diff --git a/src/core/automaticfilterparameters.cpp b/src/core/automaticfilterparameters.cpp
index ca12bdd2ad13d74d6ca3228b669127de15cdf434..531362bfcd2ddc81edc95c052d6678e822fdd0b3 100644
--- a/src/core/automaticfilterparameters.cpp
+++ b/src/core/automaticfilterparameters.cpp
@@ -1,68 +1,85 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "automaticfilterparameters.h"
AutomaticFilterParameters::AutomaticFilterParameters()
{
-
}
-AutomaticFilterParameters::AutomaticFilterParameters(const AutomaticFilterParameters& other)
+AutomaticFilterParameters::AutomaticFilterParameters(
+ const AutomaticFilterParameters &other)
{
- _filter_minimum_peptide_evalue=other._filter_minimum_peptide_evalue;
- _filter_minimum_protein_evalue=other._filter_minimum_protein_evalue;
- _filter_minimum_peptide_per_match=other._filter_minimum_peptide_per_match;
- _filter_is_cross_sample_peptide_number=other._filter_is_cross_sample_peptide_number;
+ _filter_minimum_peptide_evalue = other._filter_minimum_peptide_evalue;
+ _filter_minimum_protein_evalue = other._filter_minimum_protein_evalue;
+ _filter_minimum_peptide_per_match = other._filter_minimum_peptide_per_match;
+ _filter_is_cross_sample_peptide_number =
+ other._filter_is_cross_sample_peptide_number;
}
AutomaticFilterParameters::~AutomaticFilterParameters()
{
-
}
-void AutomaticFilterParameters::setFilterPeptideEvalue( pappso::pappso_double evalue) {
- _filter_minimum_peptide_evalue = evalue;
+void
+AutomaticFilterParameters::setFilterPeptideEvalue(pappso::pappso_double evalue)
+{
+ _filter_minimum_peptide_evalue = evalue;
}
-void AutomaticFilterParameters::setFilterProteinEvalue( pappso::pappso_double evalue) {
- _filter_minimum_protein_evalue = evalue;
+void
+AutomaticFilterParameters::setFilterProteinEvalue(pappso::pappso_double evalue)
+{
+ _filter_minimum_protein_evalue = evalue;
}
-void AutomaticFilterParameters::setFilterMinimumPeptidePerMatch(unsigned int number) {
- _filter_minimum_peptide_per_match = number;
+void
+AutomaticFilterParameters::setFilterMinimumPeptidePerMatch(unsigned int number)
+{
+ _filter_minimum_peptide_per_match = number;
}
-void AutomaticFilterParameters::setFilterCrossSamplePeptideNumber(bool cross) {
- _filter_is_cross_sample_peptide_number = cross;
+void
+AutomaticFilterParameters::setFilterCrossSamplePeptideNumber(bool cross)
+{
+ _filter_is_cross_sample_peptide_number = cross;
}
-pappso::pappso_double AutomaticFilterParameters::getFilterPeptideEvalue() const {
- return (_filter_minimum_peptide_evalue );
+pappso::pappso_double
+AutomaticFilterParameters::getFilterPeptideEvalue() const
+{
+ return (_filter_minimum_peptide_evalue);
}
-pappso::pappso_double AutomaticFilterParameters::getFilterProteinEvalue() const {
- return ( _filter_minimum_protein_evalue );
+pappso::pappso_double
+AutomaticFilterParameters::getFilterProteinEvalue() const
+{
+ return (_filter_minimum_protein_evalue);
}
-unsigned int AutomaticFilterParameters::getFilterMinimumPeptidePerMatch()const {
- return (_filter_minimum_peptide_per_match );
+unsigned int
+AutomaticFilterParameters::getFilterMinimumPeptidePerMatch() const
+{
+ return (_filter_minimum_peptide_per_match);
}
-bool AutomaticFilterParameters::getFilterCrossSamplePeptideNumber()const {
- return _filter_is_cross_sample_peptide_number ;
+bool
+AutomaticFilterParameters::getFilterCrossSamplePeptideNumber() const
+{
+ return _filter_is_cross_sample_peptide_number;
}
diff --git a/src/core/automaticfilterparameters.h b/src/core/automaticfilterparameters.h
index f76fdabe219bbc2ff21889e53dbe418588539489..b8f1e35622945a3a958052d302067ad99cea0d40 100644
--- a/src/core/automaticfilterparameters.h
+++ b/src/core/automaticfilterparameters.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef AUTOMATICFILTERPARAMETERS_H
#define AUTOMATICFILTERPARAMETERS_H
@@ -27,29 +28,28 @@
class AutomaticFilterParameters
{
-public:
- AutomaticFilterParameters();
- AutomaticFilterParameters(const AutomaticFilterParameters& other);
- ~AutomaticFilterParameters();
+ public:
+ AutomaticFilterParameters();
+ AutomaticFilterParameters(const AutomaticFilterParameters &other);
+ ~AutomaticFilterParameters();
- void setFilterPeptideEvalue( pappso::pappso_double evalue);
- void setFilterProteinEvalue( pappso::pappso_double evalue);
- void setFilterMinimumPeptidePerMatch(unsigned int number);
- void setFilterCrossSamplePeptideNumber(bool cross);
+ void setFilterPeptideEvalue(pappso::pappso_double evalue);
+ void setFilterProteinEvalue(pappso::pappso_double evalue);
+ void setFilterMinimumPeptidePerMatch(unsigned int number);
+ void setFilterCrossSamplePeptideNumber(bool cross);
- pappso::pappso_double getFilterPeptideEvalue() const;
- pappso::pappso_double getFilterProteinEvalue()const;
- unsigned int getFilterMinimumPeptidePerMatch()const;
- bool getFilterCrossSamplePeptideNumber()const;
+ pappso::pappso_double getFilterPeptideEvalue() const;
+ pappso::pappso_double getFilterProteinEvalue() const;
+ unsigned int getFilterMinimumPeptidePerMatch() const;
+ bool getFilterCrossSamplePeptideNumber() const;
-private :
-
- pappso::pappso_double _filter_minimum_peptide_evalue=1;
- pappso::pappso_double _filter_minimum_protein_evalue=1;
- unsigned int _filter_minimum_peptide_per_match=1;
- bool _filter_is_cross_sample_peptide_number=false;
+ private:
+ pappso::pappso_double _filter_minimum_peptide_evalue = 1;
+ pappso::pappso_double _filter_minimum_protein_evalue = 1;
+ unsigned int _filter_minimum_peptide_per_match = 1;
+ bool _filter_is_cross_sample_peptide_number = false;
};
#endif // AUTOMATICFILTERPARAMETERS_H
diff --git a/src/core/identification_sources/identificationdatasource.h b/src/core/identification_sources/identificationdatasource.h
index abb4a98b61e5a6e4ed3828c1990081a82e414973..519225b5ff6a9b9a48f7b4c8971a4a03ae7a5f19 100644
--- a/src/core/identification_sources/identificationdatasource.h
+++ b/src/core/identification_sources/identificationdatasource.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef IDENTIFICATIONDATASOURCE_H
#define IDENTIFICATIONDATASOURCE_H
@@ -39,106 +40,116 @@ typedef std::shared_ptr<IdentificationDataSource> IdentificationDataSourceSp;
class IdentificationDataSource
{
-public:
-
- IdentificationDataSource(const QString resource_name);
- IdentificationDataSource(const IdentificationDataSource& other);
- ~IdentificationDataSource();
- bool operator==(const IdentificationDataSource& other) const;
-
- PeptideEvidenceStore & getPeptideEvidenceStore();
- const PeptideEvidenceStore & getPeptideEvidenceStore() const;
-
- void setXmlId(const QString xmlid);
- const QString & getXmlId() const;
-
- /** @brief URL or filename containing identification data
- * */
- const QString & getResourceName () const;
-
- /** @brief get biological sample name
- * */
- const QString getSampleName () const;
- void setMsRunSp (MsRunSp ms_run_sp);
- MsRunSp getMsRunSp () const;
- /** @brief get the spectrum with scan number
- * */
- virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const;
-
-
- /** \brief read source content to store it in project
- */
- virtual void parseTo(Project* p_project)=0;
-
- /** \brief set identification engine
- */
- virtual void setIdentificationEngine(IdentificationEngine engine);
-
- /** \brief identification engine
- */
- virtual IdentificationEngine getIdentificationEngine() const;
-
- /** \brief identification engine name
- */
- const QString getIdentificationEngineName() const;
-
- /** \brief identification engine version
- */
- virtual const QString& getIdentificationEngineVersion() const;
- /** \brief set identification engine version
- */
- virtual void setIdentificationEngineVersion(const QString& version);
-
- /** \brief set identification engine parameter value
- */
- virtual void setIdentificationEngineParam(IdentificationEngineParam param, const QVariant& value);
-
-
- /** \brief get specific identification engine parameter value
- */
- virtual const QVariant getIdentificationEngineParam(IdentificationEngineParam param) const;
-
-
- /** \brief set identification engine statistics
- * any statistics on this identification run that can be told by the identification engine
- */
- virtual void setIdentificationEngineStatistics(IdentificationEngineStatistics param, const QVariant& value);
-
-
- /** \brief get specific identification engine statistics value
- */
- virtual const QVariant getIdentificationEngineStatistics(IdentificationEngineStatistics param) const;
-
- /** \brief add Fastafile used by the identification engine
- */
- void addFastaFile (FastaFileSp file);
-
- const std::vector<FastaFileSp> & getFastaFileList() const;
-
-
- /** \brief get identification engine statistics map
- */
- virtual const std::map<IdentificationEngineStatistics, QVariant> & getIdentificationEngineStatisticsMap() const;
-
- /** \brief get identification engine param map
- */
- virtual const std::map<IdentificationEngineParam, QVariant> & getIdentificationEngineParamMap() const;
-
- virtual const bool isValid(const PeptideEvidence * p_peptide_evidence, const AutomaticFilterParameters & automatic_filter_parameters) const;
-
-protected :
- QString _resource_name;
- IdentificationEngine _engine = IdentificationEngine::unknown;
-private :
- //static std::map<QString, pappso::MsRunIdSp> _map_msrunidsp;
- QString _xml_id;
- QString _version;
- MsRunSp _ms_run_sp = nullptr;
- std::map<IdentificationEngineParam, QVariant> _params;
- std::map<IdentificationEngineStatistics, QVariant> _param_stats;
- std::vector<FastaFileSp> _fastafile_list;
-
- PeptideEvidenceStore _peptide_evidence_store;
+ public:
+ IdentificationDataSource(const QString resource_name);
+ IdentificationDataSource(const IdentificationDataSource &other);
+ ~IdentificationDataSource();
+ bool operator==(const IdentificationDataSource &other) const;
+
+ PeptideEvidenceStore &getPeptideEvidenceStore();
+ const PeptideEvidenceStore &getPeptideEvidenceStore() const;
+
+ void setXmlId(const QString xmlid);
+ const QString &getXmlId() const;
+
+ /** @brief URL or filename containing identification data
+ * */
+ const QString &getResourceName() const;
+
+ /** @brief get biological sample name
+ * */
+ const QString getSampleName() const;
+ void setMsRunSp(MsRunSp ms_run_sp);
+ MsRunSp getMsRunSp() const;
+ /** @brief get the spectrum with scan number
+ * */
+ virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const;
+
+
+ /** \brief read source content to store it in project
+ */
+ virtual void parseTo(Project *p_project) = 0;
+
+ /** \brief set identification engine
+ */
+ virtual void setIdentificationEngine(IdentificationEngine engine);
+
+ /** \brief identification engine
+ */
+ virtual IdentificationEngine getIdentificationEngine() const;
+
+ /** \brief identification engine name
+ */
+ const QString getIdentificationEngineName() const;
+
+ /** \brief identification engine version
+ */
+ virtual const QString &getIdentificationEngineVersion() const;
+ /** \brief set identification engine version
+ */
+ virtual void setIdentificationEngineVersion(const QString &version);
+
+ /** \brief set identification engine parameter value
+ */
+ virtual void setIdentificationEngineParam(IdentificationEngineParam param,
+ const QVariant &value);
+
+
+ /** \brief get specific identification engine parameter value
+ */
+ virtual const QVariant
+ getIdentificationEngineParam(IdentificationEngineParam param) const;
+
+
+ /** \brief set identification engine statistics
+ * any statistics on this identification run that can be told by the
+ * identification engine
+ */
+ virtual void
+ setIdentificationEngineStatistics(IdentificationEngineStatistics param,
+ const QVariant &value);
+
+
+ /** \brief get specific identification engine statistics value
+ */
+ virtual const QVariant
+ getIdentificationEngineStatistics(IdentificationEngineStatistics param) const;
+
+ /** \brief add Fastafile used by the identification engine
+ */
+ void addFastaFile(FastaFileSp file);
+
+ const std::vector<FastaFileSp> &getFastaFileList() const;
+
+
+ /** \brief get identification engine statistics map
+ */
+ virtual const std::map<IdentificationEngineStatistics, QVariant> &
+ getIdentificationEngineStatisticsMap() const;
+
+ /** \brief get identification engine param map
+ */
+ virtual const std::map<IdentificationEngineParam, QVariant> &
+ getIdentificationEngineParamMap() const;
+
+ virtual const bool
+ isValid(const PeptideEvidence *p_peptide_evidence,
+ const AutomaticFilterParameters &automatic_filter_parameters) const;
+
+ protected:
+ QString _resource_name;
+ IdentificationEngine _engine = IdentificationEngine::unknown;
+
+ private:
+ // static std::map<QString, pappso::MsRunIdSp> _map_msrunidsp;
+ QString _xml_id;
+ QString _version;
+ MsRunSp _ms_run_sp = nullptr;
+ std::map<IdentificationEngineParam, QVariant> _params;
+ std::map<IdentificationEngineStatistics, QVariant> _param_stats;
+ std::vector<FastaFileSp> _fastafile_list;
+
+ PeptideEvidenceStore _peptide_evidence_store;
};
#endif // IDENTIFICATIONDATASOURCE_H
diff --git a/src/core/identification_sources/identificationmascotdatfile.cpp b/src/core/identification_sources/identificationmascotdatfile.cpp
index 459288fc0885774ea50763a87573eeb337827dc2..01e804a3d1f54627f28c00628559c9be54f400a7 100644
--- a/src/core/identification_sources/identificationmascotdatfile.cpp
+++ b/src/core/identification_sources/identificationmascotdatfile.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "identificationmascotdatfile.h"
@@ -33,75 +34,98 @@
#include "../project.h"
#include "../../input/mascot/mascotdatparser.h"
-IdentificationMascotDatFile::IdentificationMascotDatFile(const QFileInfo & mascot_dat_file) : IdentificationDataSource(mascot_dat_file.absoluteFilePath()), _mascot_dat_file(mascot_dat_file)
+IdentificationMascotDatFile::IdentificationMascotDatFile(
+ const QFileInfo &mascot_dat_file)
+ : IdentificationDataSource(mascot_dat_file.absoluteFilePath())
+ , _mascot_dat_file(mascot_dat_file)
{
- _engine = IdentificationEngine::mascot;
+ _engine = IdentificationEngine::mascot;
}
-IdentificationMascotDatFile::IdentificationMascotDatFile(const IdentificationMascotDatFile& other) : IdentificationDataSource(other),_mascot_dat_file (other._mascot_dat_file)
+IdentificationMascotDatFile::IdentificationMascotDatFile(
+ const IdentificationMascotDatFile &other)
+ : IdentificationDataSource(other), _mascot_dat_file(other._mascot_dat_file)
{
- _engine = IdentificationEngine::mascot;
+ _engine = IdentificationEngine::mascot;
}
IdentificationMascotDatFile::~IdentificationMascotDatFile()
{
-
}
-bool IdentificationMascotDatFile::operator==(const IdentificationMascotDatFile& other) const
+bool
+IdentificationMascotDatFile::
+operator==(const IdentificationMascotDatFile &other) const
{
-
}
-pappso::SpectrumSp IdentificationMascotDatFile::getSpectrumSp(unsigned int scan_number) const {
- pappso::SpectrumSp spectrum_sp = IdentificationDataSource::getSpectrumSp(scan_number);
- return spectrum_sp;
+pappso::SpectrumSp
+IdentificationMascotDatFile::getSpectrumSp(unsigned int scan_number) const
+{
+ pappso::SpectrumSp spectrum_sp =
+ IdentificationDataSource::getSpectrumSp(scan_number);
+ return spectrum_sp;
}
-void IdentificationMascotDatFile::parseTo(Project* p_project) {
- qDebug() << "IdentificationMascotDatFile::parseTo begin";
-
- qDebug() << "Read Mascot dat result file '" << _mascot_dat_file.absoluteFilePath() << "'";
-
- MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(QFileInfo(_mascot_dat_file).baseName());
- setMsRunSp(msrun_sp);
- std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
- IdentificationGroup * identification_group_p = nullptr;
- if (p_project->getProjectMode() == ProjectMode::combined) {
- if (identification_list.size() == 0) {
- identification_group_p = p_project->newIdentificationGroup();
+void
+IdentificationMascotDatFile::parseTo(Project *p_project)
+{
+ qDebug() << "IdentificationMascotDatFile::parseTo begin";
+
+ qDebug() << "Read Mascot dat result file '"
+ << _mascot_dat_file.absoluteFilePath() << "'";
+
+ MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(
+ QFileInfo(_mascot_dat_file).baseName());
+ setMsRunSp(msrun_sp);
+ std::vector<IdentificationGroup *> identification_list =
+ p_project->getIdentificationGroupList();
+ IdentificationGroup *identification_group_p = nullptr;
+ if(p_project->getProjectMode() == ProjectMode::combined)
+ {
+ if(identification_list.size() == 0)
+ {
+ identification_group_p = p_project->newIdentificationGroup();
}
- else {
- identification_group_p = identification_list[0];
+ else
+ {
+ identification_group_p = identification_list[0];
}
}
- else {
- for (IdentificationGroup * identification_p_flist : identification_list) {
- if (identification_p_flist->containSample(msrun_sp.get()->getSampleName())) {
- identification_group_p = identification_p_flist;
- break;
+ else
+ {
+ for(IdentificationGroup *identification_p_flist : identification_list)
+ {
+ if(identification_p_flist->containSample(
+ msrun_sp.get()->getSampleName()))
+ {
+ identification_group_p = identification_p_flist;
+ break;
}
}
- if (identification_group_p == nullptr) {
- identification_group_p = p_project->newIdentificationGroup();
+ if(identification_group_p == nullptr)
+ {
+ identification_group_p = p_project->newIdentificationGroup();
}
}
- identification_group_p->addIdentificationDataSourceP(this);
- MascotDatParser mascot_parser(p_project, identification_group_p, this);
+ identification_group_p->addIdentificationDataSourceP(this);
+ MascotDatParser mascot_parser(p_project, identification_group_p, this);
- QFile qfile(_mascot_dat_file.absoluteFilePath());
- mascot_parser.parse(&qfile);
-
- qfile.close();
+ QFile qfile(_mascot_dat_file.absoluteFilePath());
+ mascot_parser.parse(&qfile);
- qDebug() << "IdentificationMascotDatFile::parseTo end";
+ qfile.close();
+
+ qDebug() << "IdentificationMascotDatFile::parseTo end";
}
/*
-const bool IdentificationMascotDatFile::isValid(const PeptideEvidence * p_peptide_evidence, const AutomaticFilterParameters & automatic_filter_parameters) const {
-
+const bool IdentificationMascotDatFile::isValid(const PeptideEvidence *
+p_peptide_evidence, const AutomaticFilterParameters &
+automatic_filter_parameters) const {
+
return true;
}
*/
diff --git a/src/core/identification_sources/identificationmascotdatfile.h b/src/core/identification_sources/identificationmascotdatfile.h
index 4c6a8d2539cb8fadeff3b8b7dc5e24142465d9fd..a1d856f03c681a6f85555051b74500f9a5601803 100644
--- a/src/core/identification_sources/identificationmascotdatfile.h
+++ b/src/core/identification_sources/identificationmascotdatfile.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef IDENTIFICATIONMASCOTDATFILE_H
#define IDENTIFICATIONMASCOTDATFILE_H
@@ -33,21 +34,24 @@
#include "identificationdatasource.h"
#include <QFileInfo>
-class IdentificationMascotDatFile: public IdentificationDataSource
+class IdentificationMascotDatFile : public IdentificationDataSource
{
-public:
- IdentificationMascotDatFile(const QFileInfo & mascot_dat_file);
- IdentificationMascotDatFile(const IdentificationMascotDatFile& other);
- ~IdentificationMascotDatFile();
- bool operator==(const IdentificationMascotDatFile& other) const;
-
- virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const override;
- virtual void parseTo(Project* p_project) override;
-
- //virtual const bool isValid(const PeptideEvidence * p_peptide_evidence, const AutomaticFilterParameters & automatic_filter_parameters) const override;
-
-private:
- const QFileInfo _mascot_dat_file;
+ public:
+ IdentificationMascotDatFile(const QFileInfo &mascot_dat_file);
+ IdentificationMascotDatFile(const IdentificationMascotDatFile &other);
+ ~IdentificationMascotDatFile();
+ bool operator==(const IdentificationMascotDatFile &other) const;
+
+ virtual pappso::SpectrumSp
+ getSpectrumSp(unsigned int scan_number) const override;
+ virtual void parseTo(Project *p_project) override;
+
+ // virtual const bool isValid(const PeptideEvidence * p_peptide_evidence,
+ // const AutomaticFilterParameters & automatic_filter_parameters) const
+ // override;
+
+ private:
+ const QFileInfo _mascot_dat_file;
};
#endif // IDENTIFICATIONMASCOTDATFILE_H
diff --git a/src/core/identification_sources/identificationpepxmlfile.h b/src/core/identification_sources/identificationpepxmlfile.h
index 168c6dc043e6d174edf824eb34db1f94316096ad..2a66e24c6161be2b82e2964e914199fbd72f3a16 100644
--- a/src/core/identification_sources/identificationpepxmlfile.h
+++ b/src/core/identification_sources/identificationpepxmlfile.h
@@ -6,24 +6,24 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
#ifndef IDENTIFICATIONPEPXMLFILE_H
#define IDENTIFICATIONPEPXMLFILE_H
@@ -31,21 +31,24 @@
#include "identificationdatasource.h"
#include <QFileInfo>
-class IdentificationPepXmlFile: public IdentificationDataSource
+class IdentificationPepXmlFile : public IdentificationDataSource
{
-public:
- IdentificationPepXmlFile(const QFileInfo & mascot_dat_file);
- IdentificationPepXmlFile(const IdentificationPepXmlFile& other);
- ~IdentificationPepXmlFile();
- bool operator==(const IdentificationPepXmlFile& other) const;
-
- virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const override;
- virtual void parseTo(Project* p_project) override;
-
- //virtual const bool isValid(const PeptideEvidence * p_peptide_evidence, const AutomaticFilterParameters & automatic_filter_parameters) const override;
-
-private:
- const QFileInfo _pep_xml_file;
+ public:
+ IdentificationPepXmlFile(const QFileInfo &mascot_dat_file);
+ IdentificationPepXmlFile(const IdentificationPepXmlFile &other);
+ ~IdentificationPepXmlFile();
+ bool operator==(const IdentificationPepXmlFile &other) const;
+
+ virtual pappso::SpectrumSp
+ getSpectrumSp(unsigned int scan_number) const override;
+ virtual void parseTo(Project *p_project) override;
+
+ // virtual const bool isValid(const PeptideEvidence * p_peptide_evidence,
+ // const AutomaticFilterParameters & automatic_filter_parameters) const
+ // override;
+
+ private:
+ const QFileInfo _pep_xml_file;
};
#endif // IDENTIFICATIONPEPXMLFILE_H
diff --git a/src/core/identification_sources/identificationpwizfile.h b/src/core/identification_sources/identificationpwizfile.h
index 01da96a8c9f8369255d34688982f161a88f0b421..183041351028688f2098e62dcb6cefb45b667697 100644
--- a/src/core/identification_sources/identificationpwizfile.h
+++ b/src/core/identification_sources/identificationpwizfile.h
@@ -7,26 +7,27 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef IDENTIFICATIONPWIZFILE_H
#define IDENTIFICATIONPWIZFILE_H
@@ -34,19 +35,20 @@
#include "identificationdatasource.h"
#include <QFileInfo>
-class IdentificationPwizFile: public IdentificationDataSource
+class IdentificationPwizFile : public IdentificationDataSource
{
-public:
- IdentificationPwizFile(const QFileInfo & ident_file);
- IdentificationPwizFile(const IdentificationPwizFile& other);
- ~IdentificationPwizFile();
- bool operator==(const IdentificationPwizFile& other) const;
-
- virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const override;
- virtual void parseTo(Project* p_project) override;
-
-private:
- const QFileInfo _ident_file;
+ public:
+ IdentificationPwizFile(const QFileInfo &ident_file);
+ IdentificationPwizFile(const IdentificationPwizFile &other);
+ ~IdentificationPwizFile();
+ bool operator==(const IdentificationPwizFile &other) const;
+
+ virtual pappso::SpectrumSp
+ getSpectrumSp(unsigned int scan_number) const override;
+ virtual void parseTo(Project *p_project) override;
+
+ private:
+ const QFileInfo _ident_file;
};
#endif // IDENTIFICATIONPWIZFILE_H
diff --git a/src/core/identification_sources/identificationxtandemfile.cpp b/src/core/identification_sources/identificationxtandemfile.cpp
index 09da37165a928cf37f7612f232f2e37604314583..74d6313864a4cb935ac753826fccc9a6d5578995 100644
--- a/src/core/identification_sources/identificationxtandemfile.cpp
+++ b/src/core/identification_sources/identificationxtandemfile.cpp
@@ -1,108 +1,137 @@
/*******************************************************************************
-* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "identificationxtandemfile.h"
#include <pappsomspp/pappsoexception.h>
#include "../project.h"
#include "../../input/xtandemsaxhandler.h"
-IdentificationXtandemFile::IdentificationXtandemFile(const QFileInfo & xtandem_file) : IdentificationDataSource(xtandem_file.absoluteFilePath()), _xtandem_file(xtandem_file)
+IdentificationXtandemFile::IdentificationXtandemFile(
+ const QFileInfo &xtandem_file)
+ : IdentificationDataSource(xtandem_file.absoluteFilePath())
+ , _xtandem_file(xtandem_file)
{
- _engine = IdentificationEngine::XTandem;
+ _engine = IdentificationEngine::XTandem;
}
-IdentificationXtandemFile::IdentificationXtandemFile(const IdentificationXtandemFile& other) : IdentificationDataSource(other),_xtandem_file (other._xtandem_file)
+IdentificationXtandemFile::IdentificationXtandemFile(
+ const IdentificationXtandemFile &other)
+ : IdentificationDataSource(other), _xtandem_file(other._xtandem_file)
{
- _engine = IdentificationEngine::XTandem;
+ _engine = IdentificationEngine::XTandem;
}
IdentificationXtandemFile::~IdentificationXtandemFile()
{
-
}
-bool IdentificationXtandemFile::operator==(const IdentificationXtandemFile& other) const
+bool
+IdentificationXtandemFile::
+operator==(const IdentificationXtandemFile &other) const
{
-
}
-pappso::SpectrumSp IdentificationXtandemFile::getSpectrumSp(unsigned int scan_number) const {
- pappso::SpectrumSp spectrum_sp = IdentificationDataSource::getSpectrumSp(scan_number);
- return spectrum_sp;
+pappso::SpectrumSp
+IdentificationXtandemFile::getSpectrumSp(unsigned int scan_number) const
+{
+ pappso::SpectrumSp spectrum_sp =
+ IdentificationDataSource::getSpectrumSp(scan_number);
+ return spectrum_sp;
}
-void IdentificationXtandemFile::parseTo(Project* p_project) {
- qDebug() << "IdentificationXtandemFile::parseTo begin";
-
- qDebug() << "Read X!Tandem XML result file '" << _xtandem_file.absoluteFilePath() << "'";
-
- MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(QFileInfo(_xtandem_file).baseName());
- setMsRunSp(msrun_sp);
- std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
- IdentificationGroup * identification_group_p = nullptr;
- if (p_project->getProjectMode() == ProjectMode::combined) {
- if (identification_list.size() == 0) {
- identification_group_p = p_project->newIdentificationGroup();
+void
+IdentificationXtandemFile::parseTo(Project *p_project)
+{
+ qDebug() << "IdentificationXtandemFile::parseTo begin";
+
+ qDebug() << "Read X!Tandem XML result file '"
+ << _xtandem_file.absoluteFilePath() << "'";
+
+ MsRunSp msrun_sp =
+ p_project->getMsRunStore().getInstance(QFileInfo(_xtandem_file).baseName());
+ setMsRunSp(msrun_sp);
+ std::vector<IdentificationGroup *> identification_list =
+ p_project->getIdentificationGroupList();
+ IdentificationGroup *identification_group_p = nullptr;
+ if(p_project->getProjectMode() == ProjectMode::combined)
+ {
+ if(identification_list.size() == 0)
+ {
+ identification_group_p = p_project->newIdentificationGroup();
}
- else {
- identification_group_p = identification_list[0];
+ else
+ {
+ identification_group_p = identification_list[0];
}
}
- else {
- for (IdentificationGroup * identification_p_flist : identification_list) {
- if (identification_p_flist->containSample(msrun_sp.get()->getSampleName())) {
- identification_group_p = identification_p_flist;
- break;
+ else
+ {
+ for(IdentificationGroup *identification_p_flist : identification_list)
+ {
+ if(identification_p_flist->containSample(
+ msrun_sp.get()->getSampleName()))
+ {
+ identification_group_p = identification_p_flist;
+ break;
}
}
- if (identification_group_p == nullptr) {
- identification_group_p = p_project->newIdentificationGroup();
+ if(identification_group_p == nullptr)
+ {
+ identification_group_p = p_project->newIdentificationGroup();
}
}
-
- identification_group_p->addIdentificationDataSourceP(this);
- XtandemSaxHandler * parser = new XtandemSaxHandler(p_project, identification_group_p, this);
- QXmlSimpleReader simplereader;
- simplereader.setContentHandler(parser);
- simplereader.setErrorHandler(parser);
+ identification_group_p->addIdentificationDataSourceP(this);
+ XtandemSaxHandler *parser =
+ new XtandemSaxHandler(p_project, identification_group_p, this);
- QFile qfile(_xtandem_file.absoluteFilePath());
- QXmlInputSource xmlInputSource(&qfile);
+ QXmlSimpleReader simplereader;
+ simplereader.setContentHandler(parser);
+ simplereader.setErrorHandler(parser);
- if (simplereader.parse(xmlInputSource)) {
+ QFile qfile(_xtandem_file.absoluteFilePath());
+ QXmlInputSource xmlInputSource(&qfile);
- qfile.close();
- } else {
- qDebug() << parser->errorString();
- // throw PappsoException(
- // QObject::tr("error reading tandem XML result file :\n").append(
- // parser->errorString()));
+ if(simplereader.parse(xmlInputSource))
+ {
- qfile.close();
-
- throw pappso::PappsoException(QObject::tr("Error reading %1 XPIP file :\n %2").arg(_xtandem_file.absoluteFilePath()).arg(parser->errorString()));
+ qfile.close();
+ }
+ else
+ {
+ qDebug() << parser->errorString();
+ // throw PappsoException(
+ // QObject::tr("error reading tandem XML result file :\n").append(
+ // parser->errorString()));
+
+ qfile.close();
+
+ throw pappso::PappsoException(
+ QObject::tr("Error reading %1 XPIP file :\n %2")
+ .arg(_xtandem_file.absoluteFilePath())
+ .arg(parser->errorString()));
}
- qDebug() << "IdentificationXtandemFile::parseTo end";
+ qDebug() << "IdentificationXtandemFile::parseTo end";
}
diff --git a/src/core/identification_sources/identificationxtandemfile.h b/src/core/identification_sources/identificationxtandemfile.h
index 6a84fd71285727341f72d4359ce0355a8c4741ad..751eb6c9c6503150ab1b07beda784c75a6889661 100644
--- a/src/core/identification_sources/identificationxtandemfile.h
+++ b/src/core/identification_sources/identificationxtandemfile.h
@@ -1,44 +1,46 @@
/*******************************************************************************
-* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef IDENTIFICATIONXTANDEMFILE_H
#define IDENTIFICATIONXTANDEMFILE_H
#include "identificationdatasource.h"
#include <QFileInfo>
-class IdentificationXtandemFile: public IdentificationDataSource
+class IdentificationXtandemFile : public IdentificationDataSource
{
-public:
- IdentificationXtandemFile(const QFileInfo & xtandem_file);
- IdentificationXtandemFile(const IdentificationXtandemFile& other);
- ~IdentificationXtandemFile();
- bool operator==(const IdentificationXtandemFile& other) const;
+ public:
+ IdentificationXtandemFile(const QFileInfo &xtandem_file);
+ IdentificationXtandemFile(const IdentificationXtandemFile &other);
+ ~IdentificationXtandemFile();
+ bool operator==(const IdentificationXtandemFile &other) const;
- virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const override;
- virtual void parseTo(Project* p_project) override;
-
-private:
- const QFileInfo _xtandem_file;
+ virtual pappso::SpectrumSp
+ getSpectrumSp(unsigned int scan_number) const override;
+ virtual void parseTo(Project *p_project) override;
+
+ private:
+ const QFileInfo _xtandem_file;
};
#endif // IDENTIFICATIONXTANDEMFILE_H
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index ef5736adff4de3aa6544b5821218f9969e75df30..1f805b5e69e38909f4ea7352164ff997acafc84f 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -130,8 +130,7 @@ unsigned int
IdentificationGroup::countDecoyProteinMatch(ValidationState state) const
{
return std::count_if(
- _protein_match_list.begin(),
- _protein_match_list.end(),
+ _protein_match_list.begin(), _protein_match_list.end(),
[state](const ProteinMatch *p_protein_match) {
if((p_protein_match->getProteinXtpSp().get()->isDecoy()) &&
(p_protein_match->getValidationState() >= state))
@@ -210,8 +209,7 @@ IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const
unsigned int
IdentificationGroup::countProteinMatch(ValidationState state) const
{
- return std::count_if(_protein_match_list.begin(),
- _protein_match_list.end(),
+ return std::count_if(_protein_match_list.begin(), _protein_match_list.end(),
[state](const ProteinMatch *p_protein_match) {
if(p_protein_match->getValidationState() >= state)
{
@@ -304,8 +302,8 @@ IdentificationGroup::addIdentificationDataSourceP(
IdentificationDataSource *p_identification_source)
{
addMsRunSp(p_identification_source->getMsRunSp());
- auto it = std::find(
- _id_source_list.begin(), _id_source_list.end(), p_identification_source);
+ auto it = std::find(_id_source_list.begin(), _id_source_list.end(),
+ p_identification_source);
if(it == _id_source_list.end())
{
_id_source_list.push_back(p_identification_source);
@@ -355,8 +353,7 @@ IdentificationGroup::countSubGroup() const
void
IdentificationGroup::collectMhDelta(
- std::vector<pappso::pappso_double> &delta_list,
- pappso::PrecisionUnit unit,
+ std::vector<pappso::pappso_double> &delta_list, pappso::PrecisionUnit unit,
ValidationState state) const
{
std::set<const PeptideEvidence *> peptide_evidence_list;
@@ -469,9 +466,7 @@ IdentificationGroup::getProteinFdr(ValidationState state) const
void
IdentificationGroup::getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list,
- const MsRun *p_msrun,
- const PeptideXtp *p_peptide,
- unsigned int charge) const
+ const MsRun *p_msrun, const PeptideXtp *p_peptide, unsigned int charge) const
{
if(!contains(p_msrun))
return;
@@ -480,8 +475,8 @@ IdentificationGroup::getSameXicPeptideEvidenceList(
if(p_msrun == p_identification_source->getMsRunSp().get())
{
p_identification_source->getPeptideEvidenceStore()
- .getSameXicPeptideEvidenceList(
- peptide_evidence_list, p_msrun, p_peptide, charge);
+ .getSameXicPeptideEvidenceList(peptide_evidence_list, p_msrun,
+ p_peptide, charge);
}
}
}
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index eac9dd5fa7e572b8bea424846dbe18b0755e76f7..43e03e2bd4e5088115bd930ce990c92ba2220bda 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include <memory>
#include <QFileInfo>
#include "proteinmatch.h"
@@ -37,134 +38,151 @@
class Project;
-/** @brief an identification group contains one or more sample to consider for grouping
+/** @brief an identification group contains one or more sample to consider for
+ * grouping
*/
class IdentificationGroup
{
-public:
- IdentificationGroup(Project * project);
- ~IdentificationGroup();
-
- ProteinMatch * getProteinMatchInstance(const QString accession);
- const GroupStore & getGroupStore() const;
- void addProteinMatch(ProteinMatch * protein_match);
- std::vector<ProteinMatch *> & getProteinMatchList();
- const std::vector<ProteinMatch *> & getProteinMatchList() const;
- void addIdentificationDataSourceP(IdentificationDataSource * p_identification_source);
-
- const PtmGroupingExperiment * getPtmGroupingExperiment() const;
-
- /** @brief compute proto NSAF sum within msrun
- * Warning: this is not NSAF, just a part
- * @param p_msrun_id pointer on the msrun to get NSAF.
- * */
- pappso::pappso_double computeProtoNsafSum(const MsRun * p_msrun_id) const;
-
- /** @brief count groups
- * */
- std::size_t countGroup()const;
-
- /** @brief count subgroups
- * */
- std::size_t countSubGroup()const;
-
- /** @brief count proteins
- * */
- unsigned int countProteinMatch(ValidationState state) const;
-
- /** @brief count decoy proteins
- * */
- unsigned int countDecoyProteinMatch(ValidationState state) const;
-
- /** @brief count peptide evidences (peptide spectrum match + identification engine)
- * */
- unsigned int countPeptideEvidence(ValidationState state) const;
-
- /** @brief count peptide evidences (peptide spectrum match + identification engine)
- * */
- unsigned int countDecoyPeptideEvidence(ValidationState state) const;
-
- /** @brief count peptide match (peptide spectrum match + protein match)
- * */
- unsigned int countPeptideMatch(ValidationState state) const;
-
- /** @brief count decoy peptide match
- * */
- unsigned int countDecoyPeptideMatch(ValidationState state) const;
-
- /** @brief count distinct peptides overall samples(peptide+mass) including peptides from decoy proteins
- * */
- unsigned int countPeptideMass(ValidationState state) const;
-
- /** @brief count peptide (peptide+mass+sample) including peptides from decoy proteins
- * */
- unsigned int countPeptideMassSample(ValidationState state) const;
-
- /** @brief count peptide (peptide+mass+sample) only on decoy proteins
- * */
- unsigned int countDecoyPeptideMassSample(ValidationState state) const;
-
- /** @brief get False Discovery Rate of proteins
- */
- pappso::pappso_double getProteinFdr(ValidationState state = ValidationState::valid) const;
-
- /** @brief get False Discovery Rate of peptide/mass (unique sequence+modifications)
- */
- pappso::pappso_double getPeptideMassFdr(ValidationState state = ValidationState::valid) const;
-
-
- /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
- * */
- void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
-
- void startGrouping (const GroupingType & grouping_type, WorkMonitorInterface * p_work_monitor);
- /** @brief creates a new PTM grouping experiment
- * */
- void startPtmGrouping ();
-
- const std::vector<MsRunSp> & getMsRunSpList() const;
- const std::vector<IdentificationDataSource *> & getIdentificationDataSourceList() const;
-
- /** @brief get tab name for qtabwidget
- * */
- const QString getTabName() const;
-
- bool contains (const MsRun * p_msrun) const;
- bool containSample (const QString & sample) const;
-
-
- /** @brief collect mass delta between theoretical mass and observed mass
- * each peptide evidence is only counted once
- */
- void collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const;
-
-
- /** @brief look for a peptide in the same XIC
- * @param peptide_evidence_list the peptide evidence list to build
- * @param p_msrun MSrun to look for
- * @param p_peptide peptide to look for
- * @param charge charge to look for
- */
- void getSameXicPeptideEvidenceList(std::vector<const PeptideEvidence *> & peptide_evidence_list, const MsRun * p_msrun, const PeptideXtp * p_peptide, unsigned int charge) const;
-
-private :
-
- void addMsRunSp(MsRunSp ms_run_sp);
-private :
- GroupingExperiment * _p_grp_experiment= nullptr;
- PtmGroupingExperiment * _p_grp_ptm_experiment= nullptr;
-
- Project * _p_project;
-
- GroupStore _group_store;
+ public:
+ IdentificationGroup(Project *project);
+ ~IdentificationGroup();
+
+ ProteinMatch *getProteinMatchInstance(const QString accession);
+ const GroupStore &getGroupStore() const;
+ void addProteinMatch(ProteinMatch *protein_match);
+ std::vector<ProteinMatch *> &getProteinMatchList();
+ const std::vector<ProteinMatch *> &getProteinMatchList() const;
+ void addIdentificationDataSourceP(
+ IdentificationDataSource *p_identification_source);
+
+ const PtmGroupingExperiment *getPtmGroupingExperiment() const;
+
+ /** @brief compute proto NSAF sum within msrun
+ * Warning: this is not NSAF, just a part
+ * @param p_msrun_id pointer on the msrun to get NSAF.
+ * */
+ pappso::pappso_double computeProtoNsafSum(const MsRun *p_msrun_id) const;
+
+ /** @brief count groups
+ * */
+ std::size_t countGroup() const;
+
+ /** @brief count subgroups
+ * */
+ std::size_t countSubGroup() const;
+
+ /** @brief count proteins
+ * */
+ unsigned int countProteinMatch(ValidationState state) const;
+
+ /** @brief count decoy proteins
+ * */
+ unsigned int countDecoyProteinMatch(ValidationState state) const;
+
+ /** @brief count peptide evidences (peptide spectrum match + identification
+ * engine)
+ * */
+ unsigned int countPeptideEvidence(ValidationState state) const;
+
+ /** @brief count peptide evidences (peptide spectrum match + identification
+ * engine)
+ * */
+ unsigned int countDecoyPeptideEvidence(ValidationState state) const;
+
+ /** @brief count peptide match (peptide spectrum match + protein match)
+ * */
+ unsigned int countPeptideMatch(ValidationState state) const;
+
+ /** @brief count decoy peptide match
+ * */
+ unsigned int countDecoyPeptideMatch(ValidationState state) const;
+
+ /** @brief count distinct peptides overall samples(peptide+mass) including
+ * peptides from decoy proteins
+ * */
+ unsigned int countPeptideMass(ValidationState state) const;
+
+ /** @brief count peptide (peptide+mass+sample) including peptides from decoy
+ * proteins
+ * */
+ unsigned int countPeptideMassSample(ValidationState state) const;
+
+ /** @brief count peptide (peptide+mass+sample) only on decoy proteins
+ * */
+ unsigned int countDecoyPeptideMassSample(ValidationState state) const;
+
+ /** @brief get False Discovery Rate of proteins
+ */
+ pappso::pappso_double
+ getProteinFdr(ValidationState state = ValidationState::valid) const;
+
+ /** @brief get False Discovery Rate of peptide/mass (unique
+ * sequence+modifications)
+ */
+ pappso::pappso_double
+ getPeptideMassFdr(ValidationState state = ValidationState::valid) const;
+
+
+ /** @brief validate or invalidate peptides and proteins based automatic
+ * filters and manual checks
+ * */
+ void updateAutomaticFilters(
+ const AutomaticFilterParameters &automatic_filter_parameters);
+
+ void startGrouping(const GroupingType &grouping_type,
+ WorkMonitorInterface *p_work_monitor);
+ /** @brief creates a new PTM grouping experiment
+ * */
+ void startPtmGrouping();
+
+ const std::vector<MsRunSp> &getMsRunSpList() const;
+ const std::vector<IdentificationDataSource *> &
+ getIdentificationDataSourceList() const;
+
+ /** @brief get tab name for qtabwidget
+ * */
+ const QString getTabName() const;
+
+ bool contains(const MsRun *p_msrun) const;
+ bool containSample(const QString &sample) const;
+
+
+ /** @brief collect mass delta between theoretical mass and observed mass
+ * each peptide evidence is only counted once
+ */
+ void collectMhDelta(std::vector<pappso::pappso_double> &delta_list,
+ pappso::PrecisionUnit unit, ValidationState state) const;
- std::vector<ProteinMatch *> _protein_match_list;
- std::vector<MsRunSp> _ms_run_list;
- std::vector<IdentificationDataSource *> _id_source_list;
+ /** @brief look for a peptide in the same XIC
+ * @param peptide_evidence_list the peptide evidence list to build
+ * @param p_msrun MSrun to look for
+ * @param p_peptide peptide to look for
+ * @param charge charge to look for
+ */
+ void getSameXicPeptideEvidenceList(
+ std::vector<const PeptideEvidence *> &peptide_evidence_list,
+ const MsRun *p_msrun, const PeptideXtp *p_peptide,
+ unsigned int charge) const;
- std::map<QString, ProteinMatch *> _cache_accession_protein_match;
+ private:
+ void addMsRunSp(MsRunSp ms_run_sp);
+
+ private:
+ GroupingExperiment *_p_grp_experiment = nullptr;
+ PtmGroupingExperiment *_p_grp_ptm_experiment = nullptr;
+
+ Project *_p_project;
+
+ GroupStore _group_store;
+
+ std::vector<ProteinMatch *> _protein_match_list;
+
+ std::vector<MsRunSp> _ms_run_list;
+ std::vector<IdentificationDataSource *> _id_source_list;
+
+ std::map<QString, ProteinMatch *> _cache_accession_protein_match;
};
#endif // IDENTIFICATIONGROUP_H
diff --git a/src/core/labeling/label.cpp b/src/core/labeling/label.cpp
index c0a50b11eace2add49ea370a4b796497887dfbfc..4eb7b7b22f116fd4ccba995fe7f60a9781d5604f 100644
--- a/src/core/labeling/label.cpp
+++ b/src/core/labeling/label.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "label.h"
#include "../../utils/utils.h"
@@ -33,78 +34,111 @@
#include <pappsomspp/pappsoexception.h>
#include <QDebug>
-Label::Label(QDomNode & label_node) {
- //<isotope_label id="light">
- _xml_id =label_node.toElement().attribute("id");
- qDebug() <<"Label::Label begin "<<_xml_id;
- try {
- //<mod at="Nter" value="28.0" acc="MOD:00429"/>
- //<mod at="K" value="28.0" acc="MOD:00429"/>
- QDomNode child = label_node.firstChild();
- while (!child.isNull()) {
- if (child.toElement().tagName() == "mod") {
- if (child.toElement().attribute("acc").isEmpty()) {
- throw pappso::PappsoException(QObject::tr("acc attribute is empty : PSIMOD accession required"));
+Label::Label(QDomNode &label_node)
+{
+ //<isotope_label id="light">
+ _xml_id = label_node.toElement().attribute("id");
+ qDebug() << "Label::Label begin " << _xml_id;
+ try
+ {
+ //<mod at="Nter" value="28.0" acc="MOD:00429"/>
+ //<mod at="K" value="28.0" acc="MOD:00429"/>
+ QDomNode child = label_node.firstChild();
+ while(!child.isNull())
+ {
+ if(child.toElement().tagName() == "mod")
+ {
+ if(child.toElement().attribute("acc").isEmpty())
+ {
+ throw pappso::PappsoException(QObject::tr(
+ "acc attribute is empty : PSIMOD accession required"));
}
- qDebug() <<"Label::Label mod at="<<child.toElement().attribute("at") << " mod="<< child.toElement().attribute("acc");
- LabelModification label_modification = {child.toElement().attribute("at"), pappso::AaModification::getInstance( child.toElement().attribute("acc"))};
- _modification_list.push_back (label_modification);
+ qDebug() << "Label::Label mod at="
+ << child.toElement().attribute("at")
+ << " mod=" << child.toElement().attribute("acc");
+ LabelModification label_modification = {
+ child.toElement().attribute("at"),
+ pappso::AaModification::getInstance(
+ child.toElement().attribute("acc"))};
+ _modification_list.push_back(label_modification);
}
- child = child.nextSibling();
+ child = child.nextSibling();
}
}
- catch (pappso::PappsoException error) {
- throw pappso::PappsoException(QObject::tr("error creating Label : %1").arg(error.qwhat()));
+ catch(pappso::PappsoException error)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("error creating Label : %1").arg(error.qwhat()));
}
}
-Label::Label( const Label & other) {
- _xml_id = other._xml_id;
- _modification_list = other._modification_list;
+Label::Label(const Label &other)
+{
+ _xml_id = other._xml_id;
+ _modification_list = other._modification_list;
}
-bool Label::containsAaModificationP(const std::list<pappso::AaModificationP> & modification_set) const {
- for (LabelModification label_modification: _modification_list) {
- if (std::find(modification_set.begin(), modification_set.end(), label_modification.modification) != modification_set.end()) {
- return true;
+bool
+Label::containsAaModificationP(
+ const std::list<pappso::AaModificationP> &modification_set) const
+{
+ for(LabelModification label_modification : _modification_list)
+ {
+ if(std::find(modification_set.begin(), modification_set.end(),
+ label_modification.modification) != modification_set.end())
+ {
+ return true;
}
}
- return false;
+ return false;
}
-pappso::PeptideSp Label::getLabeledPeptideSp(const pappso::Peptide * p_peptide) const {
- pappso::Peptide peptide(*p_peptide);
- for (LabelModification label_modification: _modification_list) {
- peptide.removeAaModification(label_modification.modification);
+pappso::PeptideSp
+Label::getLabeledPeptideSp(const pappso::Peptide *p_peptide) const
+{
+ pappso::Peptide peptide(*p_peptide);
+ for(LabelModification label_modification : _modification_list)
+ {
+ peptide.removeAaModification(label_modification.modification);
}
- return (peptide.makePeptideSp());
+ return (peptide.makePeptideSp());
}
-const QString & Label::getXmlId() const {
- return _xml_id;
+const QString &
+Label::getXmlId() const
+{
+ return _xml_id;
}
-const std::vector<LabelModification> & Label::getLabelModifictionList() const {
- return _modification_list;
+const std::vector<LabelModification> &
+Label::getLabelModifictionList() const
+{
+ return _modification_list;
}
-void Label::writeMassChroqMl(QXmlStreamWriter* output_stream) const {
+void
+Label::writeMassChroqMl(QXmlStreamWriter *output_stream) const
+{
- //<isotope_label id="iso1">
- output_stream->writeStartElement("isotope_label");
- output_stream->writeAttribute("id",_xml_id);
- // <mod at="Nter" value="28.0" acc="MOD:00429"/>
- // <mod at="K" value="28.0" acc="MOD:00429"/>
- for (const LabelModification label_modification: _modification_list) {
- output_stream->writeStartElement("mod");
- output_stream->writeAttribute("at",label_modification.at);
- output_stream->writeAttribute("value",Utils::getXmlDouble(label_modification.modification->getMass()));
- output_stream->writeAttribute("acc",label_modification.modification->getAccession());
- output_stream->writeEndElement();
- output_stream->writeComment(label_modification.modification->getName());
+ //<isotope_label id="iso1">
+ output_stream->writeStartElement("isotope_label");
+ output_stream->writeAttribute("id", _xml_id);
+ // <mod at="Nter" value="28.0" acc="MOD:00429"/>
+ // <mod at="K" value="28.0" acc="MOD:00429"/>
+ for(const LabelModification label_modification : _modification_list)
+ {
+ output_stream->writeStartElement("mod");
+ output_stream->writeAttribute("at", label_modification.at);
+ output_stream->writeAttribute(
+ "value",
+ Utils::getXmlDouble(label_modification.modification->getMass()));
+ output_stream->writeAttribute(
+ "acc", label_modification.modification->getAccession());
+ output_stream->writeEndElement();
+ output_stream->writeComment(label_modification.modification->getName());
}
- // </isotope_label>
- output_stream->writeEndElement();
+ // </isotope_label>
+ output_stream->writeEndElement();
}
diff --git a/src/core/labeling/label.h b/src/core/labeling/label.h
index 00140c1d8de0197ceaea7bb1c4f5b9a312eebe36..ed21b41c6884825733ea69bcfa9705043f654f7c 100644
--- a/src/core/labeling/label.h
+++ b/src/core/labeling/label.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef LABEL_H
#define LABEL_H
@@ -37,27 +38,29 @@
#include <QXmlStreamWriter>
-struct LabelModification {
- QString at;
- pappso::AaModificationP modification;
+struct LabelModification
+{
+ QString at;
+ pappso::AaModificationP modification;
};
class Label
{
-public:
- Label(QDomNode & method_node);
- Label( const Label & other);
- bool containsAaModificationP(const std::list<pappso::AaModificationP> & modification_set) const;
- pappso::PeptideSp getLabeledPeptideSp(const pappso::Peptide * p_peptide) const;
- void writeMassChroqMl(QXmlStreamWriter* output_stream) const;
- const QString & getXmlId() const;
-
- const std::vector<LabelModification> & getLabelModifictionList() const;
-
-private:
- QString _xml_id;
- std::vector<LabelModification> _modification_list;
+ public:
+ Label(QDomNode &method_node);
+ Label(const Label &other);
+ bool containsAaModificationP(
+ const std::list<pappso::AaModificationP> &modification_set) const;
+ pappso::PeptideSp getLabeledPeptideSp(const pappso::Peptide *p_peptide) const;
+ void writeMassChroqMl(QXmlStreamWriter *output_stream) const;
+ const QString &getXmlId() const;
+
+ const std::vector<LabelModification> &getLabelModifictionList() const;
+
+ private:
+ QString _xml_id;
+ std::vector<LabelModification> _modification_list;
};
#endif // LABEL_H
diff --git a/src/core/labeling/labelingmethod.cpp b/src/core/labeling/labelingmethod.cpp
index bdd45035d383f1b3dc66441f82e74d9dc8cc2e49..aed64bb8558b1a6ecdf15b906f4a587f86af58c4 100644
--- a/src/core/labeling/labelingmethod.cpp
+++ b/src/core/labeling/labelingmethod.cpp
@@ -6,118 +6,149 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "labelingmethod.h"
#include <pappsomspp/pappsoexception.h>
#include <QFile>
#include <QDomDocument>
-LabelingMethod::LabelingMethod(const QString & method_id):_xml_id(method_id) {
+LabelingMethod::LabelingMethod(const QString &method_id) : _xml_id(method_id)
+{
- qDebug() <<"LabelingMethod::LabelingMethod begin "<<_xml_id;
- QDomDocument *dom = new QDomDocument("labeling_methods");
- QFile xml_doc(":/labeling/resources/catalog_label.xml");
- if(!xml_doc.open(QIODevice::ReadOnly))
+ qDebug() << "LabelingMethod::LabelingMethod begin " << _xml_id;
+ QDomDocument *dom = new QDomDocument("labeling_methods");
+ QFile xml_doc(":/labeling/resources/catalog_label.xml");
+ if(!xml_doc.open(QIODevice::ReadOnly))
{
- //error
- throw pappso::PappsoException(QObject::tr("error opening catalog_label resource file"));
+ // error
+ throw pappso::PappsoException(
+ QObject::tr("error opening catalog_label resource file"));
}
- if (!dom->setContent(&xml_doc)) {
- xml_doc.close();
- throw pappso::PappsoException(QObject::tr("error opening catalog_label xml content"));
+ if(!dom->setContent(&xml_doc))
+ {
+ xml_doc.close();
+ throw pappso::PappsoException(
+ QObject::tr("error opening catalog_label xml content"));
}
- QDomNode child = dom->documentElement().firstChild();
- while (!child.isNull()) {
- if (child.toElement().tagName() == "isotope_label_list") {
- if (child.toElement().attribute("id")== _xml_id) {
- parseMethod(child);
+ QDomNode child = dom->documentElement().firstChild();
+ while(!child.isNull())
+ {
+ if(child.toElement().tagName() == "isotope_label_list")
+ {
+ if(child.toElement().attribute("id") == _xml_id)
+ {
+ parseMethod(child);
}
}
- child = child.nextSibling();
+ child = child.nextSibling();
}
- xml_doc.close();
- delete dom;
+ xml_doc.close();
+ delete dom;
}
-Label * LabelingMethod::getLabel(const std::list<pappso::AaModificationP> & modification_set) const {
- for (Label * p_label: _label_list) {
- if (p_label->containsAaModificationP(modification_set)) {
- return p_label;
+Label *
+LabelingMethod::getLabel(
+ const std::list<pappso::AaModificationP> &modification_set) const
+{
+ for(Label *p_label : _label_list)
+ {
+ if(p_label->containsAaModificationP(modification_set))
+ {
+ return p_label;
}
}
- return nullptr;
+ return nullptr;
}
-const QString & LabelingMethod::getXmlId() const {
- return _xml_id;
+const QString &
+LabelingMethod::getXmlId() const
+{
+ return _xml_id;
}
-LabelingMethod::LabelingMethod( const LabelingMethod & other):_xml_id(other._xml_id) {
- for (Label * p_label: other._label_list) {
- _label_list.push_back( new Label(*p_label));
+LabelingMethod::LabelingMethod(const LabelingMethod &other)
+ : _xml_id(other._xml_id)
+{
+ for(Label *p_label : other._label_list)
+ {
+ _label_list.push_back(new Label(*p_label));
}
}
-LabelingMethod::~LabelingMethod() {
- for (Label * p_label: _label_list) {
- delete p_label;
+LabelingMethod::~LabelingMethod()
+{
+ for(Label *p_label : _label_list)
+ {
+ delete p_label;
}
}
-LabelingMethodSp LabelingMethod::makeLabelingMethodSp() const {
- return std::make_shared<LabelingMethod>(*this);
+LabelingMethodSp
+LabelingMethod::makeLabelingMethodSp() const
+{
+ return std::make_shared<LabelingMethod>(*this);
}
-void LabelingMethod::parseMethod(QDomNode & method_node) {
- QDomNode child = method_node.firstChild();
- while (!child.isNull()) {
- if (child.toElement().tagName() == "isotope_label") {
- _label_list.push_back( new Label(child));
+void
+LabelingMethod::parseMethod(QDomNode &method_node)
+{
+ QDomNode child = method_node.firstChild();
+ while(!child.isNull())
+ {
+ if(child.toElement().tagName() == "isotope_label")
+ {
+ _label_list.push_back(new Label(child));
}
- child = child.nextSibling();
+ child = child.nextSibling();
}
}
-void LabelingMethod::writeMassChroqMl(QXmlStreamWriter* output_stream) const {
- //<isotope_label_list>
- output_stream->writeStartElement("isotope_label_list");
- output_stream->writeComment(getXmlId());
- /*
- <isotope_label id="iso1">
- <mod at="Nter" value="28.0" acc="MOD:00429"/>
- <mod at="K" value="28.0" acc="MOD:00429"/>
- </isotope_label>
- <isotope_label id="iso2">
- <mod at="Nter" value="32.0" />
- <mod at="K" value="32.0" />
- </isotope_label>*/
- for (Label * p_label: _label_list) {
- p_label->writeMassChroqMl(output_stream);
+void
+LabelingMethod::writeMassChroqMl(QXmlStreamWriter *output_stream) const
+{
+ //<isotope_label_list>
+ output_stream->writeStartElement("isotope_label_list");
+ output_stream->writeComment(getXmlId());
+ /*
+ <isotope_label id="iso1">
+ <mod at="Nter" value="28.0" acc="MOD:00429"/>
+ <mod at="K" value="28.0" acc="MOD:00429"/>
+ </isotope_label>
+ <isotope_label id="iso2">
+ <mod at="Nter" value="32.0" />
+ <mod at="K" value="32.0" />
+ </isotope_label>*/
+ for(Label *p_label : _label_list)
+ {
+ p_label->writeMassChroqMl(output_stream);
}
- //</isotope_label_list>
- output_stream->writeEndElement();
+ //</isotope_label_list>
+ output_stream->writeEndElement();
}
-const std::vector<Label *> & LabelingMethod::getLabelList() const {
- return _label_list;
+const std::vector<Label *> &
+LabelingMethod::getLabelList() const
+{
+ return _label_list;
}
diff --git a/src/core/labeling/labelingmethod.h b/src/core/labeling/labelingmethod.h
index 6d4bf6fbeaa44c6b5f2b351aeaaedacdcb96a1e0..e0b03080cb8aaba302f310e343bad18491a0c8c5 100644
--- a/src/core/labeling/labelingmethod.h
+++ b/src/core/labeling/labelingmethod.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef LABELINGMETHOD_H
#define LABELINGMETHOD_H
@@ -41,21 +42,24 @@ typedef std::shared_ptr<LabelingMethod> LabelingMethodSp;
class LabelingMethod
{
-public:
- LabelingMethod(const QString & method_id);
- LabelingMethod( const LabelingMethod & other);
- ~LabelingMethod();
- LabelingMethodSp makeLabelingMethodSp() const;
- Label * getLabel(const std::list<pappso::AaModificationP> & modification_set) const;
- const QString & getXmlId() const;
- void writeMassChroqMl(QXmlStreamWriter* output_stream) const;
- const std::vector<Label *> & getLabelList() const;
-private :
- void parseMethod(QDomNode & method_node);
- void parseLabel(QDomNode & method_node);
-private:
- const QString _xml_id;
- std::vector<Label *> _label_list;
+ public:
+ LabelingMethod(const QString &method_id);
+ LabelingMethod(const LabelingMethod &other);
+ ~LabelingMethod();
+ LabelingMethodSp makeLabelingMethodSp() const;
+ Label *
+ getLabel(const std::list<pappso::AaModificationP> &modification_set) const;
+ const QString &getXmlId() const;
+ void writeMassChroqMl(QXmlStreamWriter *output_stream) const;
+ const std::vector<Label *> &getLabelList() const;
+
+ private:
+ void parseMethod(QDomNode &method_node);
+ void parseLabel(QDomNode &method_node);
+
+ private:
+ const QString _xml_id;
+ std::vector<Label *> _label_list;
};
#endif // LABELINGMETHOD_H
diff --git a/src/core/msrun.h b/src/core/msrun.h
index 08f04a8536662143bfc9da729f436c13659a29ef..742b3a0c48084e185c6a4fb305597d0a56bf950c 100644
--- a/src/core/msrun.h
+++ b/src/core/msrun.h
@@ -7,26 +7,27 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef MSRUN_H
@@ -43,43 +44,43 @@
class MsRun;
typedef std::shared_ptr<MsRun> MsRunSp;
-class MsRun:public pappso::MsRunId
+class MsRun : public pappso::MsRunId
{
-public:
- MsRun(const QString & location);
- MsRun(const MsRun& other);
- ~MsRun();
-
-
- /** \brief set MS run statistics
- * any statistics on this MS run file
- */
- virtual void setMsRunStatistics(MsRunStatistics param, const QVariant& value);
-
-
- /** \brief get MS run statistics
- */
- virtual const QVariant getMsRunStatistics(MsRunStatistics param) const;
-
- /** \brief get MS run statistics map
- */
- virtual const std::map<MsRunStatistics, QVariant> & getMsRunStatisticsMap() const;
-
- bool findMsRunFile();
-
- pappso::MsRunReaderSp & getMsRunReaderSp();
-
- void checkMsRunStatistics();
-
- pappso::MsRunXicExtractorSp getMsRunXicExtractorSp();
-
-private :
- std::map<MsRunStatistics, QVariant> _param_stats;
-
- pappso::MsRunReaderSp _msrun_reader_sp;
-
- pappso::MsRunXicExtractorSp _xic_extractor_sp;
-
+ public:
+ MsRun(const QString &location);
+ MsRun(const MsRun &other);
+ ~MsRun();
+
+
+ /** \brief set MS run statistics
+ * any statistics on this MS run file
+ */
+ virtual void setMsRunStatistics(MsRunStatistics param, const QVariant &value);
+
+
+ /** \brief get MS run statistics
+ */
+ virtual const QVariant getMsRunStatistics(MsRunStatistics param) const;
+
+ /** \brief get MS run statistics map
+ */
+ virtual const std::map<MsRunStatistics, QVariant> &
+ getMsRunStatisticsMap() const;
+
+ bool findMsRunFile();
+
+ pappso::MsRunReaderSp &getMsRunReaderSp();
+
+ void checkMsRunStatistics();
+
+ pappso::MsRunXicExtractorSp getMsRunXicExtractorSp();
+
+ private:
+ std::map<MsRunStatistics, QVariant> _param_stats;
+
+ pappso::MsRunReaderSp _msrun_reader_sp;
+
+ pappso::MsRunXicExtractorSp _xic_extractor_sp;
};
#endif // MSRUN_H
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index 911e1b71125f3564280b55d48536e82438d2522a..10c7e6049836c8238391142d329b2ee7db880c7c 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -1,75 +1,98 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "peptidematch.h"
#include <pappsomspp/pappsoexception.h>
-PeptideMatch::PeptideMatch() {
+PeptideMatch::PeptideMatch()
+{
}
-PeptideMatch::PeptideMatch(const PeptideMatch & other) {
- _start=other._start;
- _p_peptide_evidence = other._p_peptide_evidence;
+PeptideMatch::PeptideMatch(const PeptideMatch &other)
+{
+ _start = other._start;
+ _p_peptide_evidence = other._p_peptide_evidence;
}
-bool PeptideMatch::operator==(const PeptideMatch & other) const {
- if ((_p_peptide_evidence == other._p_peptide_evidence) && (_start == other._start)) {
- return true;
+bool
+PeptideMatch::operator==(const PeptideMatch &other) const
+{
+ if((_p_peptide_evidence == other._p_peptide_evidence) &&
+ (_start == other._start))
+ {
+ return true;
}
- return false;
+ return false;
}
-void PeptideMatch::setPeptideEvidenceSp(PeptideEvidenceSp sp_peptide_evidence) {
- _p_peptide_evidence = sp_peptide_evidence.get();
+void
+PeptideMatch::setPeptideEvidenceSp(PeptideEvidenceSp sp_peptide_evidence)
+{
+ _p_peptide_evidence = sp_peptide_evidence.get();
}
-const PeptideEvidence * PeptideMatch::getPeptideEvidence() const {
- return _p_peptide_evidence;
+const PeptideEvidence *
+PeptideMatch::getPeptideEvidence() const
+{
+ return _p_peptide_evidence;
}
-PeptideEvidence * PeptideMatch::getPeptideEvidence() {
- return _p_peptide_evidence;
+PeptideEvidence *
+PeptideMatch::getPeptideEvidence()
+{
+ return _p_peptide_evidence;
}
-void PeptideMatch::setStart(unsigned int start) {
- _start =start;
+void
+PeptideMatch::setStart(unsigned int start)
+{
+ _start = start;
}
-unsigned int PeptideMatch::getStart() const {
- return _start;
+unsigned int
+PeptideMatch::getStart() const
+{
+ return _start;
}
-unsigned int PeptideMatch::getStop() const {
- return _start+_p_peptide_evidence->getPeptideXtpSp().get()->size();
+unsigned int
+PeptideMatch::getStop() const
+{
+ return _start + _p_peptide_evidence->getPeptideXtpSp().get()->size();
}
-bool PeptideMatch::operator<(const PeptideMatch& r) const
+bool
+PeptideMatch::operator<(const PeptideMatch &r) const
{
- return std::tie(_start, _p_peptide_evidence)
- < std::tie(r._start, r._p_peptide_evidence); // keep the same order
+ return std::tie(_start, _p_peptide_evidence) <
+ std::tie(r._start, r._p_peptide_evidence); // keep the same order
}
-bool PeptideMatch::containsPosition(unsigned int position) const {
- if (position < _start) {
- return false;
+bool
+PeptideMatch::containsPosition(unsigned int position) const
+{
+ if(position < _start)
+ {
+ return false;
}
- if (position < getStop()) {
- return true;
+ if(position < getStop())
+ {
+ return true;
}
- return false;
-
+ return false;
}
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 4dc8369a734fca76f7b22a9d69391d834de99a77..c14601374efce14aa2fa173118449344cb42631c 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PEPTIDEMATCH_H
#define PEPTIDEMATCH_H
@@ -28,41 +29,42 @@
class PeptideMatch
{
-public :
- PeptideMatch();
- PeptideMatch(const PeptideMatch & other);
-
- bool operator==(const PeptideMatch & other) const;
+ public:
+ PeptideMatch();
+ PeptideMatch(const PeptideMatch &other);
+ bool operator==(const PeptideMatch &other) const;
- /** @brief set start position of this peptide inside the protein sequence
- * @param start position in the protein amino acid sequence (starts at 0)
- * */
- void setStart(unsigned int start);
- /** @brief get start position of this peptide inside the protein sequence
- * @return start position in the protein amino acid sequence (starts at 0)
- * */
- unsigned int getStart() const;
- /** @brief get stop position of this peptide inside the protein sequence
- * @return stop position in the protein amino acid sequence (starts at 0)
- * */
- unsigned int getStop() const;
- /** @brief tells if this peptide contains a protein position
- * the position is the amino acid position on the protein sequence (starts from 0)
- * */
- bool containsPosition(unsigned int position) const;
-
- void setPeptideEvidenceSp(PeptideEvidenceSp sp_peptide_evidence);
- const PeptideEvidence * getPeptideEvidence() const;
- PeptideEvidence * getPeptideEvidence();
-
-
- bool operator<(const PeptideMatch& r) const;
+ /** @brief set start position of this peptide inside the protein sequence
+ * @param start position in the protein amino acid sequence (starts at 0)
+ * */
+ void setStart(unsigned int start);
+ /** @brief get start position of this peptide inside the protein sequence
+ * @return start position in the protein amino acid sequence (starts at 0)
+ * */
+ unsigned int getStart() const;
+ /** @brief get stop position of this peptide inside the protein sequence
+ * @return stop position in the protein amino acid sequence (starts at 0)
+ * */
+ unsigned int getStop() const;
-private :
- unsigned int _start=0;
- PeptideEvidence * _p_peptide_evidence=nullptr;
+ /** @brief tells if this peptide contains a protein position
+ * the position is the amino acid position on the protein sequence (starts
+ * from 0)
+ * */
+ bool containsPosition(unsigned int position) const;
+
+ void setPeptideEvidenceSp(PeptideEvidenceSp sp_peptide_evidence);
+ const PeptideEvidence *getPeptideEvidence() const;
+ PeptideEvidence *getPeptideEvidence();
+
+
+ bool operator<(const PeptideMatch &r) const;
+
+ private:
+ unsigned int _start = 0;
+ PeptideEvidence *_p_peptide_evidence = nullptr;
};
#endif // PEPTIDEMATCH_H
diff --git a/src/core/peptidextp.cpp b/src/core/peptidextp.cpp
index 1c2abad5b06e07f92f2b61b739f57fd7ed7c23b8..d4dd5d93da24d12cfca77bf83f228631198e7647 100644
--- a/src/core/peptidextp.cpp
+++ b/src/core/peptidextp.cpp
@@ -1,112 +1,141 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "peptidextp.h"
#include <QStringList>
#include <set>
-PeptideXtp::PeptideXtp(const QString & pepstr):pappso::Peptide(pepstr)
+PeptideXtp::PeptideXtp(const QString &pepstr) : pappso::Peptide(pepstr)
{
-
}
-PeptideXtp::PeptideXtp(const PeptideXtp& other):pappso::Peptide(other)
+PeptideXtp::PeptideXtp(const PeptideXtp &other) : pappso::Peptide(other)
{
-
}
PeptideXtp::~PeptideXtp()
{
-
}
-const QString PeptideXtp::getModifString() const {
- QStringList modif_list;
- unsigned int i=1;
- for (const pappso::Aa & amino_acid:_aa_vec) {
- std::list<pappso::AaModificationP> aa_modif_list = amino_acid.getModificationList();
- QStringList aamodif;
- for (auto && aa_modif : aa_modif_list) {
- if (!aa_modif->isInternal()) {
- aamodif << QString::number(aa_modif->getMass(), 'f', 2);
+const QString
+PeptideXtp::getModifString() const
+{
+ QStringList modif_list;
+ unsigned int i = 1;
+ for(const pappso::Aa &amino_acid : _aa_vec)
+ {
+ std::list<pappso::AaModificationP> aa_modif_list =
+ amino_acid.getModificationList();
+ QStringList aamodif;
+ for(auto &&aa_modif : aa_modif_list)
+ {
+ if(!aa_modif->isInternal())
+ {
+ aamodif << QString::number(aa_modif->getMass(), 'f', 2);
}
}
- aamodif.sort();
- QString mod_str(aamodif.join("|"));
- if (!mod_str.isEmpty()) {
- modif_list << QString("%1%2:%3").arg(i).arg(amino_acid.getLetter()).arg(mod_str);
+ aamodif.sort();
+ QString mod_str(aamodif.join("|"));
+ if(!mod_str.isEmpty())
+ {
+ modif_list << QString("%1%2:%3")
+ .arg(i)
+ .arg(amino_acid.getLetter())
+ .arg(mod_str);
}
- i++;
+ i++;
}
- //return QString ("%1 %2").arg(modif_list.join(" ")).arg(this->toAbsoluteString());
- return modif_list.join(" ");
+ // return QString ("%1 %2").arg(modif_list.join("
+ // ")).arg(this->toAbsoluteString());
+ return modif_list.join(" ");
}
-PeptideXtpSp PeptideXtp::makePeptideXtpSp() const {
- return std::make_shared<PeptideXtp>(*this);
+PeptideXtpSp
+PeptideXtp::makePeptideXtpSp() const
+{
+ return std::make_shared<PeptideXtp>(*this);
}
-pappso::mz PeptideXtp::getGroupingMass() const {
- return getNativePeptideP()->getMass();
+pappso::mz
+PeptideXtp::getGroupingMass() const
+{
+ return getNativePeptideP()->getMass();
}
-void PeptideXtp::clearLabel() {
- _sp_native_peptide = nullptr;
- _p_label = nullptr;
+void
+PeptideXtp::clearLabel()
+{
+ _sp_native_peptide = nullptr;
+ _p_label = nullptr;
}
-const pappso::Peptide * PeptideXtp::getNativePeptideP() const {
- if (_sp_native_peptide.get() == nullptr) {
- return this;
+const pappso::Peptide *
+PeptideXtp::getNativePeptideP() const
+{
+ if(_sp_native_peptide.get() == nullptr)
+ {
+ return this;
}
- return _sp_native_peptide.get();
+ return _sp_native_peptide.get();
}
-bool PeptideXtp::replaceModification(pappso::AaModificationP oldmod, pappso::AaModificationP newmod) {
-
- pappso::Peptide::replaceAaModification(oldmod, newmod);
- if (_sp_native_peptide.get() != nullptr) {
- //_sp_native_peptide.get()->replaceAaModification(oldmod, newmod);
+bool
+PeptideXtp::replaceModification(pappso::AaModificationP oldmod,
+ pappso::AaModificationP newmod)
+{
+
+ pappso::Peptide::replaceAaModification(oldmod, newmod);
+ if(_sp_native_peptide.get() != nullptr)
+ {
+ //_sp_native_peptide.get()->replaceAaModification(oldmod, newmod);
}
-
}
-void PeptideXtp::applyLabelingMethod(LabelingMethodSp labeling_method_sp) {
- std::list<pappso::AaModificationP> modification_set;
- for (const pappso::Aa & amino_acid:_aa_vec) {
- std::list<pappso::AaModificationP> aa_modif_list = amino_acid.getModificationList();
- modification_set.insert(modification_set.begin(),aa_modif_list.begin(), aa_modif_list.end());
+void
+PeptideXtp::applyLabelingMethod(LabelingMethodSp labeling_method_sp)
+{
+ std::list<pappso::AaModificationP> modification_set;
+ for(const pappso::Aa &amino_acid : _aa_vec)
+ {
+ std::list<pappso::AaModificationP> aa_modif_list =
+ amino_acid.getModificationList();
+ modification_set.insert(modification_set.begin(), aa_modif_list.begin(),
+ aa_modif_list.end());
}
- modification_set.unique();
-
- _p_label = nullptr;
- Label * p_label = labeling_method_sp.get()->getLabel(modification_set);
- if (p_label != nullptr) {
- _p_label = p_label;
- _sp_native_peptide = _p_label->getLabeledPeptideSp(this);
+ modification_set.unique();
+
+ _p_label = nullptr;
+ Label *p_label = labeling_method_sp.get()->getLabel(modification_set);
+ if(p_label != nullptr)
+ {
+ _p_label = p_label;
+ _sp_native_peptide = _p_label->getLabeledPeptideSp(this);
}
}
-const Label * PeptideXtp::getLabel() const {
+const Label *
+PeptideXtp::getLabel() const
+{
return _p_label;
}
diff --git a/src/core/peptidextp.h b/src/core/peptidextp.h
index 8353eb854dd3362ee511341fea786989e5fdc0be..a1539d679b13f41f1706604f76891703461afedf 100644
--- a/src/core/peptidextp.h
+++ b/src/core/peptidextp.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PEPTIDEXTP_H
#define PEPTIDEXTP_H
@@ -35,48 +36,48 @@ typedef std::shared_ptr<PeptideXtp> PeptideXtpSp;
class PeptideXtp : public pappso::Peptide
{
-public:
- PeptideXtp(const QString & pepstr);
- PeptideXtp(const PeptideXtp& other);
- ~PeptideXtp();
-
- PeptideXtpSp makePeptideXtpSp() const;
-
- /** \brief get the theoretical mass to use for grouping
- * This mass might be different than the true peptide mass to recognize that a tagged
- * peptide with taget modification is a light, inter or heavy version of the same peptide
- */
- pappso::mz getGroupingMass() const;
-
- const pappso::Peptide * getNativePeptideP() const;
-
- /** \brief human readable string that contains modifications
- * */
- const QString getModifString() const;
-
- /** @brief replace modification in peptide
- */
- bool replaceModification(pappso::AaModificationP oldmod, pappso::AaModificationP newmod);
-
- /** @brief reset label
- * */
- void clearLabel();
- /** @brief try to apply any label from this labeling method
- * */
- void applyLabelingMethod(LabelingMethodSp labeling_method_sp);
-
- /** @brief get label
- * */
- const Label * getLabel() const;
-
-private:
- /** \brief if the peptide is tagged, this is the native peptide without tags
- */
- pappso::PeptideSp _sp_native_peptide = nullptr;
-
- Label * _p_label = nullptr;
-
-
+ public:
+ PeptideXtp(const QString &pepstr);
+ PeptideXtp(const PeptideXtp &other);
+ ~PeptideXtp();
+
+ PeptideXtpSp makePeptideXtpSp() const;
+
+ /** \brief get the theoretical mass to use for grouping
+ * This mass might be different than the true peptide mass to recognize that a
+ * tagged peptide with taget modification is a light, inter or heavy version
+ * of the same peptide
+ */
+ pappso::mz getGroupingMass() const;
+
+ const pappso::Peptide *getNativePeptideP() const;
+
+ /** \brief human readable string that contains modifications
+ * */
+ const QString getModifString() const;
+
+ /** @brief replace modification in peptide
+ */
+ bool replaceModification(pappso::AaModificationP oldmod,
+ pappso::AaModificationP newmod);
+
+ /** @brief reset label
+ * */
+ void clearLabel();
+ /** @brief try to apply any label from this labeling method
+ * */
+ void applyLabelingMethod(LabelingMethodSp labeling_method_sp);
+
+ /** @brief get label
+ * */
+ const Label *getLabel() const;
+
+ private:
+ /** \brief if the peptide is tagged, this is the native peptide without tags
+ */
+ pappso::PeptideSp _sp_native_peptide = nullptr;
+
+ Label *_p_label = nullptr;
};
#endif // PEPTIDEXTP_H
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 9beaae9a6d818bd42ca39fa7f0ad15781359aeb4..effd7a3af2d0ea19870b51d08fbbfbc0ffee3cad 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "project.h"
#include "../input/xpipsaxhandler.h"
#include "../input/xtpxpipsaxhandler.h"
@@ -29,180 +30,262 @@
Project::Project()
{
-
}
Project::~Project()
{
- auto it = _identification_goup_list.begin();
- while (it != _identification_goup_list.end()) {
- delete (*it);
- it++;
+ auto it = _identification_goup_list.begin();
+ while(it != _identification_goup_list.end())
+ {
+ delete(*it);
+ it++;
}
}
-bool Project::checkPsimodCompliance() const {
- return _peptide_store.checkPsimodCompliance();
+bool
+Project::checkPsimodCompliance() const
+{
+ return _peptide_store.checkPsimodCompliance();
}
-void Project::readResultFile(QString filename) {
- IdentificationDataSourceSp ident_source = _identification_data_source_store.getInstance(filename);
+void
+Project::readResultFile(QString filename)
+{
+ IdentificationDataSourceSp ident_source =
+ _identification_data_source_store.getInstance(filename);
- ident_source.get()->parseTo(this);
- qDebug() << "Project::readResultFile end";
+ ident_source.get()->parseTo(this);
+ qDebug() << "Project::readResultFile end";
}
-const ProjectMode Project::getProjectMode() const {
- return _project_mode;
+const ProjectMode
+Project::getProjectMode() const
+{
+ return _project_mode;
}
-void Project::setProjectMode(ProjectMode mode) {
- _project_mode = mode;
+void
+Project::setProjectMode(ProjectMode mode)
+{
+ _project_mode = mode;
}
-std::vector<IdentificationGroup *> Project::getIdentificationGroupList() {
- return _identification_goup_list;
+std::vector<IdentificationGroup *>
+Project::getIdentificationGroupList()
+{
+ return _identification_goup_list;
}
-const std::vector<IdentificationGroup *> Project::getIdentificationGroupList() const {
- return _identification_goup_list;
+const std::vector<IdentificationGroup *>
+Project::getIdentificationGroupList() const
+{
+ return _identification_goup_list;
}
-const GroupingType Project::getGroupingType() const {
- return _grouping_type;
+const GroupingType
+Project::getGroupingType() const
+{
+ return _grouping_type;
}
-FastaFileStore & Project::getFastaFileStore() {
- return _fasta_file_store;
+FastaFileStore &
+Project::getFastaFileStore()
+{
+ return _fasta_file_store;
}
-const FastaFileStore & Project::getFastaFileStore() const {
- return _fasta_file_store;
+const FastaFileStore &
+Project::getFastaFileStore() const
+{
+ return _fasta_file_store;
}
-MsRunStore & Project::getMsRunStore() {
- return _msrun_store;
+MsRunStore &
+Project::getMsRunStore()
+{
+ return _msrun_store;
}
-const MsRunStore & Project::getMsRunStore() const {
- return _msrun_store;
+const MsRunStore &
+Project::getMsRunStore() const
+{
+ return _msrun_store;
}
-PeptideStore & Project::getPeptideStore() {
- return _peptide_store;
+PeptideStore &
+Project::getPeptideStore()
+{
+ return _peptide_store;
}
-ProteinStore & Project::getProteinStore() {
- return _protein_store;
+ProteinStore &
+Project::getProteinStore()
+{
+ return _protein_store;
}
-const ProteinStore & Project::getProteinStore() const {
- return _protein_store;
+const ProteinStore &
+Project::getProteinStore() const
+{
+ return _protein_store;
}
-IdentificationDataSourceStore & Project::getIdentificationDataSourceStore() {
- return _identification_data_source_store;
+IdentificationDataSourceStore &
+Project::getIdentificationDataSourceStore()
+{
+ return _identification_data_source_store;
}
-const IdentificationDataSourceStore & Project::getIdentificationDataSourceStore() const {
- return _identification_data_source_store;
+const IdentificationDataSourceStore &
+Project::getIdentificationDataSourceStore() const
+{
+ return _identification_data_source_store;
}
-const AutomaticFilterParameters & Project::getAutomaticFilterParameters() const {
- return _automatic_filter_parameters;
+const AutomaticFilterParameters &
+Project::getAutomaticFilterParameters() const
+{
+ return _automatic_filter_parameters;
}
-void Project::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
+void
+Project::updateAutomaticFilters(
+ const AutomaticFilterParameters &automatic_filter_parameters)
+{
- qDebug() << "Project::updateAutomaticFilters begin";
- _automatic_filter_parameters = automatic_filter_parameters;
- for (auto & p_id_group : _identification_goup_list) {
- p_id_group->updateAutomaticFilters(_automatic_filter_parameters);
+ qDebug() << "Project::updateAutomaticFilters begin";
+ _automatic_filter_parameters = automatic_filter_parameters;
+ for(auto &p_id_group : _identification_goup_list)
+ {
+ p_id_group->updateAutomaticFilters(_automatic_filter_parameters);
}
- qDebug() << "Project::updateAutomaticFilters end";
+ qDebug() << "Project::updateAutomaticFilters end";
}
-ProjectSp Project::makeProjectSp() const {
- return std::make_shared<Project>(*this);
+ProjectSp
+Project::makeProjectSp() const
+{
+ return std::make_shared<Project>(*this);
}
-IdentificationGroup* Project::newIdentificationGroup() {
- _p_current_identification_group = new IdentificationGroup(this);
- _identification_goup_list.push_back(_p_current_identification_group);
- return _p_current_identification_group;
+IdentificationGroup *
+Project::newIdentificationGroup()
+{
+ _p_current_identification_group = new IdentificationGroup(this);
+ _identification_goup_list.push_back(_p_current_identification_group);
+ return _p_current_identification_group;
}
-void Project::readXpipFile(WorkMonitorInterface * p_monitor, QFileInfo xpip_fileinfo) {
- qDebug() << "Project::readXpipFile begin";
-
- XpipSaxHandler * parser_java_xpip = new XpipSaxHandler(p_monitor, this);
-
- QXmlSimpleReader simplereader;
- simplereader.setContentHandler(parser_java_xpip);
- simplereader.setErrorHandler(parser_java_xpip);
+void
+Project::readXpipFile(WorkMonitorInterface *p_monitor, QFileInfo xpip_fileinfo)
+{
+ qDebug() << "Project::readXpipFile begin";
- qDebug() << "Project::readXpipFile Read XPIP XML result file '" << xpip_fileinfo.absoluteFilePath() << "'";
+ XpipSaxHandler *parser_java_xpip = new XpipSaxHandler(p_monitor, this);
- QFile qfile(xpip_fileinfo.absoluteFilePath());
- QXmlInputSource xmlInputSource(&qfile);
+ QXmlSimpleReader simplereader;
+ simplereader.setContentHandler(parser_java_xpip);
+ simplereader.setErrorHandler(parser_java_xpip);
- if (simplereader.parse(xmlInputSource)) {
+ qDebug() << "Project::readXpipFile Read XPIP XML result file '"
+ << xpip_fileinfo.absoluteFilePath() << "'";
- qfile.close();
- } else {
- qDebug() << parser_java_xpip->errorString();
- // throw PappsoException(
- // QObject::tr("error reading tandem XML result file :\n").append(
- // parser->errorString()));
+ QFile qfile(xpip_fileinfo.absoluteFilePath());
+ QXmlInputSource xmlInputSource(&qfile);
- qfile.close();
+ if(simplereader.parse(xmlInputSource))
+ {
- if (parser_java_xpip->isJavaXpip()) {
- //delete parser_java_xpip;
- throw pappso::PappsoException(QObject::tr("Error reading %1 XPIP file :\n %2").arg(xpip_fileinfo.absoluteFilePath()).arg(parser_java_xpip->errorString()));
+ qfile.close();
+ }
+ else
+ {
+ qDebug() << parser_java_xpip->errorString();
+ // throw PappsoException(
+ // QObject::tr("error reading tandem XML result file :\n").append(
+ // parser->errorString()));
+
+ qfile.close();
+
+ if(parser_java_xpip->isJavaXpip())
+ {
+ // delete parser_java_xpip;
+ throw pappso::PappsoException(
+ QObject::tr("Error reading %1 XPIP file :\n %2")
+ .arg(xpip_fileinfo.absoluteFilePath())
+ .arg(parser_java_xpip->errorString()));
}
- else {
- XtpXpipSaxHandler * parser_xtp_xpip = new XtpXpipSaxHandler(p_monitor, this);
+ else
+ {
+ XtpXpipSaxHandler *parser_xtp_xpip =
+ new XtpXpipSaxHandler(p_monitor, this);
- QXmlSimpleReader simplereaderb;
- simplereaderb.setContentHandler(parser_xtp_xpip);
- simplereaderb.setErrorHandler(parser_xtp_xpip);
+ QXmlSimpleReader simplereaderb;
+ simplereaderb.setContentHandler(parser_xtp_xpip);
+ simplereaderb.setErrorHandler(parser_xtp_xpip);
- qDebug() << "Project::readXpipFile Read XPIP XML result file '" << xpip_fileinfo.absoluteFilePath() << "'";
+ qDebug() << "Project::readXpipFile Read XPIP XML result file '"
+ << xpip_fileinfo.absoluteFilePath() << "'";
- QFile qfileb(xpip_fileinfo.absoluteFilePath());
- QXmlInputSource xmlInputSourceb(&qfileb);
+ QFile qfileb(xpip_fileinfo.absoluteFilePath());
+ QXmlInputSource xmlInputSourceb(&qfileb);
- if (simplereaderb.parse(xmlInputSourceb)) {
- delete parser_xtp_xpip;
- qfileb.close();
- } else {
- if (parser_xtp_xpip->isXtpXpip()) {
- throw pappso::PappsoException(QObject::tr("Error reading %1 XPIP file :\n %2").arg(xpip_fileinfo.absoluteFilePath()).arg(parser_xtp_xpip->errorString()));
+ if(simplereaderb.parse(xmlInputSourceb))
+ {
+ delete parser_xtp_xpip;
+ qfileb.close();
+ }
+ else
+ {
+ if(parser_xtp_xpip->isXtpXpip())
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error reading %1 XPIP file :\n %2")
+ .arg(xpip_fileinfo.absoluteFilePath())
+ .arg(parser_xtp_xpip->errorString()));
}
- else {
- qDebug() << parser_xtp_xpip->errorString();
- throw pappso::PappsoException(QObject::tr("Error reading %1 XPIP file :\n it is not an XPIP file").arg(xpip_fileinfo.absoluteFilePath()));
+ else
+ {
+ qDebug() << parser_xtp_xpip->errorString();
+ throw pappso::PappsoException(
+ QObject::tr(
+ "Error reading %1 XPIP file :\n it is not an XPIP file")
+ .arg(xpip_fileinfo.absoluteFilePath()));
}
}
-
}
}
- delete parser_java_xpip;
+ delete parser_java_xpip;
}
-void Project::startGrouping(WorkMonitorInterface * p_work_monitor) {
- for (IdentificationGroup * p_id_group : _identification_goup_list) {
- p_id_group->startGrouping(_grouping_type, p_work_monitor);
+void
+Project::startGrouping(WorkMonitorInterface *p_work_monitor)
+{
+ for(IdentificationGroup *p_id_group : _identification_goup_list)
+ {
+ p_id_group->startGrouping(_grouping_type, p_work_monitor);
}
}
-void Project::setLabelingMethodSp(LabelingMethodSp labeling_method_sp) {
- _labeling_method_sp = labeling_method_sp;
- _peptide_store.setLabelingMethodSp(labeling_method_sp);
+void
+Project::setLabelingMethodSp(LabelingMethodSp labeling_method_sp)
+{
+ _labeling_method_sp = labeling_method_sp;
+ _peptide_store.setLabelingMethodSp(labeling_method_sp);
}
-LabelingMethodSp Project::getLabelingMethodSp() const {
- return _labeling_method_sp;
+LabelingMethodSp
+Project::getLabelingMethodSp() const
+{
+ return _labeling_method_sp;
}
-bool Project::hasPtmExperiment() const {
- if (getIdentificationGroupList().at(0)->getPtmGroupingExperiment() != nullptr) return true;
- return false;
+bool
+Project::hasPtmExperiment() const
+{
+ if(getIdentificationGroupList().at(0)->getPtmGroupingExperiment() != nullptr)
+ return true;
+ return false;
}
-void Project::getSameXicPeptideEvidenceList(std::vector<const PeptideEvidence *> & peptide_evidence_list, const MsRun * p_msrun, const PeptideXtp * p_peptide, unsigned int charge) const {
- for (const IdentificationGroup * p_ident_group: _identification_goup_list) {
- p_ident_group->getSameXicPeptideEvidenceList(peptide_evidence_list, p_msrun, p_peptide, charge);
+void
+Project::getSameXicPeptideEvidenceList(
+ std::vector<const PeptideEvidence *> &peptide_evidence_list,
+ const MsRun *p_msrun, const PeptideXtp *p_peptide, unsigned int charge) const
+{
+ for(const IdentificationGroup *p_ident_group : _identification_goup_list)
+ {
+ p_ident_group->getSameXicPeptideEvidenceList(peptide_evidence_list,
+ p_msrun, p_peptide, charge);
}
}
diff --git a/src/core/project.h b/src/core/project.h
index 3710b3d3e51e5ba73f87c2c655ae8e2ad077170a..3fbbdd7ae6dadb78b96b14a3408423b6662f9515 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -1,29 +1,30 @@
/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PROJECT_H
#define PROJECT_H
-#include<memory>
+#include <memory>
#include "identificationgroup.h"
#include "automaticfilterparameters.h"
#include "../utils/types.h"
@@ -42,75 +43,79 @@ class ProteinMatch;
class Project
{
-public:
- Project();
- ~Project();
-
- ProjectSp makeProjectSp() const;
- ProteinStore & getProteinStore();
- PeptideStore & getPeptideStore();
- const ProteinStore & getProteinStore() const;
- MsRunStore & getMsRunStore();
- const MsRunStore & getMsRunStore() const;
- FastaFileStore & getFastaFileStore();
- const FastaFileStore & getFastaFileStore() const;
- IdentificationDataSourceStore & getIdentificationDataSourceStore();
- const IdentificationDataSourceStore & getIdentificationDataSourceStore() const;
- void readXpipFile(WorkMonitorInterface * p_monitor, QFileInfo xpip_source);
- IdentificationGroup* newIdentificationGroup();
-
- /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
- * */
- void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
- const AutomaticFilterParameters & getAutomaticFilterParameters() const;
- void startGrouping(WorkMonitorInterface * p_work_monitor);
-
- const GroupingType getGroupingType() const;
- const ProjectMode getProjectMode() const;
- void setProjectMode(ProjectMode mode);
-
- std::vector<IdentificationGroup *> getIdentificationGroupList();
- const std::vector<IdentificationGroup *> getIdentificationGroupList() const;
- void readResultFile(QString filename);
-
- /** @brief check that modifications are coded with PSI MOD accessions
- */
- bool checkPsimodCompliance() const;
-
- /** @brief apply labeling method to all peptide match
- * */
- void setLabelingMethodSp(LabelingMethodSp labeling_method_sp);
-
- /** @brief get labeling method shared pointer
- * */
- LabelingMethodSp getLabelingMethodSp() const;
-
- bool hasPtmExperiment() const;
-
- /** @brief look for a peptide in the same XIC
- * @param peptide_evidence_list the peptide evidence list to build
- * @param p_msrun MSrun to look for
- * @param p_peptide peptide to look for
- * @param charge charge to look for
- */
- void getSameXicPeptideEvidenceList(std::vector<const PeptideEvidence *> & peptide_evidence_list, const MsRun * p_msrun, const PeptideXtp * p_peptide, unsigned int charge) const;
-
-private :
- LabelingMethodSp _labeling_method_sp;
- ProjectMode _project_mode = ProjectMode::combined;
- std::vector<IdentificationGroup *> _identification_goup_list;
- IdentificationGroup* _p_current_identification_group = nullptr;
-
- AutomaticFilterParameters _automatic_filter_parameters;
-
- GroupingType _grouping_type = GroupingType::PeptideMass;
-
- ProteinStore _protein_store;
- PeptideStore _peptide_store;
- IdentificationDataSourceStore _identification_data_source_store;
- MsRunStore _msrun_store;
- FastaFileStore _fasta_file_store;
-
+ public:
+ Project();
+ ~Project();
+
+ ProjectSp makeProjectSp() const;
+ ProteinStore &getProteinStore();
+ PeptideStore &getPeptideStore();
+ const ProteinStore &getProteinStore() const;
+ MsRunStore &getMsRunStore();
+ const MsRunStore &getMsRunStore() const;
+ FastaFileStore &getFastaFileStore();
+ const FastaFileStore &getFastaFileStore() const;
+ IdentificationDataSourceStore &getIdentificationDataSourceStore();
+ const IdentificationDataSourceStore &getIdentificationDataSourceStore() const;
+ void readXpipFile(WorkMonitorInterface *p_monitor, QFileInfo xpip_source);
+ IdentificationGroup *newIdentificationGroup();
+
+ /** @brief validate or invalidate peptides and proteins based automatic
+ * filters and manual checks
+ * */
+ void updateAutomaticFilters(
+ const AutomaticFilterParameters &automatic_filter_parameters);
+ const AutomaticFilterParameters &getAutomaticFilterParameters() const;
+ void startGrouping(WorkMonitorInterface *p_work_monitor);
+
+ const GroupingType getGroupingType() const;
+ const ProjectMode getProjectMode() const;
+ void setProjectMode(ProjectMode mode);
+
+ std::vector<IdentificationGroup *> getIdentificationGroupList();
+ const std::vector<IdentificationGroup *> getIdentificationGroupList() const;
+ void readResultFile(QString filename);
+
+ /** @brief check that modifications are coded with PSI MOD accessions
+ */
+ bool checkPsimodCompliance() const;
+
+ /** @brief apply labeling method to all peptide match
+ * */
+ void setLabelingMethodSp(LabelingMethodSp labeling_method_sp);
+
+ /** @brief get labeling method shared pointer
+ * */
+ LabelingMethodSp getLabelingMethodSp() const;
+
+ bool hasPtmExperiment() const;
+
+ /** @brief look for a peptide in the same XIC
+ * @param peptide_evidence_list the peptide evidence list to build
+ * @param p_msrun MSrun to look for
+ * @param p_peptide peptide to look for
+ * @param charge charge to look for
+ */
+ void getSameXicPeptideEvidenceList(
+ std::vector<const PeptideEvidence *> &peptide_evidence_list,
+ const MsRun *p_msrun, const PeptideXtp *p_peptide,
+ unsigned int charge) const;
+
+ private:
+ LabelingMethodSp _labeling_method_sp;
+ ProjectMode _project_mode = ProjectMode::combined;
+ std::vector<IdentificationGroup *> _identification_goup_list;
+ IdentificationGroup *_p_current_identification_group = nullptr;
+
+ AutomaticFilterParameters _automatic_filter_parameters;
+
+ GroupingType _grouping_type = GroupingType::PeptideMass;
+
+ ProteinStore _protein_store;
+ PeptideStore _peptide_store;
+ IdentificationDataSourceStore _identification_data_source_store;
+ MsRunStore _msrun_store;
+ FastaFileStore _fasta_file_store;
};
#endif // PROJECT_H
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 464294f979e29a47bbb60e314cfb9d43b047c77e..908c11ca894097a359c2b6178f6038c9efb7036e 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "proteinmatch.h"
#include <pappsomspp/grouping/grpprotein.h>
@@ -28,459 +29,717 @@
#include <cmath>
-QColor ProteinMatch::_color_peptide_background = QColor("yellow");
+QColor ProteinMatch::_color_peptide_background = QColor("yellow");
QColor ProteinMatch::_color_highlighted_peptide_background = QColor("#ff7878");
ProteinMatch::ProteinMatch()
{
-
}
ProteinMatch::~ProteinMatch()
{
}
-ValidationState ProteinMatch::getValidationState() const {
- if (isGrouped()) {
- return ValidationState::grouped;
- } else if (isValidAndChecked()) {
- return ValidationState::validAndChecked;
- } else if (isValid()) {
- return ValidationState::valid;
+ValidationState
+ProteinMatch::getValidationState() const
+{
+ if(isGrouped())
+ {
+ return ValidationState::grouped;
+ }
+ else if(isValidAndChecked())
+ {
+ return ValidationState::validAndChecked;
+ }
+ else if(isValid())
+ {
+ return ValidationState::valid;
}
- return ValidationState::notValid;
+ return ValidationState::notValid;
}
-void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
- //qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- _proxy_valid = false;
- unsigned int number_of_valid_peptides =0;
- bool cross_sample = automatic_filter_parameters.getFilterCrossSamplePeptideNumber();
-
- if (cross_sample) {
- number_of_valid_peptides= countSequenceLi(ValidationState::validAndChecked,nullptr);
+void
+ProteinMatch::updateAutomaticFilters(
+ const AutomaticFilterParameters &automatic_filter_parameters)
+{
+ // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _proxy_valid = false;
+ unsigned int number_of_valid_peptides = 0;
+ bool cross_sample =
+ automatic_filter_parameters.getFilterCrossSamplePeptideNumber();
+
+ if(cross_sample)
+ {
+ number_of_valid_peptides =
+ countSequenceLi(ValidationState::validAndChecked, nullptr);
}
- else {
- std::set<const MsRun *> msrun_set;
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match.getPeptideEvidence()->isValidAndChecked()) {
- msrun_set.insert(p_peptide_match.getPeptideEvidence()->getMsRunP());
+ else
+ {
+ std::set<const MsRun *> msrun_set;
+ for(auto &p_peptide_match : _peptide_match_list)
+ {
+ if(p_peptide_match.getPeptideEvidence()->isValidAndChecked())
+ {
+ msrun_set.insert(
+ p_peptide_match.getPeptideEvidence()->getMsRunP());
}
}
- for (const MsRun * p_msrun : msrun_set) {
- unsigned int count = countSequenceLi(ValidationState::validAndChecked,p_msrun);
- if (count > number_of_valid_peptides) {
- number_of_valid_peptides = count;
+ for(const MsRun *p_msrun : msrun_set)
+ {
+ unsigned int count =
+ countSequenceLi(ValidationState::validAndChecked, p_msrun);
+ if(count > number_of_valid_peptides)
+ {
+ number_of_valid_peptides = count;
}
}
}
- //qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- // qDebug() <<"ProteinMatch::updateAutomaticFilters begin 2" ;
- if (number_of_valid_peptides == 0) {
+ // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ // qDebug() <<"ProteinMatch::updateAutomaticFilters begin 2" ;
+ if(number_of_valid_peptides == 0)
+ {
- _proxy_valid = false;
- } else {
+ _proxy_valid = false;
+ }
+ else
+ {
- if (number_of_valid_peptides < automatic_filter_parameters.getFilterMinimumPeptidePerMatch()) {
+ if(number_of_valid_peptides <
+ automatic_filter_parameters.getFilterMinimumPeptidePerMatch())
+ {
}
- else {
- if (getEvalue() <= automatic_filter_parameters.getFilterProteinEvalue()) {
- _proxy_valid = true;
+ else
+ {
+ if(getEvalue() <=
+ automatic_filter_parameters.getFilterProteinEvalue())
+ {
+ _proxy_valid = true;
}
}
}
- //qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-const ProteinXtpSp & ProteinMatch::getProteinXtpSp() const {
- return _protein_sp;
+const ProteinXtpSp &
+ProteinMatch::getProteinXtpSp() const
+{
+ return _protein_sp;
}
-void ProteinMatch::setProteinXtpSp(ProteinXtpSp protein_sp) {
- _protein_sp = protein_sp;
+void
+ProteinMatch::setProteinXtpSp(ProteinXtpSp protein_sp)
+{
+ _protein_sp = protein_sp;
}
-bool ProteinMatch::isValid() const {
- return _proxy_valid;
+bool
+ProteinMatch::isValid() const
+{
+ return _proxy_valid;
}
-bool ProteinMatch::isChecked() const {
- return _checked;
+bool
+ProteinMatch::isChecked() const
+{
+ return _checked;
}
-bool ProteinMatch::isValidAndChecked() const {
- return _proxy_valid && _checked;
+bool
+ProteinMatch::isValidAndChecked() const
+{
+ return _proxy_valid && _checked;
}
-bool ProteinMatch::isGrouped() const {
- if (_sp_grp_protein.get() == nullptr) {
- return false;
+bool
+ProteinMatch::isGrouped() const
+{
+ if(_sp_grp_protein.get() == nullptr)
+ {
+ return false;
}
- if (_sp_grp_protein.get()->getGroupNumber() == 0) {
- return false;
+ if(_sp_grp_protein.get()->getGroupNumber() == 0)
+ {
+ return false;
}
- return true;
+ return true;
}
-void ProteinMatch::setChecked(bool arg1) {
- _checked = arg1;
+void
+ProteinMatch::setChecked(bool arg1)
+{
+ _checked = arg1;
}
-void ProteinMatch::addPeptideMatch(const PeptideMatch & peptide_match) {
- //qDebug() << "ProteinMatch::addPeptideMatch begin " << peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->toAbsoluteString();
- _peptide_match_list.push_back(peptide_match);
+void
+ProteinMatch::addPeptideMatch(const PeptideMatch &peptide_match)
+{
+ // qDebug() << "ProteinMatch::addPeptideMatch begin " <<
+ // peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->toAbsoluteString();
+ _peptide_match_list.push_back(peptide_match);
}
-std::vector<PeptideMatch> & ProteinMatch::getPeptideMatchList() {
- return _peptide_match_list;
+std::vector<PeptideMatch> &
+ProteinMatch::getPeptideMatchList()
+{
+ return _peptide_match_list;
}
-const std::vector<PeptideMatch> & ProteinMatch::getPeptideMatchList() const {
- return _peptide_match_list;
+const std::vector<PeptideMatch> &
+ProteinMatch::getPeptideMatchList() const
+{
+ return _peptide_match_list;
}
-void ProteinMatch::setGroupingExperiment(GroupingExperiment * p_grp_experiment) {
- _sp_grp_protein = nullptr;
- if ((isValidAndChecked() && (!_protein_sp.get()->isDecoy()))) {
- _sp_grp_protein = p_grp_experiment->getGrpProteinSp(this);
-
- for (auto & p_peptide_match : _peptide_match_list) {
- p_peptide_match.getPeptideEvidence()->setGrpPeptideSp(nullptr);
- if (p_peptide_match.getPeptideEvidence()->isValidAndChecked()) {
- p_peptide_match.getPeptideEvidence()->setGrpPeptideSp(p_grp_experiment->setGrpPeptide(_sp_grp_protein, p_peptide_match.getPeptideEvidence()));
+void
+ProteinMatch::setGroupingExperiment(GroupingExperiment *p_grp_experiment)
+{
+ _sp_grp_protein = nullptr;
+ if((isValidAndChecked() && (!_protein_sp.get()->isDecoy())))
+ {
+ _sp_grp_protein = p_grp_experiment->getGrpProteinSp(this);
+
+ for(auto &p_peptide_match : _peptide_match_list)
+ {
+ p_peptide_match.getPeptideEvidence()->setGrpPeptideSp(nullptr);
+ if(p_peptide_match.getPeptideEvidence()->isValidAndChecked())
+ {
+ p_peptide_match.getPeptideEvidence()->setGrpPeptideSp(
+ p_grp_experiment->setGrpPeptide(
+ _sp_grp_protein, p_peptide_match.getPeptideEvidence()));
}
}
- if (_protein_sp.get()->isContaminant()) {
- p_grp_experiment->addPostGroupingGrpProteinSpRemoval(_sp_grp_protein);
+ if(_protein_sp.get()->isContaminant())
+ {
+ p_grp_experiment->addPostGroupingGrpProteinSpRemoval(_sp_grp_protein);
}
-
}
}
-const pappso::GrpProteinSp & ProteinMatch::getGrpProteinSp() const {
- return _sp_grp_protein;
+const pappso::GrpProteinSp &
+ProteinMatch::getGrpProteinSp() const
+{
+ return _sp_grp_protein;
}
-void ProteinMatch::countPeptideMass(std::vector<pappso::GrpPeptide *> & count_peptide_mass, ValidationState state) const {
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match.getPeptideEvidence()->getValidationState() >= state) {
- count_peptide_mass.push_back(p_peptide_match.getPeptideEvidence()->getGrpPeptideSp().get());
+void
+ProteinMatch::countPeptideMass(
+ std::vector<pappso::GrpPeptide *> &count_peptide_mass,
+ ValidationState state) const
+{
+ for(auto &p_peptide_match : _peptide_match_list)
+ {
+ if(p_peptide_match.getPeptideEvidence()->getValidationState() >= state)
+ {
+ count_peptide_mass.push_back(
+ p_peptide_match.getPeptideEvidence()->getGrpPeptideSp().get());
}
}
}
-void ProteinMatch::countPeptideMassSample(std::vector<size_t> & count_peptide_mass_sample, ValidationState state) const {
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match.getPeptideEvidence()->getValidationState() >= state) {
- count_peptide_mass_sample.push_back(p_peptide_match.getPeptideEvidence()->getHashPeptideMassSample());
+void
+ProteinMatch::countPeptideMassSample(
+ std::vector<size_t> &count_peptide_mass_sample, ValidationState state) const
+{
+ for(auto &p_peptide_match : _peptide_match_list)
+ {
+ if(p_peptide_match.getPeptideEvidence()->getValidationState() >= state)
+ {
+ count_peptide_mass_sample.push_back(
+ p_peptide_match.getPeptideEvidence()->getHashPeptideMassSample());
}
}
}
-std::vector<PeptideMatch> ProteinMatch::getPeptideMatchList(ValidationState state, const MsRun * p_msrun_id) const {
- std::vector<PeptideMatch> peptide_match_list;
- for (auto & peptide_match : _peptide_match_list) {
- if (peptide_match.getPeptideEvidence()->getValidationState() >= state) {
- if (p_msrun_id == nullptr) {
- peptide_match_list.push_back(peptide_match);
+std::vector<PeptideMatch>
+ProteinMatch::getPeptideMatchList(ValidationState state,
+ const MsRun *p_msrun_id) const
+{
+ std::vector<PeptideMatch> peptide_match_list;
+ for(auto &peptide_match : _peptide_match_list)
+ {
+ if(peptide_match.getPeptideEvidence()->getValidationState() >= state)
+ {
+ if(p_msrun_id == nullptr)
+ {
+ peptide_match_list.push_back(peptide_match);
}
- else {
- if (peptide_match.getPeptideEvidence()->getMsRunP() == p_msrun_id) {
- peptide_match_list.push_back(peptide_match);
+ else
+ {
+ if(peptide_match.getPeptideEvidence()->getMsRunP() == p_msrun_id)
+ {
+ peptide_match_list.push_back(peptide_match);
}
}
}
}
- //it should automatically use the move semantic :
- return peptide_match_list;
+ // it should automatically use the move semantic :
+ return peptide_match_list;
}
-unsigned int ProteinMatch::countSampleScan(ValidationState state, const MsRun * p_msrun_id) const {
- std::vector<std::size_t> count_sample_scan;
- for (auto & peptide_match : _peptide_match_list) {
- const PeptideEvidence * p_peptide_evidence = peptide_match.getPeptideEvidence();
- if (p_peptide_evidence->getValidationState() >= state) {
- if(p_msrun_id == nullptr) {
- count_sample_scan.push_back(p_peptide_evidence->getHashSampleScan());
+unsigned int
+ProteinMatch::countSampleScan(ValidationState state,
+ const MsRun *p_msrun_id) const
+{
+ std::vector<std::size_t> count_sample_scan;
+ for(auto &peptide_match : _peptide_match_list)
+ {
+ const PeptideEvidence *p_peptide_evidence =
+ peptide_match.getPeptideEvidence();
+ if(p_peptide_evidence->getValidationState() >= state)
+ {
+ if(p_msrun_id == nullptr)
+ {
+ count_sample_scan.push_back(
+ p_peptide_evidence->getHashSampleScan());
}
- else {
- if (p_peptide_evidence->getMsRunP() == p_msrun_id) {
- count_sample_scan.push_back(p_peptide_evidence->getHashSampleScan());
+ else
+ {
+ if(p_peptide_evidence->getMsRunP() == p_msrun_id)
+ {
+ count_sample_scan.push_back(
+ p_peptide_evidence->getHashSampleScan());
}
}
}
}
- std::sort(count_sample_scan.begin(), count_sample_scan.end());
- auto last = std::unique(count_sample_scan.begin(),count_sample_scan.end());
- return std::distance(count_sample_scan.begin(),last);
+ std::sort(count_sample_scan.begin(), count_sample_scan.end());
+ auto last = std::unique(count_sample_scan.begin(), count_sample_scan.end());
+ return std::distance(count_sample_scan.begin(), last);
}
-unsigned int ProteinMatch::countPeptideMatch(ValidationState state) const {
- return std::count_if (_peptide_match_list.begin(), _peptide_match_list.end(), [state](const PeptideMatch & peptide_match) {
- if (peptide_match.getPeptideEvidence()->getValidationState() >= state) {
- return true;
+unsigned int
+ProteinMatch::countPeptideMatch(ValidationState state) const
+{
+ return std::count_if(
+ _peptide_match_list.begin(), _peptide_match_list.end(),
+ [state](const PeptideMatch &peptide_match) {
+ if(peptide_match.getPeptideEvidence()->getValidationState() >= state)
+ {
+ return true;
}
- else {
- return false;
+ else
+ {
+ return false;
}
});
}
-size_t ProteinMatch::countSequenceLi(ValidationState state, const MsRun * p_msrun_id) const {
- //qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- std::set<QString> sequence_list;
- for (auto & peptide_match : _peptide_match_list) {
- if (peptide_match.getPeptideEvidence()->getValidationState() >= state) {
- if(p_msrun_id != nullptr) {
- //within sample
- if (peptide_match.getPeptideEvidence()->getMsRunP() == p_msrun_id) {
- sequence_list.insert(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequenceLi());
+size_t
+ProteinMatch::countSequenceLi(ValidationState state,
+ const MsRun *p_msrun_id) const
+{
+ // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ std::set<QString> sequence_list;
+ for(auto &peptide_match : _peptide_match_list)
+ {
+ if(peptide_match.getPeptideEvidence()->getValidationState() >= state)
+ {
+ if(p_msrun_id != nullptr)
+ {
+ // within sample
+ if(peptide_match.getPeptideEvidence()->getMsRunP() == p_msrun_id)
+ {
+ sequence_list.insert(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getSequenceLi());
}
}
- else {
- //overall samples
- sequence_list.insert(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequenceLi());
+ else
+ {
+ // overall samples
+ sequence_list.insert(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getSequenceLi());
}
}
}
- //qDebug() <<"ProteinMatch::countValidAndCheckedPeptide end " << sequence_list.size();
- //qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- return sequence_list.size();
+ // qDebug() <<"ProteinMatch::countValidAndCheckedPeptide end " <<
+ // sequence_list.size(); qDebug() << __FILE__ << " " << __FUNCTION__ << " " <<
+ // __LINE__;
+ return sequence_list.size();
}
-unsigned int ProteinMatch::countDistinctMsSamples(ValidationState state) const {
- std::set<QString> sequence_list;
- for (auto & peptide_match : _peptide_match_list) {
- if (peptide_match.getPeptideEvidence()->getValidationState() >= state) {
- sequence_list.insert(QString("%1").arg(peptide_match.getPeptideEvidence()->getMsRunP()->getXmlId()));
+unsigned int
+ProteinMatch::countDistinctMsSamples(ValidationState state) const
+{
+ std::set<QString> sequence_list;
+ for(auto &peptide_match : _peptide_match_list)
+ {
+ if(peptide_match.getPeptideEvidence()->getValidationState() >= state)
+ {
+ sequence_list.insert(QString("%1").arg(
+ peptide_match.getPeptideEvidence()->getMsRunP()->getXmlId()));
}
}
- return sequence_list.size();
+ return sequence_list.size();
}
-unsigned int ProteinMatch::countPeptideMassCharge(ValidationState state, const MsRun * sp_msrun_id) const {
- std::set<QString> sequence_list;
- for (auto & peptide_match : _peptide_match_list) {
- if (peptide_match.getPeptideEvidence()->getValidationState() >= state) {
- if(sp_msrun_id != nullptr) {
- //within sample
- if (peptide_match.getPeptideEvidence()->getMsRunP() == sp_msrun_id) {
- sequence_list.insert(QString("%1-%2-%3").arg(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getNativePeptideP()->getSequenceLi()).arg(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getNativePeptideP()->getMass()).arg(peptide_match.getPeptideEvidence()->getCharge()));
+unsigned int
+ProteinMatch::countPeptideMassCharge(ValidationState state,
+ const MsRun *sp_msrun_id) const
+{
+ std::set<QString> sequence_list;
+ for(auto &peptide_match : _peptide_match_list)
+ {
+ if(peptide_match.getPeptideEvidence()->getValidationState() >= state)
+ {
+ if(sp_msrun_id != nullptr)
+ {
+ // within sample
+ if(peptide_match.getPeptideEvidence()->getMsRunP() == sp_msrun_id)
+ {
+ sequence_list.insert(
+ QString("%1-%2-%3")
+ .arg(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getNativePeptideP()
+ ->getSequenceLi())
+ .arg(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getNativePeptideP()
+ ->getMass())
+ .arg(peptide_match.getPeptideEvidence()->getCharge()));
}
}
- else {
- //overall samples
- sequence_list.insert(QString("%1-%2-%3").arg(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getNativePeptideP()->getSequenceLi()).arg(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getNativePeptideP()->getMass()).arg(peptide_match.getPeptideEvidence()->getCharge()));
+ else
+ {
+ // overall samples
+ sequence_list.insert(
+ QString("%1-%2-%3")
+ .arg(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getNativePeptideP()
+ ->getSequenceLi())
+ .arg(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getNativePeptideP()
+ ->getMass())
+ .arg(peptide_match.getPeptideEvidence()->getCharge()));
}
}
}
- return sequence_list.size();
-}
-
-pappso::pappso_double ProteinMatch::getEvalue(const MsRun * sp_msrun_id) const {
- return (std::pow ((double) 10.0,getLogEvalue(sp_msrun_id)));
-}
-
-pappso::pappso_double ProteinMatch::getLogEvalue(const MsRun * sp_msrun_id) const {
- std::map<QString, pappso::pappso_double> map_sequence_evalue;
- for (auto & peptide_match : _peptide_match_list) {
- if (peptide_match.getPeptideEvidence()->isValidAndChecked()) {
- QString sequence(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequence());
- pappso::pappso_double evalue = peptide_match.getPeptideEvidence()->getEvalue();
- if(sp_msrun_id != nullptr) {
- //within sample
- if (peptide_match.getPeptideEvidence()->getMsRunP() == sp_msrun_id) {
- auto ret = map_sequence_evalue.insert(std::pair<QString, pappso::pappso_double>(sequence, evalue));
- if (ret.second == false) {
- if (ret.first->second > evalue) {//get best evalue for sequence
- ret.first->second = evalue;
+ return sequence_list.size();
+}
+
+pappso::pappso_double
+ProteinMatch::getEvalue(const MsRun *sp_msrun_id) const
+{
+ return (std::pow((double)10.0, getLogEvalue(sp_msrun_id)));
+}
+
+pappso::pappso_double
+ProteinMatch::getLogEvalue(const MsRun *sp_msrun_id) const
+{
+ std::map<QString, pappso::pappso_double> map_sequence_evalue;
+ for(auto &peptide_match : _peptide_match_list)
+ {
+ if(peptide_match.getPeptideEvidence()->isValidAndChecked())
+ {
+ QString sequence(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getSequence());
+ pappso::pappso_double evalue =
+ peptide_match.getPeptideEvidence()->getEvalue();
+ if(sp_msrun_id != nullptr)
+ {
+ // within sample
+ if(peptide_match.getPeptideEvidence()->getMsRunP() == sp_msrun_id)
+ {
+ auto ret = map_sequence_evalue.insert(
+ std::pair<QString, pappso::pappso_double>(sequence,
+ evalue));
+ if(ret.second == false)
+ {
+ if(ret.first->second > evalue)
+ { // get best evalue for sequence
+ ret.first->second = evalue;
}
}
}
}
- else {
- //overall samples
- auto ret = map_sequence_evalue.insert(std::pair<QString, pappso::pappso_double>(sequence, evalue));
- if (ret.second == false) {
- if (ret.first->second > evalue) {//get best evalue for sequence
- ret.first->second = evalue;
+ else
+ {
+ // overall samples
+ auto ret = map_sequence_evalue.insert(
+ std::pair<QString, pappso::pappso_double>(sequence, evalue));
+ if(ret.second == false)
+ {
+ if(ret.first->second > evalue)
+ { // get best evalue for sequence
+ ret.first->second = evalue;
}
}
}
}
}
- pappso::pappso_double evalue_prot = 1;
- for (auto && peptide_pair: map_sequence_evalue) {
- evalue_prot += std::log10(peptide_pair.second);
- //evalue_prot *= peptide_pair.second;
+ pappso::pappso_double evalue_prot = 1;
+ for(auto &&peptide_pair : map_sequence_evalue)
+ {
+ evalue_prot += std::log10(peptide_pair.second);
+ // evalue_prot *= peptide_pair.second;
}
- //return (std::pow ((double) 10.0,evalue_prot));
- return (evalue_prot);
-
+ // return (std::pow ((double) 10.0,evalue_prot));
+ return (evalue_prot);
}
-pappso::pappso_double ProteinMatch::getNsaf(pappso::pappso_double proto_nsaf_sum, const MsRun * p_msrun_id) const {
- if (proto_nsaf_sum == 0) {
- throw pappso::PappsoException(QObject::tr("Error computing NSAF for protein %1 :\nproto_nsaf_sum is null").arg(this->getProteinXtpSp().get()->getAccession()));
+pappso::pappso_double
+ProteinMatch::getNsaf(pappso::pappso_double proto_nsaf_sum,
+ const MsRun *p_msrun_id) const
+{
+ if(proto_nsaf_sum == 0)
+ {
+ throw pappso::PappsoException(
+ QObject::tr(
+ "Error computing NSAF for protein %1 :\nproto_nsaf_sum is null")
+ .arg(this->getProteinXtpSp().get()->getAccession()));
}
- return (getProtoNsaf(p_msrun_id)/proto_nsaf_sum);
+ return (getProtoNsaf(p_msrun_id) / proto_nsaf_sum);
}
-pappso::pappso_double ProteinMatch::getProtoNsaf(const MsRun * sp_msrun_id) const {
- try {
- if (_protein_sp.get()->size() < 1) {
- throw pappso::PappsoException(QObject::tr("protein has no amino acid sequence"));
- }
- pappso::pappso_double proto_nsaf = (pappso::pappso_double) countSampleScan(ValidationState::validAndChecked ,sp_msrun_id) / (pappso::pappso_double) _protein_sp.get()->size();
- return proto_nsaf;
-
+pappso::pappso_double
+ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id) const
+{
+ try
+ {
+ if(_protein_sp.get()->size() < 1)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("protein has no amino acid sequence"));
+ }
+ pappso::pappso_double proto_nsaf =
+ (pappso::pappso_double)countSampleScan(ValidationState::validAndChecked,
+ sp_msrun_id) /
+ (pappso::pappso_double)_protein_sp.get()->size();
+ return proto_nsaf;
}
- catch (pappso::PappsoException error) {
- throw pappso::PappsoException(QObject::tr("Error computing proto NSAF for protein %1 :\n%2").arg(this->getProteinXtpSp().get()->getAccession()).arg(error.qwhat()));
+ catch(pappso::PappsoException error)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error computing proto NSAF for protein %1 :\n%2")
+ .arg(this->getProteinXtpSp().get()->getAccession())
+ .arg(error.qwhat()));
}
}
-pappso::pappso_double ProteinMatch::getPAI(const MsRun * sp_msrun_id) const {
- try {
- pappso::pappso_double PAI = (pappso::pappso_double) countPeptideMassCharge(ValidationState::validAndChecked ,sp_msrun_id) / (pappso::pappso_double) _protein_sp.get()->countTrypticPeptidesForPAI();
- return PAI;
-
+pappso::pappso_double
+ProteinMatch::getPAI(const MsRun *sp_msrun_id) const
+{
+ try
+ {
+ pappso::pappso_double PAI =
+ (pappso::pappso_double)countPeptideMassCharge(
+ ValidationState::validAndChecked, sp_msrun_id) /
+ (pappso::pappso_double)_protein_sp.get()->countTrypticPeptidesForPAI();
+ return PAI;
}
- catch (pappso::PappsoException error) {
- throw pappso::PappsoException(QObject::tr("Error computing PAI for protein %1 :\n%2").arg(this->getProteinXtpSp().get()->getAccession()).arg(error.qwhat()));
+ catch(pappso::PappsoException error)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error computing PAI for protein %1 :\n%2")
+ .arg(this->getProteinXtpSp().get()->getAccession())
+ .arg(error.qwhat()));
}
}
-pappso::pappso_double ProteinMatch::getEmPAI(const MsRun * sp_msrun_id) const {
- // compute emPAI, Ishihama 2005
- pappso::pappso_double value = std::pow(10.0, getPAI(sp_msrun_id)) - (pappso::pappso_double) 1.0;
+pappso::pappso_double
+ProteinMatch::getEmPAI(const MsRun *sp_msrun_id) const
+{
+ // compute emPAI, Ishihama 2005
+ pappso::pappso_double value =
+ std::pow(10.0, getPAI(sp_msrun_id)) - (pappso::pappso_double)1.0;
- return value;
+ return value;
}
-const QString ProteinMatch::getHtmlSequence(PeptideEvidence * peptide_evidence_to_locate) const
+const QString
+ProteinMatch::getHtmlSequence(PeptideEvidence *peptide_evidence_to_locate) const
{
- size_t prot_size = _protein_sp.get()->size();
- //qDebug() << "ProteinMatch::getCoverage begin prot_size=" << prot_size << " " << _protein_sp.get()-//>getSequence();
- if (prot_size == 0) return 0;
- bool cover_bool[prot_size] = {false};
- bool highlight_bool[prot_size] = {false};
- for (auto & peptide_match : _peptide_match_list) {
- if (peptide_match.getPeptideEvidence() == peptide_evidence_to_locate) {
- size_t size = peptide_evidence_to_locate->getPeptideXtpSp().get()->size();
- size_t offset = peptide_match.getStart();
- if (offset >= 0) {
- for (size_t i=0; (i < size) && (offset < prot_size) ; i++,offset++) {
- highlight_bool[offset] = true;
+ size_t prot_size = _protein_sp.get()->size();
+ // qDebug() << "ProteinMatch::getCoverage begin prot_size=" << prot_size << "
+ // " << _protein_sp.get()-//>getSequence();
+ if(prot_size == 0)
+ return 0;
+ bool cover_bool[prot_size] = {false};
+ bool highlight_bool[prot_size] = {false};
+ for(auto &peptide_match : _peptide_match_list)
+ {
+ if(peptide_match.getPeptideEvidence() == peptide_evidence_to_locate)
+ {
+ size_t size =
+ peptide_evidence_to_locate->getPeptideXtpSp().get()->size();
+ size_t offset = peptide_match.getStart();
+ if(offset >= 0)
+ {
+ for(size_t i = 0; (i < size) && (offset < prot_size);
+ i++, offset++)
+ {
+ highlight_bool[offset] = true;
}
}
}
}
- for (auto & peptide_match : _peptide_match_list) {
- if (peptide_match.getPeptideEvidence()->isValidAndChecked()) {
- size_t size = peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->size();
- size_t offset = peptide_match.getStart();
- if (offset >= 0) {
- for (size_t i=0; (i < size) && (offset < prot_size) ; i++,offset++) {
- cover_bool[offset] = true;
+ for(auto &peptide_match : _peptide_match_list)
+ {
+ if(peptide_match.getPeptideEvidence()->isValidAndChecked())
+ {
+ size_t size =
+ peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->size();
+ size_t offset = peptide_match.getStart();
+ if(offset >= 0)
+ {
+ for(size_t i = 0; (i < size) && (offset < prot_size);
+ i++, offset++)
+ {
+ cover_bool[offset] = true;
}
}
}
}
- QString sequence = getProteinXtpSp().get()->getSequence();
- QString sequence_html("<style type=\"text/css\">\nspan { margin: 0px;padding: 0px; }\n</style>");
- for (unsigned int i=0; i < prot_size; i++) {
- if(highlight_bool[i]) {
- sequence_html.append(QString("<span style=\"background-color:%2;\">%1").arg(sequence[i]).arg(_color_highlighted_peptide_background.name()));
- i++;
- for (; i < prot_size; i++) {
- if(highlight_bool[i]) {
- sequence_html.append(sequence[i]);
+ QString sequence = getProteinXtpSp().get()->getSequence();
+ QString sequence_html(
+ "<style type=\"text/css\">\nspan { margin: 0px;padding: 0px; }\n</style>");
+ for(unsigned int i = 0; i < prot_size; i++)
+ {
+ if(highlight_bool[i])
+ {
+ sequence_html.append(
+ QString("<span style=\"background-color:%2;\">%1")
+ .arg(sequence[i])
+ .arg(_color_highlighted_peptide_background.name()));
+ i++;
+ for(; i < prot_size; i++)
+ {
+ if(highlight_bool[i])
+ {
+ sequence_html.append(sequence[i]);
}
- else {
- sequence_html.append(QString("</span>"));
- i--;
- break;
+ else
+ {
+ sequence_html.append(QString("</span>"));
+ i--;
+ break;
}
}
- sequence_html.append(QString("</span>"));
+ sequence_html.append(QString("</span>"));
}
- else if(cover_bool[i]) {
- sequence_html.append(QString("<span style=\"background-color:%2;\">%1").arg(sequence[i]).arg(_color_peptide_background.name()));
- i++;
- for (; i < prot_size; i++) {
- if (highlight_bool[i]) {
- i--;
- break;
+ else if(cover_bool[i])
+ {
+ sequence_html.append(
+ QString("<span style=\"background-color:%2;\">%1")
+ .arg(sequence[i])
+ .arg(_color_peptide_background.name()));
+ i++;
+ for(; i < prot_size; i++)
+ {
+ if(highlight_bool[i])
+ {
+ i--;
+ break;
}
- if(cover_bool[i]) {
- sequence_html.append(sequence[i]);
+ if(cover_bool[i])
+ {
+ sequence_html.append(sequence[i]);
}
- else {
- sequence_html.append(QString("</span>%1").arg(sequence[i]));
- break;
+ else
+ {
+ sequence_html.append(QString("</span>%1").arg(sequence[i]));
+ break;
}
}
- sequence_html.append(QString("</span>"));
+ sequence_html.append(QString("</span>"));
}
- else {
- sequence_html.append(sequence[i]);
+ else
+ {
+ sequence_html.append(sequence[i]);
}
}
- return sequence_html;
-}
-
-pappso::pappso_double ProteinMatch::getCoverage() const {
- size_t prot_size = _protein_sp.get()->size();
- //qDebug() << "ProteinMatch::getCoverage begin prot_size=" << prot_size << " " << _protein_sp.get()-//>getSequence();
- if (prot_size == 0) return 0;
- bool cover_bool[prot_size] = {false};
- for (auto & peptide_match : _peptide_match_list) {
- if (peptide_match.getPeptideEvidence()->isValidAndChecked()) {
- size_t size = peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->size();
- size_t offset = peptide_match.getStart();
- if (offset >= 0) {
- for (size_t i=0; (i < size) && (offset < prot_size) ; i++,offset++) {
- cover_bool[offset] = true;
+ return sequence_html;
+}
+
+pappso::pappso_double
+ProteinMatch::getCoverage() const
+{
+ size_t prot_size = _protein_sp.get()->size();
+ // qDebug() << "ProteinMatch::getCoverage begin prot_size=" << prot_size << "
+ // " << _protein_sp.get()-//>getSequence();
+ if(prot_size == 0)
+ return 0;
+ bool cover_bool[prot_size] = {false};
+ for(auto &peptide_match : _peptide_match_list)
+ {
+ if(peptide_match.getPeptideEvidence()->isValidAndChecked())
+ {
+ size_t size =
+ peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->size();
+ size_t offset = peptide_match.getStart();
+ if(offset >= 0)
+ {
+ for(size_t i = 0; (i < size) && (offset < prot_size);
+ i++, offset++)
+ {
+ cover_bool[offset] = true;
}
}
}
}
- size_t count = 0;
- for (size_t i=0; i < prot_size; i++) {
- if(cover_bool[i]) count++;
+ size_t count = 0;
+ for(size_t i = 0; i < prot_size; i++)
+ {
+ if(cover_bool[i])
+ count++;
}
- //qDebug() << "ProteinMatch::getCoverage count=" << count << " prot_size=" << prot_size;
- return (((pappso::pappso_double)count)/ ((pappso::pappso_double)prot_size));
+ // qDebug() << "ProteinMatch::getCoverage count=" << count << " prot_size=" <<
+ // prot_size;
+ return (((pappso::pappso_double)count) / ((pappso::pappso_double)prot_size));
}
-const GroupingGroupSp & ProteinMatch::getGroupingGroupSp() const {
- return _sp_group;
+const GroupingGroupSp &
+ProteinMatch::getGroupingGroupSp() const
+{
+ return _sp_group;
}
-void ProteinMatch::setGroupInstance(GroupStore & group_store) {
- _sp_group = nullptr;
- if (_sp_grp_protein != nullptr) {
- unsigned int group_number = _sp_grp_protein.get()->getGroupNumber();
- if (group_number > 0) {
- _sp_group = group_store.getInstance(group_number);
- _sp_group.get()->add(this);
+void
+ProteinMatch::setGroupInstance(GroupStore &group_store)
+{
+ _sp_group = nullptr;
+ if(_sp_grp_protein != nullptr)
+ {
+ unsigned int group_number = _sp_grp_protein.get()->getGroupNumber();
+ if(group_number > 0)
+ {
+ _sp_group = group_store.getInstance(group_number);
+ _sp_group.get()->add(this);
}
}
}
-void ProteinMatch::collectPeptideEvidences(std::set<const PeptideEvidence *> & peptide_evidence_set, ValidationState state) const {
- for (auto & peptide_match : _peptide_match_list) {
- const PeptideEvidence * p_peptide_evidence = peptide_match.getPeptideEvidence();
- if (p_peptide_evidence->getValidationState() >= state) {
- peptide_evidence_set.insert(p_peptide_evidence);
+void
+ProteinMatch::collectPeptideEvidences(
+ std::set<const PeptideEvidence *> &peptide_evidence_set,
+ ValidationState state) const
+{
+ for(auto &peptide_match : _peptide_match_list)
+ {
+ const PeptideEvidence *p_peptide_evidence =
+ peptide_match.getPeptideEvidence();
+ if(p_peptide_evidence->getValidationState() >= state)
+ {
+ peptide_evidence_set.insert(p_peptide_evidence);
}
}
}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index d7e2db30d09e831b0782b5428860d541f8918130..015977cdbbb59ba570d0c1d7969b90d1515a6056 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include <QColor>
#include <vector>
@@ -39,146 +40,166 @@ class IdentificationGroup;
class ProteinMatch
{
- friend IdentificationGroup;
-public:
- ProteinMatch();
- ~ProteinMatch();
-
- const ProteinXtpSp & getProteinXtpSp() const;
-
- /** @brief compute protein log10(Evalue) within samples
- * */
- pappso::pappso_double getLogEvalue(const MsRun * sp_msrun_id = nullptr) const;
-
- /** @brief compute protein Evalue within samples
- * */
- pappso::pappso_double getEvalue(const MsRun * sp_msrun_id = nullptr) const;
-
-
- /** @brief protein coverage overall samples
- * */
- pappso::pappso_double getCoverage() const;
-
- /** @brief get coverage sequence (html representation)
- * @param peptide_match_to_locate pointer to optional peptide match to locate on protein sequence
- **/
- const QString getHtmlSequence(PeptideEvidence * peptide_evidence_to_locate = nullptr) const;
-
- /** @brief compute proto NSAF within msrun : spectral abundance factor (SAF)
- * Warning: this is not NSAF, just a part
- * @param p_msrun_id pointer on the msrun to get NSAF.
- * */
- pappso::pappso_double getProtoNsaf(const MsRun * p_msrun_id) const;
-
- /** @brief compute NSAF within msrun : normalized spectral abundance factor (NSAF)
- * Florens L., Carozza M. J. C., Swanson S. K., et al. Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods. 2006;40(4):303–311. doi: 10.1016/j.ymeth.2006.07.028.
- * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1815300/
- * @param proto_nsaf_sum the sum of SAF of all proteins within the msrun
- * @param p_msrun_id pointer on the msrun to get NSAF
- * */
- pappso::pappso_double getNsaf(pappso::pappso_double proto_nsaf_sum, const MsRun * p_msrun_id) const;
-
- /** @brief compute Protein Abundance Index (PAI) within sample
- * PAI computation (Rappsilber et al. 2002)
- * */
- pappso::pappso_double getPAI(const MsRun * sp_msrun_id = nullptr) const;
-
- /** @brief compute emPAI within sample
- * Ishihama 2005
- * */
- pappso::pappso_double getEmPAI(const MsRun * sp_msrun_id = nullptr) const;
-
- void setProteinXtpSp(ProteinXtpSp protein_sp);
- void addPeptideMatch(const PeptideMatch & peptide_match);
- std::vector<PeptideMatch> & getPeptideMatchList();
- const std::vector<PeptideMatch> & getPeptideMatchList() const;
-
- /** @brief get peptide match sublist with required validation state
- * @param state the validation state to select
- * @param sp_msrun_id the msrun to look for, if nullptr, then get peptide match overall MSruns
- * */
- std::vector<PeptideMatch> getPeptideMatchList(ValidationState state, const MsRun * sp_msrun_id = nullptr) const;
-
- void setChecked(bool arg1);
-
- bool isChecked() const;
- bool isValid() const;
- bool isValidAndChecked() const;
- bool isGrouped() const;
-
- ValidationState getValidationState() const;
-
- /** @brief count peptide match (psm) listed in this protein match
- */
- unsigned int countPeptideMatch(ValidationState state) const;
-
- /** @brief count distinct sample + scans implied in this protein identification
- */
- unsigned int countSampleScan(ValidationState state, const MsRun * p_msrun_id=nullptr) const;
-
- /** @brief count peptide (peptide+mass)
- */
- void countPeptideMass(std::vector<pappso::GrpPeptide *> & count_peptide_mass, ValidationState state) const;
-
- /** @brief count peptide (peptide+mass+sample)
- */
- void countPeptideMassSample(std::vector<size_t> & count_peptide_mass_sample, ValidationState state) const;
-
- const pappso::GrpProteinSp & getGrpProteinSp() const;
- const GroupingGroupSp & getGroupingGroupSp() const;
-
- /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
- * */
- void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
-
-
- /** @brief collect distinct peptide evidences
- */
- void collectPeptideEvidences(std::set<const PeptideEvidence *> & peptide_evidence_set, ValidationState state) const;
-
- /** @brief count distinct sequence taking into account equivalence between Leucine and Isoleucine
- * @param state validation state of peptides to count
- * @param p_msrun_id count within the specified sample
- */
- size_t countSequenceLi(ValidationState state,const MsRun * p_msrun_id=nullptr) const;
-
- /** @brief count distinct peptide+mass+charge
- * peptide is the peptide sequence LI (Leucine => Isoleucine)
- * mass is the peptide mass, not considering labelled residues (if any)
- * @param state validation state of peptides to count
- * @param p_msrun_id count within the specified sample
- */
- unsigned int countPeptideMassCharge(ValidationState state, const MsRun * sp_msrun_id=nullptr) const;
-
- /** @brief count distinct MS samples in which the protein is observed
- * @param state validation state of peptides to count
- */
- unsigned int countDistinctMsSamples(ValidationState state) const;
-protected :
-
- void setGroupingExperiment(GroupingExperiment * p_grp_experiment);
-
- void setGroupInstance(GroupStore & group_store);
-
-
-private:
- static QColor _color_peptide_background;
- static QColor _color_highlighted_peptide_background;
-
-
- pappso::GrpProteinSp _sp_grp_protein;
- GroupingGroupSp _sp_group;
-
- std::vector<PeptideMatch> _peptide_match_list;
- ProteinXtpSp _protein_sp = nullptr;
- /** @brief manually checked by user (true by default)
- */
- bool _checked = true;
-
- /** @brief automatic filter result (false by default)
- */
- bool _proxy_valid = false;
-
+ friend IdentificationGroup;
+
+ public:
+ ProteinMatch();
+ ~ProteinMatch();
+
+ const ProteinXtpSp &getProteinXtpSp() const;
+
+ /** @brief compute protein log10(Evalue) within samples
+ * */
+ pappso::pappso_double getLogEvalue(const MsRun *sp_msrun_id = nullptr) const;
+
+ /** @brief compute protein Evalue within samples
+ * */
+ pappso::pappso_double getEvalue(const MsRun *sp_msrun_id = nullptr) const;
+
+
+ /** @brief protein coverage overall samples
+ * */
+ pappso::pappso_double getCoverage() const;
+
+ /** @brief get coverage sequence (html representation)
+ * @param peptide_match_to_locate pointer to optional peptide match to locate
+ *on protein sequence
+ **/
+ const QString
+ getHtmlSequence(PeptideEvidence *peptide_evidence_to_locate = nullptr) const;
+
+ /** @brief compute proto NSAF within msrun : spectral abundance factor (SAF)
+ * Warning: this is not NSAF, just a part
+ * @param p_msrun_id pointer on the msrun to get NSAF.
+ * */
+ pappso::pappso_double getProtoNsaf(const MsRun *p_msrun_id) const;
+
+ /** @brief compute NSAF within msrun : normalized spectral abundance factor
+ * (NSAF) Florens L., Carozza M. J. C., Swanson S. K., et al. Analyzing
+ * chromatin remodeling complexes using shotgun proteomics and normalized
+ * spectral abundance factors. Methods. 2006;40(4):303–311.
+ * doi: 10.1016/j.ymeth.2006.07.028.
+ * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1815300/
+ * @param proto_nsaf_sum the sum of SAF of all proteins within the msrun
+ * @param p_msrun_id pointer on the msrun to get NSAF
+ * */
+ pappso::pappso_double getNsaf(pappso::pappso_double proto_nsaf_sum,
+ const MsRun *p_msrun_id) const;
+
+ /** @brief compute Protein Abundance Index (PAI) within sample
+ * PAI computation (Rappsilber et al. 2002)
+ * */
+ pappso::pappso_double getPAI(const MsRun *sp_msrun_id = nullptr) const;
+
+ /** @brief compute emPAI within sample
+ * Ishihama 2005
+ * */
+ pappso::pappso_double getEmPAI(const MsRun *sp_msrun_id = nullptr) const;
+
+ void setProteinXtpSp(ProteinXtpSp protein_sp);
+ void addPeptideMatch(const PeptideMatch &peptide_match);
+ std::vector<PeptideMatch> &getPeptideMatchList();
+ const std::vector<PeptideMatch> &getPeptideMatchList() const;
+
+ /** @brief get peptide match sublist with required validation state
+ * @param state the validation state to select
+ * @param sp_msrun_id the msrun to look for, if nullptr, then get peptide
+ * match overall MSruns
+ * */
+ std::vector<PeptideMatch>
+ getPeptideMatchList(ValidationState state,
+ const MsRun *sp_msrun_id = nullptr) const;
+
+ void setChecked(bool arg1);
+
+ bool isChecked() const;
+ bool isValid() const;
+ bool isValidAndChecked() const;
+ bool isGrouped() const;
+
+ ValidationState getValidationState() const;
+
+ /** @brief count peptide match (psm) listed in this protein match
+ */
+ unsigned int countPeptideMatch(ValidationState state) const;
+
+ /** @brief count distinct sample + scans implied in this protein
+ * identification
+ */
+ unsigned int countSampleScan(ValidationState state,
+ const MsRun *p_msrun_id = nullptr) const;
+
+ /** @brief count peptide (peptide+mass)
+ */
+ void countPeptideMass(std::vector<pappso::GrpPeptide *> &count_peptide_mass,
+ ValidationState state) const;
+
+ /** @brief count peptide (peptide+mass+sample)
+ */
+ void countPeptideMassSample(std::vector<size_t> &count_peptide_mass_sample,
+ ValidationState state) const;
+
+ const pappso::GrpProteinSp &getGrpProteinSp() const;
+ const GroupingGroupSp &getGroupingGroupSp() const;
+
+ /** @brief validate or invalidate peptides and proteins based automatic
+ * filters and manual checks
+ * */
+ void updateAutomaticFilters(
+ const AutomaticFilterParameters &automatic_filter_parameters);
+
+
+ /** @brief collect distinct peptide evidences
+ */
+ void collectPeptideEvidences(
+ std::set<const PeptideEvidence *> &peptide_evidence_set,
+ ValidationState state) const;
+
+ /** @brief count distinct sequence taking into account equivalence between
+ * Leucine and Isoleucine
+ * @param state validation state of peptides to count
+ * @param p_msrun_id count within the specified sample
+ */
+ size_t countSequenceLi(ValidationState state,
+ const MsRun *p_msrun_id = nullptr) const;
+
+ /** @brief count distinct peptide+mass+charge
+ * peptide is the peptide sequence LI (Leucine => Isoleucine)
+ * mass is the peptide mass, not considering labelled residues (if any)
+ * @param state validation state of peptides to count
+ * @param p_msrun_id count within the specified sample
+ */
+ unsigned int countPeptideMassCharge(ValidationState state,
+ const MsRun *sp_msrun_id = nullptr) const;
+
+ /** @brief count distinct MS samples in which the protein is observed
+ * @param state validation state of peptides to count
+ */
+ unsigned int countDistinctMsSamples(ValidationState state) const;
+
+ protected:
+ void setGroupingExperiment(GroupingExperiment *p_grp_experiment);
+
+ void setGroupInstance(GroupStore &group_store);
+
+
+ private:
+ static QColor _color_peptide_background;
+ static QColor _color_highlighted_peptide_background;
+
+
+ pappso::GrpProteinSp _sp_grp_protein;
+ GroupingGroupSp _sp_group;
+
+ std::vector<PeptideMatch> _peptide_match_list;
+ ProteinXtpSp _protein_sp = nullptr;
+ /** @brief manually checked by user (true by default)
+ */
+ bool _checked = true;
+
+ /** @brief automatic filter result (false by default)
+ */
+ bool _proxy_valid = false;
};
#endif // PROTEINMATCH_H
diff --git a/src/core/proteinxtp.cpp b/src/core/proteinxtp.cpp
index 6a59f4e27e9228fa05c324bcef4b7f45961d1ddc..b77f1a0e8e7d88cd87b61a4a660e13de555d7401 100644
--- a/src/core/proteinxtp.cpp
+++ b/src/core/proteinxtp.cpp
@@ -1,245 +1,326 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "proteinxtp.h"
#include <pappsomspp/protein/enzyme.h>
#include <pappsomspp/pappsoexception.h>
#include "../files/fastafile.h"
-DbXref::DbXref() {
+DbXref::DbXref()
+{
}
-DbXref::DbXref(ExternalDatabase database_in, const QString & accession_in):database(database_in), accession(accession_in) {
+DbXref::DbXref(ExternalDatabase database_in, const QString &accession_in)
+ : database(database_in), accession(accession_in)
+{
}
-DbXref::DbXref(const DbXref & other):database(other.database), accession(other.accession) {
+DbXref::DbXref(const DbXref &other)
+ : database(other.database), accession(other.accession)
+{
}
-const QUrl DbXref::getUrl() const {
- QUrl url;
- qDebug() << "DbXref::getUrl " << accession << " "<< (std::uint8_t)database;
- switch (database) {
-
- case ExternalDatabase::AGI_LocusCode :
- url.setUrl(QString("http://www.arabidopsis.org/servlets/TairObject?type=locus&name=%1").arg(accession));
+const QUrl
+DbXref::getUrl() const
+{
+ QUrl url;
+ qDebug() << "DbXref::getUrl " << accession << " " << (std::uint8_t)database;
+ switch(database)
+ {
+
+ case ExternalDatabase::AGI_LocusCode:
+ url.setUrl(
+ QString(
+ "http://www.arabidopsis.org/servlets/TairObject?type=locus&name=%1")
+ .arg(accession));
break;
- case ExternalDatabase::NCBI_gi :
- url.setUrl(QString("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=protein&dopt=GenBank&list_uids=%1").arg(accession));
+ case ExternalDatabase::NCBI_gi:
+ url.setUrl(
+ QString(
+ "http://www.ncbi.nlm.nih.gov/entrez/"
+ "query.fcgi?cmd=Retrieve&db=protein&dopt=GenBank&list_uids=%1")
+ .arg(accession));
break;
- case ExternalDatabase::SwissProt :
+ case ExternalDatabase::SwissProt:
url.setUrl(QString("http://www.uniprot.org/uniprot/%1").arg(accession));
break;
- case ExternalDatabase::TrEMBL :
+ case ExternalDatabase::TrEMBL:
url.setUrl(QString("http://www.uniprot.org/uniprot/%1").arg(accession));
break;
- case ExternalDatabase::ref :
+ case ExternalDatabase::ref:
break;
- case ExternalDatabase::OboPsiMod :
- QString iri(QString("http://purl.obolibrary.org/obo/%1").arg(QString(accession).replace(":","_")));
- url.setUrl(QString("http://www.ebi.ac.uk/ols/ontologies/mod/terms?iri=%1").arg(iri));
+ case ExternalDatabase::OboPsiMod:
+ QString iri(QString("http://purl.obolibrary.org/obo/%1")
+ .arg(QString(accession).replace(":", "_")));
+ url.setUrl(
+ QString("http://www.ebi.ac.uk/ols/ontologies/mod/terms?iri=%1")
+ .arg(iri));
break;
-
}
- qDebug() << "DbXref::getUrl end " << url;
- return url;
+ qDebug() << "DbXref::getUrl end " << url;
+ return url;
}
-ProteinXtp::ProteinXtp():pappso::Protein()
+ProteinXtp::ProteinXtp() : pappso::Protein()
{
-
}
-ProteinXtp::ProteinXtp(const ProteinXtp& other):pappso::Protein(other)
+ProteinXtp::ProteinXtp(const ProteinXtp &other) : pappso::Protein(other)
{
- _is_decoy=other._is_decoy;
- _is_contaminant=other._is_contaminant;
- _p_sequence_database = other._p_sequence_database;
- _p_fasta = other._p_fasta;
- _dbxref_list = other._dbxref_list;
+ _is_decoy = other._is_decoy;
+ _is_contaminant = other._is_contaminant;
+ _p_sequence_database = other._p_sequence_database;
+ _p_fasta = other._p_fasta;
+ _dbxref_list = other._dbxref_list;
}
ProteinXtp::~ProteinXtp()
{
-
}
-bool ProteinXtp::operator==(const ProteinXtp& other) const
+bool
+ProteinXtp::operator==(const ProteinXtp &other) const
{
- return pappso::Protein::operator==(other);
+ return pappso::Protein::operator==(other);
}
-ProteinXtpSp ProteinXtp::makeProteinXtpSp() const {
- return std::make_shared<ProteinXtp>(*this);
+ProteinXtpSp
+ProteinXtp::makeProteinXtpSp() const
+{
+ return std::make_shared<ProteinXtp>(*this);
}
-void ProteinXtp::setFastaFileP(const FastaFile * fasta_file) {
- _p_fasta = fasta_file;
+void
+ProteinXtp::setFastaFileP(const FastaFile *fasta_file)
+{
+ _p_fasta = fasta_file;
}
-const FastaFile * ProteinXtp::getFastaFileP() const {
- return _p_fasta;
+const FastaFile *
+ProteinXtp::getFastaFileP() const
+{
+ return _p_fasta;
}
-void ProteinXtp::setCompleteDescription(const QString & full_description) {
- setAccession (full_description.simplified().section(" ", 0,0));
- setDescription (full_description.simplified().section(" ", 1));
+void
+ProteinXtp::setCompleteDescription(const QString &full_description)
+{
+ setAccession(full_description.simplified().section(" ", 0, 0));
+ setDescription(full_description.simplified().section(" ", 1));
}
-void ProteinXtp::setIsContaminant(bool conta) {
- _is_contaminant = conta;
+void
+ProteinXtp::setIsContaminant(bool conta)
+{
+ _is_contaminant = conta;
}
-void ProteinXtp::setIsDecoy(bool conta) {
- _is_decoy = conta;
+void
+ProteinXtp::setIsDecoy(bool conta)
+{
+ _is_decoy = conta;
}
-bool ProteinXtp::isContaminant() const {
- return _is_contaminant;
+bool
+ProteinXtp::isContaminant() const
+{
+ return _is_contaminant;
}
-bool ProteinXtp::isDecoy() const {
- return _is_decoy;
+bool
+ProteinXtp::isDecoy() const
+{
+ return _is_decoy;
}
-QString ProteinXtp::getOnlyAminoAcidSequence() const {
- QString sequence(this->getSequence());
- return sequence.replace(QRegExp("[^RNDBCEQZGHILKMFPSTWYVX]"),"");
+QString
+ProteinXtp::getOnlyAminoAcidSequence() const
+{
+ QString sequence(this->getSequence());
+ return sequence.replace(QRegExp("[^RNDBCEQZGHILKMFPSTWYVX]"), "");
}
-pappso::pappso_double ProteinXtp::getMass() const {
- try {
- //qDebug() << "ProteinXtp::getMass() begin " << getOnlyAminoAcidSequence().replace("[BZX]","E");
- // replace amino acid wildcard by E, just to give an random mass (assumed it is not perfect)
- pappso::Peptide peptide(getOnlyAminoAcidSequence().replace(QRegExp("[BZX]"),"E"));
- return peptide.getMass();
-
+pappso::pappso_double
+ProteinXtp::getMass() const
+{
+ try
+ {
+ // qDebug() << "ProteinXtp::getMass() begin " <<
+ // getOnlyAminoAcidSequence().replace("[BZX]","E");
+ // replace amino acid wildcard by E, just to give an random mass (assumed
+ // it is not perfect)
+ pappso::Peptide peptide(
+ getOnlyAminoAcidSequence().replace(QRegExp("[BZX]"), "E"));
+ return peptide.getMass();
}
- catch (pappso::PappsoException error) {
- qDebug() << "ProteinXtp::getMass() " << getOnlyAminoAcidSequence().replace(QRegExp("[BZX]"),"E");
- throw pappso::PappsoException(QObject::tr("Error computing mass for protein %1 :\n%2").arg(getAccession()).arg(error.qwhat()));
+ catch(pappso::PappsoException error)
+ {
+ qDebug() << "ProteinXtp::getMass() "
+ << getOnlyAminoAcidSequence().replace(QRegExp("[BZX]"), "E");
+ throw pappso::PappsoException(
+ QObject::tr("Error computing mass for protein %1 :\n%2")
+ .arg(getAccession())
+ .arg(error.qwhat()));
}
}
-class DigestionHandler: public pappso::EnzymeProductInterface {
-public:
- void setPeptide(std::int8_t sequence_database_id, const pappso::ProteinSp & protein_sp, bool is_decoy, const QString& peptide, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme) override {
- _peptide_list.append(peptide);
- };
-
- QStringList _peptide_list;
+class DigestionHandler : public pappso::EnzymeProductInterface
+{
+ public:
+ void
+ setPeptide(std::int8_t sequence_database_id,
+ const pappso::ProteinSp &protein_sp, bool is_decoy,
+ const QString &peptide, unsigned int start, bool is_nter,
+ unsigned int missed_cleavage_number, bool semi_enzyme) override
+ {
+ _peptide_list.append(peptide);
+ };
+
+ QStringList _peptide_list;
};
-unsigned int ProteinXtp::countTrypticPeptidesForPAI() const {
- //qDebug() << "ProteinXtp::countTrypticPeptidesForPAI begin";
- try {
- pappso::Enzyme kinase;
- kinase.setMiscleavage(0);
- kinase.setTakeOnlyFirstWildcard(true);
- DigestionHandler digestion;
-
- pappso::ProteinSp protein = std::make_shared<const pappso::Protein>(this->getAccession(), this->getOnlyAminoAcidSequence());
- kinase.eat(0,protein,false,digestion);
-
- unsigned int count = 0;
- for (const QString & peptide_str: digestion._peptide_list) {
- pappso::Peptide peptide(peptide_str);
- pappso::mz mass= peptide.getMass();
- if ((mass > 800) && (mass < 2500)) {
- count ++;
+unsigned int
+ProteinXtp::countTrypticPeptidesForPAI() const
+{
+ // qDebug() << "ProteinXtp::countTrypticPeptidesForPAI begin";
+ try
+ {
+ pappso::Enzyme kinase;
+ kinase.setMiscleavage(0);
+ kinase.setTakeOnlyFirstWildcard(true);
+ DigestionHandler digestion;
+
+ pappso::ProteinSp protein = std::make_shared<const pappso::Protein>(
+ this->getAccession(), this->getOnlyAminoAcidSequence());
+ kinase.eat(0, protein, false, digestion);
+
+ unsigned int count = 0;
+ for(const QString &peptide_str : digestion._peptide_list)
+ {
+ pappso::Peptide peptide(peptide_str);
+ pappso::mz mass = peptide.getMass();
+ if((mass > 800) && (mass < 2500))
+ {
+ count++;
}
}
- //qDebug() << "ProteinXtp::countTrypticPeptidesForPAI end";
- return count;
-
+ // qDebug() << "ProteinXtp::countTrypticPeptidesForPAI end";
+ return count;
}
- catch (pappso::PappsoException error) {
- throw pappso::PappsoException(QObject::tr("Error in countTrypticPeptidesForPAI for protein %1 :\n%2").arg(getAccession()).arg(error.qwhat()));
+ catch(pappso::PappsoException error)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error in countTrypticPeptidesForPAI for protein %1 :\n%2")
+ .arg(getAccession())
+ .arg(error.qwhat()));
}
}
-void ProteinXtp::parseAccession2dbxref() {
- qDebug() << "ProteinXtp::parseAccession2dbxref begin" ;
- QStringList access_list = getAccession().split("|");
- // if (access.length == 1)
- QRegExp atg("^[Aa][Tt][MmCc1-5][Gg]\\d{5}\\.?\\d?$");
- QRegExp ncbi_gi("^[0-9]{5,8}$");
- QRegExp swiss_prot("^P[A-Z0-9]{5}$");
- QRegExp trembl("^[QOA][A-Z0-9]{5,10}$");
- QRegExp ref ("^[NZ]P\\_[0-9]{5,8}$");
- QString accession;
-
- for (unsigned int i=0; i < access_list.size(); i++) {
- accession = access_list.at(i);
- //qDebug() << "ProteinXtp::parseAccession2dbxref accession " << accession;
- if (atg.indexIn(accession, 0) != -1) {
- QStringList temp = accession.split(".");
- _dbxref_list.push_back(DbXref(ExternalDatabase::AGI_LocusCode, temp.at(0)));
- continue;
+void
+ProteinXtp::parseAccession2dbxref()
+{
+ qDebug() << "ProteinXtp::parseAccession2dbxref begin";
+ QStringList access_list = getAccession().split("|");
+ // if (access.length == 1)
+ QRegExp atg("^[Aa][Tt][MmCc1-5][Gg]\\d{5}\\.?\\d?$");
+ QRegExp ncbi_gi("^[0-9]{5,8}$");
+ QRegExp swiss_prot("^P[A-Z0-9]{5}$");
+ QRegExp trembl("^[QOA][A-Z0-9]{5,10}$");
+ QRegExp ref("^[NZ]P\\_[0-9]{5,8}$");
+ QString accession;
+
+ for(unsigned int i = 0; i < access_list.size(); i++)
+ {
+ accession = access_list.at(i);
+ // qDebug() << "ProteinXtp::parseAccession2dbxref accession " <<
+ // accession;
+ if(atg.indexIn(accession, 0) != -1)
+ {
+ QStringList temp = accession.split(".");
+ _dbxref_list.push_back(
+ DbXref(ExternalDatabase::AGI_LocusCode, temp.at(0)));
+ continue;
}
- if (swiss_prot.indexIn(accession, 0) != -1) {
- //qDebug() << "ProteinXtp::parseAccession2dbxref accession SwissProt " << accession;
- _dbxref_list.push_back(DbXref(ExternalDatabase::SwissProt, accession));
- continue;
+ if(swiss_prot.indexIn(accession, 0) != -1)
+ {
+ // qDebug() << "ProteinXtp::parseAccession2dbxref accession SwissProt
+ // " << accession;
+ _dbxref_list.push_back(
+ DbXref(ExternalDatabase::SwissProt, accession));
+ continue;
}
- if (trembl.indexIn(accession, 0) != -1) {
- //qDebug() << "ProteinXtp::parseAccession2dbxref accession TrEMBL " << accession;
- _dbxref_list.push_back(DbXref(ExternalDatabase::TrEMBL, accession));
- continue;
+ if(trembl.indexIn(accession, 0) != -1)
+ {
+ // qDebug() << "ProteinXtp::parseAccession2dbxref accession TrEMBL "
+ // << accession;
+ _dbxref_list.push_back(DbXref(ExternalDatabase::TrEMBL, accession));
+ continue;
}
- if (ref.indexIn(accession, 0) != -1) {
- _dbxref_list.push_back(DbXref(ExternalDatabase::ref, accession));
- continue;
+ if(ref.indexIn(accession, 0) != -1)
+ {
+ _dbxref_list.push_back(DbXref(ExternalDatabase::ref, accession));
+ continue;
}
- if (i > 0) {
- if ((access_list.at(i-1) == "sp")&&(accession.size() == 6)) {
- _dbxref_list.push_back(DbXref(ExternalDatabase::SwissProt, accession));
+ if(i > 0)
+ {
+ if((access_list.at(i - 1) == "sp") && (accession.size() == 6))
+ {
+ _dbxref_list.push_back(
+ DbXref(ExternalDatabase::SwissProt, accession));
}
- if ((access_list.at(i-1) == "tr")&&(accession.size() == 6)) {
- _dbxref_list.push_back(DbXref(ExternalDatabase::TrEMBL, accession));
+ if((access_list.at(i - 1) == "tr") && (accession.size() == 6))
+ {
+ _dbxref_list.push_back(
+ DbXref(ExternalDatabase::TrEMBL, accession));
}
- if ((access_list.at(i-1) == "gb")&&(ncbi_gi.indexIn(accession, 0) != -1)) {
- _dbxref_list.push_back(DbXref(ExternalDatabase::NCBI_gi, accession));
+ if((access_list.at(i - 1) == "gb") &&
+ (ncbi_gi.indexIn(accession, 0) != -1))
+ {
+ _dbxref_list.push_back(
+ DbXref(ExternalDatabase::NCBI_gi, accession));
}
-
}
- if (_dbxref_list.size() > 1) {
- _dbxref_list.sort([] (const DbXref & first, const DbXref & second)
- {
- return std::tie(first.database, first.accession) < std::tie(second.database, second.accession);
- });
- _dbxref_list.unique([] (const DbXref & first, const DbXref & second)
- {
- return ( first.database == second.database ) && (first.accession == second.accession);
- });
+ if(_dbxref_list.size() > 1)
+ {
+ _dbxref_list.sort([](const DbXref &first, const DbXref &second) {
+ return std::tie(first.database, first.accession) <
+ std::tie(second.database, second.accession);
+ });
+ _dbxref_list.unique([](const DbXref &first, const DbXref &second) {
+ return (first.database == second.database) &&
+ (first.accession == second.accession);
+ });
}
}
- //qDebug() << "ProteinXtp::parseAccession2dbxref end" ;
-
+ // qDebug() << "ProteinXtp::parseAccession2dbxref end" ;
}
-const std::list<DbXref> & ProteinXtp::getDbxrefList() const {
- return _dbxref_list;
+const std::list<DbXref> &
+ProteinXtp::getDbxrefList() const
+{
+ return _dbxref_list;
}
diff --git a/src/core/proteinxtp.h b/src/core/proteinxtp.h
index a49d39eb472258b5b707c50d559b41f0334d0ae8..a69832e41737e9f3cc74ea1029041df36c724503 100644
--- a/src/core/proteinxtp.h
+++ b/src/core/proteinxtp.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include <pappsomspp/protein/protein.h>
#include <pappsomspp/types.h>
@@ -33,13 +34,14 @@ class FastaFile;
#ifndef PROTEIN_XTP_H
#define PROTEIN_XTP_H
-struct DbXref {
- DbXref();
- DbXref(const DbXref & other);
- DbXref(ExternalDatabase database_in, const QString & accession_in);
- const QUrl getUrl() const;
- ExternalDatabase database;
- QString accession;
+struct DbXref
+{
+ DbXref();
+ DbXref(const DbXref &other);
+ DbXref(ExternalDatabase database_in, const QString &accession_in);
+ const QUrl getUrl() const;
+ ExternalDatabase database;
+ QString accession;
};
class ProteinXtp;
@@ -48,50 +50,51 @@ class ProteinXtp;
*/
typedef std::shared_ptr<ProteinXtp> ProteinXtpSp;
-class ProteinXtp : public pappso::Protein {
-public:
- ProteinXtp();
- ProteinXtp(const ProteinXtp& other);
- virtual ~ProteinXtp();
- bool operator==(const ProteinXtp& other) const;
-
-
- ProteinXtpSp makeProteinXtpSp() const;
-
- /** @brief separates accession from description based on first space separator
- */
- void setCompleteDescription(const QString & full_description);
-
- void setIsContaminant(bool conta);
- void setIsDecoy(bool conta);
- void setFastaFileP(const FastaFile * fasta_file);
- const FastaFile * getFastaFileP() const;
- bool isContaminant() const;
- bool isDecoy() const;
- unsigned int countTrypticPeptidesForPAI() const;
-
- /** @brief get only amino acid sequence
- * clean sequence of other characters : * _ ...
- */
- QString getOnlyAminoAcidSequence() const;
-
- /** @brief get protein mass in dalton
- */
- pappso::pappso_double getMass() const;
-
- /** @brief look for external database accessions in accesion text
- */
- void parseAccession2dbxref();
-
- const std::list<DbXref> & getDbxrefList() const;
-
-private:
- SequenceDatabase * _p_sequence_database;
- bool _is_decoy=false;
- bool _is_contaminant=false;
- std::list<DbXref> _dbxref_list;
-
- const FastaFile * _p_fasta=nullptr;
+class ProteinXtp : public pappso::Protein
+{
+ public:
+ ProteinXtp();
+ ProteinXtp(const ProteinXtp &other);
+ virtual ~ProteinXtp();
+ bool operator==(const ProteinXtp &other) const;
+
+
+ ProteinXtpSp makeProteinXtpSp() const;
+
+ /** @brief separates accession from description based on first space separator
+ */
+ void setCompleteDescription(const QString &full_description);
+
+ void setIsContaminant(bool conta);
+ void setIsDecoy(bool conta);
+ void setFastaFileP(const FastaFile *fasta_file);
+ const FastaFile *getFastaFileP() const;
+ bool isContaminant() const;
+ bool isDecoy() const;
+ unsigned int countTrypticPeptidesForPAI() const;
+
+ /** @brief get only amino acid sequence
+ * clean sequence of other characters : * _ ...
+ */
+ QString getOnlyAminoAcidSequence() const;
+
+ /** @brief get protein mass in dalton
+ */
+ pappso::pappso_double getMass() const;
+
+ /** @brief look for external database accessions in accesion text
+ */
+ void parseAccession2dbxref();
+
+ const std::list<DbXref> &getDbxrefList() const;
+
+ private:
+ SequenceDatabase *_p_sequence_database;
+ bool _is_decoy = false;
+ bool _is_contaminant = false;
+ std::list<DbXref> _dbxref_list;
+
+ const FastaFile *_p_fasta = nullptr;
};
#endif // PROTEIN_XTP_H
diff --git a/src/core/sequencedatabase.cpp b/src/core/sequencedatabase.cpp
index 9deb2a0c0bd49e16df6080b0a58943b093ca6a6a..54e474ea493e97d6c3d225afc70eebc68e66889e 100644
--- a/src/core/sequencedatabase.cpp
+++ b/src/core/sequencedatabase.cpp
@@ -1,34 +1,33 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "sequencedatabase.h"
SequenceDatabase::SequenceDatabase()
{
-
}
SequenceDatabase::~SequenceDatabase()
{
-
}
diff --git a/src/core/sequencedatabase.h b/src/core/sequencedatabase.h
index 4123ebd04bc2df426e71db37ae753b380873bfa5..9861374d130d3864fc29dffe6a29eb2935fb962e 100644
--- a/src/core/sequencedatabase.h
+++ b/src/core/sequencedatabase.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef SEQUENCEDATABASE_H
#define SEQUENCEDATABASE_H
@@ -34,9 +35,9 @@ typedef std::shared_ptr<SequenceDatabase> SequenceDatabaseSp;
class SequenceDatabase
{
-public:
- SequenceDatabase();
- virtual ~SequenceDatabase();
+ public:
+ SequenceDatabase();
+ virtual ~SequenceDatabase();
};
#endif // SEQUENCEDATABASE_H
diff --git a/src/core/tandem_run/tandembatchprocess.cpp b/src/core/tandem_run/tandembatchprocess.cpp
index 0437c0a124db721f2694aedcd5284137f769bffb..ba9be3d7dc654f7e9b6655001f98c9fa7e798b1c 100644
--- a/src/core/tandem_run/tandembatchprocess.cpp
+++ b/src/core/tandem_run/tandembatchprocess.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "tandembatchprocess.h"
#include <QProcess>
@@ -35,235 +36,297 @@
#include <QTemporaryDir>
#include "../../files/tandemparametersfile.h"
-TandemBatchProcess::TandemBatchProcess(MainWindow * p_main_window, WorkMonitorInterface * p_monitor, const TandemRunBatch & tandem_run_batch) {
- _p_main_window = p_main_window;
- _tandem_run_batch = tandem_run_batch;
- _p_monitor = p_monitor;
- _tmp_database_file.setAutoRemove(true);
-
- //check that output directory is writeable :
- QFileInfo fi_in_dir(_tandem_run_batch._output_directory);
- if (fi_in_dir.isDir() && fi_in_dir.isWritable()) {
- } else {
- throw pappso::PappsoException(QObject::tr("output directory is not writable. Please check permissions on %1").arg(fi_in_dir.absoluteFilePath()));
+TandemBatchProcess::TandemBatchProcess(MainWindow *p_main_window,
+ WorkMonitorInterface *p_monitor,
+ const TandemRunBatch &tandem_run_batch)
+{
+ _p_main_window = p_main_window;
+ _tandem_run_batch = tandem_run_batch;
+ _p_monitor = p_monitor;
+ _tmp_database_file.setAutoRemove(true);
+
+ // check that output directory is writeable :
+ QFileInfo fi_in_dir(_tandem_run_batch._output_directory);
+ if(fi_in_dir.isDir() && fi_in_dir.isWritable())
+ {
+ }
+ else
+ {
+ throw pappso::PappsoException(
+ QObject::tr(
+ "output directory is not writable. Please check permissions on %1")
+ .arg(fi_in_dir.absoluteFilePath()));
}
}
-TandemBatchProcess::~TandemBatchProcess() {
+TandemBatchProcess::~TandemBatchProcess()
+{
}
-bool TandemBatchProcess::shouldIstop() {
- if (_p_main_window->stopWorkerThread()) {
- return true;
+bool
+TandemBatchProcess::shouldIstop()
+{
+ if(_p_main_window->stopWorkerThread())
+ {
+ return true;
}
- return false;
+ return false;
}
-void TandemBatchProcess::writeXmlDatabaseFile (QXmlStreamWriter * p_out) {
- p_out->setAutoFormatting(true);
- p_out->writeStartDocument("1.0");
-
- //<?xml version="1.0" encoding="UTF-8"?>
- //<bioml label="x! taxon-to-file matching list">
- p_out->writeStartElement("bioml");
- p_out->writeAttribute("label","x! taxon-to-file matching list");
- //<taxon label="usedefined">
- p_out->writeStartElement("taxon");
- p_out->writeAttribute("label","usedefined");
- //<file format="peptide" URL="/gorgone/pappso/jouy/users/Didier/fasta/20170608_Delastours/contaminants_standards.fasta"></file>
- //<file format="peptide" URL="/gorgone/pappso/jouy/users/Didier/fasta/20170608_Delastours/Escherichia coli 27J42_WGS_ECOLI_1.fasta"></file>
- for (QString fasta_file:_tandem_run_batch._fasta_file_list) {
- p_out->writeStartElement("file");
- p_out->writeAttribute("format","peptide");
- p_out->writeAttribute("URL",fasta_file);
- p_out->writeEndElement();
+void
+TandemBatchProcess::writeXmlDatabaseFile(QXmlStreamWriter *p_out)
+{
+ p_out->setAutoFormatting(true);
+ p_out->writeStartDocument("1.0");
+
+ //<?xml version="1.0" encoding="UTF-8"?>
+ //<bioml label="x! taxon-to-file matching list">
+ p_out->writeStartElement("bioml");
+ p_out->writeAttribute("label", "x! taxon-to-file matching list");
+ //<taxon label="usedefined">
+ p_out->writeStartElement("taxon");
+ p_out->writeAttribute("label", "usedefined");
+ //<file format="peptide"
+ //URL="/gorgone/pappso/jouy/users/Didier/fasta/20170608_Delastours/contaminants_standards.fasta"></file>
+ //<file format="peptide"
+ //URL="/gorgone/pappso/jouy/users/Didier/fasta/20170608_Delastours/Escherichia
+ //coli 27J42_WGS_ECOLI_1.fasta"></file>
+ for(QString fasta_file : _tandem_run_batch._fasta_file_list)
+ {
+ p_out->writeStartElement("file");
+ p_out->writeAttribute("format", "peptide");
+ p_out->writeAttribute("URL", fasta_file);
+ p_out->writeEndElement();
}
- //</taxon>
- p_out->writeEndElement();
- //</bioml>
- p_out->writeEndElement();
- p_out->writeEndDocument();
+ //</taxon>
+ p_out->writeEndElement();
+ //</bioml>
+ p_out->writeEndElement();
+ p_out->writeEndDocument();
}
-void TandemBatchProcess::prepareXmlDatabaseFile() {
+void
+TandemBatchProcess::prepareXmlDatabaseFile()
+{
- if (_tmp_database_file.open())
+ if(_tmp_database_file.open())
{
- _xml_database_file = QFileInfo( _tmp_database_file.fileName()).absoluteFilePath();
- QXmlStreamWriter * p_out = new QXmlStreamWriter();
- p_out->setDevice(&_tmp_database_file);
- writeXmlDatabaseFile(p_out);
- _tmp_database_file.close();
- delete p_out;
- } else
+ _xml_database_file =
+ QFileInfo(_tmp_database_file.fileName()).absoluteFilePath();
+ QXmlStreamWriter *p_out = new QXmlStreamWriter();
+ p_out->setDevice(&_tmp_database_file);
+ writeXmlDatabaseFile(p_out);
+ _tmp_database_file.close();
+ delete p_out;
+ }
+ else
{
- throw pappso::PappsoException(QObject::tr("error : cannot open the XML database file : %1\n").arg(_tmp_database_file.fileName()));
+ throw pappso::PappsoException(
+ QObject::tr("error : cannot open the XML database file : %1\n")
+ .arg(_tmp_database_file.fileName()));
}
-
}
-void TandemBatchProcess::run() {
- qDebug() << "TandemBatchProcess::run begin " << _tandem_run_batch._preset_file;
- QTemporaryDir tmp_dir;
- if (!tmp_dir.isValid()) {
- // dir.path() returns the unique directory path
- throw pappso::PappsoException(QObject::tr("problem creating temporary directory in %1\n").arg(tmp_dir.path()));
+void
+TandemBatchProcess::run()
+{
+ qDebug() << "TandemBatchProcess::run begin "
+ << _tandem_run_batch._preset_file;
+ QTemporaryDir tmp_dir;
+ if(!tmp_dir.isValid())
+ {
+ // dir.path() returns the unique directory path
+ throw pappso::PappsoException(
+ QObject::tr("problem creating temporary directory in %1\n")
+ .arg(tmp_dir.path()));
}
- TandemParametersFile orig_parameter_file(_tandem_run_batch._preset_file);
- _preset_file = QString("%1/%2").arg(tmp_dir.path()).arg(orig_parameter_file.getFilename());
+ TandemParametersFile orig_parameter_file(_tandem_run_batch._preset_file);
+ _preset_file =
+ QString("%1/%2").arg(tmp_dir.path()).arg(orig_parameter_file.getFilename());
- TandemParametersFile new_parameter_file(_preset_file);
- TandemParameters new_param = orig_parameter_file.getTandemParameters();
- // <note type="input" label="spectrum, threads">1</note>
- new_param.setParamLabelValue("spectrum, threads",QString("%1").arg(_tandem_run_batch._number_of_threads));
- new_parameter_file.setTandemParameters(new_param);
+ TandemParametersFile new_parameter_file(_preset_file);
+ TandemParameters new_param = orig_parameter_file.getTandemParameters();
+ // <note type="input" label="spectrum, threads">1</note>
+ new_param.setParamLabelValue(
+ "spectrum, threads",
+ QString("%1").arg(_tandem_run_batch._number_of_threads));
+ new_parameter_file.setTandemParameters(new_param);
- prepareXmlDatabaseFile();
+ prepareXmlDatabaseFile();
- int i=0;
- _p_monitor->setProgressMaximumValue(_tandem_run_batch._mz_file_list.size());
- for (QString mz_file : _tandem_run_batch._mz_file_list) {
- if (shouldIstop()) {
- throw pappso::PappsoException(QObject::tr("X!Tandem stopped by the user processing %1 sample").arg(mz_file));
+ int i = 0;
+ _p_monitor->setProgressMaximumValue(_tandem_run_batch._mz_file_list.size());
+ for(QString mz_file : _tandem_run_batch._mz_file_list)
+ {
+ if(shouldIstop())
+ {
+ throw pappso::PappsoException(
+ QObject::tr("X!Tandem stopped by the user processing %1 sample")
+ .arg(mz_file));
}
- _p_monitor->message(QObject::tr("running X!Tandem on %1\n").arg(mz_file), i);
- runOne(mz_file);
- i++;
+ _p_monitor->message(QObject::tr("running X!Tandem on %1\n").arg(mz_file),
+ i);
+ runOne(mz_file);
+ i++;
}
- _p_monitor->finished(QObject::tr("%1 X!Tandem job(s) finished").arg(_tandem_run_batch._mz_file_list.size()));
- qDebug() << "TandemBatchProcess::run end" ;
+ _p_monitor->finished(QObject::tr("%1 X!Tandem job(s) finished")
+ .arg(_tandem_run_batch._mz_file_list.size()));
+ qDebug() << "TandemBatchProcess::run end";
}
-void TandemBatchProcess::writeXmlInputFile (QXmlStreamWriter * p_out, const QString & mz_file) {
-
- QFileInfo mz_file_info(mz_file);
- //<?xml version="1.0" encoding="UTF-8"?>
-
- p_out->setAutoFormatting(true);
- p_out->writeStartDocument("1.0");
-
- //<bioml label="20170405_Delastour_11.xml">
- p_out->writeStartElement("bioml");
- p_out->writeAttribute("label",mz_file_info.fileName());
-
- //<note type="heading">Paths</note>
- p_out->writeStartElement("note");
- p_out->writeAttribute("type","heading");
- p_out->writeCharacters("Paths");
- p_out->writeEndElement();
-
- //<note type="input" label="list path, default parameters">/gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/QExactive_IAM_4CPU_Classic_ClassicAvecReversed..xml</note>
- p_out->writeStartElement("note");
- p_out->writeAttribute("type","input");
- p_out->writeAttribute("label","list path, default parameters");
- p_out->writeCharacters(_preset_file);
- p_out->writeEndElement();
-
- //<note type="input" label="list path, taxonomy information">/gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/database.xml</note>
- p_out->writeStartElement("note");
- p_out->writeAttribute("type","input");
- p_out->writeAttribute("label","list path, taxonomy information");
- p_out->writeCharacters(_xml_database_file);
- p_out->writeEndElement();
-
-
- //<note type="input" label="spectrum, path">/gorgone/pappso/jouy/raw/2017_Qex/20170405_Delastours/20170405_Delastour_11.mzXML</note>
-
- p_out->writeStartElement("note");
- p_out->writeAttribute("type","input");
- p_out->writeAttribute("label","spectrum, path");
- p_out->writeCharacters(mz_file);
- p_out->writeEndElement();
-
- //<note type="heading">Protein general</note>
- p_out->writeStartElement("note");
- p_out->writeAttribute("type","heading");
- p_out->writeCharacters("Protein general");
- p_out->writeEndElement();
-
- //<note type="input" label="protein, taxon">usedefined</note>
- p_out->writeStartElement("note");
- p_out->writeAttribute("type","input");
- p_out->writeAttribute("label","protein, taxon");
- p_out->writeCharacters("usedefined");
- p_out->writeEndElement();
- //<note type="heading">Output</note>
- p_out->writeStartElement("note");
- p_out->writeAttribute("type","heading");
- p_out->writeCharacters("Output");
- p_out->writeEndElement();
-
- //<note type="input" label="output, path">/gorgone/pappso/jouy/users/Didier/Xcal2017/2017_05_04_Delastours/Interrogation_souches_sequencees/Patient27/J42/20170405_Delastour_11.xml</note>
-
- p_out->writeStartElement("note");
- p_out->writeAttribute("type","input");
- p_out->writeAttribute("label","output, path");
- p_out->writeCharacters(QString("%1/%2.xml").arg(_tandem_run_batch._output_directory).arg(mz_file_info.baseName()));
- p_out->writeEndElement();
-
- //</bioml>
- p_out->writeEndElement();
-
-
- p_out->writeEndDocument();
+void
+TandemBatchProcess::writeXmlInputFile(QXmlStreamWriter *p_out,
+ const QString &mz_file)
+{
+
+ QFileInfo mz_file_info(mz_file);
+ //<?xml version="1.0" encoding="UTF-8"?>
+
+ p_out->setAutoFormatting(true);
+ p_out->writeStartDocument("1.0");
+
+ //<bioml label="20170405_Delastour_11.xml">
+ p_out->writeStartElement("bioml");
+ p_out->writeAttribute("label", mz_file_info.fileName());
+
+ //<note type="heading">Paths</note>
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type", "heading");
+ p_out->writeCharacters("Paths");
+ p_out->writeEndElement();
+
+ //<note type="input" label="list path, default
+ //parameters">/gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/QExactive_IAM_4CPU_Classic_ClassicAvecReversed..xml</note>
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type", "input");
+ p_out->writeAttribute("label", "list path, default parameters");
+ p_out->writeCharacters(_preset_file);
+ p_out->writeEndElement();
+
+ //<note type="input" label="list path, taxonomy
+ //information">/gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/database.xml</note>
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type", "input");
+ p_out->writeAttribute("label", "list path, taxonomy information");
+ p_out->writeCharacters(_xml_database_file);
+ p_out->writeEndElement();
+
+
+ //<note type="input" label="spectrum,
+ //path">/gorgone/pappso/jouy/raw/2017_Qex/20170405_Delastours/20170405_Delastour_11.mzXML</note>
+
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type", "input");
+ p_out->writeAttribute("label", "spectrum, path");
+ p_out->writeCharacters(mz_file);
+ p_out->writeEndElement();
+
+ //<note type="heading">Protein general</note>
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type", "heading");
+ p_out->writeCharacters("Protein general");
+ p_out->writeEndElement();
+
+ //<note type="input" label="protein, taxon">usedefined</note>
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type", "input");
+ p_out->writeAttribute("label", "protein, taxon");
+ p_out->writeCharacters("usedefined");
+ p_out->writeEndElement();
+ //<note type="heading">Output</note>
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type", "heading");
+ p_out->writeCharacters("Output");
+ p_out->writeEndElement();
+
+ //<note type="input" label="output,
+ //path">/gorgone/pappso/jouy/users/Didier/Xcal2017/2017_05_04_Delastours/Interrogation_souches_sequencees/Patient27/J42/20170405_Delastour_11.xml</note>
+
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type", "input");
+ p_out->writeAttribute("label", "output, path");
+ p_out->writeCharacters(QString("%1/%2.xml")
+ .arg(_tandem_run_batch._output_directory)
+ .arg(mz_file_info.baseName()));
+ p_out->writeEndElement();
+
+ //</bioml>
+ p_out->writeEndElement();
+
+
+ p_out->writeEndDocument();
}
-void TandemBatchProcess::runOne(const QString & mz_file) {
- QTemporaryFile xml_input_file;
- xml_input_file.setAutoRemove(true);
- if (xml_input_file.open())
+void
+TandemBatchProcess::runOne(const QString &mz_file)
+{
+ QTemporaryFile xml_input_file;
+ xml_input_file.setAutoRemove(true);
+ if(xml_input_file.open())
{
- QXmlStreamWriter * p_out = new QXmlStreamWriter();
- p_out->setDevice(&xml_input_file);
+ QXmlStreamWriter *p_out = new QXmlStreamWriter();
+ p_out->setDevice(&xml_input_file);
- writeXmlInputFile(p_out, mz_file);
+ writeXmlInputFile(p_out, mz_file);
- xml_input_file.close();
- delete p_out;
- } else
+ xml_input_file.close();
+ delete p_out;
+ }
+ else
{
- throw pappso::PappsoException(QObject::tr("error : cannot open the XML X!Tandem input file : %1\n").arg(xml_input_file.fileName()));
+ throw pappso::PappsoException(
+ QObject::tr("error : cannot open the XML X!Tandem input file : %1\n")
+ .arg(xml_input_file.fileName()));
}
- QStringList arguments;
+ QStringList arguments;
- arguments << xml_input_file.fileName();
+ arguments << xml_input_file.fileName();
- QProcess * xt_process = new QProcess();
- //hk_process->setWorkingDirectory(QFileInfo(_hardklor_exe).absolutePath());
- xt_process->start(_tandem_run_batch._tandem_bin_path, arguments);
+ QProcess *xt_process = new QProcess();
+ // hk_process->setWorkingDirectory(QFileInfo(_hardklor_exe).absolutePath());
+ xt_process->start(_tandem_run_batch._tandem_bin_path, arguments);
- if (!xt_process->waitForStarted()) {
- throw pappso::PappsoException(QObject::tr("X!Tandem process failed to start"));
+ if(!xt_process->waitForStarted())
+ {
+ throw pappso::PappsoException(
+ QObject::tr("X!Tandem process failed to start"));
}
- while(xt_process->waitForReadyRead(_max_xt_time_ms)) {
- _p_monitor->appendText( xt_process->readAll().data());
- //data.append(xt_process->readAll());
- if (shouldIstop()) {
- xt_process->kill();
- delete xt_process;
- throw pappso::PappsoException(QObject::tr("X!Tandem stopped by the user processing %1 sample").arg(mz_file));
+ while(xt_process->waitForReadyRead(_max_xt_time_ms))
+ {
+ _p_monitor->appendText(xt_process->readAll().data());
+ // data.append(xt_process->readAll());
+ if(shouldIstop())
+ {
+ xt_process->kill();
+ delete xt_process;
+ throw pappso::PappsoException(
+ QObject::tr("X!Tandem stopped by the user processing %1 sample")
+ .arg(mz_file));
}
}
- /*
- if (!xt_process->waitForFinished(_max_xt_time_ms)) {
- throw pappso::PappsoException(QObject::tr("can't wait for X!Tandem process to finish : timeout at %1").arg(_max_xt_time_ms));
- }
- */
- QByteArray result = xt_process->readAll();
-
- QProcess::ExitStatus Status = xt_process->exitStatus();
-
- delete xt_process;
- if (Status != 0)
+ /*
+ if (!xt_process->waitForFinished(_max_xt_time_ms)) {
+ throw pappso::PappsoException(QObject::tr("can't wait for X!Tandem process
+ to finish : timeout at %1").arg(_max_xt_time_ms));
+ }
+ */
+ QByteArray result = xt_process->readAll();
+
+ QProcess::ExitStatus Status = xt_process->exitStatus();
+
+ delete xt_process;
+ if(Status != 0)
{
- // != QProcess::NormalExit
- throw pappso::PappsoException(QObject::tr("error executing X!Tandem Status != 0 : %1 %2\n%3").arg(_tandem_run_batch._tandem_bin_path).arg(arguments.join(" ").arg(result.data())));
+ // != QProcess::NormalExit
+ throw pappso::PappsoException(
+ QObject::tr("error executing X!Tandem Status != 0 : %1 %2\n%3")
+ .arg(_tandem_run_batch._tandem_bin_path)
+ .arg(arguments.join(" ").arg(result.data())));
}
-
}
diff --git a/src/core/tandem_run/tandembatchprocess.h b/src/core/tandem_run/tandembatchprocess.h
index 7502c4b64c094ea752b872625f9db9982e1548b8..beb8b13fa31c1d737788c10f075b296d42ce5f9e 100644
--- a/src/core/tandem_run/tandembatchprocess.h
+++ b/src/core/tandem_run/tandembatchprocess.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef TANDEMBATCHPROCESS_H
#define TANDEMBATCHPROCESS_H
@@ -37,31 +38,32 @@
class TandemBatchProcess
{
-public:
- TandemBatchProcess(MainWindow * p_main_window, WorkMonitorInterface * p_monitor, const TandemRunBatch & tandem_run_batch);
- virtual ~TandemBatchProcess();
+ public:
+ TandemBatchProcess(MainWindow *p_main_window, WorkMonitorInterface *p_monitor,
+ const TandemRunBatch &tandem_run_batch);
+ virtual ~TandemBatchProcess();
- virtual void run();
-protected:
- void writeXmlDatabaseFile (QXmlStreamWriter * p_out);
- void writeXmlInputFile (QXmlStreamWriter * p_out, const QString & mz_file);
- virtual void prepareXmlDatabaseFile();
- bool shouldIstop();
-private:
- void runOne(const QString & mz_file);
+ virtual void run();
-protected:
- QString _preset_file;
- TandemRunBatch _tandem_run_batch;
- WorkMonitorInterface * _p_monitor;
- QString _xml_database_file;
- int _max_xt_time_ms = (60000 * 60 * 24); //1 day
-
-private:
-
-
- QTemporaryFile _tmp_database_file;
- MainWindow * _p_main_window=nullptr;
+ protected:
+ void writeXmlDatabaseFile(QXmlStreamWriter *p_out);
+ void writeXmlInputFile(QXmlStreamWriter *p_out, const QString &mz_file);
+ virtual void prepareXmlDatabaseFile();
+ bool shouldIstop();
+
+ private:
+ void runOne(const QString &mz_file);
+
+ protected:
+ QString _preset_file;
+ TandemRunBatch _tandem_run_batch;
+ WorkMonitorInterface *_p_monitor;
+ QString _xml_database_file;
+ int _max_xt_time_ms = (60000 * 60 * 24); // 1 day
+
+ private:
+ QTemporaryFile _tmp_database_file;
+ MainWindow *_p_main_window = nullptr;
};
#endif // TANDEMBATCHPROCESS_H
diff --git a/src/core/tandem_run/tandemcondorprocess.h b/src/core/tandem_run/tandemcondorprocess.h
index 492dea58f6f18c01f72935fca8ef34f01e6f3dbe..2f89dabaff0e357e184458ab9d21484652aacb4d 100644
--- a/src/core/tandem_run/tandemcondorprocess.h
+++ b/src/core/tandem_run/tandemcondorprocess.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef TANDEMCONDORPROCESS_H
#define TANDEMCONDORPROCESS_H
@@ -33,36 +34,38 @@
#include "tandembatchprocess.h"
#include <QTemporaryDir>
-class TandemCondorProcess: public TandemBatchProcess
+class TandemCondorProcess : public TandemBatchProcess
{
-public:
- TandemCondorProcess(MainWindow * p_main_window, WorkMonitorInterface * p_monitor, const TandemRunBatch & tandem_run_batch);
- virtual ~TandemCondorProcess();
+ public:
+ TandemCondorProcess(MainWindow *p_main_window,
+ WorkMonitorInterface *p_monitor,
+ const TandemRunBatch &tandem_run_batch);
+ virtual ~TandemCondorProcess();
- virtual void prepareXmlDatabaseFile();
- virtual void run();
-
- unsigned int getCondorJobSize() const;
- void setCondorJobStatus(std::int8_t count_status[10]);
-
-private :
- void parseCondorJobNumber(QString condor_job);
- void surveyCondorJob();
- void getCondorJobState();
- void parseCondorQueue(QString & condor_q_xml);
- void condorRemoveJob();
-private:
- QTemporaryDir * _p_tmp_dir;
- QString _condor_submit_command;
- QString _condor_q_command;
- QString _condor_rm_command;
-
- unsigned int _condor_cluster_number;
- unsigned int _condor_job_size;
- unsigned int _condor_request_memory;
- unsigned int _condor_status_timer_millisecond= 1000;
- unsigned int _condor_completed_jobs = 0;
+ virtual void prepareXmlDatabaseFile();
+ virtual void run();
+ unsigned int getCondorJobSize() const;
+ void setCondorJobStatus(std::int8_t count_status[10]);
+
+ private:
+ void parseCondorJobNumber(QString condor_job);
+ void surveyCondorJob();
+ void getCondorJobState();
+ void parseCondorQueue(QString &condor_q_xml);
+ void condorRemoveJob();
+
+ private:
+ QTemporaryDir *_p_tmp_dir;
+ QString _condor_submit_command;
+ QString _condor_q_command;
+ QString _condor_rm_command;
+
+ unsigned int _condor_cluster_number;
+ unsigned int _condor_job_size;
+ unsigned int _condor_request_memory;
+ unsigned int _condor_status_timer_millisecond = 1000;
+ unsigned int _condor_completed_jobs = 0;
};
#endif // TANDECONDORPROCESS_H
diff --git a/src/core/tandem_run/tandemparameters.cpp b/src/core/tandem_run/tandemparameters.cpp
index 1a43c52679ae4efdc0b7f577748ea6fce3cf80f7..b20665b018599d4fdd615f0e5f9eef1f786ee756 100644
--- a/src/core/tandem_run/tandemparameters.cpp
+++ b/src/core/tandem_run/tandemparameters.cpp
@@ -6,136 +6,228 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "tandemparameters.h"
#include <QDebug>
#include <pappsomspp/exception/exceptionnotfound.h>
#include <pappsomspp/exception/exceptionnotpossible.h>
-TandemParameters::TandemParameters() {
+TandemParameters::TandemParameters()
+{
}
-TandemParameters::~TandemParameters() {
+TandemParameters::~TandemParameters()
+{
}
-TandemParameters::TandemParameters(const TandemParameters & other) {
- qDebug() << "TandemParameters::TandemParameters copy begin";
- //_map_label_value = other._map_label_value;
- _method_name = other._method_name;
+TandemParameters::TandemParameters(const TandemParameters &other)
+{
+ qDebug() << "TandemParameters::TandemParameters copy begin";
+ //_map_label_value = other._map_label_value;
+ _method_name = other._method_name;
- QMap<QString, QString>::const_iterator i = other._map_label_value.constBegin();
- while (i != other._map_label_value.constEnd()) {
- qDebug() << "TandemParameters::TandemParameters copy " << i.key() << " " << i.value();
- _map_label_value.insert(i.key(), i.value());
- i++; // added
+ QMap<QString, QString>::const_iterator i =
+ other._map_label_value.constBegin();
+ while(i != other._map_label_value.constEnd())
+ {
+ qDebug() << "TandemParameters::TandemParameters copy " << i.key() << " "
+ << i.value();
+ _map_label_value.insert(i.key(), i.value());
+ i++; // added
}
- qDebug() << "TandemParameters::TandemParameters copy end";
+ qDebug() << "TandemParameters::TandemParameters copy end";
}
-bool TandemParameters::equals(const TandemParameters & other) const {
- if (_method_name != other._method_name) {
- return false;
+bool
+TandemParameters::equals(const TandemParameters &other) const
+{
+ if(_method_name != other._method_name)
+ {
+ return false;
}
- if (_map_label_value.size() != other._map_label_value.size()) {
- return false;
+ if(_map_label_value.size() != other._map_label_value.size())
+ {
+ return false;
}
- QMap<QString, QString>::const_iterator i = _map_label_value.constBegin();
- while (i != _map_label_value.constEnd()) {
- if(i.value() != other.getValue(i.key())) {
- return false;
+ QMap<QString, QString>::const_iterator i = _map_label_value.constBegin();
+ while(i != _map_label_value.constEnd())
+ {
+ if(i.value() != other.getValue(i.key()))
+ {
+ return false;
}
- i++; // added
+ i++; // added
}
- return true;
+ return true;
}
-const QString TandemParameters::getLabelCategory(const QString & value) const {
- return value.split(", ").at(0);
+const QString
+TandemParameters::getLabelCategory(const QString &value) const
+{
+ return value.split(", ").at(0);
}
-const QString & TandemParameters::getValue(const QString & label) const {
- QMap<QString,QString>::const_iterator it = _map_label_value.constFind(label);
- if (it == _map_label_value.end()) {
- throw pappso::ExceptionNotFound(QObject::tr("X!Tandem preset label %1 not found in method %2").arg(label).arg(_method_name));
+const QString &
+TandemParameters::getValue(const QString &label) const
+{
+ QMap<QString, QString>::const_iterator it = _map_label_value.constFind(label);
+ if(it == _map_label_value.end())
+ {
+ throw pappso::ExceptionNotFound(
+ QObject::tr("X!Tandem preset label %1 not found in method %2")
+ .arg(label)
+ .arg(_method_name));
}
- return it.value();
+ return it.value();
}
-void TandemParameters::setParamLabelValue(const QString & label, const QString & value) {
- //list path
- //<note type="input" label="list path, default parameters">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/QExactive_analysis_FDR_nosemi.xml</note>
- //<note type="input" label="list path, taxonomy information">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/database.xml</note>
- if (getLabelCategory(label) == "list path") {
- return;
+void
+TandemParameters::setParamLabelValue(const QString &label, const QString &value)
+{
+ // list path
+ //<note type="input" label="list path, default
+ //parameters">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/QExactive_analysis_FDR_nosemi.xml</note>
+ //<note type="input" label="list path, taxonomy
+ //information">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/database.xml</note>
+ if(getLabelCategory(label) == "list path")
+ {
+ return;
}
- if (label == "spectrum, path") {
- return;
+ if(label == "spectrum, path")
+ {
+ return;
}
- if ((label == "spectrum, parent monoisotopic mass error units") || (label == "spectrum, fragment monoisotopic mass error units")) {
- if ((value != "Daltons") && (value != "ppm")) {
- throw pappso::ExceptionNotPossible(QObject::tr("%1 value must be Daltons or ppm (not %2)").arg(label).arg(value));
+ if((label == "spectrum, parent monoisotopic mass error units") ||
+ (label == "spectrum, fragment monoisotopic mass error units"))
+ {
+ if((value != "Daltons") && (value != "ppm"))
+ {
+ throw pappso::ExceptionNotPossible(
+ QObject::tr("%1 value must be Daltons or ppm (not %2)")
+ .arg(label)
+ .arg(value));
}
}
- if ((label == "spectrum, parent monoisotopic mass isotope error") || (label == "spectrum, use neutral loss window") || (label == "spectrum, use contrast angle") || (label == "protein, cleavage semi") || (label == "protein, quick acetyl") || (label == "protein, quick pyrolidone") || (label == "protein, stP bias") || (label == "scoring, cyclic permutation") || (label == "scoring, include reverse") || (label == "scoring, y ions") || (label == "scoring, b ions") || (label == "scoring, c ions") || (label == "scoring, z ions") || (label == "scoring, a ions") || (label == "scoring, x ions") || (label == "refine") || (label == "refine, use potential modifications for full refinement") || (label == "refine, cleavage semi") || (label == "refine, unanticipated cleavage")|| (label == "refine, spectrum synthesis")|| (label == "refine, point mutations") || (label == "output, mzid") || (label == "output, spectra") || (label == "spectrum, use noise suppression")) {
- if ((value != "yes") && (value != "no")) {
- throw pappso::ExceptionNotPossible(QObject::tr("%1 value must be yes or no (not %2)").arg(label).arg(value));
+ if((label == "spectrum, parent monoisotopic mass isotope error") ||
+ (label == "spectrum, use neutral loss window") ||
+ (label == "spectrum, use contrast angle") ||
+ (label == "protein, cleavage semi") ||
+ (label == "protein, quick acetyl") ||
+ (label == "protein, quick pyrolidone") || (label == "protein, stP bias") ||
+ (label == "scoring, cyclic permutation") ||
+ (label == "scoring, include reverse") || (label == "scoring, y ions") ||
+ (label == "scoring, b ions") || (label == "scoring, c ions") ||
+ (label == "scoring, z ions") || (label == "scoring, a ions") ||
+ (label == "scoring, x ions") || (label == "refine") ||
+ (label == "refine, use potential modifications for full refinement") ||
+ (label == "refine, cleavage semi") ||
+ (label == "refine, unanticipated cleavage") ||
+ (label == "refine, spectrum synthesis") ||
+ (label == "refine, point mutations") || (label == "output, mzid") ||
+ (label == "output, spectra") ||
+ (label == "spectrum, use noise suppression"))
+ {
+ if((value != "yes") && (value != "no"))
+ {
+ throw pappso::ExceptionNotPossible(
+ QObject::tr("%1 value must be yes or no (not %2)")
+ .arg(label)
+ .arg(value));
}
}
- if ((label == "spectrum, parent monoisotopic mass error minus") || (label == "spectrum, parent monoisotopic mass error plus")|| (label == "spectrum, dynamic range") || (label == "spectrum, minimum parent m+h") || (label == "protein, cleavage C-terminal mass change")|| (label == "protein, cleavage N-terminal mass change") || (label == "protein, C-terminal residue modification mass") || (label == "protein, N-terminal residue modification mass") || (label == "refine, maximum valid expectation value")) {
- bool ok;
- value.toDouble(&ok);
- if (!ok) {// not an integer
- throw pappso::ExceptionNotPossible(QObject::tr("%1 value must be a number (not %2)").arg(label).arg(value));
+ if((label == "spectrum, parent monoisotopic mass error minus") ||
+ (label == "spectrum, parent monoisotopic mass error plus") ||
+ (label == "spectrum, dynamic range") ||
+ (label == "spectrum, minimum parent m+h") ||
+ (label == "protein, cleavage C-terminal mass change") ||
+ (label == "protein, cleavage N-terminal mass change") ||
+ (label == "protein, C-terminal residue modification mass") ||
+ (label == "protein, N-terminal residue modification mass") ||
+ (label == "refine, maximum valid expectation value"))
+ {
+ bool ok;
+ value.toDouble(&ok);
+ if(!ok)
+ { // not an integer
+ throw pappso::ExceptionNotPossible(
+ QObject::tr("%1 value must be a number (not %2)")
+ .arg(label)
+ .arg(value));
}
}
- if ((label == "spectrum, maximum parent charge") || (label == "spectrum, total peaks") || (label == "spectrum, minimum peaks") || (label == "spectrum, sequence batch size") || (label == "spectrum, threads") || (label == "scoring, minimum ion count") || (label == "scoring, maximum missed cleavage sites")) {
- bool ok;
- value.toInt(&ok);
- if (!ok) {// not an integer
- throw pappso::ExceptionNotPossible(QObject::tr("%1 value must be an integer (not %2)").arg(label).arg(value));
+ if((label == "spectrum, maximum parent charge") ||
+ (label == "spectrum, total peaks") ||
+ (label == "spectrum, minimum peaks") ||
+ (label == "spectrum, sequence batch size") ||
+ (label == "spectrum, threads") ||
+ (label == "scoring, minimum ion count") ||
+ (label == "scoring, maximum missed cleavage sites"))
+ {
+ bool ok;
+ value.toInt(&ok);
+ if(!ok)
+ { // not an integer
+ throw pappso::ExceptionNotPossible(
+ QObject::tr("%1 value must be an integer (not %2)")
+ .arg(label)
+ .arg(value));
}
}
- if (label == "spectrum, fragment mass type") {
- if ((value != "monoisotopic") && (value != "average")) {
- throw pappso::ExceptionNotPossible(QObject::tr("%1 value must be monoisotopic or average (not %2)").arg(label).arg(value));
+ if(label == "spectrum, fragment mass type")
+ {
+ if((value != "monoisotopic") && (value != "average"))
+ {
+ throw pappso::ExceptionNotPossible(
+ QObject::tr("%1 value must be monoisotopic or average (not %2)")
+ .arg(label)
+ .arg(value));
}
}
- //text "protein, cleavage site" "protein, modified residue mass file" "residue, modification mass" || (label == "refine, potential N-terminus modifications") || (label == "refine, potential C-terminus modifications")
- //spectrum, neutral loss mass
- //spectrum, neutral loss window
+ // text "protein, cleavage site" "protein, modified residue mass file"
+ // "residue, modification mass" || (label == "refine, potential N-terminus
+ // modifications") || (label == "refine, potential C-terminus modifications")
+ // spectrum, neutral loss mass
+ // spectrum, neutral loss window
- _map_label_value.insert(label, value);
+ _map_label_value.insert(label, value);
}
-void TandemParameters::setMethodName(const QString & method) {
- _method_name = method;
+void
+TandemParameters::setMethodName(const QString &method)
+{
+ _method_name = method;
}
-const QString & TandemParameters::getMethodName() const {
- return _method_name;
+const QString &
+TandemParameters::getMethodName() const
+{
+ return _method_name;
}
-const QMap<QString, QString> & TandemParameters::getMapLabelValue() const {
- return _map_label_value;
+const QMap<QString, QString> &
+TandemParameters::getMapLabelValue() const
+{
+ return _map_label_value;
}
diff --git a/src/core/tandem_run/tandemparameters.h b/src/core/tandem_run/tandemparameters.h
index 00ae6f2fb5e0afe6655a482481617048883d27fa..5a1b75074d454a5b61e4ac733bdbc4a1bd5a1ee2 100644
--- a/src/core/tandem_run/tandemparameters.h
+++ b/src/core/tandem_run/tandemparameters.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef TANDEMPARAMETERS_H
#define TANDEMPARAMETERS_H
@@ -35,22 +36,24 @@
class TandemParameters
{
-public:
- TandemParameters();
- TandemParameters(const TandemParameters & other);
- virtual ~TandemParameters();
-
- const QString & getValue(const QString & label) const;
- void setMethodName(const QString & method);
- const QString & getMethodName() const;
- void setParamLabelValue(const QString & label, const QString & value);
- const QMap<QString, QString> & getMapLabelValue() const;
- bool equals(const TandemParameters & other) const;
-private:
- const QString getLabelCategory(const QString & value) const;
-private:
- QString _method_name;
- QMap<QString, QString> _map_label_value;
+ public:
+ TandemParameters();
+ TandemParameters(const TandemParameters &other);
+ virtual ~TandemParameters();
+
+ const QString &getValue(const QString &label) const;
+ void setMethodName(const QString &method);
+ const QString &getMethodName() const;
+ void setParamLabelValue(const QString &label, const QString &value);
+ const QMap<QString, QString> &getMapLabelValue() const;
+ bool equals(const TandemParameters &other) const;
+
+ private:
+ const QString getLabelCategory(const QString &value) const;
+
+ private:
+ QString _method_name;
+ QMap<QString, QString> _map_label_value;
};
#endif // TANDEMPARAMETERS_H
diff --git a/src/core/tandem_run/tandemrunbatch.cpp b/src/core/tandem_run/tandemrunbatch.cpp
index 64a06a41a6e405fa8e5d0bd131ccf551f26181f7..6510b4c0b5b42788c5214e4580e74d4e6e3fcfb8 100644
--- a/src/core/tandem_run/tandemrunbatch.cpp
+++ b/src/core/tandem_run/tandemrunbatch.cpp
@@ -6,25 +6,26 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "tandemrunbatch.h"
diff --git a/src/core/tandem_run/tandemrunbatch.h b/src/core/tandem_run/tandemrunbatch.h
index 64835956518636519f63c7d0f0f173ff4b46b41e..99ce0242ea8b541cd7b47732a28f2097aa1d52b0 100644
--- a/src/core/tandem_run/tandemrunbatch.h
+++ b/src/core/tandem_run/tandemrunbatch.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef TANDEMRUNBATCH_H
#define TANDEMRUNBATCH_H
@@ -34,12 +35,12 @@
#include <QMetaType>
struct TandemRunBatch
{
- QString _tandem_bin_path;
- QStringList _mz_file_list;
- QString _preset_file;
- QStringList _fasta_file_list;
- QString _output_directory;
- unsigned int _number_of_threads=1;
+ QString _tandem_bin_path;
+ QStringList _mz_file_list;
+ QString _preset_file;
+ QStringList _fasta_file_list;
+ QString _output_directory;
+ unsigned int _number_of_threads = 1;
};
-//Q_DECLARE_METATYPE(TandemRunBatch)
+// Q_DECLARE_METATYPE(TandemRunBatch)
#endif // TANDEMRUNBATCH_H
diff --git a/src/files/fastafile.cpp b/src/files/fastafile.cpp
index a4bbdef091656aa6522f037332f043c26406ce95..fe9e15ce0fc038d53aef966bac8e5a0c4374a73d 100644
--- a/src/files/fastafile.cpp
+++ b/src/files/fastafile.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "fastafile.h"
#include <pappsomspp/fasta/fastareader.h>
@@ -27,106 +28,149 @@
#include <QDebug>
#include <pappsomspp/exception/exceptionnotfound.h>
-class AccessionContaminantReader: public pappso::FastaHandlerInterface {
-public:
- AccessionContaminantReader (ProteinStore & protein_store) :_protein_store(protein_store) {
- };
+class AccessionContaminantReader : public pappso::FastaHandlerInterface
+{
+ public:
+ AccessionContaminantReader(ProteinStore &protein_store)
+ : _protein_store(protein_store){};
+
+ void
+ setSequence(const QString &description, const QString &sequence) override
+ {
+ // qDebug() << "PeptideReader::setSequence " << description << " "
+ // <<sequence;
+ QStringList descr_split = description.simplified().split(" ");
+ QString accession = descr_split.at(0);
+ // qDebug() << "PeptideReader::setSequence " << accession << " "
+ // <<accession;
+ _protein_store.setContaminantAccession(accession);
+ };
- void setSequence(const QString& description, const QString& sequence) override {
- //qDebug() << "PeptideReader::setSequence " << description << " " <<sequence;
- QStringList descr_split = description.simplified().split(" ");
- QString accession = descr_split.at(0);
- //qDebug() << "PeptideReader::setSequence " << accession << " " <<accession;
- _protein_store.setContaminantAccession(accession);
- };
-private:
- ProteinStore & _protein_store;
+ private:
+ ProteinStore &_protein_store;
};
-class AccessionDecoyReader: public pappso::FastaHandlerInterface {
-public:
- AccessionDecoyReader (ProteinStore & protein_store) :_protein_store(protein_store) {
- };
+class AccessionDecoyReader : public pappso::FastaHandlerInterface
+{
+ public:
+ AccessionDecoyReader(ProteinStore &protein_store)
+ : _protein_store(protein_store){};
+
+ void
+ setSequence(const QString &description, const QString &sequence) override
+ {
+ // qDebug() << "PeptideReader::setSequence " << description << " "
+ // <<sequence;
+ QStringList descr_split = description.simplified().split(" ");
+ QString accession = descr_split.at(0);
+ _protein_store.setDecoyAccession(accession);
+ };
- void setSequence(const QString& description, const QString& sequence) override {
- //qDebug() << "PeptideReader::setSequence " << description << " " <<sequence;
- QStringList descr_split = description.simplified().split(" ");
- QString accession = descr_split.at(0);
- _protein_store.setDecoyAccession(accession);
- };
-private:
- ProteinStore & _protein_store;
+ private:
+ ProteinStore &_protein_store;
};
-FastaFile::FastaFile(const QString & fasta_source) : _fasta_source(fasta_source)
+FastaFile::FastaFile(const QString &fasta_source) : _fasta_source(fasta_source)
{
- qDebug() << "FastaFile::FastaFile "<< fasta_source;
+ qDebug() << "FastaFile::FastaFile " << fasta_source;
}
-FastaFile::FastaFile(const QFileInfo & fasta_source): _fasta_source(fasta_source)
+FastaFile::FastaFile(const QFileInfo &fasta_source)
+ : _fasta_source(fasta_source)
{
}
-FastaFile::FastaFile(const FastaFile & other) : _fasta_source(other._fasta_source)
+FastaFile::FastaFile(const FastaFile &other)
+ : _fasta_source(other._fasta_source)
{
-
}
FastaFile::~FastaFile()
{
-
}
-void FastaFile::setXmlId(const QString xmlid) {
- _xml_id = xmlid;
+void
+FastaFile::setXmlId(const QString xmlid)
+{
+ _xml_id = xmlid;
}
-const QString & FastaFile::getXmlId() const {
- return _xml_id;
+const QString &
+FastaFile::getXmlId() const
+{
+ return _xml_id;
}
-const QString FastaFile::getFilename() const {
- return _fasta_source.fileName();
+const QString
+FastaFile::getFilename() const
+{
+ return _fasta_source.fileName();
}
-const QString FastaFile::getAbsoluteFilePath() const {
- return _fasta_source.absoluteFilePath();
+const QString
+FastaFile::getAbsoluteFilePath() const
+{
+ return _fasta_source.absoluteFilePath();
}
-void FastaFile::setContaminants(ProteinStore & protein_store) const {
- protein_store.addContaminantFastaFile(this);
- if (_fasta_source.exists()) {
- AccessionContaminantReader accession_reader(protein_store);
- pappso::FastaReader reader(accession_reader);
- QFile fasta_file(_fasta_source.absoluteFilePath());
- if (fasta_file.open(QIODevice::ReadOnly)) {
- reader.parse(&fasta_file);
- fasta_file.close();
+void
+FastaFile::setContaminants(ProteinStore &protein_store) const
+{
+ protein_store.addContaminantFastaFile(this);
+ if(_fasta_source.exists())
+ {
+ AccessionContaminantReader accession_reader(protein_store);
+ pappso::FastaReader reader(accession_reader);
+ QFile fasta_file(_fasta_source.absoluteFilePath());
+ if(fasta_file.open(QIODevice::ReadOnly))
+ {
+ reader.parse(&fasta_file);
+ fasta_file.close();
}
- else {
- qDebug() << "FastaFile::setContaminants "<< _fasta_source.absoluteFilePath() << " not open";
- throw pappso::ExceptionNotFound(QObject::tr("unable to open contaminant fasta file \"%1\"").arg(_fasta_source.absoluteFilePath()));
+ else
+ {
+ qDebug() << "FastaFile::setContaminants "
+ << _fasta_source.absoluteFilePath() << " not open";
+ throw pappso::ExceptionNotFound(
+ QObject::tr("unable to open contaminant fasta file \"%1\"")
+ .arg(_fasta_source.absoluteFilePath()));
}
}
- else {
- qDebug() << "FastaFile::setContaminants "<< _fasta_source.absoluteFilePath() << " does not exists";
- throw pappso::ExceptionNotFound(QObject::tr("contaminant fasta file \"%1\" not found").arg(_fasta_source.absoluteFilePath()));
+ else
+ {
+ qDebug() << "FastaFile::setContaminants "
+ << _fasta_source.absoluteFilePath() << " does not exists";
+ throw pappso::ExceptionNotFound(
+ QObject::tr("contaminant fasta file \"%1\" not found")
+ .arg(_fasta_source.absoluteFilePath()));
}
}
-void FastaFile::setDecoys(ProteinStore & protein_store) const {
- protein_store.addDecoyFastaFile(this);
- if (_fasta_source.exists()) {
- AccessionDecoyReader accession_reader(protein_store);
- pappso::FastaReader reader(accession_reader);
- QFile fasta_file(_fasta_source.absoluteFilePath());
- if (fasta_file.open(QIODevice::ReadOnly)) {
- reader.parse(&fasta_file);
- fasta_file.close();
+void
+FastaFile::setDecoys(ProteinStore &protein_store) const
+{
+ protein_store.addDecoyFastaFile(this);
+ if(_fasta_source.exists())
+ {
+ AccessionDecoyReader accession_reader(protein_store);
+ pappso::FastaReader reader(accession_reader);
+ QFile fasta_file(_fasta_source.absoluteFilePath());
+ if(fasta_file.open(QIODevice::ReadOnly))
+ {
+ reader.parse(&fasta_file);
+ fasta_file.close();
}
- else {
- qDebug() << "FastaFile::setDecoys "<< _fasta_source.absoluteFilePath() << " not open";
- throw pappso::ExceptionNotFound(QObject::tr("unable to open decoy fasta file \"%1\"").arg(_fasta_source.absoluteFilePath()));
+ else
+ {
+ qDebug() << "FastaFile::setDecoys "
+ << _fasta_source.absoluteFilePath() << " not open";
+ throw pappso::ExceptionNotFound(
+ QObject::tr("unable to open decoy fasta file \"%1\"")
+ .arg(_fasta_source.absoluteFilePath()));
}
}
- else {
- qDebug() << "FastaFile::setDecoys "<< _fasta_source.absoluteFilePath() << " does not exists";
- throw pappso::ExceptionNotFound(QObject::tr("decoy fasta file \"%1\" not found").arg(_fasta_source.absoluteFilePath()));
+ else
+ {
+ qDebug() << "FastaFile::setDecoys " << _fasta_source.absoluteFilePath()
+ << " does not exists";
+ throw pappso::ExceptionNotFound(
+ QObject::tr("decoy fasta file \"%1\" not found")
+ .arg(_fasta_source.absoluteFilePath()));
}
}
diff --git a/src/files/fastafile.h b/src/files/fastafile.h
index c398d3bdbcf0f16eb087bd19a29514688c00eb75..40a54c88e24dd4a876ac566b04f960963fec6db3 100644
--- a/src/files/fastafile.h
+++ b/src/files/fastafile.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef FASTAFILE_H
#define FASTAFILE_H
@@ -33,32 +34,31 @@ typedef std::shared_ptr<FastaFile> FastaFileSp;
class FastaFile
{
-public:
- FastaFile(const QString & fasta_source);
- FastaFile(const QFileInfo & fasta_source);
- FastaFile(const FastaFile & other);
- ~FastaFile();
+ public:
+ FastaFile(const QString &fasta_source);
+ FastaFile(const QFileInfo &fasta_source);
+ FastaFile(const FastaFile &other);
+ ~FastaFile();
-
- const QString getFilename() const;
- const QString getAbsoluteFilePath() const;
-
- /** @brief read fasta file and set accessions as contaminants
- * */
- void setContaminants(ProteinStore & protein_store) const;
-
- /** @brief read fasta file and set accessions as decoys
- * */
- void setDecoys(ProteinStore & protein_store) const;
-
-
- void setXmlId(const QString xmlid);
- const QString & getXmlId() const;
-private :
- const QFileInfo _fasta_source;
- QString _xml_id;
+ const QString getFilename() const;
+ const QString getAbsoluteFilePath() const;
+ /** @brief read fasta file and set accessions as contaminants
+ * */
+ void setContaminants(ProteinStore &protein_store) const;
+
+ /** @brief read fasta file and set accessions as decoys
+ * */
+ void setDecoys(ProteinStore &protein_store) const;
+
+
+ void setXmlId(const QString xmlid);
+ const QString &getXmlId() const;
+
+ private:
+ const QFileInfo _fasta_source;
+ QString _xml_id;
};
Q_DECLARE_METATYPE(FastaFile *)
diff --git a/src/files/tandemparametersfile.cpp b/src/files/tandemparametersfile.cpp
index bd98d3f5b41b9acbc2c20d4c96581f9acc8284be..498ce27eefcec8eb87f7f7868045fb65e1fc852a 100644
--- a/src/files/tandemparametersfile.cpp
+++ b/src/files/tandemparametersfile.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "tandemparametersfile.h"
#include <QXmlSimpleReader>
@@ -35,145 +36,199 @@
#include <pappsomspp/exception/exceptionnotfound.h>
#include "../input/xtandemparamsaxhandler.h"
-TandemParametersFile::TandemParametersFile(const QString & fasta_source) : _param_source(fasta_source)
+TandemParametersFile::TandemParametersFile(const QString &fasta_source)
+ : _param_source(fasta_source)
{
- qDebug() << "TandemParametersFile::TandemParametersFile "<< fasta_source;
+ qDebug() << "TandemParametersFile::TandemParametersFile " << fasta_source;
}
-TandemParametersFile::TandemParametersFile(const QFileInfo & fasta_source): _param_source(fasta_source)
+TandemParametersFile::TandemParametersFile(const QFileInfo &fasta_source)
+ : _param_source(fasta_source)
{
}
-TandemParametersFile::TandemParametersFile(const TandemParametersFile & other) : _param_source(other._param_source)
+TandemParametersFile::TandemParametersFile(const TandemParametersFile &other)
+ : _param_source(other._param_source)
{
-
}
TandemParametersFile::~TandemParametersFile()
{
-
}
-const QString TandemParametersFile::getMethodName() const {
- return _param_source.baseName();
+const QString
+TandemParametersFile::getMethodName() const
+{
+ return _param_source.baseName();
}
-const QString TandemParametersFile::getFilename() const {
- return _param_source.fileName();
+const QString
+TandemParametersFile::getFilename() const
+{
+ return _param_source.fileName();
}
-const QDir TandemParametersFile::getAbsoluteDir() const {
- return _param_source.absoluteDir();
+const QDir
+TandemParametersFile::getAbsoluteDir() const
+{
+ return _param_source.absoluteDir();
}
-const QString TandemParametersFile::getAbsoluteFilePath() const {
- return _param_source.absoluteFilePath();
+const QString
+TandemParametersFile::getAbsoluteFilePath() const
+{
+ return _param_source.absoluteFilePath();
}
-bool TandemParametersFile::exists() const
+bool
+TandemParametersFile::exists() const
{
- return _param_source.exists();
+ return _param_source.exists();
}
-void TandemParametersFile::setDirectory(const QDir & directory) {
- QFileInfo new_dir(QString("%1/%2").arg(directory.absolutePath()).arg(_param_source.fileName()));
- _param_source = new_dir;
+void
+TandemParametersFile::setDirectory(const QDir &directory)
+{
+ QFileInfo new_dir(QString("%1/%2")
+ .arg(directory.absolutePath())
+ .arg(_param_source.fileName()));
+ _param_source = new_dir;
}
-void TandemParametersFile::setTandemParameters(const TandemParameters & parameters) {
+void
+TandemParametersFile::setTandemParameters(const TandemParameters ¶meters)
+{
- QFile xml_file(_param_source.absoluteFilePath());
- QFile new_file(QString("%1/%2.xml").arg(_param_source.absolutePath()).arg(parameters.getMethodName()));
- try {
- if (_param_source.absoluteFilePath() != QFileInfo( new_file).absoluteFilePath()) {
- if (xml_file.exists()) {
- //move if renamed
- xml_file.remove();
+ QFile xml_file(_param_source.absoluteFilePath());
+ QFile new_file(QString("%1/%2.xml")
+ .arg(_param_source.absolutePath())
+ .arg(parameters.getMethodName()));
+ try
+ {
+ if(_param_source.absoluteFilePath() !=
+ QFileInfo(new_file).absoluteFilePath())
+ {
+ if(xml_file.exists())
+ {
+ // move if renamed
+ xml_file.remove();
+ }
+ }
+ QXmlStreamWriter *p_out;
+ if(new_file.open(QIODevice::WriteOnly))
+ {
+
+ _param_source.setFile(new_file);
+ p_out = new QXmlStreamWriter();
+ p_out->setDevice(&new_file);
+ writeXmlParametersFile(p_out, parameters);
+ new_file.close();
+ delete p_out;
+ }
+ else
+ {
+ throw pappso::PappsoException(
+ QObject::tr(
+ "error : cannot open the XML X!Tandem parameter file : %1\n")
+ .arg(new_file.fileName()));
}
}
- QXmlStreamWriter * p_out;
- if (new_file.open(QIODevice::WriteOnly)) {
-
- _param_source.setFile(new_file);
- p_out = new QXmlStreamWriter();
- p_out->setDevice(&new_file);
- writeXmlParametersFile(p_out, parameters);
- new_file.close();
- delete p_out;
- } else
+
+ catch(pappso::PappsoException &error_pappso)
{
- throw pappso::PappsoException(QObject::tr("error : cannot open the XML X!Tandem parameter file : %1\n").arg(new_file.fileName()));
+ throw pappso::PappsoException(
+ QObject::tr("error writing tandem preset file %1 : \n%2")
+ .arg(QFileInfo(new_file).absoluteFilePath())
+ .arg(error_pappso.qwhat()));
}
+ catch(std::exception &error)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("error writing tandem preset file %1 : \n%2")
+ .arg(QFileInfo(new_file).absoluteFilePath())
+ .arg(error.what()));
}
-
- catch (pappso::PappsoException & error_pappso) {
- throw pappso::PappsoException(QObject::tr("error writing tandem preset file %1 : \n%2").arg(QFileInfo( new_file).absoluteFilePath()).arg(error_pappso.qwhat()));
- }
- catch (std::exception & error) {
- throw pappso::PappsoException(QObject::tr("error writing tandem preset file %1 : \n%2").arg(QFileInfo( new_file).absoluteFilePath()).arg(error.what()));
- }
-
}
-TandemParameters TandemParametersFile::getTandemParameters() const {
- qDebug() << "TandemParametersFile::getTandemParameters begin";
- TandemParameters parameters;
- XtandemParamSaxHandler * parser = new XtandemParamSaxHandler(¶meters);
+TandemParameters
+TandemParametersFile::getTandemParameters() const
+{
+ qDebug() << "TandemParametersFile::getTandemParameters begin";
+ TandemParameters parameters;
+ XtandemParamSaxHandler *parser = new XtandemParamSaxHandler(¶meters);
- QXmlSimpleReader simplereader;
- simplereader.setContentHandler(parser);
- simplereader.setErrorHandler(parser);
+ QXmlSimpleReader simplereader;
+ simplereader.setContentHandler(parser);
+ simplereader.setErrorHandler(parser);
- qDebug() << "TandemParametersFile::getTandemParameters '" << _param_source.absoluteFilePath() << "'";
- parameters.setMethodName(getMethodName());
+ qDebug() << "TandemParametersFile::getTandemParameters '"
+ << _param_source.absoluteFilePath() << "'";
+ parameters.setMethodName(getMethodName());
- QFile qfile(_param_source.absoluteFilePath());
- QXmlInputSource xmlInputSource(&qfile);
+ QFile qfile(_param_source.absoluteFilePath());
+ QXmlInputSource xmlInputSource(&qfile);
- if (simplereader.parse(xmlInputSource)) {
- qDebug() << "TandemParametersFile::getTandemParameters parse ok";
- qfile.close();
- delete parser;
- } else {
+ if(simplereader.parse(xmlInputSource))
+ {
+ qDebug() << "TandemParametersFile::getTandemParameters parse ok";
+ qfile.close();
+ delete parser;
+ }
+ else
+ {
- qDebug() << "TandemParametersFile::getTandemParameters parse error";
- qfile.close();
+ qDebug() << "TandemParametersFile::getTandemParameters parse error";
+ qfile.close();
- throw pappso::PappsoException(QObject::tr("Error reading %1 X!Tandem preset file :\n %2").arg(_param_source.absoluteFilePath()).arg(parser->errorString()));
- delete parser;
+ throw pappso::PappsoException(
+ QObject::tr("Error reading %1 X!Tandem preset file :\n %2")
+ .arg(_param_source.absoluteFilePath())
+ .arg(parser->errorString()));
+ delete parser;
}
- return parameters;
+ return parameters;
}
-bool TandemParametersFile::isTandemPresetFile() const {
+bool
+TandemParametersFile::isTandemPresetFile() const
+{
- if (this->exists()) {
+ if(this->exists())
+ {
- try {
- TandemParameters param = getTandemParameters();
- param.getValue("spectrum, threads");
+ try
+ {
+ TandemParameters param = getTandemParameters();
+ param.getValue("spectrum, threads");
}
- catch (pappso::ExceptionNotFound & error) {
- return false;
+ catch(pappso::ExceptionNotFound &error)
+ {
+ return false;
}
- catch (pappso::PappsoException & error) {
- return false;
+ catch(pappso::PappsoException &error)
+ {
+ return false;
}
- return true;
+ return true;
}
- return false;
+ return false;
}
-void TandemParametersFile::writeXmlParametersFile (QXmlStreamWriter * p_out, const TandemParameters & parameters) const {
- p_out->setAutoFormatting(true);
- p_out->writeStartDocument("1.0");
-
- //<?xml version="1.0" encoding="UTF-8"?>
- //<bioml label="example api document">
- //<note type="input" label="spectrum, parent monoisotopic mass error units">ppm</note>
- //<note type="input" label="spectrum, parent monoisotopic mass error minus">10</note>
- p_out->writeStartElement("bioml");
- p_out->writeAttribute("label","example api document");
- for (const QString & label :parameters.getMapLabelValue().keys()) {
- p_out->writeStartElement("note");
- p_out->writeAttribute("type","input");
- p_out->writeAttribute("label",label);
- p_out->writeCharacters(parameters.getMapLabelValue().value(label));
- p_out->writeEndElement();
+void
+TandemParametersFile::writeXmlParametersFile(
+ QXmlStreamWriter *p_out, const TandemParameters ¶meters) const
+{
+ p_out->setAutoFormatting(true);
+ p_out->writeStartDocument("1.0");
+
+ //<?xml version="1.0" encoding="UTF-8"?>
+ //<bioml label="example api document">
+ //<note type="input" label="spectrum, parent monoisotopic mass error
+ //units">ppm</note> <note type="input" label="spectrum, parent monoisotopic
+ //mass error minus">10</note>
+ p_out->writeStartElement("bioml");
+ p_out->writeAttribute("label", "example api document");
+ for(const QString &label : parameters.getMapLabelValue().keys())
+ {
+ p_out->writeStartElement("note");
+ p_out->writeAttribute("type", "input");
+ p_out->writeAttribute("label", label);
+ p_out->writeCharacters(parameters.getMapLabelValue().value(label));
+ p_out->writeEndElement();
}
- //</bioml>
- p_out->writeEndElement();
- p_out->writeEndDocument();
+ //</bioml>
+ p_out->writeEndElement();
+ p_out->writeEndDocument();
}
diff --git a/src/files/tandemparametersfile.h b/src/files/tandemparametersfile.h
index 73dcd62116dd079941b47bd123f6800500759d66..ae2e2f58fbedc19e8e26bb1e7e77296a84376609 100644
--- a/src/files/tandemparametersfile.h
+++ b/src/files/tandemparametersfile.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef TANDEMPARAMETERSFILE_H
#define TANDEMPARAMETERSFILE_H
@@ -36,41 +37,41 @@
class TandemParametersFile
{
-
-public:
- TandemParametersFile(const QString & param_file);
- TandemParametersFile(const QFileInfo & param_file);
- TandemParametersFile(const TandemParametersFile & other);
- ~TandemParametersFile();
- const QString getMethodName() const;
- const QString getFilename() const;
- const QDir getAbsoluteDir() const;
- const QString getAbsoluteFilePath() const;
- bool exists() const;
-
- /** @brief tells if this file is really a tandem preset file
- */
- bool isTandemPresetFile() const;
-
- /** @brief read tandem parameters from XML file
- */
- TandemParameters getTandemParameters() const;
-
- /** @brief write tandem parameters to XML file
- */
- void setTandemParameters(const TandemParameters & parameters);
-
- /** @brief set param file directory
- */
- void setDirectory(const QDir & directory);
-
-private :
- void writeXmlParametersFile (QXmlStreamWriter * p_out, const TandemParameters & parameters) const;
+ public:
+ TandemParametersFile(const QString ¶m_file);
+ TandemParametersFile(const QFileInfo ¶m_file);
+ TandemParametersFile(const TandemParametersFile &other);
+ ~TandemParametersFile();
-private :
- QFileInfo _param_source;
+ const QString getMethodName() const;
+ const QString getFilename() const;
+ const QDir getAbsoluteDir() const;
+ const QString getAbsoluteFilePath() const;
+ bool exists() const;
+ /** @brief tells if this file is really a tandem preset file
+ */
+ bool isTandemPresetFile() const;
+
+ /** @brief read tandem parameters from XML file
+ */
+ TandemParameters getTandemParameters() const;
+
+ /** @brief write tandem parameters to XML file
+ */
+ void setTandemParameters(const TandemParameters ¶meters);
+
+ /** @brief set param file directory
+ */
+ void setDirectory(const QDir &directory);
+
+ private:
+ void writeXmlParametersFile(QXmlStreamWriter *p_out,
+ const TandemParameters ¶meters) const;
+
+ private:
+ QFileInfo _param_source;
};
#endif // TANDEMPARAMETERSFILE_H
diff --git a/src/files/xpipfile.cpp b/src/files/xpipfile.cpp
index 2906563f44c8ff8241048b0df55e75e9d3f39780..88ed3382d3fb4964088b2381247da6b0977b95e3 100644
--- a/src/files/xpipfile.cpp
+++ b/src/files/xpipfile.cpp
@@ -1,51 +1,52 @@
/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "xpipfile.h"
-XpipFile::XpipFile(const QUrl & xpip_source) : _xpip_source(xpip_source)
+XpipFile::XpipFile(const QUrl &xpip_source) : _xpip_source(xpip_source)
{
-
}
-XpipFile::XpipFile(const QFileInfo & xpip_source): _xpip_source(xpip_source.absoluteFilePath())
+XpipFile::XpipFile(const QFileInfo &xpip_source)
+ : _xpip_source(xpip_source.absoluteFilePath())
{
- qDebug() << "XpipFile::XpipFile begin " << _xpip_source.toString() << " " <<xpip_source.absoluteFilePath();
+ qDebug() << "XpipFile::XpipFile begin " << _xpip_source.toString() << " "
+ << xpip_source.absoluteFilePath();
}
-XpipFile::XpipFile(const XpipFile & other) : _xpip_source(other._xpip_source)
+XpipFile::XpipFile(const XpipFile &other) : _xpip_source(other._xpip_source)
{
-
}
XpipFile::~XpipFile()
{
-
}
-ProjectSp XpipFile::getProjectSp(WorkMonitorInterface * p_monitor) const {
- qDebug() << "XpipFile::getProjectSp begin " << _xpip_source.toString();
- ProjectSp project_sp = Project().makeProjectSp();
-
- project_sp.get()->readXpipFile(p_monitor, QFileInfo(_xpip_source.toString()));
+ProjectSp
+XpipFile::getProjectSp(WorkMonitorInterface *p_monitor) const
+{
+ qDebug() << "XpipFile::getProjectSp begin " << _xpip_source.toString();
+ ProjectSp project_sp = Project().makeProjectSp();
- return (project_sp);
+ project_sp.get()->readXpipFile(p_monitor, QFileInfo(_xpip_source.toString()));
+ return (project_sp);
}
diff --git a/src/files/xpipfile.h b/src/files/xpipfile.h
index 566071a109aa172b003006809a7138d293d93da9..478dbf3b9d0782ed982cadef7f152eb16a17b5ec 100644
--- a/src/files/xpipfile.h
+++ b/src/files/xpipfile.h
@@ -1,24 +1,25 @@
/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef XPIPFILE_H
#define XPIPFILE_H
@@ -29,16 +30,16 @@
class XpipFile
{
-public:
- XpipFile(const QUrl & xpip_source);
- XpipFile(const QFileInfo & xpip_source);
- XpipFile(const XpipFile & other);
- ~XpipFile();
-
- ProjectSp getProjectSp(WorkMonitorInterface * p_monitor) const;
+ public:
+ XpipFile(const QUrl &xpip_source);
+ XpipFile(const QFileInfo &xpip_source);
+ XpipFile(const XpipFile &other);
+ ~XpipFile();
-private :
- const QUrl _xpip_source;
+ ProjectSp getProjectSp(WorkMonitorInterface *p_monitor) const;
+
+ private:
+ const QUrl _xpip_source;
};
#endif // XPIPFILE_H
diff --git a/src/grouping/groupingexperiment.cpp b/src/grouping/groupingexperiment.cpp
index 25509c7ea4dc53a3bcf0ee074aa01c0bfa8d3996..631773b96063f75b2d5f605e2b3737fdc419687a 100644
--- a/src/grouping/groupingexperiment.cpp
+++ b/src/grouping/groupingexperiment.cpp
@@ -1,45 +1,51 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "groupingexperiment.h"
#include <pappsomspp/exception/exceptionnotimplemented.h>
#include "groupingpeptidemass.h"
-GroupingExperiment::GroupingExperiment(WorkMonitorInterface * p_work_monitor)
+GroupingExperiment::GroupingExperiment(WorkMonitorInterface *p_work_monitor)
{
- _p_work_monitor = p_work_monitor;
+ _p_work_monitor = p_work_monitor;
}
GroupingExperiment::~GroupingExperiment()
{
-
}
-GroupingExperiment * GroupingExperiment::newInstance(const GroupingType & grouping_type, WorkMonitorInterface * p_work_monitor) {
- if (grouping_type == GroupingType::PeptideMass) {
- return new GroupingPeptideMass(p_work_monitor);
+GroupingExperiment *
+GroupingExperiment::newInstance(const GroupingType &grouping_type,
+ WorkMonitorInterface *p_work_monitor)
+{
+ if(grouping_type == GroupingType::PeptideMass)
+ {
+ return new GroupingPeptideMass(p_work_monitor);
}
- else {
- throw pappso::ExceptionNotImplemented(QObject::tr("Grouping algorithm not yet implemented"));
+ else
+ {
+ throw pappso::ExceptionNotImplemented(
+ QObject::tr("Grouping algorithm not yet implemented"));
}
}
diff --git a/src/grouping/groupingexperiment.h b/src/grouping/groupingexperiment.h
index 0910407c3bcce9cd02cfcfc0b030911b9fd22f6e..040737c74efe0ad1873a6eac767f788a15f855fa 100644
--- a/src/grouping/groupingexperiment.h
+++ b/src/grouping/groupingexperiment.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "../utils/types.h"
@@ -34,20 +35,24 @@ class PeptideEvidence;
class GroupingExperiment
{
-public:
- GroupingExperiment(WorkMonitorInterface * p_work_monitor);
- ~GroupingExperiment();
-
- static GroupingExperiment * newInstance(const GroupingType & grouping_type, WorkMonitorInterface * p_work_monitor);
-
- virtual pappso::GrpProteinSp & getGrpProteinSp(ProteinMatch* p_protein_match) = 0;
- virtual pappso::GrpPeptideSp & setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideEvidence * p_peptide_evidence) = 0;
- virtual void addPostGroupingGrpProteinSpRemoval(pappso::GrpProteinSp sp_protein) = 0;
- virtual void startGrouping()= 0;
-
-protected:
- WorkMonitorInterface * _p_work_monitor;
-
+ public:
+ GroupingExperiment(WorkMonitorInterface *p_work_monitor);
+ ~GroupingExperiment();
+
+ static GroupingExperiment *newInstance(const GroupingType &grouping_type,
+ WorkMonitorInterface *p_work_monitor);
+
+ virtual pappso::GrpProteinSp &
+ getGrpProteinSp(ProteinMatch *p_protein_match) = 0;
+ virtual pappso::GrpPeptideSp &
+ setGrpPeptide(pappso::GrpProteinSp proteinSp,
+ PeptideEvidence *p_peptide_evidence) = 0;
+ virtual void
+ addPostGroupingGrpProteinSpRemoval(pappso::GrpProteinSp sp_protein) = 0;
+ virtual void startGrouping() = 0;
+
+ protected:
+ WorkMonitorInterface *_p_work_monitor;
};
#endif // GROUPINGEXPERIMENT_H
diff --git a/src/grouping/groupinggroup.cpp b/src/grouping/groupinggroup.cpp
index e3d85a0950dc72fbb9a6e17b64dea39c70570701..f9db8e2c868d84be4b686c4381acd2388f1214cb 100644
--- a/src/grouping/groupinggroup.cpp
+++ b/src/grouping/groupinggroup.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "groupinggroup.h"
#include <core/proteinmatch.h>
@@ -30,164 +31,252 @@
GroupingGroup::GroupingGroup()
{
-
}
GroupingGroup::~GroupingGroup()
{
-
}
-const std::vector<std::pair<unsigned int, const PeptideEvidence *>> & GroupingGroup::getPairSgNumberPeptideEvidenceList() const {
- return _pair_sg_number_peptide_evidence_list;
+const std::vector<std::pair<unsigned int, const PeptideEvidence *>> &
+GroupingGroup::getPairSgNumberPeptideEvidenceList() const
+{
+ return _pair_sg_number_peptide_evidence_list;
}
-unsigned int GroupingGroup::getGroupNumber() const {
- return _group_number;
+unsigned int
+GroupingGroup::getGroupNumber() const
+{
+ return _group_number;
}
-unsigned int GroupingGroup::getNumberOfSubgroups() const {
- return _number_of_subgroup;
+unsigned int
+GroupingGroup::getNumberOfSubgroups() const
+{
+ return _number_of_subgroup;
}
-const std::vector<const ProteinMatch *> & GroupingGroup::getProteinMatchList() const {
- return _protein_match_list;
+const std::vector<const ProteinMatch *> &
+GroupingGroup::getProteinMatchList() const
+{
+ return _protein_match_list;
}
-std::vector<const PeptideEvidence *> GroupingGroup::getPeptideEvidenceList() const {
- std::vector<const PeptideEvidence *> peptide_match_list;
- for (auto && pair_peptide_match :_pair_sg_number_peptide_evidence_list) {
- peptide_match_list.push_back(pair_peptide_match.second);
+std::vector<const PeptideEvidence *>
+GroupingGroup::getPeptideEvidenceList() const
+{
+ std::vector<const PeptideEvidence *> peptide_match_list;
+ for(auto &&pair_peptide_match : _pair_sg_number_peptide_evidence_list)
+ {
+ peptide_match_list.push_back(pair_peptide_match.second);
}
- return peptide_match_list;
+ return peptide_match_list;
}
-const QStringList GroupingGroup::getSubgroupIdList(const PeptideEvidence * p_peptide_match) const {
- std::set<unsigned int> subgroup_list;
- pappso::GrpPeptide * p_grp_peptide = p_peptide_match->getGrpPeptideSp().get();
- if (p_grp_peptide != nullptr) {
- for (auto && pair_peptide_match :_pair_sg_number_peptide_evidence_list) {
- if(pair_peptide_match.second->getGrpPeptideSp().get() == p_grp_peptide) {
- subgroup_list.insert(pair_peptide_match.first);
+const QStringList
+GroupingGroup::getSubgroupIdList(const PeptideEvidence *p_peptide_match) const
+{
+ std::set<unsigned int> subgroup_list;
+ pappso::GrpPeptide *p_grp_peptide = p_peptide_match->getGrpPeptideSp().get();
+ if(p_grp_peptide != nullptr)
+ {
+ for(auto &&pair_peptide_match : _pair_sg_number_peptide_evidence_list)
+ {
+ if(pair_peptide_match.second->getGrpPeptideSp().get() ==
+ p_grp_peptide)
+ {
+ subgroup_list.insert(pair_peptide_match.first);
}
}
}
- QStringList sg_str_list;
- for (unsigned int sgnum : subgroup_list) {
- sg_str_list << QString("%1.%2").arg(pappso::Utils::getLexicalOrderedString(_group_number)).arg(pappso::Utils::getLexicalOrderedString(sgnum));
+ QStringList sg_str_list;
+ for(unsigned int sgnum : subgroup_list)
+ {
+ sg_str_list << QString("%1.%2")
+ .arg(
+ pappso::Utils::getLexicalOrderedString(_group_number))
+ .arg(pappso::Utils::getLexicalOrderedString(sgnum));
}
- return sg_str_list;
-
+ return sg_str_list;
}
-unsigned int GroupingGroup::countSubgroupPresence(const PeptideEvidence * p_peptide_evidence) const {
- std::set<unsigned int> subgroup_list;
- pappso::GrpPeptide * p_grp_peptide = p_peptide_evidence->getGrpPeptideSp().get();
- if (p_grp_peptide != nullptr) {
- for (auto && pair_peptide_match :_pair_sg_number_peptide_evidence_list) {
- if(pair_peptide_match.second->getGrpPeptideSp().get() == p_grp_peptide) {
- subgroup_list.insert(pair_peptide_match.first);
+unsigned int
+GroupingGroup::countSubgroupPresence(
+ const PeptideEvidence *p_peptide_evidence) const
+{
+ std::set<unsigned int> subgroup_list;
+ pappso::GrpPeptide *p_grp_peptide =
+ p_peptide_evidence->getGrpPeptideSp().get();
+ if(p_grp_peptide != nullptr)
+ {
+ for(auto &&pair_peptide_match : _pair_sg_number_peptide_evidence_list)
+ {
+ if(pair_peptide_match.second->getGrpPeptideSp().get() ==
+ p_grp_peptide)
+ {
+ subgroup_list.insert(pair_peptide_match.first);
}
}
}
- return subgroup_list.size();
+ return subgroup_list.size();
}
-std::size_t GroupingGroup::countSpecificSampleScan(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun_id) const {
- if (_number_of_subgroup == 1) {
- return p_protein_match->countSampleScan(state, p_msrun_id);
+std::size_t
+GroupingGroup::countSpecificSampleScan(const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun_id) const
+{
+ if(_number_of_subgroup == 1)
+ {
+ return p_protein_match->countSampleScan(state, p_msrun_id);
}
- std::set<size_t> spectrum_list_in;
- for (auto && p_peptide_match :p_protein_match->getPeptideMatchList()) {
- if (p_peptide_match.getPeptideEvidence()->getValidationState() >= state) {
- if(p_msrun_id == nullptr) {
- spectrum_list_in.insert(p_peptide_match.getPeptideEvidence()->getHashSampleScan());
+ std::set<size_t> spectrum_list_in;
+ for(auto &&p_peptide_match : p_protein_match->getPeptideMatchList())
+ {
+ if(p_peptide_match.getPeptideEvidence()->getValidationState() >= state)
+ {
+ if(p_msrun_id == nullptr)
+ {
+ spectrum_list_in.insert(
+ p_peptide_match.getPeptideEvidence()->getHashSampleScan());
}
- else {
- if (p_peptide_match.getPeptideEvidence()->getMsRunP() == p_msrun_id) {
- spectrum_list_in.insert(p_peptide_match.getPeptideEvidence()->getHashSampleScan());
+ else
+ {
+ if(p_peptide_match.getPeptideEvidence()->getMsRunP() ==
+ p_msrun_id)
+ {
+ spectrum_list_in.insert(
+ p_peptide_match.getPeptideEvidence()->getHashSampleScan());
}
}
}
}
- std::set<size_t> spectrum_list_out;
- unsigned int sg_number = p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
- for (auto && pair_peptide_match :_pair_sg_number_peptide_evidence_list) {
- if (pair_peptide_match.first != sg_number) {
- spectrum_list_out.insert(pair_peptide_match.second->getHashSampleScan());
+ std::set<size_t> spectrum_list_out;
+ unsigned int sg_number =
+ p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
+ for(auto &&pair_peptide_match : _pair_sg_number_peptide_evidence_list)
+ {
+ if(pair_peptide_match.first != sg_number)
+ {
+ spectrum_list_out.insert(
+ pair_peptide_match.second->getHashSampleScan());
}
}
- std::size_t count = 0;
- for (size_t sample_scan: spectrum_list_in) {
- std::set<size_t>::const_iterator it = spectrum_list_out.find(sample_scan);
- if (it == spectrum_list_out.end()) {
- count++;
+ std::size_t count = 0;
+ for(size_t sample_scan : spectrum_list_in)
+ {
+ std::set<size_t>::const_iterator it = spectrum_list_out.find(sample_scan);
+ if(it == spectrum_list_out.end())
+ {
+ count++;
}
}
- return count;
+ return count;
}
-std::size_t GroupingGroup::countSpecificSequenceLi(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun_id) const {
- if (_number_of_subgroup == 1) {
- return p_protein_match->countSequenceLi(state);
+std::size_t
+GroupingGroup::countSpecificSequenceLi(const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun_id) const
+{
+ if(_number_of_subgroup == 1)
+ {
+ return p_protein_match->countSequenceLi(state);
}
- std::set<QString> sequence_list_in;
- for (auto && p_peptide_match :p_protein_match->getPeptideMatchList()) {
- if (p_peptide_match.getPeptideEvidence()->getValidationState() >= state) {
- if(p_msrun_id == nullptr) {
- sequence_list_in.insert(p_peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequenceLi());
+ std::set<QString> sequence_list_in;
+ for(auto &&p_peptide_match : p_protein_match->getPeptideMatchList())
+ {
+ if(p_peptide_match.getPeptideEvidence()->getValidationState() >= state)
+ {
+ if(p_msrun_id == nullptr)
+ {
+ sequence_list_in.insert(p_peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getSequenceLi());
}
- else {
- if (p_peptide_match.getPeptideEvidence()->getMsRunP() == p_msrun_id) {
- sequence_list_in.insert(p_peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequenceLi());
+ else
+ {
+ if(p_peptide_match.getPeptideEvidence()->getMsRunP() ==
+ p_msrun_id)
+ {
+ sequence_list_in.insert(p_peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getSequenceLi());
}
}
}
}
- std::set<QString> sequence_list_out;
- unsigned int sg_number = p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
- for (auto && pair_peptide_match :_pair_sg_number_peptide_evidence_list) {
- if (pair_peptide_match.first != sg_number) {
- sequence_list_out.insert(pair_peptide_match.second->getPeptideXtpSp().get()->getSequenceLi());
+ std::set<QString> sequence_list_out;
+ unsigned int sg_number =
+ p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
+ for(auto &&pair_peptide_match : _pair_sg_number_peptide_evidence_list)
+ {
+ if(pair_peptide_match.first != sg_number)
+ {
+ sequence_list_out.insert(pair_peptide_match.second->getPeptideXtpSp()
+ .get()
+ ->getSequenceLi());
}
}
- std::size_t count = 0;
- for (const QString & sequence: sequence_list_in) {
- std::set<QString>::const_iterator it = sequence_list_out.find(sequence);
- if (it == sequence_list_out.end()) {
- count++;
+ std::size_t count = 0;
+ for(const QString &sequence : sequence_list_in)
+ {
+ std::set<QString>::const_iterator it = sequence_list_out.find(sequence);
+ if(it == sequence_list_out.end())
+ {
+ count++;
}
}
- return count;
+ return count;
}
-unsigned int GroupingGroup::countProteinInSubgroup(unsigned int subgroup_number) const {
- return std::count_if (_protein_match_list.begin(), _protein_match_list.end(), [subgroup_number](const ProteinMatch * p_protein_match) {
- if (p_protein_match->getGrpProteinSp().get()->getSubGroupNumber() == subgroup_number) {
- return true;
+unsigned int
+GroupingGroup::countProteinInSubgroup(unsigned int subgroup_number) const
+{
+ return std::count_if(
+ _protein_match_list.begin(), _protein_match_list.end(),
+ [subgroup_number](const ProteinMatch *p_protein_match) {
+ if(p_protein_match->getGrpProteinSp().get()->getSubGroupNumber() ==
+ subgroup_number)
+ {
+ return true;
}
- else {
- return false;
+ else
+ {
+ return false;
}
});
}
-QString GroupingGroup::getProteinGroupingIdOfSubgroup(unsigned int subgroup_number) const {
- return QString("%1.%2.a1").arg(pappso::Utils::getLexicalOrderedString(_group_number)).arg(pappso::Utils::getLexicalOrderedString(subgroup_number));
+QString
+GroupingGroup::getProteinGroupingIdOfSubgroup(
+ unsigned int subgroup_number) const
+{
+ return QString("%1.%2.a1")
+ .arg(pappso::Utils::getLexicalOrderedString(_group_number))
+ .arg(pappso::Utils::getLexicalOrderedString(subgroup_number));
}
-void GroupingGroup::add(const ProteinMatch * p_protein_match) {
- _group_number = p_protein_match->getGrpProteinSp().get()->getGroupNumber();
- _protein_match_list.push_back(p_protein_match);
- if (p_protein_match->getGrpProteinSp().get()->getRank() == 1) {
- _number_of_subgroup++;
- unsigned int sg_number = p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
+void
+GroupingGroup::add(const ProteinMatch *p_protein_match)
+{
+ _group_number = p_protein_match->getGrpProteinSp().get()->getGroupNumber();
+ _protein_match_list.push_back(p_protein_match);
+ if(p_protein_match->getGrpProteinSp().get()->getRank() == 1)
+ {
+ _number_of_subgroup++;
+ unsigned int sg_number =
+ p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
- for (auto && peptide_match :p_protein_match->getPeptideMatchList()) {
- if (peptide_match.getPeptideEvidence()->isValidAndChecked()) {
- _pair_sg_number_peptide_evidence_list.push_back(std::pair<unsigned int, const PeptideEvidence * >(sg_number, peptide_match.getPeptideEvidence()));
+ for(auto &&peptide_match : p_protein_match->getPeptideMatchList())
+ {
+ if(peptide_match.getPeptideEvidence()->isValidAndChecked())
+ {
+ _pair_sg_number_peptide_evidence_list.push_back(
+ std::pair<unsigned int, const PeptideEvidence *>(
+ sg_number, peptide_match.getPeptideEvidence()));
}
}
}
}
-
diff --git a/src/grouping/groupinggroup.h b/src/grouping/groupinggroup.h
index 1789a683b2c2facdefb5c75049565e8757c024b0..5c2b006b0f1155985784adb03cf051e5f72a57ea 100644
--- a/src/grouping/groupinggroup.h
+++ b/src/grouping/groupinggroup.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef GROUPINGGROUP_H
#define GROUPINGGROUP_H
@@ -38,54 +39,61 @@ typedef std::shared_ptr<GroupingGroup> GroupingGroupSp;
class GroupingGroup
{
-public:
-
- GroupingGroup();
- ~GroupingGroup();
-
- unsigned int getGroupNumber() const ;
-
- void add(const ProteinMatch * p_protein_match);
- std::size_t countSpecificSampleScan(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun_id=nullptr) const;
- std::size_t countSpecificSequenceLi(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun_id=nullptr) const;
-
- unsigned int getNumberOfSubgroups() const;
-
- /** @brief count proteins in subgroup
- * */
- unsigned int countProteinInSubgroup(unsigned int subgroup_number) const;
-
- /** @brief count number of subgroups in which this peptide is present
- * */
- unsigned int countSubgroupPresence(const PeptideEvidence * p_peptide_evidence) const;
-
- /** @brief subgroup identifier list in which this peptide is present
- * */
- const QStringList getSubgroupIdList(const PeptideEvidence * p_peptide_evidence) const;
-
- /** @brief give the protein group id of the representant of a subgroup
- * */
- QString getProteinGroupingIdOfSubgroup(unsigned int subgroup_number) const;
-
-
- /** @brief get the list of protein match included in this group
- * */
- const std::vector<const ProteinMatch *> & getProteinMatchList() const;
-
- /** @brief get the list of peptide evidence included in this group
- * warning : it only contains the first protein representant in one subgroup
- * use a double loop with getProteinMatchList to scan every peptide match
- * */
- std::vector<const PeptideEvidence *> getPeptideEvidenceList() const;
-
- const std::vector<std::pair<unsigned int, const PeptideEvidence *>> & getPairSgNumberPeptideEvidenceList() const;
-
-private :
- unsigned int _group_number=0;
- unsigned int _number_of_subgroup=0;
- std::vector<std::pair<unsigned int, const PeptideEvidence *>> _pair_sg_number_peptide_evidence_list;
-
- std::vector<const ProteinMatch *> _protein_match_list;
+ public:
+ GroupingGroup();
+ ~GroupingGroup();
+
+ unsigned int getGroupNumber() const;
+
+ void add(const ProteinMatch *p_protein_match);
+ std::size_t countSpecificSampleScan(const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun_id = nullptr) const;
+ std::size_t countSpecificSequenceLi(const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun_id = nullptr) const;
+
+ unsigned int getNumberOfSubgroups() const;
+
+ /** @brief count proteins in subgroup
+ * */
+ unsigned int countProteinInSubgroup(unsigned int subgroup_number) const;
+
+ /** @brief count number of subgroups in which this peptide is present
+ * */
+ unsigned int
+ countSubgroupPresence(const PeptideEvidence *p_peptide_evidence) const;
+
+ /** @brief subgroup identifier list in which this peptide is present
+ * */
+ const QStringList
+ getSubgroupIdList(const PeptideEvidence *p_peptide_evidence) const;
+
+ /** @brief give the protein group id of the representant of a subgroup
+ * */
+ QString getProteinGroupingIdOfSubgroup(unsigned int subgroup_number) const;
+
+
+ /** @brief get the list of protein match included in this group
+ * */
+ const std::vector<const ProteinMatch *> &getProteinMatchList() const;
+
+ /** @brief get the list of peptide evidence included in this group
+ * warning : it only contains the first protein representant in one subgroup
+ * use a double loop with getProteinMatchList to scan every peptide match
+ * */
+ std::vector<const PeptideEvidence *> getPeptideEvidenceList() const;
+
+ const std::vector<std::pair<unsigned int, const PeptideEvidence *>> &
+ getPairSgNumberPeptideEvidenceList() const;
+
+ private:
+ unsigned int _group_number = 0;
+ unsigned int _number_of_subgroup = 0;
+ std::vector<std::pair<unsigned int, const PeptideEvidence *>>
+ _pair_sg_number_peptide_evidence_list;
+
+ std::vector<const ProteinMatch *> _protein_match_list;
};
#endif // GROUPINGGROUP_H
diff --git a/src/grouping/groupingpeptidemass.cpp b/src/grouping/groupingpeptidemass.cpp
index c55d84bfcc950e27cf075c6dd47489bb87cd28f6..4e8e373f268855aa82cf2f3ef404773ba455e65c 100644
--- a/src/grouping/groupingpeptidemass.cpp
+++ b/src/grouping/groupingpeptidemass.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "groupingpeptidemass.h"
#include "../core/proteinmatch.h"
@@ -28,67 +29,105 @@
#include <pappsomspp/grouping/grpgroupingmonitor.h>
-class GrpGroupingMonitor: public pappso::GrpGroupingMonitorInterface
+class GrpGroupingMonitor : public pappso::GrpGroupingMonitorInterface
{
-public:
- GrpGroupingMonitor(WorkMonitorInterface * p_work_monitor) {
- _p_work_monitor = p_work_monitor;
- };
- ~GrpGroupingMonitor() {
- };
- virtual void startGrouping(std::size_t total_number_protein, std::size_t total_number_peptide) override {
- _p_work_monitor->message(QObject::tr("grouping %1 proteins containing %2 unique peptides").arg(total_number_protein).arg(total_number_peptide));
- _total_number_proteins = total_number_protein;
- };
- virtual void groupingProtein() override {};
- virtual void startRemovingNonInformativeSubGroupsInAllGroups(std::size_t total_number_group)override{
- _total_number_group = total_number_group;
- };
- virtual void stopRemovingNonInformativeSubGroupsInAllGroups(std::size_t total_number_group)override{
- _total_number_group = total_number_group;
- };
- virtual void removingNonInformativeSubGroupsInGroup()override{
- _p_work_monitor->message(QObject::tr("removing non informative subgroups in %1 groups representing %2 proteins").arg(_total_number_group).arg(_total_number_proteins));
- };
- virtual void startNumberingAllGroups(std::size_t total_number_group)override{
- _p_work_monitor->message(QObject::tr("numbering in %1 groups representing %2 proteins").arg(_total_number_group).arg(_total_number_proteins));
- };
- virtual void stopGrouping()override{};
-private:
- WorkMonitorInterface * _p_work_monitor;
- std::size_t _total_number_proteins;
- std::size_t _total_number_group;
+ public:
+ GrpGroupingMonitor(WorkMonitorInterface *p_work_monitor)
+ {
+ _p_work_monitor = p_work_monitor;
+ };
+ ~GrpGroupingMonitor(){};
+ virtual void
+ startGrouping(std::size_t total_number_protein,
+ std::size_t total_number_peptide) override
+ {
+ _p_work_monitor->message(
+ QObject::tr("grouping %1 proteins containing %2 unique peptides")
+ .arg(total_number_protein)
+ .arg(total_number_peptide));
+ _total_number_proteins = total_number_protein;
+ };
+ virtual void groupingProtein() override{};
+ virtual void
+ startRemovingNonInformativeSubGroupsInAllGroups(
+ std::size_t total_number_group) override
+ {
+ _total_number_group = total_number_group;
+ };
+ virtual void
+ stopRemovingNonInformativeSubGroupsInAllGroups(
+ std::size_t total_number_group) override
+ {
+ _total_number_group = total_number_group;
+ };
+ virtual void
+ removingNonInformativeSubGroupsInGroup() override
+ {
+ _p_work_monitor->message(
+ QObject::tr("removing non informative subgroups in %1 groups "
+ "representing %2 proteins")
+ .arg(_total_number_group)
+ .arg(_total_number_proteins));
+ };
+ virtual void
+ startNumberingAllGroups(std::size_t total_number_group) override
+ {
+ _p_work_monitor->message(
+ QObject::tr("numbering in %1 groups representing %2 proteins")
+ .arg(_total_number_group)
+ .arg(_total_number_proteins));
+ };
+ virtual void stopGrouping() override{};
+
+ private:
+ WorkMonitorInterface *_p_work_monitor;
+ std::size_t _total_number_proteins;
+ std::size_t _total_number_group;
};
-GroupingPeptideMass::GroupingPeptideMass(WorkMonitorInterface * p_work_monitor): GroupingExperiment(p_work_monitor)
+GroupingPeptideMass::GroupingPeptideMass(WorkMonitorInterface *p_work_monitor)
+ : GroupingExperiment(p_work_monitor)
{
- //_p_monitor = new pappso::GrpGroupingMonitor();
- _p_monitor = new GrpGroupingMonitor(_p_work_monitor);
- _p_grp_experiment = new pappso::GrpExperiment(_p_monitor);
-
+ //_p_monitor = new pappso::GrpGroupingMonitor();
+ _p_monitor = new GrpGroupingMonitor(_p_work_monitor);
+ _p_grp_experiment = new pappso::GrpExperiment(_p_monitor);
}
GroupingPeptideMass::~GroupingPeptideMass()
{
- delete _p_grp_experiment;
- delete _p_monitor;
+ delete _p_grp_experiment;
+ delete _p_monitor;
}
-pappso::GrpProteinSp & GroupingPeptideMass::getGrpProteinSp(ProteinMatch* p_protein_match) {
- return _p_grp_experiment->getGrpProteinSp(p_protein_match->getProteinXtpSp().get()->getAccession(),p_protein_match->getProteinXtpSp().get()->getDescription());
+pappso::GrpProteinSp &
+GroupingPeptideMass::getGrpProteinSp(ProteinMatch *p_protein_match)
+{
+ return _p_grp_experiment->getGrpProteinSp(
+ p_protein_match->getProteinXtpSp().get()->getAccession(),
+ p_protein_match->getProteinXtpSp().get()->getDescription());
}
-pappso::GrpPeptideSp & GroupingPeptideMass::setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideEvidence * p_peptide_evidence) {
+pappso::GrpPeptideSp &
+GroupingPeptideMass::setGrpPeptide(pappso::GrpProteinSp proteinSp,
+ PeptideEvidence *p_peptide_evidence)
+{
- return _p_grp_experiment->setGrpPeptide(proteinSp,p_peptide_evidence->getPeptideXtpSp().get()->getSequence(), p_peptide_evidence->getPeptideXtpSp().get()->getGroupingMass());
+ return _p_grp_experiment->setGrpPeptide(
+ proteinSp, p_peptide_evidence->getPeptideXtpSp().get()->getSequence(),
+ p_peptide_evidence->getPeptideXtpSp().get()->getGroupingMass());
}
-void GroupingPeptideMass::startGrouping() {
- qDebug() << "GroupingPeptideMass::startGrouping begin";
- _p_grp_experiment->startGrouping();
- qDebug() << "GroupingPeptideMass::startGrouping end";
+void
+GroupingPeptideMass::startGrouping()
+{
+ qDebug() << "GroupingPeptideMass::startGrouping begin";
+ _p_grp_experiment->startGrouping();
+ qDebug() << "GroupingPeptideMass::startGrouping end";
}
-void GroupingPeptideMass::addPostGroupingGrpProteinSpRemoval(pappso::GrpProteinSp sp_protein) {
- _p_grp_experiment->addPostGroupingGrpProteinSpRemoval(sp_protein);
+void
+GroupingPeptideMass::addPostGroupingGrpProteinSpRemoval(
+ pappso::GrpProteinSp sp_protein)
+{
+ _p_grp_experiment->addPostGroupingGrpProteinSpRemoval(sp_protein);
}
diff --git a/src/grouping/groupingpeptidemass.h b/src/grouping/groupingpeptidemass.h
index a1d1d4e4136cab76cfba42cb8e1e99ea87899bea..0b335f28e58f6880b78b99548588dfc22f16444c 100644
--- a/src/grouping/groupingpeptidemass.h
+++ b/src/grouping/groupingpeptidemass.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "groupingexperiment.h"
#ifndef GROUPINGPEPTIDEMASS_H
@@ -27,25 +28,29 @@
class GrpGroupingMonitor;
-class GroupingPeptideMass: public GroupingExperiment
+class GroupingPeptideMass : public GroupingExperiment
{
- friend class GroupingExperiment;
-public:
+ friend class GroupingExperiment;
- virtual ~GroupingPeptideMass();
+ public:
+ virtual ~GroupingPeptideMass();
- virtual pappso::GrpProteinSp & getGrpProteinSp(ProteinMatch* p_protein_match) override;
- virtual pappso::GrpPeptideSp & setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideEvidence * p_peptide_evidence) override;
- virtual void addPostGroupingGrpProteinSpRemoval(pappso::GrpProteinSp sp_protein) override;
+ virtual pappso::GrpProteinSp &
+ getGrpProteinSp(ProteinMatch *p_protein_match) override;
+ virtual pappso::GrpPeptideSp &
+ setGrpPeptide(pappso::GrpProteinSp proteinSp,
+ PeptideEvidence *p_peptide_evidence) override;
+ virtual void
+ addPostGroupingGrpProteinSpRemoval(pappso::GrpProteinSp sp_protein) override;
- virtual void startGrouping() override;
+ virtual void startGrouping() override;
-protected :
- GroupingPeptideMass(WorkMonitorInterface * p_work_monitor);
+ protected:
+ GroupingPeptideMass(WorkMonitorInterface *p_work_monitor);
-private :
- GrpGroupingMonitor * _p_monitor = nullptr;
- pappso::GrpExperiment * _p_grp_experiment;
+ private:
+ GrpGroupingMonitor *_p_monitor = nullptr;
+ pappso::GrpExperiment *_p_grp_experiment;
};
#endif // GROUPINGPEPTIDEMASS_H
diff --git a/src/grouping/ptm/ptmgroupingexperiment.cpp b/src/grouping/ptm/ptmgroupingexperiment.cpp
index c52b912c496d49ca5e64a687c8ce58dbd0501db2..903b26226f25877255e61e8dca6a0689fc306817 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.cpp
+++ b/src/grouping/ptm/ptmgroupingexperiment.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmgroupingexperiment.h"
#include "../../grouping/ptm/ptmgroupingexperiment.h"
@@ -33,182 +34,258 @@
PtmGroupingExperiment::PtmGroupingExperiment()
{
- /*
- * accession MOD:00696
- name phosphorylated residue
- PSI-MS label Phospho
- PSI-MOD label PhosRes
- diff mono 79.966331
- diff formula H 1 O 3 P 1
-
- // dehydrated residue [MOD:00704] -18.010565
- accession MOD:00416
- name phosphorylation of an hydroxyl amino acid with prompt loss of phosphate
- PSI-MS label Methyl
- PSI-MOD label
- diff mono -18.010565
- diff formula H -2 O -1
-
-
- public boolean is_phopho_modifs() {
- if ((this.modvalue > 79.9) & (this.modvalue < 80.1))
- return true;
- boolean serthre = false;
- if (this.AA.equals("T"))
- serthre = true;
- else if (this.AA.equals("S"))
- serthre = true;
- if ((serthre) & (this.modvalue < -17.9) & (this.modvalue > -18.1))
- return true;
- return false;
- }
- */
-
-//phospho :
- _modification_list.push_back({pappso::AaModification::getInstance("MOD:00696"), {}});
- _modification_list.push_back({pappso::AaModification::getInstance("MOD:00704"), {'S','T'}});
+ /*
+ * accession MOD:00696
+ name phosphorylated residue
+ PSI-MS label Phospho
+ PSI-MOD label PhosRes
+ diff mono 79.966331
+ diff formula H 1 O 3 P 1
+
+ // dehydrated residue [MOD:00704] -18.010565
+ accession MOD:00416
+ name phosphorylation of an hydroxyl amino acid with prompt loss of phosphate
+ PSI-MS label Methyl
+ PSI-MOD label
+ diff mono -18.010565
+ diff formula H -2 O -1
+
+
+ public boolean is_phopho_modifs() {
+ if ((this.modvalue > 79.9) & (this.modvalue < 80.1))
+ return true;
+ boolean serthre = false;
+ if (this.AA.equals("T"))
+ serthre = true;
+ else if (this.AA.equals("S"))
+ serthre = true;
+ if ((serthre) & (this.modvalue < -17.9) & (this.modvalue > -18.1))
+ return true;
+ return false;
+ }
+ */
+
+ // phospho :
+ _modification_list.push_back(
+ {pappso::AaModification::getInstance("MOD:00696"), {}});
+ _modification_list.push_back(
+ {pappso::AaModification::getInstance("MOD:00704"), {'S', 'T'}});
}
PtmGroupingExperiment::~PtmGroupingExperiment()
{
-
}
-const std::vector<PtmIslandSubgroupSp> & PtmGroupingExperiment::getPtmIslandSubgroupList() const {
- return _ptm_island_subgroup_list;
+const std::vector<PtmIslandSubgroupSp> &
+PtmGroupingExperiment::getPtmIslandSubgroupList() const
+{
+ return _ptm_island_subgroup_list;
}
-const std::vector<PtmIslandGroupSp> & PtmGroupingExperiment::getPtmIslandGroupList() const {
- return _ptm_island_group_list;
+const std::vector<PtmIslandGroupSp> &
+PtmGroupingExperiment::getPtmIslandGroupList() const
+{
+ return _ptm_island_group_list;
}
-const std::vector<PtmIslandSp> & PtmGroupingExperiment::getPtmIslandList() const {
- //qDebug() << "PtmGroupingExperiment::getPtmIslandList begin" << _ptm_island_list.size();
- return _ptm_island_list;
+const std::vector<PtmIslandSp> &
+PtmGroupingExperiment::getPtmIslandList() const
+{
+ // qDebug() << "PtmGroupingExperiment::getPtmIslandList begin" <<
+ // _ptm_island_list.size();
+ return _ptm_island_list;
}
-void PtmGroupingExperiment::numbering() {
- std::sort(_ptm_island_group_list.begin(), _ptm_island_group_list.end(),[](const PtmIslandGroupSp a, const PtmIslandGroupSp b)
- {
- return *(a.get()) < *(b.get());
- });
+void
+PtmGroupingExperiment::numbering()
+{
+ std::sort(_ptm_island_group_list.begin(), _ptm_island_group_list.end(),
+ [](const PtmIslandGroupSp a, const PtmIslandGroupSp b) {
+ return *(a.get()) < *(b.get());
+ });
- unsigned int number=0;
- for (PtmIslandGroupSp ptm_island_group:_ptm_island_group_list) {
- number ++;
- ptm_island_group.get()->setGroupNumber(number);
+ unsigned int number = 0;
+ for(PtmIslandGroupSp ptm_island_group : _ptm_island_group_list)
+ {
+ number++;
+ ptm_island_group.get()->setGroupNumber(number);
}
}
-void PtmGroupingExperiment::startGrouping() {
- //we have a list of ptm island subgroups to group :
- for (PtmIslandSubgroupSp ptm_island_subgroup:_ptm_island_subgroup_list) {
- if (std::none_of(_ptm_island_group_list.begin(), _ptm_island_group_list.end(), [ptm_island_subgroup](PtmIslandGroupSp element) {
- return element.get()->mergePtmIslandSubgroupSp(ptm_island_subgroup);
- })) {
- //create a new group
- _ptm_island_group_list.push_back(std::make_shared<PtmIslandGroup>(ptm_island_subgroup));
+void
+PtmGroupingExperiment::startGrouping()
+{
+ // we have a list of ptm island subgroups to group :
+ for(PtmIslandSubgroupSp ptm_island_subgroup : _ptm_island_subgroup_list)
+ {
+ if(std::none_of(_ptm_island_group_list.begin(),
+ _ptm_island_group_list.end(),
+ [ptm_island_subgroup](PtmIslandGroupSp element) {
+ return element.get()->mergePtmIslandSubgroupSp(
+ ptm_island_subgroup);
+ }))
+ {
+ // create a new group
+ _ptm_island_group_list.push_back(
+ std::make_shared<PtmIslandGroup>(ptm_island_subgroup));
}
}
- numbering();
+ numbering();
}
-void PtmGroupingExperiment::addPtmIsland(PtmIslandSp ptm_island_sp) {
- _ptm_island_list.push_back(ptm_island_sp);
- if (std::none_of(_ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(), [ptm_island_sp](PtmIslandSubgroupSp element) {
- return element.get()->mergePtmIslandSp(ptm_island_sp);
- })) {
- //create a new subgroup
- _ptm_island_subgroup_list.push_back(std::make_shared<PtmIslandSubgroup>(ptm_island_sp));
+void
+PtmGroupingExperiment::addPtmIsland(PtmIslandSp ptm_island_sp)
+{
+ _ptm_island_list.push_back(ptm_island_sp);
+ if(std::none_of(_ptm_island_subgroup_list.begin(),
+ _ptm_island_subgroup_list.end(),
+ [ptm_island_sp](PtmIslandSubgroupSp element) {
+ return element.get()->mergePtmIslandSp(ptm_island_sp);
+ }))
+ {
+ // create a new subgroup
+ _ptm_island_subgroup_list.push_back(
+ std::make_shared<PtmIslandSubgroup>(ptm_island_sp));
}
-
}
-void PtmGroupingExperiment::setValidationState(ValidationState validation_state) {
- _peptide_validation_state = validation_state;
+void
+PtmGroupingExperiment::setValidationState(ValidationState validation_state)
+{
+ _peptide_validation_state = validation_state;
}
-void PtmGroupingExperiment::addProteinMatch(const ProteinMatch* p_protein_match) {
- if (p_protein_match->getValidationState() >= _peptide_validation_state) {
- std::vector< unsigned int > ptm_position_list = getPtmPositions(p_protein_match);
- std::vector<PtmIslandSp> ptm_island_list;
- for (unsigned int position : ptm_position_list) {
- ptm_island_list.push_back(std::make_shared<PtmIsland>(p_protein_match, position));
+void
+PtmGroupingExperiment::addProteinMatch(const ProteinMatch *p_protein_match)
+{
+ if(p_protein_match->getValidationState() >= _peptide_validation_state)
+ {
+ std::vector<unsigned int> ptm_position_list =
+ getPtmPositions(p_protein_match);
+ std::vector<PtmIslandSp> ptm_island_list;
+ for(unsigned int position : ptm_position_list)
+ {
+ ptm_island_list.push_back(
+ std::make_shared<PtmIsland>(p_protein_match, position));
}
- for (PeptideMatch & peptide_match: p_protein_match->getPeptideMatchList(_peptide_validation_state)) {
- for (PtmIslandSp ptm_island_sp:ptm_island_list) {
- ptm_island_sp.get()->addPeptideMatch(peptide_match);
+ for(PeptideMatch &peptide_match :
+ p_protein_match->getPeptideMatchList(_peptide_validation_state))
+ {
+ for(PtmIslandSp ptm_island_sp : ptm_island_list)
+ {
+ ptm_island_sp.get()->addPeptideMatch(peptide_match);
}
}
- std::vector< PtmIslandSp > protein_ptm_islands = mergePeptideMatchPtmIslandList(ptm_island_list);
- //=> ptm island subgroups (same set of sample scan numbers)
- for (PtmIslandSp ptm_island:protein_ptm_islands) {
- addPtmIsland(ptm_island);
+ std::vector<PtmIslandSp> protein_ptm_islands =
+ mergePeptideMatchPtmIslandList(ptm_island_list);
+ //=> ptm island subgroups (same set of sample scan numbers)
+ for(PtmIslandSp ptm_island : protein_ptm_islands)
+ {
+ addPtmIsland(ptm_island);
}
}
}
-std::vector< PtmIslandSp > PtmGroupingExperiment::mergePeptideMatchPtmIslandList(std::vector< PtmIslandSp > ptm_island_list) {
- std::vector< PtmIslandSp > new_ptm_island_list;
+std::vector<PtmIslandSp>
+PtmGroupingExperiment::mergePeptideMatchPtmIslandList(
+ std::vector<PtmIslandSp> ptm_island_list)
+{
+ std::vector<PtmIslandSp> new_ptm_island_list;
- for (PtmIslandSp ptm_island_sp:ptm_island_list) {
- //http://en.cppreference.com/w/cpp/algorithm/all_any_none_of
- if (std::none_of(new_ptm_island_list.begin(), new_ptm_island_list.end(), [ptm_island_sp](PtmIslandSp element) {
- return element.get()->merge(ptm_island_sp);
- })) {
- new_ptm_island_list.push_back(ptm_island_sp);
+ for(PtmIslandSp ptm_island_sp : ptm_island_list)
+ {
+ // http://en.cppreference.com/w/cpp/algorithm/all_any_none_of
+ if(std::none_of(new_ptm_island_list.begin(), new_ptm_island_list.end(),
+ [ptm_island_sp](PtmIslandSp element) {
+ return element.get()->merge(ptm_island_sp);
+ }))
+ {
+ new_ptm_island_list.push_back(ptm_island_sp);
}
}
- return new_ptm_island_list;
-
+ return new_ptm_island_list;
}
-unsigned int PtmGroupingExperiment::countPeptideMatchPtm(const PeptideMatch & peptide_match)const {
- unsigned int number=0;
- for (const ModificationAndAa & modification: _modification_list) {
- if (modification.aa_list.size() == 0) {
- number += peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getNumberOfModification(modification.modification);
+unsigned int
+PtmGroupingExperiment::countPeptideMatchPtm(
+ const PeptideMatch &peptide_match) const
+{
+ unsigned int number = 0;
+ for(const ModificationAndAa &modification : _modification_list)
+ {
+ if(modification.aa_list.size() == 0)
+ {
+ number += peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getNumberOfModification(modification.modification);
}
- else {
- number += peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->countModificationOnAa(modification.modification, modification.aa_list);
+ else
+ {
+ number += peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->countModificationOnAa(modification.modification,
+ modification.aa_list);
}
}
- return number;
+ return number;
}
-std::vector<unsigned int> PtmGroupingExperiment::getPtmPositions(const PeptideMatch & peptide_match) const {
- std::vector<unsigned int> position_list;
+std::vector<unsigned int>
+PtmGroupingExperiment::getPtmPositions(const PeptideMatch &peptide_match) const
+{
+ std::vector<unsigned int> position_list;
- for (const ModificationAndAa & modification: _modification_list) {
- if (modification.aa_list.size() == 0) {
- for (unsigned int position : peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getModificationPositionList(modification.modification)) {
- position_list.push_back(position);
+ for(const ModificationAndAa &modification : _modification_list)
+ {
+ if(modification.aa_list.size() == 0)
+ {
+ for(unsigned int position :
+ peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getModificationPositionList(modification.modification))
+ {
+ position_list.push_back(position);
}
}
- else {
- for (unsigned int position : peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getModificationPositionList(modification.modification, modification.aa_list)) {
- position_list.push_back(position);
+ else
+ {
+ for(unsigned int position :
+ peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getModificationPositionList(modification.modification,
+ modification.aa_list))
+ {
+ position_list.push_back(position);
}
}
}
- std::sort(position_list.begin(), position_list.end());
- auto last = std::unique(position_list.begin(), position_list.end());
- position_list.erase(last, position_list.end());
- return position_list;
+ std::sort(position_list.begin(), position_list.end());
+ auto last = std::unique(position_list.begin(), position_list.end());
+ position_list.erase(last, position_list.end());
+ return position_list;
}
-std::vector<unsigned int> PtmGroupingExperiment::getPtmPositions(const ProteinMatch * protein_match) const {
- std::vector<unsigned int> position_list;
+std::vector<unsigned int>
+PtmGroupingExperiment::getPtmPositions(const ProteinMatch *protein_match) const
+{
+ std::vector<unsigned int> position_list;
- for (const PeptideMatch & peptide_match: protein_match->getPeptideMatchList(_peptide_validation_state)) {
- unsigned int start = peptide_match.getStart();
- std::vector<unsigned int> positionb_list = this->getPtmPositions(peptide_match);
- for (unsigned int position: positionb_list) {
- position_list.push_back(start+position);
+ for(const PeptideMatch &peptide_match :
+ protein_match->getPeptideMatchList(_peptide_validation_state))
+ {
+ unsigned int start = peptide_match.getStart();
+ std::vector<unsigned int> positionb_list =
+ this->getPtmPositions(peptide_match);
+ for(unsigned int position : positionb_list)
+ {
+ position_list.push_back(start + position);
}
}
- std::sort(position_list.begin(), position_list.end());
- auto last = std::unique(position_list.begin(), position_list.end());
- position_list.erase(last, position_list.end());
- return position_list;
+ std::sort(position_list.begin(), position_list.end());
+ auto last = std::unique(position_list.begin(), position_list.end());
+ position_list.erase(last, position_list.end());
+ return position_list;
}
-
diff --git a/src/grouping/ptm/ptmgroupingexperiment.h b/src/grouping/ptm/ptmgroupingexperiment.h
index 541f1422fcb3e7dc0f4931ee34e586b357986874..686889bfd7a85f40960d0aed83b8b2669522cd58 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.h
+++ b/src/grouping/ptm/ptmgroupingexperiment.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMGROUPINGEXPERIMENT_H
#define PTMGROUPINGEXPERIMENT_H
@@ -37,53 +38,60 @@
#include "ptmislandgroup.h"
class PtmSampleScan;
-struct ModificationAndAa {
- pappso::AaModificationP modification;
- std::vector<char> aa_list;
+struct ModificationAndAa
+{
+ pappso::AaModificationP modification;
+ std::vector<char> aa_list;
};
class PtmGroupingExperiment
{
- friend PtmSampleScan;
-public:
- PtmGroupingExperiment();
- ~PtmGroupingExperiment();
+ friend PtmSampleScan;
+
+ public:
+ PtmGroupingExperiment();
+ ~PtmGroupingExperiment();
+
+ /** @brief choose validation state of peptide to use in PTM grouping
+ * experiment
+ */
+ void setValidationState(ValidationState validation_state);
+ void addProteinMatch(const ProteinMatch *p_protein_match);
+ void startGrouping();
+
+ /** @brief get the ptm island subgroup list
+ */
+ const std::vector<PtmIslandSubgroupSp> &getPtmIslandSubgroupList() const;
+
+ /** @brief get the ptm island group list
+ */
+ const std::vector<PtmIslandGroupSp> &getPtmIslandGroupList() const;
- /** @brief choose validation state of peptide to use in PTM grouping experiment
- */
- void setValidationState(ValidationState validation_state);
- void addProteinMatch(const ProteinMatch* p_protein_match);
- void startGrouping();
+ /** @brief get the ptm island list
+ */
+ const std::vector<PtmIslandSp> &getPtmIslandList() const;
- /** @brief get the ptm island subgroup list
- */
- const std::vector<PtmIslandSubgroupSp> & getPtmIslandSubgroupList() const;
+ /** @brief count number of modifications in a PeptideMatch
+ * */
+ unsigned int countPeptideMatchPtm(const PeptideMatch &peptide_match) const;
+ std::vector<unsigned int>
+ getPtmPositions(const PeptideMatch &peptide_match) const;
- /** @brief get the ptm island group list
- */
- const std::vector<PtmIslandGroupSp> & getPtmIslandGroupList() const;
-
- /** @brief get the ptm island list
- */
- const std::vector<PtmIslandSp> & getPtmIslandList() const;
-
- /** @brief count number of modifications in a PeptideMatch
- * */
- unsigned int countPeptideMatchPtm(const PeptideMatch & peptide_match)const;
- std::vector<unsigned int> getPtmPositions(const PeptideMatch & peptide_match) const;
+ private:
+ std::vector<unsigned int>
+ getPtmPositions(const ProteinMatch *protein_match) const;
-private:
- std::vector<unsigned int> getPtmPositions(const ProteinMatch * protein_match) const;
+ std::vector<PtmIslandSp>
+ mergePeptideMatchPtmIslandList(vector<PtmIslandSp> ptm_island_list);
+ void addPtmIsland(PtmIslandSp ptm_island);
+ void numbering();
- std::vector< PtmIslandSp > mergePeptideMatchPtmIslandList(vector< PtmIslandSp > ptm_island_list);
- void addPtmIsland(PtmIslandSp ptm_island);
- void numbering();
-private:
- std::list<ModificationAndAa> _modification_list;
- ValidationState _peptide_validation_state = ValidationState::validAndChecked;
- std::vector<PtmIslandSp> _ptm_island_list;
- std::vector<PtmIslandSubgroupSp> _ptm_island_subgroup_list;
- std::vector<PtmIslandGroupSp> _ptm_island_group_list;
+ private:
+ std::list<ModificationAndAa> _modification_list;
+ ValidationState _peptide_validation_state = ValidationState::validAndChecked;
+ std::vector<PtmIslandSp> _ptm_island_list;
+ std::vector<PtmIslandSubgroupSp> _ptm_island_subgroup_list;
+ std::vector<PtmIslandGroupSp> _ptm_island_group_list;
};
#endif // PTMGROUPINGEXPERIMENT_H
diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index 38878024962c12939450a4b5b44365acb42150cc..98c15f4a205e5caceccdb4c6a74da173cfb071b3 100644
--- a/src/grouping/ptm/ptmisland.cpp
+++ b/src/grouping/ptm/ptmisland.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmisland.h"
#include <pappsomspp/pappsoexception.h>
@@ -35,164 +36,247 @@
#include <pappsomspp/utils.h>
#include <set>
-PtmIsland::PtmIsland(const ProteinMatch* p_protein_match, unsigned int position):_protein_match_p(p_protein_match)
+PtmIsland::PtmIsland(const ProteinMatch *p_protein_match, unsigned int position)
+ : _protein_match_p(p_protein_match)
{
- _position_list.push_back(position);
+ _position_list.push_back(position);
}
-PtmIsland::PtmIsland(const PtmIsland & other):_protein_match_p(other._protein_match_p) {
- _position_list = other._position_list;
+PtmIsland::PtmIsland(const PtmIsland &other)
+ : _protein_match_p(other._protein_match_p)
+{
+ _position_list = other._position_list;
}
PtmIsland::~PtmIsland()
{
-
}
-unsigned int PtmIsland::getStart() const {
- return _protein_start;
+unsigned int
+PtmIsland::getStart() const
+{
+ return _protein_start;
}
-unsigned int PtmIsland::size() const {
- return _protein_stop - _protein_start;
+unsigned int
+PtmIsland::size() const
+{
+ return _protein_stop - _protein_start;
}
-unsigned int PtmIsland::countSampleScanMultiPtm(const PtmGroupingExperiment * p_ptm_grouping_experiment) const {
- std::set<std::size_t> sample_scan_list;
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_ptm_grouping_experiment->countPeptideMatchPtm(p_peptide_match) > 1) {
- sample_scan_list.insert(p_peptide_match.getPeptideEvidence()->getHashSampleScan());
+unsigned int
+PtmIsland::countSampleScanMultiPtm(
+ const PtmGroupingExperiment *p_ptm_grouping_experiment) const
+{
+ std::set<std::size_t> sample_scan_list;
+ for(auto &p_peptide_match : _peptide_match_list)
+ {
+ if(p_ptm_grouping_experiment->countPeptideMatchPtm(p_peptide_match) > 1)
+ {
+ sample_scan_list.insert(
+ p_peptide_match.getPeptideEvidence()->getHashSampleScan());
}
}
- return sample_scan_list.size();
+ return sample_scan_list.size();
}
-unsigned int PtmIsland::countSequence() const {
- std::set<QString> sequence_list;
- for (auto & peptide_match : _peptide_match_list) {
- sequence_list.insert(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequence());
+unsigned int
+PtmIsland::countSequence() const
+{
+ std::set<QString> sequence_list;
+ for(auto &peptide_match : _peptide_match_list)
+ {
+ sequence_list.insert(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getSequence());
}
- //qDebug() <<"ProteinMatch::countValidAndCheckedPeptide end " << sequence_list.size();
- return sequence_list.size();
+ // qDebug() <<"ProteinMatch::countValidAndCheckedPeptide end " <<
+ // sequence_list.size();
+ return sequence_list.size();
}
-const PtmIslandSubgroup * PtmIsland::getPtmIslandSubroup() const {
- return _ptm_island_subgroup_p;
+const PtmIslandSubgroup *
+PtmIsland::getPtmIslandSubroup() const
+{
+ return _ptm_island_subgroup_p;
}
-const std::vector<unsigned int> & PtmIsland::getPositionList() const {
- return _position_list;
+const std::vector<unsigned int> &
+PtmIsland::getPositionList() const
+{
+ return _position_list;
}
-const QString PtmIsland::getGroupingId() const {
- if(_prot_number==0) {
- return "";
+const QString
+PtmIsland::getGroupingId() const
+{
+ if(_prot_number == 0)
+ {
+ return "";
}
- return QString("ptm%1%2%3").arg(pappso::Utils::getLexicalOrderedString(_ptm_island_subgroup_p->getPtmIslandGroup()->getGroupNumber()))
- .arg(pappso::Utils::getLexicalOrderedString(_ptm_island_subgroup_p->getSubgroupNumber())).arg(pappso::Utils::getLexicalOrderedString(_prot_number));
+ return QString("ptm%1%2%3")
+ .arg(pappso::Utils::getLexicalOrderedString(
+ _ptm_island_subgroup_p->getPtmIslandGroup()->getGroupNumber()))
+ .arg(pappso::Utils::getLexicalOrderedString(
+ _ptm_island_subgroup_p->getSubgroupNumber()))
+ .arg(pappso::Utils::getLexicalOrderedString(_prot_number));
}
-void PtmIsland::setPtmIslandSubgroup(PtmIslandSubgroup* p_ptm_island_subgroup) {
- _ptm_island_subgroup_p = p_ptm_island_subgroup;
+void
+PtmIsland::setPtmIslandSubgroup(PtmIslandSubgroup *p_ptm_island_subgroup)
+{
+ _ptm_island_subgroup_p = p_ptm_island_subgroup;
}
-void PtmIsland::setProteinNumber(unsigned int prot_number) {
- _prot_number = prot_number;
+void
+PtmIsland::setProteinNumber(unsigned int prot_number)
+{
+ _prot_number = prot_number;
}
-const ProteinMatch * PtmIsland::getProteinMatch() const {
- return _protein_match_p;
+const ProteinMatch *
+PtmIsland::getProteinMatch() const
+{
+ return _protein_match_p;
}
-std::vector<std::size_t> PtmIsland::getSampleScanSet() const {
- std::vector<std::size_t> sample_scan_set;
- for (const PeptideMatch & peptide_match:_peptide_match_list) {
- sample_scan_set.push_back(peptide_match.getPeptideEvidence()->getHashSampleScan());
+std::vector<std::size_t>
+PtmIsland::getSampleScanSet() const
+{
+ std::vector<std::size_t> sample_scan_set;
+ for(const PeptideMatch &peptide_match : _peptide_match_list)
+ {
+ sample_scan_set.push_back(
+ peptide_match.getPeptideEvidence()->getHashSampleScan());
}
- std::sort(sample_scan_set.begin(), sample_scan_set.end());
- sample_scan_set.erase(std::unique(sample_scan_set.begin(), sample_scan_set.end()), sample_scan_set.end());
- return sample_scan_set;
+ std::sort(sample_scan_set.begin(), sample_scan_set.end());
+ sample_scan_set.erase(
+ std::unique(sample_scan_set.begin(), sample_scan_set.end()),
+ sample_scan_set.end());
+ return sample_scan_set;
}
-bool PtmIsland::containsPeptideMatch(const PeptideMatch & peptide_match) const {
+bool
+PtmIsland::containsPeptideMatch(const PeptideMatch &peptide_match) const
+{
- return std::any_of(_peptide_match_list.begin(), _peptide_match_list.end(), [peptide_match](const PeptideMatch & element) {
- return ( peptide_match == element);
- });
+ return std::any_of(_peptide_match_list.begin(), _peptide_match_list.end(),
+ [peptide_match](const PeptideMatch &element) {
+ return (peptide_match == element);
+ });
}
-void PtmIsland::addPeptideMatch(const PeptideMatch & peptide_match) {
- if (_position_list.size()==1) {
- unsigned int position = _position_list[0];
- if (peptide_match.containsPosition(position)) {
- if (_peptide_match_list.size() == 0) {
- _protein_start = peptide_match.getStart();
+void
+PtmIsland::addPeptideMatch(const PeptideMatch &peptide_match)
+{
+ if(_position_list.size() == 1)
+ {
+ unsigned int position = _position_list[0];
+ if(peptide_match.containsPosition(position))
+ {
+ if(_peptide_match_list.size() == 0)
+ {
+ _protein_start = peptide_match.getStart();
}
- _peptide_match_list.push_back(peptide_match);
- if (peptide_match.getStart() < _protein_start) {
- _protein_start = peptide_match.getStart();
+ _peptide_match_list.push_back(peptide_match);
+ if(peptide_match.getStart() < _protein_start)
+ {
+ _protein_start = peptide_match.getStart();
}
- if (peptide_match.getStop() > _protein_stop) {
- _protein_stop = peptide_match.getStop();
+ if(peptide_match.getStop() > _protein_stop)
+ {
+ _protein_stop = peptide_match.getStop();
}
}
}
- else {
- throw pappso::PappsoException(QObject::tr("not able to add peptide match if _position_list.size()!=1 (%1)").arg(_position_list.size()));
+ else
+ {
+ throw pappso::PappsoException(
+ QObject::tr(
+ "not able to add peptide match if _position_list.size()!=1 (%1)")
+ .arg(_position_list.size()));
}
}
-unsigned int PtmIsland::getProteinStartPosition() const {
- return _protein_start;
+unsigned int
+PtmIsland::getProteinStartPosition() const
+{
+ return _protein_start;
}
-bool PtmIsland::merge(PtmIslandSp ptm_island_sp) {
- if (std::none_of(_peptide_match_list.begin(), _peptide_match_list.end(), [ptm_island_sp](const PeptideMatch & element) {
- return ptm_island_sp.get()->containsPeptideMatch(element);
- })) {
- return false;
+bool
+PtmIsland::merge(PtmIslandSp ptm_island_sp)
+{
+ if(std::none_of(_peptide_match_list.begin(), _peptide_match_list.end(),
+ [ptm_island_sp](const PeptideMatch &element) {
+ return ptm_island_sp.get()->containsPeptideMatch(element);
+ }))
+ {
+ return false;
}
- else {
- //so we merge
- _peptide_match_list.insert(_peptide_match_list.begin(),ptm_island_sp.get()->_peptide_match_list.begin(),ptm_island_sp.get()->_peptide_match_list.end());
- std::sort(_peptide_match_list.begin(), _peptide_match_list.end(), [](const PeptideMatch & a, const PeptideMatch & b)
- {
- return (a.operator<(b));
- });
- auto last = std::unique(_peptide_match_list.begin(), _peptide_match_list.end());
- _peptide_match_list.erase(last, _peptide_match_list.end());
+ else
+ {
+ // so we merge
+ _peptide_match_list.insert(
+ _peptide_match_list.begin(),
+ ptm_island_sp.get()->_peptide_match_list.begin(),
+ ptm_island_sp.get()->_peptide_match_list.end());
+ std::sort(_peptide_match_list.begin(), _peptide_match_list.end(),
+ [](const PeptideMatch &a, const PeptideMatch &b) {
+ return (a.operator<(b));
+ });
+ auto last =
+ std::unique(_peptide_match_list.begin(), _peptide_match_list.end());
+ _peptide_match_list.erase(last, _peptide_match_list.end());
- _position_list.insert(_position_list.begin(),ptm_island_sp.get()->_position_list.begin(),ptm_island_sp.get()->_position_list.end());
- std::sort(_position_list.begin(), _position_list.end());
- _position_list.erase(std::unique(_position_list.begin(), _position_list.end()), _position_list.end());
+ _position_list.insert(_position_list.begin(),
+ ptm_island_sp.get()->_position_list.begin(),
+ ptm_island_sp.get()->_position_list.end());
+ std::sort(_position_list.begin(), _position_list.end());
+ _position_list.erase(
+ std::unique(_position_list.begin(), _position_list.end()),
+ _position_list.end());
- std::vector<PeptideMatch>::const_iterator it_result = std::max_element(_peptide_match_list.begin(), _peptide_match_list.end(), [](const PeptideMatch & a, const PeptideMatch & b)
- {
- return (a.getStop() < b.getStop());
- });
- _protein_stop = it_result->getStop();
+ std::vector<PeptideMatch>::const_iterator it_result =
+ std::max_element(_peptide_match_list.begin(), _peptide_match_list.end(),
+ [](const PeptideMatch &a, const PeptideMatch &b) {
+ return (a.getStop() < b.getStop());
+ });
+ _protein_stop = it_result->getStop();
- it_result = std::min_element(_peptide_match_list.begin(), _peptide_match_list.end(), [](const PeptideMatch & a, const PeptideMatch & b)
- {
- return a.getStart() < b.getStart();
- });
- _protein_start = it_result->getStart();
- return true;
+ it_result =
+ std::min_element(_peptide_match_list.begin(), _peptide_match_list.end(),
+ [](const PeptideMatch &a, const PeptideMatch &b) {
+ return a.getStart() < b.getStart();
+ });
+ _protein_start = it_result->getStart();
+ return true;
}
}
-const std::vector<PeptideMatch> & PtmIsland::getPeptideMatchList() const {
- return _peptide_match_list;
+const std::vector<PeptideMatch> &
+PtmIsland::getPeptideMatchList() const
+{
+ return _peptide_match_list;
}
-std::vector<PtmSampleScanSp> PtmIsland::getPtmSampleScanSpList() const {
- qDebug() << "PtmIsland::getPtmSampleScanSpList begin" ;
- std::vector<PtmSampleScanSp> sample_scan_list;
- for (const PeptideMatch & peptide_match:_peptide_match_list) {
+std::vector<PtmSampleScanSp>
+PtmIsland::getPtmSampleScanSpList() const
+{
+ qDebug() << "PtmIsland::getPtmSampleScanSpList begin";
+ std::vector<PtmSampleScanSp> sample_scan_list;
+ for(const PeptideMatch &peptide_match : _peptide_match_list)
+ {
- std::vector<PtmSampleScanSp>::iterator it_ptm = sample_scan_list.begin();
- std::vector<PtmSampleScanSp>::iterator it_ptm_end = sample_scan_list.end();
- while ((it_ptm != it_ptm_end) && (it_ptm->get()->add(peptide_match) == false)) {
- //peptide added
- it_ptm++;
+ std::vector<PtmSampleScanSp>::iterator it_ptm = sample_scan_list.begin();
+ std::vector<PtmSampleScanSp>::iterator it_ptm_end =
+ sample_scan_list.end();
+ while((it_ptm != it_ptm_end) &&
+ (it_ptm->get()->add(peptide_match) == false))
+ {
+ // peptide added
+ it_ptm++;
}
- if (it_ptm == it_ptm_end) {
- //peptide NOT added
- sample_scan_list.push_back(std::make_shared<PtmSampleScan>(peptide_match));
+ if(it_ptm == it_ptm_end)
+ {
+ // peptide NOT added
+ sample_scan_list.push_back(
+ std::make_shared<PtmSampleScan>(peptide_match));
}
}
- qDebug() << "PtmIsland::getPtmSampleScanSpList end" ;
- return sample_scan_list;
+ qDebug() << "PtmIsland::getPtmSampleScanSpList end";
+ return sample_scan_list;
}
diff --git a/src/grouping/ptm/ptmisland.h b/src/grouping/ptm/ptmisland.h
index 7d66eaa3d7b341a536f30e7ab52de47412b35af8..a4b8985f9fdb375eaf94b1dc024da24db8859ebe 100644
--- a/src/grouping/ptm/ptmisland.h
+++ b/src/grouping/ptm/ptmisland.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMISLAND_H
#define PTMISLAND_H
@@ -46,48 +47,50 @@ typedef std::shared_ptr<PtmIsland> PtmIslandSp;
class PtmIsland
{
-public:
- PtmIsland(const ProteinMatch* p_protein_match, unsigned int position);
- PtmIsland(const PtmIsland & other);
- ~PtmIsland();
- void addPeptideMatch(const PeptideMatch & peptide_match);
-
- /** @brief merge with the given ptm island if there is at least one common peptide match
- * */
- bool merge(PtmIslandSp ptm_island_sp);
-
- bool containsPeptideMatch(const PeptideMatch & element) const;
- std::vector<std::size_t> getSampleScanSet() const;
- const ProteinMatch * getProteinMatch() const;
- unsigned int getProteinStartPosition() const;
- void setPtmIslandSubgroup(PtmIslandSubgroup* p_ptm_island_subgroup);
- void setProteinNumber(unsigned int prot_number);
-
-
- const QString getGroupingId() const;
- const std::vector<unsigned int> & getPositionList() const;
- const PtmIslandSubgroup * getPtmIslandSubroup() const;
- unsigned int countSequence() const;
- unsigned int countSampleScanMultiPtm(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
-
- unsigned int getStart() const;
- unsigned int size() const;
-
- std::vector<PtmSampleScanSp> getPtmSampleScanSpList() const;
-
- const std::vector<PeptideMatch> & getPeptideMatchList() const;
-
-private:
- const ProteinMatch * _protein_match_p;
- std::vector<PeptideMatch> _peptide_match_list;
- //std::vector<std::size_t> _sample_scan_set;
- std::vector<unsigned int> _position_list;
- unsigned int _protein_stop=0;
- unsigned int _protein_start=0;
- /** @brief protein rank number in the PTM subgroup
- * */
- unsigned int _prot_number=0;
- PtmIslandSubgroup * _ptm_island_subgroup_p = nullptr;
+ public:
+ PtmIsland(const ProteinMatch *p_protein_match, unsigned int position);
+ PtmIsland(const PtmIsland &other);
+ ~PtmIsland();
+ void addPeptideMatch(const PeptideMatch &peptide_match);
+
+ /** @brief merge with the given ptm island if there is at least one common
+ * peptide match
+ * */
+ bool merge(PtmIslandSp ptm_island_sp);
+
+ bool containsPeptideMatch(const PeptideMatch &element) const;
+ std::vector<std::size_t> getSampleScanSet() const;
+ const ProteinMatch *getProteinMatch() const;
+ unsigned int getProteinStartPosition() const;
+ void setPtmIslandSubgroup(PtmIslandSubgroup *p_ptm_island_subgroup);
+ void setProteinNumber(unsigned int prot_number);
+
+
+ const QString getGroupingId() const;
+ const std::vector<unsigned int> &getPositionList() const;
+ const PtmIslandSubgroup *getPtmIslandSubroup() const;
+ unsigned int countSequence() const;
+ unsigned int countSampleScanMultiPtm(
+ const PtmGroupingExperiment *p_ptm_grouping_experiment) const;
+
+ unsigned int getStart() const;
+ unsigned int size() const;
+
+ std::vector<PtmSampleScanSp> getPtmSampleScanSpList() const;
+
+ const std::vector<PeptideMatch> &getPeptideMatchList() const;
+
+ private:
+ const ProteinMatch *_protein_match_p;
+ std::vector<PeptideMatch> _peptide_match_list;
+ // std::vector<std::size_t> _sample_scan_set;
+ std::vector<unsigned int> _position_list;
+ unsigned int _protein_stop = 0;
+ unsigned int _protein_start = 0;
+ /** @brief protein rank number in the PTM subgroup
+ * */
+ unsigned int _prot_number = 0;
+ PtmIslandSubgroup *_ptm_island_subgroup_p = nullptr;
};
#endif // PTMISLAND_H
diff --git a/src/grouping/ptm/ptmislandgroup.cpp b/src/grouping/ptm/ptmislandgroup.cpp
index cf79ed89d7249fa83658a3bcec6ff0d13ea543ae..0f3a2b3843cc90cc434e0dba4634b5a567ba7e09 100644
--- a/src/grouping/ptm/ptmislandgroup.cpp
+++ b/src/grouping/ptm/ptmislandgroup.cpp
@@ -6,106 +6,139 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmislandgroup.h"
PtmIslandGroup::PtmIslandGroup(PtmIslandSubgroupSp ptm_island_subgroup_sp)
{
- _ptm_island_subgroup_list.push_back(ptm_island_subgroup_sp);
+ _ptm_island_subgroup_list.push_back(ptm_island_subgroup_sp);
}
-PtmIslandGroup::PtmIslandGroup(const PtmIslandGroup& other)
+PtmIslandGroup::PtmIslandGroup(const PtmIslandGroup &other)
{
- _ptm_island_subgroup_list = other._ptm_island_subgroup_list;
+ _ptm_island_subgroup_list = other._ptm_island_subgroup_list;
}
PtmIslandGroup::~PtmIslandGroup()
{
-
}
-QString PtmIslandGroup::getFirstAccession() const {
- if (_ptm_island_subgroup_list.size() == 0) return QString();
- QStringList accession_list;
- for (PtmIslandSubgroupSp ptm_island_subgroup:_ptm_island_subgroup_list) {
- for (PtmIslandSp ptm_island: ptm_island_subgroup.get()->getPtmIslandList()) {
- accession_list << ptm_island.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession();
+QString
+PtmIslandGroup::getFirstAccession() const
+{
+ if(_ptm_island_subgroup_list.size() == 0)
+ return QString();
+ QStringList accession_list;
+ for(PtmIslandSubgroupSp ptm_island_subgroup : _ptm_island_subgroup_list)
+ {
+ for(PtmIslandSp ptm_island :
+ ptm_island_subgroup.get()->getPtmIslandList())
+ {
+ accession_list << ptm_island.get()
+ ->getProteinMatch()
+ ->getProteinXtpSp()
+ .get()
+ ->getAccession();
}
}
- accession_list.sort();
+ accession_list.sort();
- return accession_list[0];
+ return accession_list[0];
}
-unsigned int PtmIslandGroup::getGroupNumber() const {
- return _group_number;
+unsigned int
+PtmIslandGroup::getGroupNumber() const
+{
+ return _group_number;
}
-void PtmIslandGroup::setGroupNumber(unsigned int number) {
- _group_number = number;
- for (PtmIslandSubgroupSp ptm_island_subgroup:_ptm_island_subgroup_list) {
- ptm_island_subgroup.get()->setPtmIslandGroup(this);
- }
- std::sort(_ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(), [](const PtmIslandSubgroupSp& a, const PtmIslandSubgroupSp& b)
+void
+PtmIslandGroup::setGroupNumber(unsigned int number)
+{
+ _group_number = number;
+ for(PtmIslandSubgroupSp ptm_island_subgroup : _ptm_island_subgroup_list)
{
- return (a.get()->getFirstPtmIsland()->getProteinStartPosition() < b.get()->getFirstPtmIsland()->getProteinStartPosition());
- });
+ ptm_island_subgroup.get()->setPtmIslandGroup(this);
+ }
+ std::sort(_ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(),
+ [](const PtmIslandSubgroupSp &a, const PtmIslandSubgroupSp &b) {
+ return (a.get()->getFirstPtmIsland()->getProteinStartPosition() <
+ b.get()->getFirstPtmIsland()->getProteinStartPosition());
+ });
- unsigned int sg_number=0;
- for (PtmIslandSubgroupSp ptm_island_subgroup:_ptm_island_subgroup_list) {
- sg_number ++;
- ptm_island_subgroup.get()->setSubgroupNumber(sg_number);
+ unsigned int sg_number = 0;
+ for(PtmIslandSubgroupSp ptm_island_subgroup : _ptm_island_subgroup_list)
+ {
+ sg_number++;
+ ptm_island_subgroup.get()->setSubgroupNumber(sg_number);
}
}
-bool PtmIslandGroup::operator<(const PtmIslandGroup& other) const {
- //if (_ptm_island_subgroup_list.size() == other._ptm_island_subgroup_list.size()) {
- if (maxCountSampleScan() == other.maxCountSampleScan()) {
- return (getFirstAccession() < other.getFirstAccession());
+bool
+PtmIslandGroup::operator<(const PtmIslandGroup &other) const
+{
+ // if (_ptm_island_subgroup_list.size() ==
+ // other._ptm_island_subgroup_list.size()) {
+ if(maxCountSampleScan() == other.maxCountSampleScan())
+ {
+ return (getFirstAccession() < other.getFirstAccession());
}
- else {
- return (maxCountSampleScan() > other.maxCountSampleScan());
+ else
+ {
+ return (maxCountSampleScan() > other.maxCountSampleScan());
}
- //}
- //else {
- // return (_ptm_island_subgroup_list.size() < other._ptm_island_subgroup_list.size());
- //}
+ //}
+ // else {
+ // return (_ptm_island_subgroup_list.size() <
+ // other._ptm_island_subgroup_list.size());
+ //}
}
-unsigned int PtmIslandGroup::maxCountSampleScan() const {
- std::vector<PtmIslandSubgroupSp>::const_iterator it_result = std::max_element(_ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(), [](const PtmIslandSubgroupSp & a, const PtmIslandSubgroupSp & b)
- {
- return (a.get()->countSampleScan() < b.get()->countSampleScan());
+unsigned int
+PtmIslandGroup::maxCountSampleScan() const
+{
+ std::vector<PtmIslandSubgroupSp>::const_iterator it_result = std::max_element(
+ _ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(),
+ [](const PtmIslandSubgroupSp &a, const PtmIslandSubgroupSp &b) {
+ return (a.get()->countSampleScan() < b.get()->countSampleScan());
});
- return it_result->get()->countSampleScan();
+ return it_result->get()->countSampleScan();
}
-bool PtmIslandGroup::mergePtmIslandSubgroupSp(PtmIslandSubgroupSp ptm_island_subgroup_sp) {
+bool
+PtmIslandGroup::mergePtmIslandSubgroupSp(
+ PtmIslandSubgroupSp ptm_island_subgroup_sp)
+{
- //http://en.cppreference.com/w/cpp/algorithm/all_any_none_of
- if (std::any_of(_ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(), [ptm_island_subgroup_sp](PtmIslandSubgroupSp element) {
- return element.get()->containsProteinMatchFrom( ptm_island_subgroup_sp.get());
- })) {
- //accept this subgroup
- _ptm_island_subgroup_list.push_back(ptm_island_subgroup_sp);
- return true;
+ // http://en.cppreference.com/w/cpp/algorithm/all_any_none_of
+ if(std::any_of(_ptm_island_subgroup_list.begin(),
+ _ptm_island_subgroup_list.end(),
+ [ptm_island_subgroup_sp](PtmIslandSubgroupSp element) {
+ return element.get()->containsProteinMatchFrom(
+ ptm_island_subgroup_sp.get());
+ }))
+ {
+ // accept this subgroup
+ _ptm_island_subgroup_list.push_back(ptm_island_subgroup_sp);
+ return true;
}
- return false;
+ return false;
}
diff --git a/src/grouping/ptm/ptmislandgroup.h b/src/grouping/ptm/ptmislandgroup.h
index bb3702d1ffdd0c03aee4dad15f74e9014fdd2f37..26e98bf53e34234bf83e948d7f2ab180922c9424 100644
--- a/src/grouping/ptm/ptmislandgroup.h
+++ b/src/grouping/ptm/ptmislandgroup.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMISLANDGROUP_H
#define PTMISLANDGROUP_H
@@ -42,23 +43,24 @@ typedef std::shared_ptr<PtmIslandGroup> PtmIslandGroupSp;
class PtmIslandGroup
{
-public:
- PtmIslandGroup(PtmIslandSubgroupSp ptm_island_subgroup_sp);
- PtmIslandGroup(const PtmIslandGroup& other);
- ~PtmIslandGroup();
- bool operator<(const PtmIslandGroup& other) const;
- /** @brief merge with the given ptm island subgroup if at least one protein is shared
- * */
- bool mergePtmIslandSubgroupSp(PtmIslandSubgroupSp ptm_island_subgroup_sp);
-
- unsigned int maxCountSampleScan() const;
- QString getFirstAccession() const;
- void setGroupNumber(unsigned int number);
- unsigned int getGroupNumber() const;
+ public:
+ PtmIslandGroup(PtmIslandSubgroupSp ptm_island_subgroup_sp);
+ PtmIslandGroup(const PtmIslandGroup &other);
+ ~PtmIslandGroup();
+ bool operator<(const PtmIslandGroup &other) const;
+ /** @brief merge with the given ptm island subgroup if at least one protein is
+ * shared
+ * */
+ bool mergePtmIslandSubgroupSp(PtmIslandSubgroupSp ptm_island_subgroup_sp);
-private :
- std::vector<PtmIslandSubgroupSp> _ptm_island_subgroup_list;
- unsigned int _group_number;
+ unsigned int maxCountSampleScan() const;
+ QString getFirstAccession() const;
+ void setGroupNumber(unsigned int number);
+ unsigned int getGroupNumber() const;
+
+ private:
+ std::vector<PtmIslandSubgroupSp> _ptm_island_subgroup_list;
+ unsigned int _group_number;
};
#endif // PTMISLANDGROUP_H
diff --git a/src/grouping/ptm/ptmislandsubgroup.cpp b/src/grouping/ptm/ptmislandsubgroup.cpp
index f1df0c12361c5cfad670f748f0d935fd3d5416d8..d43c016a88b6ab81de3aa763192dfd0517f50d6f 100644
--- a/src/grouping/ptm/ptmislandsubgroup.cpp
+++ b/src/grouping/ptm/ptmislandsubgroup.cpp
@@ -2,107 +2,140 @@
* \file grouping/ptm/ptmislandsubgroup.cpp
* \date 29/5/2017
* \author Olivier Langella
- * \brief object to group ptm islands sharing the same set of sample scans with different proteins
+ * \brief object to group ptm islands sharing the same set of sample scans with
+ * different proteins
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmislandsubgroup.h"
PtmIslandSubgroup::PtmIslandSubgroup(PtmIslandSp ptm_island_sp)
{
- _ptm_island_list.push_back(ptm_island_sp);
- _sample_scan_set = ptm_island_sp.get()->getSampleScanSet();
+ _ptm_island_list.push_back(ptm_island_sp);
+ _sample_scan_set = ptm_island_sp.get()->getSampleScanSet();
}
-PtmIslandSubgroup::PtmIslandSubgroup(const PtmIslandSubgroup& other)
+PtmIslandSubgroup::PtmIslandSubgroup(const PtmIslandSubgroup &other)
{
- _ptm_island_list = other._ptm_island_list;
- _sample_scan_set = other._sample_scan_set;
-
+ _ptm_island_list = other._ptm_island_list;
+ _sample_scan_set = other._sample_scan_set;
}
PtmIslandSubgroup::~PtmIslandSubgroup()
{
-
}
-const PtmIsland * PtmIslandSubgroup::getFirstPtmIsland() const {
- return _ptm_island_list.begin()->get();
+const PtmIsland *
+PtmIslandSubgroup::getFirstPtmIsland() const
+{
+ return _ptm_island_list.begin()->get();
}
-const PtmIslandGroup * PtmIslandSubgroup::getPtmIslandGroup() const {
- return _ptm_island_group_p;
+const PtmIslandGroup *
+PtmIslandSubgroup::getPtmIslandGroup() const
+{
+ return _ptm_island_group_p;
}
-unsigned int PtmIslandSubgroup::getSubgroupNumber() const {
- return _subgroup_number;
+unsigned int
+PtmIslandSubgroup::getSubgroupNumber() const
+{
+ return _subgroup_number;
}
-void PtmIslandSubgroup::setSubgroupNumber(unsigned int number) {
- _subgroup_number = number;
+void
+PtmIslandSubgroup::setSubgroupNumber(unsigned int number)
+{
+ _subgroup_number = number;
- for (PtmIslandSp ptm_island:_ptm_island_list) {
- ptm_island.get()->setPtmIslandSubgroup(this);
- }
- std::sort(_ptm_island_list.begin(), _ptm_island_list.end(), [](const PtmIslandSp& a, const PtmIslandSp& b)
+ for(PtmIslandSp ptm_island : _ptm_island_list)
{
- return (a.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession() < b.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession());
+ ptm_island.get()->setPtmIslandSubgroup(this);
+ }
+ std::sort(
+ _ptm_island_list.begin(), _ptm_island_list.end(),
+ [](const PtmIslandSp &a, const PtmIslandSp &b) {
+ return (
+ a.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession() <
+ b.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession());
});
- unsigned int prot_number=0;
- for (PtmIslandSp ptm_island:_ptm_island_list) {
- prot_number ++;
- ptm_island.get()->setProteinNumber(prot_number);
+ unsigned int prot_number = 0;
+ for(PtmIslandSp ptm_island : _ptm_island_list)
+ {
+ prot_number++;
+ ptm_island.get()->setProteinNumber(prot_number);
}
}
-void PtmIslandSubgroup::setPtmIslandGroup(PtmIslandGroup * p_ptm_island_group) {
- _ptm_island_group_p = p_ptm_island_group;
- std::sort(_ptm_island_list.begin(), _ptm_island_list.end(), [](const PtmIslandSp& a, const PtmIslandSp& b)
- {
- return (a.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession() < b.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession());
+void
+PtmIslandSubgroup::setPtmIslandGroup(PtmIslandGroup *p_ptm_island_group)
+{
+ _ptm_island_group_p = p_ptm_island_group;
+ std::sort(
+ _ptm_island_list.begin(), _ptm_island_list.end(),
+ [](const PtmIslandSp &a, const PtmIslandSp &b) {
+ return (
+ a.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession() <
+ b.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession());
});
}
-const std::vector< PtmIslandSp > & PtmIslandSubgroup::getPtmIslandList() const {
- return _ptm_island_list;
+const std::vector<PtmIslandSp> &
+PtmIslandSubgroup::getPtmIslandList() const
+{
+ return _ptm_island_list;
}
-unsigned int PtmIslandSubgroup::countSampleScan() const {
- return _sample_scan_set.size();
+unsigned int
+PtmIslandSubgroup::countSampleScan() const
+{
+ return _sample_scan_set.size();
}
-bool PtmIslandSubgroup::containsProteinMatchFrom(PtmIslandSubgroup* ptm_island_subgroup_p) {
- for (PtmIslandSp ptm_island_sp :_ptm_island_list) {
- if (std::any_of(ptm_island_subgroup_p->_ptm_island_list.begin(), ptm_island_subgroup_p->_ptm_island_list.end(), [ptm_island_sp](PtmIslandSp element) {
- return (element.get()->getProteinMatch() == ptm_island_sp.get()->getProteinMatch());
- })) {
- return true;
+bool
+PtmIslandSubgroup::containsProteinMatchFrom(
+ PtmIslandSubgroup *ptm_island_subgroup_p)
+{
+ for(PtmIslandSp ptm_island_sp : _ptm_island_list)
+ {
+ if(std::any_of(ptm_island_subgroup_p->_ptm_island_list.begin(),
+ ptm_island_subgroup_p->_ptm_island_list.end(),
+ [ptm_island_sp](PtmIslandSp element) {
+ return (element.get()->getProteinMatch() ==
+ ptm_island_sp.get()->getProteinMatch());
+ }))
+ {
+ return true;
}
}
- return false;
+ return false;
}
-bool PtmIslandSubgroup::mergePtmIslandSp(PtmIslandSp ptm_island_sp) {
- if (_sample_scan_set == ptm_island_sp.get()->getSampleScanSet()) {
- //merge
- _ptm_island_list.push_back(ptm_island_sp);
- return true;
+bool
+PtmIslandSubgroup::mergePtmIslandSp(PtmIslandSp ptm_island_sp)
+{
+ if(_sample_scan_set == ptm_island_sp.get()->getSampleScanSet())
+ {
+ // merge
+ _ptm_island_list.push_back(ptm_island_sp);
+ return true;
}
- return false;
+ return false;
}
diff --git a/src/grouping/ptm/ptmislandsubgroup.h b/src/grouping/ptm/ptmislandsubgroup.h
index 0f83c6df713ca9de89ebc80ca36667e85adaf9d9..92629a4e165f602a64caf2cf7b703ee99e0533cc 100644
--- a/src/grouping/ptm/ptmislandsubgroup.h
+++ b/src/grouping/ptm/ptmislandsubgroup.h
@@ -2,30 +2,32 @@
* \file grouping/ptm/ptmislandsubgroup.h
* \date 29/5/2017
* \author Olivier Langella
- * \brief object to group ptm islands sharing the same set of sample scans with different proteins
+ * \brief object to group ptm islands sharing the same set of sample scans with
+ * different proteins
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMISLANDSUBGROUP_H
#define PTMISLANDSUBGROUP_H
@@ -43,33 +45,32 @@ class PtmIslandGroup;
class PtmIslandSubgroup
{
-public:
- PtmIslandSubgroup(PtmIslandSp ptm_island_sp);
- PtmIslandSubgroup(const PtmIslandSubgroup& other);
- ~PtmIslandSubgroup();
+ public:
+ PtmIslandSubgroup(PtmIslandSp ptm_island_sp);
+ PtmIslandSubgroup(const PtmIslandSubgroup &other);
+ ~PtmIslandSubgroup();
- /** @brief merge with the given ptm island if all sample scans are shared
- * */
- bool mergePtmIslandSp(PtmIslandSp ptm_island_sp);
- bool containsProteinMatchFrom(PtmIslandSubgroup* ptm_island_subgroup_p);
-
- unsigned int countSampleScan() const;
-
- const std::vector< PtmIslandSp > & getPtmIslandList() const;
-
- void setPtmIslandGroup(PtmIslandGroup * p_ptm_island_group);
-
- const PtmIsland * getFirstPtmIsland() const;
- unsigned int getSubgroupNumber() const;
- void setSubgroupNumber(unsigned int number);
- const PtmIslandGroup * getPtmIslandGroup() const;
+ /** @brief merge with the given ptm island if all sample scans are shared
+ * */
+ bool mergePtmIslandSp(PtmIslandSp ptm_island_sp);
+ bool containsProteinMatchFrom(PtmIslandSubgroup *ptm_island_subgroup_p);
-private:
- std::vector< PtmIslandSp > _ptm_island_list;
- std::vector<std::size_t> _sample_scan_set;
- PtmIslandGroup * _ptm_island_group_p = nullptr;
- unsigned int _subgroup_number;
+ unsigned int countSampleScan() const;
+ const std::vector<PtmIslandSp> &getPtmIslandList() const;
+
+ void setPtmIslandGroup(PtmIslandGroup *p_ptm_island_group);
+
+ const PtmIsland *getFirstPtmIsland() const;
+ unsigned int getSubgroupNumber() const;
+ void setSubgroupNumber(unsigned int number);
+ const PtmIslandGroup *getPtmIslandGroup() const;
+
+ private:
+ std::vector<PtmIslandSp> _ptm_island_list;
+ std::vector<std::size_t> _sample_scan_set;
+ PtmIslandGroup *_ptm_island_group_p = nullptr;
+ unsigned int _subgroup_number;
};
#endif // PTMISLANDSUBGROUP_H
diff --git a/src/grouping/ptm/ptmpeptide.cpp b/src/grouping/ptm/ptmpeptide.cpp
index 498858ee91776256d4730719c05b67ca674741e7..9f07274cffbc68203d6ff6504bbafe6a91985190 100644
--- a/src/grouping/ptm/ptmpeptide.cpp
+++ b/src/grouping/ptm/ptmpeptide.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmpeptide.h"
diff --git a/src/grouping/ptm/ptmpeptide.h b/src/grouping/ptm/ptmpeptide.h
index 775a07474155f350e787f189f72b4f5b3c8a2aa5..e1f79e7b3a002ddc92246c7411ed31c8afbd66df 100644
--- a/src/grouping/ptm/ptmpeptide.h
+++ b/src/grouping/ptm/ptmpeptide.h
@@ -2,30 +2,32 @@
* \file core/grouping/ptm/ptmpeptide.h
* \date 14/3/2018
* \author Olivier Langella
- * \brief collection of PTM PeptideMatch sharing the same peptide sequence + mass
+ * \brief collection of PTM PeptideMatch sharing the same peptide sequence +
+ * mass
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMPEPTIDE_H
diff --git a/src/grouping/ptm/ptmsamplescan.cpp b/src/grouping/ptm/ptmsamplescan.cpp
index d35d16908649f76777bad44a4ad0db237ef3516b..623eb6d9d4560d27fa637695c9394ef8f0afef56 100644
--- a/src/grouping/ptm/ptmsamplescan.cpp
+++ b/src/grouping/ptm/ptmsamplescan.cpp
@@ -6,146 +6,214 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmsamplescan.h"
#include "../../grouping/ptm/ptmgroupingexperiment.h"
-QColor PtmSampleScan::_color_best = QColor("red");
+QColor PtmSampleScan::_color_best = QColor("red");
QColor PtmSampleScan::_color_other_best = QColor("#ff7878");
-QColor PtmSampleScan::_color_no_best = QColor("yellow");
+QColor PtmSampleScan::_color_no_best = QColor("yellow");
-PtmSampleScan::PtmSampleScan(const PeptideMatch & peptide_match) {
- _peptide_match_list.push_back(peptide_match);
+PtmSampleScan::PtmSampleScan(const PeptideMatch &peptide_match)
+{
+ _peptide_match_list.push_back(peptide_match);
}
-PtmSampleScan::PtmSampleScan(const PtmSampleScan& other) {
- _peptide_match_list = other._peptide_match_list;
+PtmSampleScan::PtmSampleScan(const PtmSampleScan &other)
+{
+ _peptide_match_list = other._peptide_match_list;
}
-PtmSampleScan::~PtmSampleScan() {
+PtmSampleScan::~PtmSampleScan()
+{
}
-const PeptideMatch & PtmSampleScan::getRepresentativePeptideMatch() const {
- //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " " << _peptide_match_list.size();
- return _peptide_match_list[0];
+const PeptideMatch &
+PtmSampleScan::getRepresentativePeptideMatch() const
+{
+ // qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " " <<
+ // _peptide_match_list.size();
+ return _peptide_match_list[0];
}
-bool PtmSampleScan::add(const PeptideMatch & peptide_match) {
- //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ ;
- if(getRepresentativePeptideMatch().getPeptideEvidence()->getHashSampleScan() != peptide_match.getPeptideEvidence()->getHashSampleScan()) {
- return false;
+bool
+PtmSampleScan::add(const PeptideMatch &peptide_match)
+{
+ // qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ ;
+ if(getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getHashSampleScan() !=
+ peptide_match.getPeptideEvidence()->getHashSampleScan())
+ {
+ return false;
}
-
- //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ ;
- if(getRepresentativePeptideMatch().getPeptideEvidence()->getPeptideXtpSp().get()->getSequence() != peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequence()) {
- return false;
+
+ // qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ ;
+ if(getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getSequence() !=
+ peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequence())
+ {
+ return false;
}
-
- //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ ;
- if(getRepresentativePeptideMatch().getPeptideEvidence()->getPeptideXtpSp().get()->getMass() != peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getMass()) {
- return false;
+
+ // qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ ;
+ if(getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getMass() !=
+ peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getMass())
+ {
+ return false;
}
- _peptide_match_list.push_back(peptide_match);
-
- //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ ;
+ _peptide_match_list.push_back(peptide_match);
- //sort list
- std::sort(_peptide_match_list.begin(),_peptide_match_list.end(),[](const PeptideMatch & first, const PeptideMatch & second) {
- return (first.getPeptideEvidence()->getEvalue() < second.getPeptideEvidence()->getEvalue()) ;
- });
+ // qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ ;
- //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " " << true;
- return true;
-}
+ // sort list
+ std::sort(_peptide_match_list.begin(), _peptide_match_list.end(),
+ [](const PeptideMatch &first, const PeptideMatch &second) {
+ return (first.getPeptideEvidence()->getEvalue() <
+ second.getPeptideEvidence()->getEvalue());
+ });
-std::vector<unsigned int> PtmSampleScan::getBestPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const {
- return p_ptm_grouping_experiment->getPtmPositions(getRepresentativePeptideMatch());
+ // qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " " <<
+ // true;
+ return true;
}
-std::vector<unsigned int> PtmSampleScan::getObservedPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const {
- std::vector<unsigned int> position_list;
+std::vector<unsigned int>
+PtmSampleScan::getBestPtmPositionList(
+ const PtmGroupingExperiment *p_ptm_grouping_experiment) const
+{
+ return p_ptm_grouping_experiment->getPtmPositions(
+ getRepresentativePeptideMatch());
+}
- for (const PeptideMatch & peptide_match: _peptide_match_list) {
- std::vector<unsigned int> positionb_list = p_ptm_grouping_experiment->getPtmPositions(peptide_match);
- for (unsigned int position: positionb_list) {
- position_list.push_back(position);
+std::vector<unsigned int>
+PtmSampleScan::getObservedPtmPositionList(
+ const PtmGroupingExperiment *p_ptm_grouping_experiment) const
+{
+ std::vector<unsigned int> position_list;
+
+ for(const PeptideMatch &peptide_match : _peptide_match_list)
+ {
+ std::vector<unsigned int> positionb_list =
+ p_ptm_grouping_experiment->getPtmPositions(peptide_match);
+ for(unsigned int position : positionb_list)
+ {
+ position_list.push_back(position);
}
}
- std::sort(position_list.begin(), position_list.end());
- auto last = std::unique(position_list.begin(), position_list.end());
- position_list.erase(last, position_list.end());
- return position_list;
+ std::sort(position_list.begin(), position_list.end());
+ auto last = std::unique(position_list.begin(), position_list.end());
+ position_list.erase(last, position_list.end());
+ return position_list;
}
-const QString PtmSampleScan::getHtmlSequence(const PtmGroupingExperiment * p_ptm_grouping_experiment) const
+const QString
+PtmSampleScan::getHtmlSequence(
+ const PtmGroupingExperiment *p_ptm_grouping_experiment) const
{
- const PeptideMatch & representative_peptide = getRepresentativePeptideMatch();
- size_t pep_size = representative_peptide.getPeptideEvidence()->getPeptideXtpSp().get()->size();
- //qDebug() << "ProteinMatch::getCoverage begin prot_size=" << prot_size << " " << _protein_sp.get()-//>getSequence();
- if (pep_size == 0) return 0;
- bool best_bool[pep_size] = {false};
- bool other_best_bool[pep_size] = {false};
- bool nobest_bool[pep_size] = {false};
- double best_evalue = representative_peptide.getPeptideEvidence()->getEvalue();
-
-
- for (auto & peptide_match : _peptide_match_list) {
- bool is_best= false;
- if (peptide_match.getPeptideEvidence()->getEvalue() == best_evalue) {
- is_best= true;
+ const PeptideMatch &representative_peptide = getRepresentativePeptideMatch();
+ size_t pep_size = representative_peptide.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->size();
+ // qDebug() << "ProteinMatch::getCoverage begin prot_size=" << prot_size << "
+ // " << _protein_sp.get()-//>getSequence();
+ if(pep_size == 0)
+ return 0;
+ bool best_bool[pep_size] = {false};
+ bool other_best_bool[pep_size] = {false};
+ bool nobest_bool[pep_size] = {false};
+ double best_evalue = representative_peptide.getPeptideEvidence()->getEvalue();
+
+
+ for(auto &peptide_match : _peptide_match_list)
+ {
+ bool is_best = false;
+ if(peptide_match.getPeptideEvidence()->getEvalue() == best_evalue)
+ {
+ is_best = true;
}
- std::vector<unsigned int> position_list = p_ptm_grouping_experiment->getPtmPositions(peptide_match);
- for (unsigned int position :position_list) {
- if (representative_peptide == peptide_match) {
- best_bool[position] = true;
+ std::vector<unsigned int> position_list =
+ p_ptm_grouping_experiment->getPtmPositions(peptide_match);
+ for(unsigned int position : position_list)
+ {
+ if(representative_peptide == peptide_match)
+ {
+ best_bool[position] = true;
}
- else if (is_best) {
- other_best_bool[position] = true;
+ else if(is_best)
+ {
+ other_best_bool[position] = true;
}
- else {
- nobest_bool[position] = true;
+ else
+ {
+ nobest_bool[position] = true;
}
}
}
- QString sequence = representative_peptide.getPeptideEvidence()->getPeptideXtpSp().get()->getSequence();
- QString sequence_html;
- for (unsigned int i=0; i < pep_size; i++) {
- if (best_bool[i]) {
- sequence_html.append(QString("<span style=\"color:%2;\">%1</span>").arg(sequence[i]).arg(_color_best.name()));
+ QString sequence = representative_peptide.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getSequence();
+ QString sequence_html;
+ for(unsigned int i = 0; i < pep_size; i++)
+ {
+ if(best_bool[i])
+ {
+ sequence_html.append(QString("<span style=\"color:%2;\">%1</span>")
+ .arg(sequence[i])
+ .arg(_color_best.name()));
}
- else if (other_best_bool[i]) {
- sequence_html.append(QString("<span style=\"color:%2;\">%1</span>").arg(sequence[i]).arg(_color_other_best.name()));
+ else if(other_best_bool[i])
+ {
+ sequence_html.append(QString("<span style=\"color:%2;\">%1</span>")
+ .arg(sequence[i])
+ .arg(_color_other_best.name()));
}
- else if (nobest_bool[i]) {
- sequence_html.append(QString("<span style=\"color:%2;\">%1</span>").arg(sequence[i]).arg(_color_no_best.name()));
+ else if(nobest_bool[i])
+ {
+ sequence_html.append(QString("<span style=\"color:%2;\">%1</span>")
+ .arg(sequence[i])
+ .arg(_color_no_best.name()));
}
- else {
- sequence_html.append(sequence[i]);
+ else
+ {
+ sequence_html.append(sequence[i]);
}
}
- return sequence_html;
+ return sequence_html;
}
-std::vector<PeptideMatch> & PtmSampleScan::getPeptideMatchList() {
- return _peptide_match_list;
+std::vector<PeptideMatch> &
+PtmSampleScan::getPeptideMatchList()
+{
+ return _peptide_match_list;
}
diff --git a/src/grouping/ptm/ptmsamplescan.h b/src/grouping/ptm/ptmsamplescan.h
index 50427558790b6124407bb85b2d6f3c58b25798aa..46d0a576e9fbf115b4e1c087bfe5b2872e955833 100644
--- a/src/grouping/ptm/ptmsamplescan.h
+++ b/src/grouping/ptm/ptmsamplescan.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMSAMPLESCAN_H
#define PTMSAMPLESCAN_H
@@ -43,32 +44,35 @@ typedef std::shared_ptr<PtmSampleScan> PtmSampleScanSp;
class PtmSampleScan
{
-public:
- PtmSampleScan(const PeptideMatch & peptide_match);
- PtmSampleScan(const PtmSampleScan& other);
- ~PtmSampleScan();
-
- /** @brief get the best peptide Match (Evalue)
- * peptide match are sorted in this sample/scan by Evalue
- * The representative peptide match is the first in the sorted array
- */
- const PeptideMatch & getRepresentativePeptideMatch() const;
- bool add(const PeptideMatch & peptide_match);
- std::vector<unsigned int> getBestPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
-
- /** @brief get all observed PTM positions for this sample/scan
- * positions are intended in a peptide (not protein), from 0 (first amino acid) to size-1 (last amino acid)
- */
- std::vector<unsigned int> getObservedPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
- const QString getHtmlSequence(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
- std::vector<PeptideMatch> & getPeptideMatchList();
-
-private:
- std::vector<PeptideMatch> _peptide_match_list;
- static QColor _color_best;
- static QColor _color_other_best;
- static QColor _color_no_best;
+ public:
+ PtmSampleScan(const PeptideMatch &peptide_match);
+ PtmSampleScan(const PtmSampleScan &other);
+ ~PtmSampleScan();
+ /** @brief get the best peptide Match (Evalue)
+ * peptide match are sorted in this sample/scan by Evalue
+ * The representative peptide match is the first in the sorted array
+ */
+ const PeptideMatch &getRepresentativePeptideMatch() const;
+ bool add(const PeptideMatch &peptide_match);
+ std::vector<unsigned int> getBestPtmPositionList(
+ const PtmGroupingExperiment *p_ptm_grouping_experiment) const;
+
+ /** @brief get all observed PTM positions for this sample/scan
+ * positions are intended in a peptide (not protein), from 0 (first amino
+ * acid) to size-1 (last amino acid)
+ */
+ std::vector<unsigned int> getObservedPtmPositionList(
+ const PtmGroupingExperiment *p_ptm_grouping_experiment) const;
+ const QString
+ getHtmlSequence(const PtmGroupingExperiment *p_ptm_grouping_experiment) const;
+ std::vector<PeptideMatch> &getPeptideMatchList();
+
+ private:
+ std::vector<PeptideMatch> _peptide_match_list;
+ static QColor _color_best;
+ static QColor _color_other_best;
+ static QColor _color_no_best;
};
Q_DECLARE_METATYPE(PtmSampleScan *)
diff --git a/src/gui/about_dialog/aboutdialog.cpp b/src/gui/about_dialog/aboutdialog.cpp
index 8fa0094f5ce16f1f1dc893c0c258295cb9f20a43..1aefbcbc962dad0d5d8cad8b82210b27234741eb 100644
--- a/src/gui/about_dialog/aboutdialog.cpp
+++ b/src/gui/about_dialog/aboutdialog.cpp
@@ -1,51 +1,50 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "aboutdialog.h"
#include <QDebug>
#include "ui_about_dialog.h"
-AboutDialog::AboutDialog(QWidget * parent):
- QDialog(parent),
- ui(new Ui::AboutDialog)
+AboutDialog::AboutDialog(QWidget *parent)
+ : QDialog(parent), ui(new Ui::AboutDialog)
{
- qDebug() << "AboutDialog::AboutDialog begin";
- ui->setupUi(this);
- this->setModal(true);
-
+ qDebug() << "AboutDialog::AboutDialog begin";
+ ui->setupUi(this);
+ this->setModal(true);
+
#if QT_VERSION >= 0x050000
- // Qt5 code
+ // Qt5 code
#else
-// Qt4 code
+ // Qt4 code
#endif
-
}
AboutDialog::~AboutDialog()
{
- qDebug() << "AboutDialog::~AboutDialog";
- delete ui;
-
- qDebug() << "AboutDialog::~AboutDialog end";
+ qDebug() << "AboutDialog::~AboutDialog";
+ delete ui;
+
+ qDebug() << "AboutDialog::~AboutDialog end";
}
diff --git a/src/gui/about_dialog/aboutdialog.h b/src/gui/about_dialog/aboutdialog.h
index 299a6b33188cbeb7086a1e387fbb8fcfa3f07462..fe2b90f2b675fff928daa1702965bd0c42070983 100644
--- a/src/gui/about_dialog/aboutdialog.h
+++ b/src/gui/about_dialog/aboutdialog.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef ABOUTDIALOG_H
#define ABOUTDIALOG_H
@@ -27,21 +28,21 @@
#include <QDialog>
-namespace Ui {
-class AboutDialog;
+namespace Ui
+{
+ class AboutDialog;
}
class AboutDialog : public QDialog
{
- Q_OBJECT
-
-public:
- explicit AboutDialog(QWidget * parent);
- ~AboutDialog();
+ Q_OBJECT
-private:
- Ui::AboutDialog *ui;
+ public:
+ explicit AboutDialog(QWidget *parent);
+ ~AboutDialog();
+ private:
+ Ui::AboutDialog *ui;
};
#endif // ABOUTDIALOG_H
diff --git a/src/gui/choose_modification_dialog/choosemodificationdialog.cpp b/src/gui/choose_modification_dialog/choosemodificationdialog.cpp
index 3120ad714f45b11d3471ad89f93af2ba6d0dbde6..9d682cdc99739a62841e5bc3c59874097cf427bf 100644
--- a/src/gui/choose_modification_dialog/choosemodificationdialog.cpp
+++ b/src/gui/choose_modification_dialog/choosemodificationdialog.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "choosemodificationdialog.h"
@@ -33,81 +34,100 @@
#include <pappsomspp/obo/filterobopsimodtermname.h>
#include "../../utils/utils.h"
-ChooseModificationDialog::ChooseModificationDialog(QWidget * parent):
- QDialog(parent),
- ui(new Ui::ChooseModificationDialog)
+ChooseModificationDialog::ChooseModificationDialog(QWidget *parent)
+ : QDialog(parent), ui(new Ui::ChooseModificationDialog)
{
- qDebug() << "ChooseModificationDialog::ChooseModificationDialog begin";
- ui->setupUi(this);
- this->setModal(true);
+ qDebug() << "ChooseModificationDialog::ChooseModificationDialog begin";
+ ui->setupUi(this);
+ this->setModal(true);
- _p_modification_str_li = new QStandardItemModel();
- ui->modification_listview->setModel(_p_modification_str_li);
- //param.setFilterCrossSamplePeptideNumber(settings.value("automatic_filter/cross_sample", "true").toBool());
+ _p_modification_str_li = new QStandardItemModel();
+ ui->modification_listview->setModel(_p_modification_str_li);
+ // param.setFilterCrossSamplePeptideNumber(settings.value("automatic_filter/cross_sample",
+ // "true").toBool());
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect(ui->modification_listview,&QListView::clicked,this,&ChooseModificationDialog::ItemClicked);
- connect(ui->modification_listview,&QListView::doubleClicked,this,&ChooseModificationDialog::ItemDoubleClicked);
+ // Qt5 code
+ connect(ui->modification_listview, &QListView::clicked, this,
+ &ChooseModificationDialog::ItemClicked);
+ connect(ui->modification_listview, &QListView::doubleClicked, this,
+ &ChooseModificationDialog::ItemDoubleClicked);
#else
-// Qt4 code
+ // Qt4 code
- connect(ui->modification_listview,SIGNAL(clicked(const QModelIndex)),this,SLOT(ItemClicked(QModelIndex)));
- connect(ui->modification_listview,SIGNAL(doubleClicked(const QModelIndex)),this,SLOT(ItemDoubleClicked(QModelIndex)));
+ connect(ui->modification_listview, SIGNAL(clicked(const QModelIndex)), this,
+ SLOT(ItemClicked(QModelIndex)));
+ connect(ui->modification_listview, SIGNAL(doubleClicked(const QModelIndex)),
+ this, SLOT(ItemDoubleClicked(QModelIndex)));
#endif
-
}
ChooseModificationDialog::~ChooseModificationDialog()
{
- qDebug() << "ChooseModificationDialog::~ChooseModificationDialog";
- delete ui;
-
- qDebug() << "ChooseModificationDialog::~ChooseModificationDialog end";
-}
-
-void ChooseModificationDialog::setMassRange(const pappso::MassRange & massrange) {
-
- qDebug() << "ChooseModificationDialog::setMassRange " << massrange.toString();
- _selected_modification = nullptr;
- _p_modification_str_li->removeRows(0,_p_modification_str_li->rowCount());
- pappso::FilterOboPsiModSink term_list;
+ qDebug() << "ChooseModificationDialog::~ChooseModificationDialog";
+ delete ui;
- pappso::OboPsiModHandlerInterface * last_men_standing = &term_list;
- pappso::FilterOboPsiModTermDiffMono * p_filter_mass = nullptr;
- //FilterOboPsiModTermLabel * p_filter_label = nullptr;
- //FilterOboPsiModTermName * p_filter_name = nullptr;
+ qDebug() << "ChooseModificationDialog::~ChooseModificationDialog end";
+}
- p_filter_mass = new pappso::FilterOboPsiModTermDiffMono(*last_men_standing, massrange);
- pappso::OboPsiMod psimodb(*p_filter_mass);
- for (pappso::OboPsiModTerm term : term_list.getOboPsiModTermList() ) {
+void
+ChooseModificationDialog::setMassRange(const pappso::MassRange &massrange)
+{
- QStandardItem *item;
- item = new QStandardItem(QString("[%1] %2").arg(term._accession).arg(term._name));
- item->setEditable(false);
- _p_modification_str_li->appendRow(item);
- item->setData(QVariant(QString("%1").arg(term._accession)),Qt::UserRole);
+ qDebug() << "ChooseModificationDialog::setMassRange " << massrange.toString();
+ _selected_modification = nullptr;
+ _p_modification_str_li->removeRows(0, _p_modification_str_li->rowCount());
+ pappso::FilterOboPsiModSink term_list;
+
+ pappso::OboPsiModHandlerInterface *last_men_standing = &term_list;
+ pappso::FilterOboPsiModTermDiffMono *p_filter_mass = nullptr;
+ // FilterOboPsiModTermLabel * p_filter_label = nullptr;
+ // FilterOboPsiModTermName * p_filter_name = nullptr;
+
+ p_filter_mass =
+ new pappso::FilterOboPsiModTermDiffMono(*last_men_standing, massrange);
+ pappso::OboPsiMod psimodb(*p_filter_mass);
+ for(pappso::OboPsiModTerm term : term_list.getOboPsiModTermList())
+ {
+
+ QStandardItem *item;
+ item = new QStandardItem(
+ QString("[%1] %2").arg(term._accession).arg(term._name));
+ item->setEditable(false);
+ _p_modification_str_li->appendRow(item);
+ item->setData(QVariant(QString("%1").arg(term._accession)), Qt::UserRole);
}
}
-void ChooseModificationDialog::ItemDoubleClicked (QModelIndex index )
+void
+ChooseModificationDialog::ItemDoubleClicked(QModelIndex index)
{
- qDebug() << "ChooseModificationDialog::ItemClicked data=" << index.data().toString();
- qDebug() << "ChooseModificationDialog::ItemClicked acc=" << _p_modification_str_li->data(index,Qt::UserRole).toString();
- QDesktopServices::openUrl (Utils::getOlsUrl(_p_modification_str_li->data(index,Qt::UserRole).toString())) ;
+ qDebug() << "ChooseModificationDialog::ItemClicked data="
+ << index.data().toString();
+ qDebug() << "ChooseModificationDialog::ItemClicked acc="
+ << _p_modification_str_li->data(index, Qt::UserRole).toString();
+ QDesktopServices::openUrl(Utils::getOlsUrl(
+ _p_modification_str_li->data(index, Qt::UserRole).toString()));
}
-void ChooseModificationDialog::ItemClicked (QModelIndex index )
+void
+ChooseModificationDialog::ItemClicked(QModelIndex index)
{
- qDebug() << "ChooseModificationDialog::ItemClicked data=" << index.data().toString();
- qDebug() << "ChooseModificationDialog::ItemClicked acc=" << _p_modification_str_li->data(index,Qt::UserRole).toString();
- qDebug() << "ChooseModificationDialog::ItemClicked str=" << _p_modification_str_li->data(index,Qt::DisplayRole).toString();
- pappso::AaModificationP modification = pappso::AaModification::getInstance(index.data(Qt::UserRole).toString());
- _selected_modification = modification;
+ qDebug() << "ChooseModificationDialog::ItemClicked data="
+ << index.data().toString();
+ qDebug() << "ChooseModificationDialog::ItemClicked acc="
+ << _p_modification_str_li->data(index, Qt::UserRole).toString();
+ qDebug() << "ChooseModificationDialog::ItemClicked str="
+ << _p_modification_str_li->data(index, Qt::DisplayRole).toString();
+ pappso::AaModificationP modification =
+ pappso::AaModification::getInstance(index.data(Qt::UserRole).toString());
+ _selected_modification = modification;
}
-pappso::AaModificationP ChooseModificationDialog::getSelectedModification()const {
- return _selected_modification;
+pappso::AaModificationP
+ChooseModificationDialog::getSelectedModification() const
+{
+ return _selected_modification;
}
diff --git a/src/gui/choose_modification_dialog/choosemodificationdialog.h b/src/gui/choose_modification_dialog/choosemodificationdialog.h
index 83445bd8e2f6feb354443e41612944dbe0835a6c..32479c43f0df2f0580077b4b128a5ce536d9ee4d 100644
--- a/src/gui/choose_modification_dialog/choosemodificationdialog.h
+++ b/src/gui/choose_modification_dialog/choosemodificationdialog.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef CHOOSEMODIFICATIONDIALOG_H
#define CHOOSEMODIFICATIONDIALOG_H
@@ -30,30 +31,30 @@
#include <pappsomspp/amino_acid/aamodification.h>
-namespace Ui {
-class ChooseModificationDialog;
+namespace Ui
+{
+ class ChooseModificationDialog;
}
class ChooseModificationDialog : public QDialog
{
- Q_OBJECT
+ Q_OBJECT
-public:
- explicit ChooseModificationDialog(QWidget * parent);
- ~ChooseModificationDialog();
+ public:
+ explicit ChooseModificationDialog(QWidget *parent);
+ ~ChooseModificationDialog();
- void setMassRange(const pappso::MassRange & massrange);
- public slots:
- void ItemClicked (QModelIndex index );
- void ItemDoubleClicked (QModelIndex index );
-
- pappso::AaModificationP getSelectedModification() const;
+ void setMassRange(const pappso::MassRange &massrange);
+ public slots:
+ void ItemClicked(QModelIndex index);
+ void ItemDoubleClicked(QModelIndex index);
-private:
- Ui::ChooseModificationDialog *ui;
- QStandardItemModel * _p_modification_str_li=nullptr;
- pappso::AaModificationP _selected_modification;
+ pappso::AaModificationP getSelectedModification() const;
+ private:
+ Ui::ChooseModificationDialog *ui;
+ QStandardItemModel *_p_modification_str_li = nullptr;
+ pappso::AaModificationP _selected_modification;
};
#endif // CHOOSEMODIFICATIONDIALOG_H
diff --git a/src/gui/edit_label_methods/editlabelmethods.cpp b/src/gui/edit_label_methods/editlabelmethods.cpp
index e59a14685d002b2e19e753c89c3d58abbb3852df..738841833d8f7b7c7494483a8d518feb7d11eaed 100644
--- a/src/gui/edit_label_methods/editlabelmethods.cpp
+++ b/src/gui/edit_label_methods/editlabelmethods.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "editlabelmethods.h"
#include "../project_view/projectwindow.h"
@@ -28,82 +29,96 @@
#include <QDomDocument>
#include <QMessageBox>
-EditLabelMethods::EditLabelMethods(ProjectWindow *parent):
- QDialog(),
- ui(new Ui::EditLabelMethodView)
+EditLabelMethods::EditLabelMethods(ProjectWindow *parent)
+ : QDialog(), ui(new Ui::EditLabelMethodView)
{
- ui->setupUi(this);
- _project_window = parent;
- _p_label_method_str_li = new QStandardItemModel();
- ui->method_list_view->setModel(_p_label_method_str_li);
-this->setModal(true);
+ ui->setupUi(this);
+ _project_window = parent;
+ _p_label_method_str_li = new QStandardItemModel();
+ ui->method_list_view->setModel(_p_label_method_str_li);
+ this->setModal(true);
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect(ui->method_list_view,&QListView::clicked,this,&EditLabelMethods::ItemClicked);
+ // Qt5 code
+ connect(ui->method_list_view, &QListView::clicked, this,
+ &EditLabelMethods::ItemClicked);
#else
- connect(ui->method_list_view,SIGNAL(clicked(const QModelIndex)),this,SLOT(ItemClicked(QModelIndex)));
+ connect(ui->method_list_view, SIGNAL(clicked(const QModelIndex)), this,
+ SLOT(ItemClicked(QModelIndex)));
#endif
}
-EditLabelMethods::~EditLabelMethods() {
-
- qDebug() << "EditLabelMethods::~EditLabelMethods";
- delete ui;
- qDebug() << "EditLabelMethods::~EditLabelMethods end";
+EditLabelMethods::~EditLabelMethods()
+{
+
+ qDebug() << "EditLabelMethods::~EditLabelMethods";
+ delete ui;
+ qDebug() << "EditLabelMethods::~EditLabelMethods end";
}
-void EditLabelMethods::setProjectSp(ProjectSp project_sp) {
+void
+EditLabelMethods::setProjectSp(ProjectSp project_sp)
+{
- _project_sp = project_sp;
- _p_label_method_str_li->removeRows(0,_p_label_method_str_li->rowCount());
- ui->ok_button->setDisabled(true);
+ _project_sp = project_sp;
+ _p_label_method_str_li->removeRows(0, _p_label_method_str_li->rowCount());
+ ui->ok_button->setDisabled(true);
- QDomDocument *dom = new QDomDocument("labeling_methods");
- QFile xml_doc(":/labeling/resources/catalog_label.xml");
- if(!xml_doc.open(QIODevice::ReadOnly))
+ QDomDocument *dom = new QDomDocument("labeling_methods");
+ QFile xml_doc(":/labeling/resources/catalog_label.xml");
+ if(!xml_doc.open(QIODevice::ReadOnly))
{
- //error
- QMessageBox::warning(this,tr("error"),tr("error opening catalog_label resource file"));
- return;
+ // error
+ QMessageBox::warning(this, tr("error"),
+ tr("error opening catalog_label resource file"));
+ return;
}
- if (!dom->setContent(&xml_doc)) {
- xml_doc.close();
- QMessageBox::warning(this,tr("error"), tr("error setting catalog_label xml content"));
- return;
+ if(!dom->setContent(&xml_doc))
+ {
+ xml_doc.close();
+ QMessageBox::warning(this, tr("error"),
+ tr("error setting catalog_label xml content"));
+ return;
}
- QDomNode child = dom->documentElement().firstChild();
- while (!child.isNull()) {
- if (child.toElement().tagName() == "isotope_label_list") {
- QStandardItem *item;
- item = new QStandardItem(QString("%1").arg(child.toElement().attribute("id")));
- item->setEditable(false);
- _p_label_method_str_li->appendRow(item);
- item->setData(QVariant(QString("%1").arg(child.toElement().attribute("id"))),Qt::UserRole);
+ QDomNode child = dom->documentElement().firstChild();
+ while(!child.isNull())
+ {
+ if(child.toElement().tagName() == "isotope_label_list")
+ {
+ QStandardItem *item;
+ item = new QStandardItem(
+ QString("%1").arg(child.toElement().attribute("id")));
+ item->setEditable(false);
+ _p_label_method_str_li->appendRow(item);
+ item->setData(
+ QVariant(QString("%1").arg(child.toElement().attribute("id"))),
+ Qt::UserRole);
}
- child = child.nextSibling();
+ child = child.nextSibling();
}
-
- xml_doc.close();
- delete dom;
+ xml_doc.close();
+ delete dom;
}
-void EditLabelMethods::ItemClicked (QModelIndex index )
+void
+EditLabelMethods::ItemClicked(QModelIndex index)
{
- qDebug() << "EditLabelMethods::ItemClicked begin" << index.data().toString();
- ui->ok_button->setDisabled(false);
-
- LabelingMethod method(index.data().toString());
-
- _sp_labeling_method = method.makeLabelingMethodSp();
+ qDebug() << "EditLabelMethods::ItemClicked begin" << index.data().toString();
+ ui->ok_button->setDisabled(false);
+
+ LabelingMethod method(index.data().toString());
+
+ _sp_labeling_method = method.makeLabelingMethodSp();
}
-LabelingMethodSp EditLabelMethods::getLabelingMethodSp() const {
- //_project_sp.get()->setLabelingMethodSp(_sp_labeling_method);
- return _sp_labeling_method;
+LabelingMethodSp
+EditLabelMethods::getLabelingMethodSp() const
+{
+ //_project_sp.get()->setLabelingMethodSp(_sp_labeling_method);
+ return _sp_labeling_method;
}
diff --git a/src/gui/edit_label_methods/editlabelmethods.h b/src/gui/edit_label_methods/editlabelmethods.h
index 09f1afcf0f9e5067cdda2c24512902f91f4006f8..5b05b7b325c514f396a79c1603452bc418be570d 100644
--- a/src/gui/edit_label_methods/editlabelmethods.h
+++ b/src/gui/edit_label_methods/editlabelmethods.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef EDITLABELMETHODS_H
#define EDITLABELMETHODS_H
@@ -32,30 +33,30 @@
class ProjectWindow;
-namespace Ui {
-class EditLabelMethodView;
+namespace Ui
+{
+ class EditLabelMethodView;
}
-class EditLabelMethods: public QDialog {
- Q_OBJECT
-public:
-
- explicit EditLabelMethods(ProjectWindow * parent = 0);
- ~EditLabelMethods();
-
- void setProjectSp(ProjectSp project_sp);
- LabelingMethodSp getLabelingMethodSp() const;
-
-public slots:
- void ItemClicked (QModelIndex index );
-
-private :
-
-private:
- Ui::EditLabelMethodView *ui;
- ProjectWindow * _project_window;
- ProjectSp _project_sp;
- QStandardItemModel * _p_label_method_str_li=nullptr;
- LabelingMethodSp _sp_labeling_method;
+class EditLabelMethods : public QDialog
+{
+ Q_OBJECT
+ public:
+ explicit EditLabelMethods(ProjectWindow *parent = 0);
+ ~EditLabelMethods();
+
+ void setProjectSp(ProjectSp project_sp);
+ LabelingMethodSp getLabelingMethodSp() const;
+
+ public slots:
+ void ItemClicked(QModelIndex index);
+
+ private:
+ private:
+ Ui::EditLabelMethodView *ui;
+ ProjectWindow *_project_window;
+ ProjectSp _project_sp;
+ QStandardItemModel *_p_label_method_str_li = nullptr;
+ LabelingMethodSp _sp_labeling_method;
};
#endif // EDITLABELMETHODS_H
diff --git a/src/gui/edit_modifications/editmodifications.cpp b/src/gui/edit_modifications/editmodifications.cpp
index ad688acd01474b94077f8d34873e214d62518b46..8cfacd24f4eb3261cd04aa8faa064d18d44f51ab 100644
--- a/src/gui/edit_modifications/editmodifications.cpp
+++ b/src/gui/edit_modifications/editmodifications.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "editmodifications.h"
#include "../project_view/projectwindow.h"
@@ -28,139 +29,176 @@
#include "ui_edit_modifications.h"
-EditModifications::EditModifications(ProjectWindow *parent):
- QMainWindow(parent),
- ui(new Ui::EditModificationView)
+EditModifications::EditModifications(ProjectWindow *parent)
+ : QMainWindow(parent), ui(new Ui::EditModificationView)
{
- ui->setupUi(this);
- _project_window = parent;
- _p_modification_str_li = new QStandardItemModel();
- ui->modification_list_view->setModel(_p_modification_str_li);
+ ui->setupUi(this);
+ _project_window = parent;
+ _p_modification_str_li = new QStandardItemModel();
+ ui->modification_list_view->setModel(_p_modification_str_li);
- _p_browse_modification_dialog = new ChooseModificationDialog(this);
+ _p_browse_modification_dialog = new ChooseModificationDialog(this);
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect(ui->modification_list_view,&QListView::clicked,this,&EditModifications::ItemClicked);
- connect(ui->modification_list_view,&QListView::doubleClicked,this,&EditModifications::ItemDoubleClicked);
-
- connect(_p_browse_modification_dialog, &ChooseModificationDialog::accepted, this,&EditModifications::doAcceptedBrowseDialog);
+ // Qt5 code
+ connect(ui->modification_list_view, &QListView::clicked, this,
+ &EditModifications::ItemClicked);
+ connect(ui->modification_list_view, &QListView::doubleClicked, this,
+ &EditModifications::ItemDoubleClicked);
+
+ connect(_p_browse_modification_dialog, &ChooseModificationDialog::accepted,
+ this, &EditModifications::doAcceptedBrowseDialog);
#else
- connect(ui->modification_list_view,SIGNAL(clicked(const QModelIndex)),this,SLOT(ItemClicked(QModelIndex)));
- connect(ui->modification_list_view,SIGNAL(doubleClicked(const QModelIndex)),this,SLOT(ItemDoubleClicked(QModelIndex)));
+ connect(ui->modification_list_view, SIGNAL(clicked(const QModelIndex)), this,
+ SLOT(ItemClicked(QModelIndex)));
+ connect(ui->modification_list_view, SIGNAL(doubleClicked(const QModelIndex)),
+ this, SLOT(ItemDoubleClicked(QModelIndex)));
- connect(_p_browse_modification_dialog, SIGNAL(accepted()), this,SLOT(doAcceptedBrowseDialog()));
+ connect(_p_browse_modification_dialog, SIGNAL(accepted()), this,
+ SLOT(doAcceptedBrowseDialog()));
#endif
}
-EditModifications::~EditModifications() {
- qDebug() << "EditModifications::~EditModifications";
-
- delete ui;
- //delete _project_window;
- delete _p_browse_modification_dialog;
- delete _p_modification_str_li;
- qDebug() << "EditModifications::~EditModifications end";
+EditModifications::~EditModifications()
+{
+ qDebug() << "EditModifications::~EditModifications";
+ delete ui;
+ // delete _project_window;
+ delete _p_browse_modification_dialog;
+ delete _p_modification_str_li;
+ qDebug() << "EditModifications::~EditModifications end";
}
-void EditModifications::setProjectSp(ProjectSp project_sp) {
-
- _project_sp = project_sp;
- ui->selected_modification_groupbox->setVisible(false);
- _p_modification_str_li->removeRows(0,_p_modification_str_li->rowCount());
+void
+EditModifications::setProjectSp(ProjectSp project_sp)
+{
- std::set<pappso::AaModificationP> mod_list = project_sp.get()->getPeptideStore().getModificationCollection();
- //_p_modification_str_li->insertRows(0, mod_list.size());
- for (pappso::AaModificationP modification :mod_list) {
- if (modification->isInternal()) {
+ _project_sp = project_sp;
+ ui->selected_modification_groupbox->setVisible(false);
+ _p_modification_str_li->removeRows(0, _p_modification_str_li->rowCount());
+
+ std::set<pappso::AaModificationP> mod_list =
+ project_sp.get()->getPeptideStore().getModificationCollection();
+ //_p_modification_str_li->insertRows(0, mod_list.size());
+ for(pappso::AaModificationP modification : mod_list)
+ {
+ if(modification->isInternal())
+ {
}
- else {
- QStandardItem *item;
- item = new QStandardItem(QString("[%1] %2").arg(modification->getAccession()).arg(modification->getName()));
- item->setEditable(false);
- _p_modification_str_li->appendRow(item);
- item->setData(QVariant(QString("%1").arg(modification->getAccession())),Qt::UserRole);
+ else
+ {
+ QStandardItem *item;
+ item = new QStandardItem(QString("[%1] %2")
+ .arg(modification->getAccession())
+ .arg(modification->getName()));
+ item->setEditable(false);
+ _p_modification_str_li->appendRow(item);
+ item->setData(
+ QVariant(QString("%1").arg(modification->getAccession())),
+ Qt::UserRole);
}
}
-
}
-
-void EditModifications::ItemDoubleClicked (QModelIndex index )
+void
+EditModifications::ItemDoubleClicked(QModelIndex index)
{
- qDebug() << "EditModifications::ItemClicked data=" << index.data().toString();
- qDebug() << "EditModifications::ItemClicked acc=" << _p_modification_str_li->data(index,Qt::UserRole).toString();
- QDesktopServices::openUrl (Utils::getOlsUrl(_p_modification_str_li->data(index,Qt::UserRole).toString())) ;
+ qDebug() << "EditModifications::ItemClicked data=" << index.data().toString();
+ qDebug() << "EditModifications::ItemClicked acc="
+ << _p_modification_str_li->data(index, Qt::UserRole).toString();
+ QDesktopServices::openUrl(Utils::getOlsUrl(
+ _p_modification_str_li->data(index, Qt::UserRole).toString()));
}
-void EditModifications::ItemClicked (QModelIndex index )
+void
+EditModifications::ItemClicked(QModelIndex index)
{
- qDebug() << "EditModifications::ItemClicked data=" << index.data().toString();
- qDebug() << "EditModifications::ItemClicked acc=" << _p_modification_str_li->data(index,Qt::UserRole).toString();
- qDebug() << "EditModifications::ItemClicked str=" << _p_modification_str_li->data(index,Qt::DisplayRole).toString();
- pappso::AaModificationP modification = pappso::AaModification::getInstance(index.data(Qt::UserRole).toString());
- setSelectedModification(modification);
- setReplaceModification(nullptr);
+ qDebug() << "EditModifications::ItemClicked data=" << index.data().toString();
+ qDebug() << "EditModifications::ItemClicked acc="
+ << _p_modification_str_li->data(index, Qt::UserRole).toString();
+ qDebug() << "EditModifications::ItemClicked str="
+ << _p_modification_str_li->data(index, Qt::DisplayRole).toString();
+ pappso::AaModificationP modification =
+ pappso::AaModification::getInstance(index.data(Qt::UserRole).toString());
+ setSelectedModification(modification);
+ setReplaceModification(nullptr);
}
-void EditModifications::setReplaceModification (pappso::AaModificationP modification)
+void
+EditModifications::setReplaceModification(pappso::AaModificationP modification)
{
- _replace_modification = modification;
- if (_replace_modification == nullptr) {
- ui->replace_accession_label->setText("");
- ui->replace_description_label->setText("");
- ui->replace_delta_label->setText("");
+ _replace_modification = modification;
+ if(_replace_modification == nullptr)
+ {
+ ui->replace_accession_label->setText("");
+ ui->replace_description_label->setText("");
+ ui->replace_delta_label->setText("");
}
- else {
- ui->replace_accession_label->setText(_replace_modification->getAccession());
- ui->replace_description_label->setText(_replace_modification->getName());
- ui->replace_delta_label->setText(QString::number(_replace_modification->getMass(), 'f', 10));
+ else
+ {
+ ui->replace_accession_label->setText(
+ _replace_modification->getAccession());
+ ui->replace_description_label->setText(_replace_modification->getName());
+ ui->replace_delta_label->setText(
+ QString::number(_replace_modification->getMass(), 'f', 10));
}
-
}
-void EditModifications::setSelectedModification (pappso::AaModificationP modification)
+void
+EditModifications::setSelectedModification(pappso::AaModificationP modification)
{
- qDebug() << "EditModifications::setSelectedModification acc=" << modification->getAccession();
- _selected_modification = modification;
- ui->selected_modification_groupbox->setVisible(true);
- ui->accession_label->setText(modification->getAccession());
- ui->description_label->setText(modification->getName());
- ui->delta_label->setText(QString::number(modification->getMass(), 'f', 10));
-
+ qDebug() << "EditModifications::setSelectedModification acc="
+ << modification->getAccession();
+ _selected_modification = modification;
+ ui->selected_modification_groupbox->setVisible(true);
+ ui->accession_label->setText(modification->getAccession());
+ ui->description_label->setText(modification->getName());
+ ui->delta_label->setText(QString::number(modification->getMass(), 'f', 10));
}
-void EditModifications::doActionBrowse() {
- qDebug() << "EditModifications::doActionBrowse begin";
- if (_selected_modification != nullptr) {
- pappso::MassRange massrange(_selected_modification->getMass(), pappso::Precision::getDaltonInstance(0.05));
- _p_browse_modification_dialog->setMassRange(massrange);
- _p_browse_modification_dialog->show();
- _p_browse_modification_dialog->raise();
- _p_browse_modification_dialog->activateWindow();
+void
+EditModifications::doActionBrowse()
+{
+ qDebug() << "EditModifications::doActionBrowse begin";
+ if(_selected_modification != nullptr)
+ {
+ pappso::MassRange massrange(_selected_modification->getMass(),
+ pappso::Precision::getDaltonInstance(0.05));
+ _p_browse_modification_dialog->setMassRange(massrange);
+ _p_browse_modification_dialog->show();
+ _p_browse_modification_dialog->raise();
+ _p_browse_modification_dialog->activateWindow();
}
- qDebug() << "EditModifications::doActionBrowse end";
+ qDebug() << "EditModifications::doActionBrowse end";
}
-void EditModifications::doActionReplace() {
- qDebug() << "EditModifications::doActionReplace begin";
- if (_selected_modification != nullptr) {
- if (_replace_modification != nullptr) {
- _project_sp.get()->getPeptideStore().replaceModification(_selected_modification, _replace_modification);
-
- _project_window->doAutomaticFilterParametersChanged(_project_sp.get()->getAutomaticFilterParameters());
- setProjectSp(_project_sp);
+void
+EditModifications::doActionReplace()
+{
+ qDebug() << "EditModifications::doActionReplace begin";
+ if(_selected_modification != nullptr)
+ {
+ if(_replace_modification != nullptr)
+ {
+ _project_sp.get()->getPeptideStore().replaceModification(
+ _selected_modification, _replace_modification);
+
+ _project_window->doAutomaticFilterParametersChanged(
+ _project_sp.get()->getAutomaticFilterParameters());
+ setProjectSp(_project_sp);
}
}
- qDebug() << "EditModifications::doActionReplace end";
+ qDebug() << "EditModifications::doActionReplace end";
}
-void EditModifications::doAcceptedBrowseDialog() {
- setReplaceModification(_p_browse_modification_dialog->getSelectedModification());
-
+void
+EditModifications::doAcceptedBrowseDialog()
+{
+ setReplaceModification(
+ _p_browse_modification_dialog->getSelectedModification());
}
diff --git a/src/gui/edit_modifications/editmodifications.h b/src/gui/edit_modifications/editmodifications.h
index 04a6dce6c0db1fb2486581eb89bc3660e3070405..36f0b1416084fd06e2dccb8ff6e9f6bf422ae184 100644
--- a/src/gui/edit_modifications/editmodifications.h
+++ b/src/gui/edit_modifications/editmodifications.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef EDITMODIFICATIONS_H
#define EDITMODIFICATIONS_H
@@ -32,38 +33,40 @@
class ProjectWindow;
-//http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
-namespace Ui {
-class EditModificationView;
+// http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
+namespace Ui
+{
+ class EditModificationView;
}
-class EditModifications: public QMainWindow {
- Q_OBJECT
-public:
+class EditModifications : public QMainWindow
+{
+ Q_OBJECT
+ public:
+ explicit EditModifications(ProjectWindow *parent = 0);
+ ~EditModifications();
- explicit EditModifications(ProjectWindow * parent = 0);
- ~EditModifications();
+ void setProjectSp(ProjectSp project_sp);
- void setProjectSp(ProjectSp project_sp);
+ public slots:
+ void ItemClicked(QModelIndex index);
+ void ItemDoubleClicked(QModelIndex index);
+ private slots:
+ void doAcceptedBrowseDialog();
+ void doActionReplace();
+ void doActionBrowse();
-public slots:
- void ItemClicked (QModelIndex index );
- void ItemDoubleClicked (QModelIndex index );
-private slots:
- void doAcceptedBrowseDialog();
- void doActionReplace();
- void doActionBrowse();
-private :
- void setSelectedModification (pappso::AaModificationP modification);
- void setReplaceModification (pappso::AaModificationP modification);
+ private:
+ void setSelectedModification(pappso::AaModificationP modification);
+ void setReplaceModification(pappso::AaModificationP modification);
-private:
- Ui::EditModificationView *ui;
- ProjectWindow * _project_window;
- ProjectSp _project_sp;
- ChooseModificationDialog * _p_browse_modification_dialog;
- QStandardItemModel * _p_modification_str_li=nullptr;
- pappso::AaModificationP _selected_modification;
- pappso::AaModificationP _replace_modification;
+ private:
+ Ui::EditModificationView *ui;
+ ProjectWindow *_project_window;
+ ProjectSp _project_sp;
+ ChooseModificationDialog *_p_browse_modification_dialog;
+ QStandardItemModel *_p_modification_str_li = nullptr;
+ pappso::AaModificationP _selected_modification;
+ pappso::AaModificationP _replace_modification;
};
#endif // EDITMODIFICATIONS_H
diff --git a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
index 8a94d4a5f803a3289cc155a98885f221e4ed8d2b..0f08ef9f348d833061c47b6a5ff9192c66af5bac 100644
--- a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
+++ b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "edittandempresetdialog.h"
#include <QDebug>
@@ -39,1006 +40,1280 @@
#include <QMessageBox>
-EditTandemPresetDialog::EditTandemPresetDialog(QWidget * parent):
- QDialog(parent),
- ui(new Ui::EditTandemPresetView)
+EditTandemPresetDialog::EditTandemPresetDialog(QWidget *parent)
+ : QDialog(parent), ui(new Ui::EditTandemPresetView)
{
- qDebug() << "EditTandemPresetDialog::EditTandemPresetDialog begin";
- ui->setupUi(this);
- this->setModal(true);
+ qDebug() << "EditTandemPresetDialog::EditTandemPresetDialog begin";
+ ui->setupUi(this);
+ this->setModal(true);
- ui->splitter->setStretchFactor(0, 1);
+ ui->splitter->setStretchFactor(0, 1);
#if QT_VERSION >= 0x050000
- // Qt5 code
+ // Qt5 code
#else
-// Qt4 code
+ // Qt4 code
#endif
- qDebug() << "EditTandemPresetDialog::EditTandemPresetDialog end";
+ qDebug() << "EditTandemPresetDialog::EditTandemPresetDialog end";
}
EditTandemPresetDialog::~EditTandemPresetDialog()
{
- delete ui;
- if (_p_tandem_preset_file != nullptr) {
- delete _p_tandem_preset_file;
+ delete ui;
+ if(_p_tandem_preset_file != nullptr)
+ {
+ delete _p_tandem_preset_file;
}
}
-void EditTandemPresetDialog::setTandemParametersFile(const TandemParametersFile & tandem_preset_file) {
+void
+EditTandemPresetDialog::setTandemParametersFile(
+ const TandemParametersFile &tandem_preset_file)
+{
- if (tandem_preset_file.exists()) {
- _p_tandem_preset_file = new TandemParametersFile( tandem_preset_file);
- _preset_directory = _p_tandem_preset_file->getAbsoluteDir().absolutePath();
- _tandem_params = _p_tandem_preset_file->getTandemParameters();
- } else {
- _p_tandem_preset_file = new TandemParametersFile(":/tandem/resources/model/QExactive_analysis_FDR_nosemi.xml");
- _tandem_params = _p_tandem_preset_file->getTandemParameters();
- QSettings settings;
- _preset_directory = settings.value("path/tandemrun_preset_directory", "").toString();
- _p_tandem_preset_file->setDirectory(QDir(_preset_directory));
+ if(tandem_preset_file.exists())
+ {
+ _p_tandem_preset_file = new TandemParametersFile(tandem_preset_file);
+ _preset_directory =
+ _p_tandem_preset_file->getAbsoluteDir().absolutePath();
+ _tandem_params = _p_tandem_preset_file->getTandemParameters();
+ }
+ else
+ {
+ _p_tandem_preset_file = new TandemParametersFile(
+ ":/tandem/resources/model/QExactive_analysis_FDR_nosemi.xml");
+ _tandem_params = _p_tandem_preset_file->getTandemParameters();
+ QSettings settings;
+ _preset_directory =
+ settings.value("path/tandemrun_preset_directory", "").toString();
+ _p_tandem_preset_file->setDirectory(QDir(_preset_directory));
}
- fillPresetComboBox();
- populate();
+ fillPresetComboBox();
+ populate();
}
-void EditTandemPresetDialog::doCopy() {
- ui->method_name_line_edit->setText("untitled");
- readUi();
- if (_p_tandem_preset_file == nullptr) {
+void
+EditTandemPresetDialog::doCopy()
+{
+ ui->method_name_line_edit->setText("untitled");
+ readUi();
+ if(_p_tandem_preset_file == nullptr)
+ {
- throw pappso::PappsoException(QObject::tr("_p_tandem_preset_file == nullptr"));
+ throw pappso::PappsoException(
+ QObject::tr("_p_tandem_preset_file == nullptr"));
}
- else {
- delete _p_tandem_preset_file;
+ else
+ {
+ delete _p_tandem_preset_file;
}
- _p_tandem_preset_file = new TandemParametersFile(QString("%1/untitled.xml").arg(_preset_directory));
+ _p_tandem_preset_file =
+ new TandemParametersFile(QString("%1/untitled.xml").arg(_preset_directory));
}
-void EditTandemPresetDialog::doSelectDir() {
- try {
+void
+EditTandemPresetDialog::doSelectDir()
+{
+ try
+ {
- QString directory = QFileDialog::getExistingDirectory(this,tr("Choose preset directory"),_preset_directory );
+ QString directory = QFileDialog::getExistingDirectory(
+ this, tr("Choose preset directory"), _preset_directory);
- QFileInfo my_dir(directory);
- if (!directory.isEmpty() && ! directory.isNull()) {
- if (!my_dir.isWritable()) {
- throw pappso::PappsoException(QObject::tr("this directory is not writable, check permissions (%1)").arg(my_dir.absoluteFilePath()));
+ QFileInfo my_dir(directory);
+ if(!directory.isEmpty() && !directory.isNull())
+ {
+ if(!my_dir.isWritable())
+ {
+ throw pappso::PappsoException(
+ QObject::tr(
+ "this directory is not writable, check permissions (%1)")
+ .arg(my_dir.absoluteFilePath()));
}
- _preset_directory = directory;
- fillPresetComboBox();
+ _preset_directory = directory;
+ fillPresetComboBox();
}
-
}
- catch (pappso::PappsoException & error) {
- QMessageBox::warning(this,tr("Error :"), tr("Error choosing preset directory : %1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ QMessageBox::warning(
+ this, tr("Error :"),
+ tr("Error choosing preset directory : %1").arg(error.qwhat()));
}
}
-void EditTandemPresetDialog::doSave() {
- readUi();
- if (_p_tandem_preset_file == nullptr) {
- throw pappso::PappsoException(QObject::tr("_p_tandem_preset_file == nullptr"));
+void
+EditTandemPresetDialog::doSave()
+{
+ readUi();
+ if(_p_tandem_preset_file == nullptr)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("_p_tandem_preset_file == nullptr"));
}
- _p_tandem_preset_file->setDirectory(QDir(_preset_directory));
- _p_tandem_preset_file->setTandemParameters(_tandem_params);
- fillPresetComboBox();
- populate();
+ _p_tandem_preset_file->setDirectory(QDir(_preset_directory));
+ _p_tandem_preset_file->setTandemParameters(_tandem_params);
+ fillPresetComboBox();
+ populate();
}
-void EditTandemPresetDialog::doLoad() {
- int index = ui->preset_combo_box->currentIndex();
- if ( index != -1 ) { // -1 for not found
- TandemParametersFile * p_tandem_preset_file = new TandemParametersFile(
- ui->preset_combo_box->itemData(index).value<QString>());
- if (p_tandem_preset_file->isTandemPresetFile()) {
- if (_p_tandem_preset_file == nullptr) {
- throw pappso::PappsoException(QObject::tr("_p_tandem_preset_file == nullptr"));
+void
+EditTandemPresetDialog::doLoad()
+{
+ int index = ui->preset_combo_box->currentIndex();
+ if(index != -1)
+ { // -1 for not found
+ TandemParametersFile *p_tandem_preset_file = new TandemParametersFile(
+ ui->preset_combo_box->itemData(index).value<QString>());
+ if(p_tandem_preset_file->isTandemPresetFile())
+ {
+ if(_p_tandem_preset_file == nullptr)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("_p_tandem_preset_file == nullptr"));
}
- else {
- delete _p_tandem_preset_file;
+ else
+ {
+ delete _p_tandem_preset_file;
}
- _p_tandem_preset_file = p_tandem_preset_file;
- _tandem_params = _p_tandem_preset_file->getTandemParameters();
- populate();
+ _p_tandem_preset_file = p_tandem_preset_file;
+ _tandem_params = _p_tandem_preset_file->getTandemParameters();
+ populate();
}
- else {
- QMessageBox::warning(this,tr("Error :"), tr("%1 is not an X!Tandem parameter file").arg(p_tandem_preset_file->getAbsoluteFilePath()));
+ else
+ {
+ QMessageBox::warning(
+ this, tr("Error :"),
+ tr("%1 is not an X!Tandem parameter file")
+ .arg(p_tandem_preset_file->getAbsoluteFilePath()));
}
}
}
-const TandemParametersFile & EditTandemPresetDialog::getTandemParametersFile() const {
- if (_p_tandem_preset_file == nullptr) {
- throw pappso::PappsoException(QObject::tr("_p_tandem_preset_file == nullptr"));
+const TandemParametersFile &
+EditTandemPresetDialog::getTandemParametersFile() const
+{
+ if(_p_tandem_preset_file == nullptr)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("_p_tandem_preset_file == nullptr"));
}
- if (!_p_tandem_preset_file->exists()) {
- throw pappso::PappsoException(QObject::tr("preset file %1 does not exists").arg(_p_tandem_preset_file->getAbsoluteFilePath()));
+ if(!_p_tandem_preset_file->exists())
+ {
+ throw pappso::PappsoException(
+ QObject::tr("preset file %1 does not exists")
+ .arg(_p_tandem_preset_file->getAbsoluteFilePath()));
}
- return *_p_tandem_preset_file;
+ return *_p_tandem_preset_file;
}
-void EditTandemPresetDialog::fillPresetComboBox() {
- ui->preset_combo_box->clear();
- QString default_preset_name = _tandem_params.getMethodName();
+void
+EditTandemPresetDialog::fillPresetComboBox()
+{
+ ui->preset_combo_box->clear();
+ QString default_preset_name = _tandem_params.getMethodName();
- QDir preset_dir(_preset_directory);
- QStringList filters;
- filters << "*.xml";
- preset_dir.setNameFilters(filters);
- for (QFileInfo file_info: preset_dir.entryInfoList() ) {
- ui->preset_combo_box->addItem(file_info.baseName(), QVariant(file_info.absoluteFilePath()));
+ QDir preset_dir(_preset_directory);
+ QStringList filters;
+ filters << "*.xml";
+ preset_dir.setNameFilters(filters);
+ for(QFileInfo file_info : preset_dir.entryInfoList())
+ {
+ ui->preset_combo_box->addItem(file_info.baseName(),
+ QVariant(file_info.absoluteFilePath()));
}
- int index = ui->preset_combo_box->findText(default_preset_name);
- if ( index != -1 ) { // -1 for not found
- ui->preset_combo_box->setCurrentIndex(index);
+ int index = ui->preset_combo_box->findText(default_preset_name);
+ if(index != -1)
+ { // -1 for not found
+ ui->preset_combo_box->setCurrentIndex(index);
}
-
}
-void EditTandemPresetDialog::doEdit(QString value) {
- QObject *senderObj = sender();
- QString senderObjName = senderObj->objectName();
- qDebug() << "EditTandemPresetDialog::doEdit begin " << senderObjName << " " << value;
- qDebug() << "EditTandemPresetDialog::doEdit end " << senderObjName;
+void
+EditTandemPresetDialog::doEdit(QString value)
+{
+ QObject *senderObj = sender();
+ QString senderObjName = senderObj->objectName();
+ qDebug() << "EditTandemPresetDialog::doEdit begin " << senderObjName << " "
+ << value;
+ qDebug() << "EditTandemPresetDialog::doEdit end " << senderObjName;
}
-void EditTandemPresetDialog::doHelp() {
- QObject *senderObj = sender();
- QString senderObjName = senderObj->objectName();
- qDebug() << "EditTandemPresetDialog::doHelp begin " << senderObjName;
- QFile html_doc;
- if(senderObjName == "spmmeu_push_button")
+void
+EditTandemPresetDialog::doHelp()
+{
+ QObject *senderObj = sender();
+ QString senderObjName = senderObj->objectName();
+ qDebug() << "EditTandemPresetDialog::doHelp begin " << senderObjName;
+ QFile html_doc;
+ if(senderObjName == "spmmeu_push_button")
{
- //spmmeu.html
- html_doc.setFileName(":/tandem/resources/html_doc/spmmeu.html");
+ // spmmeu.html
+ html_doc.setFileName(":/tandem/resources/html_doc/spmmeu.html");
}
- if(senderObjName == "smpc_push_button")
+ if(senderObjName == "smpc_push_button")
{
- //spmmeu.html
- html_doc.setFileName(":/tandem/resources/html_doc/smpc.html");
+ // spmmeu.html
+ html_doc.setFileName(":/tandem/resources/html_doc/smpc.html");
}
- if(senderObjName == "spmmem_push_button")
+ if(senderObjName == "spmmem_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/spmmem.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/spmmem.html");
}
- if(senderObjName == "spmmep_push_button")
+ if(senderObjName == "spmmep_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/spmmep.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/spmmep.html");
}
- if(senderObjName == "spmmie_push_button")
+ if(senderObjName == "spmmie_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/spmmie.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/spmmie.html");
}
- if(senderObjName == "sfmt_push_button")
+ if(senderObjName == "sfmt_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/sfmt.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/sfmt.html");
}
- if(senderObjName == "sfmmeu_push_button")
+ if(senderObjName == "sfmmeu_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/sfmmeu.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/sfmmeu.html");
}
- if(senderObjName == "sfmme_push_button")
+ if(senderObjName == "sfmme_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/sfmme.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/sfmme.html");
}
- if(senderObjName == "sunlw_push_button")
+ if(senderObjName == "sunlw_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/sunlw.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/sunlw.html");
}
- if(senderObjName == "snlm_push_button")
+ if(senderObjName == "snlm_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/snlm.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/snlm.html");
}
- if(senderObjName == "snlw_push_button")
+ if(senderObjName == "snlw_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/snlw.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/snlw.html");
}
- if(senderObjName == "suns_push_button")
+ if(senderObjName == "suns_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/suns.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/suns.html");
}
- if(senderObjName == "sdr_push_button")
+ if(senderObjName == "sdr_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/sdr.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/sdr.html");
}
- if(senderObjName == "stp_push_button")
+ if(senderObjName == "stp_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/stp.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/stp.html");
}
- if(senderObjName == "smp_push_button")
+ if(senderObjName == "smp_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/smp.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/smp.html");
}
- if(senderObjName == "smfmz_push_button")
+ if(senderObjName == "smfmz_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/smfmz.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/smfmz.html");
}
- if(senderObjName == "smpmh_push_button")
+ if(senderObjName == "smpmh_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/smpmh.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/smpmh.html");
}
- if(senderObjName == "spsbs_push_button")
+ if(senderObjName == "spsbs_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/spsbs.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/spsbs.html");
}
- if(senderObjName == "suca_push_button")
+ if(senderObjName == "suca_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/suca.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/suca.html");
}
- if(senderObjName == "st_push_button")
+ if(senderObjName == "st_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/st.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/st.html");
}
- if(senderObjName == "pcs_push_button")
+ if(senderObjName == "pcs_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/pcs.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/pcs.html");
}
- if(senderObjName == "pcsemi_push_button")
+ if(senderObjName == "pcsemi_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/pcsemi.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/pcsemi.html");
}
- if(senderObjName == "pcctmc_push_button")
+ if(senderObjName == "pcctmc_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/pcctmc.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/pcctmc.html");
}
- if(senderObjName == "pcntmc_push_button")
+ if(senderObjName == "pcntmc_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/pcntmc.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/pcntmc.html");
}
- if(senderObjName == "pctrmm_push_button")
+ if(senderObjName == "pctrmm_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/pctrmm.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/pctrmm.html");
}
- if(senderObjName == "pntrmm_push_button")
+ if(senderObjName == "pntrmm_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/pntrmm.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/pntrmm.html");
}
- if(senderObjName == "pqa_push_button")
+ if(senderObjName == "pqa_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/pqa.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/pqa.html");
}
- if(senderObjName == "pqp_push_button")
+ if(senderObjName == "pqp_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/pqp.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/pqp.html");
}
- if(senderObjName == "pstpb_push_button")
+ if(senderObjName == "pstpb_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/pstpb.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/pstpb.html");
}
- if(senderObjName == "pmrmf_push_button")
+ if(senderObjName == "pmrmf_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/pmrmf.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/pmrmf.html");
}
- if ((senderObjName == "rmm_push_button") || (senderObjName == "rmm1_push_button") || (senderObjName == "rmm2_push_button"))
+ if((senderObjName == "rmm_push_button") ||
+ (senderObjName == "rmm1_push_button") ||
+ (senderObjName == "rmm2_push_button"))
{
- html_doc.setFileName(":/tandem/resources/html_doc/rmm.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/rmm.html");
}
- if ((senderObjName == "rpmm_push_button") || (senderObjName == "rpmm1_push_button") || (senderObjName == "rpmm2_push_button"))
+ if((senderObjName == "rpmm_push_button") ||
+ (senderObjName == "rpmm1_push_button") ||
+ (senderObjName == "rpmm2_push_button"))
{
- html_doc.setFileName(":/tandem/resources/html_doc/rpmm.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/rpmm.html");
}
- if ((senderObjName == "rpmmotif_push_button") || (senderObjName == "rpmmotif1_push_button") || (senderObjName == "rpmmotif2_push_button"))
+ if((senderObjName == "rpmmotif_push_button") ||
+ (senderObjName == "rpmmotif1_push_button") ||
+ (senderObjName == "rpmmotif2_push_button"))
{
- html_doc.setFileName(":/tandem/resources/html_doc/rpmmotif.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/rpmmotif.html");
}
- if(senderObjName == "smic_push_button")
+ if(senderObjName == "smic_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/smic.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/smic.html");
}
- if(senderObjName == "smmcs_push_button")
+ if(senderObjName == "smmcs_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/smmcs.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/smmcs.html");
}
- if(senderObjName == "scp_push_button")
+ if(senderObjName == "scp_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/scp.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/scp.html");
}
- if(senderObjName == "sir_push_button")
+ if(senderObjName == "sir_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/sir.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/sir.html");
}
- if(senderObjName == "syi_push_button")
+ if(senderObjName == "syi_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/syi.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/syi.html");
}
- if(senderObjName == "sbi_push_button")
+ if(senderObjName == "sbi_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/sbi.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/sbi.html");
}
- if(senderObjName == "sci_push_button")
+ if(senderObjName == "sci_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/sci.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/sci.html");
}
- if(senderObjName == "szi_push_button")
+ if(senderObjName == "szi_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/szi.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/szi.html");
}
- if(senderObjName == "sai_push_button")
+ if(senderObjName == "sai_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/sai.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/sai.html");
}
- if(senderObjName == "sxi_push_button")
+ if(senderObjName == "sxi_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/sxi.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/sxi.html");
}
- if(senderObjName == "refine_push_button")
+ if(senderObjName == "refine_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/refine.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/refine.html");
}
- if(senderObjName == "rmvev_push_button")
+ if(senderObjName == "rmvev_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/rmvev.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/rmvev.html");
}
- if(senderObjName == "refpntm_push_button")
+ if(senderObjName == "refpntm_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/refpntm.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/refpntm.html");
}
- if(senderObjName == "refpctm_push_button")
+ if(senderObjName == "refpctm_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/refpctm.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/refpctm.html");
}
- if ((senderObjName == "refmm_push_button")|| (senderObjName == "refmm1_push_button")|| (senderObjName == "refmm2_push_button"))
+ if((senderObjName == "refmm_push_button") ||
+ (senderObjName == "refmm1_push_button") ||
+ (senderObjName == "refmm2_push_button"))
{
- html_doc.setFileName(":/tandem/resources/html_doc/refmm.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/refmm.html");
}
- if ((senderObjName == "refpmm_push_button")|| (senderObjName == "refpmm1_push_button")|| (senderObjName == "refpmm2_push_button"))
+ if((senderObjName == "refpmm_push_button") ||
+ (senderObjName == "refpmm1_push_button") ||
+ (senderObjName == "refpmm2_push_button"))
{
- html_doc.setFileName(":/tandem/resources/html_doc/refpmm.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/refpmm.html");
}
- if ((senderObjName == "refpmmotif_push_button")|| (senderObjName == "refpmmotif1_push_button")|| (senderObjName == "refpmmotif2_push_button"))
+ if((senderObjName == "refpmmotif_push_button") ||
+ (senderObjName == "refpmmotif1_push_button") ||
+ (senderObjName == "refpmmotif2_push_button"))
{
- html_doc.setFileName(":/tandem/resources/html_doc/refpmmotif.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/refpmmotif.html");
}
- if(senderObjName == "rupmffr_push_button")
+ if(senderObjName == "rupmffr_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/rupmffr.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/rupmffr.html");
}
- if(senderObjName == "rcsemi_push_button")
+ if(senderObjName == "rcsemi_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/rcsemi.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/rcsemi.html");
}
- if(senderObjName == "ruc_push_button")
+ if(senderObjName == "ruc_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/ruc.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/ruc.html");
}
- if(senderObjName == "rss_push_button")
+ if(senderObjName == "rss_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/rss.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/rss.html");
}
- if(senderObjName == "rpm_push_button")
+ if(senderObjName == "rpm_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/rpm.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/rpm.html");
}
- if ((senderObjName == "omvev_push_button") || (senderObjName == "omvpev_push_button"))
+ if((senderObjName == "omvev_push_button") ||
+ (senderObjName == "omvpev_push_button"))
{
- html_doc.setFileName(":/tandem/resources/html_doc/omvev.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/omvev.html");
}
- if (senderObjName == "oresu_push_button")
+ if(senderObjName == "oresu_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/oresu.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/oresu.html");
}
- if (senderObjName == "osrb_push_button")
+ if(senderObjName == "osrb_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/osrb.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/osrb.html");
}
- if (senderObjName == "oprot_push_button")
+ if(senderObjName == "oprot_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/oprot.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/oprot.html");
}
- if (senderObjName == "oseq_push_button")
+ if(senderObjName == "oseq_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/oseq.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/oseq.html");
}
- if (senderObjName == "oosc_push_button")
+ if(senderObjName == "oosc_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/oosc.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/oosc.html");
}
- if (senderObjName == "ospec_push_button")
+ if(senderObjName == "ospec_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/ospec.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/ospec.html");
}
- if (senderObjName == "opara_push_button")
+ if(senderObjName == "opara_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/opara.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/opara.html");
}
- if (senderObjName == "ohist_push_button")
+ if(senderObjName == "ohist_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/ohist.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/ohist.html");
}
- if (senderObjName == "ohcw_push_button")
+ if(senderObjName == "ohcw_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/ohcw.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/ohcw.html");
}
- if (senderObjName == "oph_push_button")
+ if(senderObjName == "oph_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/oph.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/oph.html");
}
- if (senderObjName == "oxp_push_button")
+ if(senderObjName == "oxp_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/oxp.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/oxp.html");
}
- if (senderObjName == "mzid_push_button")
+ if(senderObjName == "mzid_push_button")
{
- html_doc.setFileName(":/tandem/resources/html_doc/mzid.html");
+ html_doc.setFileName(":/tandem/resources/html_doc/mzid.html");
}
- if (html_doc.open(QFile::ReadOnly | QFile::Text)) {
- QTextStream in(&html_doc);
- ui->doc_plain_text_edit->setHtml(in.readAll());
- qDebug() << "EditTandemPresetDialog::doHelp doc " << in.readAll();
+ if(html_doc.open(QFile::ReadOnly | QFile::Text))
+ {
+ QTextStream in(&html_doc);
+ ui->doc_plain_text_edit->setHtml(in.readAll());
+ qDebug() << "EditTandemPresetDialog::doHelp doc " << in.readAll();
}
- else {
- qDebug() << "EditTandemPresetDialog::doHelp doc not found";
+ else
+ {
+ qDebug() << "EditTandemPresetDialog::doHelp doc not found";
}
- qDebug() << "EditTandemPresetDialog::doHelp end " << senderObjName;
+ qDebug() << "EditTandemPresetDialog::doHelp end " << senderObjName;
}
-void EditTandemPresetDialog::readUi() {
- try {
- _tandem_params.setMethodName(ui->method_name_line_edit->text());
- _tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass error units", "Daltons");
- if (ui->spmmeu_ppm_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass error units", "ppm");
+void
+EditTandemPresetDialog::readUi()
+{
+ try
+ {
+ _tandem_params.setMethodName(ui->method_name_line_edit->text());
+ _tandem_params.setParamLabelValue(
+ "spectrum, parent monoisotopic mass error units", "Daltons");
+ if(ui->spmmeu_ppm_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue(
+ "spectrum, parent monoisotopic mass error units", "ppm");
}
- _tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass error minus", ui->parent_ion_lower_window_edit->text());
+ _tandem_params.setParamLabelValue(
+ "spectrum, parent monoisotopic mass error minus",
+ ui->parent_ion_lower_window_edit->text());
- _tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass error plus", ui->parent_ion_upper_window_edit->text());
+ _tandem_params.setParamLabelValue(
+ "spectrum, parent monoisotopic mass error plus",
+ ui->parent_ion_upper_window_edit->text());
- _tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass isotope error", "no");
- if (ui->spmmie_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass isotope error", "yes");
+ _tandem_params.setParamLabelValue(
+ "spectrum, parent monoisotopic mass isotope error", "no");
+ if(ui->spmmie_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue(
+ "spectrum, parent monoisotopic mass isotope error", "yes");
}
- _tandem_params.setParamLabelValue("spectrum, maximum parent charge", ui->smpc_edit->text());
+ _tandem_params.setParamLabelValue("spectrum, maximum parent charge",
+ ui->smpc_edit->text());
- _tandem_params.setParamLabelValue("spectrum, fragment mass type", ui->sfmt_combo_box->currentText());
+ _tandem_params.setParamLabelValue("spectrum, fragment mass type",
+ ui->sfmt_combo_box->currentText());
- _tandem_params.setParamLabelValue("spectrum, fragment monoisotopic mass error units", "Daltons");
- if (ui->sfmmeu_ppm_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("spectrum, fragment monoisotopic mass error units", "ppm");
+ _tandem_params.setParamLabelValue(
+ "spectrum, fragment monoisotopic mass error units", "Daltons");
+ if(ui->sfmmeu_ppm_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue(
+ "spectrum, fragment monoisotopic mass error units", "ppm");
}
- _tandem_params.setParamLabelValue("spectrum, fragment monoisotopic mass error", ui->sfmme_edit->text());
- _tandem_params.setParamLabelValue("spectrum, use neutral loss window", "no");
- if (ui->sunlw_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("spectrum, use neutral loss window", "yes");
+ _tandem_params.setParamLabelValue(
+ "spectrum, fragment monoisotopic mass error", ui->sfmme_edit->text());
+ _tandem_params.setParamLabelValue("spectrum, use neutral loss window",
+ "no");
+ if(ui->sunlw_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("spectrum, use neutral loss window",
+ "yes");
}
- _tandem_params.setParamLabelValue("spectrum, neutral loss mass", ui->snlm_edit->text());
- _tandem_params.setParamLabelValue("spectrum, neutral loss window", ui->snlw_edit->text());
- _tandem_params.setParamLabelValue("spectrum, use noise suppression", "no");
- if (ui->suns_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("spectrum, use noise suppression", "yes");
+ _tandem_params.setParamLabelValue("spectrum, neutral loss mass",
+ ui->snlm_edit->text());
+ _tandem_params.setParamLabelValue("spectrum, neutral loss window",
+ ui->snlw_edit->text());
+ _tandem_params.setParamLabelValue("spectrum, use noise suppression",
+ "no");
+ if(ui->suns_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("spectrum, use noise suppression",
+ "yes");
}
- _tandem_params.setParamLabelValue("spectrum, dynamic range", ui->sdr_edit->text());
- _tandem_params.setParamLabelValue("spectrum, total peaks", ui->stp_edit->text());
- _tandem_params.setParamLabelValue("spectrum, minimum peaks", ui->smp_edit->text());
- _tandem_params.setParamLabelValue("spectrum, minimum fragment mz", ui->smfmz_edit->text());
- _tandem_params.setParamLabelValue("spectrum, minimum parent m+h", ui->smpmh_edit->text());
- _tandem_params.setParamLabelValue("spectrum, sequence batch size", ui->spsbs_edit->text());
- _tandem_params.setParamLabelValue("spectrum, use contrast angle", "no");
- if (ui->suca_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("spectrum, use contrast angle", "yes");
+ _tandem_params.setParamLabelValue("spectrum, dynamic range",
+ ui->sdr_edit->text());
+ _tandem_params.setParamLabelValue("spectrum, total peaks",
+ ui->stp_edit->text());
+ _tandem_params.setParamLabelValue("spectrum, minimum peaks",
+ ui->smp_edit->text());
+ _tandem_params.setParamLabelValue("spectrum, minimum fragment mz",
+ ui->smfmz_edit->text());
+ _tandem_params.setParamLabelValue("spectrum, minimum parent m+h",
+ ui->smpmh_edit->text());
+ _tandem_params.setParamLabelValue("spectrum, sequence batch size",
+ ui->spsbs_edit->text());
+ _tandem_params.setParamLabelValue("spectrum, use contrast angle", "no");
+ if(ui->suca_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("spectrum, use contrast angle",
+ "yes");
}
- _tandem_params.setParamLabelValue("spectrum, threads", ui->st_edit->text());
+ _tandem_params.setParamLabelValue("spectrum, threads",
+ ui->st_edit->text());
- _tandem_params.setParamLabelValue("protein, cleavage site", ui->pcs_edit->text());
- _tandem_params.setParamLabelValue("protein, cleavage semi", "no");
- if (ui->pcsemi_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("protein, cleavage semi", "yes");
+ _tandem_params.setParamLabelValue("protein, cleavage site",
+ ui->pcs_edit->text());
+ _tandem_params.setParamLabelValue("protein, cleavage semi", "no");
+ if(ui->pcsemi_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("protein, cleavage semi", "yes");
}
- _tandem_params.setParamLabelValue("protein, cleavage C-terminal mass change", ui->pcctmc_edit->text());
- _tandem_params.setParamLabelValue("protein, cleavage N-terminal mass change", ui->pcntmc_edit->text());
- _tandem_params.setParamLabelValue("protein, quick acetyl", "no");
- if (ui->pqa_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("protein, quick acetyl", "yes");
+ _tandem_params.setParamLabelValue(
+ "protein, cleavage C-terminal mass change", ui->pcctmc_edit->text());
+ _tandem_params.setParamLabelValue(
+ "protein, cleavage N-terminal mass change", ui->pcntmc_edit->text());
+ _tandem_params.setParamLabelValue("protein, quick acetyl", "no");
+ if(ui->pqa_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("protein, quick acetyl", "yes");
}
- _tandem_params.setParamLabelValue("protein, quick pyrolidone", "no");
- if (ui->pqp_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("protein, quick pyrolidone", "yes");
+ _tandem_params.setParamLabelValue("protein, quick pyrolidone", "no");
+ if(ui->pqp_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("protein, quick pyrolidone", "yes");
}
- _tandem_params.setParamLabelValue("protein, stP bias", "no");
- if (ui->pstpb_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("protein, stP bias", "yes");
+ _tandem_params.setParamLabelValue("protein, stP bias", "no");
+ if(ui->pstpb_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("protein, stP bias", "yes");
}
- _tandem_params.setParamLabelValue("protein, modified residue mass file", ui->pmrmf_edit->text());
-
-
-
- _tandem_params.setParamLabelValue("residue, modification mass", ui->rmm_edit->text());
- _tandem_params.setParamLabelValue("residue, modification mass 1", ui->rmm1_edit->text());
- _tandem_params.setParamLabelValue("residue, modification mass 2", ui->rmm2_edit->text());
- _tandem_params.setParamLabelValue("residue, potential modification mass", ui->rpmm_edit->text());
- _tandem_params.setParamLabelValue("residue, potential modification mass 1", ui->rpmm1_edit->text());
- _tandem_params.setParamLabelValue("residue, potential modification mass 2", ui->rpmm2_edit->text());
- _tandem_params.setParamLabelValue("residue, potential modification motif", ui->rpmmotif_edit->text());
- _tandem_params.setParamLabelValue("residue, potential modification motif 1", ui->rpmmotif1_edit->text());
- _tandem_params.setParamLabelValue("residue, potential modification motif 2", ui->rpmmotif2_edit->text());
- _tandem_params.setParamLabelValue("scoring, maximum missed cleavage sites", ui->smmcs_edit->text());
- _tandem_params.setParamLabelValue("scoring, cyclic permutation", "no");
- if (ui->scp_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("scoring, cyclic permutation", "yes");
+ _tandem_params.setParamLabelValue("protein, modified residue mass file",
+ ui->pmrmf_edit->text());
+
+
+ _tandem_params.setParamLabelValue("residue, modification mass",
+ ui->rmm_edit->text());
+ _tandem_params.setParamLabelValue("residue, modification mass 1",
+ ui->rmm1_edit->text());
+ _tandem_params.setParamLabelValue("residue, modification mass 2",
+ ui->rmm2_edit->text());
+ _tandem_params.setParamLabelValue("residue, potential modification mass",
+ ui->rpmm_edit->text());
+ _tandem_params.setParamLabelValue(
+ "residue, potential modification mass 1", ui->rpmm1_edit->text());
+ _tandem_params.setParamLabelValue(
+ "residue, potential modification mass 2", ui->rpmm2_edit->text());
+ _tandem_params.setParamLabelValue("residue, potential modification motif",
+ ui->rpmmotif_edit->text());
+ _tandem_params.setParamLabelValue(
+ "residue, potential modification motif 1", ui->rpmmotif1_edit->text());
+ _tandem_params.setParamLabelValue(
+ "residue, potential modification motif 2", ui->rpmmotif2_edit->text());
+ _tandem_params.setParamLabelValue(
+ "scoring, maximum missed cleavage sites", ui->smmcs_edit->text());
+ _tandem_params.setParamLabelValue("scoring, cyclic permutation", "no");
+ if(ui->scp_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("scoring, cyclic permutation",
+ "yes");
}
- _tandem_params.setParamLabelValue("scoring, include reverse", "no");
- if (ui->sir_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("scoring, include reverse", "yes");
+ _tandem_params.setParamLabelValue("scoring, include reverse", "no");
+ if(ui->sir_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("scoring, include reverse", "yes");
}
- _tandem_params.setParamLabelValue("scoring, minimum ion count", ui->smic_edit->text());
+ _tandem_params.setParamLabelValue("scoring, minimum ion count",
+ ui->smic_edit->text());
- _tandem_params.setParamLabelValue("scoring, y ions", "no");
- if (ui->syi_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("scoring, y ions", "yes");
+ _tandem_params.setParamLabelValue("scoring, y ions", "no");
+ if(ui->syi_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("scoring, y ions", "yes");
}
- _tandem_params.setParamLabelValue("scoring, b ions", "no");
- if (ui->sbi_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("scoring, b ions", "yes");
+ _tandem_params.setParamLabelValue("scoring, b ions", "no");
+ if(ui->sbi_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("scoring, b ions", "yes");
}
- _tandem_params.setParamLabelValue("scoring, c ions", "no");
- if (ui->sci_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("scoring, c ions", "yes");
+ _tandem_params.setParamLabelValue("scoring, c ions", "no");
+ if(ui->sci_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("scoring, c ions", "yes");
}
- _tandem_params.setParamLabelValue("scoring, z ions", "no");
- if (ui->szi_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("scoring, z ions", "yes");
+ _tandem_params.setParamLabelValue("scoring, z ions", "no");
+ if(ui->szi_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("scoring, z ions", "yes");
}
- _tandem_params.setParamLabelValue("scoring, a ions", "no");
- if (ui->sai_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("scoring, a ions", "yes");
+ _tandem_params.setParamLabelValue("scoring, a ions", "no");
+ if(ui->sai_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("scoring, a ions", "yes");
}
- _tandem_params.setParamLabelValue("scoring, x ions", "no");
- if (ui->sxi_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("scoring, x ions", "yes");
+ _tandem_params.setParamLabelValue("scoring, x ions", "no");
+ if(ui->sxi_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("scoring, x ions", "yes");
}
- _tandem_params.setParamLabelValue("refine", "no");
- if (ui->refine_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("refine", "yes");
+ _tandem_params.setParamLabelValue("refine", "no");
+ if(ui->refine_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("refine", "yes");
}
- _tandem_params.setParamLabelValue("refine, maximum valid expectation value", ui->rmvev_edit->text());
-
- _tandem_params.setParamLabelValue("refine, potential N-terminus modifications", ui->refpntm_edit->text());
- _tandem_params.setParamLabelValue("refine, potential C-terminus modifications", ui->refpctm_edit->text());
- _tandem_params.setParamLabelValue("refine, modification mass", ui->refmm_edit->text());
- _tandem_params.setParamLabelValue("refine, modification mass 1", ui->refmm1_edit->text());
- _tandem_params.setParamLabelValue("refine, modification mass 2", ui->refmm2_edit->text());
- _tandem_params.setParamLabelValue("refine, potential modification mass", ui->refpmm_edit->text());
- _tandem_params.setParamLabelValue("refine, potential modification mass 1", ui->refpmm1_edit->text());
- _tandem_params.setParamLabelValue("refine, potential modification mass 2", ui->refpmm2_edit->text());
- _tandem_params.setParamLabelValue("refine, potential modification motif", ui->refpmmotif_edit->text());
- _tandem_params.setParamLabelValue("refine, potential modification motif 1", ui->refpmmotif1_edit->text());
- _tandem_params.setParamLabelValue("refine, potential modification motif 2", ui->refpmmotif2_edit->text());
- _tandem_params.setParamLabelValue("refine, use potential modifications for full refinement", "no");
- if (ui->rupmffr_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("refine, use potential modifications for full refinement", "yes");
+ _tandem_params.setParamLabelValue(
+ "refine, maximum valid expectation value", ui->rmvev_edit->text());
+
+ _tandem_params.setParamLabelValue(
+ "refine, potential N-terminus modifications", ui->refpntm_edit->text());
+ _tandem_params.setParamLabelValue(
+ "refine, potential C-terminus modifications", ui->refpctm_edit->text());
+ _tandem_params.setParamLabelValue("refine, modification mass",
+ ui->refmm_edit->text());
+ _tandem_params.setParamLabelValue("refine, modification mass 1",
+ ui->refmm1_edit->text());
+ _tandem_params.setParamLabelValue("refine, modification mass 2",
+ ui->refmm2_edit->text());
+ _tandem_params.setParamLabelValue("refine, potential modification mass",
+ ui->refpmm_edit->text());
+ _tandem_params.setParamLabelValue("refine, potential modification mass 1",
+ ui->refpmm1_edit->text());
+ _tandem_params.setParamLabelValue("refine, potential modification mass 2",
+ ui->refpmm2_edit->text());
+ _tandem_params.setParamLabelValue("refine, potential modification motif",
+ ui->refpmmotif_edit->text());
+ _tandem_params.setParamLabelValue(
+ "refine, potential modification motif 1", ui->refpmmotif1_edit->text());
+ _tandem_params.setParamLabelValue(
+ "refine, potential modification motif 2", ui->refpmmotif2_edit->text());
+ _tandem_params.setParamLabelValue(
+ "refine, use potential modifications for full refinement", "no");
+ if(ui->rupmffr_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue(
+ "refine, use potential modifications for full refinement", "yes");
}
- _tandem_params.setParamLabelValue("refine, cleavage semi", "no");
- if (ui->rcsemi_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("refine, cleavage semi", "yes");
+ _tandem_params.setParamLabelValue("refine, cleavage semi", "no");
+ if(ui->rcsemi_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("refine, cleavage semi", "yes");
}
- _tandem_params.setParamLabelValue("refine, unanticipated cleavage", "no");
- if (ui->ruc_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("refine, unanticipated cleavage", "yes");
+ _tandem_params.setParamLabelValue("refine, unanticipated cleavage", "no");
+ if(ui->ruc_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("refine, unanticipated cleavage",
+ "yes");
}
- _tandem_params.setParamLabelValue("refine, spectrum synthesis", "no");
- if (ui->rss_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("refine, spectrum synthesis", "yes");
+ _tandem_params.setParamLabelValue("refine, spectrum synthesis", "no");
+ if(ui->rss_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("refine, spectrum synthesis",
+ "yes");
}
- _tandem_params.setParamLabelValue("refine, point mutations", "no");
- if (ui->rpm_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("refine, point mutations", "yes");
+ _tandem_params.setParamLabelValue("refine, point mutations", "no");
+ if(ui->rpm_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("refine, point mutations", "yes");
}
- _tandem_params.setParamLabelValue("output, maximum valid expectation value", ui->omvev_edit->text());
+ _tandem_params.setParamLabelValue(
+ "output, maximum valid expectation value", ui->omvev_edit->text());
- _tandem_params.setParamLabelValue("output, maximum valid protein expectation value", ui->omvpev_edit->text());
+ _tandem_params.setParamLabelValue(
+ "output, maximum valid protein expectation value",
+ ui->omvpev_edit->text());
- _tandem_params.setParamLabelValue("output, results", "valid");
- if (ui->oresu_all_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("output, results", "all");
+ _tandem_params.setParamLabelValue("output, results", "valid");
+ if(ui->oresu_all_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("output, results", "all");
}
- if (ui->oresu_stochastic_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("output, results", "stochastic");
+ if(ui->oresu_stochastic_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("output, results", "stochastic");
}
- _tandem_params.setParamLabelValue("output, spectra", "no");
- if (ui->ospec_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("output, spectra", "yes");
+ _tandem_params.setParamLabelValue("output, spectra", "no");
+ if(ui->ospec_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("output, spectra", "yes");
}
- _tandem_params.setParamLabelValue("output, histogram column width", "30");
+ _tandem_params.setParamLabelValue("output, histogram column width", "30");
- _tandem_params.setParamLabelValue("output, xsl path", ui->oxp_edit->text());
- _tandem_params.setParamLabelValue("output, mzid", "no");
- if (ui->mzid_yes_radio_button->isChecked()) {
- _tandem_params.setParamLabelValue("output, mzid", "yes");
+ _tandem_params.setParamLabelValue("output, xsl path",
+ ui->oxp_edit->text());
+ _tandem_params.setParamLabelValue("output, mzid", "no");
+ if(ui->mzid_yes_radio_button->isChecked())
+ {
+ _tandem_params.setParamLabelValue("output, mzid", "yes");
}
-
}
- catch (pappso::PappsoException & error) {
- QMessageBox::warning(this,tr("Error in parameters :"), error.qwhat());
+ catch(pappso::PappsoException &error)
+ {
+ QMessageBox::warning(this, tr("Error in parameters :"), error.qwhat());
}
}
-void EditTandemPresetDialog::populate() {
- qDebug() << "EditTandemPresetDialog::populate begin";
- try {
- ui->method_name_line_edit->setText(_tandem_params.getMethodName());
- /*
- * <note type="input" label="spectrum, parent monoisotopic mass error units">ppm</note>
- * */
- ui->spmmeu_daltons_radio_button->setChecked(true);
- ui->spmmeu_ppm_radio_button->setChecked(false);
- if ( _tandem_params.getValue("spectrum, parent monoisotopic mass error units") == "ppm" ) { // -1 for not found
- ui->spmmeu_daltons_radio_button->setChecked(false);
- ui->spmmeu_ppm_radio_button->setChecked(true);
+void
+EditTandemPresetDialog::populate()
+{
+ qDebug() << "EditTandemPresetDialog::populate begin";
+ try
+ {
+ ui->method_name_line_edit->setText(_tandem_params.getMethodName());
+ /*
+ * <note type="input" label="spectrum, parent monoisotopic mass error
+ * units">ppm</note>
+ * */
+ ui->spmmeu_daltons_radio_button->setChecked(true);
+ ui->spmmeu_ppm_radio_button->setChecked(false);
+ if(_tandem_params.getValue(
+ "spectrum, parent monoisotopic mass error units") == "ppm")
+ { // -1 for not found
+ ui->spmmeu_daltons_radio_button->setChecked(false);
+ ui->spmmeu_ppm_radio_button->setChecked(true);
}
- //<note type="input" label="spectrum, parent monoisotopic mass error minus">10</note>
- ui->parent_ion_lower_window_edit->setText(_tandem_params.getValue("spectrum, parent monoisotopic mass error minus"));
- //<note type="input" label="spectrum, parent monoisotopic mass error plus">10</note>
- ui->parent_ion_upper_window_edit->setText(_tandem_params.getValue("spectrum, parent monoisotopic mass error plus"));
- //<note type="input" label="spectrum, parent monoisotopic mass isotope error">yes</note>
- ui->spmmie_yes_radio_button->setChecked(true);
- ui->spmmie_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("spectrum, parent monoisotopic mass isotope error") == "no" ) { // -1 for not found
- ui->spmmie_yes_radio_button->setChecked(false);
- ui->spmmie_no_radio_button->setChecked(true);
+ //<note type="input" label="spectrum, parent monoisotopic mass error
+ //minus">10</note>
+ ui->parent_ion_lower_window_edit->setText(_tandem_params.getValue(
+ "spectrum, parent monoisotopic mass error minus"));
+ //<note type="input" label="spectrum, parent monoisotopic mass error
+ //plus">10</note>
+ ui->parent_ion_upper_window_edit->setText(_tandem_params.getValue(
+ "spectrum, parent monoisotopic mass error plus"));
+ //<note type="input" label="spectrum, parent monoisotopic mass isotope
+ //error">yes</note>
+ ui->spmmie_yes_radio_button->setChecked(true);
+ ui->spmmie_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue(
+ "spectrum, parent monoisotopic mass isotope error") == "no")
+ { // -1 for not found
+ ui->spmmie_yes_radio_button->setChecked(false);
+ ui->spmmie_no_radio_button->setChecked(true);
}
- //<note type="input" label="spectrum, maximum parent charge">4</note>
- ui->smpc_edit->setText(_tandem_params.getValue("spectrum, maximum parent charge"));
-
- //<note type="input" label="spectrum, fragment mass type">monoisotopic</note>
- auto index = ui->sfmt_combo_box->findText("monoisotopic");
- if ( index != -1 ) { // -1 for not found
- ui->sfmt_combo_box->setCurrentIndex(index);
+ //<note type="input" label="spectrum, maximum parent charge">4</note>
+ ui->smpc_edit->setText(
+ _tandem_params.getValue("spectrum, maximum parent charge"));
+
+ //<note type="input" label="spectrum, fragment mass
+ //type">monoisotopic</note>
+ auto index = ui->sfmt_combo_box->findText("monoisotopic");
+ if(index != -1)
+ { // -1 for not found
+ ui->sfmt_combo_box->setCurrentIndex(index);
}
- //<note type="input" label="spectrum, fragment monoisotopic mass error units">Daltons</note>
- ui->sfmmeu_daltons_radio_button->setChecked(true);
- ui->sfmmeu_ppm_radio_button->setChecked(false);
- if ( _tandem_params.getValue("spectrum, fragment monoisotopic mass error units") == "ppm" ) { // -1 for not found
- ui->sfmmeu_daltons_radio_button->setChecked(false);
- ui->sfmmeu_ppm_radio_button->setChecked(true);
+ //<note type="input" label="spectrum, fragment monoisotopic mass error
+ //units">Daltons</note>
+ ui->sfmmeu_daltons_radio_button->setChecked(true);
+ ui->sfmmeu_ppm_radio_button->setChecked(false);
+ if(_tandem_params.getValue(
+ "spectrum, fragment monoisotopic mass error units") == "ppm")
+ { // -1 for not found
+ ui->sfmmeu_daltons_radio_button->setChecked(false);
+ ui->sfmmeu_ppm_radio_button->setChecked(true);
}
- //<note type="input" label="spectrum, fragment monoisotopic mass error">0.02</note>
- ui->sfmme_edit->setText(_tandem_params.getValue("spectrum, fragment monoisotopic mass error"));
+ //<note type="input" label="spectrum, fragment monoisotopic mass
+ //error">0.02</note>
+ ui->sfmme_edit->setText(
+ _tandem_params.getValue("spectrum, fragment monoisotopic mass error"));
- //<note type="input" label="spectrum, use neutral loss window">yes</note>
- ui->sunlw_yes_radio_button->setChecked(true);
- ui->sunlw_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("spectrum, use neutral loss window") == "no" ) { // -1 for not found
- ui->sunlw_yes_radio_button->setChecked(false);
- ui->sunlw_no_radio_button->setChecked(true);
+ //<note type="input" label="spectrum, use neutral loss window">yes</note>
+ ui->sunlw_yes_radio_button->setChecked(true);
+ ui->sunlw_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("spectrum, use neutral loss window") == "no")
+ { // -1 for not found
+ ui->sunlw_yes_radio_button->setChecked(false);
+ ui->sunlw_no_radio_button->setChecked(true);
}
-
- //<note type="input" label="spectrum, neutral loss mass">18.01057</note>
- ui->snlm_edit->setText(_tandem_params.getValue("spectrum, neutral loss mass"));
- //<note type="input" label="spectrum, neutral loss window">0.02</note>
- ui->snlw_edit->setText(_tandem_params.getValue("spectrum, neutral loss window"));
- //<note type="input" label="spectrum, use noise suppression">yes</note>
- ui->suns_yes_radio_button->setChecked(true);
- ui->suns_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("spectrum, use noise suppression") == "no" ) { // -1 for not found
- ui->suns_yes_radio_button->setChecked(false);
- ui->suns_no_radio_button->setChecked(true);
+ //<note type="input" label="spectrum, neutral loss mass">18.01057</note>
+ ui->snlm_edit->setText(
+ _tandem_params.getValue("spectrum, neutral loss mass"));
+ //<note type="input" label="spectrum, neutral loss window">0.02</note>
+ ui->snlw_edit->setText(
+ _tandem_params.getValue("spectrum, neutral loss window"));
+ //<note type="input" label="spectrum, use noise suppression">yes</note>
+ ui->suns_yes_radio_button->setChecked(true);
+ ui->suns_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("spectrum, use noise suppression") == "no")
+ { // -1 for not found
+ ui->suns_yes_radio_button->setChecked(false);
+ ui->suns_no_radio_button->setChecked(true);
}
- //<note type="input" label="spectrum, dynamic range">100.0</note>
- ui->sdr_edit->setText(_tandem_params.getValue("spectrum, dynamic range"));
+ //<note type="input" label="spectrum, dynamic range">100.0</note>
+ ui->sdr_edit->setText(_tandem_params.getValue("spectrum, dynamic range"));
- //<note type="input" label="spectrum, total peaks">100</note>
- ui->stp_edit->setText(_tandem_params.getValue("spectrum, total peaks"));
+ //<note type="input" label="spectrum, total peaks">100</note>
+ ui->stp_edit->setText(_tandem_params.getValue("spectrum, total peaks"));
- ui->smp_edit->setText(_tandem_params.getValue("spectrum, minimum peaks"));
+ ui->smp_edit->setText(_tandem_params.getValue("spectrum, minimum peaks"));
- //<note type="input" label="spectrum, minimum fragment mz">150.0</note>
- ui->smfmz_edit->setText(_tandem_params.getValue("spectrum, minimum fragment mz"));
- //<note type="input" label="spectrum, minimum parent m+h">500.0</note>
- ui->smpmh_edit->setText(_tandem_params.getValue("spectrum, minimum parent m+h"));
+ //<note type="input" label="spectrum, minimum fragment mz">150.0</note>
+ ui->smfmz_edit->setText(
+ _tandem_params.getValue("spectrum, minimum fragment mz"));
+ //<note type="input" label="spectrum, minimum parent m+h">500.0</note>
+ ui->smpmh_edit->setText(
+ _tandem_params.getValue("spectrum, minimum parent m+h"));
- //<note type="input" label="spectrum, sequence batch size">1000</note>
- ui->spsbs_edit->setText(_tandem_params.getValue("spectrum, sequence batch size"));
- //<note type="input" label="spectrum, use contrast angle">no</note>
- ui->suca_yes_radio_button->setChecked(true);
- ui->suca_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("spectrum, use contrast angle") == "no" ) { // -1 for not found
- ui->suca_yes_radio_button->setChecked(false);
- ui->suca_no_radio_button->setChecked(true);
+ //<note type="input" label="spectrum, sequence batch size">1000</note>
+ ui->spsbs_edit->setText(
+ _tandem_params.getValue("spectrum, sequence batch size"));
+ //<note type="input" label="spectrum, use contrast angle">no</note>
+ ui->suca_yes_radio_button->setChecked(true);
+ ui->suca_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("spectrum, use contrast angle") == "no")
+ { // -1 for not found
+ ui->suca_yes_radio_button->setChecked(false);
+ ui->suca_no_radio_button->setChecked(true);
}
- //<note type="input" label="spectrum, threads">1</note>
- ui->st_edit->setText(_tandem_params.getValue("spectrum, threads"));
+ //<note type="input" label="spectrum, threads">1</note>
+ ui->st_edit->setText(_tandem_params.getValue("spectrum, threads"));
- //<note type="input" label="protein, cleavage site">[RK]|{P}</note>
- ui->pcs_edit->setText(_tandem_params.getValue("protein, cleavage site"));
- //<note type="input" label="protein, cleavage semi">no</note>
- ui->pcsemi_yes_radio_button->setChecked(true);
- ui->pcsemi_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("protein, cleavage semi") == "no" ) { // -1 for not found
- ui->pcsemi_yes_radio_button->setChecked(false);
- ui->pcsemi_no_radio_button->setChecked(true);
+ //<note type="input" label="protein, cleavage site">[RK]|{P}</note>
+ ui->pcs_edit->setText(_tandem_params.getValue("protein, cleavage site"));
+ //<note type="input" label="protein, cleavage semi">no</note>
+ ui->pcsemi_yes_radio_button->setChecked(true);
+ ui->pcsemi_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("protein, cleavage semi") == "no")
+ { // -1 for not found
+ ui->pcsemi_yes_radio_button->setChecked(false);
+ ui->pcsemi_no_radio_button->setChecked(true);
}
- //<note type="input" label="protein, cleavage C-terminal mass change">+17.00305</note>
- ui->pcctmc_edit->setText(_tandem_params.getValue("protein, cleavage C-terminal mass change"));
- //<note type="input" label="protein, cleavage N-terminal mass change">+1.00794</note>
- ui->pcntmc_edit->setText(_tandem_params.getValue("protein, cleavage N-terminal mass change"));
-
- //<note type="input" label="protein, C-terminal residue modification mass">0.0</note>
- ui->pctrmm_edit->setText(_tandem_params.getValue("protein, C-terminal residue modification mass"));
- //<note type="input" label="protein, N-terminal residue modification mass">0.0</note>
- ui->pntrmm_edit->setText(_tandem_params.getValue("protein, N-terminal residue modification mass"));
-
- //<note type="input" label="protein, quick acetyl">yes</note>
- ui->pqa_yes_radio_button->setChecked(true);
- ui->pqa_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("protein, quick acetyl") == "no" ) { // -1 for not found
- ui->pqa_yes_radio_button->setChecked(false);
- ui->pqa_no_radio_button->setChecked(true);
+ //<note type="input" label="protein, cleavage C-terminal mass
+ //change">+17.00305</note>
+ ui->pcctmc_edit->setText(
+ _tandem_params.getValue("protein, cleavage C-terminal mass change"));
+ //<note type="input" label="protein, cleavage N-terminal mass
+ //change">+1.00794</note>
+ ui->pcntmc_edit->setText(
+ _tandem_params.getValue("protein, cleavage N-terminal mass change"));
+
+ //<note type="input" label="protein, C-terminal residue modification
+ //mass">0.0</note>
+ ui->pctrmm_edit->setText(_tandem_params.getValue(
+ "protein, C-terminal residue modification mass"));
+ //<note type="input" label="protein, N-terminal residue modification
+ //mass">0.0</note>
+ ui->pntrmm_edit->setText(_tandem_params.getValue(
+ "protein, N-terminal residue modification mass"));
+
+ //<note type="input" label="protein, quick acetyl">yes</note>
+ ui->pqa_yes_radio_button->setChecked(true);
+ ui->pqa_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("protein, quick acetyl") == "no")
+ { // -1 for not found
+ ui->pqa_yes_radio_button->setChecked(false);
+ ui->pqa_no_radio_button->setChecked(true);
}
- //<note type="input" label="protein, quick pyrolidone">yes</note>
- ui->pqp_yes_radio_button->setChecked(true);
- ui->pqp_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("protein, quick pyrolidone") == "no" ) { // -1 for not found
- ui->pqp_yes_radio_button->setChecked(false);
- ui->pqp_no_radio_button->setChecked(true);
+ //<note type="input" label="protein, quick pyrolidone">yes</note>
+ ui->pqp_yes_radio_button->setChecked(true);
+ ui->pqp_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("protein, quick pyrolidone") == "no")
+ { // -1 for not found
+ ui->pqp_yes_radio_button->setChecked(false);
+ ui->pqp_no_radio_button->setChecked(true);
}
- //<note type="input" label="protein, stP bias">yes</note>
- ui->pstpb_yes_radio_button->setChecked(true);
- ui->pstpb_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("protein, stP bias") == "no" ) { // -1 for not found
- ui->pstpb_yes_radio_button->setChecked(false);
- ui->pstpb_no_radio_button->setChecked(true);
+ //<note type="input" label="protein, stP bias">yes</note>
+ ui->pstpb_yes_radio_button->setChecked(true);
+ ui->pstpb_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("protein, stP bias") == "no")
+ { // -1 for not found
+ ui->pstpb_yes_radio_button->setChecked(false);
+ ui->pstpb_no_radio_button->setChecked(true);
}
- //<note type="input" label="protein, modified residue mass file"></note>
- ui->pmrmf_edit->setText(_tandem_params.getValue("protein, modified residue mass file"));
-
- //<note type="input" label="residue, modification mass">57.02146@C</note>
- ui->rmm_edit->setText(_tandem_params.getValue("residue, modification mass"));
-
- //<note type="input" label="residue, modification mass 1"></note>
- ui->rmm1_edit->setText(_tandem_params.getValue("residue, modification mass 1"));
- //<note type="input" label="residue, modification mass 2"></note>
- ui->rmm2_edit->setText(_tandem_params.getValue("residue, modification mass 2"));
-
-
- //<note type="input" label="residue, potential modification mass">15.99491@M</note>
- ui->rpmm_edit->setText(_tandem_params.getValue("residue, potential modification mass"));
- //<note type="input" label="residue, potential modification mass 1"></note>
- ui->rpmm1_edit->setText(_tandem_params.getValue("residue, potential modification mass 1"));
- //<note type="input" label="residue, potential modification mass 2"></note>
- ui->rpmm2_edit->setText(_tandem_params.getValue("residue, potential modification mass 2"));
- //<note type="input" label="residue, potential modification motif"></note>
- ui->rpmmotif_edit->setText(_tandem_params.getValue("residue, potential modification motif"));
- //<note type="input" label="residue, potential modification motif 1"></note>
- ui->rpmmotif1_edit->setText(_tandem_params.getValue("residue, potential modification motif 1"));
- //<note type="input" label="residue, potential modification motif 2"></note>
- ui->rpmmotif2_edit->setText(_tandem_params.getValue("residue, potential modification motif 2"));
-
- //<note type="input" label="scoring, minimum ion count">4</note>
- ui->smic_edit->setText(_tandem_params.getValue("scoring, minimum ion count"));
- //<note type="input" label="scoring, maximum missed cleavage sites">1</note>
- ui->smmcs_edit->setText(_tandem_params.getValue("scoring, maximum missed cleavage sites"));
- //<note type="input" label="scoring, cyclic permutation">yes</note>
- ui->scp_yes_radio_button->setChecked(true);
- ui->scp_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("scoring, cyclic permutation") == "no" ) { // -1 for not found
- ui->scp_yes_radio_button->setChecked(false);
- ui->scp_no_radio_button->setChecked(true);
+ //<note type="input" label="protein, modified residue mass file"></note>
+ ui->pmrmf_edit->setText(
+ _tandem_params.getValue("protein, modified residue mass file"));
+
+ //<note type="input" label="residue, modification mass">57.02146@C</note>
+ ui->rmm_edit->setText(
+ _tandem_params.getValue("residue, modification mass"));
+
+ //<note type="input" label="residue, modification mass 1"></note>
+ ui->rmm1_edit->setText(
+ _tandem_params.getValue("residue, modification mass 1"));
+ //<note type="input" label="residue, modification mass 2"></note>
+ ui->rmm2_edit->setText(
+ _tandem_params.getValue("residue, modification mass 2"));
+
+
+ //<note type="input" label="residue, potential modification
+ //mass">15.99491@M</note>
+ ui->rpmm_edit->setText(
+ _tandem_params.getValue("residue, potential modification mass"));
+ //<note type="input" label="residue, potential modification mass
+ //1"></note>
+ ui->rpmm1_edit->setText(
+ _tandem_params.getValue("residue, potential modification mass 1"));
+ //<note type="input" label="residue, potential modification mass
+ //2"></note>
+ ui->rpmm2_edit->setText(
+ _tandem_params.getValue("residue, potential modification mass 2"));
+ //<note type="input" label="residue, potential modification motif"></note>
+ ui->rpmmotif_edit->setText(
+ _tandem_params.getValue("residue, potential modification motif"));
+ //<note type="input" label="residue, potential modification motif
+ //1"></note>
+ ui->rpmmotif1_edit->setText(
+ _tandem_params.getValue("residue, potential modification motif 1"));
+ //<note type="input" label="residue, potential modification motif
+ //2"></note>
+ ui->rpmmotif2_edit->setText(
+ _tandem_params.getValue("residue, potential modification motif 2"));
+
+ //<note type="input" label="scoring, minimum ion count">4</note>
+ ui->smic_edit->setText(
+ _tandem_params.getValue("scoring, minimum ion count"));
+ //<note type="input" label="scoring, maximum missed cleavage
+ //sites">1</note>
+ ui->smmcs_edit->setText(
+ _tandem_params.getValue("scoring, maximum missed cleavage sites"));
+ //<note type="input" label="scoring, cyclic permutation">yes</note>
+ ui->scp_yes_radio_button->setChecked(true);
+ ui->scp_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("scoring, cyclic permutation") == "no")
+ { // -1 for not found
+ ui->scp_yes_radio_button->setChecked(false);
+ ui->scp_no_radio_button->setChecked(true);
}
- //<note type="input" label="scoring, include reverse">yes</note>
- ui->sir_yes_radio_button->setChecked(true);
- ui->sir_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("scoring, include reverse") == "no" ) { // -1 for not found
- ui->sir_yes_radio_button->setChecked(false);
- ui->sir_no_radio_button->setChecked(true);
+ //<note type="input" label="scoring, include reverse">yes</note>
+ ui->sir_yes_radio_button->setChecked(true);
+ ui->sir_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("scoring, include reverse") == "no")
+ { // -1 for not found
+ ui->sir_yes_radio_button->setChecked(false);
+ ui->sir_no_radio_button->setChecked(true);
}
- //<note type="input" label="scoring, y ions">yes</note>
- ui->syi_yes_radio_button->setChecked(true);
- ui->syi_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("scoring, y ions") == "no" ) { // -1 for not found
- ui->syi_yes_radio_button->setChecked(false);
- ui->syi_no_radio_button->setChecked(true);
+ //<note type="input" label="scoring, y ions">yes</note>
+ ui->syi_yes_radio_button->setChecked(true);
+ ui->syi_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("scoring, y ions") == "no")
+ { // -1 for not found
+ ui->syi_yes_radio_button->setChecked(false);
+ ui->syi_no_radio_button->setChecked(true);
}
- //<note type="input" label="scoring, b ions">yes</note>
- ui->sbi_yes_radio_button->setChecked(true);
- ui->sbi_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("scoring, b ions") == "no" ) { // -1 for not found
- ui->sbi_yes_radio_button->setChecked(false);
- ui->sbi_no_radio_button->setChecked(true);
+ //<note type="input" label="scoring, b ions">yes</note>
+ ui->sbi_yes_radio_button->setChecked(true);
+ ui->sbi_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("scoring, b ions") == "no")
+ { // -1 for not found
+ ui->sbi_yes_radio_button->setChecked(false);
+ ui->sbi_no_radio_button->setChecked(true);
}
- //<note type="input" label="scoring, c ions">no</note>
- ui->sci_yes_radio_button->setChecked(true);
- ui->sci_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("scoring, c ions") == "no" ) { // -1 for not found
- ui->sci_yes_radio_button->setChecked(false);
- ui->sci_no_radio_button->setChecked(true);
+ //<note type="input" label="scoring, c ions">no</note>
+ ui->sci_yes_radio_button->setChecked(true);
+ ui->sci_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("scoring, c ions") == "no")
+ { // -1 for not found
+ ui->sci_yes_radio_button->setChecked(false);
+ ui->sci_no_radio_button->setChecked(true);
}
- //<note type="input" label="scoring, z ions">no</note>
- ui->szi_yes_radio_button->setChecked(true);
- ui->szi_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("scoring, z ions") == "no" ) { // -1 for not found
- ui->szi_yes_radio_button->setChecked(false);
- ui->szi_no_radio_button->setChecked(true);
+ //<note type="input" label="scoring, z ions">no</note>
+ ui->szi_yes_radio_button->setChecked(true);
+ ui->szi_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("scoring, z ions") == "no")
+ { // -1 for not found
+ ui->szi_yes_radio_button->setChecked(false);
+ ui->szi_no_radio_button->setChecked(true);
}
- //<note type="input" label="scoring, a ions">no</note>
- ui->sai_yes_radio_button->setChecked(true);
- ui->sai_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("scoring, a ions") == "no" ) { // -1 for not found
- ui->sai_yes_radio_button->setChecked(false);
- ui->sai_no_radio_button->setChecked(true);
+ //<note type="input" label="scoring, a ions">no</note>
+ ui->sai_yes_radio_button->setChecked(true);
+ ui->sai_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("scoring, a ions") == "no")
+ { // -1 for not found
+ ui->sai_yes_radio_button->setChecked(false);
+ ui->sai_no_radio_button->setChecked(true);
}
- //<note type="input" label="scoring, x ions">no</note>
- ui->sxi_yes_radio_button->setChecked(true);
- ui->sxi_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("scoring, x ions") == "no" ) { // -1 for not found
- ui->sxi_yes_radio_button->setChecked(false);
- ui->sxi_no_radio_button->setChecked(true);
+ //<note type="input" label="scoring, x ions">no</note>
+ ui->sxi_yes_radio_button->setChecked(true);
+ ui->sxi_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("scoring, x ions") == "no")
+ { // -1 for not found
+ ui->sxi_yes_radio_button->setChecked(false);
+ ui->sxi_no_radio_button->setChecked(true);
}
- //<note type="input" label="refine">yes</note>
- ui->refine_yes_radio_button->setChecked(true);
- ui->refine_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("refine") == "no" ) { // -1 for not found
- ui->refine_yes_radio_button->setChecked(false);
- ui->refine_no_radio_button->setChecked(true);
+ //<note type="input" label="refine">yes</note>
+ ui->refine_yes_radio_button->setChecked(true);
+ ui->refine_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("refine") == "no")
+ { // -1 for not found
+ ui->refine_yes_radio_button->setChecked(false);
+ ui->refine_no_radio_button->setChecked(true);
}
- //<note type="input" label="refine, maximum valid expectation value">0.01</note>
- ui->rmvev_edit->setText(_tandem_params.getValue("refine, maximum valid expectation value"));
-
- //<note type="input" label="refine, potential N-terminus modifications">+42.01056@[</note>
- ui->refpntm_edit->setText(_tandem_params.getValue("refine, potential N-terminus modifications"));
- //<note type="input" label="refine, potential C-terminus modifications"></note>
- ui->refpctm_edit->setText(_tandem_params.getValue("refine, potential C-terminus modifications"));
- //<note type="input" label="refine, modification mass">57.02146@C</note>
- ui->refmm_edit->setText(_tandem_params.getValue("refine, modification mass"));
- //<note type="input" label="refine, modification mass 1"></note>
- ui->refmm1_edit->setText(_tandem_params.getValue("refine, modification mass 1"));
- //<note type="input" label="refine, modification mass 2"></note>
- ui->refmm2_edit->setText(_tandem_params.getValue("refine, modification mass 2"));
- //<note type="input" label="refine, potential modification mass">15.99491@M</note>
- ui->refpmm_edit->setText(_tandem_params.getValue("refine, potential modification mass"));
- //<note type="input" label="refine, potential modification mass 1"></note>
- ui->refpmm1_edit->setText(_tandem_params.getValue("refine, potential modification mass 1"));
- //<note type="input" label="refine, potential modification mass 2"></note>
- ui->refpmm2_edit->setText(_tandem_params.getValue("refine, potential modification mass 2"));
- //<note type="input" label="refine, potential modification motif"></note>
- ui->refpmmotif_edit->setText(_tandem_params.getValue("refine, potential modification motif"));
- //<note type="input" label="refine, potential modification motif 1"></note>
- ui->refpmmotif1_edit->setText(_tandem_params.getValue("refine, potential modification motif 1"));
- //<note type="input" label="refine, potential modification motif 2"></note>
- ui->refpmmotif2_edit->setText(_tandem_params.getValue("refine, potential modification motif 2"));
- //<note type="input" label="refine, use potential modifications for full refinement">yes</note>
- ui->rupmffr_yes_radio_button->setChecked(true);
- ui->rupmffr_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("refine, use potential modifications for full refinement") == "no" ) { // -1 for not found
- ui->rupmffr_yes_radio_button->setChecked(false);
- ui->rupmffr_no_radio_button->setChecked(true);
+ //<note type="input" label="refine, maximum valid expectation
+ //value">0.01</note>
+ ui->rmvev_edit->setText(
+ _tandem_params.getValue("refine, maximum valid expectation value"));
+
+ //<note type="input" label="refine, potential N-terminus
+ //modifications">+42.01056@[</note>
+ ui->refpntm_edit->setText(
+ _tandem_params.getValue("refine, potential N-terminus modifications"));
+ //<note type="input" label="refine, potential C-terminus
+ //modifications"></note>
+ ui->refpctm_edit->setText(
+ _tandem_params.getValue("refine, potential C-terminus modifications"));
+ //<note type="input" label="refine, modification mass">57.02146@C</note>
+ ui->refmm_edit->setText(
+ _tandem_params.getValue("refine, modification mass"));
+ //<note type="input" label="refine, modification mass 1"></note>
+ ui->refmm1_edit->setText(
+ _tandem_params.getValue("refine, modification mass 1"));
+ //<note type="input" label="refine, modification mass 2"></note>
+ ui->refmm2_edit->setText(
+ _tandem_params.getValue("refine, modification mass 2"));
+ //<note type="input" label="refine, potential modification
+ //mass">15.99491@M</note>
+ ui->refpmm_edit->setText(
+ _tandem_params.getValue("refine, potential modification mass"));
+ //<note type="input" label="refine, potential modification mass 1"></note>
+ ui->refpmm1_edit->setText(
+ _tandem_params.getValue("refine, potential modification mass 1"));
+ //<note type="input" label="refine, potential modification mass 2"></note>
+ ui->refpmm2_edit->setText(
+ _tandem_params.getValue("refine, potential modification mass 2"));
+ //<note type="input" label="refine, potential modification motif"></note>
+ ui->refpmmotif_edit->setText(
+ _tandem_params.getValue("refine, potential modification motif"));
+ //<note type="input" label="refine, potential modification motif
+ //1"></note>
+ ui->refpmmotif1_edit->setText(
+ _tandem_params.getValue("refine, potential modification motif 1"));
+ //<note type="input" label="refine, potential modification motif
+ //2"></note>
+ ui->refpmmotif2_edit->setText(
+ _tandem_params.getValue("refine, potential modification motif 2"));
+ //<note type="input" label="refine, use potential modifications for full
+ //refinement">yes</note>
+ ui->rupmffr_yes_radio_button->setChecked(true);
+ ui->rupmffr_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue(
+ "refine, use potential modifications for full refinement") == "no")
+ { // -1 for not found
+ ui->rupmffr_yes_radio_button->setChecked(false);
+ ui->rupmffr_no_radio_button->setChecked(true);
}
- //<note type="input" label="refine, cleavage semi">no</note>
- ui->rcsemi_yes_radio_button->setChecked(true);
- ui->rcsemi_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("refine, cleavage semi") == "no" ) { // -1 for not found
- ui->rcsemi_yes_radio_button->setChecked(false);
- ui->rcsemi_no_radio_button->setChecked(true);
+ //<note type="input" label="refine, cleavage semi">no</note>
+ ui->rcsemi_yes_radio_button->setChecked(true);
+ ui->rcsemi_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("refine, cleavage semi") == "no")
+ { // -1 for not found
+ ui->rcsemi_yes_radio_button->setChecked(false);
+ ui->rcsemi_no_radio_button->setChecked(true);
}
- //<note type="input" label="refine, unanticipated cleavage">no</note>
- ui->ruc_yes_radio_button->setChecked(true);
- ui->ruc_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("refine, unanticipated cleavage") == "no" ) { // -1 for not found
- ui->ruc_yes_radio_button->setChecked(false);
- ui->ruc_no_radio_button->setChecked(true);
+ //<note type="input" label="refine, unanticipated cleavage">no</note>
+ ui->ruc_yes_radio_button->setChecked(true);
+ ui->ruc_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("refine, unanticipated cleavage") == "no")
+ { // -1 for not found
+ ui->ruc_yes_radio_button->setChecked(false);
+ ui->ruc_no_radio_button->setChecked(true);
}
- //<note type="input" label="refine, spectrum synthesis">yes</note>
- ui->rss_yes_radio_button->setChecked(true);
- ui->rss_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("refine, spectrum synthesis") == "no" ) { // -1 for not found
- ui->rss_yes_radio_button->setChecked(false);
- ui->rss_no_radio_button->setChecked(true);
+ //<note type="input" label="refine, spectrum synthesis">yes</note>
+ ui->rss_yes_radio_button->setChecked(true);
+ ui->rss_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("refine, spectrum synthesis") == "no")
+ { // -1 for not found
+ ui->rss_yes_radio_button->setChecked(false);
+ ui->rss_no_radio_button->setChecked(true);
}
- //<note type="input" label="refine, point mutations">no</note>
- ui->rpm_yes_radio_button->setChecked(true);
- ui->rpm_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("refine, point mutations") == "no" ) { // -1 for not found
- ui->rpm_yes_radio_button->setChecked(false);
- ui->rpm_no_radio_button->setChecked(true);
+ //<note type="input" label="refine, point mutations">no</note>
+ ui->rpm_yes_radio_button->setChecked(true);
+ ui->rpm_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("refine, point mutations") == "no")
+ { // -1 for not found
+ ui->rpm_yes_radio_button->setChecked(false);
+ ui->rpm_no_radio_button->setChecked(true);
}
- //<note type="input" label="output, maximum valid expectation value">0.05</note>
- ui->omvev_edit->setText(_tandem_params.getValue("output, maximum valid expectation value"));
- //<note type="input" label="output, maximum valid protein expectation value">0.05</note>
- ui->omvpev_edit->setText(_tandem_params.getValue("output, maximum valid protein expectation value"));
- //<note type="input" label="output, results">valid</note>
- ui->oresu_all_radio_button->setChecked(false);
- ui->oresu_valid_radio_button->setChecked(true);
- ui->oresu_stochastic_radio_button->setChecked(false);
- if ( _tandem_params.getValue("output, results") == "all" ) { // -1 for not found
- ui->oresu_all_radio_button->setChecked(true);
- ui->oresu_valid_radio_button->setChecked(false);
- ui->oresu_stochastic_radio_button->setChecked(false);
+ //<note type="input" label="output, maximum valid expectation
+ //value">0.05</note>
+ ui->omvev_edit->setText(
+ _tandem_params.getValue("output, maximum valid expectation value"));
+ //<note type="input" label="output, maximum valid protein expectation
+ //value">0.05</note>
+ ui->omvpev_edit->setText(_tandem_params.getValue(
+ "output, maximum valid protein expectation value"));
+ //<note type="input" label="output, results">valid</note>
+ ui->oresu_all_radio_button->setChecked(false);
+ ui->oresu_valid_radio_button->setChecked(true);
+ ui->oresu_stochastic_radio_button->setChecked(false);
+ if(_tandem_params.getValue("output, results") == "all")
+ { // -1 for not found
+ ui->oresu_all_radio_button->setChecked(true);
+ ui->oresu_valid_radio_button->setChecked(false);
+ ui->oresu_stochastic_radio_button->setChecked(false);
}
- if ( _tandem_params.getValue("output, results") == "stochastic" ) { // -1 for not found
- ui->oresu_all_radio_button->setChecked(false);
- ui->oresu_valid_radio_button->setChecked(false);
- ui->oresu_stochastic_radio_button->setChecked(true);
+ if(_tandem_params.getValue("output, results") == "stochastic")
+ { // -1 for not found
+ ui->oresu_all_radio_button->setChecked(false);
+ ui->oresu_valid_radio_button->setChecked(false);
+ ui->oresu_stochastic_radio_button->setChecked(true);
}
- //<note type="input" label="output, sort results by">spectrum</note>
- //<note type="input" label="output, proteins">yes</note>
- //<note type="input" label="output, sequences">yes</note>
- //<note type="input" label="output, one sequence copy">yes</note>
- //<note type="input" label="output, spectra">yes</note>
- ui->ospec_yes_radio_button->setChecked(true);
- ui->ospec_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("output, spectra") == "no" ) { // -1 for not found
- ui->ospec_yes_radio_button->setChecked(false);
- ui->ospec_no_radio_button->setChecked(true);
+ //<note type="input" label="output, sort results by">spectrum</note>
+ //<note type="input" label="output, proteins">yes</note>
+ //<note type="input" label="output, sequences">yes</note>
+ //<note type="input" label="output, one sequence copy">yes</note>
+ //<note type="input" label="output, spectra">yes</note>
+ ui->ospec_yes_radio_button->setChecked(true);
+ ui->ospec_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("output, spectra") == "no")
+ { // -1 for not found
+ ui->ospec_yes_radio_button->setChecked(false);
+ ui->ospec_no_radio_button->setChecked(true);
}
- //<note type="input" label="output, parameters">yes</note>
- //<note type="input" label="output, performance">yes</note>
- //<note type="input" label="output, histograms">yes</note>
- //<note type="input" label="output, histogram column width">30</note>
- //<note type="input" label="output, path hashing">no</note>
- //<note type="input" label="output, xsl path">tandem-style.xsl</note>
- ui->oxp_edit->setText(_tandem_params.getValue("output, xsl path"));
- //<note type="input" label="output, mzid">no</note>
- ui->mzid_yes_radio_button->setChecked(true);
- ui->mzid_no_radio_button->setChecked(false);
- if ( _tandem_params.getValue("output, mzid") == "no" ) { // -1 for not found
- ui->mzid_yes_radio_button->setChecked(false);
- ui->mzid_no_radio_button->setChecked(true);
+ //<note type="input" label="output, parameters">yes</note>
+ //<note type="input" label="output, performance">yes</note>
+ //<note type="input" label="output, histograms">yes</note>
+ //<note type="input" label="output, histogram column width">30</note>
+ //<note type="input" label="output, path hashing">no</note>
+ //<note type="input" label="output, xsl path">tandem-style.xsl</note>
+ ui->oxp_edit->setText(_tandem_params.getValue("output, xsl path"));
+ //<note type="input" label="output, mzid">no</note>
+ ui->mzid_yes_radio_button->setChecked(true);
+ ui->mzid_no_radio_button->setChecked(false);
+ if(_tandem_params.getValue("output, mzid") == "no")
+ { // -1 for not found
+ ui->mzid_yes_radio_button->setChecked(false);
+ ui->mzid_no_radio_button->setChecked(true);
}
}
- catch (pappso::ExceptionNotFound & error) {
- QMessageBox::warning(this,tr("Parameter not found :"), error.qwhat());
+ catch(pappso::ExceptionNotFound &error)
+ {
+ QMessageBox::warning(this, tr("Parameter not found :"), error.qwhat());
}
- catch (pappso::PappsoException & error) {
- QMessageBox::warning(this,tr("Error in parameters :"), error.qwhat());
+ catch(pappso::PappsoException &error)
+ {
+ QMessageBox::warning(this, tr("Error in parameters :"), error.qwhat());
}
- qDebug() << "EditTandemPresetDialog::populate end";
+ qDebug() << "EditTandemPresetDialog::populate end";
}
-void EditTandemPresetDialog::done(int r)
+void
+EditTandemPresetDialog::done(int r)
{
- if(QDialog::Accepted == r) // ok was pressed
+ if(QDialog::Accepted == r) // ok was pressed
{
- readUi();
- if (!_p_tandem_preset_file->exists()) {
- QMessageBox::warning(this,
- tr("Save parameters"), tr("Parameters file does not exists.\nPlease save it before pressing ok or cancel edition"));
- return;
+ readUi();
+ if(!_p_tandem_preset_file->exists())
+ {
+ QMessageBox::warning(
+ this, tr("Save parameters"),
+ tr("Parameters file does not exists.\nPlease save it before "
+ "pressing ok or cancel edition"));
+ return;
}
- TandemParameters ref_params = _p_tandem_preset_file->getTandemParameters();
- if(ref_params.equals(_tandem_params)) // validate the data somehow
+ TandemParameters ref_params =
+ _p_tandem_preset_file->getTandemParameters();
+ if(ref_params.equals(_tandem_params)) // validate the data somehow
{
- QDialog::done(r);
- return;
+ QDialog::done(r);
+ return;
}
- else
+ else
{
- QMessageBox::warning(this,
- tr("Save parameters"), tr("Parameters modified but not saved.\nPlease save it before pressing ok or cancel edition"));
- return;
+ QMessageBox::warning(
+ this, tr("Save parameters"),
+ tr("Parameters modified but not saved.\nPlease save it before "
+ "pressing ok or cancel edition"));
+ return;
}
}
- else // cancel, close or exc was pressed
+ else // cancel, close or exc was pressed
{
- QDialog::done(r);
- return;
+ QDialog::done(r);
+ return;
}
}
diff --git a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.h b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.h
index 509b3d58991f5e126df14fa3b977b0ff1f797335..fffcef16775658a557d0f997f20e5605de315601 100644
--- a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.h
+++ b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.h
@@ -6,69 +6,72 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef EDITTANDEMPRESETDIALOG_H
#define EDITTANDEMPRESETDIALOG_H
#include "../../files/tandemparametersfile.h"
-#include<QDialog>
+#include <QDialog>
-namespace Ui {
-class EditTandemPresetView;
+namespace Ui
+{
+ class EditTandemPresetView;
}
-class EditTandemPresetDialog: public QDialog
+class EditTandemPresetDialog : public QDialog
{
- Q_OBJECT
+ Q_OBJECT
+
+ public:
+ explicit EditTandemPresetDialog(QWidget *parent);
+ ~EditTandemPresetDialog();
+
+ void setTandemParametersFile(const TandemParametersFile &tandem_preset_file);
+
+ const TandemParametersFile &getTandemParametersFile() const;
+
+ protected:
+ void done(int r) override;
-public:
- explicit EditTandemPresetDialog(QWidget * parent);
- ~EditTandemPresetDialog();
-
- void setTandemParametersFile(const TandemParametersFile & tandem_preset_file);
-
- const TandemParametersFile & getTandemParametersFile() const;
-
-protected:
- void done(int r) override;
+ public slots:
+ void doHelp();
+ void doSave();
+ void doCopy();
+ void doEdit(QString value);
+ void doLoad();
+ void doSelectDir();
-public slots:
- void doHelp ();
- void doSave();
- void doCopy();
- void doEdit(QString value);
- void doLoad();
- void doSelectDir();
-private:
- void fillPresetComboBox();
- void populate();
- void readUi();
+ private:
+ void fillPresetComboBox();
+ void populate();
+ void readUi();
-private:
- Ui::EditTandemPresetView *ui;
- TandemParametersFile * _p_tandem_preset_file = nullptr;
- TandemParameters _tandem_params;
- QString _preset_directory;
+ private:
+ Ui::EditTandemPresetView *ui;
+ TandemParametersFile *_p_tandem_preset_file = nullptr;
+ TandemParameters _tandem_params;
+ QString _preset_directory;
};
#endif // EDITTANDEMPRESETDIALOG_H
diff --git a/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.cpp b/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.cpp
index 60ec8e679e5f2fe95129034b0bfbac944cc6e1ac..28231401cb20cc3660b4486f1489cbfff8598eee 100644
--- a/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.cpp
+++ b/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.cpp
@@ -1,229 +1,286 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ui_export_spreadsheet_dialog.h"
#include "exportspreadsheetdialog.h"
#include <QDebug>
#include <QSettings>
-ExportSpreadsheetDialog::ExportSpreadsheetDialog(QWidget * parent):
- QDialog(parent),
- ui(new Ui::ExportSpreadsheetDialog)
+ExportSpreadsheetDialog::ExportSpreadsheetDialog(QWidget *parent)
+ : QDialog(parent), ui(new Ui::ExportSpreadsheetDialog)
{
- qDebug() << "ExportSpreadsheetDialog::ExportSpreadsheetDialog begin";
- ui->setupUi(this);
- this->setModal(true);
+ qDebug() << "ExportSpreadsheetDialog::ExportSpreadsheetDialog begin";
+ ui->setupUi(this);
+ this->setModal(true);
+ QSettings settings;
- QSettings settings;
-
- ui->groups_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/groups", "true").toBool()) {
- ui->groups_checkbox->setCheckState(Qt::Checked);
+ ui->groups_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/groups", "true").toBool())
+ {
+ ui->groups_checkbox->setCheckState(Qt::Checked);
}
- //ui->simple_checkbox->setVisible(false);
- //ui->simple_checkbox->setCheckState(Qt::Unchecked);
- //if (settings.value("export_ods/simple", "false").toBool()) {
- // ui->simple_checkbox->setCheckState(Qt::Checked);
- //}
- ui->protein_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/proteins", "true").toBool()) {
- ui->protein_checkbox->setCheckState(Qt::Checked);
+ // ui->simple_checkbox->setVisible(false);
+ // ui->simple_checkbox->setCheckState(Qt::Unchecked);
+ // if (settings.value("export_ods/simple", "false").toBool()) {
+ // ui->simple_checkbox->setCheckState(Qt::Checked);
+ //}
+ ui->protein_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/proteins", "true").toBool())
+ {
+ ui->protein_checkbox->setCheckState(Qt::Checked);
}
- ui->peptide_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/peptides", "true").toBool()) {
- ui->peptide_checkbox->setCheckState(Qt::Checked);
+ ui->peptide_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/peptides", "true").toBool())
+ {
+ ui->peptide_checkbox->setCheckState(Qt::Checked);
}
- ui->spectra_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/spectra", "true").toBool()) {
- ui->spectra_checkbox->setCheckState(Qt::Checked);
+ ui->spectra_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/spectra", "true").toBool())
+ {
+ ui->spectra_checkbox->setCheckState(Qt::Checked);
}
- ui->peptidepos_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/peptidepos", "true").toBool()) {
- ui->peptidepos_checkbox->setCheckState(Qt::Checked);
+ ui->peptidepos_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/peptidepos", "true").toBool())
+ {
+ ui->peptidepos_checkbox->setCheckState(Qt::Checked);
}
- ui->comparspectra_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/comparspectra", "true").toBool()) {
- ui->comparspectra_checkbox->setCheckState(Qt::Checked);
+ ui->comparspectra_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/comparspectra", "true").toBool())
+ {
+ ui->comparspectra_checkbox->setCheckState(Qt::Checked);
}
- ui->comparspecificspectra_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/comparspecificspectra", "true").toBool()) {
- ui->comparspecificspectra_checkbox->setCheckState(Qt::Checked);
+ ui->comparspecificspectra_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/comparspecificspectra", "true").toBool())
+ {
+ ui->comparspecificspectra_checkbox->setCheckState(Qt::Checked);
}
- ui->comparuniquesequence_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/comparuniquesequence", "true").toBool()) {
- ui->comparuniquesequence_checkbox->setCheckState(Qt::Checked);
+ ui->comparuniquesequence_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/comparuniquesequence", "true").toBool())
+ {
+ ui->comparuniquesequence_checkbox->setCheckState(Qt::Checked);
}
- ui->comparspecificuniquesequence_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/comparspecificuniquesequence", "true").toBool()) {
- ui->comparspecificuniquesequence_checkbox->setCheckState(Qt::Checked);
+ ui->comparspecificuniquesequence_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/comparspecificuniquesequence", "true").toBool())
+ {
+ ui->comparspecificuniquesequence_checkbox->setCheckState(Qt::Checked);
}
- ui->comparpai_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/comparpai", "true").toBool()) {
- ui->comparpai_checkbox->setCheckState(Qt::Checked);
+ ui->comparpai_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/comparpai", "true").toBool())
+ {
+ ui->comparpai_checkbox->setCheckState(Qt::Checked);
}
- ui->comparempai_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/comparempai", "true").toBool()) {
- ui->comparempai_checkbox->setCheckState(Qt::Checked);
+ ui->comparempai_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/comparempai", "true").toBool())
+ {
+ ui->comparempai_checkbox->setCheckState(Qt::Checked);
}
- ui->comparnsaf_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/comparnsaf", "true").toBool()) {
- ui->comparnsaf_checkbox->setCheckState(Qt::Checked);
+ ui->comparnsaf_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/comparnsaf", "true").toBool())
+ {
+ ui->comparnsaf_checkbox->setCheckState(Qt::Checked);
}
- ui->samples_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/samples", "true").toBool()) {
- ui->samples_checkbox->setCheckState(Qt::Checked);
+ ui->samples_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/samples", "true").toBool())
+ {
+ ui->samples_checkbox->setCheckState(Qt::Checked);
}
- ui->ptmislands_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/ptmislands", "true").toBool()) {
- ui->ptmislands_checkbox->setCheckState(Qt::Checked);
+ ui->ptmislands_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/ptmislands", "true").toBool())
+ {
+ ui->ptmislands_checkbox->setCheckState(Qt::Checked);
}
- ui->ptmspectra_checkbox->setCheckState(Qt::Unchecked);
- if (settings.value("export_ods/ptmspectra", "true").toBool()) {
- ui->ptmspectra_checkbox->setCheckState(Qt::Checked);
+ ui->ptmspectra_checkbox->setCheckState(Qt::Unchecked);
+ if(settings.value("export_ods/ptmspectra", "true").toBool())
+ {
+ ui->ptmspectra_checkbox->setCheckState(Qt::Checked);
}
- //param.setFilterCrossSamplePeptideNumber(settings.value("automatic_filter/cross_sample", "true").toBool());
+ // param.setFilterCrossSamplePeptideNumber(settings.value("automatic_filter/cross_sample",
+ // "true").toBool());
#if QT_VERSION >= 0x050000
// Qt5 code
#else
-// Qt4 code
+ // Qt4 code
#endif
- qDebug() << "ExportSpreadsheetDialog::ExportSpreadsheetDialog end";
+ qDebug() << "ExportSpreadsheetDialog::ExportSpreadsheetDialog end";
}
ExportSpreadsheetDialog::~ExportSpreadsheetDialog()
{
- delete ui;
+ delete ui;
}
-void ExportSpreadsheetDialog::doPeptides(bool simple) {
+void
+ExportSpreadsheetDialog::doPeptides(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/peptides", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/peptides", QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doProteins(bool simple) {
+void
+ExportSpreadsheetDialog::doProteins(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/proteins", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/proteins", QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doSamples(bool simple) {
+void
+ExportSpreadsheetDialog::doSamples(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/samples", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/samples", QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doSpectra(bool simple) {
+void
+ExportSpreadsheetDialog::doSpectra(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/spectra", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/spectra", QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doComparSpectra(bool simple) {
+void
+ExportSpreadsheetDialog::doComparSpectra(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/comparspectra", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/comparspectra", QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doComparSpecificSpectra(bool simple) {
+void
+ExportSpreadsheetDialog::doComparSpecificSpectra(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/comparspecificspectra", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/comparspecificspectra",
+ QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doComparUniqueSequence(bool simple) {
+void
+ExportSpreadsheetDialog::doComparUniqueSequence(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/comparuniquesequence", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/comparuniquesequence",
+ QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doComparSpecificUniqueSequence(bool simple) {
+void
+ExportSpreadsheetDialog::doComparSpecificUniqueSequence(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/comparspecificuniquesequence", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/comparspecificuniquesequence",
+ QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doComparEmpai(bool simple) {
+void
+ExportSpreadsheetDialog::doComparEmpai(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/comparempai", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/comparempai", QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doComparPai(bool simple) {
+void
+ExportSpreadsheetDialog::doComparPai(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/comparpai", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/comparpai", QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doComparNsaf(bool simple) {
+void
+ExportSpreadsheetDialog::doComparNsaf(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/comparnsaf", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/comparnsaf", QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doPeptidePos(bool simple) {
+void
+ExportSpreadsheetDialog::doPeptidePos(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/peptidepos", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/peptidepos", QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doGroups(bool simple) {
+void
+ExportSpreadsheetDialog::doGroups(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/groups", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/groups", QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doSimpleProteinPeptideList(bool simple) {
+void
+ExportSpreadsheetDialog::doSimpleProteinPeptideList(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/simple", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/simple", QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doProteinList(bool simple) {
+void
+ExportSpreadsheetDialog::doProteinList(bool simple)
+{
- QSettings settings;
- settings.setValue("export_ods/proteins", QString("%1").arg(simple));
+ QSettings settings;
+ settings.setValue("export_ods/proteins", QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doPtmIslands(bool simple) {
- QSettings settings;
- settings.setValue("export_ods/ptmislands", QString("%1").arg(simple));
+void
+ExportSpreadsheetDialog::doPtmIslands(bool simple)
+{
+ QSettings settings;
+ settings.setValue("export_ods/ptmislands", QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::doPtmSpectra(bool simple) {
- QSettings settings;
- settings.setValue("export_ods/ptmspectra", QString("%1").arg(simple));
+void
+ExportSpreadsheetDialog::doPtmSpectra(bool simple)
+{
+ QSettings settings;
+ settings.setValue("export_ods/ptmspectra", QString("%1").arg(simple));
}
-void ExportSpreadsheetDialog::setProject(const Project * p_project) {
+void
+ExportSpreadsheetDialog::setProject(const Project *p_project)
+{
- if (p_project->getProjectMode() == ProjectMode::individual) {
- ui->compar_groupbox->setDisabled(true);
+ if(p_project->getProjectMode() == ProjectMode::individual)
+ {
+ ui->compar_groupbox->setDisabled(true);
}
- else {
- ui->compar_groupbox->setDisabled(false);
+ else
+ {
+ ui->compar_groupbox->setDisabled(false);
}
- if (p_project->hasPtmExperiment()) {
- ui->ptm_groupbox->setEnabled(true);
+ if(p_project->hasPtmExperiment())
+ {
+ ui->ptm_groupbox->setEnabled(true);
}
- else {
- ui->ptm_groupbox->setEnabled(false);
+ else
+ {
+ ui->ptm_groupbox->setEnabled(false);
}
-
}
diff --git a/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.h b/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.h
index 0214e871e9fb28895658429659930b5f9c44b44e..f03559d09d5b992dddbc7bd14ab69a11c1ced9ad 100644
--- a/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.h
+++ b/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef EXPORTSPREADSHEETDIALOG_H
#define EXPORTSPREADSHEETDIALOG_H
@@ -30,44 +31,44 @@
#include "../../core/project.h"
-namespace Ui {
-class ExportSpreadsheetDialog;
+namespace Ui
+{
+ class ExportSpreadsheetDialog;
}
class ExportSpreadsheetDialog : public QDialog
{
- Q_OBJECT
+ Q_OBJECT
-public:
- explicit ExportSpreadsheetDialog(QWidget * parent);
- ~ExportSpreadsheetDialog();
+ public:
+ explicit ExportSpreadsheetDialog(QWidget *parent);
+ ~ExportSpreadsheetDialog();
- void setProject(const Project * p_project);
+ void setProject(const Project *p_project);
-public slots:
- void doSimpleProteinPeptideList(bool simple);
- void doProteinList(bool simple);
- void doGroups(bool simple);
- void doPeptidePos(bool simple);
- void doComparEmpai(bool simple);
- void doComparNsaf(bool simple);
- void doComparPai(bool simple);
- void doComparSpecificUniqueSequence(bool simple);
- void doComparUniqueSequence(bool simple);
- void doComparSpecificSpectra(bool simple);
- void doComparSpectra(bool simple);
- void doSamples(bool simple);
- void doSpectra(bool simple);
- void doPeptides(bool simple);
- void doProteins(bool simple);
- void doPtmIslands(bool simple);
- void doPtmSpectra(bool simple);
-
-signals:
+ public slots:
+ void doSimpleProteinPeptideList(bool simple);
+ void doProteinList(bool simple);
+ void doGroups(bool simple);
+ void doPeptidePos(bool simple);
+ void doComparEmpai(bool simple);
+ void doComparNsaf(bool simple);
+ void doComparPai(bool simple);
+ void doComparSpecificUniqueSequence(bool simple);
+ void doComparUniqueSequence(bool simple);
+ void doComparSpecificSpectra(bool simple);
+ void doComparSpectra(bool simple);
+ void doSamples(bool simple);
+ void doSpectra(bool simple);
+ void doPeptides(bool simple);
+ void doProteins(bool simple);
+ void doPtmIslands(bool simple);
+ void doPtmSpectra(bool simple);
-private:
- Ui::ExportSpreadsheetDialog *ui;
+ signals:
+ private:
+ Ui::ExportSpreadsheetDialog *ui;
};
#endif // EXPORTSPREADSHEETDIALOG_H
diff --git a/src/gui/load_results_dialog/loadresultsdialog.cpp b/src/gui/load_results_dialog/loadresultsdialog.cpp
index 5843021bd48bfad38011bd44ea5569bd749685b9..a83d1f34d03b9228f6c56cb03f4d22b350e4343f 100644
--- a/src/gui/load_results_dialog/loadresultsdialog.cpp
+++ b/src/gui/load_results_dialog/loadresultsdialog.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "loadresultsdialog.h"
#include "ui_load_results_dialog.h"
@@ -30,81 +31,104 @@
#include <pappsomspp/pappsoexception.h>
-LoadResultsDialog::LoadResultsDialog(QWidget * parent):
- QDialog(parent),
- ui(new Ui::LoadResultsDialog)
+LoadResultsDialog::LoadResultsDialog(QWidget *parent)
+ : QDialog(parent), ui(new Ui::LoadResultsDialog)
{
- qDebug() << "LoadResultsDialog::LoadResultsDialog begin";
- ui->setupUi(this);
- this->setModal(true);
- _p_file_list = new QStringListModel();
-
- QSettings settings;
- AutomaticFilterParameters param = ui->automatic_filter_widget->getAutomaticFilterParameters();
- param.setFilterCrossSamplePeptideNumber(settings.value("automatic_filter/cross_sample", "true").toBool());
- param.setFilterMinimumPeptidePerMatch((unsigned int) settings.value("automatic_filter/peptide_number", "2").toInt());
- param.setFilterPeptideEvalue(settings.value("automatic_filter/peptide_evalue", "0.05").toDouble());
- param.setFilterProteinEvalue(settings.value("automatic_filter/protein_evalue", "0.01").toDouble());
- ui->automatic_filter_widget->setAutomaticFilterParameters(param);
-
+ qDebug() << "LoadResultsDialog::LoadResultsDialog begin";
+ ui->setupUi(this);
+ this->setModal(true);
+ _p_file_list = new QStringListModel();
+
+ QSettings settings;
+ AutomaticFilterParameters param =
+ ui->automatic_filter_widget->getAutomaticFilterParameters();
+ param.setFilterCrossSamplePeptideNumber(
+ settings.value("automatic_filter/cross_sample", "true").toBool());
+ param.setFilterMinimumPeptidePerMatch(
+ (unsigned int)settings.value("automatic_filter/peptide_number", "2")
+ .toInt());
+ param.setFilterPeptideEvalue(
+ settings.value("automatic_filter/peptide_evalue", "0.05").toDouble());
+ param.setFilterProteinEvalue(
+ settings.value("automatic_filter/protein_evalue", "0.01").toDouble());
+ ui->automatic_filter_widget->setAutomaticFilterParameters(param);
#if QT_VERSION >= 0x050000
- // Qt5 code
+ // Qt5 code
#else
-// Qt4 code
+ // Qt4 code
#endif
- qDebug() << "LoadResultsDialog::LoadResultsDialog end";
+ qDebug() << "LoadResultsDialog::LoadResultsDialog end";
}
LoadResultsDialog::~LoadResultsDialog()
{
- delete _p_file_list;
- delete ui;
+ delete _p_file_list;
+ delete ui;
}
-bool LoadResultsDialog::isIndividual() const {
- if (ui->individual_radio->isChecked()) {
- return true;
+bool
+LoadResultsDialog::isIndividual() const
+{
+ if(ui->individual_radio->isChecked())
+ {
+ return true;
}
}
-QStringList LoadResultsDialog::getFileList() const {
- return _p_file_list->stringList();
+QStringList
+LoadResultsDialog::getFileList() const
+{
+ return _p_file_list->stringList();
}
-AutomaticFilterParameters LoadResultsDialog::getAutomaticFilterParameters() const {
- return ui->automatic_filter_widget->getAutomaticFilterParameters();
+AutomaticFilterParameters
+LoadResultsDialog::getAutomaticFilterParameters() const
+{
+ return ui->automatic_filter_widget->getAutomaticFilterParameters();
}
-void LoadResultsDialog::clearFileList() {
- _p_file_list->removeRows( 0, _p_file_list->rowCount() );
+void
+LoadResultsDialog::clearFileList()
+{
+ _p_file_list->removeRows(0, _p_file_list->rowCount());
}
-void LoadResultsDialog::chooseFiles() {
- try {
- QSettings settings;
- QString default_location = settings.value("path/identificationfiles", "").toString();
-
- QStringList filenames = QFileDialog::getOpenFileNames(this,tr("identification files"),default_location,
- tr("X!Tandem, Mascot DAT or mzIdentML files (*.xml *.mzid *.dat *.pepxml *.pepXML);;all files (*)") );
-
- if (filenames.size() > 0) {
- settings.setValue("path/identificationfiles", QFileInfo(filenames[0]).absolutePath());
+void
+LoadResultsDialog::chooseFiles()
+{
+ try
+ {
+ QSettings settings;
+ QString default_location =
+ settings.value("path/identificationfiles", "").toString();
+
+ QStringList filenames = QFileDialog::getOpenFileNames(
+ this, tr("identification files"), default_location,
+ tr("X!Tandem, Mascot DAT or mzIdentML files (*.xml *.mzid *.dat "
+ "*.pepxml *.pepXML);;all files (*)"));
+
+ if(filenames.size() > 0)
+ {
+ settings.setValue("path/identificationfiles",
+ QFileInfo(filenames[0]).absolutePath());
}
- QStringList file_list = _p_file_list->stringList();
- file_list.append(filenames);
- _p_file_list->setStringList(file_list);
- ui->file_list_view->setModel(_p_file_list);
-
+ QStringList file_list = _p_file_list->stringList();
+ file_list.append(filenames);
+ _p_file_list->setStringList(file_list);
+ ui->file_list_view->setModel(_p_file_list);
}
- catch (pappso::PappsoException & error) {
- //QMessageBox::warning(this,
- // tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
+ catch(pappso::PappsoException &error)
+ {
+ // QMessageBox::warning(this,
+ // tr("Error choosing identification result files :
+ // %1").arg(error.qwhat()), error);
}
}
-void LoadResultsDialog::setProjectContaminants(Project * p_project) const {
- ui->contaminant_widget->setProjectContaminants(p_project);
+void
+LoadResultsDialog::setProjectContaminants(Project *p_project) const
+{
+ ui->contaminant_widget->setProjectContaminants(p_project);
}
-
diff --git a/src/gui/load_results_dialog/loadresultsdialog.h b/src/gui/load_results_dialog/loadresultsdialog.h
index c4b7c9440b9ef053d20cfec430326232713ae352..613e058c2f3d273e1a51cb210692da82f4b2660e 100644
--- a/src/gui/load_results_dialog/loadresultsdialog.h
+++ b/src/gui/load_results_dialog/loadresultsdialog.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef LOADRESULTSDIALOG_H
#define LOADRESULTSDIALOG_H
@@ -30,33 +31,33 @@
#include "../../core/project.h"
-namespace Ui {
-class LoadResultsDialog;
+namespace Ui
+{
+ class LoadResultsDialog;
}
class LoadResultsDialog : public QDialog
{
- Q_OBJECT
-
-public:
- explicit LoadResultsDialog(QWidget * parent);
- ~LoadResultsDialog();
+ Q_OBJECT
- AutomaticFilterParameters getAutomaticFilterParameters() const;
- QStringList getFileList() const;
- bool isIndividual() const;
- void setProjectContaminants(Project * p_project) const;
-public slots:
- void chooseFiles();
- void clearFileList();
+ public:
+ explicit LoadResultsDialog(QWidget *parent);
+ ~LoadResultsDialog();
-signals:
+ AutomaticFilterParameters getAutomaticFilterParameters() const;
+ QStringList getFileList() const;
+ bool isIndividual() const;
+ void setProjectContaminants(Project *p_project) const;
+ public slots:
+ void chooseFiles();
+ void clearFileList();
-private:
- Ui::LoadResultsDialog *ui;
- QStringListModel * _p_file_list;
+ signals:
+ private:
+ Ui::LoadResultsDialog *ui;
+ QStringListModel *_p_file_list;
};
#endif // LOADRESULTSDIALOG_H
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 48d803e001abfdd596c1e4ae940b904c23c9d858..ee7bc639fd2815433814c06162028e4e957ad8d4 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include <QSettings>
#include <QFileDialog>
@@ -36,527 +37,662 @@
#include "workerthread.h"
#include "output/xpip.h"
-MainWindow::MainWindow(QWidget *parent):
- QMainWindow(parent),
- ui(new Ui::Main)
+MainWindow::MainWindow(QWidget *parent) : QMainWindow(parent), ui(new Ui::Main)
{
- _p_app = QCoreApplication::instance();
- ui->setupUi(this);
- setWindowTitle(QString("%1 %2").arg(SOFTWARE_NAME).arg(XTPCPP_VERSION));
- setWindowIcon(QIcon(":/xtpcpp_icon/resources/xtandempipeline_icon.svg"));
+ _p_app = QCoreApplication::instance();
+ ui->setupUi(this);
+ setWindowTitle(QString("%1 %2").arg(SOFTWARE_NAME).arg(XTPCPP_VERSION));
+ setWindowIcon(QIcon(":/xtpcpp_icon/resources/xtandempipeline_icon.svg"));
- WorkerThread *worker = new WorkerThread(this);
- worker->moveToThread(&_worker_thread);
- _worker_thread.start();
+ WorkerThread *worker = new WorkerThread(this);
+ worker->moveToThread(&_worker_thread);
+ _worker_thread.start();
- _p_load_results_dialog = new LoadResultsDialog(this);
- _p_export_spreadsheet_dialog = new ExportSpreadsheetDialog(this);
- _p_waiting_message_dialog = new WaitingMessageDialog(this);
- _p_tandem_run_dialog = new TandemRunDialog(this);
+ _p_load_results_dialog = new LoadResultsDialog(this);
+ _p_export_spreadsheet_dialog = new ExportSpreadsheetDialog(this);
+ _p_waiting_message_dialog = new WaitingMessageDialog(this);
+ _p_tandem_run_dialog = new TandemRunDialog(this);
- _project_window = new ProjectWindow(this);
+ _project_window = new ProjectWindow(this);
- ui->menu_export_files->setDisabled(true);
- ui->centralwidget->layout()->addWidget(_project_window);
- _project_window->hide();
- ui->action_save_project->setDisabled(true);
- ui->default_display_widget->show();
- //_protein_list_window = new ProteinListWindow(this);
- //QDockWidget *dock = new QDockWidget(tr("Protein List"), this);
- //dock->setWidget(_protein_list_window);
- //addDockWidget(Qt::RightDockWidgetArea, dock);
+ ui->menu_export_files->setDisabled(true);
+ ui->centralwidget->layout()->addWidget(_project_window);
+ _project_window->hide();
+ ui->action_save_project->setDisabled(true);
+ ui->default_display_widget->show();
+ //_protein_list_window = new ProteinListWindow(this);
+ // QDockWidget *dock = new QDockWidget(tr("Protein List"), this);
+ // dock->setWidget(_protein_list_window);
+ // addDockWidget(Qt::RightDockWidgetArea, dock);
- qRegisterMetaType<ProjectSp>("ProjectSp");
- qRegisterMetaType<AutomaticFilterParameters>("AutomaticFilterParameters");
- qRegisterMetaType<GroupingType>("GroupingType");
+ qRegisterMetaType<ProjectSp>("ProjectSp");
+ qRegisterMetaType<AutomaticFilterParameters>("AutomaticFilterParameters");
+ qRegisterMetaType<GroupingType>("GroupingType");
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect(_p_tandem_run_dialog, &TandemRunDialog::accepted, this, &MainWindow::doAcceptedTandemRunDialog);
- connect(_p_load_results_dialog, &LoadResultsDialog::accepted, this,&MainWindow::doAcceptedLoadResultDialog);
- connect(_p_export_spreadsheet_dialog, &ExportSpreadsheetDialog::accepted, this,&MainWindow::doAcceptedExportSpreadsheetDialog);
+ // Qt5 code
+ connect(_p_tandem_run_dialog, &TandemRunDialog::accepted, this,
+ &MainWindow::doAcceptedTandemRunDialog);
+ connect(_p_load_results_dialog, &LoadResultsDialog::accepted, this,
+ &MainWindow::doAcceptedLoadResultDialog);
+ connect(_p_export_spreadsheet_dialog, &ExportSpreadsheetDialog::accepted,
+ this, &MainWindow::doAcceptedExportSpreadsheetDialog);
#else
-// Qt4 code
+ // Qt4 code
- connect(_p_tandem_run_dialog, SIGNAL(accepted()), this,SLOT(doAcceptedTandemRunDialog()));
- connect(_p_load_results_dialog, SIGNAL(accepted()), this,SLOT(doAcceptedLoadResultDialog()));
- connect(_p_export_spreadsheet_dialog, SIGNAL(accepted()), this,SLOT(doAcceptedExportSpreadsheetDialog()));
+ connect(_p_tandem_run_dialog, SIGNAL(accepted()), this,
+ SLOT(doAcceptedTandemRunDialog()));
+ connect(_p_load_results_dialog, SIGNAL(accepted()), this,
+ SLOT(doAcceptedLoadResultDialog()));
+ connect(_p_export_spreadsheet_dialog, SIGNAL(accepted()), this,
+ SLOT(doAcceptedExportSpreadsheetDialog()));
#endif
}
MainWindow::~MainWindow()
{
- qDebug() << "MainWindow::~MainWindow";
- _worker_thread.quit();
- _worker_thread.wait();
- //if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
- delete ui;
- //delete _project_window;
- delete _p_load_results_dialog;
- delete _p_export_spreadsheet_dialog;
- delete _p_waiting_message_dialog;
- qDebug() << "MainWindow::~MainWindow end";
-
-}
-
-bool MainWindow::stopWorkerThread() {
- return _p_waiting_message_dialog->stopWorkerThread();
+ qDebug() << "MainWindow::~MainWindow";
+ _worker_thread.quit();
+ _worker_thread.wait();
+ // if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
+ delete ui;
+ // delete _project_window;
+ delete _p_load_results_dialog;
+ delete _p_export_spreadsheet_dialog;
+ delete _p_waiting_message_dialog;
+ qDebug() << "MainWindow::~MainWindow end";
+}
+
+bool
+MainWindow::stopWorkerThread()
+{
+ return _p_waiting_message_dialog->stopWorkerThread();
}
-void MainWindow::closeEvent(QCloseEvent * event) {
- if (true) {
- event->accept();
- } else {
- event->ignore();
+void
+MainWindow::closeEvent(QCloseEvent *event)
+{
+ if(true)
+ {
+ event->accept();
+ }
+ else
+ {
+ event->ignore();
}
}
-void MainWindow::viewError(QString error) {
- hideWaitingMessage();
- QMessageBox::warning(this,
- tr("Oops! an error occurred in XTPCPP. Dont Panic :"), error);
+void
+MainWindow::viewError(QString error)
+{
+ hideWaitingMessage();
+ QMessageBox::warning(
+ this, tr("Oops! an error occurred in XTPCPP. Dont Panic :"), error);
}
-void MainWindow::doDisplayJobFinished(QString message) {
- qDebug() << "MainWindow::doDisplayJobFinished " << message;
- hideWaitingMessage();
- QMessageBox::information(this,
- tr("job finished"), message);
-
-
+void
+MainWindow::doDisplayJobFinished(QString message)
+{
+ qDebug() << "MainWindow::doDisplayJobFinished " << message;
+ hideWaitingMessage();
+ QMessageBox::information(this, tr("job finished"), message);
}
-void MainWindow::doDisplayLoadingMessage(QString message) {
- qDebug() << "MainWindow::doDisplayLoadingMessage " << message;
- _p_waiting_message_dialog->message(message);
- ui->statusbar->showMessage(message);
+void
+MainWindow::doDisplayLoadingMessage(QString message)
+{
+ qDebug() << "MainWindow::doDisplayLoadingMessage " << message;
+ _p_waiting_message_dialog->message(message);
+ ui->statusbar->showMessage(message);
}
-void MainWindow::doDisplayLoadingMessagePercent(QString message, int value) {
- qDebug() << "MainWindow::doDisplayLoadingMessagePercent " << message << " " << value;
- _p_waiting_message_dialog->message(message, value);
- ui->statusbar->showMessage(message);
+void
+MainWindow::doDisplayLoadingMessagePercent(QString message, int value)
+{
+ qDebug() << "MainWindow::doDisplayLoadingMessagePercent " << message << " "
+ << value;
+ _p_waiting_message_dialog->message(message, value);
+ ui->statusbar->showMessage(message);
}
-void MainWindow::doWorkerSetText(QString text) {
- _p_waiting_message_dialog->setText(text);
+void
+MainWindow::doWorkerSetText(QString text)
+{
+ _p_waiting_message_dialog->setText(text);
}
-void MainWindow::doWorkerAppendText(char * text) {
- _p_waiting_message_dialog->appendText(text);
+void
+MainWindow::doWorkerAppendText(char *text)
+{
+ _p_waiting_message_dialog->appendText(text);
}
-void MainWindow::doActionQuit() {
- qDebug() << "MainWindow::doActionQuit begin";
- this->close();
+void
+MainWindow::doActionQuit()
+{
+ qDebug() << "MainWindow::doActionQuit begin";
+ this->close();
}
-void MainWindow::doAcceptedExportSpreadsheetDialog() {
- qDebug() << "MainWindow::doAcceptedExportSpreadsheetDialog begin";
- try {
- QSettings settings;
- QString default_location = settings.value("path/export_ods", "").toString();
-
- QString filename = QFileDialog::getSaveFileName(this, tr("Save ODS file"),
- QString("%1/untitled.ods").arg(default_location),
- tr("Open Document Spreadsheet (*.ods)"));
-
- if (filename.isEmpty()) {
- return;
+void
+MainWindow::doAcceptedExportSpreadsheetDialog()
+{
+ qDebug() << "MainWindow::doAcceptedExportSpreadsheetDialog begin";
+ try
+ {
+ QSettings settings;
+ QString default_location =
+ settings.value("path/export_ods", "").toString();
+
+ QString filename = QFileDialog::getSaveFileName(
+ this, tr("Save ODS file"),
+ QString("%1/untitled.ods").arg(default_location),
+ tr("Open Document Spreadsheet (*.ods)"));
+
+ if(filename.isEmpty())
+ {
+ return;
}
- settings.setValue("path/export_ods", QFileInfo(filename).absolutePath());
+ settings.setValue("path/export_ods", QFileInfo(filename).absolutePath());
- showWaitingMessage(tr("writing %1 ODS file").arg(QFileInfo(filename).fileName()));
- emit operateWritingOdsFile(filename, _project_sp);
- //emit operateXpipFile(filename);
+ showWaitingMessage(
+ tr("writing %1 ODS file").arg(QFileInfo(filename).fileName()));
+ emit operateWritingOdsFile(filename, _project_sp);
+ // emit operateXpipFile(filename);
}
- catch (pappso::PappsoException & error) {
- viewError(tr("Error while writing ODS file :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ viewError(tr("Error while writing ODS file :\n%1").arg(error.qwhat()));
}
- qDebug() << "MainWindow::doAcceptedExportSpreadsheetDialog end";
+ qDebug() << "MainWindow::doAcceptedExportSpreadsheetDialog end";
}
-void MainWindow::doAcceptedTandemRunDialog()
+void
+MainWindow::doAcceptedTandemRunDialog()
{
- qDebug() << "MainWindow::doAcceptedTandemRunDialog begin";
- showWaitingMessage(tr("Running X!Tandem"));
- emit operateRunningXtandem(_p_tandem_run_dialog->getTandemRunBatch());
- qDebug() << "MainWindow::doAcceptedTandemRunDialog end";
-}
-
-void MainWindow::doAcceptedLoadResultDialog() {
- qDebug() << "MainWindow::doAcceptedLoadResultDialog begin";
- AutomaticFilterParameters param = _p_load_results_dialog->getAutomaticFilterParameters();
- QSettings settings;
- settings.setValue("automatic_filter/cross_sample", QString("%1").arg(param.getFilterCrossSamplePeptideNumber()));
- settings.setValue("automatic_filter/peptide_number", QString("%1").arg(param.getFilterMinimumPeptidePerMatch()));
- settings.setValue("automatic_filter/peptide_evalue", QString("%1").arg(param.getFilterPeptideEvalue()));
- settings.setValue("automatic_filter/protein_evalue", QString("%1").arg(param.getFilterProteinEvalue()));
-
- QStringList file_list = _p_load_results_dialog->getFileList();
- bool is_individual = _p_load_results_dialog->isIndividual();
-
- showWaitingMessage(tr("Loading files"));
- emit operateLoadingResults(is_individual, param, file_list);
- qDebug() << "MainWindow::doAcceptedLoadResultDialog end";
+ qDebug() << "MainWindow::doAcceptedTandemRunDialog begin";
+ showWaitingMessage(tr("Running X!Tandem"));
+ emit operateRunningXtandem(_p_tandem_run_dialog->getTandemRunBatch());
+ qDebug() << "MainWindow::doAcceptedTandemRunDialog end";
}
-void MainWindow::doOperationFailed(QString error) {
- hideWaitingMessage();
- viewError(error);
+void
+MainWindow::doAcceptedLoadResultDialog()
+{
+ qDebug() << "MainWindow::doAcceptedLoadResultDialog begin";
+ AutomaticFilterParameters param =
+ _p_load_results_dialog->getAutomaticFilterParameters();
+ QSettings settings;
+ settings.setValue(
+ "automatic_filter/cross_sample",
+ QString("%1").arg(param.getFilterCrossSamplePeptideNumber()));
+ settings.setValue("automatic_filter/peptide_number",
+ QString("%1").arg(param.getFilterMinimumPeptidePerMatch()));
+ settings.setValue("automatic_filter/peptide_evalue",
+ QString("%1").arg(param.getFilterPeptideEvalue()));
+ settings.setValue("automatic_filter/protein_evalue",
+ QString("%1").arg(param.getFilterProteinEvalue()));
+
+ QStringList file_list = _p_load_results_dialog->getFileList();
+ bool is_individual = _p_load_results_dialog->isIndividual();
+
+ showWaitingMessage(tr("Loading files"));
+ emit operateLoadingResults(is_individual, param, file_list);
+ qDebug() << "MainWindow::doAcceptedLoadResultDialog end";
+}
+
+void
+MainWindow::doOperationFailed(QString error)
+{
+ hideWaitingMessage();
+ viewError(error);
}
-void MainWindow::doOperationFinished() {
- hideWaitingMessage();
+void
+MainWindow::doOperationFinished()
+{
+ hideWaitingMessage();
}
-void MainWindow::doGroupingFinished() {
- hideWaitingMessage();
- _project_window->setProjectSp(_project_sp);
-
+void
+MainWindow::doGroupingFinished()
+{
+ hideWaitingMessage();
+ _project_window->setProjectSp(_project_sp);
}
-void MainWindow::doLoadingResultsReady(ProjectSp project_sp) {
- qDebug() << "MainWindow::doLoadingResultsReady begin";
- if (_p_load_results_dialog != nullptr) {
- _p_load_results_dialog->setProjectContaminants(project_sp.get());
+void
+MainWindow::doLoadingResultsReady(ProjectSp project_sp)
+{
+ qDebug() << "MainWindow::doLoadingResultsReady begin";
+ if(_p_load_results_dialog != nullptr)
+ {
+ _p_load_results_dialog->setProjectContaminants(project_sp.get());
}
- doProjectReady(project_sp);
- qDebug() << "MainWindow::doLoadingResultsReady end";
+ doProjectReady(project_sp);
+ qDebug() << "MainWindow::doLoadingResultsReady end";
}
-void MainWindow::doProjectReady(ProjectSp project_sp) {
+void
+MainWindow::doProjectReady(ProjectSp project_sp)
+{
- qDebug() << "MainWindow::doProjectReady begin";
- qDebug() << "MainWindow::doProjectReady begin a " << project_sp.get()->getFastaFileStore().getFastaFileList().size() ;
- _project_sp = project_sp;
+ qDebug() << "MainWindow::doProjectReady begin";
+ qDebug() << "MainWindow::doProjectReady begin a "
+ << project_sp.get()->getFastaFileStore().getFastaFileList().size();
+ _project_sp = project_sp;
- qDebug() << "MainWindow::doProjectReady begin b " << _project_sp.get()->getFastaFileStore().getFastaFileList().size() ;
+ qDebug() << "MainWindow::doProjectReady begin b "
+ << _project_sp.get()->getFastaFileStore().getFastaFileList().size();
- showWaitingMessage(tr("grouping proteins"));
- emit operateGrouping(project_sp);
+ showWaitingMessage(tr("grouping proteins"));
+ emit operateGrouping(project_sp);
- ui->menu_export_files->setDisabled(false);
- ui->menu_edit->setDisabled(false);
+ ui->menu_export_files->setDisabled(false);
+ ui->menu_edit->setDisabled(false);
- _project_window->show();
- ui->default_display_widget->hide();
- ui->action_save_project->setDisabled(false);
+ _project_window->show();
+ ui->default_display_widget->hide();
+ ui->action_save_project->setDisabled(false);
- qDebug() << "MainWindow::doProjectReady end";
+ qDebug() << "MainWindow::doProjectReady end";
}
-void MainWindow::doActionLabelingMethods () {
- _project_window->editLabelingMethods();
+void
+MainWindow::doActionLabelingMethods()
+{
+ _project_window->editLabelingMethods();
}
-void MainWindow::doActionModifications() {
- _project_window->editModifications();
+void
+MainWindow::doActionModifications()
+{
+ _project_window->editModifications();
}
-void MainWindow::doProjectNotReady(QString error) {
- viewError(error);
+void
+MainWindow::doProjectNotReady(QString error)
+{
+ viewError(error);
}
-void MainWindow::doActionTandemRun() {
- _p_tandem_run_dialog->show();
- _p_tandem_run_dialog->raise();
- _p_tandem_run_dialog->activateWindow();
+void
+MainWindow::doActionTandemRun()
+{
+ _p_tandem_run_dialog->show();
+ _p_tandem_run_dialog->raise();
+ _p_tandem_run_dialog->activateWindow();
}
-void MainWindow::loadResults() {
-
- _p_load_results_dialog->show();
- _p_load_results_dialog->raise();
- _p_load_results_dialog->activateWindow();
+void
+MainWindow::loadResults()
+{
+ _p_load_results_dialog->show();
+ _p_load_results_dialog->raise();
+ _p_load_results_dialog->activateWindow();
}
-void MainWindow::hideWaitingMessage() {
+void
+MainWindow::hideWaitingMessage()
+{
- _p_waiting_message_dialog->hide();
- ui->statusbar->showMessage("");
+ _p_waiting_message_dialog->hide();
+ ui->statusbar->showMessage("");
}
-void MainWindow::showWaitingMessage(const QString title) {
- _p_waiting_message_dialog->setWindowTitle(title);
- _p_waiting_message_dialog->show();
- _p_waiting_message_dialog->raise();
- _p_waiting_message_dialog->activateWindow();
-
+void
+MainWindow::showWaitingMessage(const QString title)
+{
+ _p_waiting_message_dialog->setWindowTitle(title);
+ _p_waiting_message_dialog->show();
+ _p_waiting_message_dialog->raise();
+ _p_waiting_message_dialog->activateWindow();
}
-void MainWindow::selectXpipFile() {
- try {
- QSettings settings;
- QString default_location = settings.value("path/xpipfile", "").toString();
+void
+MainWindow::selectXpipFile()
+{
+ try
+ {
+ QSettings settings;
+ QString default_location = settings.value("path/xpipfile", "").toString();
- QString filename = QFileDialog::getOpenFileName(this,
- tr("Open XPIP File"), default_location,
- tr("xpip files (*.xpip);;all files (*)"));
+ QString filename = QFileDialog::getOpenFileName(
+ this, tr("Open XPIP File"), default_location,
+ tr("xpip files (*.xpip);;all files (*)"));
- if (filename.isEmpty()) {
- return;
+ if(filename.isEmpty())
+ {
+ return;
}
- settings.setValue("path/xpipfile", QFileInfo(filename).absolutePath());
- showWaitingMessage(tr("Loading %1 XPIP file").arg(QFileInfo(filename).fileName()));
- emit operateXpipFile(filename);
+ settings.setValue("path/xpipfile", QFileInfo(filename).absolutePath());
+ showWaitingMessage(
+ tr("Loading %1 XPIP file").arg(QFileInfo(filename).fileName()));
+ emit operateXpipFile(filename);
}
- catch (pappso::PappsoException & error) {
- viewError(tr("Error while reading XPIP file :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ viewError(tr("Error while reading XPIP file :\n%1").arg(error.qwhat()));
}
-
}
-void MainWindow::doActionSaveProject() {
- try {
- //QMessageBox::warning(this,
- // tr("Experimental feature"), "WARNING : project files export is not ready");
- QSettings settings;
- QString default_location = settings.value("path/xpipfile", "").toString();
+void
+MainWindow::doActionSaveProject()
+{
+ try
+ {
+ // QMessageBox::warning(this,
+ // tr("Experimental feature"), "WARNING : project
+ // files export is not ready");
+ QSettings settings;
+ QString default_location = settings.value("path/xpipfile", "").toString();
- QString filename = QFileDialog::getSaveFileName(this, tr("Save XPIP file"),
- QString("%1/untitled.xpip").arg(default_location),
- tr("XPIP (*.xpip)"));
+ QString filename = QFileDialog::getSaveFileName(
+ this, tr("Save XPIP file"),
+ QString("%1/untitled.xpip").arg(default_location), tr("XPIP (*.xpip)"));
- if (filename.isEmpty()) {
- return;
+ if(filename.isEmpty())
+ {
+ return;
}
- settings.setValue("path/xpipfile", QFileInfo(filename).absolutePath());
- showWaitingMessage(tr("Writing %1 XPIP file").arg(QFileInfo(filename).fileName()));
- emit operateWritingXpipFile(filename, _project_sp);
-
+ settings.setValue("path/xpipfile", QFileInfo(filename).absolutePath());
+ showWaitingMessage(
+ tr("Writing %1 XPIP file").arg(QFileInfo(filename).fileName()));
+ emit operateWritingXpipFile(filename, _project_sp);
}
- catch (pappso::PappsoException & error) {
- viewError(tr("Error while writing XPIP file :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ viewError(tr("Error while writing XPIP file :\n%1").arg(error.qwhat()));
}
-
}
-void MainWindow::doActionSpreadsheet() {
- qDebug() << "MainWindow::doActionSpreadsheet begin";
- try {
- if (_project_sp.get() != nullptr) {
- _p_export_spreadsheet_dialog->setProject(_project_sp.get());
+void
+MainWindow::doActionSpreadsheet()
+{
+ qDebug() << "MainWindow::doActionSpreadsheet begin";
+ try
+ {
+ if(_project_sp.get() != nullptr)
+ {
+ _p_export_spreadsheet_dialog->setProject(_project_sp.get());
}
- _p_export_spreadsheet_dialog->show();
- _p_export_spreadsheet_dialog->raise();
- _p_export_spreadsheet_dialog->activateWindow();
+ _p_export_spreadsheet_dialog->show();
+ _p_export_spreadsheet_dialog->raise();
+ _p_export_spreadsheet_dialog->activateWindow();
}
- catch (pappso::PappsoException & error) {
- viewError(tr("Error doActionSpreadsheet :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ viewError(tr("Error doActionSpreadsheet :\n%1").arg(error.qwhat()));
}
- qDebug() << "MainWindow::doActionSpreadsheet end";
+ qDebug() << "MainWindow::doActionSpreadsheet end";
}
-void MainWindow::doActionSpectralCountingMcq()
+void
+MainWindow::doActionSpectralCountingMcq()
{
- qDebug() << "MainWindow::doActionSpectralCountingMcq begin";
+ qDebug() << "MainWindow::doActionSpectralCountingMcq begin";
- QSettings settings;
- QString default_location = settings.value("path/scmcqfile", "").toString();
+ QSettings settings;
+ QString default_location = settings.value("path/scmcqfile", "").toString();
- QString filename = QFileDialog::getSaveFileName(this, tr("Save spectral count TSV file"),
- QString("%1/untitled.tsv").arg(default_location),
- tr("TSV (*.tsv)"));
+ QString filename = QFileDialog::getSaveFileName(
+ this, tr("Save spectral count TSV file"),
+ QString("%1/untitled.tsv").arg(default_location), tr("TSV (*.tsv)"));
- if (filename.isEmpty()) {
- return;
+ if(filename.isEmpty())
+ {
+ return;
}
- settings.setValue("path/scmcqfile", QFileInfo(filename).absolutePath());
+ settings.setValue("path/scmcqfile", QFileInfo(filename).absolutePath());
- showWaitingMessage(tr("Writing %1 spectral count file for MassChroqR").arg(QFileInfo(filename).fileName()));
- emit operateWritingMcqrSpectralCountFile(filename, _project_sp);
+ showWaitingMessage(tr("Writing %1 spectral count file for MassChroqR")
+ .arg(QFileInfo(filename).fileName()));
+ emit operateWritingMcqrSpectralCountFile(filename, _project_sp);
- qDebug() << "MainWindow::doActionSpectralCountingMcq end";
+ qDebug() << "MainWindow::doActionSpectralCountingMcq end";
}
-void MainWindow::doActionFasta() {
- try {
+void
+MainWindow::doActionFasta()
+{
+ try
+ {
- QSettings settings;
- QString default_location = settings.value("path/fastafile", "").toString();
+ QSettings settings;
+ QString default_location =
+ settings.value("path/fastafile", "").toString();
- QString filename = QFileDialog::getSaveFileName(this, tr("Save FASTA file"),
- QString("%1/untitled.fasta").arg(default_location),
- tr("FASTA (*.fasta)"));
+ QString filename = QFileDialog::getSaveFileName(
+ this, tr("Save FASTA file"),
+ QString("%1/untitled.fasta").arg(default_location),
+ tr("FASTA (*.fasta)"));
- if (filename.isEmpty()) {
- return;
+ if(filename.isEmpty())
+ {
+ return;
}
- settings.setValue("path/fastafile", QFileInfo(filename).absolutePath());
-
-
-
- QFile outFile;
- outFile.setFileName(filename);
- outFile.open(QIODevice::WriteOnly);
- QTextStream * p_outputStream = new QTextStream(&outFile);
-
-
- pappso::FastaOutputStream fasta_output(*p_outputStream);
-
- for (IdentificationGroup * identification:_project_sp.get()->getIdentificationGroupList()) {
- for (ProteinMatch * protein_match : identification->getProteinMatchList()) {
- if (protein_match->getValidationState() >= ValidationState::grouped) {
- pappso::Protein protein(QString("%1 %2").arg(protein_match->getProteinXtpSp().get()->getAccession()).arg(protein_match->getProteinXtpSp().get()->getDescription()),protein_match->getProteinXtpSp().get()->getSequence());
- fasta_output.writeProtein(protein);
+ settings.setValue("path/fastafile", QFileInfo(filename).absolutePath());
+
+
+ QFile outFile;
+ outFile.setFileName(filename);
+ outFile.open(QIODevice::WriteOnly);
+ QTextStream *p_outputStream = new QTextStream(&outFile);
+
+
+ pappso::FastaOutputStream fasta_output(*p_outputStream);
+
+ for(IdentificationGroup *identification :
+ _project_sp.get()->getIdentificationGroupList())
+ {
+ for(ProteinMatch *protein_match :
+ identification->getProteinMatchList())
+ {
+ if(protein_match->getValidationState() >=
+ ValidationState::grouped)
+ {
+ pappso::Protein protein(
+ QString("%1 %2")
+ .arg(
+ protein_match->getProteinXtpSp().get()->getAccession())
+ .arg(protein_match->getProteinXtpSp()
+ .get()
+ ->getDescription()),
+ protein_match->getProteinXtpSp().get()->getSequence());
+ fasta_output.writeProtein(protein);
}
}
}
- p_outputStream->flush();
- delete p_outputStream;
- outFile.close();
- //emit operateXpipFile(filename);
+ p_outputStream->flush();
+ delete p_outputStream;
+ outFile.close();
+ // emit operateXpipFile(filename);
}
- catch (pappso::PappsoException & error) {
- viewError(tr("Error while writing MassChroqML file :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ viewError(
+ tr("Error while writing MassChroqML file :\n%1").arg(error.qwhat()));
}
}
-void MainWindow::doActionMassChroQ() {
- qDebug() << "MainWindow::doActionMassChroQ begin";
- try {
- _project_sp.get()->checkPsimodCompliance();
+void
+MainWindow::doActionMassChroQ()
+{
+ qDebug() << "MainWindow::doActionMassChroQ begin";
+ try
+ {
+ _project_sp.get()->checkPsimodCompliance();
- QSettings settings;
- QString default_location = settings.value("path/mcqfile", "").toString();
+ QSettings settings;
+ QString default_location = settings.value("path/mcqfile", "").toString();
- QString filename = QFileDialog::getSaveFileName(this, tr("Save MassChroqML file"),
- QString("%1/untitled.masschroqml").arg(default_location),
- tr("MassChroqML (*.masschroqml)"));
+ QString filename = QFileDialog::getSaveFileName(
+ this, tr("Save MassChroqML file"),
+ QString("%1/untitled.masschroqml").arg(default_location),
+ tr("MassChroqML (*.masschroqml)"));
- if (filename.isEmpty()) {
- return;
+ if(filename.isEmpty())
+ {
+ return;
}
- settings.setValue("path/mcqfile", QFileInfo(filename).absolutePath());
+ settings.setValue("path/mcqfile", QFileInfo(filename).absolutePath());
- showWaitingMessage(tr("Writing %1 MassChroqML file").arg(QFileInfo(filename).fileName()));
- emit operateWritingMassChroqFile(filename, _project_sp);
- //emit operateXpipFile(filename);
+ showWaitingMessage(
+ tr("Writing %1 MassChroqML file").arg(QFileInfo(filename).fileName()));
+ emit operateWritingMassChroqFile(filename, _project_sp);
+ // emit operateXpipFile(filename);
}
- catch (pappso::PappsoException & error) {
- viewError(tr("Error while writing MassChroqML file :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ viewError(
+ tr("Error while writing MassChroqML file :\n%1").arg(error.qwhat()));
}
- qDebug() << "MainWindow::doActionMassChroQ end";
+ qDebug() << "MainWindow::doActionMassChroQ end";
}
-void MainWindow::doActionMassChroqPRM() {
- qDebug() << "MainWindow::doActionMassChroqPRM begin";
- try {
- _project_sp.get()->checkPsimodCompliance();
+void
+MainWindow::doActionMassChroqPRM()
+{
+ qDebug() << "MainWindow::doActionMassChroqPRM begin";
+ try
+ {
+ _project_sp.get()->checkPsimodCompliance();
- QSettings settings;
- QString default_location = settings.value("path/mcqprmfile", "").toString();
+ QSettings settings;
+ QString default_location =
+ settings.value("path/mcqprmfile", "").toString();
- QString filename = QFileDialog::getSaveFileName(this, tr("Save MassChroqPRM file"),
- QString("%1/untitled.masschroqprm").arg(default_location),
- tr("MassChroqPRM (*.masschroqprm)"));
+ QString filename = QFileDialog::getSaveFileName(
+ this, tr("Save MassChroqPRM file"),
+ QString("%1/untitled.masschroqprm").arg(default_location),
+ tr("MassChroqPRM (*.masschroqprm)"));
- if (filename.isEmpty()) {
- return;
+ if(filename.isEmpty())
+ {
+ return;
}
- settings.setValue("path/mcqprmfile", QFileInfo(filename).absolutePath());
+ settings.setValue("path/mcqprmfile", QFileInfo(filename).absolutePath());
- showWaitingMessage(tr("Writing %1 MassChroqPRM file").arg(QFileInfo(filename).fileName()));
- emit operateWritingMassChroqPrmFile(filename, _project_sp);
- //emit operateXpipFile(filename);
+ showWaitingMessage(
+ tr("Writing %1 MassChroqPRM file").arg(QFileInfo(filename).fileName()));
+ emit operateWritingMassChroqPrmFile(filename, _project_sp);
+ // emit operateXpipFile(filename);
}
- catch (pappso::PappsoException & error) {
- viewError(tr("Error while writing MassChroqML file :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ viewError(
+ tr("Error while writing MassChroqML file :\n%1").arg(error.qwhat()));
}
- qDebug() << "MainWindow::doActionMassChroqPRM end";
+ qDebug() << "MainWindow::doActionMassChroqPRM end";
}
-void MainWindow::doActionProticDb() {
- qDebug() << "MainWindow::doActionProticDb begin";
- try {
- _project_sp.get()->checkPsimodCompliance();
+void
+MainWindow::doActionProticDb()
+{
+ qDebug() << "MainWindow::doActionProticDb begin";
+ try
+ {
+ _project_sp.get()->checkPsimodCompliance();
- QSettings settings;
- QString default_location = settings.value("path/proticfile", "").toString();
+ QSettings settings;
+ QString default_location =
+ settings.value("path/proticfile", "").toString();
- QString filename = QFileDialog::getSaveFileName(this, tr("Save PROTICdbML file"),
- QString("%1/untitled.proticdbml").arg(default_location),
- tr("PROTICdbML (*.proticdbml)"));
+ QString filename = QFileDialog::getSaveFileName(
+ this, tr("Save PROTICdbML file"),
+ QString("%1/untitled.proticdbml").arg(default_location),
+ tr("PROTICdbML (*.proticdbml)"));
- if (filename.isEmpty()) {
- return;
+ if(filename.isEmpty())
+ {
+ return;
}
- settings.setValue("path/proticfile", QFileInfo(filename).absolutePath());
+ settings.setValue("path/proticfile", QFileInfo(filename).absolutePath());
- showWaitingMessage(tr("Writing %1 PROTICdbML file").arg(QFileInfo(filename).fileName()));
- emit operateWritingProticFile(filename, _project_sp);
- //emit operateXpipFile(filename);
+ showWaitingMessage(
+ tr("Writing %1 PROTICdbML file").arg(QFileInfo(filename).fileName()));
+ emit operateWritingProticFile(filename, _project_sp);
+ // emit operateXpipFile(filename);
}
- catch (pappso::PappsoException & error) {
- viewError(tr("Error while writing PROTICdbML file :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ viewError(
+ tr("Error while writing PROTICdbML file :\n%1").arg(error.qwhat()));
}
- qDebug() << "MainWindow::doActionProticDb end";
+ qDebug() << "MainWindow::doActionProticDb end";
}
-void MainWindow::doActionAbout() {
- qDebug() << "MainWindow::doActionAbout begin";
- if (_p_about_dialog == nullptr) {
- _p_about_dialog = new AboutDialog(this);
+void
+MainWindow::doActionAbout()
+{
+ qDebug() << "MainWindow::doActionAbout begin";
+ if(_p_about_dialog == nullptr)
+ {
+ _p_about_dialog = new AboutDialog(this);
}
- _p_about_dialog->show();
- _p_about_dialog->raise();
- _p_about_dialog->activateWindow();
+ _p_about_dialog->show();
+ _p_about_dialog->raise();
+ _p_about_dialog->activateWindow();
- qDebug() << "MainWindow::doActionAbout end";
+ qDebug() << "MainWindow::doActionAbout end";
}
-
-
// 10ms after the application starts this method will run
// all QT messaging is running at this point so threads, signals and slots
// will all work as expected.
-void MainWindow::run()
+void
+MainWindow::run()
{
- QTextStream errorStream(stderr, QIODevice::WriteOnly);
+ QTextStream errorStream(stderr, QIODevice::WriteOnly);
- try {
- qDebug() << "MainWindow::run() begin";
- QCommandLineParser parser;
+ try
+ {
+ qDebug() << "MainWindow::run() begin";
+ QCommandLineParser parser;
- //throw pappso::PappsoException("test");
- parser.setApplicationDescription(QString(SOFTWARE_NAME).append(" ").append(XTPCPP_VERSION));
- parser.addHelpOption();
- parser.addVersionOption();
- parser.addPositionalArgument("XPIP project file", QCoreApplication::translate("main", "Project file to open."));
+ // throw pappso::PappsoException("test");
+ parser.setApplicationDescription(
+ QString(SOFTWARE_NAME).append(" ").append(XTPCPP_VERSION));
+ parser.addHelpOption();
+ parser.addVersionOption();
+ parser.addPositionalArgument(
+ "XPIP project file",
+ QCoreApplication::translate("main", "Project file to open."));
- qDebug() << "MainWindow::run() 1";
+ qDebug() << "MainWindow::run() 1";
- // Process the actual command line arguments given by the user
- parser.process(*_p_app);
+ // Process the actual command line arguments given by the user
+ parser.process(*_p_app);
- QStringList xpip_list = parser.positionalArguments();
- if (xpip_list.size() > 0) {
- showWaitingMessage(tr("Loading %1 XPIP file").arg(xpip_list.at(0)));
- emit operateXpipFile(xpip_list.at(0));
+ QStringList xpip_list = parser.positionalArguments();
+ if(xpip_list.size() > 0)
+ {
+ showWaitingMessage(tr("Loading %1 XPIP file").arg(xpip_list.at(0)));
+ emit operateXpipFile(xpip_list.at(0));
}
-
}
- catch (pappso::PappsoException& error)
+ catch(pappso::PappsoException &error)
{
- viewError(tr("Oops! an error occurred in X!TandemPipeline. Dont Panic :\n%1").arg(error.qwhat()));
+ viewError(
+ tr("Oops! an error occurred in X!TandemPipeline. Dont Panic :\n%1")
+ .arg(error.qwhat()));
}
- catch (std::exception& error)
+ catch(std::exception &error)
{
- viewError(tr("Oops! an error occurred in X!TandemPipeline. Dont Panic :\n%1").arg(error.what()));
+ viewError(
+ tr("Oops! an error occurred in X!TandemPipeline. Dont Panic :\n%1")
+ .arg(error.what()));
}
-
-
}
diff --git a/src/gui/mainwindow.h b/src/gui/mainwindow.h
index 3aed2e9b0eefc7f8c6f3eb8f23467cbafca51314..e3dde336e878d55e5ffe043872c6c07c6f093a57 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef MAINWINDOW_H
@@ -41,95 +42,95 @@
#include "core/tandem_run/tandemrunbatch.h"
-
-namespace Ui {
-class Main;
+namespace Ui
+{
+ class Main;
}
-class MainWindow: public QMainWindow {
- Q_OBJECT
-
-public:
-
- explicit MainWindow(QWidget * parent = 0);
- ~MainWindow();
-
- /** @brief tells if the worker should stop running his job
- * @param bool true asks to stop
- */
- bool stopWorkerThread();
-
-public slots:
- void run();
- void loadResults();
- void selectXpipFile();
- void doActionAbout();
- void doActionQuit();
- void doActionFasta();
- void doActionMassChroQ();
- void doActionMassChroqPRM();
- void doActionProticDb();
- void doActionLabelingMethods();
- void doActionTandemRun();
- void doActionSpreadsheet();
- void doActionModifications();
- void doActionSaveProject();
- void doDisplayLoadingMessage(QString message);
- void doDisplayLoadingMessagePercent(QString message, int value);
- void doDisplayJobFinished(QString message);
- void doWorkerAppendText(char *);
- void doWorkerSetText(QString);
- void doProjectReady(ProjectSp project_sp);
- void doLoadingResultsReady(ProjectSp project_sp);
- void doProjectNotReady(QString error);
- void doAcceptedLoadResultDialog();
- void doAcceptedTandemRunDialog();
- void doAcceptedExportSpreadsheetDialog();
- void doOperationFailed(QString);
- void doOperationFinished();
- void doGroupingFinished();
- void doActionSpectralCountingMcq();
- //void peptideEdited(QString peptideStr);
- // void setColor(const QColor &color);
- // void setShape(Shape shape);
-signals:
- //void peptideChanged(pappso::PeptideSp peptide);
- void operateXpipFile(QString xpip_file);
- void operateLoadingResults(bool is_individual, AutomaticFilterParameters param, QStringList file_list);
- void operateWritingXpipFile(QString filename, ProjectSp project_sp);
- void operateWritingOdsFile(QString filename, ProjectSp project_sp);
- void operateWritingMassChroqFile(QString filename, ProjectSp project_sp);
- void operateWritingMassChroqPrmFile(QString filename, ProjectSp project_sp);
- void operateWritingProticFile(QString filename, ProjectSp project_sp);
- void operateWritingMcqrSpectralCountFile(QString filename, ProjectSp project_sp);
- void operateGrouping(ProjectSp project_sp);
- void operateRunningXtandem(TandemRunBatch tandem_run_batch);
-
-protected:
-
- void closeEvent(QCloseEvent *event) override;
- void setProjectSp(ProjectSp project_sp);
-
-
-private:
-
- void showWaitingMessage(const QString title);
- void hideWaitingMessage();
- void viewError(QString error);
-
-private :
- QCoreApplication * _p_app;
- Ui::Main *ui;
- QThread _worker_thread;
- ProjectSp _project_sp=nullptr;
-
- ProjectWindow * _project_window=nullptr;
- LoadResultsDialog * _p_load_results_dialog=nullptr;
- ExportSpreadsheetDialog * _p_export_spreadsheet_dialog;
- WaitingMessageDialog * _p_waiting_message_dialog;
- AboutDialog * _p_about_dialog=nullptr;
- TandemRunDialog * _p_tandem_run_dialog=nullptr;
-
+class MainWindow : public QMainWindow
+{
+ Q_OBJECT
+
+ public:
+ explicit MainWindow(QWidget *parent = 0);
+ ~MainWindow();
+
+ /** @brief tells if the worker should stop running his job
+ * @param bool true asks to stop
+ */
+ bool stopWorkerThread();
+
+ public slots:
+ void run();
+ void loadResults();
+ void selectXpipFile();
+ void doActionAbout();
+ void doActionQuit();
+ void doActionFasta();
+ void doActionMassChroQ();
+ void doActionMassChroqPRM();
+ void doActionProticDb();
+ void doActionLabelingMethods();
+ void doActionTandemRun();
+ void doActionSpreadsheet();
+ void doActionModifications();
+ void doActionSaveProject();
+ void doDisplayLoadingMessage(QString message);
+ void doDisplayLoadingMessagePercent(QString message, int value);
+ void doDisplayJobFinished(QString message);
+ void doWorkerAppendText(char *);
+ void doWorkerSetText(QString);
+ void doProjectReady(ProjectSp project_sp);
+ void doLoadingResultsReady(ProjectSp project_sp);
+ void doProjectNotReady(QString error);
+ void doAcceptedLoadResultDialog();
+ void doAcceptedTandemRunDialog();
+ void doAcceptedExportSpreadsheetDialog();
+ void doOperationFailed(QString);
+ void doOperationFinished();
+ void doGroupingFinished();
+ void doActionSpectralCountingMcq();
+ // void peptideEdited(QString peptideStr);
+ // void setColor(const QColor &color);
+ // void setShape(Shape shape);
+ signals:
+ // void peptideChanged(pappso::PeptideSp peptide);
+ void operateXpipFile(QString xpip_file);
+ void operateLoadingResults(bool is_individual,
+ AutomaticFilterParameters param,
+ QStringList file_list);
+ void operateWritingXpipFile(QString filename, ProjectSp project_sp);
+ void operateWritingOdsFile(QString filename, ProjectSp project_sp);
+ void operateWritingMassChroqFile(QString filename, ProjectSp project_sp);
+ void operateWritingMassChroqPrmFile(QString filename, ProjectSp project_sp);
+ void operateWritingProticFile(QString filename, ProjectSp project_sp);
+ void operateWritingMcqrSpectralCountFile(QString filename,
+ ProjectSp project_sp);
+ void operateGrouping(ProjectSp project_sp);
+ void operateRunningXtandem(TandemRunBatch tandem_run_batch);
+
+ protected:
+ void closeEvent(QCloseEvent *event) override;
+ void setProjectSp(ProjectSp project_sp);
+
+
+ private:
+ void showWaitingMessage(const QString title);
+ void hideWaitingMessage();
+ void viewError(QString error);
+
+ private:
+ QCoreApplication *_p_app;
+ Ui::Main *ui;
+ QThread _worker_thread;
+ ProjectSp _project_sp = nullptr;
+
+ ProjectWindow *_project_window = nullptr;
+ LoadResultsDialog *_p_load_results_dialog = nullptr;
+ ExportSpreadsheetDialog *_p_export_spreadsheet_dialog;
+ WaitingMessageDialog *_p_waiting_message_dialog;
+ AboutDialog *_p_about_dialog = nullptr;
+ TandemRunDialog *_p_tandem_run_dialog = nullptr;
};
#endif // MAINWINDOW_H
diff --git a/src/gui/peptide_detail_view/peptidewindow.cpp b/src/gui/peptide_detail_view/peptidewindow.cpp
index 9e8591291ce5fdc56aa8add50c3e7bb9a4556d6e..c4fcb4abb31a89b19adc27c22c6ea0b3e5e3ab84 100644
--- a/src/gui/peptide_detail_view/peptidewindow.cpp
+++ b/src/gui/peptide_detail_view/peptidewindow.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "peptidewindow.h"
#include "../project_view/projectwindow.h"
@@ -37,317 +38,424 @@
#include <QSpacerItem>
-void SpectrumSpLoaderThread::doLoadSpectrumSp (PeptideEvidence * p_peptide_evidence) {
- qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp begin";
- pappso::SpectrumSp spectrum;
- try {
- spectrum = p_peptide_evidence->getIdentificationDataSource()->getSpectrumSp(p_peptide_evidence->getScan());
- emit spectrumSpReady(spectrum, QString(""), QString(""));
+void
+SpectrumSpLoaderThread::doLoadSpectrumSp(PeptideEvidence *p_peptide_evidence)
+{
+ qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp begin";
+ pappso::SpectrumSp spectrum;
+ try
+ {
+ spectrum =
+ p_peptide_evidence->getIdentificationDataSource()->getSpectrumSp(
+ p_peptide_evidence->getScan());
+ emit spectrumSpReady(spectrum, QString(""), QString(""));
}
- catch (pappso::ExceptionNotFound & error) {
- qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp error " << error.qwhat();
- emit spectrumSpReady(spectrum, error.qwhat(), QString(""));
+ catch(pappso::ExceptionNotFound &error)
+ {
+ qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp error "
+ << error.qwhat();
+ emit spectrumSpReady(spectrum, error.qwhat(), QString(""));
}
- catch (pappso::PappsoException & error) {
- qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp error " << error.qwhat();
- emit spectrumSpReady(spectrum, QString(""), error.qwhat());
+ catch(pappso::PappsoException &error)
+ {
+ qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp error "
+ << error.qwhat();
+ emit spectrumSpReady(spectrum, QString(""), error.qwhat());
}
- catch (std::exception & error) {
- qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp error " << error.what();
- emit spectrumSpReady(spectrum, QString(""), QString(error.what()));
+ catch(std::exception &error)
+ {
+ qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp error "
+ << error.what();
+ emit spectrumSpReady(spectrum, QString(""), QString(error.what()));
}
- qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp end";
+ qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp end";
}
-PeptideWindow::PeptideWindow(ProjectWindow *parent):
- QMainWindow(parent),
- ui(new Ui::PeptideDetailView)
+PeptideWindow::PeptideWindow(ProjectWindow *parent)
+ : QMainWindow(parent), ui(new Ui::PeptideDetailView)
{
- qDebug() << "PeptideWindow::PeptideWindow begin";
- _p_project_window = parent;
- ui->setupUi(this);
- /*
- */
- SpectrumSpLoaderThread * worker = new SpectrumSpLoaderThread;
- worker->moveToThread(&_spectrum_loader_thread);
- _spectrum_loader_thread.start();
+ qDebug() << "PeptideWindow::PeptideWindow begin";
+ _p_project_window = parent;
+ ui->setupUi(this);
+ /*
+ */
+ SpectrumSpLoaderThread *worker = new SpectrumSpLoaderThread;
+ worker->moveToThread(&_spectrum_loader_thread);
+ _spectrum_loader_thread.start();
- QSettings settings;
- QString precision_str = settings.value("peptideview/precision", "0.2 dalton").toString();
+ QSettings settings;
+ QString precision_str =
+ settings.value("peptideview/precision", "0.2 dalton").toString();
- _p_precision = pappso::Precision::fromString(precision_str);
+ _p_precision = pappso::Precision::fromString(precision_str);
- ui->file_not_found->setVisible(false);
+ ui->file_not_found->setVisible(false);
- _mz_label = new QLabel("");
- ui->statusbar->addWidget(_mz_label);
- QWidget * p_spacer = new QWidget();
- p_spacer->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Minimum);
- ui->statusbar->addWidget(p_spacer);
- _peak_label = new QLabel("");
- ui->statusbar->addWidget(_peak_label);
- _ion_label = new QLabel("");
- ui->statusbar->addWidget(_ion_label);
+ _mz_label = new QLabel("");
+ ui->statusbar->addWidget(_mz_label);
+ QWidget *p_spacer = new QWidget();
+ p_spacer->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Minimum);
+ ui->statusbar->addWidget(p_spacer);
+ _peak_label = new QLabel("");
+ ui->statusbar->addWidget(_peak_label);
+ _ion_label = new QLabel("");
+ ui->statusbar->addWidget(_ion_label);
- ui->spectrum_widget->setMaximumIsotopeNumber(3);
- ui->spectrum_widget->setMaximumIsotopeRank(6);
+ ui->spectrum_widget->setMaximumIsotopeNumber(3);
+ ui->spectrum_widget->setMaximumIsotopeRank(6);
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect (_p_project_window, &ProjectWindow::identificationGroupGrouped, this,&PeptideWindow::doIdentificationGroupGrouped);
-
- connect (this, &PeptideWindow::loadSpectrumSp, worker,&SpectrumSpLoaderThread::doLoadSpectrumSp);
- connect (worker, &SpectrumSpLoaderThread::spectrumSpReady, this,&PeptideWindow::doSpectrumSpReady);
- connect (ui->spectrum_widget,&pappso::SpectrumWidget::mzChanged, this, &PeptideWindow::setMz);
- connect (ui->spectrum_widget,&pappso::SpectrumWidget::peakChanged, this, &PeptideWindow::setPeak);
- connect (ui->spectrum_widget,&pappso::SpectrumWidget::ionChanged, this, &PeptideWindow::setIon);
+ // Qt5 code
+ connect(_p_project_window, &ProjectWindow::identificationGroupGrouped, this,
+ &PeptideWindow::doIdentificationGroupGrouped);
+
+ connect(this, &PeptideWindow::loadSpectrumSp, worker,
+ &SpectrumSpLoaderThread::doLoadSpectrumSp);
+ connect(worker, &SpectrumSpLoaderThread::spectrumSpReady, this,
+ &PeptideWindow::doSpectrumSpReady);
+ connect(ui->spectrum_widget, &pappso::SpectrumWidget::mzChanged, this,
+ &PeptideWindow::setMz);
+ connect(ui->spectrum_widget, &pappso::SpectrumWidget::peakChanged, this,
+ &PeptideWindow::setPeak);
+ connect(ui->spectrum_widget, &pappso::SpectrumWidget::ionChanged, this,
+ &PeptideWindow::setIon);
#else
-// Qt4 code
- connect (_p_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
-
- connect (this, SIGNAL(loadSpectrumSp(PeptideMatch *)), worker,SLOT(doLoadSpectrumSp(PeptideMatch *)));
- connect (worker, SIGNAL(spectrumSpReady(pappso::SpectrumSp, QString, QString)), this,SLOT(doSpectrumSpReady(pappso::SpectrumSp, QString, QString)));
- connect (_p_spectrum_overlay,SIGNAL(mzChanged(double)), this, SLOT(setMz(double)));
- //connect(_protein_table_model_p, SIGNAL(layoutChanged()), this, SLOT(updateStatusBar()));
+ // Qt4 code
+ connect(_p_project_window,
+ SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
+ SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
+
+ connect(this, SIGNAL(loadSpectrumSp(PeptideMatch *)), worker,
+ SLOT(doLoadSpectrumSp(PeptideMatch *)));
+ connect(worker, SIGNAL(spectrumSpReady(pappso::SpectrumSp, QString, QString)),
+ this, SLOT(doSpectrumSpReady(pappso::SpectrumSp, QString, QString)));
+ connect(_p_spectrum_overlay, SIGNAL(mzChanged(double)), this,
+ SLOT(setMz(double)));
+ // connect(_protein_table_model_p, SIGNAL(layoutChanged()), this,
+ // SLOT(updateStatusBar()));
#endif
- qDebug() << "PeptideWindow::PeptideWindow end";
+ qDebug() << "PeptideWindow::PeptideWindow end";
}
PeptideWindow::~PeptideWindow()
{
- delete ui;
+ delete ui;
}
-void PeptideWindow::setIon(pappso::PeakIonIsotopeMatch ion) {
- QString plusstr = "+";
- plusstr = plusstr.repeated(ion.getCharge());
- _ion_label->setText(QString("%1%2%3 (+%4) - th. isotope ratio %5%").arg(ion.getPeptideFragmentIonSp().get()->getPeptideIonName()).arg(ion.getPeptideFragmentIonSp().get()->size()).arg(plusstr).arg(ion.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber()).arg((int)(ion.getPeptideNaturalIsotopeAverageSp().get()->getIntensityRatio()*100)));
-
-
+void
+PeptideWindow::setIon(pappso::PeakIonIsotopeMatch ion)
+{
+ QString plusstr = "+";
+ plusstr = plusstr.repeated(ion.getCharge());
+ _ion_label->setText(
+ QString("%1%2%3 (+%4) - th. isotope ratio %5%")
+ .arg(ion.getPeptideFragmentIonSp().get()->getPeptideIonName())
+ .arg(ion.getPeptideFragmentIonSp().get()->size())
+ .arg(plusstr)
+ .arg(ion.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber())
+ .arg((int)(ion.getPeptideNaturalIsotopeAverageSp()
+ .get()
+ ->getIntensityRatio() *
+ 100)));
}
-void PeptideWindow::setPeak(const pappso::Peak * p_peak_match) {
- qDebug() << "PeptideWindow::setPeak begin" << p_peak_match;
- if (p_peak_match == nullptr) {
- _peak_label->setText(QString("no peak"));
- _ion_label->setText("");
+void
+PeptideWindow::setPeak(const pappso::Peak *p_peak_match)
+{
+ qDebug() << "PeptideWindow::setPeak begin" << p_peak_match;
+ if(p_peak_match == nullptr)
+ {
+ _peak_label->setText(QString("no peak"));
+ _ion_label->setText("");
}
- else {
- _peak_label->setText(QString("peak mz=%1 intensity=%2").arg(QString::number(p_peak_match->mz, 'g', 10)).arg(p_peak_match->intensity));
+ else
+ {
+ _peak_label->setText(QString("peak mz=%1 intensity=%2")
+ .arg(QString::number(p_peak_match->mz, 'g', 10))
+ .arg(p_peak_match->intensity));
}
}
-void PeptideWindow::setMz(double mz) {
- if (mz >0 ) {
- _mz_label->setText(QString("mz=%1").arg(QString::number(mz, 'g', 10)));
+void
+PeptideWindow::setMz(double mz)
+{
+ if(mz > 0)
+ {
+ _mz_label->setText(QString("mz=%1").arg(QString::number(mz, 'g', 10)));
}
- else {
- _mz_label->setText("");
+ else
+ {
+ _mz_label->setText("");
}
}
-void PeptideWindow::doIdentificationGroupGrouped(IdentificationGroup * p_identification_group) {
- updateDisplay();
+void
+PeptideWindow::doIdentificationGroupGrouped(
+ IdentificationGroup *p_identification_group)
+{
+ updateDisplay();
}
-void PeptideWindow::updateDisplay() {
- try {
- ui->sequence_label->setText(_p_peptide_evidence->getPeptideXtpSp().get()->toString());
- ui->mz_label->setText(QString("%1").arg(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(_p_peptide_evidence->getCharge())));
- ui->z_label->setText(QString("%1").arg(_p_peptide_evidence->getCharge()));
- ui->scan_label->setText(QString("%1").arg(_p_peptide_evidence->getScan()));
- ui->sample_label->setText(_p_peptide_evidence->getMsRunP()->getSampleName());
- ui->modification_label->setText(_p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
- ui->hyperscore_label->setText(_p_peptide_evidence->getParam(PeptideEvidenceParam::tandem_hyperscore).toString());
- ui->evalue_label->setText(QString::number(_p_peptide_evidence->getEvalue(), 'g', 4));
- ui->mh_label->setText(QString::number(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(1), 'f', 4));
- ui->mz_label->setText(QString::number(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(_p_peptide_evidence->getCharge()), 'f', 4));
- ui->expmz_label->setText(QString::number(_p_peptide_evidence->getExperimentalMz(), 'f', 4));
- ui->delta_label->setText(QString::number(_p_peptide_evidence->getDeltaMass(), 'g', 4));
- ui->retention_time_label->setText(QString::number(_p_peptide_evidence->getRetentionTime(), 'f', 2));
- ui->retention_time_min_label->setText(QString::number(_p_peptide_evidence->getRetentionTime()/60, 'f', 2));
-
-
+void
+PeptideWindow::updateDisplay()
+{
+ try
+ {
+ ui->sequence_label->setText(
+ _p_peptide_evidence->getPeptideXtpSp().get()->toString());
+ ui->mz_label->setText(
+ QString("%1").arg(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(
+ _p_peptide_evidence->getCharge())));
+ ui->z_label->setText(QString("%1").arg(_p_peptide_evidence->getCharge()));
+ ui->scan_label->setText(
+ QString("%1").arg(_p_peptide_evidence->getScan()));
+ ui->sample_label->setText(
+ _p_peptide_evidence->getMsRunP()->getSampleName());
+ ui->modification_label->setText(
+ _p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
+ ui->hyperscore_label->setText(
+ _p_peptide_evidence->getParam(PeptideEvidenceParam::tandem_hyperscore)
+ .toString());
+ ui->evalue_label->setText(
+ QString::number(_p_peptide_evidence->getEvalue(), 'g', 4));
+ ui->mh_label->setText(QString::number(
+ _p_peptide_evidence->getPeptideXtpSp().get()->getMz(1), 'f', 4));
+ ui->mz_label->setText(
+ QString::number(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(
+ _p_peptide_evidence->getCharge()),
+ 'f', 4));
+ ui->expmz_label->setText(
+ QString::number(_p_peptide_evidence->getExperimentalMz(), 'f', 4));
+ ui->delta_label->setText(
+ QString::number(_p_peptide_evidence->getDeltaMass(), 'g', 4));
+ ui->retention_time_label->setText(
+ QString::number(_p_peptide_evidence->getRetentionTime(), 'f', 2));
+ ui->retention_time_min_label->setText(
+ QString::number(_p_peptide_evidence->getRetentionTime() / 60, 'f', 2));
}
- catch (pappso::PappsoException exception_pappso) {
- QMessageBox::warning(this,
- tr("Unable to display peptide details :"), exception_pappso.qwhat());
+ catch(pappso::PappsoException exception_pappso)
+ {
+ QMessageBox::warning(this, tr("Unable to display peptide details :"),
+ exception_pappso.qwhat());
}
- catch (std::exception exception_std) {
- QMessageBox::warning(this,
- tr("Unable to display peptide details :"), exception_std.what());
+ catch(std::exception exception_std)
+ {
+ QMessageBox::warning(this, tr("Unable to display peptide details :"),
+ exception_std.what());
}
-
}
-void PeptideWindow::chooseDefaultMzDataDir() {
- QSettings settings;
- QString default_location = settings.value("path/mzdatadir", "").toString();
+void
+PeptideWindow::chooseDefaultMzDataDir()
+{
+ QSettings settings;
+ QString default_location = settings.value("path/mzdatadir", "").toString();
- QString filename = QFileDialog::getExistingDirectory(this,
- tr("Choose default mz data directory"), default_location,
- QFileDialog::ShowDirsOnly);
+ QString filename = QFileDialog::getExistingDirectory(
+ this, tr("Choose default mz data directory"), default_location,
+ QFileDialog::ShowDirsOnly);
- if (filename.isEmpty()) {
- return;
+ if(filename.isEmpty())
+ {
+ return;
}
- QString path = QFileInfo(filename).absoluteFilePath();
- settings.setValue("path/mzdatadir", path);
- ui->mz_data_dir_label->setText(path);
-
+ QString path = QFileInfo(filename).absoluteFilePath();
+ settings.setValue("path/mzdatadir", path);
+ ui->mz_data_dir_label->setText(path);
- qDebug() << "PeptideWindow::chooseDefaultMzDataDir begin";
- ui->file_not_found->setVisible(false);
- ui->xic_button->setEnabled(true);
- ui->spectrum_widget->setVisible(true);
- emit loadSpectrumSp(_p_peptide_evidence);
- ui->statusbar->showMessage(tr("loading spectrum"));
+ qDebug() << "PeptideWindow::chooseDefaultMzDataDir begin";
+ ui->file_not_found->setVisible(false);
+ ui->xic_button->setEnabled(true);
+ ui->spectrum_widget->setVisible(true);
+ emit loadSpectrumSp(_p_peptide_evidence);
+ ui->statusbar->showMessage(tr("loading spectrum"));
}
-void PeptideWindow::openInPeptideViewer() {
- QSettings settings;
- QString program = settings.value("application/peptideviewer", "/usr/bin/pt-peptideviewer").toString();
- QStringList arguments;
- arguments << _p_peptide_evidence->getPeptideXtpSp().get()->toString() << QString("%1").arg(_p_peptide_evidence->getCharge()) << _p_peptide_evidence->getMsRunP()->getFilename() << QString("%1").arg(_p_peptide_evidence->getScan());
-
- qDebug() << "PeptideWindow::openInPeptideViewer " << program << " " << arguments.join(" ");
- QProcess *myProcess = new QProcess(this);
- myProcess->start(program, arguments);
+void
+PeptideWindow::openInPeptideViewer()
+{
+ QSettings settings;
+ QString program =
+ settings.value("application/peptideviewer", "/usr/bin/pt-peptideviewer")
+ .toString();
+ QStringList arguments;
+ arguments << _p_peptide_evidence->getPeptideXtpSp().get()->toString()
+ << QString("%1").arg(_p_peptide_evidence->getCharge())
+ << _p_peptide_evidence->getMsRunP()->getFilename()
+ << QString("%1").arg(_p_peptide_evidence->getScan());
+
+ qDebug() << "PeptideWindow::openInPeptideViewer " << program << " "
+ << arguments.join(" ");
+ QProcess *myProcess = new QProcess(this);
+ myProcess->start(program, arguments);
}
-void PeptideWindow::openInXicViewer() {
- _p_project_window->openInXicViewer(_p_peptide_evidence);
+void
+PeptideWindow::openInXicViewer()
+{
+ _p_project_window->openInXicViewer(_p_peptide_evidence);
}
-void PeptideWindow::doSpectrumSpReady(pappso::SpectrumSp spectrum_sp, QString error, QString fatal_error) {
- qDebug() << "PeptideWindow::doSpectrumSpReady begin error=" << error << " fatal_error=" << fatal_error;
- if ((error.isEmpty()) && (fatal_error.isEmpty())) {
- ui->statusbar->showMessage(tr(""));
- ui->file_not_found->setVisible(false);
- ui->spectrum_widget->setVisible(true);
- ui->xic_button->setEnabled(true);
-
- ui->spectrum_widget->setMsLevel(2);
- ui->spectrum_widget->setSpectrumSp(spectrum_sp);
- qDebug() << "PeptideWindow::doSpectrumSpReady plot";
- ui->spectrum_widget->plot();
- qDebug() << "PeptideWindow::doSpectrumSpReady rescale";
- ui->spectrum_widget->rescale();
- _spectrum_is_ready = true;
-
+void
+PeptideWindow::doSpectrumSpReady(pappso::SpectrumSp spectrum_sp, QString error,
+ QString fatal_error)
+{
+ qDebug() << "PeptideWindow::doSpectrumSpReady begin error=" << error
+ << " fatal_error=" << fatal_error;
+ if((error.isEmpty()) && (fatal_error.isEmpty()))
+ {
+ ui->statusbar->showMessage(tr(""));
+ ui->file_not_found->setVisible(false);
+ ui->spectrum_widget->setVisible(true);
+ ui->xic_button->setEnabled(true);
+
+ ui->spectrum_widget->setMsLevel(2);
+ ui->spectrum_widget->setSpectrumSp(spectrum_sp);
+ qDebug() << "PeptideWindow::doSpectrumSpReady plot";
+ ui->spectrum_widget->plot();
+ qDebug() << "PeptideWindow::doSpectrumSpReady rescale";
+ ui->spectrum_widget->rescale();
+ _spectrum_is_ready = true;
}
- if (!error.isEmpty()) {
- //not found
+ if(!error.isEmpty())
+ {
+ // not found
- ui->statusbar->showMessage(tr("spectrum not found"));
- QSettings settings;
- QString path = settings.value("path/mzdatadir", "").toString();
+ ui->statusbar->showMessage(tr("spectrum not found"));
+ QSettings settings;
+ QString path = settings.value("path/mzdatadir", "").toString();
- ui->mz_data_dir_label->setText(path);
+ ui->mz_data_dir_label->setText(path);
- ui->file_not_found->setVisible(true);
- ui->spectrum_widget->setVisible(false);
- ui->xic_button->setEnabled(false);
- _spectrum_is_ready = false;
+ ui->file_not_found->setVisible(true);
+ ui->spectrum_widget->setVisible(false);
+ ui->xic_button->setEnabled(false);
+ _spectrum_is_ready = false;
}
- if (!fatal_error.isEmpty()) {
- //fatal_error
-
- QMessageBox::warning(this,
- tr("Oops! an error occurred in XTPCPP. Dont Panic :"), fatal_error);
- ui->statusbar->showMessage(tr("ERROR reading spectrum"));
- QSettings settings;
- QString path = settings.value("path/mzdatadir", "").toString();
-
- ui->mz_data_dir_label->setText(path);
-
- ui->file_not_found->setVisible(true);
- ui->spectrum_widget->setVisible(false);
- _spectrum_is_ready = false;
+ if(!fatal_error.isEmpty())
+ {
+ // fatal_error
+
+ QMessageBox::warning(
+ this, tr("Oops! an error occurred in XTPCPP. Dont Panic :"),
+ fatal_error);
+ ui->statusbar->showMessage(tr("ERROR reading spectrum"));
+ QSettings settings;
+ QString path = settings.value("path/mzdatadir", "").toString();
+
+ ui->mz_data_dir_label->setText(path);
+
+ ui->file_not_found->setVisible(true);
+ ui->spectrum_widget->setVisible(false);
+ _spectrum_is_ready = false;
}
- qDebug() << "PeptideWindow::doSpectrumSpReady end";
-
+ qDebug() << "PeptideWindow::doSpectrumSpReady end";
}
-void PeptideWindow::setPeptideEvidence(PeptideEvidence * p_peptide_evidence) {
- qDebug() << "PeptideWindow::setPeptideEvidence begin " << p_peptide_evidence;
- _p_peptide_evidence = p_peptide_evidence;
- _spectrum_is_ready = false;
-
- qDebug() << "PeptideWindow::setPeptideEvidence 1";
-
- ui->file_not_found->setVisible(false);
- ui->spectrum_widget->setVisible(true);
- ui->statusbar->showMessage(tr("loading spectrum"));
-
- qDebug() << "PeptideWindow::setPeptideEvidence 2";
- pappso::PeptideSp peptide = _p_peptide_evidence->getPeptideXtpSp();
- qDebug() << "PeptideWindow::setPeptideEvidence 3";
- ui->spectrum_widget->setMs2Precision(_p_precision);
- ui->spectrum_widget->setPeptideCharge(_p_peptide_evidence->getCharge());
- ui->spectrum_widget->setPeptideSp(peptide);
-
- qDebug() << "PeptideWindow::setPeptideEvidence 4";
- //ui->spectrum_widget->plot();
-
- updateDisplay();
- qDebug() << "PeptideWindow::setPeptideEvidence emit loadSpectrumSp(_p_peptide_match)";
- emit loadSpectrumSp(_p_peptide_evidence);
- qDebug() << "PeptideWindow::setPeptideEvidence end";
+void
+PeptideWindow::setPeptideEvidence(PeptideEvidence *p_peptide_evidence)
+{
+ qDebug() << "PeptideWindow::setPeptideEvidence begin " << p_peptide_evidence;
+ _p_peptide_evidence = p_peptide_evidence;
+ _spectrum_is_ready = false;
+
+ qDebug() << "PeptideWindow::setPeptideEvidence 1";
+
+ ui->file_not_found->setVisible(false);
+ ui->spectrum_widget->setVisible(true);
+ ui->statusbar->showMessage(tr("loading spectrum"));
+
+ qDebug() << "PeptideWindow::setPeptideEvidence 2";
+ pappso::PeptideSp peptide = _p_peptide_evidence->getPeptideXtpSp();
+ qDebug() << "PeptideWindow::setPeptideEvidence 3";
+ ui->spectrum_widget->setMs2Precision(_p_precision);
+ ui->spectrum_widget->setPeptideCharge(_p_peptide_evidence->getCharge());
+ ui->spectrum_widget->setPeptideSp(peptide);
+
+ qDebug() << "PeptideWindow::setPeptideEvidence 4";
+ // ui->spectrum_widget->plot();
+
+ updateDisplay();
+ qDebug() << "PeptideWindow::setPeptideEvidence emit "
+ "loadSpectrumSp(_p_peptide_match)";
+ emit loadSpectrumSp(_p_peptide_evidence);
+ qDebug() << "PeptideWindow::setPeptideEvidence end";
}
-void PeptideWindow::doMsmsPrecisionChanged(pappso::PrecisionP precision) {
+void
+PeptideWindow::doMsmsPrecisionChanged(pappso::PrecisionP precision)
+{
- qDebug() << "PeptideWindow::doMsmsPrecisionChanged begin " << precision->toString();
- QSettings settings;
- _p_precision = precision;
- ui->spectrum_widget->setMs2Precision(_p_precision);
- qDebug() << "PeptideWindow::doMsmsPrecisionUnitChanged plot ";
- ui->spectrum_widget->plot();
+ qDebug() << "PeptideWindow::doMsmsPrecisionChanged begin "
+ << precision->toString();
+ QSettings settings;
+ _p_precision = precision;
+ ui->spectrum_widget->setMs2Precision(_p_precision);
+ qDebug() << "PeptideWindow::doMsmsPrecisionUnitChanged plot ";
+ ui->spectrum_widget->plot();
- settings.setValue("peptideview/precision", precision->toString());
+ settings.setValue("peptideview/precision", precision->toString());
- qDebug() << "PeptideWindow::doMsmsPrecisionUnitChanged end ";
+ qDebug() << "PeptideWindow::doMsmsPrecisionUnitChanged end ";
}
-void PeptideWindow::doSaveSvg() {
-
- try {
- QSettings settings;
- QString default_location = settings.value("path/export_svg", "").toString();
-
- QString proposed_filename = QString("%1/%2_%3.svg").arg(default_location).arg(_p_peptide_evidence->getMsRunP()->getSampleName()).arg(_p_peptide_evidence->getScan());
+void
+PeptideWindow::doSaveSvg()
+{
- if (_p_peptide_evidence->getValidationState() == ValidationState::grouped) {
- proposed_filename = QString("%1/%2_%3_%4.svg").arg(default_location).arg(_p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId()).arg(_p_peptide_evidence->getMsRunP()->getSampleName()).arg(_p_peptide_evidence->getScan());
+ try
+ {
+ QSettings settings;
+ QString default_location =
+ settings.value("path/export_svg", "").toString();
+
+ QString proposed_filename =
+ QString("%1/%2_%3.svg")
+ .arg(default_location)
+ .arg(_p_peptide_evidence->getMsRunP()->getSampleName())
+ .arg(_p_peptide_evidence->getScan());
+
+ if(_p_peptide_evidence->getValidationState() == ValidationState::grouped)
+ {
+ proposed_filename =
+ QString("%1/%2_%3_%4.svg")
+ .arg(default_location)
+ .arg(
+ _p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId())
+ .arg(_p_peptide_evidence->getMsRunP()->getSampleName())
+ .arg(_p_peptide_evidence->getScan());
}
- QString filename = QFileDialog::getSaveFileName(this, tr("Save SVG file"),
- proposed_filename,
- tr("Scalable Vector Graphic (*.svg)"));
+ QString filename = QFileDialog::getSaveFileName(
+ this, tr("Save SVG file"), proposed_filename,
+ tr("Scalable Vector Graphic (*.svg)"));
- if (filename.isEmpty()) {
- return;
+ if(filename.isEmpty())
+ {
+ return;
}
- settings.setValue("path/export_svg", QFileInfo(filename).absolutePath());
+ settings.setValue("path/export_svg", QFileInfo(filename).absolutePath());
- ui->spectrum_widget->toSvgFile(filename,tr("%1 SVG spectrum generator").arg(SOFTWARE_NAME), tr("This is an annotated SVG spectrum"), QSize(1200,500) );
- //emit operateXpipFile(filename);
+ ui->spectrum_widget->toSvgFile(
+ filename, tr("%1 SVG spectrum generator").arg(SOFTWARE_NAME),
+ tr("This is an annotated SVG spectrum"), QSize(1200, 500));
+ // emit operateXpipFile(filename);
}
- catch (pappso::PappsoException & error) {
- QMessageBox::warning(this,
- tr("Error trying to save spectrum to SVG file :"), error.qwhat());
+ catch(pappso::PappsoException &error)
+ {
+ QMessageBox::warning(
+ this, tr("Error trying to save spectrum to SVG file :"), error.qwhat());
}
}
diff --git a/src/gui/peptide_detail_view/peptidewindow.h b/src/gui/peptide_detail_view/peptidewindow.h
index c165f164957649720ae2e4a072626d3073cd3fa1..cfc6e33a866a6b970232e131c751be087d14b80b 100644
--- a/src/gui/peptide_detail_view/peptidewindow.h
+++ b/src/gui/peptide_detail_view/peptidewindow.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PEPTIDEWINDOW_H
#define PEPTIDEWINDOW_H
@@ -35,72 +36,71 @@
class ProjectWindow;
-namespace Ui {
-class PeptideDetailView;
+namespace Ui
+{
+ class PeptideDetailView;
}
class SpectrumSpLoaderThread : public QObject
{
- Q_OBJECT
-public:
-
-
-public slots:
- void doLoadSpectrumSp(PeptideEvidence * p_peptide_evidence);
-
-signals:
- void spectrumSpReady(pappso::SpectrumSp spectrum_sp, QString error, QString fatal_error);
+ Q_OBJECT
+ public:
+ public slots:
+ void doLoadSpectrumSp(PeptideEvidence *p_peptide_evidence);
-protected:
-
- void closeEvent(QCloseEvent *event);
+ signals:
+ void spectrumSpReady(pappso::SpectrumSp spectrum_sp, QString error,
+ QString fatal_error);
+ protected:
+ void closeEvent(QCloseEvent *event);
};
-class PeptideWindow: public QMainWindow {
- Q_OBJECT
-
-public:
-
- explicit PeptideWindow(ProjectWindow * parent = 0);
- ~PeptideWindow();
- void setPeptideEvidence(PeptideEvidence * p_peptide_evidence);
-
-public slots:
- void doIdentificationGroupGrouped(IdentificationGroup * p_identification_group);
- void setMz(double);
- void setPeak(const pappso::Peak * p_peak_match);
- void setIon(pappso::PeakIonIsotopeMatch ion);
-
-signals:
- void loadSpectrumSp(PeptideEvidence * p_peptide_evidence);
-
-protected slots:
- void doSpectrumSpReady(pappso::SpectrumSp spectrum_sp, QString error, QString fatal_error);
- void doMsmsPrecisionChanged(pappso::PrecisionP);
- void doSaveSvg();
- void chooseDefaultMzDataDir();
- void openInPeptideViewer();
- void openInXicViewer();
-protected :
- void updateDisplay();
-
-private:
-
- QThread _spectrum_loader_thread;
- QLabel * _mz_label;
- QLabel * _peak_label;
- QLabel * _ion_label;
-
- Ui::PeptideDetailView *ui;
- ProjectWindow * _p_project_window;
- PeptideEvidence * _p_peptide_evidence = nullptr;
- pappso::PrecisionP _p_precision;
-
- bool _spectrum_is_ready=false;
-
+class PeptideWindow : public QMainWindow
+{
+ Q_OBJECT
+
+ public:
+ explicit PeptideWindow(ProjectWindow *parent = 0);
+ ~PeptideWindow();
+ void setPeptideEvidence(PeptideEvidence *p_peptide_evidence);
+
+ public slots:
+ void
+ doIdentificationGroupGrouped(IdentificationGroup *p_identification_group);
+ void setMz(double);
+ void setPeak(const pappso::Peak *p_peak_match);
+ void setIon(pappso::PeakIonIsotopeMatch ion);
+
+ signals:
+ void loadSpectrumSp(PeptideEvidence *p_peptide_evidence);
+
+ protected slots:
+ void doSpectrumSpReady(pappso::SpectrumSp spectrum_sp, QString error,
+ QString fatal_error);
+ void doMsmsPrecisionChanged(pappso::PrecisionP);
+ void doSaveSvg();
+ void chooseDefaultMzDataDir();
+ void openInPeptideViewer();
+ void openInXicViewer();
+
+ protected:
+ void updateDisplay();
+
+ private:
+ QThread _spectrum_loader_thread;
+ QLabel *_mz_label;
+ QLabel *_peak_label;
+ QLabel *_ion_label;
+
+ Ui::PeptideDetailView *ui;
+ ProjectWindow *_p_project_window;
+ PeptideEvidence *_p_peptide_evidence = nullptr;
+ pappso::PrecisionP _p_precision;
+
+ bool _spectrum_is_ready = false;
};
#endif // PEPTIDEWINDOW_H
diff --git a/src/gui/peptide_list_view/peptidetablemodel.h b/src/gui/peptide_list_view/peptidetablemodel.h
index aa2bea21b3fb15621b2e04ef6d2918dc9d52a8da..82addadd8757bfac6d28c98547af3114c3eef8ee 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.h
+++ b/src/gui/peptide_list_view/peptidetablemodel.h
@@ -68,7 +68,7 @@ enum class PeptideListColumn : std::int8_t
msgfplus_energy = 30, ///< MS:1002051 "MS-GF energy score." [PSI:PI]
msgfplus_SpecEValue = 31, ///< MS:1002052 "MS-GF spectral E-value." [PSI:PI]
msgfplus_EValue = 32, ///< MS:1002053 "MS-GF E-value." [PSI:PI]
- msgfplus_isotope_error = 33, ///< MS:1002053 "MS-GF E-value." [PSI:PI]
+ msgfplus_isotope_error = 33, ///< MS:1002053 "MS-GF E-value." [PSI:PI]
comet_xcorr = 34, ///< MS:1002252 "The Comet result 'XCorr'." [PSI:PI]
comet_deltacn = 35, ///< MS:1002253 "The Comet result 'DeltaCn'." [PSI:PI]
comet_deltacnstar =
diff --git a/src/gui/peptide_list_view/peptidetableproxymodel.cpp b/src/gui/peptide_list_view/peptidetableproxymodel.cpp
index 6099b50b0b160d7c3b1dff58c784da6eb51d2cfd..3993cd41216919b5d97d242828271b8d9e6a68f6 100644
--- a/src/gui/peptide_list_view/peptidetableproxymodel.cpp
+++ b/src/gui/peptide_list_view/peptidetableproxymodel.cpp
@@ -43,10 +43,7 @@ PeptideTableProxyModel::PeptideTableProxyModel(
for(std::size_t i = 0; i < _column_display.size(); i++)
{
_column_display[i] =
- settings
- .value(QString("peptide_list_columns/c%1")
- .arg(i),
- "true")
+ settings.value(QString("peptide_list_columns/c%1").arg(i), "true")
.toBool();
}
_mass_delegate = new MassItemDelegate(_p_peptide_list_window);
@@ -380,9 +377,8 @@ PeptideTableProxyModel::setPeptideListColumnDisplay(PeptideListColumn column,
<< toggled;
beginResetModel();
QSettings settings;
- settings.setValue(QString("peptide_list_columns/c%1")
- .arg((std::int8_t) column),
- toggled);
+ settings.setValue(
+ QString("peptide_list_columns/c%1").arg((std::int8_t)column), toggled);
_column_display[(std::int8_t)column] = toggled;
endResetModel();
diff --git a/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp b/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
index 23304334f1d7211bc05602016cc2273c7b4af9e6..ac279cfd175267a5f3910cf46ca4e66874a5a4ad 100644
--- a/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
+++ b/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
@@ -1,86 +1,108 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "identificationgroupwidget.h"
#include "ui_identification_group_widget.h"
#include <QDebug>
-IdentificationGroupWidget::IdentificationGroupWidget(QWidget * parent):
- QWidget(parent),
- ui(new Ui::IdentificationGroupWidget)
+IdentificationGroupWidget::IdentificationGroupWidget(QWidget *parent)
+ : QWidget(parent), ui(new Ui::IdentificationGroupWidget)
{
- ui->setupUi(this);
- qDebug() << "IdentificationGroupWidget::IdentificationGroupWidget begin";
+ ui->setupUi(this);
+ qDebug() << "IdentificationGroupWidget::IdentificationGroupWidget begin";
- qDebug() << "IdentificationGroupWidget::IdentificationGroupWidget end";
+ qDebug() << "IdentificationGroupWidget::IdentificationGroupWidget end";
}
IdentificationGroupWidget::~IdentificationGroupWidget()
{
- qDebug() << "IdentificationGroupWidget::~IdentificationGroupWidget";
- delete ui;
- qDebug() << "IdentificationGroupWidget::~IdentificationGroupWidget end";
+ qDebug() << "IdentificationGroupWidget::~IdentificationGroupWidget";
+ delete ui;
+ qDebug() << "IdentificationGroupWidget::~IdentificationGroupWidget end";
}
-void IdentificationGroupWidget::setIdentificationGroup(ProjectWindow * parent, IdentificationGroup* p_identification_group) {
- _p_identification_group = p_identification_group;
-
- _p_project_window = parent;
+void
+IdentificationGroupWidget::setIdentificationGroup(
+ ProjectWindow *parent, IdentificationGroup *p_identification_group)
+{
+ _p_identification_group = p_identification_group;
+
+ _p_project_window = parent;
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect (_p_project_window, &ProjectWindow::identificationGroupGrouped, this,&IdentificationGroupWidget::doIdentificationGroupGrouped);
+ // Qt5 code
+ connect(_p_project_window, &ProjectWindow::identificationGroupGrouped, this,
+ &IdentificationGroupWidget::doIdentificationGroupGrouped);
#else
-// Qt4 code
+ // Qt4 code
- connect (_p_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
+ connect(_p_project_window,
+ SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
+ SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
#endif
}
-void IdentificationGroupWidget::doViewPtmIslandList() {
- qDebug() << "IdentificationGroupWidget::doViewPtmIslandList begin " << _p_identification_group;
- _p_project_window->doViewPtmIslandList(_p_identification_group);
- qDebug() << "IdentificationGroupWidget::doViewPtmIslandList end";
+void
+IdentificationGroupWidget::doViewPtmIslandList()
+{
+ qDebug() << "IdentificationGroupWidget::doViewPtmIslandList begin "
+ << _p_identification_group;
+ _p_project_window->doViewPtmIslandList(_p_identification_group);
+ qDebug() << "IdentificationGroupWidget::doViewPtmIslandList end";
}
-void IdentificationGroupWidget::doViewProteinList() {
- qDebug() << "IdentificationGroupWidget::doViewProteinList begin " << _p_identification_group;
- _p_project_window->doViewProteinList(_p_identification_group);
- qDebug() << "IdentificationGroupWidget::doViewProteinList end";
+void
+IdentificationGroupWidget::doViewProteinList()
+{
+ qDebug() << "IdentificationGroupWidget::doViewProteinList begin "
+ << _p_identification_group;
+ _p_project_window->doViewProteinList(_p_identification_group);
+ qDebug() << "IdentificationGroupWidget::doViewProteinList end";
}
-void IdentificationGroupWidget::doIdentificationGroupGrouped(IdentificationGroup * p_identification_group) {
- qDebug() << "IdentificationGroupWidget::doIdentificationGroupGrouped begin " << _p_identification_group << " " << p_identification_group;
- if (_p_identification_group == p_identification_group) {
- vector< MsRunSp > ms_run_list = _p_identification_group->getMsRunSpList();
- ui->sample_number_display->setText(QString("%1").arg(ms_run_list.size()));
+void
+IdentificationGroupWidget::doIdentificationGroupGrouped(
+ IdentificationGroup *p_identification_group)
+{
+ qDebug() << "IdentificationGroupWidget::doIdentificationGroupGrouped begin "
+ << _p_identification_group << " " << p_identification_group;
+ if(_p_identification_group == p_identification_group)
+ {
+ vector<MsRunSp> ms_run_list = _p_identification_group->getMsRunSpList();
+ ui->sample_number_display->setText(QString("%1").arg(ms_run_list.size()));
- ui->group_number_display->setText(QString("%1").arg(_p_identification_group->countGroup()));
- ui->subgroup_number_display->setText(QString("%1").arg(_p_identification_group->countSubGroup()));
- ui->protein_number_display->setText(QString("%1").arg(_p_identification_group->countProteinMatch(ValidationState::grouped)));
- ui->grouped_peptide_display->setText(QString("%1").arg(_p_identification_group->countPeptideMass(ValidationState::grouped)));
- _p_identification_group->countPeptideMatch(ValidationState::grouped);
+ ui->group_number_display->setText(
+ QString("%1").arg(_p_identification_group->countGroup()));
+ ui->subgroup_number_display->setText(
+ QString("%1").arg(_p_identification_group->countSubGroup()));
+ ui->protein_number_display->setText(QString("%1").arg(
+ _p_identification_group->countProteinMatch(ValidationState::grouped)));
+ ui->grouped_peptide_display->setText(QString("%1").arg(
+ _p_identification_group->countPeptideMass(ValidationState::grouped)));
+ _p_identification_group->countPeptideMatch(ValidationState::grouped);
}
- qDebug() << "IdentificationGroupWidget::doIdentificationGroupGrouped end " << _p_identification_group;
+ qDebug() << "IdentificationGroupWidget::doIdentificationGroupGrouped end "
+ << _p_identification_group;
}
diff --git a/src/gui/project_view/identification_group_widget/identificationgroupwidget.h b/src/gui/project_view/identification_group_widget/identificationgroupwidget.h
index 79ff9a1f8376494f5b1d2344b29fb8689a19c7f3..94d03b4be10e66674a09776ee399a786e35ef7af 100644
--- a/src/gui/project_view/identification_group_widget/identificationgroupwidget.h
+++ b/src/gui/project_view/identification_group_widget/identificationgroupwidget.h
@@ -1,58 +1,61 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef IDENTIFICATIONGROUPWIDGET_H
#define IDENTIFICATIONGROUPWIDGET_H
#include "../projectwindow.h"
-namespace Ui {
-class IdentificationGroupWidget;
+namespace Ui
+{
+ class IdentificationGroupWidget;
}
class IdentificationGroupWidget : public QWidget
{
- Q_OBJECT
+ Q_OBJECT
-public:
+ public:
+ explicit IdentificationGroupWidget(QWidget *parent);
+ ~IdentificationGroupWidget();
- explicit IdentificationGroupWidget(QWidget * parent);
- ~IdentificationGroupWidget();
-
-public:
- void setIdentificationGroup(ProjectWindow * parent, IdentificationGroup* p_identification_group);
+ public:
+ void setIdentificationGroup(ProjectWindow *parent,
+ IdentificationGroup *p_identification_group);
-public slots:
- void doViewProteinList();
- void doViewPtmIslandList();
- void doIdentificationGroupGrouped(IdentificationGroup * p_identification_group);
+ public slots:
+ void doViewProteinList();
+ void doViewPtmIslandList();
+ void
+ doIdentificationGroupGrouped(IdentificationGroup *p_identification_group);
-private:
- Ui::IdentificationGroupWidget *ui;
- ProjectWindow *_p_project_window;
- IdentificationGroup* _p_identification_group;
+ private:
+ Ui::IdentificationGroupWidget *ui;
+ ProjectWindow *_p_project_window;
+ IdentificationGroup *_p_identification_group;
};
Q_DECLARE_METATYPE(IdentificationGroupWidget *)
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 7af5685639bf5792d2b475eb65621eba69332d27..b270acd287e5f5d5259587a88694a1d075a99745 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "projectwindow.h"
#include "ui_project_view.h"
@@ -39,772 +40,963 @@
#include <qcustomplot.h>
-
-ProjectWindow::ProjectWindow(MainWindow *parent):
- QMainWindow(parent),
- ui(new Ui::ProjectView)
+ProjectWindow::ProjectWindow(MainWindow *parent)
+ : QMainWindow(parent), ui(new Ui::ProjectView)
{
- main_window = parent;
+ main_window = parent;
- ui->setupUi(this);
- WorkerThread * p_worker = new WorkerThread(this);
- p_worker->moveToThread(&_worker_thread);
- _worker_thread.start();
+ ui->setupUi(this);
+ WorkerThread *p_worker = new WorkerThread(this);
+ p_worker->moveToThread(&_worker_thread);
+ _worker_thread.start();
- _p_fasta_str_li = new QStandardItemModel();
- ui->decoy_database_listview->setModel(_p_fasta_str_li);
- ui->decoy_database_listview->setSelectionMode(QAbstractItemView::MultiSelection);
+ _p_fasta_str_li = new QStandardItemModel();
+ ui->decoy_database_listview->setModel(_p_fasta_str_li);
+ ui->decoy_database_listview->setSelectionMode(
+ QAbstractItemView::MultiSelection);
- _p_edit_modifications = new EditModifications(this);
- _p_edit_label_methods = new EditLabelMethods(this);
- _p_waiting_message_dialog = new WaitingMessageDialog(this);
+ _p_edit_modifications = new EditModifications(this);
+ _p_edit_label_methods = new EditLabelMethods(this);
+ _p_waiting_message_dialog = new WaitingMessageDialog(this);
- ui->mass_histogram_widget->xAxis->setLabel("mass delta");
- ui->mass_histogram_widget->yAxis->setLabel("count");
- ui->mass_histogram_widget->setInteractions(QCP::iRangeDrag | QCP::iRangeZoom );
- ui->mass_histogram_widget->axisRects().at(0)->setRangeDrag(Qt::Horizontal);
- ui->mass_histogram_widget->axisRects().at(0)->setRangeZoom(Qt::Horizontal);
- //legend->setVisible(false);
- ui->mass_histogram_widget->legend->setFont(QFont("Helvetica",9));
-// set locale to english, so we get english decimal separator:
-//setLocale(QLocale(QLocale::English, QLocale::UnitedKingdom));
- setFocusPolicy(Qt::ClickFocus);
+ ui->mass_histogram_widget->xAxis->setLabel("mass delta");
+ ui->mass_histogram_widget->yAxis->setLabel("count");
+ ui->mass_histogram_widget->setInteractions(QCP::iRangeDrag | QCP::iRangeZoom);
+ ui->mass_histogram_widget->axisRects().at(0)->setRangeDrag(Qt::Horizontal);
+ ui->mass_histogram_widget->axisRects().at(0)->setRangeZoom(Qt::Horizontal);
+ // legend->setVisible(false);
+ ui->mass_histogram_widget->legend->setFont(QFont("Helvetica", 9));
+ // set locale to english, so we get english decimal separator:
+ // setLocale(QLocale(QLocale::English, QLocale::UnitedKingdom));
+ setFocusPolicy(Qt::ClickFocus);
- QCPGraph * p_graph = ui->mass_histogram_widget->addGraph();
- //p_graph->setName("raw xic");
- //QPen pen;
- //pen.setColor(getNewColors());
- //graph()->setPen(pen);
- //graph()->setName(lineNames.at(i-QCPGraph::lsNone));
- p_graph->setLineStyle(QCPGraph::LineStyle::lsStepCenter);
- //p_graph->setScatterStyle(QCPScatterStyle(QCPScatterStyle::ssDisc, 2.0));
+ QCPGraph *p_graph = ui->mass_histogram_widget->addGraph();
+ // p_graph->setName("raw xic");
+ // QPen pen;
+ // pen.setColor(getNewColors());
+ // graph()->setPen(pen);
+ // graph()->setName(lineNames.at(i-QCPGraph::lsNone));
+ p_graph->setLineStyle(QCPGraph::LineStyle::lsStepCenter);
+ // p_graph->setScatterStyle(QCPScatterStyle(QCPScatterStyle::ssDisc, 2.0));
- QVBoxLayout * p_layout = new QVBoxLayout();
- ui->identifications_widget->setLayout(p_layout);
+ QVBoxLayout *p_layout = new QVBoxLayout();
+ ui->identifications_widget->setLayout(p_layout);
- ui->apply_filter_button->setEnabled(false);
+ ui->apply_filter_button->setEnabled(false);
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect (ui->filter_parameter_widget, &AutomaticFilterWidget::automaticFilterParametersChanged, this,&ProjectWindow::doAutomaticFilterParametersChanged);
- connect (ui->contaminant_widget, &ContaminantWidget::changed, this,&ProjectWindow::doContaminantSelectionChanged);
+ // Qt5 code
+ connect(ui->filter_parameter_widget,
+ &AutomaticFilterWidget::automaticFilterParametersChanged, this,
+ &ProjectWindow::doAutomaticFilterParametersChanged);
+ connect(ui->contaminant_widget, &ContaminantWidget::changed, this,
+ &ProjectWindow::doContaminantSelectionChanged);
- connect(_p_edit_label_methods, &EditLabelMethods::accepted, this,&ProjectWindow::doAcceptedLabelingMethod);
+ connect(_p_edit_label_methods, &EditLabelMethods::accepted, this,
+ &ProjectWindow::doAcceptedLabelingMethod);
#else
-// Qt4 code
- //connect (_protein_list_window, SIGNAL(proteinMatchClicked(ProteinMatch *)), this //,SLOT(doProteinMatchClicked(ProteinMatch *)));
- connect (_p_automatic_filter_widget, SIGNAL(automaticFilterParametersChanged(AutomaticFilterParameters)), this,SLOT(doAutomaticFilterParametersChanged(AutomaticFilterParameters)));
-
- connect(_p_edit_label_methods, SIGNAL(accepted()), this,SLOT(doAcceptedLabelingMethod()));
-
- //connect(this, SIGNAL(operateGrouping(ProjectSp)), p_worker,SLOT(doGrouping(ProjectSp)));
+ // Qt4 code
+ // connect (_protein_list_window, SIGNAL(proteinMatchClicked(ProteinMatch *)),
+ // this //,SLOT(doProteinMatchClicked(ProteinMatch *)));
+ connect(_p_automatic_filter_widget,
+ SIGNAL(automaticFilterParametersChanged(AutomaticFilterParameters)),
+ this,
+ SLOT(doAutomaticFilterParametersChanged(AutomaticFilterParameters)));
+
+ connect(_p_edit_label_methods, SIGNAL(accepted()), this,
+ SLOT(doAcceptedLabelingMethod()));
+
+ // connect(this, SIGNAL(operateGrouping(ProjectSp)),
+ // p_worker,SLOT(doGrouping(ProjectSp)));
#endif
- /*
- */
-
- this->setDisabled(true);
-
+ /*
+ */
+ this->setDisabled(true);
}
ProjectWindow::~ProjectWindow()
{
- qDebug() << "ProjectWindow::~ProjectWindow";
-
- //if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
- _worker_thread.quit();
- _worker_thread.wait();
- qDebug() << "ProjectWindow::~ProjectWindow1";
- delete ui;
- qDebug() << "ProjectWindow::~ProjectWindow2";
- delete _p_fasta_str_li ;
- qDebug() << "ProjectWindow::~ProjectWindow3";
- delete _p_edit_modifications;
- qDebug() << "ProjectWindow::~ProjectWindow5";
- delete _p_edit_label_methods ;
- qDebug() << "ProjectWindow::~ProjectWindow6";
- delete _p_waiting_message_dialog;
- qDebug() << "ProjectWindow::~ProjectWindow end";
-
-
-}
-
-Project * ProjectWindow::getProjectP() {
- return _project_sp.get();
-}
-void ProjectWindow::setDefaultProteinListWindow(ProteinListWindow* p_protein_list_window) {
- qDebug() << "ProjectWindow::setDefaultProteinListWindow begin";
- _p_current_protein_list_window = p_protein_list_window;
- qDebug() << "ProjectWindow::setDefaultProteinListWindow end";
+ qDebug() << "ProjectWindow::~ProjectWindow";
+
+ // if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
+ _worker_thread.quit();
+ _worker_thread.wait();
+ qDebug() << "ProjectWindow::~ProjectWindow1";
+ delete ui;
+ qDebug() << "ProjectWindow::~ProjectWindow2";
+ delete _p_fasta_str_li;
+ qDebug() << "ProjectWindow::~ProjectWindow3";
+ delete _p_edit_modifications;
+ qDebug() << "ProjectWindow::~ProjectWindow5";
+ delete _p_edit_label_methods;
+ qDebug() << "ProjectWindow::~ProjectWindow6";
+ delete _p_waiting_message_dialog;
+ qDebug() << "ProjectWindow::~ProjectWindow end";
+}
+
+Project *
+ProjectWindow::getProjectP()
+{
+ return _project_sp.get();
}
-
-void ProjectWindow::connectNewPtmIslandListWindow() {
- qDebug() << "ProjectWindow::connectNewPtmIslandListWindow begin";
- _p_current_ptm_island_list_window = new PtmIslandListWindow(this);
- _ptm_island_list_window_collection.push_back(_p_current_ptm_island_list_window);
- qDebug() << "ProjectWindow::connectNewPtmIslandListWindow end";
+void
+ProjectWindow::setDefaultProteinListWindow(
+ ProteinListWindow *p_protein_list_window)
+{
+ qDebug() << "ProjectWindow::setDefaultProteinListWindow begin";
+ _p_current_protein_list_window = p_protein_list_window;
+ qDebug() << "ProjectWindow::setDefaultProteinListWindow end";
}
-void ProjectWindow::connectNewProteinListWindow() {
- qDebug() << "ProjectWindow::connectNewProteinListWindow begin";
- _p_current_protein_list_window = new ProteinListWindow(this);
- _protein_list_window_collection.push_back(_p_current_protein_list_window);
+void
+ProjectWindow::connectNewPtmIslandListWindow()
+{
+ qDebug() << "ProjectWindow::connectNewPtmIslandListWindow begin";
+ _p_current_ptm_island_list_window = new PtmIslandListWindow(this);
+ _ptm_island_list_window_collection.push_back(
+ _p_current_ptm_island_list_window);
+ qDebug() << "ProjectWindow::connectNewPtmIslandListWindow end";
+}
+void
+ProjectWindow::connectNewProteinListWindow()
+{
+ qDebug() << "ProjectWindow::connectNewProteinListWindow begin";
+ _p_current_protein_list_window = new ProteinListWindow(this);
- qDebug() << "ProjectWindow::connectNewProteinListWindow end";
+ _protein_list_window_collection.push_back(_p_current_protein_list_window);
+ qDebug() << "ProjectWindow::connectNewProteinListWindow end";
}
-void ProjectWindow::connectNewProteinDetailWindow() {
- qDebug() << "ProjectWindow::connectNewProteinDetailWindow begin";
- _p_current_protein_detail_window = new ProteinWindow(this);
- _protein_detail_window_collection.push_back(_p_current_protein_detail_window);
-
- qDebug() << "ProjectWindow::connectNewProteinDetailWindow end";
+void
+ProjectWindow::connectNewProteinDetailWindow()
+{
+ qDebug() << "ProjectWindow::connectNewProteinDetailWindow begin";
+ _p_current_protein_detail_window = new ProteinWindow(this);
+ _protein_detail_window_collection.push_back(_p_current_protein_detail_window);
+ qDebug() << "ProjectWindow::connectNewProteinDetailWindow end";
}
-void ProjectWindow::connectNewPeptideDetailWindow() {
- qDebug() << "ProjectWindow::connectNewPeptideDetailWindow begin";
- _p_current_peptide_detail_window = new PeptideWindow(this);
- _peptide_detail_window_collection.push_back(_p_current_peptide_detail_window);
-
- qDebug() << "ProjectWindow::connectNewPeptideDetailWindow end";
+void
+ProjectWindow::connectNewPeptideDetailWindow()
+{
+ qDebug() << "ProjectWindow::connectNewPeptideDetailWindow begin";
+ _p_current_peptide_detail_window = new PeptideWindow(this);
+ _peptide_detail_window_collection.push_back(_p_current_peptide_detail_window);
+ qDebug() << "ProjectWindow::connectNewPeptideDetailWindow end";
}
-void ProjectWindow::connectNewPeptideListWindow() {
- qDebug() << "ProjectWindow::connectNewPeptideListWindow begin";
- _p_current_peptide_list_window = new PeptideListWindow(this);
- _peptide_list_window_collection.push_back(_p_current_peptide_list_window);
-
- qDebug() << "ProjectWindow::connectNewPeptideListWindow end";
+void
+ProjectWindow::connectNewPeptideListWindow()
+{
+ qDebug() << "ProjectWindow::connectNewPeptideListWindow begin";
+ _p_current_peptide_list_window = new PeptideListWindow(this);
+ _peptide_list_window_collection.push_back(_p_current_peptide_list_window);
+ qDebug() << "ProjectWindow::connectNewPeptideListWindow end";
}
-void ProjectWindow::refreshPtmGroup(IdentificationGroup * p_ident_group) {
- qDebug() << "ProjectWindow::refreshPtmGroup begin";
- hideWaitingMessage();
- if (p_ident_group == nullptr) {
- qDebug() << "ProjectWindow::refreshPtmGroup p_ident_group == nullptr";
- }
- else {
- try {
- emit identificationPtmGroupGrouped(p_ident_group);
+void
+ProjectWindow::refreshPtmGroup(IdentificationGroup *p_ident_group)
+{
+ qDebug() << "ProjectWindow::refreshPtmGroup begin";
+ hideWaitingMessage();
+ if(p_ident_group == nullptr)
+ {
+ qDebug() << "ProjectWindow::refreshPtmGroup p_ident_group == nullptr";
+ }
+ else
+ {
+ try
+ {
+ emit identificationPtmGroupGrouped(p_ident_group);
}
- catch (pappso::PappsoException exception_pappso) {
- QMessageBox::warning(this,
- tr("Unable to display project :"), exception_pappso.qwhat());
+ catch(pappso::PappsoException exception_pappso)
+ {
+ QMessageBox::warning(this, tr("Unable to display project :"),
+ exception_pappso.qwhat());
}
- catch (std::exception exception_std) {
- QMessageBox::warning(this,
- tr("Unable to display project :"), exception_std.what());
+ catch(std::exception exception_std)
+ {
+ QMessageBox::warning(this, tr("Unable to display project :"),
+ exception_std.what());
}
}
- qDebug() << "ProjectWindow::refreshPtmGroup end";
+ qDebug() << "ProjectWindow::refreshPtmGroup end";
}
-void ProjectWindow::refreshGroup(IdentificationGroup * p_ident_group) {
- qDebug() << "ProjectWindow::refreshGroup begin";
- hideWaitingMessage();
- if (p_ident_group == nullptr) {
- qDebug() << "ProjectWindow::refreshGroup p_ident_group == nullptr";
- }
- else {
- try {
- emit identificationGroupGrouped(p_ident_group);
+void
+ProjectWindow::refreshGroup(IdentificationGroup *p_ident_group)
+{
+ qDebug() << "ProjectWindow::refreshGroup begin";
+ hideWaitingMessage();
+ if(p_ident_group == nullptr)
+ {
+ qDebug() << "ProjectWindow::refreshGroup p_ident_group == nullptr";
+ }
+ else
+ {
+ try
+ {
+ emit identificationGroupGrouped(p_ident_group);
}
- catch (pappso::PappsoException exception_pappso) {
- QMessageBox::warning(this,
- tr("Unable to display project :"), exception_pappso.qwhat());
+ catch(pappso::PappsoException exception_pappso)
+ {
+ QMessageBox::warning(this, tr("Unable to display project :"),
+ exception_pappso.qwhat());
}
- catch (std::exception exception_std) {
- QMessageBox::warning(this,
- tr("Unable to display project :"), exception_std.what());
+ catch(std::exception exception_std)
+ {
+ QMessageBox::warning(this, tr("Unable to display project :"),
+ exception_std.what());
}
}
- qDebug() << "ProjectWindow::refreshGroup end";
-}
-
-void ProjectWindow::computeFdr() {
- qDebug() << "ProjectWindow::computeFdr begin ";
- try {
- ValidationState state = ValidationState::valid;
- pappso::pappso_double total_prot=0;
- pappso::pappso_double false_prot=0;
- pappso::pappso_double total_peptide=0;
- pappso::pappso_double false_peptide=0;
- for (IdentificationGroup * identification_group : _project_sp.get()->getIdentificationGroupList()) {
- total_prot += identification_group->countProteinMatch(state);
- false_prot += identification_group->countDecoyProteinMatch(state);
- total_peptide += identification_group->countPeptideEvidence(state);
- false_peptide += identification_group->countDecoyPeptideEvidence(state);
- }
- ui->protein_fdr_label->setText(QString("%1 %").arg(QString::number((false_prot/total_prot)*100.0,'f',2)));
- ui->peptide_fdr_label->setText(QString("%1 %").arg(QString::number((false_peptide/total_peptide)*100.0,'f',2)));
+ qDebug() << "ProjectWindow::refreshGroup end";
+}
+void
+ProjectWindow::computeFdr()
+{
+ qDebug() << "ProjectWindow::computeFdr begin ";
+ try
+ {
+ ValidationState state = ValidationState::valid;
+ pappso::pappso_double total_prot = 0;
+ pappso::pappso_double false_prot = 0;
+ pappso::pappso_double total_peptide = 0;
+ pappso::pappso_double false_peptide = 0;
+ for(IdentificationGroup *identification_group :
+ _project_sp.get()->getIdentificationGroupList())
+ {
+ total_prot += identification_group->countProteinMatch(state);
+ false_prot += identification_group->countDecoyProteinMatch(state);
+ total_peptide += identification_group->countPeptideEvidence(state);
+ false_peptide +=
+ identification_group->countDecoyPeptideEvidence(state);
+ }
+ ui->protein_fdr_label->setText(QString("%1 %").arg(
+ QString::number((false_prot / total_prot) * 100.0, 'f', 2)));
+ ui->peptide_fdr_label->setText(QString("%1 %").arg(
+ QString::number((false_peptide / total_peptide) * 100.0, 'f', 2)));
}
- catch (pappso::PappsoException exception_pappso) {
- QMessageBox::warning(this,
- tr("Unable to compute FDR :"), exception_pappso.qwhat());
+ catch(pappso::PappsoException exception_pappso)
+ {
+ QMessageBox::warning(this, tr("Unable to compute FDR :"),
+ exception_pappso.qwhat());
}
- catch (std::exception exception_std) {
- QMessageBox::warning(this,
- tr("Unable to compute FDR :"), exception_std.what());
+ catch(std::exception exception_std)
+ {
+ QMessageBox::warning(this, tr("Unable to compute FDR :"),
+ exception_std.what());
}
- qDebug() << "ProjectWindow::computeFdr end";
+ qDebug() << "ProjectWindow::computeFdr end";
}
-void ProjectWindow::computeMassPrecision() {
- qDebug() << "ProjectWindow::computeMassPrecision begin";
- try {
- ValidationState state = ValidationState::validAndChecked;
- std::vector< pappso::pappso_double> delta_list;
- pappso::PrecisionUnit unit = pappso::PrecisionUnit::dalton;
- if (ui->precision_unit_combobox->currentText() == "ppm") {
- unit = pappso::PrecisionUnit::ppm;
+void
+ProjectWindow::computeMassPrecision()
+{
+ qDebug() << "ProjectWindow::computeMassPrecision begin";
+ try
+ {
+ ValidationState state = ValidationState::validAndChecked;
+ std::vector<pappso::pappso_double> delta_list;
+ pappso::PrecisionUnit unit = pappso::PrecisionUnit::dalton;
+ if(ui->precision_unit_combobox->currentText() == "ppm")
+ {
+ unit = pappso::PrecisionUnit::ppm;
}
- for (IdentificationGroup * identification_group : _project_sp.get()->getIdentificationGroupList()) {
- identification_group->collectMhDelta(delta_list, unit, state);
+ for(IdentificationGroup *identification_group :
+ _project_sp.get()->getIdentificationGroupList())
+ {
+ identification_group->collectMhDelta(delta_list, unit, state);
}
- qDebug() << "ProjectWindow::computeMassPrecision accumulate";
- pappso::pappso_double sum = std::accumulate(delta_list.begin(), delta_list.end(), 0);
+ qDebug() << "ProjectWindow::computeMassPrecision accumulate";
+ pappso::pappso_double sum =
+ std::accumulate(delta_list.begin(), delta_list.end(), 0);
- qDebug() << "ProjectWindow::computeMassPrecision delta_list.size()=" << delta_list.size();
- pappso::pappso_double mean = 0;
- if (delta_list.size() > 0) {
- mean = sum / ((pappso::pappso_double) delta_list.size());
+ qDebug() << "ProjectWindow::computeMassPrecision delta_list.size()="
+ << delta_list.size();
+ pappso::pappso_double mean = 0;
+ if(delta_list.size() > 0)
+ {
+ mean = sum / ((pappso::pappso_double)delta_list.size());
}
- else {
- throw pappso::PappsoException(QObject::tr("division by zero : no valid peptide found. Please check your filter parameters (decoy regexp or database particularly)"));
+ else
+ {
+ throw pappso::PappsoException(QObject::tr(
+ "division by zero : no valid peptide found. Please check your "
+ "filter parameters (decoy regexp or database particularly)"));
}
- std::sort(delta_list.begin(), delta_list.end());
- pappso::pappso_double median = delta_list[(delta_list.size()/2)];
+ std::sort(delta_list.begin(), delta_list.end());
+ pappso::pappso_double median = delta_list[(delta_list.size() / 2)];
- qDebug() << "ProjectWindow::computeMassPrecision sd";
- pappso::pappso_double sd = 0;
- for (pappso::pappso_double val : delta_list) {
- //sd = sd + ((val - mean) * (val - mean));
- sd += std::pow((val - mean), 2);
+ qDebug() << "ProjectWindow::computeMassPrecision sd";
+ pappso::pappso_double sd = 0;
+ for(pappso::pappso_double val : delta_list)
+ {
+ // sd = sd + ((val - mean) * (val - mean));
+ sd += std::pow((val - mean), 2);
}
- sd = sd / delta_list.size();
- sd = std::sqrt(sd);
+ sd = sd / delta_list.size();
+ sd = std::sqrt(sd);
- ui->mass_precision_mean_label->setText(QString::number(mean,'f',10));
- ui->mass_precision_median_label->setText(QString::number(median,'f',10));
- ui->mass_precision_sd_label->setText(QString::number(sd,'f',10));
+ ui->mass_precision_mean_label->setText(QString::number(mean, 'f', 10));
+ ui->mass_precision_median_label->setText(
+ QString::number(median, 'f', 10));
+ ui->mass_precision_sd_label->setText(QString::number(sd, 'f', 10));
- std::vector< std::pair<pappso::pappso_double, size_t >> histogram = Utils::getHistogram(delta_list, 100);
- // generate some data:
- QVector<double> x, y;
- for (std::pair<pappso::pappso_double, size_t > & mass_pair: histogram)
+ std::vector<std::pair<pappso::pappso_double, size_t>> histogram =
+ Utils::getHistogram(delta_list, 100);
+ // generate some data:
+ QVector<double> x, y;
+ for(std::pair<pappso::pappso_double, size_t> &mass_pair : histogram)
{
- x.push_back(mass_pair.first);
- y.push_back(mass_pair.second);
+ x.push_back(mass_pair.first);
+ y.push_back(mass_pair.second);
}
- QCPGraph * p_graph = ui->mass_histogram_widget->graph();
- p_graph->setData(x,y);
- p_graph->rescaleAxes(true);
- ui->mass_histogram_widget->rescaleAxes();
- ui->mass_histogram_widget->replot();
- }
- catch (pappso::PappsoException exception_pappso) {
- ui->mass_precision_mean_label->setText("0");
- ui->mass_precision_median_label->setText("0");
- ui->mass_precision_sd_label->setText("0");
- QMessageBox::warning(this,
- tr("Unable to compute mass precision :"), exception_pappso.qwhat());
- }
- catch (std::exception exception_std) {
- ui->mass_precision_mean_label->setText("0");
- ui->mass_precision_median_label->setText("0");
- ui->mass_precision_sd_label->setText("0");
- QMessageBox::warning(this,
- tr("Unable to compute mass precision :"), exception_std.what());
- }
- qDebug() << "ProjectWindow::computeMassPrecision end";
-}
-
-void ProjectWindow::doFdrChanged() {
- qDebug() << "ProjectWindow::doFdrChanged begin ";
- try {
- showWaitingMessage(tr("FDR modifications"));
- doDisplayLoadingMessage(tr("tagging decoy proteins"));
- if (ui->decoy_regexp_radiobutton->isChecked()) {
- _project_sp.get()->getProteinStore().setRegexpDecoyPattern(ui->decoy_protein_regexp_line_edit->text());
+ QCPGraph *p_graph = ui->mass_histogram_widget->graph();
+ p_graph->setData(x, y);
+ p_graph->rescaleAxes(true);
+ ui->mass_histogram_widget->rescaleAxes();
+ ui->mass_histogram_widget->replot();
+ }
+ catch(pappso::PappsoException exception_pappso)
+ {
+ ui->mass_precision_mean_label->setText("0");
+ ui->mass_precision_median_label->setText("0");
+ ui->mass_precision_sd_label->setText("0");
+ QMessageBox::warning(this, tr("Unable to compute mass precision :"),
+ exception_pappso.qwhat());
+ }
+ catch(std::exception exception_std)
+ {
+ ui->mass_precision_mean_label->setText("0");
+ ui->mass_precision_median_label->setText("0");
+ ui->mass_precision_sd_label->setText("0");
+ QMessageBox::warning(this, tr("Unable to compute mass precision :"),
+ exception_std.what());
+ }
+ qDebug() << "ProjectWindow::computeMassPrecision end";
+}
+
+void
+ProjectWindow::doFdrChanged()
+{
+ qDebug() << "ProjectWindow::doFdrChanged begin ";
+ try
+ {
+ showWaitingMessage(tr("FDR modifications"));
+ doDisplayLoadingMessage(tr("tagging decoy proteins"));
+ if(ui->decoy_regexp_radiobutton->isChecked())
+ {
+ _project_sp.get()->getProteinStore().setRegexpDecoyPattern(
+ ui->decoy_protein_regexp_line_edit->text());
}
- else {
- _project_sp.get()->getProteinStore().clearDecoys();
- QModelIndexList index_list = ui->decoy_database_listview->selectionModel()->selectedIndexes();
- if (index_list.size() > 0) {
- qDebug() << "ProjectWindow::doFdrChanged index_list.size()=" << index_list.size();
- for (QModelIndex index :index_list) {
- if (index.data(Qt::UserRole).canConvert<FastaFile *>()) {
- FastaFile * p_fasta_file = index.data(Qt::UserRole).value<FastaFile *>();
- p_fasta_file->setDecoys(_project_sp.get()->getProteinStore());
+ else
+ {
+ _project_sp.get()->getProteinStore().clearDecoys();
+ QModelIndexList index_list =
+ ui->decoy_database_listview->selectionModel()->selectedIndexes();
+ if(index_list.size() > 0)
+ {
+ qDebug() << "ProjectWindow::doFdrChanged index_list.size()="
+ << index_list.size();
+ for(QModelIndex index : index_list)
+ {
+ if(index.data(Qt::UserRole).canConvert<FastaFile *>())
+ {
+ FastaFile *p_fasta_file =
+ index.data(Qt::UserRole).value<FastaFile *>();
+ p_fasta_file->setDecoys(
+ _project_sp.get()->getProteinStore());
}
- else {
- throw pappso::PappsoException(QObject::tr("can not convert to FastaFile index.data().canConvert<FastaFile *>()"));
+ else
+ {
+ throw pappso::PappsoException(
+ QObject::tr("can not convert to FastaFile "
+ "index.data().canConvert<FastaFile *>()"));
}
}
}
}
- doDisplayLoadingMessage(tr("updating filters"));
- _project_sp.get()->updateAutomaticFilters(_project_sp.get()->getAutomaticFilterParameters());
+ doDisplayLoadingMessage(tr("updating filters"));
+ _project_sp.get()->updateAutomaticFilters(
+ _project_sp.get()->getAutomaticFilterParameters());
- //re group
- emit operateGrouping(_project_sp);
+ // re group
+ emit operateGrouping(_project_sp);
}
- catch (pappso::PappsoException exception_pappso) {
- hideWaitingMessage();
- QMessageBox::warning(this,
- tr("Unable to compute FDR :"), exception_pappso.qwhat());
+ catch(pappso::PappsoException exception_pappso)
+ {
+ hideWaitingMessage();
+ QMessageBox::warning(this, tr("Unable to compute FDR :"),
+ exception_pappso.qwhat());
}
- catch (std::exception exception_std) {
- hideWaitingMessage();
- QMessageBox::warning(this,
- tr("Unable to compute FDR :"), exception_std.what());
+ catch(std::exception exception_std)
+ {
+ hideWaitingMessage();
+ QMessageBox::warning(this, tr("Unable to compute FDR :"),
+ exception_std.what());
}
- qDebug() << "ProjectWindow::doFdrChanged end ";
+ qDebug() << "ProjectWindow::doFdrChanged end ";
}
-void ProjectWindow::refresh() {
- qDebug() << "ProjectWindow::refresh begin ";
- computeFdr();
- computeMassPrecision();
- qDebug() << "ProjectWindow::refresh end ";
-
+void
+ProjectWindow::refresh()
+{
+ qDebug() << "ProjectWindow::refresh begin ";
+ computeFdr();
+ computeMassPrecision();
+ qDebug() << "ProjectWindow::refresh end ";
}
-void ProjectWindow::doContaminantSelectionChanged() {
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- ui->apply_filter_button->setEnabled(true);
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+void
+ProjectWindow::doContaminantSelectionChanged()
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ ui->apply_filter_button->setEnabled(true);
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-void ProjectWindow::doAutomaticFilterParametersChanged(AutomaticFilterParameters parameters) {
- qDebug() << "ProjectWindow::doAutomaticFilterParametersChanged begin ";
- ui->apply_filter_button->setEnabled(true);
- qDebug() << "ProjectWindow::doAutomaticFilterParametersChanged end ";
+void
+ProjectWindow::doAutomaticFilterParametersChanged(
+ AutomaticFilterParameters parameters)
+{
+ qDebug() << "ProjectWindow::doAutomaticFilterParametersChanged begin ";
+ ui->apply_filter_button->setEnabled(true);
+ qDebug() << "ProjectWindow::doAutomaticFilterParametersChanged end ";
}
-void ProjectWindow::doOperationFailed(QString error) {
- hideWaitingMessage();
- viewError(error);
+void
+ProjectWindow::doOperationFailed(QString error)
+{
+ hideWaitingMessage();
+ viewError(error);
}
-void ProjectWindow::doOperationFinished() {
- hideWaitingMessage();
+void
+ProjectWindow::doOperationFinished()
+{
+ hideWaitingMessage();
}
-void ProjectWindow::doDisplayLoadingMessage(QString message) {
- qDebug() << "ProjectWindow::doDisplayLoadingMessage " << message;
- _p_waiting_message_dialog->message(message);
+void
+ProjectWindow::doDisplayLoadingMessage(QString message)
+{
+ qDebug() << "ProjectWindow::doDisplayLoadingMessage " << message;
+ _p_waiting_message_dialog->message(message);
}
-void ProjectWindow::doDisplayLoadingMessagePercent(QString message, int value) {
- qDebug() << "ProjectWindow::doDisplayLoadingMessagePercent " << message << " " << value;
- _p_waiting_message_dialog->message(message, value);
+void
+ProjectWindow::doDisplayLoadingMessagePercent(QString message, int value)
+{
+ qDebug() << "ProjectWindow::doDisplayLoadingMessagePercent " << message << " "
+ << value;
+ _p_waiting_message_dialog->message(message, value);
}
-void ProjectWindow::doGroupingFinished() {
- qDebug() << "ProjectWindow::doGroupingFinished begin " ;
- hideWaitingMessage();
-
- //re group
- for (IdentificationGroup * p_ident_group : _project_sp.get()->getIdentificationGroupList()) {
- refreshGroup(p_ident_group);
+void
+ProjectWindow::doGroupingFinished()
+{
+ qDebug() << "ProjectWindow::doGroupingFinished begin ";
+ hideWaitingMessage();
+ // re group
+ for(IdentificationGroup *p_ident_group :
+ _project_sp.get()->getIdentificationGroupList())
+ {
+ refreshGroup(p_ident_group);
}
- refresh();
+ refresh();
- qDebug() << "ProjectWindow::doGroupingFinished end";
+ qDebug() << "ProjectWindow::doGroupingFinished end";
}
-void ProjectWindow::doMassPrecisionUnitChanged(QString combo_value) {
- qDebug() << "ProjectWindow::doMassPrecisionUnitChanged begin "<< combo_value;
+void
+ProjectWindow::doMassPrecisionUnitChanged(QString combo_value)
+{
+ qDebug() << "ProjectWindow::doMassPrecisionUnitChanged begin " << combo_value;
- refresh();
- qDebug() << "ProjectWindow::doMassPrecisionUnitChanged end ";
+ refresh();
+ qDebug() << "ProjectWindow::doMassPrecisionUnitChanged end ";
}
-void ProjectWindow::doViewPeptideList(IdentificationGroup * p_ident_group, ProteinMatch * protein_match) {
+void
+ProjectWindow::doViewPeptideList(IdentificationGroup *p_ident_group,
+ ProteinMatch *protein_match)
+{
- qDebug() << "ProjectWindow::doViewPeptideList begin";
- if (_peptide_list_window_collection.size() == 0) {
- connectNewPeptideListWindow();
+ qDebug() << "ProjectWindow::doViewPeptideList begin";
+ if(_peptide_list_window_collection.size() == 0)
+ {
+ connectNewPeptideListWindow();
}
- Qt::KeyboardModifiers modifier = QApplication::keyboardModifiers();
- if (modifier == Qt::ControlModifier) {
- connectNewPeptideListWindow();
+ Qt::KeyboardModifiers modifier = QApplication::keyboardModifiers();
+ if(modifier == Qt::ControlModifier)
+ {
+ connectNewPeptideListWindow();
}
- _p_current_peptide_list_window->setProteinMatch(p_ident_group, protein_match);
- _p_current_peptide_list_window->show();
- //_p_current_peptide_list_window->raise();
- //_p_current_peptide_list_window->activateWindow();
- qDebug() << "ProjectWindow::doViewPeptideList end";
+ _p_current_peptide_list_window->setProteinMatch(p_ident_group, protein_match);
+ _p_current_peptide_list_window->show();
+ //_p_current_peptide_list_window->raise();
+ //_p_current_peptide_list_window->activateWindow();
+ qDebug() << "ProjectWindow::doViewPeptideList end";
}
-void ProjectWindow::doViewPeptideDetail(PeptideEvidence * peptide_evidence) {
+void
+ProjectWindow::doViewPeptideDetail(PeptideEvidence *peptide_evidence)
+{
- qDebug() << "ProjectWindow::doViewPeptideDetail begin " << peptide_evidence;
- if (_peptide_detail_window_collection.size() == 0) {
- connectNewPeptideDetailWindow();
+ qDebug() << "ProjectWindow::doViewPeptideDetail begin " << peptide_evidence;
+ if(_peptide_detail_window_collection.size() == 0)
+ {
+ connectNewPeptideDetailWindow();
}
- Qt::KeyboardModifiers modifier = QApplication::keyboardModifiers();
- if (modifier == Qt::ControlModifier) {
- connectNewPeptideDetailWindow();
+ Qt::KeyboardModifiers modifier = QApplication::keyboardModifiers();
+ if(modifier == Qt::ControlModifier)
+ {
+ connectNewPeptideDetailWindow();
}
- _p_current_peptide_detail_window->setPeptideEvidence(peptide_evidence);
- _p_current_peptide_detail_window->show();
- //_p_current_peptide_detail_window->raise();
- //_p_current_peptide_detail_window->activateWindow();
+ _p_current_peptide_detail_window->setPeptideEvidence(peptide_evidence);
+ _p_current_peptide_detail_window->show();
+ //_p_current_peptide_detail_window->raise();
+ //_p_current_peptide_detail_window->activateWindow();
- emit peptideEvidenceSelected(peptide_evidence);
- qDebug() << "ProjectWindow::doViewPeptideDetail end";
+ emit peptideEvidenceSelected(peptide_evidence);
+ qDebug() << "ProjectWindow::doViewPeptideDetail end";
}
-void ProjectWindow::doViewProteinDetail(ProteinMatch * protein_match) {
+void
+ProjectWindow::doViewProteinDetail(ProteinMatch *protein_match)
+{
- qDebug() << "ProjectWindow::doViewProteinDetail begin";
- if (_protein_detail_window_collection.size() == 0) {
- connectNewProteinDetailWindow();
+ qDebug() << "ProjectWindow::doViewProteinDetail begin";
+ if(_protein_detail_window_collection.size() == 0)
+ {
+ connectNewProteinDetailWindow();
}
- Qt::KeyboardModifiers modifier = QApplication::keyboardModifiers();
- if (modifier == Qt::ControlModifier) {
- connectNewProteinDetailWindow();
+ Qt::KeyboardModifiers modifier = QApplication::keyboardModifiers();
+ if(modifier == Qt::ControlModifier)
+ {
+ connectNewProteinDetailWindow();
}
- _p_current_protein_detail_window->setProteinMatch(protein_match);
- _p_current_protein_detail_window->show();
- //_p_current_protein_detail_window->raise();
- //_p_current_protein_detail_window->activateWindow();
- qDebug() << "ProjectWindow::doViewProteinDetail end";
+ _p_current_protein_detail_window->setProteinMatch(protein_match);
+ _p_current_protein_detail_window->show();
+ //_p_current_protein_detail_window->raise();
+ //_p_current_protein_detail_window->activateWindow();
+ qDebug() << "ProjectWindow::doViewProteinDetail end";
}
-void ProjectWindow::doPtmIslandGrouping(IdentificationGroup* p_identification_group) {
+void
+ProjectWindow::doPtmIslandGrouping(IdentificationGroup *p_identification_group)
+{
- if (p_identification_group->getPtmGroupingExperiment() == nullptr) {
- showWaitingMessage(tr("Computing PTM islands"));
- emit operatePtmGroupingOnIdentification(p_identification_group);
+ if(p_identification_group->getPtmGroupingExperiment() == nullptr)
+ {
+ showWaitingMessage(tr("Computing PTM islands"));
+ emit operatePtmGroupingOnIdentification(p_identification_group);
}
-
}
-void ProjectWindow::doViewPtmIslandList(IdentificationGroup* p_identification_group) {
- qDebug() << "ProjectWindow::doViewPtmIslandList begin " << p_identification_group;
- //if (p_identification_group == nullptr) {
- //}
- if (_ptm_island_list_window_collection.size() == 0) {
- connectNewPtmIslandListWindow();
+void
+ProjectWindow::doViewPtmIslandList(IdentificationGroup *p_identification_group)
+{
+ qDebug() << "ProjectWindow::doViewPtmIslandList begin "
+ << p_identification_group;
+ // if (p_identification_group == nullptr) {
+ //}
+ if(_ptm_island_list_window_collection.size() == 0)
+ {
+ connectNewPtmIslandListWindow();
}
- Qt::KeyboardModifiers modifier = QApplication::keyboardModifiers();
- if (modifier == Qt::ControlModifier) {
- connectNewPtmIslandListWindow();
+ Qt::KeyboardModifiers modifier = QApplication::keyboardModifiers();
+ if(modifier == Qt::ControlModifier)
+ {
+ connectNewPtmIslandListWindow();
}
- _p_current_ptm_island_list_window->show();
- //_p_current_protein_list_window->raise();
- //_p_current_protein_list_window->activateWindow();
+ _p_current_ptm_island_list_window->show();
+ //_p_current_protein_list_window->raise();
+ //_p_current_protein_list_window->activateWindow();
- qDebug() << "ProjectWindow::doViewPtmIslandList end " << p_identification_group;
- _p_current_ptm_island_list_window->setIdentificationGroup(p_identification_group);
+ qDebug() << "ProjectWindow::doViewPtmIslandList end "
+ << p_identification_group;
+ _p_current_ptm_island_list_window->setIdentificationGroup(
+ p_identification_group);
- doPtmIslandGrouping(p_identification_group);
- //emit identificationGroupGrouped(p_identification_group);
- qDebug() << "ProjectWindow::doViewPtmIslandList end";
+ doPtmIslandGrouping(p_identification_group);
+ // emit identificationGroupGrouped(p_identification_group);
+ qDebug() << "ProjectWindow::doViewPtmIslandList end";
}
-void ProjectWindow::doViewProteinList(IdentificationGroup* p_identification_group) {
- qDebug() << "ProjectWindow::doViewProteinList begin " << p_identification_group;
- //if (p_identification_group == nullptr) {
- //}
- if (_protein_list_window_collection.size() == 0) {
- connectNewProteinListWindow();
+void
+ProjectWindow::doViewProteinList(IdentificationGroup *p_identification_group)
+{
+ qDebug() << "ProjectWindow::doViewProteinList begin "
+ << p_identification_group;
+ // if (p_identification_group == nullptr) {
+ //}
+ if(_protein_list_window_collection.size() == 0)
+ {
+ connectNewProteinListWindow();
}
- Qt::KeyboardModifiers modifier = QApplication::keyboardModifiers();
- if (modifier == Qt::ControlModifier) {
- connectNewProteinListWindow();
+ Qt::KeyboardModifiers modifier = QApplication::keyboardModifiers();
+ if(modifier == Qt::ControlModifier)
+ {
+ connectNewProteinListWindow();
}
- _p_current_protein_list_window->show();
- _p_current_protein_list_window->raise();
- _p_current_protein_list_window->activateWindow();
+ _p_current_protein_list_window->show();
+ _p_current_protein_list_window->raise();
+ _p_current_protein_list_window->activateWindow();
- qDebug() << "ProjectWindow::doViewProteinList end " << p_identification_group;
- _p_current_protein_list_window->setIdentificationGroup(p_identification_group);
+ qDebug() << "ProjectWindow::doViewProteinList end " << p_identification_group;
+ _p_current_protein_list_window->setIdentificationGroup(
+ p_identification_group);
- emit identificationGroupGrouped(p_identification_group);
- qDebug() << "ProjectWindow::doViewProteinList end";
+ emit identificationGroupGrouped(p_identification_group);
+ qDebug() << "ProjectWindow::doViewProteinList end";
}
-void ProjectWindow::setProjectSp(ProjectSp project_sp) {
- qDebug() << "ProjectWindow::setProjectSp begin" ;
+void
+ProjectWindow::setProjectSp(ProjectSp project_sp)
+{
+ qDebug() << "ProjectWindow::setProjectSp begin";
- _project_sp = project_sp;
- ui->decoy_regexp_radiobutton->setChecked(true);
- ui->decoy_regexp_groupbox->setVisible(true);
- ui->decoy_database_groupbox->setVisible(false);
- if (_project_sp.get()->getProteinStore().getDecoyFastaFileList().size() > 0) {
- ui->decoy_database_files_radiobutton->setChecked(true);
- ui->decoy_regexp_groupbox->setVisible(false);
- ui->decoy_database_groupbox->setVisible(true);
+ _project_sp = project_sp;
+ ui->decoy_regexp_radiobutton->setChecked(true);
+ ui->decoy_regexp_groupbox->setVisible(true);
+ ui->decoy_database_groupbox->setVisible(false);
+ if(_project_sp.get()->getProteinStore().getDecoyFastaFileList().size() > 0)
+ {
+ ui->decoy_database_files_radiobutton->setChecked(true);
+ ui->decoy_regexp_groupbox->setVisible(false);
+ ui->decoy_database_groupbox->setVisible(true);
}
- ui->contaminant_widget->getProjectContaminants(_project_sp.get());
+ ui->contaminant_widget->getProjectContaminants(_project_sp.get());
- qDebug() << "ProjectWindow::setProjectSp begin " << _project_sp.get()->getFastaFileStore().getFastaFileList().size() ;
- _fastafile_list = _project_sp.get()->getFastaFileStore().getFastaFileList();
+ qDebug() << "ProjectWindow::setProjectSp begin "
+ << _project_sp.get()->getFastaFileStore().getFastaFileList().size();
+ _fastafile_list = _project_sp.get()->getFastaFileStore().getFastaFileList();
- _p_fasta_str_li->removeRows(0, _p_fasta_str_li->rowCount());
- for (FastaFileSp fasta_file : _fastafile_list ) {
+ _p_fasta_str_li->removeRows(0, _p_fasta_str_li->rowCount());
+ for(FastaFileSp fasta_file : _fastafile_list)
+ {
- QStandardItem *item;
- item = new QStandardItem(QString("%1").arg(fasta_file.get()->getFilename()));
- item->setEditable(false);
- item->setData(QVariant::fromValue(fasta_file.get()), Qt::UserRole);
- _p_fasta_str_li->appendRow(item);
- //item->setData(QVariant(QString("%1").arg(fasta_file.get()->getAbsoluteFilePath())),Qt::UserRole);
+ QStandardItem *item;
+ item =
+ new QStandardItem(QString("%1").arg(fasta_file.get()->getFilename()));
+ item->setEditable(false);
+ item->setData(QVariant::fromValue(fasta_file.get()), Qt::UserRole);
+ _p_fasta_str_li->appendRow(item);
+ // item->setData(QVariant(QString("%1").arg(fasta_file.get()->getAbsoluteFilePath())),Qt::UserRole);
}
- for (auto && p_window :_ptm_island_list_window_collection) {
- delete p_window;
+ for(auto &&p_window : _ptm_island_list_window_collection)
+ {
+ delete p_window;
}
- _ptm_island_list_window_collection.clear();
- _p_current_ptm_island_list_window = nullptr;
+ _ptm_island_list_window_collection.clear();
+ _p_current_ptm_island_list_window = nullptr;
- for (auto && p_window :_peptide_list_window_collection) {
- delete p_window;
+ for(auto &&p_window : _peptide_list_window_collection)
+ {
+ delete p_window;
}
- _peptide_list_window_collection.clear();
- _p_current_peptide_list_window = nullptr;
+ _peptide_list_window_collection.clear();
+ _p_current_peptide_list_window = nullptr;
- for (auto && p_window :_protein_list_window_collection) {
- delete p_window;
+ for(auto &&p_window : _protein_list_window_collection)
+ {
+ delete p_window;
}
- _protein_list_window_collection.clear();
- _p_current_protein_list_window = nullptr;
+ _protein_list_window_collection.clear();
+ _p_current_protein_list_window = nullptr;
- for (auto && p_window :_protein_detail_window_collection) {
- delete p_window;
+ for(auto &&p_window : _protein_detail_window_collection)
+ {
+ delete p_window;
}
- _protein_detail_window_collection.clear();
- _p_current_protein_detail_window = nullptr;
+ _protein_detail_window_collection.clear();
+ _p_current_protein_detail_window = nullptr;
- for (auto && p_window :_peptide_detail_window_collection) {
- delete p_window;
+ for(auto &&p_window : _peptide_detail_window_collection)
+ {
+ delete p_window;
}
- _peptide_detail_window_collection.clear();
- _p_current_peptide_detail_window = nullptr;
+ _peptide_detail_window_collection.clear();
+ _p_current_peptide_detail_window = nullptr;
- if (_p_identification_widget != nullptr) {
- delete _p_identification_widget;
+ if(_p_identification_widget != nullptr)
+ {
+ delete _p_identification_widget;
}
- std::vector<IdentificationGroup *> identification_list = _project_sp.get()->getIdentificationGroupList();
+ std::vector<IdentificationGroup *> identification_list =
+ _project_sp.get()->getIdentificationGroupList();
- doViewProteinList(identification_list[0]);
+ doViewProteinList(identification_list[0]);
- //qDeleteAll(ui->identifications_widget->children());
- QLayoutItem *wItem;
- while (wItem = ui->identifications_widget->layout()->takeAt(0)) {
- wItem->widget()->setVisible(false);
- delete wItem;
+ // qDeleteAll(ui->identifications_widget->children());
+ QLayoutItem *wItem;
+ while(wItem = ui->identifications_widget->layout()->takeAt(0))
+ {
+ wItem->widget()->setVisible(false);
+ delete wItem;
}
- if (_p_xic_window != nullptr) {
- _p_xic_window->clear();
- _p_xic_window->hide();
- delete _p_xic_window;
- _p_xic_window = nullptr;
+ if(_p_xic_window != nullptr)
+ {
+ _p_xic_window->clear();
+ _p_xic_window->hide();
+ delete _p_xic_window;
+ _p_xic_window = nullptr;
}
- qDebug() << " ProjectWindow::setProjectSp size=" << identification_list.size();
- if (identification_list.size() == 1) {
- ui->identifications_combobox->setVisible(false);
+ qDebug() << " ProjectWindow::setProjectSp size="
+ << identification_list.size();
+ if(identification_list.size() == 1)
+ {
+ ui->identifications_combobox->setVisible(false);
- IdentificationGroupWidget * p_identification_widget = new IdentificationGroupWidget(this);
- p_identification_widget->setIdentificationGroup(this, identification_list[0]);
+ IdentificationGroupWidget *p_identification_widget =
+ new IdentificationGroupWidget(this);
+ p_identification_widget->setIdentificationGroup(this,
+ identification_list[0]);
- ui->identifications_widget->layout()->addWidget(p_identification_widget);
+ ui->identifications_widget->layout()->addWidget(p_identification_widget);
- refreshGroup(identification_list[0]);
+ refreshGroup(identification_list[0]);
}
- else {
- ui->identifications_combobox->clear();
- ui->identifications_combobox->setVisible(true);
+ else
+ {
+ ui->identifications_combobox->clear();
+ ui->identifications_combobox->setVisible(true);
- for (IdentificationGroup * identification_group : identification_list) {
- IdentificationGroupWidget * p_identification_widget = new IdentificationGroupWidget(this);
- p_identification_widget->setVisible(false);
+ for(IdentificationGroup *identification_group : identification_list)
+ {
+ IdentificationGroupWidget *p_identification_widget =
+ new IdentificationGroupWidget(this);
+ p_identification_widget->setVisible(false);
- ui->identifications_combobox->addItem(identification_group->getTabName(), QVariant::fromValue(p_identification_widget));
+ ui->identifications_combobox->addItem(
+ identification_group->getTabName(),
+ QVariant::fromValue(p_identification_widget));
- p_identification_widget->setIdentificationGroup(this, identification_group);
+ p_identification_widget->setIdentificationGroup(this,
+ identification_group);
- ui->identifications_widget->layout()->addWidget(p_identification_widget);
+ ui->identifications_widget->layout()->addWidget(
+ p_identification_widget);
- refreshGroup(identification_group);
+ refreshGroup(identification_group);
}
- ui->identifications_combobox->setCurrentIndex(0);
- qobject_cast<IdentificationGroupWidget*>(qvariant_cast<QObject*>(ui->identifications_combobox->itemData( ui->identifications_combobox->currentIndex())))->setVisible(true);
+ ui->identifications_combobox->setCurrentIndex(0);
+ qobject_cast<IdentificationGroupWidget *>(
+ qvariant_cast<QObject *>(ui->identifications_combobox->itemData(
+ ui->identifications_combobox->currentIndex())))
+ ->setVisible(true);
}
- AutomaticFilterParameters params = _project_sp.get()->getAutomaticFilterParameters();
-
- ui->filter_parameter_widget->setAutomaticFilterParameters(params);
- //_protein_list_window->setIdentificationGroup(_project_sp.get()->getCurrentIdentificationGroupP());
- //_protein_list_window->show();
+ AutomaticFilterParameters params =
+ _project_sp.get()->getAutomaticFilterParameters();
- ui->decoy_protein_regexp_line_edit->setText(_project_sp.get()->getProteinStore().getRegexpDecoy().pattern());
+ ui->filter_parameter_widget->setAutomaticFilterParameters(params);
+ //_protein_list_window->setIdentificationGroup(_project_sp.get()->getCurrentIdentificationGroupP());
+ //_protein_list_window->show();
- refresh();
- this->setEnabled(true);
+ ui->decoy_protein_regexp_line_edit->setText(
+ _project_sp.get()->getProteinStore().getRegexpDecoy().pattern());
- //doAutomaticFilterParametersChanged(params);
- //doFdrChanged();
+ refresh();
+ this->setEnabled(true);
+ // doAutomaticFilterParametersChanged(params);
+ // doFdrChanged();
}
-void ProjectWindow::doIdentificationsComboboxChanged(int index_in) {
- qDebug() << "ProjectWindow::doIdentificationsComboboxChanged begin ";
- for (int index = 0; index < ui->identifications_combobox->count(); index++) {
- qobject_cast<IdentificationGroupWidget*>(qvariant_cast<QObject*>(ui->identifications_combobox->itemData(index)))->setVisible(false);
+void
+ProjectWindow::doIdentificationsComboboxChanged(int index_in)
+{
+ qDebug() << "ProjectWindow::doIdentificationsComboboxChanged begin ";
+ for(int index = 0; index < ui->identifications_combobox->count(); index++)
+ {
+ qobject_cast<IdentificationGroupWidget *>(
+ qvariant_cast<QObject *>(ui->identifications_combobox->itemData(index)))
+ ->setVisible(false);
}
- qobject_cast<IdentificationGroupWidget*>(qvariant_cast<QObject*>(ui->identifications_combobox->itemData(index_in)))->setVisible(true);
- qDebug() << "ProjectWindow::doIdentificationsComboboxChanged end ";
+ qobject_cast<IdentificationGroupWidget *>(
+ qvariant_cast<QObject *>(ui->identifications_combobox->itemData(index_in)))
+ ->setVisible(true);
+ qDebug() << "ProjectWindow::doIdentificationsComboboxChanged end ";
}
-void ProjectWindow::editModifications() {
- _p_edit_modifications->setProjectSp(_project_sp);
- _p_edit_modifications->show();
- _p_edit_modifications->raise();
- _p_edit_modifications->activateWindow();
-
+void
+ProjectWindow::editModifications()
+{
+ _p_edit_modifications->setProjectSp(_project_sp);
+ _p_edit_modifications->show();
+ _p_edit_modifications->raise();
+ _p_edit_modifications->activateWindow();
}
-void ProjectWindow::editLabelingMethods() {
- _p_edit_label_methods->setProjectSp(_project_sp);
- _p_edit_label_methods->show();
- _p_edit_label_methods->raise();
- _p_edit_label_methods->activateWindow();
-
+void
+ProjectWindow::editLabelingMethods()
+{
+ _p_edit_label_methods->setProjectSp(_project_sp);
+ _p_edit_label_methods->show();
+ _p_edit_label_methods->raise();
+ _p_edit_label_methods->activateWindow();
}
-void ProjectWindow::hideWaitingMessage() {
+void
+ProjectWindow::hideWaitingMessage()
+{
- _p_waiting_message_dialog->hide();
+ _p_waiting_message_dialog->hide();
}
-void ProjectWindow::showWaitingMessage(const QString title) {
- _p_waiting_message_dialog->setWindowTitle(title);
- _p_waiting_message_dialog->show();
- _p_waiting_message_dialog->raise();
- _p_waiting_message_dialog->activateWindow();
-
+void
+ProjectWindow::showWaitingMessage(const QString title)
+{
+ _p_waiting_message_dialog->setWindowTitle(title);
+ _p_waiting_message_dialog->show();
+ _p_waiting_message_dialog->raise();
+ _p_waiting_message_dialog->activateWindow();
}
-void ProjectWindow::doIdentificationGroupEdited(IdentificationGroup* p_identification_group) {
- showWaitingMessage(tr("Updating identification group"));
+void
+ProjectWindow::doIdentificationGroupEdited(
+ IdentificationGroup *p_identification_group)
+{
+ showWaitingMessage(tr("Updating identification group"));
- qDebug() << "ProjectWindow::doIdentificationGroupEdited emit operateGroupingOnIdentification(_project_sp) ";
- emit operateGroupingOnIdentification(p_identification_group, _project_sp.get()->getGroupingType());
+ qDebug() << "ProjectWindow::doIdentificationGroupEdited emit "
+ "operateGroupingOnIdentification(_project_sp) ";
+ emit operateGroupingOnIdentification(p_identification_group,
+ _project_sp.get()->getGroupingType());
}
-void ProjectWindow::viewError(QString error) {
- QMessageBox::warning(this,
- tr("Oops! an error occurred in XTPCPP. Dont Panic :"), error);
+void
+ProjectWindow::viewError(QString error)
+{
+ QMessageBox::warning(
+ this, tr("Oops! an error occurred in XTPCPP. Dont Panic :"), error);
}
-void ProjectWindow::doAcceptedLabelingMethod() {
- qDebug() << "ProjectWindow::doAcceptedLabelingMethod";
- showWaitingMessage(tr("Apply labeling method"));
-
- LabelingMethodSp labeling_method_sp = _p_edit_label_methods->getLabelingMethodSp();
- _project_sp.get()->setLabelingMethodSp(labeling_method_sp);
- //_p_edit_label_methods->applyLabelingMethodInProject();
+void
+ProjectWindow::doAcceptedLabelingMethod()
+{
+ qDebug() << "ProjectWindow::doAcceptedLabelingMethod";
+ showWaitingMessage(tr("Apply labeling method"));
- doDisplayLoadingMessage(tr("labeling peptides"));
+ LabelingMethodSp labeling_method_sp =
+ _p_edit_label_methods->getLabelingMethodSp();
+ _project_sp.get()->setLabelingMethodSp(labeling_method_sp);
+ //_p_edit_label_methods->applyLabelingMethodInProject();
- qDebug() << "ProjectWindow::doAcceptedLabelingMethod emit operateGrouping(_project_sp) ";
- emit operateGrouping(_project_sp);
+ doDisplayLoadingMessage(tr("labeling peptides"));
+ qDebug() << "ProjectWindow::doAcceptedLabelingMethod emit "
+ "operateGrouping(_project_sp) ";
+ emit operateGrouping(_project_sp);
}
-void ProjectWindow::openInXicViewer(const PeptideEvidence * p_peptide_evidence) {
- qDebug() << "ProjectWindow::openInXicViewer begin";
- if (_p_xic_window == nullptr) {
- _p_xic_window = new XicWindow(this);
+void
+ProjectWindow::openInXicViewer(const PeptideEvidence *p_peptide_evidence)
+{
+ qDebug() << "ProjectWindow::openInXicViewer begin";
+ if(_p_xic_window == nullptr)
+ {
+ _p_xic_window = new XicWindow(this);
}
- _p_xic_window->show();
+ _p_xic_window->show();
- _p_xic_window->addXic(p_peptide_evidence);
- qDebug() << "ProjectWindow::openInXicViewer end";
+ _p_xic_window->addXic(p_peptide_evidence);
+ qDebug() << "ProjectWindow::openInXicViewer end";
}
-void ProjectWindow::doSelectDecoySource() {
- qDebug() << "ProjectWindow::doSelectDecoySource begin";
- ui->decoy_database_groupbox->setVisible(false);
- ui->decoy_regexp_groupbox->setVisible(false);
- if (ui->decoy_database_files_radiobutton->isChecked()) {
- ui->decoy_database_groupbox->setVisible(true);
+void
+ProjectWindow::doSelectDecoySource()
+{
+ qDebug() << "ProjectWindow::doSelectDecoySource begin";
+ ui->decoy_database_groupbox->setVisible(false);
+ ui->decoy_regexp_groupbox->setVisible(false);
+ if(ui->decoy_database_files_radiobutton->isChecked())
+ {
+ ui->decoy_database_groupbox->setVisible(true);
}
- else {
- ui->decoy_regexp_groupbox->setVisible(true);
+ else
+ {
+ ui->decoy_regexp_groupbox->setVisible(true);
}
- qDebug() << "ProjectWindow::doSelectDecoySource end";
+ qDebug() << "ProjectWindow::doSelectDecoySource end";
}
-void ProjectWindow::doFilterChanged() {
- ui->apply_filter_button->setEnabled(true);
+void
+ProjectWindow::doFilterChanged()
+{
+ ui->apply_filter_button->setEnabled(true);
}
-void ProjectWindow::doApplyFilter() {
- ui->apply_filter_button->setEnabled(false);
- AutomaticFilterParameters automatic_filter = ui->filter_parameter_widget->getAutomaticFilterParameters();
- //doAutomaticFilterParametersChanged(automatic_filter);
- try {
- showWaitingMessage(tr("Updating filters"));
-
- doDisplayLoadingMessage(tr("tagging contaminant proteins"));
-
- ui->contaminant_widget->setProjectContaminants(_project_sp.get());
- doDisplayLoadingMessage(tr("updating filters"));
- _project_sp.get()->updateAutomaticFilters(automatic_filter);
-
- qDebug() << "ProjectWindow::doAutomaticFilterParametersChanged emit operateGrouping(_project_sp) ";
- emit operateGrouping(_project_sp);
- }
- catch (pappso::PappsoException exception_pappso) {
- hideWaitingMessage();
- QMessageBox::warning(this,
- tr("Error filtering results :"), exception_pappso.qwhat());
- }
- catch (std::exception exception_std) {
- hideWaitingMessage();
- QMessageBox::warning(this,
- tr("Error filtering results :"), exception_std.what());
+void
+ProjectWindow::doApplyFilter()
+{
+ ui->apply_filter_button->setEnabled(false);
+ AutomaticFilterParameters automatic_filter =
+ ui->filter_parameter_widget->getAutomaticFilterParameters();
+ // doAutomaticFilterParametersChanged(automatic_filter);
+ try
+ {
+ showWaitingMessage(tr("Updating filters"));
+
+ doDisplayLoadingMessage(tr("tagging contaminant proteins"));
+
+ ui->contaminant_widget->setProjectContaminants(_project_sp.get());
+ doDisplayLoadingMessage(tr("updating filters"));
+ _project_sp.get()->updateAutomaticFilters(automatic_filter);
+
+ qDebug() << "ProjectWindow::doAutomaticFilterParametersChanged emit "
+ "operateGrouping(_project_sp) ";
+ emit operateGrouping(_project_sp);
+ }
+ catch(pappso::PappsoException exception_pappso)
+ {
+ hideWaitingMessage();
+ QMessageBox::warning(this, tr("Error filtering results :"),
+ exception_pappso.qwhat());
+ }
+ catch(std::exception exception_std)
+ {
+ hideWaitingMessage();
+ QMessageBox::warning(this, tr("Error filtering results :"),
+ exception_std.what());
}
-
}
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index f1f8f2f399adc9eb2162304d88add404e93c718c..7855d705dcbc082d3ec45ee288c78d145617979c 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PROJECTWINDOW_H
#define PROJECTWINDOW_H
@@ -42,106 +43,111 @@
class MainWindow;
-//http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
-namespace Ui {
-class ProjectView;
+// http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
+namespace Ui
+{
+ class ProjectView;
}
-class ProjectWindow: public QMainWindow {
- Q_OBJECT
-
- friend class ProteinListWindow;
- friend class PeptideListWindow;
-public:
-
- explicit ProjectWindow(MainWindow * parent = 0);
- Project * getProjectP();
- void setProjectSp(ProjectSp project_sp);
- void editModifications();
- void editLabelingMethods();
- void openInXicViewer(const PeptideEvidence * p_peptide_evidence);
- ~ProjectWindow();
-
-public slots:
- void doViewPtmIslandList(IdentificationGroup* p_identification_group);
- void doPtmIslandGrouping(IdentificationGroup* p_identification_group);
- void doViewProteinList(IdentificationGroup* p_identification_group =nullptr);
- void setDefaultProteinListWindow(ProteinListWindow* p_protein_list_window);
- void doAutomaticFilterParametersChanged(AutomaticFilterParameters parameters);
- void doFdrChanged();
- void doSelectDecoySource();
- void doMassPrecisionUnitChanged(QString combo_value);
- void doOperationFailed(QString);
- void doOperationFinished();
- void doGroupingFinished();
- void doIdentificationsComboboxChanged(int index);
- void doDisplayLoadingMessage(QString message);
- void doDisplayLoadingMessagePercent(QString message, int value);
- void refreshGroup(IdentificationGroup * p_ident_group);
- void refreshPtmGroup(IdentificationGroup * p_ident_group);
- void doAcceptedLabelingMethod();
- void doViewPeptideDetail(PeptideEvidence * peptide_evidence);
- void doFilterChanged();
- void doApplyFilter();
- // void setColor(const QColor &color);
- // void setShape(Shape shape);
-signals:
- void identificationGroupGrouped(IdentificationGroup * p_identification_group);
- void identificationPtmGroupGrouped(IdentificationGroup * p_identification_group);
- void peptideEvidenceSelected(PeptideEvidence * peptide_evidence);
- void operateGrouping(ProjectSp project_sp);
- void operatePtmGroupingOnIdentification(IdentificationGroup * p_identification_group);
- void operateGroupingOnIdentification(IdentificationGroup * p_identification_group, GroupingType grouping_type);
- //void peptideChanged(pappso::PeptideSp peptide);
-
-protected :
- void doViewPeptideList(IdentificationGroup * p_ident_group, ProteinMatch * protein_match);
- void doViewProteinDetail(ProteinMatch * protein_match);
- void doIdentificationGroupEdited(IdentificationGroup* p_identification_group);
- void doContaminantSelectionChanged();
- void computeFdr();
- void computeMassPrecision();
-
-private :
- void connectNewPtmIslandListWindow();
- void connectNewProteinListWindow();
- void connectNewPeptideListWindow();
- void connectNewProteinDetailWindow();
- void connectNewPeptideDetailWindow();
- void refresh();
- void showWaitingMessage(const QString title);
- void hideWaitingMessage();
- void viewError(QString error);
-
-
-private:
- QThread _worker_thread;
- Ui::ProjectView *ui;
- QWidget * _p_identification_widget = nullptr;
- MainWindow * main_window;
- std::list <ProteinListWindow *> _protein_list_window_collection;
- ProteinListWindow * _p_current_protein_list_window = nullptr;
- std::list <PeptideListWindow *> _peptide_list_window_collection;
- PeptideListWindow * _p_current_peptide_list_window = nullptr;
- std::list <ProteinWindow *> _protein_detail_window_collection;
- ProteinWindow * _p_current_protein_detail_window = nullptr;
- std::list <PeptideWindow *> _peptide_detail_window_collection;
- PeptideWindow * _p_current_peptide_detail_window = nullptr;
- std::list <PtmIslandListWindow *> _ptm_island_list_window_collection;
- PtmIslandListWindow * _p_current_ptm_island_list_window = nullptr;
-
- EditModifications * _p_edit_modifications = nullptr;
- EditLabelMethods * _p_edit_label_methods = nullptr;
- XicWindow * _p_xic_window = nullptr;
-
- ProjectSp _project_sp;
-
- QStandardItemModel * _p_fasta_str_li;
- std::vector<FastaFileSp> _fastafile_list;
- WaitingMessageDialog * _p_waiting_message_dialog;
- //QCPBars *_p_bars;
+class ProjectWindow : public QMainWindow
+{
+ Q_OBJECT
+ friend class ProteinListWindow;
+ friend class PeptideListWindow;
+ public:
+ explicit ProjectWindow(MainWindow *parent = 0);
+ Project *getProjectP();
+ void setProjectSp(ProjectSp project_sp);
+ void editModifications();
+ void editLabelingMethods();
+ void openInXicViewer(const PeptideEvidence *p_peptide_evidence);
+ ~ProjectWindow();
+
+ public slots:
+ void doViewPtmIslandList(IdentificationGroup *p_identification_group);
+ void doPtmIslandGrouping(IdentificationGroup *p_identification_group);
+ void doViewProteinList(IdentificationGroup *p_identification_group = nullptr);
+ void setDefaultProteinListWindow(ProteinListWindow *p_protein_list_window);
+ void doAutomaticFilterParametersChanged(AutomaticFilterParameters parameters);
+ void doFdrChanged();
+ void doSelectDecoySource();
+ void doMassPrecisionUnitChanged(QString combo_value);
+ void doOperationFailed(QString);
+ void doOperationFinished();
+ void doGroupingFinished();
+ void doIdentificationsComboboxChanged(int index);
+ void doDisplayLoadingMessage(QString message);
+ void doDisplayLoadingMessagePercent(QString message, int value);
+ void refreshGroup(IdentificationGroup *p_ident_group);
+ void refreshPtmGroup(IdentificationGroup *p_ident_group);
+ void doAcceptedLabelingMethod();
+ void doViewPeptideDetail(PeptideEvidence *peptide_evidence);
+ void doFilterChanged();
+ void doApplyFilter();
+ // void setColor(const QColor &color);
+ // void setShape(Shape shape);
+ signals:
+ void identificationGroupGrouped(IdentificationGroup *p_identification_group);
+ void
+ identificationPtmGroupGrouped(IdentificationGroup *p_identification_group);
+ void peptideEvidenceSelected(PeptideEvidence *peptide_evidence);
+ void operateGrouping(ProjectSp project_sp);
+ void operatePtmGroupingOnIdentification(
+ IdentificationGroup *p_identification_group);
+ void
+ operateGroupingOnIdentification(IdentificationGroup *p_identification_group,
+ GroupingType grouping_type);
+ // void peptideChanged(pappso::PeptideSp peptide);
+
+ protected:
+ void doViewPeptideList(IdentificationGroup *p_ident_group,
+ ProteinMatch *protein_match);
+ void doViewProteinDetail(ProteinMatch *protein_match);
+ void doIdentificationGroupEdited(IdentificationGroup *p_identification_group);
+ void doContaminantSelectionChanged();
+ void computeFdr();
+ void computeMassPrecision();
+
+ private:
+ void connectNewPtmIslandListWindow();
+ void connectNewProteinListWindow();
+ void connectNewPeptideListWindow();
+ void connectNewProteinDetailWindow();
+ void connectNewPeptideDetailWindow();
+ void refresh();
+ void showWaitingMessage(const QString title);
+ void hideWaitingMessage();
+ void viewError(QString error);
+
+
+ private:
+ QThread _worker_thread;
+ Ui::ProjectView *ui;
+ QWidget *_p_identification_widget = nullptr;
+ MainWindow *main_window;
+ std::list<ProteinListWindow *> _protein_list_window_collection;
+ ProteinListWindow *_p_current_protein_list_window = nullptr;
+ std::list<PeptideListWindow *> _peptide_list_window_collection;
+ PeptideListWindow *_p_current_peptide_list_window = nullptr;
+ std::list<ProteinWindow *> _protein_detail_window_collection;
+ ProteinWindow *_p_current_protein_detail_window = nullptr;
+ std::list<PeptideWindow *> _peptide_detail_window_collection;
+ PeptideWindow *_p_current_peptide_detail_window = nullptr;
+ std::list<PtmIslandListWindow *> _ptm_island_list_window_collection;
+ PtmIslandListWindow *_p_current_ptm_island_list_window = nullptr;
+
+ EditModifications *_p_edit_modifications = nullptr;
+ EditLabelMethods *_p_edit_label_methods = nullptr;
+ XicWindow *_p_xic_window = nullptr;
+
+ ProjectSp _project_sp;
+
+ QStandardItemModel *_p_fasta_str_li;
+ std::vector<FastaFileSp> _fastafile_list;
+ WaitingMessageDialog *_p_waiting_message_dialog;
+ // QCPBars *_p_bars;
};
diff --git a/src/gui/protein_list_view/proteinlistwindow.cpp b/src/gui/protein_list_view/proteinlistwindow.cpp
index e043d0cdd75bb3b54f1c62ab3894e2fec4f0a85f..73648355426d11880bc79d9f6c6fcf09d939c753 100644
--- a/src/gui/protein_list_view/proteinlistwindow.cpp
+++ b/src/gui/protein_list_view/proteinlistwindow.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "proteinlistwindow.h"
@@ -27,324 +28,423 @@
#include "../mainwindow.h"
#include <QSettings>
-ProteinListQactionColumn::ProteinListQactionColumn(ProteinListWindow * parent, ProteinListColumn column):QAction(parent) {
+ProteinListQactionColumn::ProteinListQactionColumn(ProteinListWindow *parent,
+ ProteinListColumn column)
+ : QAction(parent)
+{
- this->setText(ProteinTableModel::getTitle(column));
+ this->setText(ProteinTableModel::getTitle(column));
- this->setCheckable(true);
- this->setChecked(parent->getProteinListColumnDisplay(column));
+ this->setCheckable(true);
+ this->setChecked(parent->getProteinListColumnDisplay(column));
- //evalue_action.setChecked(_display_evalue);
- //connect(p_action, SIGNAL(toggled(bool)), this, SLOT(showEvalueColumn(bool)));
- _column = column;
- _p_protein_list_window = parent;
+ // evalue_action.setChecked(_display_evalue);
+ // connect(p_action, SIGNAL(toggled(bool)), this,
+ // SLOT(showEvalueColumn(bool)));
+ _column = column;
+ _p_protein_list_window = parent;
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect (this, &ProteinListQactionColumn::toggled, this,&ProteinListQactionColumn::doToggled);
+ // Qt5 code
+ connect(this, &ProteinListQactionColumn::toggled, this,
+ &ProteinListQactionColumn::doToggled);
#else
-// Qt4 code
- connect (this, SIGNAL(toggled(bool)), this,SLOT(doToggled(bool)));
+ // Qt4 code
+ connect(this, SIGNAL(toggled(bool)), this, SLOT(doToggled(bool)));
#endif
}
ProteinListQactionColumn::~ProteinListQactionColumn()
{
- //if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
- qDebug() << "ProteinListQactionColumn::~ProteinListQactionColumn begin ";
-
+ // if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
+ qDebug() << "ProteinListQactionColumn::~ProteinListQactionColumn begin ";
}
-void ProteinListQactionColumn::doToggled(bool toggled) {
- qDebug() << "ProteinListQactionColumn::doToggled begin " << toggled;
- setChecked(toggled);
- _p_protein_list_window->setProteinListColumnDisplay(_column, toggled);
+void
+ProteinListQactionColumn::doToggled(bool toggled)
+{
+ qDebug() << "ProteinListQactionColumn::doToggled begin " << toggled;
+ setChecked(toggled);
+ _p_protein_list_window->setProteinListColumnDisplay(_column, toggled);
- qDebug() << "ProteinListQactionColumn::doToggled end";
+ qDebug() << "ProteinListQactionColumn::doToggled end";
}
-ProteinListWindow::ProteinListWindow(ProjectWindow *parent):
- QMainWindow(parent),
- ui(new Ui::ProteinView)
+ProteinListWindow::ProteinListWindow(ProjectWindow *parent)
+ : QMainWindow(parent), ui(new Ui::ProteinView)
{
- _project_window = parent;
- ui->setupUi(this);
- setWindowIcon(QIcon(":/xtpcpp_icon/resources/xtandempipeline_icon.svg"));
- /*
- */
- _protein_table_model_p = new ProteinTableModel(this);
-
-
- _p_proxy_model = new ProteinTableProxyModel(this, _protein_table_model_p);
- _p_proxy_model->setSourceModel(_protein_table_model_p);
- _p_proxy_model->setDynamicSortFilter(true);
- ui->tableView->setModel( _p_proxy_model );
- ui->tableView->setSortingEnabled(true);
- ui->tableView->setAlternatingRowColors(true);
-
- QSettings settings;
- bool hide = settings.value("proteinview/hidenotvalid", "true").toBool();
- if (hide) {
- ui->hideNotValidCheckBox->setCheckState(Qt::Checked);
+ _project_window = parent;
+ ui->setupUi(this);
+ setWindowIcon(QIcon(":/xtpcpp_icon/resources/xtandempipeline_icon.svg"));
+ /*
+ */
+ _protein_table_model_p = new ProteinTableModel(this);
+
+
+ _p_proxy_model = new ProteinTableProxyModel(this, _protein_table_model_p);
+ _p_proxy_model->setSourceModel(_protein_table_model_p);
+ _p_proxy_model->setDynamicSortFilter(true);
+ ui->tableView->setModel(_p_proxy_model);
+ ui->tableView->setSortingEnabled(true);
+ ui->tableView->setAlternatingRowColors(true);
+
+ QSettings settings;
+ bool hide = settings.value("proteinview/hidenotvalid", "true").toBool();
+ if(hide)
+ {
+ ui->hideNotValidCheckBox->setCheckState(Qt::Checked);
}
- _p_proxy_model->hideNotValid(hide);
- hide = settings.value("proteinview/hidenotchecked", "false").toBool();
- if (hide) {
- ui->hideNotCheckedCheckBox->setCheckState(Qt::Checked);
+ _p_proxy_model->hideNotValid(hide);
+ hide = settings.value("proteinview/hidenotchecked", "false").toBool();
+ if(hide)
+ {
+ ui->hideNotCheckedCheckBox->setCheckState(Qt::Checked);
}
- _p_proxy_model->hideNotChecked(hide);
- hide = settings.value("proteinview/hidenotgrouped", "false").toBool();
- if (hide) {
- ui->hideNotGroupedCheckBox->setCheckState(Qt::Checked);
+ _p_proxy_model->hideNotChecked(hide);
+ hide = settings.value("proteinview/hidenotgrouped", "false").toBool();
+ if(hide)
+ {
+ ui->hideNotGroupedCheckBox->setCheckState(Qt::Checked);
}
- _p_proxy_model->hideNotGrouped(hide);
-
-
+ _p_proxy_model->hideNotGrouped(hide);
- ui->scan_number_edit->setVisible(false);
- ui->msrun_auto_completion->setVisible(false);
- ui->mod_auto_completion->setVisible(false);
- ui->protein_search_edit->setVisible(true);
+ ui->scan_number_edit->setVisible(false);
+ ui->msrun_auto_completion->setVisible(false);
+ ui->mod_auto_completion->setVisible(false);
+ ui->protein_search_edit->setVisible(true);
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect (_project_window, &ProjectWindow::identificationGroupGrouped, this,&ProteinListWindow::doIdentificationGroupGrouped);
-
- connect (this, &ProteinListWindow::proteinDataChanged, _protein_table_model_p, &ProteinTableModel::onProteinDataChanged);
- connect(ui->tableView, &QTableView::clicked, _p_proxy_model, &ProteinTableProxyModel::onTableClicked);
- connect(ui->centralwidget, &QWidget::customContextMenuRequested,
- this, &ProteinListWindow::showContextMenu);
- connect(_protein_table_model_p, &ProteinTableModel::layoutChanged, this, &ProteinListWindow::updateStatusBar);
+ // Qt5 code
+ connect(_project_window, &ProjectWindow::identificationGroupGrouped, this,
+ &ProteinListWindow::doIdentificationGroupGrouped);
+
+ connect(this, &ProteinListWindow::proteinDataChanged, _protein_table_model_p,
+ &ProteinTableModel::onProteinDataChanged);
+ connect(ui->tableView, &QTableView::clicked, _p_proxy_model,
+ &ProteinTableProxyModel::onTableClicked);
+ connect(ui->centralwidget, &QWidget::customContextMenuRequested, this,
+ &ProteinListWindow::showContextMenu);
+ connect(_protein_table_model_p, &ProteinTableModel::layoutChanged, this,
+ &ProteinListWindow::updateStatusBar);
#else
-// Qt4 code
- connect (_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
-
- connect (this, SIGNAL(proteinDataChanged()), _protein_table_model_p, SLOT(onProteinDataChanged()));
- connect(ui->tableView, SIGNAL(clicked(const QModelIndex &)), _p_proxy_model, SLOT(onTableClicked(const QModelIndex &)));
- //connect(ui->tableView, SIGNAL(doubleClicked(const QModelIndex &)), _p_proxy_model, SLOT(onTableDoubleClicked(const QModelIndex &)));
- //connect(ui->protein_search_edit, SIGNAL(textChanged(QString)), this, SLOT(onProteinSearchEdit(QString)));
-
-
- //connect( this, SIGNAL( focusReceived(bool) ),this, SLOT(doFocusReceived(bool)) );
- connect(ui->centralwidget, SIGNAL(customContextMenuRequested(const QPoint &)),
- this, SLOT(showContextMenu(const QPoint &)));
- //connect(_p_proxy_model, SIGNAL(layoutChanged()),
- // this, SLOT(doProxyLayoutChanged()));
- connect(_protein_table_model_p, SIGNAL(layoutChanged()), this, SLOT(updateStatusBar()));
+ // Qt4 code
+ connect(_project_window,
+ SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
+ SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
+
+ connect(this, SIGNAL(proteinDataChanged()), _protein_table_model_p,
+ SLOT(onProteinDataChanged()));
+ connect(ui->tableView, SIGNAL(clicked(const QModelIndex &)), _p_proxy_model,
+ SLOT(onTableClicked(const QModelIndex &)));
+ // connect(ui->tableView, SIGNAL(doubleClicked(const QModelIndex &)),
+ // _p_proxy_model, SLOT(onTableDoubleClicked(const QModelIndex &)));
+ // connect(ui->protein_search_edit, SIGNAL(textChanged(QString)), this,
+ // SLOT(onProteinSearchEdit(QString)));
+
+
+ // connect( this, SIGNAL( focusReceived(bool) ),this,
+ // SLOT(doFocusReceived(bool)) );
+ connect(ui->centralwidget, SIGNAL(customContextMenuRequested(const QPoint &)),
+ this, SLOT(showContextMenu(const QPoint &)));
+ // connect(_p_proxy_model, SIGNAL(layoutChanged()),
+ // this, SLOT(doProxyLayoutChanged()));
+ connect(_protein_table_model_p, SIGNAL(layoutChanged()), this,
+ SLOT(updateStatusBar()));
#endif
}
-void ProteinListWindow::doProxyLayoutChanged() {
- qDebug() << "ProteinListWindow::doProxyLayoutChanged begin";
- //updateStatusBar();
- qDebug() << "ProteinListWindow::doProxyLayoutChanged end";
+void
+ProteinListWindow::doProxyLayoutChanged()
+{
+ qDebug() << "ProteinListWindow::doProxyLayoutChanged begin";
+ // updateStatusBar();
+ qDebug() << "ProteinListWindow::doProxyLayoutChanged end";
}
-void ProteinListWindow::askPeptideListView(ProteinMatch * p_protein_match) {
- qDebug() << "ProteinListWindow::askPeptideListView begin";
- _project_window->doViewPeptideList(_p_identification_group, p_protein_match);
- qDebug() << "ProteinListWindow::askPeptideListView end";
- //updateStatusBar();
+void
+ProteinListWindow::askPeptideListView(ProteinMatch *p_protein_match)
+{
+ qDebug() << "ProteinListWindow::askPeptideListView begin";
+ _project_window->doViewPeptideList(_p_identification_group, p_protein_match);
+ qDebug() << "ProteinListWindow::askPeptideListView end";
+ // updateStatusBar();
}
-void ProteinListWindow::askProteinDetailView(ProteinMatch * p_protein_match) {
- qDebug() << "ProteinListWindow::askProteinDetailView begin";
- _project_window->doViewProteinDetail(p_protein_match);
- qDebug() << "ProteinListWindow::askProteinDetailView end";
- //updateStatusBar();
+void
+ProteinListWindow::askProteinDetailView(ProteinMatch *p_protein_match)
+{
+ qDebug() << "ProteinListWindow::askProteinDetailView begin";
+ _project_window->doViewProteinDetail(p_protein_match);
+ qDebug() << "ProteinListWindow::askProteinDetailView end";
+ // updateStatusBar();
}
-void ProteinListWindow::doFocusReceived(bool has_focus) {
- if (has_focus ) {
- qDebug() << "ProteinListWindow::doFocusReceived begin";
- _project_window->setDefaultProteinListWindow(this);
- qDebug() << "ProteinListWindow::doFocusReceived end";
+void
+ProteinListWindow::doFocusReceived(bool has_focus)
+{
+ if(has_focus)
+ {
+ qDebug() << "ProteinListWindow::doFocusReceived begin";
+ _project_window->setDefaultProteinListWindow(this);
+ qDebug() << "ProteinListWindow::doFocusReceived end";
}
}
-void ProteinListWindow::showContextMenu(const QPoint & pos) {
- if (_p_context_menu == nullptr) {
- _p_context_menu = new QMenu(tr("Context menu"), this);
+void
+ProteinListWindow::showContextMenu(const QPoint &pos)
+{
+ if(_p_context_menu == nullptr)
+ {
+ _p_context_menu = new QMenu(tr("Context menu"), this);
- ProteinListQactionColumn * p_action;
- for (unsigned int i=0; i < _protein_table_model_p->columnCount(); i++) {
- p_action = new ProteinListQactionColumn(this,ProteinTableModel::getProteinListColumn(i));
- _p_context_menu->addAction(p_action);
+ ProteinListQactionColumn *p_action;
+ for(unsigned int i = 0; i < _protein_table_model_p->columnCount(); i++)
+ {
+ p_action = new ProteinListQactionColumn(
+ this, ProteinTableModel::getProteinListColumn(i));
+ _p_context_menu->addAction(p_action);
}
- _p_context_menu->exec(mapToGlobal(pos));
+ _p_context_menu->exec(mapToGlobal(pos));
}
- _p_context_menu->move(mapToGlobal(pos));
- _p_context_menu->show();
+ _p_context_menu->move(mapToGlobal(pos));
+ _p_context_menu->show();
}
ProteinListWindow::~ProteinListWindow()
{
- //if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
- delete ui;
- if (_p_context_menu != nullptr) {
- delete _p_context_menu;
+ // if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
+ delete ui;
+ if(_p_context_menu != nullptr)
+ {
+ delete _p_context_menu;
}
-
}
-void ProteinListWindow::edited() {
- qDebug() << "ProteinListWindow::edited begin";
- //emit dataChanged(index, index);
- _project_window->doIdentificationGroupEdited(_p_identification_group);
- //updateStatusBar();
+void
+ProteinListWindow::edited()
+{
+ qDebug() << "ProteinListWindow::edited begin";
+ // emit dataChanged(index, index);
+ _project_window->doIdentificationGroupEdited(_p_identification_group);
+ // updateStatusBar();
- qDebug() << "ProteinListWindow::edited end";
+ qDebug() << "ProteinListWindow::edited end";
}
-void ProteinListWindow::doNotValidHide(bool hide) {
- qDebug() << "ProteinListWindow::doNotValidHide begin";
- _p_proxy_model->hideNotValid(hide);
- QSettings settings;
- settings.setValue("proteinview/hidenotvalid", QString("%1").arg(hide));
- emit proteinDataChanged();
- qDebug() << "ProteinListWindow::doNotValidHide end";
+void
+ProteinListWindow::doNotValidHide(bool hide)
+{
+ qDebug() << "ProteinListWindow::doNotValidHide begin";
+ _p_proxy_model->hideNotValid(hide);
+ QSettings settings;
+ settings.setValue("proteinview/hidenotvalid", QString("%1").arg(hide));
+ emit proteinDataChanged();
+ qDebug() << "ProteinListWindow::doNotValidHide end";
}
-void ProteinListWindow::doNotCheckedHide(bool hide) {
- qDebug() << "ProteinListWindow::doNotCheckedHide begin";
- _p_proxy_model->hideNotChecked(hide);
- QSettings settings;
- settings.setValue("proteinview/hidenotchecked", QString("%1").arg(hide));
- emit proteinDataChanged();
- qDebug() << "ProteinListWindow::doNotCheckedHide end";
+void
+ProteinListWindow::doNotCheckedHide(bool hide)
+{
+ qDebug() << "ProteinListWindow::doNotCheckedHide begin";
+ _p_proxy_model->hideNotChecked(hide);
+ QSettings settings;
+ settings.setValue("proteinview/hidenotchecked", QString("%1").arg(hide));
+ emit proteinDataChanged();
+ qDebug() << "ProteinListWindow::doNotCheckedHide end";
}
-void ProteinListWindow::doNotGroupedHide(bool hide) {
- qDebug() << "ProteinListWindow::doNotGroupedHide begin";
- _p_proxy_model->hideNotGrouped(hide);
- QSettings settings;
- settings.setValue("proteinview/hidenotgrouped", QString("%1").arg(hide));
- emit proteinDataChanged();
- qDebug() << "ProteinListWindow::doNotGroupedHide end";
+void
+ProteinListWindow::doNotGroupedHide(bool hide)
+{
+ qDebug() << "ProteinListWindow::doNotGroupedHide begin";
+ _p_proxy_model->hideNotGrouped(hide);
+ QSettings settings;
+ settings.setValue("proteinview/hidenotgrouped", QString("%1").arg(hide));
+ emit proteinDataChanged();
+ qDebug() << "ProteinListWindow::doNotGroupedHide end";
}
-void ProteinListWindow::doSearchOn(QString search_on) {
- qDebug() << "ProteinTableProxyModel::doSearchOn begin " << search_on;
- _p_proxy_model->setSearchOn( search_on);
- ui->mod_auto_completion->setVisible(false);
- ui->scan_number_edit->setVisible(false);
- ui->msrun_auto_completion->setVisible(false);
- ui->protein_search_edit->setVisible(false);
- if (search_on == "msrun/scan" ) {
-
- qDebug() << "ProteinTableProxyModel::doSearchOn visible " << search_on;
- ui->scan_number_edit->setVisible(true);
- ui->msrun_auto_completion->setVisible(true);
- } else if (search_on == "modifications" ) {
-
- qDebug() << "ProteinTableProxyModel::doSearchOn visible " << search_on;
- ui->mod_auto_completion->setVisible(true);
+void
+ProteinListWindow::doSearchOn(QString search_on)
+{
+ qDebug() << "ProteinTableProxyModel::doSearchOn begin " << search_on;
+ _p_proxy_model->setSearchOn(search_on);
+ ui->mod_auto_completion->setVisible(false);
+ ui->scan_number_edit->setVisible(false);
+ ui->msrun_auto_completion->setVisible(false);
+ ui->protein_search_edit->setVisible(false);
+ if(search_on == "msrun/scan")
+ {
+
+ qDebug() << "ProteinTableProxyModel::doSearchOn visible " << search_on;
+ ui->scan_number_edit->setVisible(true);
+ ui->msrun_auto_completion->setVisible(true);
+ }
+ else if(search_on == "modifications")
+ {
+
+ qDebug() << "ProteinTableProxyModel::doSearchOn visible " << search_on;
+ ui->mod_auto_completion->setVisible(true);
}
- else {
- qDebug() << "ProteinTableProxyModel::doSearchOn hidden " << search_on;
- ui->protein_search_edit->setVisible(true);
+ else
+ {
+ qDebug() << "ProteinTableProxyModel::doSearchOn hidden " << search_on;
+ ui->protein_search_edit->setVisible(true);
}
- emit proteinDataChanged();
+ emit proteinDataChanged();
}
-void ProteinListWindow::doMsrunFileSearch(QString msr_run_file_search) {
- //_p_proxy_model->setMsrunFileSearch(msr_run_file_search);
- emit proteinDataChanged();
+void
+ProteinListWindow::doMsrunFileSearch(QString msr_run_file_search)
+{
+ //_p_proxy_model->setMsrunFileSearch(msr_run_file_search);
+ emit proteinDataChanged();
}
-void ProteinListWindow::doModificationSearch(QString mod_search) {
- emit proteinDataChanged();
+void
+ProteinListWindow::doModificationSearch(QString mod_search)
+{
+ emit proteinDataChanged();
}
-void ProteinListWindow::doScanNumberSearch(int scan_num) {
- emit proteinDataChanged();
+void
+ProteinListWindow::doScanNumberSearch(int scan_num)
+{
+ emit proteinDataChanged();
}
-void ProteinListWindow::onProteinSearchEdit(QString protein_search_string) {
- qDebug() << "ProteinTableProxyModel::onProteinSearchEdit begin " << protein_search_string;
- _p_proxy_model->setProteinSearchString(protein_search_string);
- emit proteinDataChanged();
+void
+ProteinListWindow::onProteinSearchEdit(QString protein_search_string)
+{
+ qDebug() << "ProteinTableProxyModel::onProteinSearchEdit begin "
+ << protein_search_string;
+ _p_proxy_model->setProteinSearchString(protein_search_string);
+ emit proteinDataChanged();
}
-void ProteinListWindow::doIdentificationGroupGrouped(IdentificationGroup * p_identification_group) {
- qDebug() << "ProteinListWindow::doIdentificationGroupGrouped begin";
- if (_p_identification_group == p_identification_group) {
- //_protein_table_model_p->setIdentificationGroup(p_identification_group);
- //_p_proxy_model->setSourceModel(_protein_table_model_p);
- emit proteinDataChanged();
+void
+ProteinListWindow::doIdentificationGroupGrouped(
+ IdentificationGroup *p_identification_group)
+{
+ qDebug() << "ProteinListWindow::doIdentificationGroupGrouped begin";
+ if(_p_identification_group == p_identification_group)
+ {
+ //_protein_table_model_p->setIdentificationGroup(p_identification_group);
+ //_p_proxy_model->setSourceModel(_protein_table_model_p);
+ emit proteinDataChanged();
}
- qDebug() << "ProteinListWindow::doIdentificationGroupGrouped end";
+ qDebug() << "ProteinListWindow::doIdentificationGroupGrouped end";
}
-void ProteinListWindow::setIdentificationGroup(IdentificationGroup * p_identification_group) {
- qDebug() << "ProteinListWindow::setIdentificationGroup begin " ;
- if (p_identification_group != nullptr) {
- qDebug() << "ProteinListWindow::setIdentificationGroup not null";
- _p_identification_group = p_identification_group;
- _protein_table_model_p->setIdentificationGroup(p_identification_group);
- //_p_proxy_model->setSourceModel(_protein_table_model_p);
-
- if (_project_window->getProjectP()->getProjectMode() == ProjectMode::individual ) {
- this->setWindowTitle(QString("%1 protein list").arg(_p_identification_group->getTabName()));
+void
+ProteinListWindow::setIdentificationGroup(
+ IdentificationGroup *p_identification_group)
+{
+ qDebug() << "ProteinListWindow::setIdentificationGroup begin ";
+ if(p_identification_group != nullptr)
+ {
+ qDebug() << "ProteinListWindow::setIdentificationGroup not null";
+ _p_identification_group = p_identification_group;
+ _protein_table_model_p->setIdentificationGroup(p_identification_group);
+ //_p_proxy_model->setSourceModel(_protein_table_model_p);
+
+ if(_project_window->getProjectP()->getProjectMode() ==
+ ProjectMode::individual)
+ {
+ this->setWindowTitle(QString("%1 protein list")
+ .arg(_p_identification_group->getTabName()));
}
- QStringList msrun_list;
- for (MsRunSp msrun_sp : _p_identification_group->getMsRunSpList()) {
- msrun_list << msrun_sp.get()->getFilename();
- qDebug() << "ProteinListWindow::setIdentificationGroup " << msrun_sp.get()->getFilename();
+ QStringList msrun_list;
+ for(MsRunSp msrun_sp : _p_identification_group->getMsRunSpList())
+ {
+ msrun_list << msrun_sp.get()->getFilename();
+ qDebug() << "ProteinListWindow::setIdentificationGroup "
+ << msrun_sp.get()->getFilename();
}
- QCompleter *completer = new QCompleter(msrun_list, this);
- completer->setCaseSensitivity(Qt::CaseInsensitive);
-
- completer->setCompletionMode(QCompleter::PopupCompletion);
- completer->setModelSorting(QCompleter::CaseSensitivelySortedModel);
- completer->setFilterMode(Qt::MatchContains);
- ui->msrun_auto_completion->setCompleter(completer);
-
-
- QStringList mod_list;
- for (pappso::AaModificationP mod :_project_window->getProjectP()->getPeptideStore().getModificationCollection()) {
- mod_list << QString("[%1] %2 %3").arg(mod->getAccession()).arg(mod->getName()).arg(mod->getMass());
- //qDebug() << "ProteinListWindow::setIdentificationGroup " << msrun_sp.get()->getFilename();
+ QCompleter *completer = new QCompleter(msrun_list, this);
+ completer->setCaseSensitivity(Qt::CaseInsensitive);
+
+ completer->setCompletionMode(QCompleter::PopupCompletion);
+ completer->setModelSorting(QCompleter::CaseSensitivelySortedModel);
+ completer->setFilterMode(Qt::MatchContains);
+ ui->msrun_auto_completion->setCompleter(completer);
+
+
+ QStringList mod_list;
+ for(pappso::AaModificationP mod : _project_window->getProjectP()
+ ->getPeptideStore()
+ .getModificationCollection())
+ {
+ mod_list << QString("[%1] %2 %3")
+ .arg(mod->getAccession())
+ .arg(mod->getName())
+ .arg(mod->getMass());
+ // qDebug() << "ProteinListWindow::setIdentificationGroup " <<
+ // msrun_sp.get()->getFilename();
}
- completer = new QCompleter(mod_list, this);
- completer->setCaseSensitivity(Qt::CaseInsensitive);
+ completer = new QCompleter(mod_list, this);
+ completer->setCaseSensitivity(Qt::CaseInsensitive);
- completer->setCompletionMode(QCompleter::PopupCompletion);
- completer->setModelSorting(QCompleter::CaseSensitivelySortedModel);
- completer->setFilterMode(Qt::MatchContains);
- ui->mod_auto_completion->setCompleter(completer);
+ completer->setCompletionMode(QCompleter::PopupCompletion);
+ completer->setModelSorting(QCompleter::CaseSensitivelySortedModel);
+ completer->setFilterMode(Qt::MatchContains);
+ ui->mod_auto_completion->setCompleter(completer);
- _p_proxy_model->resteItemDelegates();
+ _p_proxy_model->resteItemDelegates();
}
- else {
- qDebug() << "ProteinListWindow::setIdentificationGroup null";
+ else
+ {
+ qDebug() << "ProteinListWindow::setIdentificationGroup null";
}
- qDebug() << "ProteinListWindow::setIdentificationGroup end";
+ qDebug() << "ProteinListWindow::setIdentificationGroup end";
}
-void ProteinListWindow::updateStatusBar() {
- if (_p_identification_group == nullptr) {
+void
+ProteinListWindow::updateStatusBar()
+{
+ if(_p_identification_group == nullptr)
+ {
}
- else {
- ui->statusbar->showMessage(tr("proteins all:%1 valid:%2 valid&checked:%3 grouped:%4 displayed:%5").arg(_p_identification_group->countProteinMatch(ValidationState::notValid)).arg(_p_identification_group->countProteinMatch(ValidationState::valid)).arg(_p_identification_group->countProteinMatch(ValidationState::validAndChecked)).arg(_p_identification_group->countProteinMatch(ValidationState::grouped)).arg(_p_proxy_model->rowCount()));
+ else
+ {
+ ui->statusbar->showMessage(
+ tr("proteins all:%1 valid:%2 valid&checked:%3 grouped:%4 displayed:%5")
+ .arg(_p_identification_group->countProteinMatch(
+ ValidationState::notValid))
+ .arg(
+ _p_identification_group->countProteinMatch(ValidationState::valid))
+ .arg(_p_identification_group->countProteinMatch(
+ ValidationState::validAndChecked))
+ .arg(_p_identification_group->countProteinMatch(
+ ValidationState::grouped))
+ .arg(_p_proxy_model->rowCount()));
}
}
-void ProteinListWindow::setProteinListColumnDisplay(ProteinListColumn column, bool toggled) {
- _p_proxy_model->setProteinListColumnDisplay(column, toggled);
+void
+ProteinListWindow::setProteinListColumnDisplay(ProteinListColumn column,
+ bool toggled)
+{
+ _p_proxy_model->setProteinListColumnDisplay(column, toggled);
}
-bool ProteinListWindow::getProteinListColumnDisplay(ProteinListColumn column) const {
- return _p_proxy_model->getProteinListColumnDisplay(column);
+bool
+ProteinListWindow::getProteinListColumnDisplay(ProteinListColumn column) const
+{
+ return _p_proxy_model->getProteinListColumnDisplay(column);
}
-void ProteinListWindow::resizeColumnsToContents() {
- ui->tableView->resizeColumnsToContents();
+void
+ProteinListWindow::resizeColumnsToContents()
+{
+ ui->tableView->resizeColumnsToContents();
}
-ProjectWindow * ProteinListWindow::getProjectWindow() {
- return _project_window;
+ProjectWindow *
+ProteinListWindow::getProjectWindow()
+{
+ return _project_window;
}
diff --git a/src/gui/protein_list_view/proteinlistwindow.h b/src/gui/protein_list_view/proteinlistwindow.h
index e5d1d9d7163ebf27993b51e103bf703bf67bb721..a1015a9a3cb4dae50f4d6ba401aacd6fc6ad002b 100644
--- a/src/gui/protein_list_view/proteinlistwindow.h
+++ b/src/gui/protein_list_view/proteinlistwindow.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PROTEINLISTWINDOW_H
#define PROTEINLISTWINDOW_H
@@ -33,84 +34,86 @@
class ProjectWindow;
-//http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
-namespace Ui {
-class ProteinView;
+// http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
+namespace Ui
+{
+ class ProteinView;
}
class ProteinListWindow;
-class ProteinListQactionColumn: public QAction {
- Q_OBJECT
-public:
-
- explicit ProteinListQactionColumn(ProteinListWindow * parent, ProteinListColumn column);
- ~ProteinListQactionColumn();
-
-public slots:
- void doToggled(bool toggled);
-
-private:
- ProteinListWindow * _p_protein_list_window;
- ProteinListColumn _column;
+class ProteinListQactionColumn : public QAction
+{
+ Q_OBJECT
+ public:
+ explicit ProteinListQactionColumn(ProteinListWindow *parent,
+ ProteinListColumn column);
+ ~ProteinListQactionColumn();
+
+ public slots:
+ void doToggled(bool toggled);
+
+ private:
+ ProteinListWindow *_p_protein_list_window;
+ ProteinListColumn _column;
};
-class ProteinListWindow: public QMainWindow {
- Q_OBJECT
-
- friend class ProteinTableModel;
- friend class ProteinTableProxyModel;
-public:
-
- explicit ProteinListWindow(ProjectWindow * parent = 0);
- ~ProteinListWindow();
- void setIdentificationGroup(IdentificationGroup * p_identification_group);
- void setProteinListColumnDisplay(ProteinListColumn column, bool toggled);
- bool getProteinListColumnDisplay(ProteinListColumn column) const;
- void resizeColumnsToContents();
-
- void edited();
-
-public slots:
- void doFocusReceived(bool has_focus);
- void doIdentificationGroupGrouped(IdentificationGroup * p_identification_group);
- //void peptideEdited(QString peptideStr);
- // void setColor(const QColor &color);
- // void setShape(Shape shape);
-signals:
- void identificationGroupEdited(IdentificationGroup * p_identification_group);
- void proteinDataChanged();
-
-
-protected slots:
- void doNotValidHide(bool hide);
- void doNotCheckedHide(bool hide);
- void doNotGroupedHide(bool hide);
- void doMsrunFileSearch(QString msr_run_file_search);
- void doModificationSearch(QString mod_search);
- void doScanNumberSearch(int scan_num);
- void doProxyLayoutChanged();
- void showContextMenu(const QPoint &);
- void updateStatusBar();
- void onProteinSearchEdit(QString protein_search_string);
- void doSearchOn(QString search_on);
-
-protected :
- void askProteinDetailView(ProteinMatch * p_protein_match);
- void askPeptideListView(ProteinMatch * p_protein_match);
- ProjectWindow * getProjectWindow();
-
-
-
-private:
- IdentificationGroup * _p_identification_group=nullptr;
- Ui::ProteinView *ui;
- ProteinTableModel * _protein_table_model_p = nullptr;
- ProteinTableProxyModel * _p_proxy_model = nullptr;
- ProjectWindow * _project_window;
- QMenu * _p_context_menu = nullptr;
- bool _display_evalue = true;
- bool _display_accession = true;
-
+class ProteinListWindow : public QMainWindow
+{
+ Q_OBJECT
+
+ friend class ProteinTableModel;
+ friend class ProteinTableProxyModel;
+
+ public:
+ explicit ProteinListWindow(ProjectWindow *parent = 0);
+ ~ProteinListWindow();
+ void setIdentificationGroup(IdentificationGroup *p_identification_group);
+ void setProteinListColumnDisplay(ProteinListColumn column, bool toggled);
+ bool getProteinListColumnDisplay(ProteinListColumn column) const;
+ void resizeColumnsToContents();
+
+ void edited();
+
+ public slots:
+ void doFocusReceived(bool has_focus);
+ void
+ doIdentificationGroupGrouped(IdentificationGroup *p_identification_group);
+ // void peptideEdited(QString peptideStr);
+ // void setColor(const QColor &color);
+ // void setShape(Shape shape);
+ signals:
+ void identificationGroupEdited(IdentificationGroup *p_identification_group);
+ void proteinDataChanged();
+
+
+ protected slots:
+ void doNotValidHide(bool hide);
+ void doNotCheckedHide(bool hide);
+ void doNotGroupedHide(bool hide);
+ void doMsrunFileSearch(QString msr_run_file_search);
+ void doModificationSearch(QString mod_search);
+ void doScanNumberSearch(int scan_num);
+ void doProxyLayoutChanged();
+ void showContextMenu(const QPoint &);
+ void updateStatusBar();
+ void onProteinSearchEdit(QString protein_search_string);
+ void doSearchOn(QString search_on);
+
+ protected:
+ void askProteinDetailView(ProteinMatch *p_protein_match);
+ void askPeptideListView(ProteinMatch *p_protein_match);
+ ProjectWindow *getProjectWindow();
+
+
+ private:
+ IdentificationGroup *_p_identification_group = nullptr;
+ Ui::ProteinView *ui;
+ ProteinTableModel *_protein_table_model_p = nullptr;
+ ProteinTableProxyModel *_p_proxy_model = nullptr;
+ ProjectWindow *_project_window;
+ QMenu *_p_context_menu = nullptr;
+ bool _display_evalue = true;
+ bool _display_accession = true;
};
#endif // PROTEINLISTWINDOW_H
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index efd5d1f62a417553f2f1f6e6e3505a5a3ef272af..490f40bb9af62e4406a2325e0be34d837bfa13f1 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "proteintablemodel.h"
#include <pappsomspp/grouping/grpprotein.h>
@@ -30,314 +31,434 @@
#include "proteinlistwindow.h"
#include "../../utils/types.h"
-IdentificationGroup * ProteinTableModel::getIdentificationGroup() {
- return _p_identification_group;
+IdentificationGroup *
+ProteinTableModel::getIdentificationGroup()
+{
+ return _p_identification_group;
}
-ProteinTableModel::ProteinTableModel(ProteinListWindow * p_protein_list_window)
- :QAbstractTableModel(p_protein_list_window)
+ProteinTableModel::ProteinTableModel(ProteinListWindow *p_protein_list_window)
+ : QAbstractTableModel(p_protein_list_window)
{
- _p_protein_list_window = p_protein_list_window;
- _p_identification_group = nullptr;
+ _p_protein_list_window = p_protein_list_window;
+ _p_identification_group = nullptr;
}
-void ProteinTableModel::setIdentificationGroup(IdentificationGroup * p_identification_group) {
- qDebug() << "ProteinTableModel::setIdentificationGroup begin " << p_identification_group->getProteinMatchList().size();
- beginResetModel();
- _p_identification_group = p_identification_group;
-
- //emit headerDataChanged(Qt::Horizontal, 0,11);
- //refresh();
- qDebug() << "ProteinTableModel::setIdentificationGroup end ";
- endResetModel();
-
- _p_protein_list_window->resizeColumnsToContents();
+void
+ProteinTableModel::setIdentificationGroup(
+ IdentificationGroup *p_identification_group)
+{
+ qDebug() << "ProteinTableModel::setIdentificationGroup begin "
+ << p_identification_group->getProteinMatchList().size();
+ beginResetModel();
+ _p_identification_group = p_identification_group;
+
+ // emit headerDataChanged(Qt::Horizontal, 0,11);
+ // refresh();
+ qDebug() << "ProteinTableModel::setIdentificationGroup end ";
+ endResetModel();
+
+ _p_protein_list_window->resizeColumnsToContents();
}
-int ProteinTableModel::rowCount(const QModelIndex &parent ) const {
- //qDebug() << "ProteinTableModel::rowCount begin ";
- if (_p_identification_group != nullptr) {
- //qDebug() << "ProteinTableModel::rowCount(const QModelIndex &parent ) " << _p_identification_group->getProteinMatchList().size();
- return (int) _p_identification_group->getProteinMatchList().size();
+int
+ProteinTableModel::rowCount(const QModelIndex &parent) const
+{
+ // qDebug() << "ProteinTableModel::rowCount begin ";
+ if(_p_identification_group != nullptr)
+ {
+ // qDebug() << "ProteinTableModel::rowCount(const QModelIndex &parent ) "
+ // << _p_identification_group->getProteinMatchList().size();
+ return (int)_p_identification_group->getProteinMatchList().size();
}
- return 0;
+ return 0;
}
-int ProteinTableModel::columnCount(const QModelIndex &parent ) const {
- //qDebug() << "ProteinTableModel::columnCount begin ";
- if (_p_identification_group != nullptr) {
- return 14;
+int
+ProteinTableModel::columnCount(const QModelIndex &parent) const
+{
+ // qDebug() << "ProteinTableModel::columnCount begin ";
+ if(_p_identification_group != nullptr)
+ {
+ return 14;
}
- return 0;
+ return 0;
}
-const QString ProteinTableModel::getTitle(ProteinListColumn column) {
- qDebug() << "ProteinTableModel::getTitle begin ";
- return ProteinTableModel::getTitle((std::int8_t) column);
- //qDebug() << "ProteinTableModel::getTitle end ";
+const QString
+ProteinTableModel::getTitle(ProteinListColumn column)
+{
+ qDebug() << "ProteinTableModel::getTitle begin ";
+ return ProteinTableModel::getTitle((std::int8_t)column);
+ // qDebug() << "ProteinTableModel::getTitle end ";
}
-const QString ProteinTableModel::getDescription(ProteinListColumn column) {
- qDebug() << "ProteinTableModel::columnCount begin ";
- return ProteinTableModel::getDescription((std::int8_t) column);
- //qDebug() << "ProteinTableModel::columnCount end ";
+const QString
+ProteinTableModel::getDescription(ProteinListColumn column)
+{
+ qDebug() << "ProteinTableModel::columnCount begin ";
+ return ProteinTableModel::getDescription((std::int8_t)column);
+ // qDebug() << "ProteinTableModel::columnCount end ";
}
-const QString ProteinTableModel::getTitle(std::int8_t column) {
+const QString
+ProteinTableModel::getTitle(std::int8_t column)
+{
- qDebug() << "ProteinTableModel::getTitle begin " << column;
- switch (column) {
+ qDebug() << "ProteinTableModel::getTitle begin " << column;
+ switch(column)
+ {
- case (std::int8_t) ProteinListColumn::checked:
+ case(std::int8_t)ProteinListColumn::checked:
return "checked";
break;
- case (std::int8_t) ProteinListColumn::protein_grouping_id:
+ case(std::int8_t)ProteinListColumn::protein_grouping_id:
return "group";
break;
- case (std::int8_t) ProteinListColumn::accession:
+ case(std::int8_t)ProteinListColumn::accession:
return "accession";
break;
- case (std::int8_t) ProteinListColumn::description:
+ case(std::int8_t)ProteinListColumn::description:
return "description";
break;
- case (std::int8_t) ProteinListColumn::log_evalue:
+ case(std::int8_t)ProteinListColumn::log_evalue:
return "log(Evalue)";
break;
- case (std::int8_t) ProteinListColumn::evalue:
+ case(std::int8_t)ProteinListColumn::evalue:
return "Evalue";
break;
- case (std::int8_t) ProteinListColumn::spectrum:
+ case(std::int8_t)ProteinListColumn::spectrum:
return "spectra";
break;
- case (std::int8_t) ProteinListColumn::specific_spectrum:
+ case(std::int8_t)ProteinListColumn::specific_spectrum:
return "specific spectra";
break;
- case (std::int8_t) ProteinListColumn::sequence:
+ case(std::int8_t)ProteinListColumn::sequence:
return "sequences";
break;
- case (std::int8_t) ProteinListColumn::coverage:
+ case(std::int8_t)ProteinListColumn::coverage:
return "coverage";
break;
- case (std::int8_t) ProteinListColumn::pai:
+ case(std::int8_t)ProteinListColumn::pai:
return "PAI";
break;
- case (std::int8_t) ProteinListColumn::empai:
+ case(std::int8_t)ProteinListColumn::empai:
return "emPAI";
break;
- case (std::int8_t) ProteinListColumn::specific_sequence:
+ case(std::int8_t)ProteinListColumn::specific_sequence:
return "specific sequences";
- case (std::int8_t) ProteinListColumn::molecular_weight:
+ case(std::int8_t)ProteinListColumn::molecular_weight:
return "MW";
break;
-
-
}
- return "";
+ return "";
}
-const QString ProteinTableModel::getDescription(std::int8_t column) {
+const QString
+ProteinTableModel::getDescription(std::int8_t column)
+{
- qDebug() << "ProteinTableModel::getDescription begin " << column;
- switch (column) {
+ qDebug() << "ProteinTableModel::getDescription begin " << column;
+ switch(column)
+ {
- case (std::int8_t) ProteinListColumn::checked:
+ case(std::int8_t)ProteinListColumn::checked:
return "manual protein check";
break;
- case (std::int8_t) ProteinListColumn::protein_grouping_id:
+ case(std::int8_t)ProteinListColumn::protein_grouping_id:
return "unique protein identifier within this grouping experiment";
break;
- case (std::int8_t) ProteinListColumn::accession:
+ case(std::int8_t)ProteinListColumn::accession:
return "protein accession";
break;
- case (std::int8_t) ProteinListColumn::description:
+ case(std::int8_t)ProteinListColumn::description:
return "protein description";
break;
- case (std::int8_t) ProteinListColumn::log_evalue:
+ case(std::int8_t)ProteinListColumn::log_evalue:
return "log(Evalue)";
break;
- case (std::int8_t) ProteinListColumn::evalue:
+ case(std::int8_t)ProteinListColumn::evalue:
return "protein Evalue";
break;
- case (std::int8_t) ProteinListColumn::spectrum:
+ case(std::int8_t)ProteinListColumn::spectrum:
return "number of distinct MS spectrum assigned to this protein";
break;
- case (std::int8_t) ProteinListColumn::specific_spectrum:
- return "number of distinct MS spectrum only assigned to this protein within the group";
+ case(std::int8_t)ProteinListColumn::specific_spectrum:
+ return "number of distinct MS spectrum only assigned to this protein "
+ "within the group";
break;
- case (std::int8_t) ProteinListColumn::sequence:
+ case(std::int8_t)ProteinListColumn::sequence:
return "number of unique distinct peptide sequences";
break;
- case (std::int8_t) ProteinListColumn::coverage:
+ case(std::int8_t)ProteinListColumn::coverage:
return "protein coverage (ratio)";
break;
- case (std::int8_t) ProteinListColumn::pai:
+ case(std::int8_t)ProteinListColumn::pai:
return "Protein Abundance Index (Rappsilber et al. 2002)";
break;
- case (std::int8_t) ProteinListColumn::empai:
- return "Exponentially Modified Protein Abundance Index (emPAI) as described by Ishihama 2005";
+ case(std::int8_t)ProteinListColumn::empai:
+ return "Exponentially Modified Protein Abundance Index (emPAI) as "
+ "described by Ishihama 2005";
break;
- case (std::int8_t) ProteinListColumn::specific_sequence:
- return "number of unique distinct peptide sequences only assigned to this protein within the group";
+ case(std::int8_t)ProteinListColumn::specific_sequence:
+ return "number of unique distinct peptide sequences only assigned to "
+ "this protein within the group";
- case (std::int8_t) ProteinListColumn::molecular_weight:
+ case(std::int8_t)ProteinListColumn::molecular_weight:
return "protein molecular weight in Dalton";
}
- return "";
+ return "";
}
-QVariant ProteinTableModel::headerData(int section, Qt::Orientation orientation, int role) const
+QVariant
+ProteinTableModel::headerData(int section, Qt::Orientation orientation,
+ int role) const
{
- if (_p_identification_group == nullptr) return QVariant();
- if (orientation == Qt::Horizontal)
+ if(_p_identification_group == nullptr)
+ return QVariant();
+ if(orientation == Qt::Horizontal)
{
- switch (role) {
- case Qt::DisplayRole :
+ switch(role)
+ {
+ case Qt::DisplayRole:
return QVariant(getTitle(section));
break;
- case Qt::ToolTipRole :
+ case Qt::ToolTipRole:
return QVariant(getDescription(section));
break;
- case Qt::SizeHintRole :
- //qDebug() << "ProteinTableModel::headerData " << ProteinTableModel::getColumnWidth(section);
- return QSize( ProteinTableModel::getColumnWidth(section), 40 );
+ case Qt::SizeHintRole:
+ // qDebug() << "ProteinTableModel::headerData " <<
+ // ProteinTableModel::getColumnWidth(section);
+ return QSize(ProteinTableModel::getColumnWidth(section), 40);
break;
}
}
- return QVariant();
+ return QVariant();
}
-int ProteinTableModel::getColumnWidth(int column) {
- qDebug() << "ProteinTableModel::getColumnWidth " << column;
- switch (column) {
+int
+ProteinTableModel::getColumnWidth(int column)
+{
+ qDebug() << "ProteinTableModel::getColumnWidth " << column;
+ switch(column)
+ {
- case (int) ProteinListColumn::checked:
+ case(int)ProteinListColumn::checked:
break;
- case (int) ProteinListColumn::protein_grouping_id:
+ case(int)ProteinListColumn::protein_grouping_id:
return 120;
break;
- case (int) ProteinListColumn::accession:
+ case(int)ProteinListColumn::accession:
qDebug() << "ProteinTableModel::getColumnWidth accession " << column;
return 250;
break;
- case (int) ProteinListColumn::description:
+ case(int)ProteinListColumn::description:
return 400;
break;
}
- return 100;
+ return 100;
}
-ProteinListColumn ProteinTableModel::getProteinListColumn(std::int8_t column) {
- return static_cast<ProteinListColumn>(column);
+ProteinListColumn
+ProteinTableModel::getProteinListColumn(std::int8_t column)
+{
+ return static_cast<ProteinListColumn>(column);
}
-QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
- // generate a log message when this method gets called
- if (_p_identification_group == nullptr) return QVariant();
- int row = index.row();
- int col = index.column();
- // qDebug() << QString("row %1, col%2, role %3")
- // .arg(row).arg(col).arg(role);
-
- switch(role) {
- case Qt::CheckStateRole:
+QVariant
+ProteinTableModel::data(const QModelIndex &index, int role) const
+{
+ // generate a log message when this method gets called
+ if(_p_identification_group == nullptr)
+ return QVariant();
+ int row = index.row();
+ int col = index.column();
+ // qDebug() << QString("row %1, col%2, role %3")
+ // .arg(row).arg(col).arg(role);
- if (col == 0) //add a checkbox to cell(1,0)
- {
- if ( _p_identification_group->getProteinMatchList().at(row)->isChecked()) {
+ switch(role)
+ {
+ case Qt::CheckStateRole:
+
+ if(col == 0) // add a checkbox to cell(1,0)
+ {
+ if(_p_identification_group->getProteinMatchList()
+ .at(row)
+ ->isChecked())
+ {
return Qt::Checked;
- }
- else {
+ }
+ else
+ {
return Qt::Unchecked;
- }
- }
- break;
- case Qt::SizeHintRole :
- //qDebug() << "ProteinTableModel::headerData " << ProteinTableModel::getColumnWidth(section);
- return QSize( ProteinTableModel::getColumnWidth(col), 30 );
- break;
- case Qt::BackgroundRole:
- if (_p_identification_group->getProteinMatchList().at(row)->isValid() == false)
- {
+ }
+ }
+ break;
+ case Qt::SizeHintRole:
+ // qDebug() << "ProteinTableModel::headerData " <<
+ // ProteinTableModel::getColumnWidth(section);
+ return QSize(ProteinTableModel::getColumnWidth(col), 30);
+ break;
+ case Qt::BackgroundRole:
+ if(_p_identification_group->getProteinMatchList().at(row)->isValid() ==
+ false)
+ {
return QVariant(QColor("grey"));
- }
- if (_p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->isDecoy() == true)
- {
+ }
+ if(_p_identification_group->getProteinMatchList()
+ .at(row)
+ ->getProteinXtpSp()
+ .get()
+ ->isDecoy() == true)
+ {
return QVariant(QColor("orange"));
- }
- if (_p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->isContaminant() == true)
- {
+ }
+ if(_p_identification_group->getProteinMatchList()
+ .at(row)
+ ->getProteinXtpSp()
+ .get()
+ ->isContaminant() == true)
+ {
return QVariant(QColor("orange"));
- }
+ }
break;
- case Qt::DisplayRole:
- if (_p_identification_group == nullptr) {
- return QVariant();
- }
- switch (col) {
- case (std::int8_t)ProteinListColumn::checked:
- return QVariant();
- break;
-
- case (std::int8_t)ProteinListColumn::protein_grouping_id:
- pappso::GrpProtein * p_grp_prot = _p_identification_group->getProteinMatchList().at(row)->getGrpProteinSp().get();
- if (p_grp_prot != nullptr) return p_grp_prot->getGroupingId();
+ case Qt::DisplayRole:
+ if(_p_identification_group == nullptr)
+ {
return QVariant();
- break;
- }
- if (col == (std::int8_t) ProteinListColumn::accession ) {
- return QVariant(_p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getAccession());
-
- }
-
- if (col == (std::int8_t) ProteinListColumn::description ) {
- return _p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getDescription();
- }
- if (col == (std::int8_t) ProteinListColumn::log_evalue ) {
- return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getLogEvalue());
- }
-
- if (col == (std::int8_t) ProteinListColumn::evalue ) {
- return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getEvalue());
- }
- if (col == (std::int8_t) ProteinListColumn::spectrum ) {
- return QVariant ((qreal) _p_identification_group->getProteinMatchList().at(row)->countSampleScan(ValidationState::validAndChecked));
- }
-
- if (col == (std::int8_t) ProteinListColumn::specific_spectrum ) {
- GroupingGroup * p_groupin_group = _p_identification_group->getProteinMatchList().at(row)->getGroupingGroupSp().get();
- if (p_groupin_group != nullptr) {
- return QVariant ((qreal) p_groupin_group->countSpecificSampleScan(_p_identification_group->getProteinMatchList().at(row),ValidationState::validAndChecked));
- }
- }
-
- if (col == (std::int8_t) ProteinListColumn::sequence ) {
- return QVariant ((qreal) _p_identification_group->getProteinMatchList().at(row)->countSequenceLi(ValidationState::validAndChecked));
- }
- if (col == (std::int8_t) ProteinListColumn::specific_sequence ) {
- GroupingGroup * p_groupin_group = _p_identification_group->getProteinMatchList().at(row)->getGroupingGroupSp().get();
- if (p_groupin_group != nullptr) {
- return QVariant ((qreal) p_groupin_group->countSpecificSequenceLi(_p_identification_group->getProteinMatchList().at(row),ValidationState::validAndChecked));
- }
- }
- if (col == (std::int8_t) ProteinListColumn::coverage ) {
- return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getCoverage());
- }
-
- if (col == (std::int8_t) ProteinListColumn::pai ) {
- return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getPAI());
- }
- if (col == (std::int8_t) ProteinListColumn::empai ) {
- return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getEmPAI());
- }
- if (col == (std::int8_t) ProteinListColumn::molecular_weight ) {
- return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getMass());
- }
+ }
+ switch(col)
+ {
+ case(std::int8_t)ProteinListColumn::checked:
+ return QVariant();
+ break;
+
+ case(std::int8_t)ProteinListColumn::protein_grouping_id:
+ pappso::GrpProtein *p_grp_prot =
+ _p_identification_group->getProteinMatchList()
+ .at(row)
+ ->getGrpProteinSp()
+ .get();
+ if(p_grp_prot != nullptr)
+ return p_grp_prot->getGroupingId();
+ return QVariant();
+ break;
+ }
+ if(col == (std::int8_t)ProteinListColumn::accession)
+ {
+ return QVariant(_p_identification_group->getProteinMatchList()
+ .at(row)
+ ->getProteinXtpSp()
+ .get()
+ ->getAccession());
+ }
+
+ if(col == (std::int8_t)ProteinListColumn::description)
+ {
+ return _p_identification_group->getProteinMatchList()
+ .at(row)
+ ->getProteinXtpSp()
+ .get()
+ ->getDescription();
+ }
+ if(col == (std::int8_t)ProteinListColumn::log_evalue)
+ {
+ return QVariant(
+ (qreal)_p_identification_group->getProteinMatchList()
+ .at(row)
+ ->getLogEvalue());
+ }
+
+ if(col == (std::int8_t)ProteinListColumn::evalue)
+ {
+ return QVariant(
+ (qreal)_p_identification_group->getProteinMatchList()
+ .at(row)
+ ->getEvalue());
+ }
+ if(col == (std::int8_t)ProteinListColumn::spectrum)
+ {
+ return QVariant(
+ (qreal)_p_identification_group->getProteinMatchList()
+ .at(row)
+ ->countSampleScan(ValidationState::validAndChecked));
+ }
+
+ if(col == (std::int8_t)ProteinListColumn::specific_spectrum)
+ {
+ GroupingGroup *p_groupin_group =
+ _p_identification_group->getProteinMatchList()
+ .at(row)
+ ->getGroupingGroupSp()
+ .get();
+ if(p_groupin_group != nullptr)
+ {
+ return QVariant((qreal)p_groupin_group->countSpecificSampleScan(
+ _p_identification_group->getProteinMatchList().at(row),
+ ValidationState::validAndChecked));
+ }
+ }
+
+ if(col == (std::int8_t)ProteinListColumn::sequence)
+ {
+ return QVariant(
+ (qreal)_p_identification_group->getProteinMatchList()
+ .at(row)
+ ->countSequenceLi(ValidationState::validAndChecked));
+ }
+ if(col == (std::int8_t)ProteinListColumn::specific_sequence)
+ {
+ GroupingGroup *p_groupin_group =
+ _p_identification_group->getProteinMatchList()
+ .at(row)
+ ->getGroupingGroupSp()
+ .get();
+ if(p_groupin_group != nullptr)
+ {
+ return QVariant((qreal)p_groupin_group->countSpecificSequenceLi(
+ _p_identification_group->getProteinMatchList().at(row),
+ ValidationState::validAndChecked));
+ }
+ }
+ if(col == (std::int8_t)ProteinListColumn::coverage)
+ {
+ return QVariant(
+ (qreal)_p_identification_group->getProteinMatchList()
+ .at(row)
+ ->getCoverage());
+ }
+
+ if(col == (std::int8_t)ProteinListColumn::pai)
+ {
+ return QVariant(
+ (qreal)_p_identification_group->getProteinMatchList()
+ .at(row)
+ ->getPAI());
+ }
+ if(col == (std::int8_t)ProteinListColumn::empai)
+ {
+ return QVariant(
+ (qreal)_p_identification_group->getProteinMatchList()
+ .at(row)
+ ->getEmPAI());
+ }
+ if(col == (std::int8_t)ProteinListColumn::molecular_weight)
+ {
+ return QVariant(
+ (qreal)_p_identification_group->getProteinMatchList()
+ .at(row)
+ ->getProteinXtpSp()
+ .get()
+ ->getMass());
+ }
return QVariant();
}
- return QVariant();
+ return QVariant();
}
-void ProteinTableModel::onProteinDataChanged() {
- qDebug() << "ProteinTableModel::onProteinDataChanged begin " << rowCount();
- emit layoutAboutToBeChanged();
- emit layoutChanged();
+void
+ProteinTableModel::onProteinDataChanged()
+{
+ qDebug() << "ProteinTableModel::onProteinDataChanged begin " << rowCount();
+ emit layoutAboutToBeChanged();
+ emit layoutChanged();
}
diff --git a/src/gui/protein_list_view/proteintablemodel.h b/src/gui/protein_list_view/proteintablemodel.h
index a3f103260b31cb002f89ab043ae3e69519d17543..6cdaa1ce25844a2f4998f71d9d9dcc886edb3b90 100644
--- a/src/gui/protein_list_view/proteintablemodel.h
+++ b/src/gui/protein_list_view/proteintablemodel.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PROTEINTABLEMODEL_H
#define PROTEINTABLEMODEL_H
@@ -32,53 +33,59 @@
*
*/
-enum class ProteinListColumn: std::int8_t {
- checked=0, ///< manual checked
- protein_grouping_id=1, ///< protein grouping id
- accession=2, ///< accession
- description=3, ///< protein description
- log_evalue=4, ///< log(Evalue)
- evalue=5, ///< Evalue
- spectrum=6, ///< spectrum count
- specific_spectrum=7, ///< specific spectrum count
- sequence=8, ///< unique sequence count
- specific_sequence=9, ///< specific unique sequence
- coverage=10, ///< protein coverage
- molecular_weight=11, ///< protein molecular weight in Dalton
- pai=12, ///< PAI
- empai=13, ///< emPAI
+enum class ProteinListColumn : std::int8_t
+{
+ checked = 0, ///< manual checked
+ protein_grouping_id = 1, ///< protein grouping id
+ accession = 2, ///< accession
+ description = 3, ///< protein description
+ log_evalue = 4, ///< log(Evalue)
+ evalue = 5, ///< Evalue
+ spectrum = 6, ///< spectrum count
+ specific_spectrum = 7, ///< specific spectrum count
+ sequence = 8, ///< unique sequence count
+ specific_sequence = 9, ///< specific unique sequence
+ coverage = 10, ///< protein coverage
+ molecular_weight = 11, ///< protein molecular weight in Dalton
+ pai = 12, ///< PAI
+ empai = 13, ///< emPAI
};
class ProteinListWindow;
-class ProteinTableModel: public QAbstractTableModel
+class ProteinTableModel : public QAbstractTableModel
{
- Q_OBJECT
-public:
- ProteinTableModel(ProteinListWindow * p_protein_list_window);
- virtual int rowCount(const QModelIndex &parent = QModelIndex()) const override;
- virtual int columnCount(const QModelIndex &parent = QModelIndex()) const override;
- virtual QVariant headerData(int section, Qt::Orientation orientation, int role) const override;
- virtual QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override;
+ Q_OBJECT
+ public:
+ ProteinTableModel(ProteinListWindow *p_protein_list_window);
+ virtual int
+ rowCount(const QModelIndex &parent = QModelIndex()) const override;
+ virtual int
+ columnCount(const QModelIndex &parent = QModelIndex()) const override;
+ virtual QVariant headerData(int section, Qt::Orientation orientation,
+ int role) const override;
+ virtual QVariant data(const QModelIndex &index,
+ int role = Qt::DisplayRole) const override;
+
+ static const QString getTitle(ProteinListColumn column);
+ static const QString getDescription(ProteinListColumn column);
+ static const QString getTitle(std::int8_t column);
+ static const QString getDescription(std::int8_t column);
+ static ProteinListColumn getProteinListColumn(std::int8_t column);
- static const QString getTitle(ProteinListColumn column);
- static const QString getDescription(ProteinListColumn column);
- static const QString getTitle(std::int8_t column);
- static const QString getDescription(std::int8_t column);
- static ProteinListColumn getProteinListColumn(std::int8_t column);
+ void setIdentificationGroup(IdentificationGroup *p_identification_group);
+ IdentificationGroup *getIdentificationGroup();
+ public slots:
+ void onProteinDataChanged();
- void setIdentificationGroup(IdentificationGroup * p_identification_group);
- IdentificationGroup * getIdentificationGroup();
-public slots:
- void onProteinDataChanged();
-private :
+ private:
+ static int getColumnWidth(int column);
+ void refresh();
- static int getColumnWidth(int column);
- void refresh();
-private :
- IdentificationGroup * _p_identification_group = nullptr;
- ProteinListWindow * _p_protein_list_window;
+ private:
+ IdentificationGroup *_p_identification_group = nullptr;
+ ProteinListWindow *_p_protein_list_window;
};
#endif // PROTEINTABLEMODEL_H
diff --git a/src/gui/protein_view/proteinwindow.cpp b/src/gui/protein_view/proteinwindow.cpp
index 31c8e83ea8cb2e71035dc2c7ce30a0bd11103d82..0e69385626f0834edfb0da01fffb16ea19c61246 100644
--- a/src/gui/protein_view/proteinwindow.cpp
+++ b/src/gui/protein_view/proteinwindow.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "proteinwindow.h"
#include "../project_view/projectwindow.h"
@@ -33,223 +34,277 @@
//#include <QWebEnginePage>
//#include <QtWebEngine>
-DbXrefButton::DbXrefButton(QWidget * parent, DbXref dbxref): QPushButton(parent) {
- _dbxref = dbxref;
+DbXrefButton::DbXrefButton(QWidget *parent, DbXref dbxref) : QPushButton(parent)
+{
+ _dbxref = dbxref;
#if QT_VERSION >= 0x050000
- // Qt5 code
- QObject::connect(this, &DbXrefButton::clicked,this, &DbXrefButton::clickedSlot);
+ // Qt5 code
+ QObject::connect(this, &DbXrefButton::clicked, this,
+ &DbXrefButton::clickedSlot);
#else
-// Qt4 code
- QObject::connect(this, SIGNAL(clicked()),this, SLOT(clickedSlot()));
+ // Qt4 code
+ QObject::connect(this, SIGNAL(clicked()), this, SLOT(clickedSlot()));
#endif
- setText(_dbxref.accession);
+ setText(_dbxref.accession);
}
-void DbXrefButton::clickedSlot() {
- qDebug() << "DbXrefButton::clickedSlot " << _dbxref.getUrl();
- QDesktopServices::openUrl (_dbxref.getUrl()) ;
+void
+DbXrefButton::clickedSlot()
+{
+ qDebug() << "DbXrefButton::clickedSlot " << _dbxref.getUrl();
+ QDesktopServices::openUrl(_dbxref.getUrl());
}
-ProteinWindow::ProteinWindow(ProjectWindow *parent):
- QMainWindow(parent),
- ui(new Ui::ProteinDetailView)
+ProteinWindow::ProteinWindow(ProjectWindow *parent)
+ : QMainWindow(parent), ui(new Ui::ProteinDetailView)
{
- _p_project_window = parent;
- ui->setupUi(this);
- /*
- */
+ _p_project_window = parent;
+ ui->setupUi(this);
+ /*
+ */
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect (_p_project_window, &ProjectWindow::identificationGroupGrouped, this,&ProteinWindow::doIdentificationGroupGrouped);
- connect (_p_project_window, &ProjectWindow::peptideEvidenceSelected, this,&ProteinWindow::doPeptideEvidenceSelected);
+ // Qt5 code
+ connect(_p_project_window, &ProjectWindow::identificationGroupGrouped, this,
+ &ProteinWindow::doIdentificationGroupGrouped);
+ connect(_p_project_window, &ProjectWindow::peptideEvidenceSelected, this,
+ &ProteinWindow::doPeptideEvidenceSelected);
#else
-// Qt4 code
- connect (_p_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
- connect (_p_project_window, SIGNAL(peptideMatchSelected(PeptideMatch*)), this,SLOT(doPeptideMatchSelected(PeptideMatch*)));
-
- //connect(_protein_table_model_p, SIGNAL(layoutChanged()), this, SLOT(updateStatusBar()));
+ // Qt4 code
+ connect(_p_project_window,
+ SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
+ SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
+ connect(_p_project_window, SIGNAL(peptideMatchSelected(PeptideMatch *)), this,
+ SLOT(doPeptideMatchSelected(PeptideMatch *)));
+
+ // connect(_protein_table_model_p, SIGNAL(layoutChanged()), this,
+ // SLOT(updateStatusBar()));
#endif
}
ProteinWindow::~ProteinWindow()
{
- clearDbXrefLayout();
- delete ui;
+ clearDbXrefLayout();
+ delete ui;
}
-void ProteinWindow::doIdentificationGroupGrouped(IdentificationGroup * p_identification_group) {
- updateDisplay();
+void
+ProteinWindow::doIdentificationGroupGrouped(
+ IdentificationGroup *p_identification_group)
+{
+ updateDisplay();
}
-void ProteinWindow::doPeptideEvidenceSelected(PeptideEvidence * peptide_evidence) {
- if (peptide_evidence != nullptr) {
- ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence(peptide_evidence));
-
+void
+ProteinWindow::doPeptideEvidenceSelected(PeptideEvidence *peptide_evidence)
+{
+ if(peptide_evidence != nullptr)
+ {
+ ui->sequenceTextEdit->setText(
+ _p_protein_match->getHtmlSequence(peptide_evidence));
}
}
-void ProteinWindow::clearDbXrefLayout() {
- for (int i = 0; i < ui->dbxref_list_layout->count(); ++i)
+void
+ProteinWindow::clearDbXrefLayout()
+{
+ for(int i = 0; i < ui->dbxref_list_layout->count(); ++i)
{
- delete ui->dbxref_list_layout->itemAt(i)->widget();
+ delete ui->dbxref_list_layout->itemAt(i)->widget();
}
}
-void ProteinWindow::browseUrl(int i) {
+void
+ProteinWindow::browseUrl(int i)
+{
}
-void ProteinWindow::updateDisplay() {
- try {
- clearDbXrefLayout();
- ui->valid_checkbox->setCheckState(Qt::Unchecked);
- if (_p_protein_match->isValid()) ui->valid_checkbox->setCheckState(Qt::Checked);
- ui->decoy_checkbox->setCheckState(Qt::Unchecked);
- if (_p_protein_match->getProteinXtpSp().get()->isDecoy()) ui->decoy_checkbox->setCheckState(Qt::Checked);
- ui->accession_label->setText(_p_protein_match->getProteinXtpSp().get()->getAccession());
- for (const DbXref & dbxref:_p_protein_match->getProteinXtpSp().get()->getDbxrefList()) {
- QString accession = ui->accession_label->text().replace(dbxref.accession, QString("<span style=\"color:%2;\">%1</span>").arg(dbxref.accession).arg("blue"));
- ui->accession_label->setText(accession);
- qDebug() << "ProteinWindow::updateDisplay " << accession;
-
- DbXrefButton * dbxref_button = new DbXrefButton(this,dbxref);
- ui->dbxref_list_layout->addWidget(dbxref_button);
+void
+ProteinWindow::updateDisplay()
+{
+ try
+ {
+ clearDbXrefLayout();
+ ui->valid_checkbox->setCheckState(Qt::Unchecked);
+ if(_p_protein_match->isValid())
+ ui->valid_checkbox->setCheckState(Qt::Checked);
+ ui->decoy_checkbox->setCheckState(Qt::Unchecked);
+ if(_p_protein_match->getProteinXtpSp().get()->isDecoy())
+ ui->decoy_checkbox->setCheckState(Qt::Checked);
+ ui->accession_label->setText(
+ _p_protein_match->getProteinXtpSp().get()->getAccession());
+ for(const DbXref &dbxref :
+ _p_protein_match->getProteinXtpSp().get()->getDbxrefList())
+ {
+ QString accession = ui->accession_label->text().replace(
+ dbxref.accession, QString("<span style=\"color:%2;\">%1</span>")
+ .arg(dbxref.accession)
+ .arg("blue"));
+ ui->accession_label->setText(accession);
+ qDebug() << "ProteinWindow::updateDisplay " << accession;
+
+ DbXrefButton *dbxref_button = new DbXrefButton(this, dbxref);
+ ui->dbxref_list_layout->addWidget(dbxref_button);
}
- ui->button_layout->setVisible(true);
- if (ui->dbxref_list_layout->count() == 0) {
- ui->button_layout->setVisible(false);
+ ui->button_layout->setVisible(true);
+ if(ui->dbxref_list_layout->count() == 0)
+ {
+ ui->button_layout->setVisible(false);
}
- ui->description_label->setText(_p_protein_match->getProteinXtpSp().get()->getDescription());
- ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence());
- ui->coverage_label->setText(QString("%1 %").arg(_p_protein_match->getCoverage()*100));
- ui->mw_label->setText(QString("%1 kDa").arg(_p_protein_match->getProteinXtpSp().get()->getMass()/1000));
- ui->evalue_label->setText(QString("%1 (log10: %2)").arg(_p_protein_match->getEvalue()).arg(_p_protein_match->getLogEvalue()));
+ ui->description_label->setText(
+ _p_protein_match->getProteinXtpSp().get()->getDescription());
+ ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence());
+ ui->coverage_label->setText(
+ QString("%1 %").arg(_p_protein_match->getCoverage() * 100));
+ ui->mw_label->setText(QString("%1 kDa").arg(
+ _p_protein_match->getProteinXtpSp().get()->getMass() / 1000));
+ ui->evalue_label->setText(QString("%1 (log10: %2)")
+ .arg(_p_protein_match->getEvalue())
+ .arg(_p_protein_match->getLogEvalue()));
}
- catch (pappso::PappsoException exception_pappso) {
- QMessageBox::warning(this,
- tr("Unable to display protein details :"), exception_pappso.qwhat());
+ catch(pappso::PappsoException exception_pappso)
+ {
+ QMessageBox::warning(this, tr("Unable to display protein details :"),
+ exception_pappso.qwhat());
}
- catch (std::exception exception_std) {
- QMessageBox::warning(this,
- tr("Unable to display protein details :"), exception_std.what());
+ catch(std::exception exception_std)
+ {
+ QMessageBox::warning(this, tr("Unable to display protein details :"),
+ exception_std.what());
}
-
}
-void ProteinWindow::setProteinMatch(ProteinMatch * p_protein_match) {
- _p_protein_match = p_protein_match;
- updateDisplay();
+void
+ProteinWindow::setProteinMatch(ProteinMatch *p_protein_match)
+{
+ _p_protein_match = p_protein_match;
+ updateDisplay();
}
-void ProteinWindow::doSaveSvg() {
+void
+ProteinWindow::doSaveSvg()
+{
- try {
- QSettings settings;
- QString default_location = settings.value("path/export_svg", "").toString();
+ try
+ {
+ QSettings settings;
+ QString default_location =
+ settings.value("path/export_svg", "").toString();
- QString proposed_filename = QString("%1/protein_%1.pdf").arg(_p_protein_match->getProteinXtpSp().get()->getAccession());
+ QString proposed_filename =
+ QString("%1/protein_%1.pdf")
+ .arg(_p_protein_match->getProteinXtpSp().get()->getAccession());
- QString filename = QFileDialog::getSaveFileName(this, tr("Save PDF file"),
- proposed_filename,
- tr("pdf (*.pdf)"));
+ QString filename = QFileDialog::getSaveFileName(
+ this, tr("Save PDF file"), proposed_filename, tr("pdf (*.pdf)"));
- if (filename.isEmpty()) {
- return;
+ if(filename.isEmpty())
+ {
+ return;
}
- settings.setValue("path/export_svg", QFileInfo(filename).absolutePath());
-
- //https://bugreports.qt.io/browse/QTBUG-52538
- QPrinter printer(QPrinter::PrinterResolution);
- printer.setOutputFormat(QPrinter::PdfFormat);
- printer.setPaperSize(QPrinter::A4);
- printer.setOutputFileName(filename);
- /*
- QSvgGenerator generator;
- //generator.setOutputDevice(&buffer);
- QSize size(600, 1000);
- generator.setFileName(filename);
- generator.setSize(size);
- generator.setViewBox(QRect(0, 0, size.width(), size.height()));
- generator.setTitle(_p_protein_match->getProteinXtpSp().get()->getAccession());
- */
-
- //generator.setDescription(description);
- //QPainter painter;
- //painter.begin(&generator);
- //painter.setViewport(0,0, size.width(), size.height());
-
- // ui->sequenceTextEdit->document()->drawContents(&painter);
- // painter.end();
- //QFont::Monospace
- QFont font("Monospace");
- font.setStyleHint(QFont::Monospace);
- font.setLetterSpacing(QFont::AbsoluteSpacing,0);
- font.setPointSize(10); //generator.setDefaultFont(font);
-
- QTextOption text_option;
- text_option.setWrapMode(QTextOption::WrapAnywhere);
- text_option.setFlags(QTextOption::IncludeTrailingSpaces|QTextOption::ShowTabsAndSpaces);
- text_option.setUseDesignMetrics(0);
-
- //QTextDocument *doc = ui->sequenceTextEdit->document()->clone();
- QTextDocument *doc = new QTextDocument();
- doc->setHtml(QString("<p>%1</p><p>%2</p><p>%3</p>").arg(_p_protein_match->getProteinXtpSp().get()->getAccession()).arg(_p_protein_match->getProteinXtpSp().get()->getDescription()).arg(ui->sequenceTextEdit->toHtml()));
- doc->setUndoRedoEnabled(false);
- //doc->setHtml("<p><span style=\"color:#000000; font-weight:600\">"+text_x+"</span></p>");
- doc->setTextWidth(printer.pageRect().size().width());
- doc->setDefaultFont(font);
- doc->setPageSize(printer.pageRect().size());
- //// height from doc QTextDocument
- //// http://fop-miniscribus.googlecode.com/svn/trunk/fop_miniscribus.1.0.0/src/floating_box/floatdiagram.cpp
- //////setMaximumHeight(DocumentHighgtActual());
- doc->setPageSize(printer.pageRect().size()); // This is necessary if you want to hide the page number
- doc->print(&printer);
-
- /*
- QPainter *painter = new QPainter(&generator);
- painter->setRenderHint(QPainter::Antialiasing, true);
- painter->setFont(font);
- doc->drawContents(painter);
- painter->end();
- */
-
-
- /*
- QSvgGenerator svg;
- svg.setFileName(filename);
- QTextDocument *doc = ui->sequenceTextEdit->document()->clone();
- QRect rectSize(0, 0, (int) doc->size().width(), (int) doc->size().height());
- QPainter painter(&svg);
- //painter.setViewport(rectSize);
- //doc->documentLayout()->setPaintDevice(&svg);
- doc->drawContents(&painter);
- */
-
- /*
- QtWebEngine::initialize();
- QWebEnginePage page;
- QEventLoop loop;
- loop.connect(&page, &QWebEnginePage::loadFinished, [&page, &loop, &filename]() {
- page.printToPdf([&loop, &filename] (QByteArray ba) {
- QFile f(filename);
- if (f.open(QIODevice::WriteOnly))
- {
- f.write(ba);
- f.close();
- } else {
- qDebug() << "Error opening file for writing" << filename << f.errorString();
- }
- loop.exit();
- });
- });
- qDebug() << ui->sequenceTextEdit->toHtml();
- page.setHtml(ui->sequenceTextEdit->toHtml());
- loop.exec();
- */
+ settings.setValue("path/export_svg", QFileInfo(filename).absolutePath());
+
+ // https://bugreports.qt.io/browse/QTBUG-52538
+ QPrinter printer(QPrinter::PrinterResolution);
+ printer.setOutputFormat(QPrinter::PdfFormat);
+ printer.setPaperSize(QPrinter::A4);
+ printer.setOutputFileName(filename);
+ /*
+ QSvgGenerator generator;
+ //generator.setOutputDevice(&buffer);
+ QSize size(600, 1000);
+ generator.setFileName(filename);
+ generator.setSize(size);
+ generator.setViewBox(QRect(0, 0, size.width(), size.height()));
+ generator.setTitle(_p_protein_match->getProteinXtpSp().get()->getAccession());
+ */
+
+ // generator.setDescription(description);
+ // QPainter painter;
+ // painter.begin(&generator);
+ // painter.setViewport(0,0, size.width(), size.height());
+
+ // ui->sequenceTextEdit->document()->drawContents(&painter);
+ // painter.end();
+ // QFont::Monospace
+ QFont font("Monospace");
+ font.setStyleHint(QFont::Monospace);
+ font.setLetterSpacing(QFont::AbsoluteSpacing, 0);
+ font.setPointSize(10); // generator.setDefaultFont(font);
+
+ QTextOption text_option;
+ text_option.setWrapMode(QTextOption::WrapAnywhere);
+ text_option.setFlags(QTextOption::IncludeTrailingSpaces |
+ QTextOption::ShowTabsAndSpaces);
+ text_option.setUseDesignMetrics(0);
+
+ // QTextDocument *doc = ui->sequenceTextEdit->document()->clone();
+ QTextDocument *doc = new QTextDocument();
+ doc->setHtml(
+ QString("<p>%1</p><p>%2</p><p>%3</p>")
+ .arg(_p_protein_match->getProteinXtpSp().get()->getAccession())
+ .arg(_p_protein_match->getProteinXtpSp().get()->getDescription())
+ .arg(ui->sequenceTextEdit->toHtml()));
+ doc->setUndoRedoEnabled(false);
+ // doc->setHtml("<p><span style=\"color:#000000;
+ // font-weight:600\">"+text_x+"</span></p>");
+ doc->setTextWidth(printer.pageRect().size().width());
+ doc->setDefaultFont(font);
+ doc->setPageSize(printer.pageRect().size());
+ //// height from doc QTextDocument
+ ////
+ ///http://fop-miniscribus.googlecode.com/svn/trunk/fop_miniscribus.1.0.0/src/floating_box/floatdiagram.cpp
+ //////setMaximumHeight(DocumentHighgtActual());
+ doc->setPageSize(
+ printer.pageRect()
+ .size()); // This is necessary if you want to hide the page number
+ doc->print(&printer);
+
+ /*
+ QPainter *painter = new QPainter(&generator);
+ painter->setRenderHint(QPainter::Antialiasing, true);
+ painter->setFont(font);
+ doc->drawContents(painter);
+ painter->end();
+ */
+
+
+ /*
+ QSvgGenerator svg;
+ svg.setFileName(filename);
+ QTextDocument *doc = ui->sequenceTextEdit->document()->clone();
+ QRect rectSize(0, 0, (int) doc->size().width(), (int)
+ doc->size().height()); QPainter painter(&svg);
+ //painter.setViewport(rectSize);
+ //doc->documentLayout()->setPaintDevice(&svg);
+ doc->drawContents(&painter);
+ */
+
+ /*
+ QtWebEngine::initialize();
+ QWebEnginePage page;
+ QEventLoop loop;
+ loop.connect(&page, &QWebEnginePage::loadFinished, [&page, &loop,
+ &filename]() { page.printToPdf([&loop, &filename] (QByteArray ba) { QFile
+ f(filename); if (f.open(QIODevice::WriteOnly))
+ {
+ f.write(ba);
+ f.close();
+ } else {
+ qDebug() << "Error opening file for writing" << filename
+ << f.errorString();
+ }
+ loop.exit();
+ });
+ });
+ qDebug() << ui->sequenceTextEdit->toHtml();
+ page.setHtml(ui->sequenceTextEdit->toHtml());
+ loop.exec();
+ */
}
- catch (pappso::PappsoException & error) {
- QMessageBox::warning(this,
- tr("Error trying to save spectrum to SVG file :"), error.qwhat());
+ catch(pappso::PappsoException &error)
+ {
+ QMessageBox::warning(
+ this, tr("Error trying to save spectrum to SVG file :"), error.qwhat());
}
-
}
diff --git a/src/gui/protein_view/proteinwindow.h b/src/gui/protein_view/proteinwindow.h
index c0862c185040388e53bbe6d71758751640e8966e..8bb6fcf33d8d49ce293db8ed755a560169e8409b 100644
--- a/src/gui/protein_view/proteinwindow.h
+++ b/src/gui/protein_view/proteinwindow.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PROTEINWINDOW_H
#define PROTEINWINDOW_H
@@ -29,48 +30,51 @@
#include <QPushButton>
#include "../../core/proteinmatch.h"
-class DbXrefButton: public QPushButton {
- Q_OBJECT
-public :
- DbXrefButton(QWidget * parent, DbXref dbxref);
-protected slots:
- void clickedSlot();
-private:
- DbXref _dbxref;
+class DbXrefButton : public QPushButton
+{
+ Q_OBJECT
+ public:
+ DbXrefButton(QWidget *parent, DbXref dbxref);
+ protected slots:
+ void clickedSlot();
+
+ private:
+ DbXref _dbxref;
};
class ProjectWindow;
-namespace Ui {
-class ProteinDetailView;
+namespace Ui
+{
+ class ProteinDetailView;
}
-class ProteinWindow: public QMainWindow {
- Q_OBJECT
-
-public:
-
- explicit ProteinWindow(ProjectWindow * parent = 0);
- ~ProteinWindow();
- void setProteinMatch(ProteinMatch * p_protein_match);
+class ProteinWindow : public QMainWindow
+{
+ Q_OBJECT
-public slots:
- void doIdentificationGroupGrouped(IdentificationGroup * p_identification_group);
- void doPeptideEvidenceSelected(PeptideEvidence * peptide_evidence);
-protected slots:
- void browseUrl(int i);
- void doSaveSvg();
+ public:
+ explicit ProteinWindow(ProjectWindow *parent = 0);
+ ~ProteinWindow();
+ void setProteinMatch(ProteinMatch *p_protein_match);
-protected :
- void updateDisplay();
- void clearDbXrefLayout();
+ public slots:
+ void
+ doIdentificationGroupGrouped(IdentificationGroup *p_identification_group);
+ void doPeptideEvidenceSelected(PeptideEvidence *peptide_evidence);
+ protected slots:
+ void browseUrl(int i);
+ void doSaveSvg();
-private:
- Ui::ProteinDetailView *ui;
- QTextDocument sequence_text;
- ProjectWindow * _p_project_window;
- ProteinMatch * _p_protein_match = nullptr;
+ protected:
+ void updateDisplay();
+ void clearDbXrefLayout();
+ private:
+ Ui::ProteinDetailView *ui;
+ QTextDocument sequence_text;
+ ProjectWindow *_p_project_window;
+ ProteinMatch *_p_protein_match = nullptr;
};
#endif // PROTEINWINDOW_H
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index f3b0d219599b215608741c5d287634c47966b889..5114d8f0d6450f6ebcad0c3d370d3c34f0e6af36 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmislandlistwindow.h"
@@ -36,153 +37,198 @@
#include "../ptm_peptide_list_view/ptmpeptidelistwindow.h"
-PtmIslandListWindow::PtmIslandListWindow(ProjectWindow *parent):
- QMainWindow(parent),
- ui(new Ui::PtmIslandListWindow)
+PtmIslandListWindow::PtmIslandListWindow(ProjectWindow *parent)
+ : QMainWindow(parent), ui(new Ui::PtmIslandListWindow)
{
- _project_window = parent;
- ui->setupUi(this);
- /*
- */
- _ptm_table_model_p = new PtmIslandTableModel(this);
+ _project_window = parent;
+ ui->setupUi(this);
+ /*
+ */
+ _ptm_table_model_p = new PtmIslandTableModel(this);
- _ptm_proxy_model_p = new PtmIslandProxyModel(this, _ptm_table_model_p);
- _ptm_proxy_model_p->setSourceModel(_ptm_table_model_p);
- _ptm_proxy_model_p->setDynamicSortFilter(true);
- ui->ptm_island_tableview->setModel( _ptm_proxy_model_p );
- ui->ptm_island_tableview->setSortingEnabled(true);
- ui->ptm_island_tableview->setAlternatingRowColors(true);
+ _ptm_proxy_model_p = new PtmIslandProxyModel(this, _ptm_table_model_p);
+ _ptm_proxy_model_p->setSourceModel(_ptm_table_model_p);
+ _ptm_proxy_model_p->setDynamicSortFilter(true);
+ ui->ptm_island_tableview->setModel(_ptm_proxy_model_p);
+ ui->ptm_island_tableview->setSortingEnabled(true);
+ ui->ptm_island_tableview->setAlternatingRowColors(true);
+ _statusbar_ptm_islands_label = new QLabel("");
+ ui->statusbar->addWidget(_statusbar_ptm_islands_label);
- _statusbar_ptm_islands_label = new QLabel("");
- ui->statusbar->addWidget(_statusbar_ptm_islands_label);
-
- _statusbar_displayed_label = new QLabel("");
- ui->statusbar->addWidget(_statusbar_displayed_label);
+ _statusbar_displayed_label = new QLabel("");
+ ui->statusbar->addWidget(_statusbar_displayed_label);
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect (this, &PtmIslandListWindow::ptmIslandDataChanged, _ptm_table_model_p, &PtmIslandTableModel::onPtmIslandDataChanged);
-
- connect (_project_window, &ProjectWindow::identificationPtmGroupGrouped, this,&PtmIslandListWindow::doIdentificationPtmGroupGrouped);
- connect (_project_window, &ProjectWindow::identificationGroupGrouped, this,&PtmIslandListWindow::doIdentificationGroupGrouped);
- connect(ui->ptm_island_tableview, &QTableView::clicked, _ptm_proxy_model_p, &PtmIslandProxyModel::onTableClicked);
- connect(_ptm_table_model_p, &PtmIslandTableModel::layoutChanged, this, &PtmIslandListWindow::updateStatusBar);
+ // Qt5 code
+ connect(this, &PtmIslandListWindow::ptmIslandDataChanged, _ptm_table_model_p,
+ &PtmIslandTableModel::onPtmIslandDataChanged);
+
+ connect(_project_window, &ProjectWindow::identificationPtmGroupGrouped, this,
+ &PtmIslandListWindow::doIdentificationPtmGroupGrouped);
+ connect(_project_window, &ProjectWindow::identificationGroupGrouped, this,
+ &PtmIslandListWindow::doIdentificationGroupGrouped);
+ connect(ui->ptm_island_tableview, &QTableView::clicked, _ptm_proxy_model_p,
+ &PtmIslandProxyModel::onTableClicked);
+ connect(_ptm_table_model_p, &PtmIslandTableModel::layoutChanged, this,
+ &PtmIslandListWindow::updateStatusBar);
#else
-// Qt4 code
- connect (this, SIGNAL(ptmIslandDataChanged()), _ptm_table_model_p, SLOT(onPtmIslandDataChanged()));
-
- connect (_project_window, SIGNAL(identificationPtmGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationPtmGroupGrouped(IdentificationGroup *)));
- connect (_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
- connect(ui->ptm_island_tableview, SIGNAL(clicked(const QModelIndex &)), _ptm_proxy_model_p, SLOT(onTableClicked(const QModelIndex &)));
+ // Qt4 code
+ connect(this, SIGNAL(ptmIslandDataChanged()), _ptm_table_model_p,
+ SLOT(onPtmIslandDataChanged()));
+
+ connect(_project_window,
+ SIGNAL(identificationPtmGroupGrouped(IdentificationGroup *)), this,
+ SLOT(doIdentificationPtmGroupGrouped(IdentificationGroup *)));
+ connect(_project_window,
+ SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
+ SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
+ connect(ui->ptm_island_tableview, SIGNAL(clicked(const QModelIndex &)),
+ _ptm_proxy_model_p, SLOT(onTableClicked(const QModelIndex &)));
#endif
}
PtmIslandListWindow::~PtmIslandListWindow()
{
- delete _ptm_table_model_p;
- delete _ptm_proxy_model_p;
- delete _statusbar_displayed_label;
+ delete _ptm_table_model_p;
+ delete _ptm_proxy_model_p;
+ delete _statusbar_displayed_label;
}
-ProjectWindow * PtmIslandListWindow::getProjectWindowP() {
- return _project_window;
+ProjectWindow *
+PtmIslandListWindow::getProjectWindowP()
+{
+ return _project_window;
}
-void PtmIslandListWindow::setIdentificationGroup(IdentificationGroup * p_identification_group) {
-
- qDebug() << "PtmIslandListWindow::setIdentificationGroup begin " ;
- if (p_identification_group != nullptr) {
- qDebug() << "PtmIslandListWindow::setIdentificationGroup not null";
- _p_identification_group = p_identification_group;
- _ptm_table_model_p->setIdentificationGroup(p_identification_group);
- //_p_proxy_model->setSourceModel(_protein_table_model_p);
-
+void
+PtmIslandListWindow::setIdentificationGroup(
+ IdentificationGroup *p_identification_group)
+{
+ qDebug() << "PtmIslandListWindow::setIdentificationGroup begin ";
+ if(p_identification_group != nullptr)
+ {
+ qDebug() << "PtmIslandListWindow::setIdentificationGroup not null";
+ _p_identification_group = p_identification_group;
+ _ptm_table_model_p->setIdentificationGroup(p_identification_group);
+ //_p_proxy_model->setSourceModel(_protein_table_model_p);
}
- else {
- qDebug() << "PtmIslandListWindow::setIdentificationGroup null";
+ else
+ {
+ qDebug() << "PtmIslandListWindow::setIdentificationGroup null";
}
- qDebug() << "PtmIslandListWindow::setIdentificationGroup end";
+ qDebug() << "PtmIslandListWindow::setIdentificationGroup end";
}
-void PtmIslandListWindow::doIdentificationGroupGrouped(IdentificationGroup * p_identification_group) {
- qDebug() << "PtmIslandListWindow::doIdentificationGroupGrouped begin";
- if (_p_identification_group == p_identification_group) {
- //ui->ptm_island_tableview->resizeRowToContents(_ptm_table_model_p->rowCount());
- _project_window->doPtmIslandGrouping(p_identification_group);
- //emit ptmIslandDataChanged();
+void
+PtmIslandListWindow::doIdentificationGroupGrouped(
+ IdentificationGroup *p_identification_group)
+{
+ qDebug() << "PtmIslandListWindow::doIdentificationGroupGrouped begin";
+ if(_p_identification_group == p_identification_group)
+ {
+ // ui->ptm_island_tableview->resizeRowToContents(_ptm_table_model_p->rowCount());
+ _project_window->doPtmIslandGrouping(p_identification_group);
+ // emit ptmIslandDataChanged();
}
- qDebug() << "PtmIslandListWindow::doIdentificationGroupGrouped end";
+ qDebug() << "PtmIslandListWindow::doIdentificationGroupGrouped end";
}
-void PtmIslandListWindow::doIdentificationPtmGroupGrouped(IdentificationGroup * p_identification_group) {
- qDebug() << "PtmIslandListWindow::doIdentificationPtmGroupGrouped begin";
- if (_p_identification_group == p_identification_group) {
- //ui->ptm_island_tableview->resizeRowToContents(0);
- //_protein_table_model_p->setIdentificationGroup(p_identification_group);
- //_p_proxy_model->setSourceModel(_protein_table_model_p);
- _ptm_table_model_p->setIdentificationGroup(p_identification_group);
- emit ptmIslandDataChanged();
-
- const PtmGroupingExperiment * p_ptm_grouping_experiment = p_identification_group->getPtmGroupingExperiment();
- _statusbar_ptm_islands_label->setText(tr("ptm island groups:%1 ptm island subgroups:%2 ptm islands:%3").arg(p_ptm_grouping_experiment->getPtmIslandGroupList().size()).arg(p_ptm_grouping_experiment->getPtmIslandSubgroupList().size()).arg(p_ptm_grouping_experiment->getPtmIslandList().size()));
- //ui->ptm_island_tableview->resizeRowToContents(_ptm_table_model_p->rowCount());
+void
+PtmIslandListWindow::doIdentificationPtmGroupGrouped(
+ IdentificationGroup *p_identification_group)
+{
+ qDebug() << "PtmIslandListWindow::doIdentificationPtmGroupGrouped begin";
+ if(_p_identification_group == p_identification_group)
+ {
+ // ui->ptm_island_tableview->resizeRowToContents(0);
+ //_protein_table_model_p->setIdentificationGroup(p_identification_group);
+ //_p_proxy_model->setSourceModel(_protein_table_model_p);
+ _ptm_table_model_p->setIdentificationGroup(p_identification_group);
+ emit ptmIslandDataChanged();
+
+ const PtmGroupingExperiment *p_ptm_grouping_experiment =
+ p_identification_group->getPtmGroupingExperiment();
+ _statusbar_ptm_islands_label->setText(
+ tr("ptm island groups:%1 ptm island subgroups:%2 ptm islands:%3")
+ .arg(p_ptm_grouping_experiment->getPtmIslandGroupList().size())
+ .arg(p_ptm_grouping_experiment->getPtmIslandSubgroupList().size())
+ .arg(p_ptm_grouping_experiment->getPtmIslandList().size()));
+ // ui->ptm_island_tableview->resizeRowToContents(_ptm_table_model_p->rowCount());
}
- qDebug() << "PtmIslandListWindow::doIdentificationPtmGroupGrouped end";
+ qDebug() << "PtmIslandListWindow::doIdentificationPtmGroupGrouped end";
}
-void PtmIslandListWindow::resizeColumnsToContents() {
- ui->ptm_island_tableview->resizeColumnsToContents();
+void
+PtmIslandListWindow::resizeColumnsToContents()
+{
+ ui->ptm_island_tableview->resizeColumnsToContents();
}
-void PtmIslandListWindow::connectNewPtmPeptideListWindow() {
- qDebug() << "PtmIslandListWindow::connectNewPtmPeptideListWindow begin";
- _p_current_ptm_peptide_list_window = new PtmPeptideListWindow(this);
- _ptm_peptide_list_window_collection.push_back(_p_current_ptm_peptide_list_window);
-
- qDebug() << "PtmIslandListWindow::connectNewPtmPeptideListWindow end";
+void
+PtmIslandListWindow::connectNewPtmPeptideListWindow()
+{
+ qDebug() << "PtmIslandListWindow::connectNewPtmPeptideListWindow begin";
+ _p_current_ptm_peptide_list_window = new PtmPeptideListWindow(this);
+ _ptm_peptide_list_window_collection.push_back(
+ _p_current_ptm_peptide_list_window);
+ qDebug() << "PtmIslandListWindow::connectNewPtmPeptideListWindow end";
}
-void PtmIslandListWindow::askViewPtmPeptideList(PtmIsland * ptm_island) {
- if (_ptm_peptide_list_window_collection.size() == 0) {
- connectNewPtmPeptideListWindow();
+void
+PtmIslandListWindow::askViewPtmPeptideList(PtmIsland *ptm_island)
+{
+ if(_ptm_peptide_list_window_collection.size() == 0)
+ {
+ connectNewPtmPeptideListWindow();
}
- Qt::KeyboardModifiers modifier = QApplication::keyboardModifiers();
- if (modifier == Qt::ControlModifier) {
- connectNewPtmPeptideListWindow();
+ Qt::KeyboardModifiers modifier = QApplication::keyboardModifiers();
+ if(modifier == Qt::ControlModifier)
+ {
+ connectNewPtmPeptideListWindow();
}
- _p_current_ptm_peptide_list_window->setPtmIsland(ptm_island);
- _p_current_ptm_peptide_list_window->show();
-
+ _p_current_ptm_peptide_list_window->setPtmIsland(ptm_island);
+ _p_current_ptm_peptide_list_window->show();
}
-const IdentificationGroup * PtmIslandListWindow::getIdentificationGroup() const {
- return _p_identification_group;
+const IdentificationGroup *
+PtmIslandListWindow::getIdentificationGroup() const
+{
+ return _p_identification_group;
}
-void PtmIslandListWindow::updateStatusBar() {
- if (_p_identification_group == nullptr) {
+void
+PtmIslandListWindow::updateStatusBar()
+{
+ if(_p_identification_group == nullptr)
+ {
}
- else {
- _statusbar_displayed_label->setText(tr("displayed: %1").arg(_ptm_proxy_model_p->rowCount()));
+ else
+ {
+ _statusbar_displayed_label->setText(
+ tr("displayed: %1").arg(_ptm_proxy_model_p->rowCount()));
}
}
-void PtmIslandListWindow::doPtmSearchEdit(QString ptm_search_string) {
- _ptm_proxy_model_p->setPtmSearchString(ptm_search_string);
- emit ptmIslandDataChanged();
+void
+PtmIslandListWindow::doPtmSearchEdit(QString ptm_search_string)
+{
+ _ptm_proxy_model_p->setPtmSearchString(ptm_search_string);
+ emit ptmIslandDataChanged();
}
-void PtmIslandListWindow::doSearchOn(QString search_on) {
- _ptm_proxy_model_p->setSearchOn(search_on);
- emit ptmIslandDataChanged();
+void
+PtmIslandListWindow::doSearchOn(QString search_on)
+{
+ _ptm_proxy_model_p->setSearchOn(search_on);
+ emit ptmIslandDataChanged();
}
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.h b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
index cb460570dd9c82afe281c3120d422e257af767ed..70cb8e16864ed226b8bd6f18e014e76351cec23c 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.h
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMISLANDLISTWINDOW_H
#define PTMISLANDLISTWINDOW_H
@@ -38,53 +39,59 @@
class ProjectWindow;
class PtmPeptideListWindow;
-//http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
-namespace Ui {
-class PtmIslandListWindow;
+// http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
+namespace Ui
+{
+ class PtmIslandListWindow;
}
-class PtmIslandListWindow: public QMainWindow {
- Q_OBJECT
- friend PtmIslandProxyModel;
-public:
- explicit PtmIslandListWindow(ProjectWindow * parent = 0);
- ~PtmIslandListWindow();
- void setIdentificationGroup(IdentificationGroup * p_identification_group);
- void resizeColumnsToContents();
- const IdentificationGroup * getIdentificationGroup() const;
- ProjectWindow * getProjectWindowP();
+class PtmIslandListWindow : public QMainWindow
+{
+ Q_OBJECT
+ friend PtmIslandProxyModel;
+ public:
+ explicit PtmIslandListWindow(ProjectWindow *parent = 0);
+ ~PtmIslandListWindow();
+ void setIdentificationGroup(IdentificationGroup *p_identification_group);
+ void resizeColumnsToContents();
+ const IdentificationGroup *getIdentificationGroup() const;
+ ProjectWindow *getProjectWindowP();
-public slots:
- void doIdentificationPtmGroupGrouped(IdentificationGroup * p_identification_group);
- void doIdentificationGroupGrouped(IdentificationGroup * p_identification_group);
-protected slots:
- void updateStatusBar();
- void doPtmSearchEdit(QString ptm_search_string);
- void doSearchOn(QString search_on);
+ public slots:
+ void
+ doIdentificationPtmGroupGrouped(IdentificationGroup *p_identification_group);
+ void
+ doIdentificationGroupGrouped(IdentificationGroup *p_identification_group);
+ protected slots:
+ void updateStatusBar();
+ void doPtmSearchEdit(QString ptm_search_string);
+ void doSearchOn(QString search_on);
-signals:
- void ptmIslandDataChanged();
-protected:
- void askViewPtmPeptideList(PtmIsland * ptm_island);
-private:
- void connectNewPtmPeptideListWindow();
-private:
- IdentificationGroup * _p_identification_group=nullptr;
- Ui::PtmIslandListWindow *ui;
- PtmIslandTableModel * _ptm_table_model_p = nullptr;
- PtmIslandProxyModel * _ptm_proxy_model_p = nullptr;
- ProjectWindow * _project_window;
+ signals:
+ void ptmIslandDataChanged();
- PtmPeptideListWindow * _p_current_ptm_peptide_list_window;
- std::vector<PtmPeptideListWindow *> _ptm_peptide_list_window_collection;
+ protected:
+ void askViewPtmPeptideList(PtmIsland *ptm_island);
- QLabel * _statusbar_displayed_label;
- QLabel * _statusbar_ptm_islands_label;
+ private:
+ void connectNewPtmPeptideListWindow();
+ private:
+ IdentificationGroup *_p_identification_group = nullptr;
+ Ui::PtmIslandListWindow *ui;
+ PtmIslandTableModel *_ptm_table_model_p = nullptr;
+ PtmIslandProxyModel *_ptm_proxy_model_p = nullptr;
+ ProjectWindow *_project_window;
+
+ PtmPeptideListWindow *_p_current_ptm_peptide_list_window;
+ std::vector<PtmPeptideListWindow *> _ptm_peptide_list_window_collection;
+
+ QLabel *_statusbar_displayed_label;
+ QLabel *_statusbar_ptm_islands_label;
};
#endif // PTMISLANDLISTWINDOW_H
diff --git a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
index be015191e27cfe8afba36fe9778c010186822a1e..d9634eeb5c654e8c6f98e386894e04a58393a24c 100644
--- a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmislandproxymodel.h"
#include "ptmislandtablemodel.h"
@@ -34,111 +35,173 @@
#include "../../grouping/ptm/ptmisland.h"
#include <pappsomspp/pappsoexception.h>
-PtmIslandProxyModel::PtmIslandProxyModel(PtmIslandListWindow * p_ptm_island_list_window, PtmIslandTableModel* ptm_table_model_p)
+PtmIslandProxyModel::PtmIslandProxyModel(
+ PtmIslandListWindow *p_ptm_island_list_window,
+ PtmIslandTableModel *ptm_table_model_p)
{
- _p_ptm_island_list_window = p_ptm_island_list_window;
- _p_ptm_island_table_model = ptm_table_model_p;
- _ptm_search_string = "";
- _search_on = "accession";
+ _p_ptm_island_list_window = p_ptm_island_list_window;
+ _p_ptm_island_table_model = ptm_table_model_p;
+ _ptm_search_string = "";
+ _search_on = "accession";
}
PtmIslandProxyModel::~PtmIslandProxyModel()
{
-
}
-bool PtmIslandProxyModel::filterAcceptsRow(int source_row,
- const QModelIndex &source_parent) const {
- try {
- //qDebug() << "ProteinTableProxyModel::filterAcceptsRow begin " << source_row;
- PtmIslandSp sp_ptm_island = _p_ptm_island_table_model->getPtmGroupingExperiment()->getPtmIslandList().at(source_row);
- //qDebug() << "ProteinTableProxyModel::filterAcceptsRow protein_match " << source_row;
-
- if (!_ptm_search_string.isEmpty()) {
- if (_search_on == "accession") {
- if (!sp_ptm_island.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession().contains(_ptm_search_string)) {
- return false;
+bool
+PtmIslandProxyModel::filterAcceptsRow(int source_row,
+ const QModelIndex &source_parent) const
+{
+ try
+ {
+ // qDebug() << "ProteinTableProxyModel::filterAcceptsRow begin " <<
+ // source_row;
+ PtmIslandSp sp_ptm_island =
+ _p_ptm_island_table_model->getPtmGroupingExperiment()
+ ->getPtmIslandList()
+ .at(source_row);
+ // qDebug() << "ProteinTableProxyModel::filterAcceptsRow protein_match "
+ // << source_row;
+
+ if(!_ptm_search_string.isEmpty())
+ {
+ if(_search_on == "accession")
+ {
+ if(!sp_ptm_island.get()
+ ->getProteinMatch()
+ ->getProteinXtpSp()
+ .get()
+ ->getAccession()
+ .contains(_ptm_search_string))
+ {
+ return false;
}
}
- else if (_search_on == "group") {
- if (!sp_ptm_island.get()->getGroupingId().startsWith(QString("ptm%1").arg(_ptm_search_string))) {
- return false;
+ else if(_search_on == "group")
+ {
+ if(!sp_ptm_island.get()->getGroupingId().startsWith(
+ QString("ptm%1").arg(_ptm_search_string)))
+ {
+ return false;
}
-
}
- else if (_search_on == "sequence") {
- if (!sp_ptm_island.get()->getProteinMatch()->getProteinXtpSp().get()->getSequence().contains(_ptm_search_string)) {
- return false;
+ else if(_search_on == "sequence")
+ {
+ if(!sp_ptm_island.get()
+ ->getProteinMatch()
+ ->getProteinXtpSp()
+ .get()
+ ->getSequence()
+ .contains(_ptm_search_string))
+ {
+ return false;
}
}
- else if (_search_on == "peptide") {
- QString peptide_search_string = QString(_ptm_search_string).replace("L","I");
- for (const PeptideMatch & p_peptide_match: sp_ptm_island.get()->getProteinMatch()->getPeptideMatchList()) {
- if (p_peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequenceLi().contains(peptide_search_string)) {
- return true;
+ else if(_search_on == "peptide")
+ {
+ QString peptide_search_string =
+ QString(_ptm_search_string).replace("L", "I");
+ for(const PeptideMatch &p_peptide_match :
+ sp_ptm_island.get()->getProteinMatch()->getPeptideMatchList())
+ {
+ if(p_peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getSequenceLi()
+ .contains(peptide_search_string))
+ {
+ return true;
}
}
- return false;
+ return false;
}
- else if (_search_on == "description") {
- //description
- if (!sp_ptm_island.get()->getProteinMatch()->getProteinXtpSp().get()->getDescription().contains(_ptm_search_string)) {
- return false;
+ else if(_search_on == "description")
+ {
+ // description
+ if(!sp_ptm_island.get()
+ ->getProteinMatch()
+ ->getProteinXtpSp()
+ .get()
+ ->getDescription()
+ .contains(_ptm_search_string))
+ {
+ return false;
}
}
}
- if (sp_ptm_island != nullptr) {
- return true;
+ if(sp_ptm_island != nullptr)
+ {
+ return true;
}
- return false;
+ return false;
}
- catch (pappso::PappsoException exception_pappso) {
- //QMessageBox::warning(this,
- // tr("Error in ProteinTableModel::acceptRow :"), exception_pappso.qwhat());
- qDebug() << "Error in PtmIslandProxyModel::acceptRow :" << exception_pappso.qwhat();
+ catch(pappso::PappsoException exception_pappso)
+ {
+ // QMessageBox::warning(this,
+ // tr("Error in ProteinTableModel::acceptRow :"),
+ // exception_pappso.qwhat());
+ qDebug() << "Error in PtmIslandProxyModel::acceptRow :"
+ << exception_pappso.qwhat();
}
- catch (std::exception exception_std) {
- //QMessageBox::warning(this,
- // tr("Error in ProteinTableModel::acceptRow :"), exception_std.what());
- qDebug() << "Error in PtmIslandProxyModel::acceptRow :" << exception_std.what();
+ catch(std::exception exception_std)
+ {
+ // QMessageBox::warning(this,
+ // tr("Error in ProteinTableModel::acceptRow :"),
+ // exception_std.what());
+ qDebug() << "Error in PtmIslandProxyModel::acceptRow :"
+ << exception_std.what();
}
- return true;
+ return true;
- //return true;
+ // return true;
}
-void PtmIslandProxyModel::onTableClicked(const QModelIndex &index)
+void
+PtmIslandProxyModel::onTableClicked(const QModelIndex &index)
{
- qDebug() << "PtmIslandProxyModel::onTableClicked begin " << index.row();
- qDebug() << "PtmIslandProxyModel::onTableClicked begin " << this->mapToSource(index).row();
-
- //_protein_table_model_p->onTableClicked(this->mapToSource(index));
- QModelIndex source_index(this->mapToSource(index));
- int row = source_index.row();
- int col = source_index.column();
-
- //ProteinMatch* p_protein_match = _p_ptm_island_table_model->getIdentificationGroup()->getProteinMatchList().at(row);
-
- if ((col == (std::int8_t) PtmIslandListColumn::accession)||(col == (std::int8_t) PtmIslandListColumn::description)) {
- //_p_ptm_island_table_model->askPtmProteinDetailView(p_protein_match);
+ qDebug() << "PtmIslandProxyModel::onTableClicked begin " << index.row();
+ qDebug() << "PtmIslandProxyModel::onTableClicked begin "
+ << this->mapToSource(index).row();
+
+ //_protein_table_model_p->onTableClicked(this->mapToSource(index));
+ QModelIndex source_index(this->mapToSource(index));
+ int row = source_index.row();
+ int col = source_index.column();
+
+ // ProteinMatch* p_protein_match =
+ // _p_ptm_island_table_model->getIdentificationGroup()->getProteinMatchList().at(row);
+
+ if((col == (std::int8_t)PtmIslandListColumn::accession) ||
+ (col == (std::int8_t)PtmIslandListColumn::description))
+ {
+ //_p_ptm_island_table_model->askPtmProteinDetailView(p_protein_match);
}
- else {
- _p_ptm_island_list_window->askViewPtmPeptideList(_p_ptm_island_table_model->getPtmGroupingExperiment()->getPtmIslandList().at(row).get());
+ else
+ {
+ _p_ptm_island_list_window->askViewPtmPeptideList(
+ _p_ptm_island_table_model->getPtmGroupingExperiment()
+ ->getPtmIslandList()
+ .at(row)
+ .get());
}
- qDebug() << "PtmIslandProxyModel::onTableClicked end " << index.row();
-
+ qDebug() << "PtmIslandProxyModel::onTableClicked end " << index.row();
}
-void PtmIslandProxyModel::setSearchOn(QString search_on) {
- _search_on = search_on;
+void
+PtmIslandProxyModel::setSearchOn(QString search_on)
+{
+ _search_on = search_on;
}
-void PtmIslandProxyModel::setPtmSearchString(QString ptm_search_string) {
- _ptm_search_string = ptm_search_string;
+void
+PtmIslandProxyModel::setPtmSearchString(QString ptm_search_string)
+{
+ _ptm_search_string = ptm_search_string;
}
diff --git a/src/gui/ptm_island_list_view/ptmislandproxymodel.h b/src/gui/ptm_island_list_view/ptmislandproxymodel.h
index 71eaf6d34045197cad1f16a1803f3141e560b8a4..b65464b89f63b4e8c7c3eb660906511195df60d0 100644
--- a/src/gui/ptm_island_list_view/ptmislandproxymodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandproxymodel.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMISLANDPROXYMODEL_H
#define PTMISLANDPROXYMODEL_H
@@ -37,28 +38,28 @@
class PtmIslandListWindow;
class PtmIslandTableModel;
-class PtmIslandProxyModel: public QSortFilterProxyModel
+class PtmIslandProxyModel : public QSortFilterProxyModel
{
- Q_OBJECT
-public:
- PtmIslandProxyModel(PtmIslandListWindow * p_ptm_island_list_window, PtmIslandTableModel* ptm_table_model_p);
- ~PtmIslandProxyModel();
- bool filterAcceptsRow(int source_row,
- const QModelIndex &source_parent) const override;
+ Q_OBJECT
+ public:
+ PtmIslandProxyModel(PtmIslandListWindow *p_ptm_island_list_window,
+ PtmIslandTableModel *ptm_table_model_p);
+ ~PtmIslandProxyModel();
+ bool filterAcceptsRow(int source_row,
+ const QModelIndex &source_parent) const override;
- void setSearchOn(QString search_on);
+ void setSearchOn(QString search_on);
- void setPtmSearchString(QString ptm_search_string) ;
+ void setPtmSearchString(QString ptm_search_string);
-public slots:
- void onTableClicked(const QModelIndex &index);
-
-private:
- PtmIslandListWindow * _p_ptm_island_list_window;
- PtmIslandTableModel * _p_ptm_island_table_model;
- QString _search_on;
- QString _ptm_search_string;
+ public slots:
+ void onTableClicked(const QModelIndex &index);
+ private:
+ PtmIslandListWindow *_p_ptm_island_list_window;
+ PtmIslandTableModel *_p_ptm_island_table_model;
+ QString _search_on;
+ QString _ptm_search_string;
};
#endif // PTMISLANDPROXYMODEL_H
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
index a51a54093c63dddc17d0830052725820a87d4acb..d039db1fe402edff4d6d9ff8fcea4b678fba7991 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
@@ -6,243 +6,325 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmislandtablemodel.h"
#include "ptmislandlistwindow.h"
-
-PtmIslandTableModel::PtmIslandTableModel(PtmIslandListWindow * p_ptm_island_list_window)
+PtmIslandTableModel::PtmIslandTableModel(
+ PtmIslandListWindow *p_ptm_island_list_window)
{
-_p_ptm_island_list_window = p_ptm_island_list_window;
+ _p_ptm_island_list_window = p_ptm_island_list_window;
}
PtmIslandTableModel::~PtmIslandTableModel()
{
-
}
-const QString PtmIslandTableModel::getTitle(PtmIslandListColumn column) {
- qDebug() << "PtmIslandTableModel::getTitle begin ";
- return PtmIslandTableModel::getTitle((std::int8_t) column);
- //qDebug() << "ProteinTableModel::getTitle end ";
+const QString
+PtmIslandTableModel::getTitle(PtmIslandListColumn column)
+{
+ qDebug() << "PtmIslandTableModel::getTitle begin ";
+ return PtmIslandTableModel::getTitle((std::int8_t)column);
+ // qDebug() << "ProteinTableModel::getTitle end ";
}
-const QString PtmIslandTableModel::getDescription(PtmIslandListColumn column) {
- qDebug() << "PtmIslandTableModel::columnCount begin ";
- return PtmIslandTableModel::getDescription((std::int8_t) column);
- //qDebug() << "ProteinTableModel::columnCount end ";
+const QString
+PtmIslandTableModel::getDescription(PtmIslandListColumn column)
+{
+ qDebug() << "PtmIslandTableModel::columnCount begin ";
+ return PtmIslandTableModel::getDescription((std::int8_t)column);
+ // qDebug() << "ProteinTableModel::columnCount end ";
}
-const QString PtmIslandTableModel::getTitle(std::int8_t column) {
- switch (column) {
+const QString
+PtmIslandTableModel::getTitle(std::int8_t column)
+{
+ switch(column)
+ {
- case (std::int8_t) PtmIslandListColumn::spectrum:
+ case(std::int8_t)PtmIslandListColumn::spectrum:
return "spectrum";
break;
- case (std::int8_t) PtmIslandListColumn::description:
+ case(std::int8_t)PtmIslandListColumn::description:
return "description";
break;
- case (std::int8_t) PtmIslandListColumn::multiptm:
+ case(std::int8_t)PtmIslandListColumn::multiptm:
return "multi PTM";
break;
- case (std::int8_t) PtmIslandListColumn::sequence:
+ case(std::int8_t)PtmIslandListColumn::sequence:
return "sequence";
break;
- case (std::int8_t) PtmIslandListColumn::ptm_island_id:
+ case(std::int8_t)PtmIslandListColumn::ptm_island_id:
return "PTM island ID";
break;
- case (std::int8_t) PtmIslandListColumn::accession:
+ case(std::int8_t)PtmIslandListColumn::accession:
return "accession";
break;
- case (std::int8_t) PtmIslandListColumn::ptm_position_list:
+ case(std::int8_t)PtmIslandListColumn::ptm_position_list:
return "ptm positions";
break;
- case (std::int8_t) PtmIslandListColumn::ptm_island_start:
+ case(std::int8_t)PtmIslandListColumn::ptm_island_start:
return "start";
break;
- case (std::int8_t) PtmIslandListColumn::ptm_island_length:
+ case(std::int8_t)PtmIslandListColumn::ptm_island_length:
return "length";
-
}
- return "";
+ return "";
}
-const QString PtmIslandTableModel::getDescription(std::int8_t column) {
- switch (column) {
+const QString
+PtmIslandTableModel::getDescription(std::int8_t column)
+{
+ switch(column)
+ {
- case (std::int8_t) PtmIslandListColumn::spectrum:
+ case(std::int8_t)PtmIslandListColumn::spectrum:
return "number of distinct spectrum assigned to this PTM island";
break;
- case (std::int8_t) PtmIslandListColumn::description:
+ case(std::int8_t)PtmIslandListColumn::description:
return "protein description";
break;
- case (std::int8_t) PtmIslandListColumn::multiptm:
+ case(std::int8_t)PtmIslandListColumn::multiptm:
return "number of distinct spectrum containing more than 1 ptm";
break;
- case (std::int8_t) PtmIslandListColumn::sequence:
+ case(std::int8_t)PtmIslandListColumn::sequence:
return "number of unique peptide sequence";
break;
- case (std::int8_t) PtmIslandListColumn::ptm_island_id:
+ case(std::int8_t)PtmIslandListColumn::ptm_island_id:
return "unique PTM island identifier";
break;
- case (std::int8_t) PtmIslandListColumn::accession:
+ case(std::int8_t)PtmIslandListColumn::accession:
return "protein accession";
break;
- case (std::int8_t) PtmIslandListColumn::ptm_position_list:
+ case(std::int8_t)PtmIslandListColumn::ptm_position_list:
return "PTM positions observed in this PTM island";
break;
- case (std::int8_t) PtmIslandListColumn::ptm_island_start:
+ case(std::int8_t)PtmIslandListColumn::ptm_island_start:
return "PTM island start on the protein";
break;
- case (std::int8_t) PtmIslandListColumn::ptm_island_length:
+ case(std::int8_t)PtmIslandListColumn::ptm_island_length:
return "PTM island length";
-
}
- return "";
+ return "";
}
-void PtmIslandTableModel::setIdentificationGroup(IdentificationGroup * p_identification_group) {
- qDebug() << "PtmIslandTableModel::setIdentificationGroup begin ";
-
- beginResetModel();
- _p_identification_group = p_identification_group;
-
- //emit headerDataChanged(Qt::Horizontal, 0,11);
- //refresh();
- qDebug() << "PtmIslandTableModel::setIdentificationGroup end ";
- endResetModel();
-
- this->_p_ptm_island_list_window->resizeColumnsToContents();
-
+void
+PtmIslandTableModel::setIdentificationGroup(
+ IdentificationGroup *p_identification_group)
+{
+ qDebug() << "PtmIslandTableModel::setIdentificationGroup begin ";
+
+ beginResetModel();
+ _p_identification_group = p_identification_group;
+
+ // emit headerDataChanged(Qt::Horizontal, 0,11);
+ // refresh();
+ qDebug() << "PtmIslandTableModel::setIdentificationGroup end ";
+ endResetModel();
+
+ this->_p_ptm_island_list_window->resizeColumnsToContents();
}
-const PtmGroupingExperiment * PtmIslandTableModel::getPtmGroupingExperiment() const {
- if (_p_identification_group == nullptr) {
- return nullptr;
+const PtmGroupingExperiment *
+PtmIslandTableModel::getPtmGroupingExperiment() const
+{
+ if(_p_identification_group == nullptr)
+ {
+ return nullptr;
}
- return _p_identification_group->getPtmGroupingExperiment();
+ return _p_identification_group->getPtmGroupingExperiment();
}
-int PtmIslandTableModel::rowCount(const QModelIndex &parent ) const {
- //qDebug() << "PtmIslandTableModel::rowCount begin ";
- if (getPtmGroupingExperiment() != nullptr) {
- //qDebug() << "PtmIslandTableModel::rowCount(const QModelIndex &parent ) " << getPtmGroupingExperiment()->getPtmIslandList().size();
- return (int) getPtmGroupingExperiment()->getPtmIslandList().size();
+int
+PtmIslandTableModel::rowCount(const QModelIndex &parent) const
+{
+ // qDebug() << "PtmIslandTableModel::rowCount begin ";
+ if(getPtmGroupingExperiment() != nullptr)
+ {
+ // qDebug() << "PtmIslandTableModel::rowCount(const QModelIndex &parent )
+ // " << getPtmGroupingExperiment()->getPtmIslandList().size();
+ return (int)getPtmGroupingExperiment()->getPtmIslandList().size();
}
- return 0;
+ return 0;
}
-int PtmIslandTableModel::columnCount(const QModelIndex &parent ) const {
- //qDebug() << "ProteinTableModel::columnCount begin ";
- if (getPtmGroupingExperiment() != nullptr) {
- return 9;
+int
+PtmIslandTableModel::columnCount(const QModelIndex &parent) const
+{
+ // qDebug() << "ProteinTableModel::columnCount begin ";
+ if(getPtmGroupingExperiment() != nullptr)
+ {
+ return 9;
}
- return 0;
+ return 0;
}
-QVariant PtmIslandTableModel::headerData(int section, Qt::Orientation orientation, int role) const
+QVariant
+PtmIslandTableModel::headerData(int section, Qt::Orientation orientation,
+ int role) const
{
- if (getPtmGroupingExperiment() == nullptr) return QVariant();
- if (orientation == Qt::Horizontal)
+ if(getPtmGroupingExperiment() == nullptr)
+ return QVariant();
+ if(orientation == Qt::Horizontal)
{
- switch (role) {
- case Qt::DisplayRole :
+ switch(role)
+ {
+ case Qt::DisplayRole:
return QVariant(getTitle(section));
break;
- case Qt::ToolTipRole :
- return QVariant(getDescription(section));
+ case Qt::ToolTipRole:
+ return QVariant(getDescription(section));
break;
-
}
}
- return QVariant();
+ return QVariant();
}
-QVariant PtmIslandTableModel::data(const QModelIndex &index, int role ) const {
- // generate a log message when this method gets called
- if (getPtmGroupingExperiment() == nullptr) return QVariant();
- int row = index.row();
- int col = index.column();
- switch(role) {
- case Qt::SizeHintRole :
- //qDebug() << "ProteinTableModel::headerData " << ProteinTableModel::getColumnWidth(section);
- return QSize( PtmIslandTableModel::getColumnWidth(col), 30 );
- break;
- case Qt::DisplayRole:
- if (_p_identification_group == nullptr) {
+QVariant
+PtmIslandTableModel::data(const QModelIndex &index, int role) const
+{
+ // generate a log message when this method gets called
+ if(getPtmGroupingExperiment() == nullptr)
+ return QVariant();
+ int row = index.row();
+ int col = index.column();
+ switch(role)
+ {
+ case Qt::SizeHintRole:
+ // qDebug() << "ProteinTableModel::headerData " <<
+ // ProteinTableModel::getColumnWidth(section);
+ return QSize(PtmIslandTableModel::getColumnWidth(col), 30);
+ break;
+ case Qt::DisplayRole:
+ if(_p_identification_group == nullptr)
+ {
return QVariant();
- }
- switch (col) {
+ }
+ switch(col)
+ {
- case (std::int8_t) PtmIslandListColumn::spectrum:
- return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getPtmIslandSubroup()->countSampleScan());
- break;
+ case(std::int8_t)PtmIslandListColumn::spectrum:
+ return QVariant(getPtmGroupingExperiment()
+ ->getPtmIslandList()
+ .at(row)
+ .get()
+ ->getPtmIslandSubroup()
+ ->countSampleScan());
+ break;
- case (std::int8_t) PtmIslandListColumn::description:
- return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getProteinMatch()->getProteinXtpSp().get()->getDescription());
- break;
- case (std::int8_t) PtmIslandListColumn::multiptm:
- return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->countSampleScanMultiPtm(getPtmGroupingExperiment()));
- break;
- case (std::int8_t) PtmIslandListColumn::sequence:
- return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->countSequence());
- break;
- case (std::int8_t) PtmIslandListColumn::ptm_island_id:
- return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getGroupingId());
- break;
- case (std::int8_t) PtmIslandListColumn::accession:
- return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getProteinMatch()->getProteinXtpSp().get()->getAccession());
- break;
- case (std::int8_t) PtmIslandListColumn::ptm_island_start:
- return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getStart()+1);
- break;
- case (std::int8_t) PtmIslandListColumn::ptm_island_length:
- return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->size());
- break;
- case (std::int8_t) PtmIslandListColumn::ptm_position_list:
- QStringList position_list;
- for (unsigned int position :getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getPositionList()) {
- position_list << QString("%1").arg(position+1);
- }
- return QVariant(position_list.join(" "));
- }
+ case(std::int8_t)PtmIslandListColumn::description:
+ return QVariant(getPtmGroupingExperiment()
+ ->getPtmIslandList()
+ .at(row)
+ .get()
+ ->getProteinMatch()
+ ->getProteinXtpSp()
+ .get()
+ ->getDescription());
+ break;
+ case(std::int8_t)PtmIslandListColumn::multiptm:
+ return QVariant(
+ getPtmGroupingExperiment()
+ ->getPtmIslandList()
+ .at(row)
+ .get()
+ ->countSampleScanMultiPtm(getPtmGroupingExperiment()));
+ break;
+ case(std::int8_t)PtmIslandListColumn::sequence:
+ return QVariant(getPtmGroupingExperiment()
+ ->getPtmIslandList()
+ .at(row)
+ .get()
+ ->countSequence());
+ break;
+ case(std::int8_t)PtmIslandListColumn::ptm_island_id:
+ return QVariant(getPtmGroupingExperiment()
+ ->getPtmIslandList()
+ .at(row)
+ .get()
+ ->getGroupingId());
+ break;
+ case(std::int8_t)PtmIslandListColumn::accession:
+ return QVariant(getPtmGroupingExperiment()
+ ->getPtmIslandList()
+ .at(row)
+ .get()
+ ->getProteinMatch()
+ ->getProteinXtpSp()
+ .get()
+ ->getAccession());
+ break;
+ case(std::int8_t)PtmIslandListColumn::ptm_island_start:
+ return QVariant(getPtmGroupingExperiment()
+ ->getPtmIslandList()
+ .at(row)
+ .get()
+ ->getStart() +
+ 1);
+ break;
+ case(std::int8_t)PtmIslandListColumn::ptm_island_length:
+ return QVariant(getPtmGroupingExperiment()
+ ->getPtmIslandList()
+ .at(row)
+ .get()
+ ->size());
+ break;
+ case(std::int8_t)PtmIslandListColumn::ptm_position_list:
+ QStringList position_list;
+ for(unsigned int position : getPtmGroupingExperiment()
+ ->getPtmIslandList()
+ .at(row)
+ .get()
+ ->getPositionList())
+ {
+ position_list << QString("%1").arg(position + 1);
+ }
+ return QVariant(position_list.join(" "));
+ }
}
- return QVariant();
+ return QVariant();
}
-void PtmIslandTableModel::onPtmIslandDataChanged() {
- qDebug() << "PtmIslandTableModel::onPtmIslandDataChanged begin " << rowCount();
- emit layoutAboutToBeChanged();
- emit layoutChanged();
+void
+PtmIslandTableModel::onPtmIslandDataChanged()
+{
+ qDebug() << "PtmIslandTableModel::onPtmIslandDataChanged begin "
+ << rowCount();
+ emit layoutAboutToBeChanged();
+ emit layoutChanged();
}
-int PtmIslandTableModel::getColumnWidth(int column) {
- qDebug() << "PtmIslandTableModel::getColumnWidth " << column;
- switch (column) {
- case (int) PtmIslandListColumn::accession:
+int
+PtmIslandTableModel::getColumnWidth(int column)
+{
+ qDebug() << "PtmIslandTableModel::getColumnWidth " << column;
+ switch(column)
+ {
+ case(int)PtmIslandListColumn::accession:
qDebug() << "PtmIslandTableModel::getColumnWidth accession " << column;
return 250;
break;
- case (int) PtmIslandListColumn::description:
+ case(int)PtmIslandListColumn::description:
return 400;
break;
}
- return 100;
+ return 100;
}
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.h b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
index 948b1bddf466b6526f87521e8cd5868fcdf9524d..2cee9bc6260f1f14c7bd0a7ab96649de8104208e 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMISLANDTABLEMODEL_H
#define PTMISLANDTABLEMODEL_H
@@ -35,54 +36,61 @@
#include "../../grouping/ptm/ptmgroupingexperiment.h"
-
-/** \def PtmIslandListColumn list of available fields to display in ptm island list
+/** \def PtmIslandListColumn list of available fields to display in ptm island
+ * list
*
*/
-enum class PtmIslandListColumn: std::int8_t {
- ptm_island_id=0, ///< ptm_island_id
- accession=1, ///< protein accession
- description=2, ///< protein description
- ptm_position_list=3, ///< ptm position list
- spectrum=4, ///< count sample scans
- sequence=5, ///< unique sequence count
- multiptm=6, ///< count multi ptm peptide match
- ptm_island_start=7, ///< start position of the ptm island on the protein
- ptm_island_length=8, ///< length of the ptm island
+enum class PtmIslandListColumn : std::int8_t
+{
+ ptm_island_id = 0, ///< ptm_island_id
+ accession = 1, ///< protein accession
+ description = 2, ///< protein description
+ ptm_position_list = 3, ///< ptm position list
+ spectrum = 4, ///< count sample scans
+ sequence = 5, ///< unique sequence count
+ multiptm = 6, ///< count multi ptm peptide match
+ ptm_island_start = 7, ///< start position of the ptm island on the protein
+ ptm_island_length = 8, ///< length of the ptm island
};
class PtmIslandListWindow;
-class PtmIslandTableModel: public QAbstractTableModel
+class PtmIslandTableModel : public QAbstractTableModel
{
- Q_OBJECT
-public:
- PtmIslandTableModel(PtmIslandListWindow * p_ptm_island_list_window);
-
- ~PtmIslandTableModel();
-
- void setIdentificationGroup(IdentificationGroup * p_identification_group);
- virtual int rowCount(const QModelIndex &parent = QModelIndex()) const override;
- virtual int columnCount(const QModelIndex &parent = QModelIndex()) const override;
- virtual QVariant headerData(int section, Qt::Orientation orientation, int role) const override;
- virtual QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override;
-
- static const QString getTitle(PtmIslandListColumn column);
- static const QString getDescription(PtmIslandListColumn column);
-
- const PtmGroupingExperiment * getPtmGroupingExperiment() const;
-
-public slots:
- void onPtmIslandDataChanged();
-private :
- static int getColumnWidth(int column);
- static const QString getTitle(std::int8_t column);
- static const QString getDescription(std::int8_t column);
-private :
- IdentificationGroup * _p_identification_group=nullptr;
- PtmIslandListWindow * _p_ptm_island_list_window=nullptr;
+ Q_OBJECT
+ public:
+ PtmIslandTableModel(PtmIslandListWindow *p_ptm_island_list_window);
+
+ ~PtmIslandTableModel();
+
+ void setIdentificationGroup(IdentificationGroup *p_identification_group);
+ virtual int
+ rowCount(const QModelIndex &parent = QModelIndex()) const override;
+ virtual int
+ columnCount(const QModelIndex &parent = QModelIndex()) const override;
+ virtual QVariant headerData(int section, Qt::Orientation orientation,
+ int role) const override;
+ virtual QVariant data(const QModelIndex &index,
+ int role = Qt::DisplayRole) const override;
+
+ static const QString getTitle(PtmIslandListColumn column);
+ static const QString getDescription(PtmIslandListColumn column);
+
+ const PtmGroupingExperiment *getPtmGroupingExperiment() const;
+
+ public slots:
+ void onPtmIslandDataChanged();
+
+ private:
+ static int getColumnWidth(int column);
+ static const QString getTitle(std::int8_t column);
+ static const QString getDescription(std::int8_t column);
+
+ private:
+ IdentificationGroup *_p_identification_group = nullptr;
+ PtmIslandListWindow *_p_ptm_island_list_window = nullptr;
};
#endif // PTMISLANDTABLEMODEL_H
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
index 7babd9b4ba2106bde6d45b52309aa526310b1b22..f2b0b68b5139d7e68b911f18f9198a7e51e0b1b6 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmpeptidelistwindow.h"
#include "../ptm_island_list_view/ptmislandlistwindow.h"
@@ -36,56 +37,76 @@
#include "ui_ptm_peptide_list_view.h"
+PtmPeptideListWindow::PtmPeptideListWindow(PtmIslandListWindow *parent)
+ : QMainWindow(parent), ui(new Ui::PtmPeptideListWindow)
+{
+ _p_ptm_island_list_window = parent;
+ ui->setupUi(this);
+ /*
+ */
+ _ptm_table_model_p = new PtmPeptideTableModel(this);
-PtmPeptideListWindow::PtmPeptideListWindow(PtmIslandListWindow * parent):QMainWindow(parent),
- ui(new Ui::PtmPeptideListWindow) {
- _p_ptm_island_list_window = parent;
-
- ui->setupUi(this);
- /*
- */
- _ptm_table_model_p = new PtmPeptideTableModel(this);
-
-
- _ptm_proxy_model_p = new PtmPeptideTableProxyModel(this, _ptm_table_model_p);
- _ptm_proxy_model_p->setSourceModel(_ptm_table_model_p);
- _ptm_proxy_model_p->setDynamicSortFilter(true);
- ui->ptm_peptide_tableview->setModel( _ptm_proxy_model_p );
- ui->ptm_peptide_tableview->setSortingEnabled(true);
- ui->ptm_peptide_tableview->setAlternatingRowColors(true);
- PtmSequenceDelegate * p_sequence_delegate = new PtmSequenceDelegate(_p_ptm_island_list_window, this);
- ui->ptm_peptide_tableview->setItemDelegateForColumn((std::int8_t) PtmPeptideListColumn::sequence, p_sequence_delegate);
+ _ptm_proxy_model_p = new PtmPeptideTableProxyModel(this, _ptm_table_model_p);
+ _ptm_proxy_model_p->setSourceModel(_ptm_table_model_p);
+ _ptm_proxy_model_p->setDynamicSortFilter(true);
+ ui->ptm_peptide_tableview->setModel(_ptm_proxy_model_p);
+ ui->ptm_peptide_tableview->setSortingEnabled(true);
+ ui->ptm_peptide_tableview->setAlternatingRowColors(true);
+ PtmSequenceDelegate *p_sequence_delegate =
+ new PtmSequenceDelegate(_p_ptm_island_list_window, this);
+ ui->ptm_peptide_tableview->setItemDelegateForColumn(
+ (std::int8_t)PtmPeptideListColumn::sequence, p_sequence_delegate);
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect(ui->ptm_peptide_tableview, &QTableView::clicked, _ptm_proxy_model_p, &PtmPeptideTableProxyModel::onTableClicked);
- connect (this, &PtmPeptideListWindow::requestPeptideDetailView, _p_ptm_island_list_window->getProjectWindowP(),&ProjectWindow::doViewPeptideDetail);
+ // Qt5 code
+ connect(ui->ptm_peptide_tableview, &QTableView::clicked, _ptm_proxy_model_p,
+ &PtmPeptideTableProxyModel::onTableClicked);
+ connect(this, &PtmPeptideListWindow::requestPeptideDetailView,
+ _p_ptm_island_list_window->getProjectWindowP(),
+ &ProjectWindow::doViewPeptideDetail);
#else
-// Qt4 code
- //connect (this, SIGNAL(ptmIslandDataChanged()), _ptm_table_model_p, SLOT(onPtmIslandDataChanged()));
+ // Qt4 code
+ // connect (this, SIGNAL(ptmIslandDataChanged()), _ptm_table_model_p,
+ // SLOT(onPtmIslandDataChanged()));
- //connect (_project_window, SIGNAL(identificationPtmGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationPtmGroupGrouped(IdentificationGroup *)));
- //connect (_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
- connect(ui->ptm_peptide_tableview, SIGNAL(clicked(const QModelIndex &)), _ptm_proxy_model_p, SLOT(onTableClicked(const QModelIndex &)));
- connect (this, SIGNAL(requestPeptideDetailView(PeptideMatch *)), _p_ptm_island_list_window->getProjectWindowP(),SLOT(doViewPeptideDetail(PeptideMatch *)));
+ // connect (_project_window,
+ // SIGNAL(identificationPtmGroupGrouped(IdentificationGroup *)),
+ // this,SLOT(doIdentificationPtmGroupGrouped(IdentificationGroup *))); connect
+ // (_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)),
+ // this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
+ connect(ui->ptm_peptide_tableview, SIGNAL(clicked(const QModelIndex &)),
+ _ptm_proxy_model_p, SLOT(onTableClicked(const QModelIndex &)));
+ connect(this, SIGNAL(requestPeptideDetailView(PeptideMatch *)),
+ _p_ptm_island_list_window->getProjectWindowP(),
+ SLOT(doViewPeptideDetail(PeptideMatch *)));
#endif
}
-PtmPeptideListWindow::~PtmPeptideListWindow() {
+PtmPeptideListWindow::~PtmPeptideListWindow()
+{
}
-void PtmPeptideListWindow::setPtmIsland(PtmIsland * p_ptm_island) {
- _p_ptm_island = p_ptm_island;
- _ptm_table_model_p->setPtmIsland(_p_ptm_island_list_window->getIdentificationGroup()->getPtmGroupingExperiment(), _p_ptm_island);
+void
+PtmPeptideListWindow::setPtmIsland(PtmIsland *p_ptm_island)
+{
+ _p_ptm_island = p_ptm_island;
+ _ptm_table_model_p->setPtmIsland(
+ _p_ptm_island_list_window->getIdentificationGroup()
+ ->getPtmGroupingExperiment(),
+ _p_ptm_island);
}
-void PtmPeptideListWindow::askPeptideDetailView(PeptideEvidence * p_peptide_evidence) {
- qDebug() << "PtmPeptideListWindow::askPeptideDetailView begin " << p_peptide_evidence;
- //PeptideMatch peptide_match(* p_peptide_match);
- //qDebug() << "PtmPeptideListWindow::askPeptideDetailView begin " << peptide_match.getPeptideEvidence();
- emit requestPeptideDetailView(p_peptide_evidence);
- qDebug() << "PtmPeptideListWindow::askPeptideDetailView end";
- //updateStatusBar();
+void
+PtmPeptideListWindow::askPeptideDetailView(PeptideEvidence *p_peptide_evidence)
+{
+ qDebug() << "PtmPeptideListWindow::askPeptideDetailView begin "
+ << p_peptide_evidence;
+ // PeptideMatch peptide_match(* p_peptide_match);
+ // qDebug() << "PtmPeptideListWindow::askPeptideDetailView begin " <<
+ // peptide_match.getPeptideEvidence();
+ emit requestPeptideDetailView(p_peptide_evidence);
+ qDebug() << "PtmPeptideListWindow::askPeptideDetailView end";
+ // updateStatusBar();
}
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
index b467c3aea7fa2198f5302d2b799daf62d72578e5..d49489ef74f2197e0e22c0dca384ecd5e8b6046c 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMPEPTIDELISTWINDOW_H
#define PTMPEPTIDELISTWINDOW_H
@@ -37,32 +38,32 @@
class PtmIslandListWindow;
-namespace Ui {
-class PtmPeptideListWindow;
+namespace Ui
+{
+ class PtmPeptideListWindow;
}
-class PtmPeptideListWindow: public QMainWindow {
- Q_OBJECT
-public:
+class PtmPeptideListWindow : public QMainWindow
+{
+ Q_OBJECT
+ public:
+ explicit PtmPeptideListWindow(PtmIslandListWindow *parent = 0);
+ ~PtmPeptideListWindow();
+ void setPtmIsland(PtmIsland *p_ptm_island);
+ void askPeptideDetailView(PeptideEvidence *p_peptide_evidence);
- explicit PtmPeptideListWindow(PtmIslandListWindow * parent = 0);
- ~PtmPeptideListWindow();
- void setPtmIsland(PtmIsland * p_ptm_island);
- void askPeptideDetailView(PeptideEvidence * p_peptide_evidence);
-
-signals:
- void requestPeptideDetailView(PeptideEvidence * p_peptide_evidence);
+ signals:
+ void requestPeptideDetailView(PeptideEvidence *p_peptide_evidence);
-
-private:
- PtmIsland * _p_ptm_island=nullptr;
- Ui::PtmPeptideListWindow *ui;
- PtmPeptideTableModel * _ptm_table_model_p = nullptr;
- PtmPeptideTableProxyModel * _ptm_proxy_model_p = nullptr;
- PtmIslandListWindow * _p_ptm_island_list_window;
- QMenu * _p_context_menu = nullptr;
+ private:
+ PtmIsland *_p_ptm_island = nullptr;
+ Ui::PtmPeptideListWindow *ui;
+ PtmPeptideTableModel *_ptm_table_model_p = nullptr;
+ PtmPeptideTableProxyModel *_ptm_proxy_model_p = nullptr;
+ PtmIslandListWindow *_p_ptm_island_list_window;
+ QMenu *_p_context_menu = nullptr;
};
#endif // PTMPEPTIDELISTWINDOW_H
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
index 20a4f59fa8703b267eee86443f97c975533322f7..ca333c6a2eb8909b7351cb914800d21ba344f689 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
@@ -5,262 +5,358 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmpeptidetablemodel.h"
#include "ptmpeptidelistwindow.h"
#include <QDebug>
#include <QStringList>
-PtmPeptideTableModel::PtmPeptideTableModel(PtmPeptideListWindow * p_ptm_peptide_list_window) {
+PtmPeptideTableModel::PtmPeptideTableModel(
+ PtmPeptideListWindow *p_ptm_peptide_list_window)
+{
}
-PtmPeptideTableModel::~PtmPeptideTableModel() {
+PtmPeptideTableModel::~PtmPeptideTableModel()
+{
}
- const PtmGroupingExperiment * PtmPeptideTableModel::getPtmGroupingExperiment() const {
- return _p_ptm_grouping_experiment;
- }
-const std::vector<PtmSampleScanSp> & PtmPeptideTableModel::getPtmSampleScanSpList() const {
- return _ptm_sample_scan_list;
+const PtmGroupingExperiment *
+PtmPeptideTableModel::getPtmGroupingExperiment() const
+{
+ return _p_ptm_grouping_experiment;
+}
+const std::vector<PtmSampleScanSp> &
+PtmPeptideTableModel::getPtmSampleScanSpList() const
+{
+ return _ptm_sample_scan_list;
}
-const QString PtmPeptideTableModel::getTitle(PtmPeptideListColumn column) {
- qDebug() << "PtmPeptideTableModel::getTitle begin ";
- return PtmPeptideTableModel::getTitle((std::int8_t) column);
- //qDebug() << "ProteinTableModel::getTitle end ";
+const QString
+PtmPeptideTableModel::getTitle(PtmPeptideListColumn column)
+{
+ qDebug() << "PtmPeptideTableModel::getTitle begin ";
+ return PtmPeptideTableModel::getTitle((std::int8_t)column);
+ // qDebug() << "ProteinTableModel::getTitle end ";
}
-const QString PtmPeptideTableModel::getDescription(PtmPeptideListColumn column) {
- qDebug() << "PtmPeptideTableModel::columnCount begin ";
- return PtmPeptideTableModel::getDescription((std::int8_t) column);
- //qDebug() << "ProteinTableModel::columnCount end ";
+const QString
+PtmPeptideTableModel::getDescription(PtmPeptideListColumn column)
+{
+ qDebug() << "PtmPeptideTableModel::columnCount begin ";
+ return PtmPeptideTableModel::getDescription((std::int8_t)column);
+ // qDebug() << "ProteinTableModel::columnCount end ";
}
-const QString PtmPeptideTableModel::getTitle(std::int8_t column) {
- switch (column) {
+const QString
+PtmPeptideTableModel::getTitle(std::int8_t column)
+{
+ switch(column)
+ {
- case (std::int8_t) PtmPeptideListColumn::peptide_ptm_grouping_id:
+ case(std::int8_t)PtmPeptideListColumn::peptide_ptm_grouping_id:
return "peptide ID";
break;
- case (std::int8_t) PtmPeptideListColumn::sample:
+ case(std::int8_t)PtmPeptideListColumn::sample:
return "sample";
break;
- case (std::int8_t) PtmPeptideListColumn::scan:
+ case(std::int8_t)PtmPeptideListColumn::scan:
return "scan";
break;
- case (std::int8_t) PtmPeptideListColumn::rt:
+ case(std::int8_t)PtmPeptideListColumn::rt:
return "RT";
break;
- case (std::int8_t) PtmPeptideListColumn::charge:
+ case(std::int8_t)PtmPeptideListColumn::charge:
return "charge";
break;
- case (std::int8_t) PtmPeptideListColumn::sequence:
+ case(std::int8_t)PtmPeptideListColumn::sequence:
return "sequence";
break;
- case (std::int8_t) PtmPeptideListColumn::modifs:
+ case(std::int8_t)PtmPeptideListColumn::modifs:
return "modifs";
break;
- case (std::int8_t) PtmPeptideListColumn::start:
+ case(std::int8_t)PtmPeptideListColumn::start:
return "start";
break;
- case (std::int8_t) PtmPeptideListColumn::length:
+ case(std::int8_t)PtmPeptideListColumn::length:
return "length";
break;
- case (std::int8_t) PtmPeptideListColumn::bestEvalue:
+ case(std::int8_t)PtmPeptideListColumn::bestEvalue:
return "top Evalue";
break;
- case (std::int8_t) PtmPeptideListColumn::theoretical_mhplus:
+ case(std::int8_t)PtmPeptideListColumn::theoretical_mhplus:
return "theoretical MH+";
break;
- case (std::int8_t) PtmPeptideListColumn::delta_mhplus:
+ case(std::int8_t)PtmPeptideListColumn::delta_mhplus:
return "delta MH+";
break;
- case (std::int8_t) PtmPeptideListColumn::besthyperscore:
+ case(std::int8_t)PtmPeptideListColumn::besthyperscore:
return "top hyperscore";
- case (std::int8_t) PtmPeptideListColumn::bestposition:
+ case(std::int8_t)PtmPeptideListColumn::bestposition:
return "top PTM positions";
- case (std::int8_t) PtmPeptideListColumn::allobservedposition:
+ case(std::int8_t)PtmPeptideListColumn::allobservedposition:
return "observed PTM positions";
-
}
- return "";
+ return "";
}
-const QString PtmPeptideTableModel::getDescription(std::int8_t column) {
- switch (column) {
+const QString
+PtmPeptideTableModel::getDescription(std::int8_t column)
+{
+ switch(column)
+ {
- case (std::int8_t) PtmPeptideListColumn::peptide_ptm_grouping_id:
- return "unique PTM peptide identifier within this PTM grouping experiment";
+ case(std::int8_t)PtmPeptideListColumn::peptide_ptm_grouping_id:
+ return "unique PTM peptide identifier within this PTM grouping "
+ "experiment";
break;
- case (std::int8_t) PtmPeptideListColumn::sample:
+ case(std::int8_t)PtmPeptideListColumn::sample:
return "MS sample name";
break;
- case (std::int8_t) PtmPeptideListColumn::scan:
+ case(std::int8_t)PtmPeptideListColumn::scan:
return "scan number";
break;
- case (std::int8_t) PtmPeptideListColumn::rt:
+ case(std::int8_t)PtmPeptideListColumn::rt:
return "retention time in seconds";
break;
- case (std::int8_t) PtmPeptideListColumn::charge:
+ case(std::int8_t)PtmPeptideListColumn::charge:
return "peptide charge";
break;
- case (std::int8_t) PtmPeptideListColumn::sequence:
+ case(std::int8_t)PtmPeptideListColumn::sequence:
return "peptide sequence";
break;
- case (std::int8_t) PtmPeptideListColumn::modifs:
+ case(std::int8_t)PtmPeptideListColumn::modifs:
return "peptide modifications";
break;
- case (std::int8_t) PtmPeptideListColumn::start:
+ case(std::int8_t)PtmPeptideListColumn::start:
return "peptide start position on protein";
break;
- case (std::int8_t) PtmPeptideListColumn::length:
+ case(std::int8_t)PtmPeptideListColumn::length:
return "peptide length";
break;
- case (std::int8_t) PtmPeptideListColumn::bestEvalue:
+ case(std::int8_t)PtmPeptideListColumn::bestEvalue:
return "best peptide Evalue";
break;
- case (std::int8_t) PtmPeptideListColumn::theoretical_mhplus:
+ case(std::int8_t)PtmPeptideListColumn::theoretical_mhplus:
return "peptide theoretical MH+";
break;
- case (std::int8_t) PtmPeptideListColumn::delta_mhplus:
- return "peptide mass difference between observed mass and theoretical mass";
+ case(std::int8_t)PtmPeptideListColumn::delta_mhplus:
+ return "peptide mass difference between observed mass and theoretical "
+ "mass";
break;
- case (std::int8_t) PtmPeptideListColumn::besthyperscore:
+ case(std::int8_t)PtmPeptideListColumn::besthyperscore:
return "best X!Tandem hyperscore";
- case (std::int8_t) PtmPeptideListColumn::bestposition:
- return "PTM positions of the top identified peptide (best Evalue) for this scan";
- case (std::int8_t) PtmPeptideListColumn::allobservedposition:
+ case(std::int8_t)PtmPeptideListColumn::bestposition:
+ return "PTM positions of the top identified peptide (best Evalue) for "
+ "this scan";
+ case(std::int8_t)PtmPeptideListColumn::allobservedposition:
return "all observed PTM positions for the same scan";
-
}
- return "";
+ return "";
}
-int PtmPeptideTableModel::rowCount(const QModelIndex &parent ) const {
- qDebug() << "PtmPeptideTableModel::rowCount begin ";
- return _ptm_sample_scan_list.size();
+int
+PtmPeptideTableModel::rowCount(const QModelIndex &parent) const
+{
+ qDebug() << "PtmPeptideTableModel::rowCount begin ";
+ return _ptm_sample_scan_list.size();
}
-int PtmPeptideTableModel::columnCount(const QModelIndex &parent ) const {
- //qDebug() << "ProteinTableModel::columnCount begin ";
- return 15;
+int
+PtmPeptideTableModel::columnCount(const QModelIndex &parent) const
+{
+ // qDebug() << "ProteinTableModel::columnCount begin ";
+ return 15;
}
-QVariant PtmPeptideTableModel::headerData(int section, Qt::Orientation orientation, int role) const
+QVariant
+PtmPeptideTableModel::headerData(int section, Qt::Orientation orientation,
+ int role) const
{
- if (orientation == Qt::Horizontal)
+ if(orientation == Qt::Horizontal)
{
- switch (role) {
- case Qt::DisplayRole :
+ switch(role)
+ {
+ case Qt::DisplayRole:
return QVariant(getTitle(section));
break;
- case Qt::ToolTipRole :
- return QVariant(getDescription(section));
+ case Qt::ToolTipRole:
+ return QVariant(getDescription(section));
break;
-
}
}
- return QVariant();
+ return QVariant();
}
-QVariant PtmPeptideTableModel::data(const QModelIndex &index, int role ) const {
- // generate a log message when this method gets called
- int row = index.row();
- int col = index.column();
- QStringList position_list;
-
- if (row >= _ptm_sample_scan_list.size()) return QVariant();
- switch(role) {
- case Qt::DisplayRole:
- switch (col) {
+QVariant
+PtmPeptideTableModel::data(const QModelIndex &index, int role) const
+{
+ // generate a log message when this method gets called
+ int row = index.row();
+ int col = index.column();
+ QStringList position_list;
- case (std::int8_t)PtmPeptideListColumn::peptide_ptm_grouping_id:
- return QVariant (_ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getGrpPeptideSp().get()->getGroupingId());
- break;
- case (std::int8_t)PtmPeptideListColumn::sample:
- return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getIdentificationDataSource()->getSampleName();
- break;
- case (std::int8_t)PtmPeptideListColumn::scan:
- return QVariant ((quint32) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getScan());
- break;
- case (std::int8_t)PtmPeptideListColumn::rt:
- return QVariant ((qreal) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getRetentionTime());
- break;
- case (std::int8_t)PtmPeptideListColumn::charge:
- return QVariant ((quint32) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getCharge());
- break;
- case (std::int8_t)PtmPeptideListColumn::sequence:
- return QVariant::fromValue( _ptm_sample_scan_list.at(row).get());
- break;
- case (std::int8_t)PtmPeptideListColumn::modifs:
- return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getPeptideXtpSp().get()->getModifString();
- break;
- case (std::int8_t)PtmPeptideListColumn::start:
- return QVariant((quint32) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getStart()+1);
- break;
- case (std::int8_t)PtmPeptideListColumn::length:
- return QVariant((quint32) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getPeptideXtpSp().get()->size());
- break;
- case (std::int8_t)PtmPeptideListColumn::bestEvalue:
- return QVariant((qreal) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getEvalue());
- break;
- case (std::int8_t)PtmPeptideListColumn::theoretical_mhplus:
- return QVariant((qreal) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getPeptideXtpSp().get()->getMz(1));
- break;
- case (std::int8_t)PtmPeptideListColumn::delta_mhplus:
- return QVariant((qreal) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getDeltaMass());
- break;
- case (std::int8_t)PtmPeptideListColumn::besthyperscore:
- return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getParam(PeptideEvidenceParam::tandem_hyperscore);
- break;
- case (std::int8_t)PtmPeptideListColumn::bestposition:
- for (unsigned int position :_ptm_sample_scan_list.at(row).get()->getBestPtmPositionList(_p_ptm_grouping_experiment)) {
- position_list << QString("%1").arg(position+1);
+ if(row >= _ptm_sample_scan_list.size())
+ return QVariant();
+ switch(role)
+ {
+ case Qt::DisplayRole:
+ switch(col)
+ {
+
+ case(std::int8_t)PtmPeptideListColumn::peptide_ptm_grouping_id:
+ return QVariant(_ptm_sample_scan_list.at(row)
+ .get()
+ ->getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getGrpPeptideSp()
+ .get()
+ ->getGroupingId());
+ break;
+ case(std::int8_t)PtmPeptideListColumn::sample:
+ return _ptm_sample_scan_list.at(row)
+ .get()
+ ->getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getIdentificationDataSource()
+ ->getSampleName();
+ break;
+ case(std::int8_t)PtmPeptideListColumn::scan:
+ return QVariant((quint32)_ptm_sample_scan_list.at(row)
+ .get()
+ ->getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getScan());
+ break;
+ case(std::int8_t)PtmPeptideListColumn::rt:
+ return QVariant((qreal)_ptm_sample_scan_list.at(row)
+ .get()
+ ->getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getRetentionTime());
+ break;
+ case(std::int8_t)PtmPeptideListColumn::charge:
+ return QVariant((quint32)_ptm_sample_scan_list.at(row)
+ .get()
+ ->getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getCharge());
+ break;
+ case(std::int8_t)PtmPeptideListColumn::sequence:
+ return QVariant::fromValue(_ptm_sample_scan_list.at(row).get());
+ break;
+ case(std::int8_t)PtmPeptideListColumn::modifs:
+ return _ptm_sample_scan_list.at(row)
+ .get()
+ ->getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getModifString();
+ break;
+ case(std::int8_t)PtmPeptideListColumn::start:
+ return QVariant((quint32)_ptm_sample_scan_list.at(row)
+ .get()
+ ->getRepresentativePeptideMatch()
+ .getStart() +
+ 1);
+ break;
+ case(std::int8_t)PtmPeptideListColumn::length:
+ return QVariant((quint32)_ptm_sample_scan_list.at(row)
+ .get()
+ ->getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->size());
+ break;
+ case(std::int8_t)PtmPeptideListColumn::bestEvalue:
+ return QVariant((qreal)_ptm_sample_scan_list.at(row)
+ .get()
+ ->getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getEvalue());
+ break;
+ case(std::int8_t)PtmPeptideListColumn::theoretical_mhplus:
+ return QVariant((qreal)_ptm_sample_scan_list.at(row)
+ .get()
+ ->getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getMz(1));
+ break;
+ case(std::int8_t)PtmPeptideListColumn::delta_mhplus:
+ return QVariant((qreal)_ptm_sample_scan_list.at(row)
+ .get()
+ ->getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getDeltaMass());
+ break;
+ case(std::int8_t)PtmPeptideListColumn::besthyperscore:
+ return _ptm_sample_scan_list.at(row)
+ .get()
+ ->getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::tandem_hyperscore);
+ break;
+ case(std::int8_t)PtmPeptideListColumn::bestposition:
+ for(unsigned int position :
+ _ptm_sample_scan_list.at(row).get()->getBestPtmPositionList(
+ _p_ptm_grouping_experiment))
+ {
+ position_list << QString("%1").arg(position + 1);
}
- return QVariant(position_list.join(" "));
- break;
- case (std::int8_t)PtmPeptideListColumn::allobservedposition:
- //return _ptm_sample_scan_list.at(row).get()->getObservedPtmPositionList();
- for (unsigned int position :_ptm_sample_scan_list.at(row).get()->getObservedPtmPositionList(_p_ptm_grouping_experiment)) {
- position_list << QString("%1").arg(position+1);
+ return QVariant(position_list.join(" "));
+ break;
+ case(std::int8_t)PtmPeptideListColumn::allobservedposition:
+ // return
+ // _ptm_sample_scan_list.at(row).get()->getObservedPtmPositionList();
+ for(unsigned int position :
+ _ptm_sample_scan_list.at(row)
+ .get()
+ ->getObservedPtmPositionList(_p_ptm_grouping_experiment))
+ {
+ position_list << QString("%1").arg(position + 1);
}
- return QVariant(position_list.join(" "));
- break;
-
- }
+ return QVariant(position_list.join(" "));
+ break;
+ }
}
- return QVariant();
+ return QVariant();
}
-void PtmPeptideTableModel::setPtmIsland(const PtmGroupingExperiment * p_ptm_grouping_experiment, PtmIsland * ptm_island) {
- qDebug() << "tmPeptideTableModel::setPtmIsland begin ";
-
- beginResetModel();
- _p_ptm_grouping_experiment = p_ptm_grouping_experiment;
- _p_ptm_island = ptm_island;
-_ptm_sample_scan_list = ptm_island->getPtmSampleScanSpList();
- //emit headerDataChanged(Qt::Horizontal, 0,11);
- //refresh();
- qDebug() << "tmPeptideTableModel::setPtmIsland end ";
- endResetModel();
-
- //this->_p_ptm_island_list_window->resizeColumnsToContents();
+void
+PtmPeptideTableModel::setPtmIsland(
+ const PtmGroupingExperiment *p_ptm_grouping_experiment, PtmIsland *ptm_island)
+{
+ qDebug() << "tmPeptideTableModel::setPtmIsland begin ";
+
+ beginResetModel();
+ _p_ptm_grouping_experiment = p_ptm_grouping_experiment;
+ _p_ptm_island = ptm_island;
+ _ptm_sample_scan_list = ptm_island->getPtmSampleScanSpList();
+ // emit headerDataChanged(Qt::Horizontal, 0,11);
+ // refresh();
+ qDebug() << "tmPeptideTableModel::setPtmIsland end ";
+ endResetModel();
+ // this->_p_ptm_island_list_window->resizeColumnsToContents();
}
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
index cbd8344d0d42732629282b2c032e6b371a86ab93..76c02ce65b2f5ac008d2fe0dbb74427e876171c1 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
@@ -5,26 +5,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMPEPTIDETABLEMODEL_H
#define PTMPEPTIDETABLEMODEL_H
@@ -34,58 +35,64 @@
#include "../../grouping/ptm/ptmisland.h"
-
-/** \def PtmPeptideListColumn list of available fields to display in ptm peptide list
+/** \def PtmPeptideListColumn list of available fields to display in ptm peptide
+ * list
*
*/
-enum class PtmPeptideListColumn: std::int8_t {
- peptide_ptm_grouping_id=0, ///< peptide PTM grouping id
- sample=1,
- scan=2,
- rt=3,
- charge=4,
- sequence=5,
- modifs=6,
- start=7,
- length=8,
- bestEvalue=9,
- theoretical_mhplus=10,
- delta_mhplus=11,
- besthyperscore=12,
- bestposition=13,
- allobservedposition=14
+enum class PtmPeptideListColumn : std::int8_t
+{
+ peptide_ptm_grouping_id = 0, ///< peptide PTM grouping id
+ sample = 1,
+ scan = 2,
+ rt = 3,
+ charge = 4,
+ sequence = 5,
+ modifs = 6,
+ start = 7,
+ length = 8,
+ bestEvalue = 9,
+ theoretical_mhplus = 10,
+ delta_mhplus = 11,
+ besthyperscore = 12,
+ bestposition = 13,
+ allobservedposition = 14
};
class PtmPeptideListWindow;
-class PtmPeptideTableModel: public QAbstractTableModel
+class PtmPeptideTableModel : public QAbstractTableModel
{
- Q_OBJECT
-public:
- PtmPeptideTableModel(PtmPeptideListWindow * p_ptm_peptide_list_window);
- virtual int rowCount(const QModelIndex &parent = QModelIndex()) const override;
- virtual int columnCount(const QModelIndex &parent = QModelIndex()) const override;
- virtual QVariant headerData(int section, Qt::Orientation orientation, int role) const override;
- virtual QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override;
- static const QString getTitle(PtmPeptideListColumn column);
- static const QString getDescription(PtmPeptideListColumn column);
+ Q_OBJECT
+ public:
+ PtmPeptideTableModel(PtmPeptideListWindow *p_ptm_peptide_list_window);
+ virtual int
+ rowCount(const QModelIndex &parent = QModelIndex()) const override;
+ virtual int
+ columnCount(const QModelIndex &parent = QModelIndex()) const override;
+ virtual QVariant headerData(int section, Qt::Orientation orientation,
+ int role) const override;
+ virtual QVariant data(const QModelIndex &index,
+ int role = Qt::DisplayRole) const override;
+ static const QString getTitle(PtmPeptideListColumn column);
+ static const QString getDescription(PtmPeptideListColumn column);
+
+ ~PtmPeptideTableModel();
+ void setPtmIsland(const PtmGroupingExperiment *p_ptm_grouping_experiment,
+ PtmIsland *ptm_island);
+
+ const std::vector<PtmSampleScanSp> &getPtmSampleScanSpList() const;
+ const PtmGroupingExperiment *getPtmGroupingExperiment() const;
+
+ private:
+ static const QString getTitle(std::int8_t column);
+ static const QString getDescription(std::int8_t column);
- ~PtmPeptideTableModel();
- void setPtmIsland(const PtmGroupingExperiment * p_ptm_grouping_experiment, PtmIsland * ptm_island);
-
- const std::vector<PtmSampleScanSp> & getPtmSampleScanSpList() const;
- const PtmGroupingExperiment * getPtmGroupingExperiment() const;
-
-private :
- static const QString getTitle(std::int8_t column);
- static const QString getDescription(std::int8_t column);
-
-private:
- std::vector<PtmSampleScanSp> _ptm_sample_scan_list;
- const PtmIsland * _p_ptm_island;
- const PtmGroupingExperiment * _p_ptm_grouping_experiment;
+ private:
+ std::vector<PtmSampleScanSp> _ptm_sample_scan_list;
+ const PtmIsland *_p_ptm_island;
+ const PtmGroupingExperiment *_p_ptm_grouping_experiment;
};
#endif // PTMPEPTIDETABLEMODEL_H
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
index 2110b928879c2f6f99e252d80c126ac5283defd0..2d4e4368cc6dbb01a64520034d3ba5fc21c0356a 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
@@ -5,26 +5,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmpeptidetableproxymodel.h"
#include "ptmpeptidetablemodel.h"
@@ -32,135 +33,197 @@
#include "../../grouping/ptm/ptmgroupingexperiment.h"
#include <QTextDocument>
-PtmPeptideMenuQicon::PtmPeptideMenuQicon(const PtmGroupingExperiment * p_ptm_grouping_experiment, const PtmSampleScan * p_ptm_sample, const PeptideMatch * p_peptide_match):QIcon(), _peptide_match(*p_peptide_match) {
- _p_ptm_sample_scan = p_ptm_sample;
- _p_ptm_grouping_experiment = p_ptm_grouping_experiment;
+PtmPeptideMenuQicon::PtmPeptideMenuQicon(
+ const PtmGroupingExperiment *p_ptm_grouping_experiment,
+ const PtmSampleScan *p_ptm_sample, const PeptideMatch *p_peptide_match)
+ : QIcon(), _peptide_match(*p_peptide_match)
+{
+ _p_ptm_sample_scan = p_ptm_sample;
+ _p_ptm_grouping_experiment = p_ptm_grouping_experiment;
}
-PtmPeptideMenuQicon::~PtmPeptideMenuQicon( ) {
+PtmPeptideMenuQicon::~PtmPeptideMenuQicon()
+{
}
-void PtmPeptideMenuQicon::paint(QPainter *painter, const QRect &rect, Qt::Alignment alignment, Mode mode, State state) const
+void
+PtmPeptideMenuQicon::paint(QPainter *painter, const QRect &rect,
+ Qt::Alignment alignment, Mode mode,
+ State state) const
{
- // if (option.state & QStyle::State_Selected)
- // painter->fillRect(option.rect, option.palette.highlight());
- QTextDocument document;
- document.setDocumentMargin(2);
- document.setHtml(_p_ptm_sample_scan->getHtmlSequence(_p_ptm_grouping_experiment));
- //painter->translate(option.rect.topLeft());
- document.drawContents(painter);
- //painter->translate(-option.rect.topLeft());
-
- //edit_seq.render(painter);
- //edit..paint(painter, option.rect, option.palette,
- // StarRating::ReadOnly);
+ // if (option.state & QStyle::State_Selected)
+ // painter->fillRect(option.rect, option.palette.highlight());
+ QTextDocument document;
+ document.setDocumentMargin(2);
+ document.setHtml(
+ _p_ptm_sample_scan->getHtmlSequence(_p_ptm_grouping_experiment));
+ // painter->translate(option.rect.topLeft());
+ document.drawContents(painter);
+ // painter->translate(-option.rect.topLeft());
+
+ // edit_seq.render(painter);
+ // edit..paint(painter, option.rect, option.palette,
+ // StarRating::ReadOnly);
}
-PtmPeptideMenuQaction::PtmPeptideMenuQaction(PtmPeptideTableProxyModel * parent, const PtmGroupingExperiment * p_ptm_grouping_experiment, const PtmSampleScan * p_ptm_sample, PeptideMatch * p_peptide_match):QAction(parent) {
-
- _p_ptm_peptide_table_proxy_model = parent;
- _peptide_match = *p_peptide_match;
- this->setIcon(PtmPeptideMenuQicon(p_ptm_grouping_experiment, p_ptm_sample, p_peptide_match));
- //this->setText(p_peptide_match->getPeptideXtpSp().get()->getSequence());
+PtmPeptideMenuQaction::PtmPeptideMenuQaction(
+ PtmPeptideTableProxyModel *parent,
+ const PtmGroupingExperiment *p_ptm_grouping_experiment,
+ const PtmSampleScan *p_ptm_sample, PeptideMatch *p_peptide_match)
+ : QAction(parent)
+{
- QStringList position_list;
- for (unsigned int position : p_ptm_grouping_experiment->getPtmPositions(*p_peptide_match)) {
- position_list << QString("%1").arg(position+1);
+ _p_ptm_peptide_table_proxy_model = parent;
+ _peptide_match = *p_peptide_match;
+ this->setIcon(PtmPeptideMenuQicon(p_ptm_grouping_experiment, p_ptm_sample,
+ p_peptide_match));
+ // this->setText(p_peptide_match->getPeptideXtpSp().get()->getSequence());
+
+ QStringList position_list;
+ for(unsigned int position :
+ p_ptm_grouping_experiment->getPtmPositions(*p_peptide_match))
+ {
+ position_list << QString("%1").arg(position + 1);
}
- this->setText(QString("%1 (%2)").arg(p_peptide_match->getPeptideEvidence()->getPeptideXtpSp().get()->toString()).arg(position_list.join(" ")));
- //evalue_action.setChecked(_display_evalue);
- //connect(p_action, SIGNAL(toggled(bool)), this, SLOT(showEvalueColumn(bool)));
+ this->setText(QString("%1 (%2)")
+ .arg(p_peptide_match->getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->toString())
+ .arg(position_list.join(" ")));
+ // evalue_action.setChecked(_display_evalue);
+ // connect(p_action, SIGNAL(toggled(bool)), this,
+ // SLOT(showEvalueColumn(bool)));
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect (this, &PtmPeptideMenuQaction::triggered, this,&PtmPeptideMenuQaction::doTriggered);
+ // Qt5 code
+ connect(this, &PtmPeptideMenuQaction::triggered, this,
+ &PtmPeptideMenuQaction::doTriggered);
#else
-// Qt4 code
- connect (this, SIGNAL(triggered(bool)), this,SLOT(doTriggered(bool)));
+ // Qt4 code
+ connect(this, SIGNAL(triggered(bool)), this, SLOT(doTriggered(bool)));
#endif
}
-void PtmPeptideMenuQaction::doTriggered(bool triggered) {
- PeptideEvidence * p_peptide_evidence = _peptide_match.getPeptideEvidence();
- qDebug() << "PtmPeptideMenuQaction::doTriggered begin" << _peptide_match.getPeptideEvidence();
- qDebug() << "PtmPeptideMenuQaction::doTriggered begin 2 " << p_peptide_evidence;
- qDebug() << "PtmPeptideMenuQaction::doTriggered begin 3 " << p_peptide_evidence->getPeptideXtpSp().get()->toString();
- _p_ptm_peptide_table_proxy_model->getPtmPeptideListWindowP()->askPeptideDetailView(p_peptide_evidence);
+void
+PtmPeptideMenuQaction::doTriggered(bool triggered)
+{
+ PeptideEvidence *p_peptide_evidence = _peptide_match.getPeptideEvidence();
+ qDebug() << "PtmPeptideMenuQaction::doTriggered begin"
+ << _peptide_match.getPeptideEvidence();
+ qDebug() << "PtmPeptideMenuQaction::doTriggered begin 2 "
+ << p_peptide_evidence;
+ qDebug() << "PtmPeptideMenuQaction::doTriggered begin 3 "
+ << p_peptide_evidence->getPeptideXtpSp().get()->toString();
+ _p_ptm_peptide_table_proxy_model->getPtmPeptideListWindowP()
+ ->askPeptideDetailView(p_peptide_evidence);
}
PtmPeptideMenuQaction::~PtmPeptideMenuQaction()
{
- //if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
- qDebug() << "PtmPeptideMenuQaction::~PtmPeptideMenuQaction begin ";
-
+ // if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
+ qDebug() << "PtmPeptideMenuQaction::~PtmPeptideMenuQaction begin ";
}
-PtmPeptideTableProxyModel::PtmPeptideTableProxyModel(PtmPeptideListWindow * p_ptm_peptide_list_window, PtmPeptideTableModel* ptm_table_model_p)
+PtmPeptideTableProxyModel::PtmPeptideTableProxyModel(
+ PtmPeptideListWindow *p_ptm_peptide_list_window,
+ PtmPeptideTableModel *ptm_table_model_p)
{
- _p_ptm_peptide_list_window = p_ptm_peptide_list_window;
- _p_ptm_table_model = ptm_table_model_p;
+ _p_ptm_peptide_list_window = p_ptm_peptide_list_window;
+ _p_ptm_table_model = ptm_table_model_p;
}
PtmPeptideTableProxyModel::~PtmPeptideTableProxyModel()
{
-
}
-PtmPeptideListWindow * PtmPeptideTableProxyModel::getPtmPeptideListWindowP() {
- return _p_ptm_peptide_list_window;
+PtmPeptideListWindow *
+PtmPeptideTableProxyModel::getPtmPeptideListWindowP()
+{
+ return _p_ptm_peptide_list_window;
}
-bool PtmPeptideTableProxyModel::lessThan(const QModelIndex &left,
- const QModelIndex &right) const
+bool
+PtmPeptideTableProxyModel::lessThan(const QModelIndex &left,
+ const QModelIndex &right) const
{
- QVariant leftData = sourceModel()->data(left);
- QVariant rightData = sourceModel()->data(right);
-
- if (leftData.canConvert<PtmSampleScan *>()) {
- PtmSampleScan * p_ptm_sample_scan_left = qvariant_cast<PtmSampleScan *>(leftData);
- PtmSampleScan * p_ptm_sample_scan_right = qvariant_cast<PtmSampleScan *>(rightData);
- return p_ptm_sample_scan_left->getRepresentativePeptideMatch().getPeptideEvidence()->getPeptideXtpSp().get()->toAbsoluteString() < p_ptm_sample_scan_right->getRepresentativePeptideMatch().getPeptideEvidence()->getPeptideXtpSp().get()->toAbsoluteString();
- } else {
- return QSortFilterProxyModel::lessThan(left, right);
+ QVariant leftData = sourceModel()->data(left);
+ QVariant rightData = sourceModel()->data(right);
+
+ if(leftData.canConvert<PtmSampleScan *>())
+ {
+ PtmSampleScan *p_ptm_sample_scan_left =
+ qvariant_cast<PtmSampleScan *>(leftData);
+ PtmSampleScan *p_ptm_sample_scan_right =
+ qvariant_cast<PtmSampleScan *>(rightData);
+ return p_ptm_sample_scan_left->getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->toAbsoluteString() <
+ p_ptm_sample_scan_right->getRepresentativePeptideMatch()
+ .getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->toAbsoluteString();
+ }
+ else
+ {
+ return QSortFilterProxyModel::lessThan(left, right);
}
}
-void PtmPeptideTableProxyModel::showContextMenu(const QModelIndex &index) {
- if (_p_context_menu == nullptr) {
- _p_context_menu = new QMenu(tr("Context menu"));
+void
+PtmPeptideTableProxyModel::showContextMenu(const QModelIndex &index)
+{
+ if(_p_context_menu == nullptr)
+ {
+ _p_context_menu = new QMenu(tr("Context menu"));
}
- _p_context_menu->clear();
- QModelIndex source_index(this->mapToSource(index));
- int row = source_index.row();
- PtmSampleScanSp sp_ptm_sample_scan = _p_ptm_table_model->getPtmSampleScanSpList().at(row);
-
- PtmPeptideMenuQaction * p_action;
- for (auto p_peptide_match : sp_ptm_sample_scan.get()->getPeptideMatchList()) {
- p_action = new PtmPeptideMenuQaction(this, _p_ptm_table_model->getPtmGroupingExperiment(), sp_ptm_sample_scan.get(), &p_peptide_match);
- _p_context_menu->addAction(p_action);
+ _p_context_menu->clear();
+ QModelIndex source_index(this->mapToSource(index));
+ int row = source_index.row();
+ PtmSampleScanSp sp_ptm_sample_scan =
+ _p_ptm_table_model->getPtmSampleScanSpList().at(row);
+
+ PtmPeptideMenuQaction *p_action;
+ for(auto p_peptide_match : sp_ptm_sample_scan.get()->getPeptideMatchList())
+ {
+ p_action = new PtmPeptideMenuQaction(
+ this, _p_ptm_table_model->getPtmGroupingExperiment(),
+ sp_ptm_sample_scan.get(), &p_peptide_match);
+ _p_context_menu->addAction(p_action);
}
- _p_context_menu->exec(QCursor::pos());
+ _p_context_menu->exec(QCursor::pos());
- //_p_context_menu->exec(_p_ptm_peptide_list_window-> mapToGlobal(QCursor::pos()));
+ //_p_context_menu->exec(_p_ptm_peptide_list_window->
+ //mapToGlobal(QCursor::pos()));
- _p_context_menu->show();
+ _p_context_menu->show();
}
-void PtmPeptideTableProxyModel::onTableClicked(const QModelIndex &index)
+void
+PtmPeptideTableProxyModel::onTableClicked(const QModelIndex &index)
{
- qDebug() << "PtmPeptideTableProxyModel::onTableClicked begin " << index.row();
- qDebug() << "PtmPeptideTableProxyModel::onTableClicked begin " << this->mapToSource(index).row();
-
- //_protein_table_model_p->onTableClicked(this->mapToSource(index));
- QModelIndex source_index(this->mapToSource(index));
- int row = source_index.row();
- int col = source_index.column();
- PtmSampleScanSp sp_ptm_sample_scan = _p_ptm_table_model->getPtmSampleScanSpList().at(row);
-
- if (sp_ptm_sample_scan.get()->getPeptideMatchList().size() == 1) {
- _p_ptm_peptide_list_window->askPeptideDetailView(sp_ptm_sample_scan.get()->getPeptideMatchList().at(0).getPeptideEvidence());
+ qDebug() << "PtmPeptideTableProxyModel::onTableClicked begin " << index.row();
+ qDebug() << "PtmPeptideTableProxyModel::onTableClicked begin "
+ << this->mapToSource(index).row();
+
+ //_protein_table_model_p->onTableClicked(this->mapToSource(index));
+ QModelIndex source_index(this->mapToSource(index));
+ int row = source_index.row();
+ int col = source_index.column();
+ PtmSampleScanSp sp_ptm_sample_scan =
+ _p_ptm_table_model->getPtmSampleScanSpList().at(row);
+
+ if(sp_ptm_sample_scan.get()->getPeptideMatchList().size() == 1)
+ {
+ _p_ptm_peptide_list_window->askPeptideDetailView(sp_ptm_sample_scan.get()
+ ->getPeptideMatchList()
+ .at(0)
+ .getPeptideEvidence());
}
- else {
- this->showContextMenu(index);
+ else
+ {
+ this->showContextMenu(index);
}
- qDebug() << "PtmPeptideTableProxyModel::onTableClicked end " << index.row();
-
+ qDebug() << "PtmPeptideTableProxyModel::onTableClicked end " << index.row();
}
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
index 373ca4d30f17a0f3c7b89b85f1b6903a4b765305..3b458883bfd391828b05e20202daed9b4270f104 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
@@ -5,26 +5,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMPEPTIDETABLEPROXYMODEL_H
#define PTMPEPTIDETABLEPROXYMODEL_H
@@ -40,56 +41,65 @@ class PtmPeptideListWindow;
class PtmPeptideTableModel;
class PtmPeptideTableProxyModel;
-class PtmPeptideMenuQicon: public QIcon {
-public:
-
- explicit PtmPeptideMenuQicon(const PtmGroupingExperiment * p_ptm_grouping_experiment, const PtmSampleScan * p_ptm_sample, const PeptideMatch * p_peptide_match);
- ~PtmPeptideMenuQicon();
-
- void paint(QPainter *painter, const QRect &rect, Qt::Alignment alignment = Qt::AlignCenter, Mode mode = Normal, State state = Off) const;
-
-private:
- const PtmSampleScan * _p_ptm_sample_scan;
- const PeptideMatch _peptide_match;
- const PtmGroupingExperiment * _p_ptm_grouping_experiment;
+class PtmPeptideMenuQicon : public QIcon
+{
+ public:
+ explicit PtmPeptideMenuQicon(
+ const PtmGroupingExperiment *p_ptm_grouping_experiment,
+ const PtmSampleScan *p_ptm_sample, const PeptideMatch *p_peptide_match);
+ ~PtmPeptideMenuQicon();
+
+ void paint(QPainter *painter, const QRect &rect,
+ Qt::Alignment alignment = Qt::AlignCenter, Mode mode = Normal,
+ State state = Off) const;
+
+ private:
+ const PtmSampleScan *_p_ptm_sample_scan;
+ const PeptideMatch _peptide_match;
+ const PtmGroupingExperiment *_p_ptm_grouping_experiment;
};
-class PtmPeptideMenuQaction: public QAction {
- Q_OBJECT
-public:
-
- explicit PtmPeptideMenuQaction(PtmPeptideTableProxyModel * parent, const PtmGroupingExperiment * p_ptm_grouping_experiment, const PtmSampleScan * p_ptm_sample, PeptideMatch * p_peptide_match);
- ~PtmPeptideMenuQaction();
-
-public slots:
- void doTriggered(bool triggered);
-
-private:
- PeptideMatch _peptide_match;
- PtmPeptideTableProxyModel * _p_ptm_peptide_table_proxy_model;
+class PtmPeptideMenuQaction : public QAction
+{
+ Q_OBJECT
+ public:
+ explicit PtmPeptideMenuQaction(
+ PtmPeptideTableProxyModel *parent,
+ const PtmGroupingExperiment *p_ptm_grouping_experiment,
+ const PtmSampleScan *p_ptm_sample, PeptideMatch *p_peptide_match);
+ ~PtmPeptideMenuQaction();
+
+ public slots:
+ void doTriggered(bool triggered);
+
+ private:
+ PeptideMatch _peptide_match;
+ PtmPeptideTableProxyModel *_p_ptm_peptide_table_proxy_model;
};
-class PtmPeptideTableProxyModel: public QSortFilterProxyModel
+class PtmPeptideTableProxyModel : public QSortFilterProxyModel
{
- Q_OBJECT
-public:
- PtmPeptideTableProxyModel(PtmPeptideListWindow * p_ptm_peptide_list_window, PtmPeptideTableModel* ptm_table_model_p);
- ~PtmPeptideTableProxyModel();
-
- PtmPeptideListWindow * getPtmPeptideListWindowP();
-
-public slots:
- void onTableClicked(const QModelIndex &index);
-
-protected:
- bool lessThan(const QModelIndex &left, const QModelIndex &right) const override;
- void showContextMenu(const QModelIndex &index);
-
-private:
- PtmPeptideListWindow * _p_ptm_peptide_list_window;
- PtmPeptideTableModel* _p_ptm_table_model;
- QMenu * _p_context_menu = nullptr;
+ Q_OBJECT
+ public:
+ PtmPeptideTableProxyModel(PtmPeptideListWindow *p_ptm_peptide_list_window,
+ PtmPeptideTableModel *ptm_table_model_p);
+ ~PtmPeptideTableProxyModel();
+
+ PtmPeptideListWindow *getPtmPeptideListWindowP();
+
+ public slots:
+ void onTableClicked(const QModelIndex &index);
+
+ protected:
+ bool lessThan(const QModelIndex &left,
+ const QModelIndex &right) const override;
+ void showContextMenu(const QModelIndex &index);
+
+ private:
+ PtmPeptideListWindow *_p_ptm_peptide_list_window;
+ PtmPeptideTableModel *_p_ptm_table_model;
+ QMenu *_p_context_menu = nullptr;
};
#endif // PTMPEPTIDETABLEPROXYMODEL_H
diff --git a/src/gui/ptm_peptide_list_view/ptmsequencedelegate.cpp b/src/gui/ptm_peptide_list_view/ptmsequencedelegate.cpp
index 57a2c504e492c1bf6cb4623c5fbb16928630f0ac..a477e0a95c5be3238ea11efa83f7cfbd9cfa7c45 100644
--- a/src/gui/ptm_peptide_list_view/ptmsequencedelegate.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmsequencedelegate.cpp
@@ -5,26 +5,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmsequencedelegate.h"
#include "../../grouping/ptm/ptmsamplescan.h"
@@ -32,29 +33,39 @@
#include <QTextDocument>
#include <QPainter>
-PtmSequenceDelegate::PtmSequenceDelegate(PtmIslandListWindow * p_ptm_island_list_window, QWidget *parent) : QStyledItemDelegate(parent) {
- _p_ptm_island_list_window = p_ptm_island_list_window;
+PtmSequenceDelegate::PtmSequenceDelegate(
+ PtmIslandListWindow *p_ptm_island_list_window, QWidget *parent)
+ : QStyledItemDelegate(parent)
+{
+ _p_ptm_island_list_window = p_ptm_island_list_window;
}
-void PtmSequenceDelegate::paint(QPainter *painter, const QStyleOptionViewItem &option,
- const QModelIndex &index) const
+void
+PtmSequenceDelegate::paint(QPainter *painter,
+ const QStyleOptionViewItem &option,
+ const QModelIndex &index) const
{
- if (index.data().canConvert<PtmSampleScan *>()) {
- PtmSampleScan * p_ptm_sample_scan = index.data().value<PtmSampleScan *>();
+ if(index.data().canConvert<PtmSampleScan *>())
+ {
+ PtmSampleScan *p_ptm_sample_scan = index.data().value<PtmSampleScan *>();
+
+ // if (option.state & QStyle::State_Selected)
+ // painter->fillRect(option.rect, option.palette.highlight());
+ QTextDocument document;
+ document.setDocumentMargin(2);
+ document.setHtml(p_ptm_sample_scan->getHtmlSequence(
+ _p_ptm_island_list_window->getIdentificationGroup()
+ ->getPtmGroupingExperiment()));
+ painter->translate(option.rect.topLeft());
+ document.drawContents(painter);
+ painter->translate(-option.rect.topLeft());
- // if (option.state & QStyle::State_Selected)
- // painter->fillRect(option.rect, option.palette.highlight());
- QTextDocument document;
- document.setDocumentMargin(2);
- document.setHtml(p_ptm_sample_scan->getHtmlSequence(_p_ptm_island_list_window->getIdentificationGroup()->getPtmGroupingExperiment()));
- painter->translate(option.rect.topLeft());
- document.drawContents(painter);
- painter->translate(-option.rect.topLeft());
-
- //edit_seq.render(painter);
- //edit..paint(painter, option.rect, option.palette,
- // StarRating::ReadOnly);
- } else {
- QStyledItemDelegate::paint(painter, option, index);
+ // edit_seq.render(painter);
+ // edit..paint(painter, option.rect, option.palette,
+ // StarRating::ReadOnly);
+ }
+ else
+ {
+ QStyledItemDelegate::paint(painter, option, index);
}
}
diff --git a/src/gui/ptm_peptide_list_view/ptmsequencedelegate.h b/src/gui/ptm_peptide_list_view/ptmsequencedelegate.h
index ab98fc180ea9d18f2438533759cc766175a7eb60..e9b786bcc63c4700a6db961e0def62f88408155d 100644
--- a/src/gui/ptm_peptide_list_view/ptmsequencedelegate.h
+++ b/src/gui/ptm_peptide_list_view/ptmsequencedelegate.h
@@ -5,26 +5,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMSEQUENCEDELEGATE_H
#define PTMSEQUENCEDELEGATE_H
@@ -34,21 +35,22 @@ class PtmIslandListWindow;
class PtmSequenceDelegate : public QStyledItemDelegate
{
- Q_OBJECT
+ Q_OBJECT
-public:
- PtmSequenceDelegate(PtmIslandListWindow * p_ptm_island_list_window, QWidget *parent = 0);
+ public:
+ PtmSequenceDelegate(PtmIslandListWindow *p_ptm_island_list_window,
+ QWidget *parent = 0);
- void paint(QPainter *painter, const QStyleOptionViewItem &option,
- const QModelIndex &index) const override;
- //QSize sizeHint(const QStyleOptionViewItem &option,
- // const QModelIndex &index) const override;
- //QWidget *createEditor(QWidget *parent, const QStyleOptionViewItem &option,
- // const QModelIndex &index) const override;
- //void setEditorData(QWidget *editor, const QModelIndex &index) const override;
- //void setModelData(QWidget *editor, QAbstractItemModel *model,
- // const QModelIndex &index) const override;
-private:
- PtmIslandListWindow * _p_ptm_island_list_window;
+ void paint(QPainter *painter, const QStyleOptionViewItem &option,
+ const QModelIndex &index) const override;
+ // QSize sizeHint(const QStyleOptionViewItem &option,
+ // const QModelIndex &index) const override;
+ // QWidget *createEditor(QWidget *parent, const QStyleOptionViewItem &option,
+ // const QModelIndex &index) const override;
+ // void setEditorData(QWidget *editor, const QModelIndex &index) const
+ // override; void setModelData(QWidget *editor, QAbstractItemModel *model,
+ // const QModelIndex &index) const override;
+ private:
+ PtmIslandListWindow *_p_ptm_island_list_window;
};
#endif // PTMSEQUENCEDELEGATE_H
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.cpp b/src/gui/tandem_run_dialog/tandemrundialog.cpp
index 0d4cb8ad9ba0c3887e43f8326da39c1e9cd0e215..3337ec9fba3d0f8428261331212a12f1ee3da4b0 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.cpp
+++ b/src/gui/tandem_run_dialog/tandemrundialog.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "tandemrundialog.h"
#include "ui_tandem_run_dialog.h"
@@ -36,325 +37,422 @@
#include <pappsomspp/pappsoexception.h>
#include "../../files/tandemparametersfile.h"
-//Q_DECLARE_METATYPE(QFileInfo)
+// Q_DECLARE_METATYPE(QFileInfo)
-TandemRunDialog::TandemRunDialog(QWidget * parent):
- QDialog(parent),
- ui(new Ui::TandemRunDialog)
+TandemRunDialog::TandemRunDialog(QWidget *parent)
+ : QDialog(parent), ui(new Ui::TandemRunDialog)
{
- qDebug() << "TandemRunDialog::TandemRunDialog begin";
- ui->setupUi(this);
- this->setModal(true);
- _p_fasta_file_list = new QStringListModel();
- _p_mz_file_list = new QStringListModel();
- ui->fasta_file_listview->setModel(_p_fasta_file_list);
- ui->mz_file_listview->setModel(_p_mz_file_list);
- ui->exe_group_widget->setVisible(false);
-
- QSettings settings;
- /*
- QString condor_tmp_dir = QString("%1/xtpcpp").arg(settings.value("condor/tmp_dir", "/tmp").toString());
- _p_tmp_dir = new QTemporaryDir(condor_tmp_dir);
- _p_tmp_dir->setAutoRemove(settings.value("condor/tmp_dir_autoremove", true).toBool());
- _condor_submit_command = settings.value("condor/submit", "/usr/bin/condor_submit").toString();
- _condor_q_command = settings.value("condor/condor_q", "/usr/bin/condor_q").toString();
- _condor_rm_command = settings.value("condor/condor_rm", "/usr/bin/condor_rm").toString();
- _condor_request_memory = settings.value("condor/request_memory", "10000").toUInt();
-
- QString default_preset_name = ;
- */
-
- ui->use_htcondor_groupbox->setChecked(settings.value("tandem/use_HTCondor", "false").toBool());
- ui->request_memory_edit->setText(settings.value("tandem/condor_request_memory", "5000").toString());
-
- settings.value("condor/tmp_dir", "/gorgone/pappso/tmp");
+ qDebug() << "TandemRunDialog::TandemRunDialog begin";
+ ui->setupUi(this);
+ this->setModal(true);
+ _p_fasta_file_list = new QStringListModel();
+ _p_mz_file_list = new QStringListModel();
+ ui->fasta_file_listview->setModel(_p_fasta_file_list);
+ ui->mz_file_listview->setModel(_p_mz_file_list);
+ ui->exe_group_widget->setVisible(false);
+
+ QSettings settings;
+ /*
+ QString condor_tmp_dir =
+ QString("%1/xtpcpp").arg(settings.value("condor/tmp_dir", "/tmp").toString());
+ _p_tmp_dir = new QTemporaryDir(condor_tmp_dir);
+ _p_tmp_dir->setAutoRemove(settings.value("condor/tmp_dir_autoremove",
+ true).toBool()); _condor_submit_command = settings.value("condor/submit",
+ "/usr/bin/condor_submit").toString(); _condor_q_command =
+ settings.value("condor/condor_q", "/usr/bin/condor_q").toString();
+ _condor_rm_command = settings.value("condor/condor_rm",
+ "/usr/bin/condor_rm").toString(); _condor_request_memory =
+ settings.value("condor/request_memory", "10000").toUInt();
+
+ QString default_preset_name = ;
+ */
+
+ ui->use_htcondor_groupbox->setChecked(
+ settings.value("tandem/use_HTCondor", "false").toBool());
+ ui->request_memory_edit->setText(
+ settings.value("tandem/condor_request_memory", "5000").toString());
+
+ settings.value("condor/tmp_dir", "/gorgone/pappso/tmp");
#if QT_VERSION >= 0x050000
- // Qt5 code
+ // Qt5 code
#else
-// Qt4 code
+ // Qt4 code
#endif
- reset();
- fillPresetComboBox();
- qDebug() << "TandemRunDialog::TandemRunDialog end";
+ reset();
+ fillPresetComboBox();
+ qDebug() << "TandemRunDialog::TandemRunDialog end";
}
TandemRunDialog::~TandemRunDialog()
{
- delete ui;
- delete _p_fasta_file_list;
- delete _p_mz_file_list;
+ delete ui;
+ delete _p_fasta_file_list;
+ delete _p_mz_file_list;
}
-void TandemRunDialog::exeGroupBoxClicked(bool clicked) {
- qDebug() << "TandemRunDialog::exeGroupBoxClicked begin";
- ui->exe_group_widget->setVisible(false);
- if (clicked) {
- ui->exe_group_widget->setVisible(true);
+void
+TandemRunDialog::exeGroupBoxClicked(bool clicked)
+{
+ qDebug() << "TandemRunDialog::exeGroupBoxClicked begin";
+ ui->exe_group_widget->setVisible(false);
+ if(clicked)
+ {
+ ui->exe_group_widget->setVisible(true);
}
- qDebug() << "TandemRunDialog::exeGroupBoxClicked end";
+ qDebug() << "TandemRunDialog::exeGroupBoxClicked end";
}
-void TandemRunDialog::setPresetName(QString preset_name) {
- qDebug() << "TandemRunDialog::setPresetName begin";
- if (!preset_name.isEmpty() && !preset_name.isNull()) {
-
- qDebug() << "TandemRunDialog::setPresetName not null";
- //test if this is an X!Tandem preset file:
- //get presets :
- TandemParametersFile param_file(ui->preset_combobox->itemData(ui->preset_combobox->currentIndex()).value<QString>());
-
- if (param_file.isTandemPresetFile()) {
- QSettings settings;
- settings.setValue("tandem/preset_name", preset_name);
-
+void
+TandemRunDialog::setPresetName(QString preset_name)
+{
+ qDebug() << "TandemRunDialog::setPresetName begin";
+ if(!preset_name.isEmpty() && !preset_name.isNull())
+ {
- if (_previous_preset_file != param_file.getAbsoluteFilePath()) {
- _previous_preset_file = param_file.getAbsoluteFilePath();
- ui->thread_spin_box->setValue(param_file.getTandemParameters().getValue("spectrum, threads").toInt());
+ qDebug() << "TandemRunDialog::setPresetName not null";
+ // test if this is an X!Tandem preset file:
+ // get presets :
+ TandemParametersFile param_file(
+ ui->preset_combobox->itemData(ui->preset_combobox->currentIndex())
+ .value<QString>());
+
+ if(param_file.isTandemPresetFile())
+ {
+ QSettings settings;
+ settings.setValue("tandem/preset_name", preset_name);
+
+
+ if(_previous_preset_file != param_file.getAbsoluteFilePath())
+ {
+ _previous_preset_file = param_file.getAbsoluteFilePath();
+ ui->thread_spin_box->setValue(param_file.getTandemParameters()
+ .getValue("spectrum, threads")
+ .toInt());
}
}
}
- qDebug() << "TandemRunDialog::setPresetName end";
+ qDebug() << "TandemRunDialog::setPresetName end";
}
-void TandemRunDialog::fillPresetComboBox() {
- qDebug() << "TandemRunDialog::fillPresetComboBox begin";
- ui->preset_combobox->clear();
- QSettings settings;
- QString default_preset_location = settings.value("path/tandemrun_preset_directory", "").toString();
- QString default_preset_name = settings.value("tandem/preset_name", "").toString();
-
- qDebug() << "TandemRunDialog::fillPresetComboBox default_preset_location=" << default_preset_location;
- qDebug() << "TandemRunDialog::fillPresetComboBox default_preset_name=" << default_preset_name;
- QDir preset_dir(default_preset_location);
- QStringList filters;
- filters << "*.xml";
- preset_dir.setNameFilters(filters);
- for (QFileInfo file_info: preset_dir.entryInfoList() ) {
- TandemParametersFile param_file(file_info.absoluteFilePath());
- if (param_file.isTandemPresetFile()) {
- ui->preset_combobox->addItem(file_info.baseName(), QVariant(file_info.absoluteFilePath()));
+void
+TandemRunDialog::fillPresetComboBox()
+{
+ qDebug() << "TandemRunDialog::fillPresetComboBox begin";
+ ui->preset_combobox->clear();
+ QSettings settings;
+ QString default_preset_location =
+ settings.value("path/tandemrun_preset_directory", "").toString();
+ QString default_preset_name =
+ settings.value("tandem/preset_name", "").toString();
+
+ qDebug() << "TandemRunDialog::fillPresetComboBox default_preset_location="
+ << default_preset_location;
+ qDebug() << "TandemRunDialog::fillPresetComboBox default_preset_name="
+ << default_preset_name;
+ QDir preset_dir(default_preset_location);
+ QStringList filters;
+ filters << "*.xml";
+ preset_dir.setNameFilters(filters);
+ for(QFileInfo file_info : preset_dir.entryInfoList())
+ {
+ TandemParametersFile param_file(file_info.absoluteFilePath());
+ if(param_file.isTandemPresetFile())
+ {
+ ui->preset_combobox->addItem(file_info.baseName(),
+ QVariant(file_info.absoluteFilePath()));
}
}
- int index = ui->preset_combobox->findText(default_preset_name);
- if ( index != -1 ) { // -1 for not found
- ui->preset_combobox->setCurrentIndex(index);
+ int index = ui->preset_combobox->findText(default_preset_name);
+ if(index != -1)
+ { // -1 for not found
+ ui->preset_combobox->setCurrentIndex(index);
}
-
}
-void TandemRunDialog::reset() {
- QSettings settings;
- QString default_output_location = settings.value("path/identificationfiles", "").toString();
- QString tandem_bin_path = settings.value("path/tandem_bin", "/usr/bin/tandem").toString();
-
- ui->output_directory_label->setText(default_output_location);
- ui->tandem_bin_label->setText(tandem_bin_path);
-
- _p_fasta_file_list->stringList().clear();
- _p_mz_file_list->stringList().clear();
- /*
- if (filenames.size() > 0) {
- settings.setValue("path/identificationfiles", QFileInfo(filenames[0]).absolutePath());
- }*/
+void
+TandemRunDialog::reset()
+{
+ QSettings settings;
+ QString default_output_location =
+ settings.value("path/identificationfiles", "").toString();
+ QString tandem_bin_path =
+ settings.value("path/tandem_bin", "/usr/bin/tandem").toString();
+
+ ui->output_directory_label->setText(default_output_location);
+ ui->tandem_bin_label->setText(tandem_bin_path);
+
+ _p_fasta_file_list->stringList().clear();
+ _p_mz_file_list->stringList().clear();
+ /*
+ if (filenames.size() > 0) {
+ settings.setValue("path/identificationfiles",
+ QFileInfo(filenames[0]).absolutePath());
+ }*/
}
-void TandemRunDialog::selectPresetDirectory() {
- try {
- QSettings settings;
- QString default_preset_location = settings.value("path/tandemrun_preset_directory", "").toString();
+void
+TandemRunDialog::selectPresetDirectory()
+{
+ try
+ {
+ QSettings settings;
+ QString default_preset_location =
+ settings.value("path/tandemrun_preset_directory", "").toString();
- QString directory = QFileDialog::getExistingDirectory(this,tr("Choose preset directory"),default_preset_location );
+ QString directory = QFileDialog::getExistingDirectory(
+ this, tr("Choose preset directory"), default_preset_location);
- if (!directory.isEmpty() && ! directory.isNull()) {
- settings.setValue("path/tandemrun_preset_directory", directory);
- fillPresetComboBox();
+ if(!directory.isEmpty() && !directory.isNull())
+ {
+ settings.setValue("path/tandemrun_preset_directory", directory);
+ fillPresetComboBox();
}
-
}
- catch (pappso::PappsoException & error) {
- //QMessageBox::warning(this,
- // tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
+ catch(pappso::PappsoException &error)
+ {
+ // QMessageBox::warning(this,
+ // tr("Error choosing identification result files :
+ // %1").arg(error.qwhat()), error);
}
}
-void TandemRunDialog::editPresets() {
- QSettings settings;
- QString default_preset_location = settings.value("path/tandemrun_preset_directory", "").toString();
+void
+TandemRunDialog::editPresets()
+{
+ QSettings settings;
+ QString default_preset_location =
+ settings.value("path/tandemrun_preset_directory", "").toString();
- if (_p_preset_dialog == nullptr) {
- _p_preset_dialog = new EditTandemPresetDialog(this);
+ if(_p_preset_dialog == nullptr)
+ {
+ _p_preset_dialog = new EditTandemPresetDialog(this);
}
- _p_preset_dialog->setTandemParametersFile(TandemParametersFile(ui->preset_combobox->itemData(ui->preset_combobox->currentIndex()).value<QString>()));
- _p_preset_dialog->show();
+ _p_preset_dialog->setTandemParametersFile(TandemParametersFile(
+ ui->preset_combobox->itemData(ui->preset_combobox->currentIndex())
+ .value<QString>()));
+ _p_preset_dialog->show();
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect(_p_preset_dialog, &EditTandemPresetDialog::accepted, this, &TandemRunDialog::acceptPresetEdit);
- connect(_p_preset_dialog, &EditTandemPresetDialog::rejected, this, &TandemRunDialog::rejectPresetEdit);
+ // Qt5 code
+ connect(_p_preset_dialog, &EditTandemPresetDialog::accepted, this,
+ &TandemRunDialog::acceptPresetEdit);
+ connect(_p_preset_dialog, &EditTandemPresetDialog::rejected, this,
+ &TandemRunDialog::rejectPresetEdit);
#else
-// Qt4 code
+ // Qt4 code
#endif
}
-void TandemRunDialog::rejectPresetEdit() {
- fillPresetComboBox();
+void
+TandemRunDialog::rejectPresetEdit()
+{
+ fillPresetComboBox();
}
-void TandemRunDialog::acceptPresetEdit() {
- TandemParametersFile param_file = _p_preset_dialog->getTandemParametersFile();
- QSettings settings;
- settings.setValue("path/tandemrun_preset_directory", param_file.getAbsoluteDir().absolutePath());
- settings.setValue("tandem/preset_name", param_file.getMethodName());
-
+void
+TandemRunDialog::acceptPresetEdit()
+{
+ TandemParametersFile param_file = _p_preset_dialog->getTandemParametersFile();
+ QSettings settings;
+ settings.setValue("path/tandemrun_preset_directory",
+ param_file.getAbsoluteDir().absolutePath());
+ settings.setValue("tandem/preset_name", param_file.getMethodName());
- fillPresetComboBox();
+ fillPresetComboBox();
}
-void TandemRunDialog::selectOutputDirectory() {
- try {
- QSettings settings;
- QString default_output_location = settings.value("path/identificationfiles", "").toString();
+void
+TandemRunDialog::selectOutputDirectory()
+{
+ try
+ {
+ QSettings settings;
+ QString default_output_location =
+ settings.value("path/identificationfiles", "").toString();
- QString directory = QFileDialog::getExistingDirectory(this,tr("Choose output directory"),default_output_location );
+ QString directory = QFileDialog::getExistingDirectory(
+ this, tr("Choose output directory"), default_output_location);
- if (!directory.isEmpty()) {
- settings.setValue("path/identificationfiles", directory);
- ui->output_directory_label->setText(directory);
+ if(!directory.isEmpty())
+ {
+ settings.setValue("path/identificationfiles", directory);
+ ui->output_directory_label->setText(directory);
}
-
-
}
- catch (pappso::PappsoException & error) {
- //QMessageBox::warning(this,
- // tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
+ catch(pappso::PappsoException &error)
+ {
+ // QMessageBox::warning(this,
+ // tr("Error choosing identification result files :
+ // %1").arg(error.qwhat()), error);
}
}
-void TandemRunDialog::clearFastaFiles() {
- _p_fasta_file_list->removeRows( 0, _p_fasta_file_list->rowCount() );
+void
+TandemRunDialog::clearFastaFiles()
+{
+ _p_fasta_file_list->removeRows(0, _p_fasta_file_list->rowCount());
}
-void TandemRunDialog::selectFastaFiles() {
- try {
- QSettings settings;
- QString default_fasta_location = settings.value("path/tandemrun_fastafiles_directory", "").toString();
-
- QStringList filenames = QFileDialog::getOpenFileNames(this,tr("FASTA files"),default_fasta_location,
- tr("FASTA files (*.fasta);;all files (*)") );
-
- if (filenames.size() > 0) {
- settings.setValue("path/tandemrun_fastafiles_directory", QFileInfo(filenames[0]).absolutePath());
+void
+TandemRunDialog::selectFastaFiles()
+{
+ try
+ {
+ QSettings settings;
+ QString default_fasta_location =
+ settings.value("path/tandemrun_fastafiles_directory", "").toString();
+
+ QStringList filenames = QFileDialog::getOpenFileNames(
+ this, tr("FASTA files"), default_fasta_location,
+ tr("FASTA files (*.fasta);;all files (*)"));
+
+ if(filenames.size() > 0)
+ {
+ settings.setValue("path/tandemrun_fastafiles_directory",
+ QFileInfo(filenames[0]).absolutePath());
}
- QStringList file_list = _p_fasta_file_list->stringList();
- file_list.append(filenames);
- _p_fasta_file_list->setStringList(file_list);
-
+ QStringList file_list = _p_fasta_file_list->stringList();
+ file_list.append(filenames);
+ _p_fasta_file_list->setStringList(file_list);
}
- catch (pappso::PappsoException & error) {
- //QMessageBox::warning(this,
- // tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
+ catch(pappso::PappsoException &error)
+ {
+ // QMessageBox::warning(this,
+ // tr("Error choosing identification result files :
+ // %1").arg(error.qwhat()), error);
}
}
-void TandemRunDialog::selectXtandemExe() {
- try {
- QSettings settings;
- QString tandem_bin_path = settings.value("path/tandem_bin", "/usr/bin/tandem").toString();
-
-
- QString filename = QFileDialog::getOpenFileName(this,tr("select X!Tandem executable"),QDir(tandem_bin_path).absolutePath(),
- tr("all files (*);;exe files (*.exe)") );
-
- if (!filename.isEmpty()) {
- QFileInfo tandem_bin(filename);
- filename = tandem_bin.absoluteFilePath();
- if (tandem_bin.isExecutable()) {
- ui->tandem_bin_label->setText(filename);
- settings.setValue("path/tandem_bin", filename);
+void
+TandemRunDialog::selectXtandemExe()
+{
+ try
+ {
+ QSettings settings;
+ QString tandem_bin_path =
+ settings.value("path/tandem_bin", "/usr/bin/tandem").toString();
+
+
+ QString filename =
+ QFileDialog::getOpenFileName(this, tr("select X!Tandem executable"),
+ QDir(tandem_bin_path).absolutePath(),
+ tr("all files (*);;exe files (*.exe)"));
+
+ if(!filename.isEmpty())
+ {
+ QFileInfo tandem_bin(filename);
+ filename = tandem_bin.absoluteFilePath();
+ if(tandem_bin.isExecutable())
+ {
+ ui->tandem_bin_label->setText(filename);
+ settings.setValue("path/tandem_bin", filename);
}
- else {
- QMessageBox::warning(this,
- tr("Wrong X!Tandem exe file"), tr("%1 is not executable.").arg(filename));
+ else
+ {
+ QMessageBox::warning(this, tr("Wrong X!Tandem exe file"),
+ tr("%1 is not executable.").arg(filename));
}
}
}
- catch (pappso::PappsoException & error) {
- //QMessageBox::warning(this,
- // tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
+ catch(pappso::PappsoException &error)
+ {
+ // QMessageBox::warning(this,
+ // tr("Error choosing identification result files :
+ // %1").arg(error.qwhat()), error);
}
}
-void TandemRunDialog::selectMzFiles() {
- try {
- QSettings settings;
- QString default_mz_location = settings.value("path/tandemrun_mzfiles_directory", "").toString();
-
- QStringList filenames = QFileDialog::getOpenFileNames(this,tr("select peak list files"),default_mz_location,
- tr("any mz files (*.mzXML *.mzxml *.mzML *.mzml *.mgf);;mzXML (*.mzXML *.mzxml);;mzML (*.mzML *.mzml);;MGF (*.mgf);;all files (*)") );
-
- if (filenames.size() > 0) {
- settings.setValue("path/tandemrun_mzfiles_directory", QFileInfo(filenames[0]).absolutePath());
+void
+TandemRunDialog::selectMzFiles()
+{
+ try
+ {
+ QSettings settings;
+ QString default_mz_location =
+ settings.value("path/tandemrun_mzfiles_directory", "").toString();
+
+ QStringList filenames = QFileDialog::getOpenFileNames(
+ this, tr("select peak list files"), default_mz_location,
+ tr("any mz files (*.mzXML *.mzxml *.mzML *.mzml *.mgf);;mzXML (*.mzXML "
+ "*.mzxml);;mzML (*.mzML *.mzml);;MGF (*.mgf);;all files (*)"));
+
+ if(filenames.size() > 0)
+ {
+ settings.setValue("path/tandemrun_mzfiles_directory",
+ QFileInfo(filenames[0]).absolutePath());
}
- QStringList file_list = _p_mz_file_list->stringList();
- file_list.append(filenames);
- _p_mz_file_list->setStringList(file_list);
-
+ QStringList file_list = _p_mz_file_list->stringList();
+ file_list.append(filenames);
+ _p_mz_file_list->setStringList(file_list);
}
- catch (pappso::PappsoException & error) {
- //QMessageBox::warning(this,
- // tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
+ catch(pappso::PappsoException &error)
+ {
+ // QMessageBox::warning(this,
+ // tr("Error choosing identification result files :
+ // %1").arg(error.qwhat()), error);
}
}
-void TandemRunDialog::clearMzFiles() {
- _p_mz_file_list->removeRows( 0, _p_mz_file_list->rowCount() );
+void
+TandemRunDialog::clearMzFiles()
+{
+ _p_mz_file_list->removeRows(0, _p_mz_file_list->rowCount());
}
-TandemRunBatch TandemRunDialog::getTandemRunBatch() const {
- TandemRunBatch tandem_run_batch;
- tandem_run_batch._tandem_bin_path = ui->tandem_bin_label->text();
- tandem_run_batch._mz_file_list = _p_mz_file_list->stringList();
- tandem_run_batch._fasta_file_list = _p_fasta_file_list->stringList();
- //tandem_run_batch._preset_file = ui->preset_combobox->itemData(ui->preset_combobox->currentIndex()).value<QFileInfo>().absoluteFilePath();
- tandem_run_batch._preset_file = ui->preset_combobox->itemData(ui->preset_combobox->currentIndex()).value<QString>();
- tandem_run_batch._output_directory = ui->output_directory_label->text();
- tandem_run_batch._number_of_threads = ui->thread_spin_box->value();
- return tandem_run_batch;
+TandemRunBatch
+TandemRunDialog::getTandemRunBatch() const
+{
+ TandemRunBatch tandem_run_batch;
+ tandem_run_batch._tandem_bin_path = ui->tandem_bin_label->text();
+ tandem_run_batch._mz_file_list = _p_mz_file_list->stringList();
+ tandem_run_batch._fasta_file_list = _p_fasta_file_list->stringList();
+ // tandem_run_batch._preset_file =
+ // ui->preset_combobox->itemData(ui->preset_combobox->currentIndex()).value<QFileInfo>().absoluteFilePath();
+ tandem_run_batch._preset_file =
+ ui->preset_combobox->itemData(ui->preset_combobox->currentIndex())
+ .value<QString>();
+ tandem_run_batch._output_directory = ui->output_directory_label->text();
+ tandem_run_batch._number_of_threads = ui->thread_spin_box->value();
+ return tandem_run_batch;
}
-void TandemRunDialog::done(int r)
+void
+TandemRunDialog::done(int r)
{
- if(QDialog::Accepted == r) // ok was pressed
+ if(QDialog::Accepted == r) // ok was pressed
{
- QSettings settings;
- settings.setValue("tandem/use_HTCondor", "false");
- if ( ui->use_htcondor_groupbox->isChecked()) {
- settings.setValue("tandem/use_HTCondor", "true");
+ QSettings settings;
+ settings.setValue("tandem/use_HTCondor", "false");
+ if(ui->use_htcondor_groupbox->isChecked())
+ {
+ settings.setValue("tandem/use_HTCondor", "true");
}
- //QString condor_tmp_dir = QString("%1/xtpcpp").arg(settings.value("condor/tmp_dir", "/tmp").toString());
- //_p_tmp_dir = new QTemporaryDir(condor_tmp_dir);
- //_p_tmp_dir->setAutoRemove(settings.value("condor/tmp_dir_autoremove", true).toBool());
- //_condor_submit_command = settings.value("condor/submit", "/usr/bin/condor_submit").toString();
- //_condor_q_command = settings.value("condor/condor_q", "/usr/bin/condor_q").toString();
- //_condor_rm_command = settings.value("condor/condor_rm", "/usr/bin/condor_rm").toString();
- settings.setValue("tandem/condor_request_memory", ui->request_memory_edit->text());
-
- QDialog::done(r);
- return;
+ // QString condor_tmp_dir =
+ // QString("%1/xtpcpp").arg(settings.value("condor/tmp_dir",
+ // "/tmp").toString()); _p_tmp_dir = new QTemporaryDir(condor_tmp_dir);
+ //_p_tmp_dir->setAutoRemove(settings.value("condor/tmp_dir_autoremove",
+ //true).toBool()); _condor_submit_command =
+ //settings.value("condor/submit", "/usr/bin/condor_submit").toString();
+ //_condor_q_command = settings.value("condor/condor_q",
+ //"/usr/bin/condor_q").toString(); _condor_rm_command =
+ //settings.value("condor/condor_rm", "/usr/bin/condor_rm").toString();
+ settings.setValue("tandem/condor_request_memory",
+ ui->request_memory_edit->text());
+
+ QDialog::done(r);
+ return;
}
- else // cancel, close or exc was pressed
+ else // cancel, close or exc was pressed
{
- QDialog::done(r);
- return;
+ QDialog::done(r);
+ return;
}
}
-
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.h b/src/gui/tandem_run_dialog/tandemrundialog.h
index c7dcdee799c717f04d5fc77b22630ae2c142da43..edd690fdcf43c724733aecb5d7b0784bfaf4607d 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.h
+++ b/src/gui/tandem_run_dialog/tandemrundialog.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef TANDEMRUNDIALOG_H
#define TANDEMRUNDIALOG_H
@@ -35,49 +36,50 @@
#include "../../core/tandem_run/tandemrunbatch.h"
#include "../edit_tandem_preset_dialog/edittandempresetdialog.h"
-namespace Ui {
-class TandemRunDialog;
+namespace Ui
+{
+ class TandemRunDialog;
}
class TandemRunDialog : public QDialog
{
- Q_OBJECT
+ Q_OBJECT
+
+ public:
+ explicit TandemRunDialog(QWidget *parent);
+ ~TandemRunDialog();
-public:
- explicit TandemRunDialog(QWidget * parent);
- ~TandemRunDialog();
+ TandemRunBatch getTandemRunBatch() const;
+ void reset();
+ public slots:
+ void exeGroupBoxClicked(bool clicked);
+ void selectFastaFiles();
+ void clearFastaFiles();
+ void selectXtandemExe();
+ void selectMzFiles();
+ void clearMzFiles();
+ void selectOutputDirectory();
+ void selectPresetDirectory();
+ void editPresets();
+ void setPresetName(QString preset_name);
+ void acceptPresetEdit();
+ void rejectPresetEdit();
+ signals:
- TandemRunBatch getTandemRunBatch() const;
- void reset();
-public slots:
- void exeGroupBoxClicked(bool clicked);
- void selectFastaFiles();
- void clearFastaFiles();
- void selectXtandemExe();
- void selectMzFiles();
- void clearMzFiles();
- void selectOutputDirectory();
- void selectPresetDirectory();
- void editPresets();
- void setPresetName(QString preset_name);
- void acceptPresetEdit();
- void rejectPresetEdit();
-signals:
-
-protected:
- void done(int r) override;
+ protected:
+ void done(int r) override;
-private:
- void fillPresetComboBox();
-private:
- Ui::TandemRunDialog *ui;
- EditTandemPresetDialog * _p_preset_dialog=nullptr;
- QStringListModel * _p_fasta_file_list;
- QStringListModel * _p_mz_file_list;
- QString _previous_preset_file;
+ private:
+ void fillPresetComboBox();
+ private:
+ Ui::TandemRunDialog *ui;
+ EditTandemPresetDialog *_p_preset_dialog = nullptr;
+ QStringListModel *_p_fasta_file_list;
+ QStringListModel *_p_mz_file_list;
+ QString _previous_preset_file;
};
#endif // TANDEMRUNDIALOG_H
diff --git a/src/gui/waiting_message_dialog/waitingmessagedialog.cpp b/src/gui/waiting_message_dialog/waitingmessagedialog.cpp
index 9b37ca64c71fc91642ec0aa51fa554b20d3759ca..ff1f67e724891117c70b13c4a362cc686f7e6107 100644
--- a/src/gui/waiting_message_dialog/waitingmessagedialog.cpp
+++ b/src/gui/waiting_message_dialog/waitingmessagedialog.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ui_waiting_message_dialog.h"
#include "waitingmessagedialog.h"
@@ -27,95 +28,113 @@
#include <QLabel>
#include <QMutexLocker>
-WaitingMessageDialog::WaitingMessageDialog(QWidget * parent):
- QDialog(parent),
- ui(new Ui::WaitingMessageDialog)
+WaitingMessageDialog::WaitingMessageDialog(QWidget *parent)
+ : QDialog(parent), ui(new Ui::WaitingMessageDialog)
{
- qDebug() << "WaitingMessageDialog::WaitingMessageDialog begin";
- ui->setupUi(this);
- this->setModal(true);
- this->setWindowFlags(Qt::Window | Qt::WindowTitleHint | Qt::CustomizeWindowHint);
- //this->setWindowFlags(Qt::FramelessWindowHint);
- //this->setWindowFlags(Qt::WindowTitleHint);
-
- _p_movie = new QMovie(":/xtpcpp_icon/resources/xtandempipeline_animated_gif.gif");
- if (!_p_movie->isValid())
+ qDebug() << "WaitingMessageDialog::WaitingMessageDialog begin";
+ ui->setupUi(this);
+ this->setModal(true);
+ this->setWindowFlags(Qt::Window | Qt::WindowTitleHint |
+ Qt::CustomizeWindowHint);
+ // this->setWindowFlags(Qt::FramelessWindowHint);
+ // this->setWindowFlags(Qt::WindowTitleHint);
+
+ _p_movie =
+ new QMovie(":/xtpcpp_icon/resources/xtandempipeline_animated_gif.gif");
+ if(!_p_movie->isValid())
{
- qDebug() << "WaitingMessageDialog::WaitingMessageDialog animation not found";
+ qDebug()
+ << "WaitingMessageDialog::WaitingMessageDialog animation not found";
}
- ui->movie_label->setMovie(_p_movie);
- ui->progress_bar->setVisible(false);
-
- ui->progress_bar->setMaximum(100);
- ui->progress_bar->setMinimum(0);
- ui->console_plaintextedit->setHidden(true);
- ui->stop_push_button->setVisible(false);
- _asked_to_stop = false;
- //movie->start();
- qDebug() << "WaitingMessageDialog::WaitingMessageDialog end";
+ ui->movie_label->setMovie(_p_movie);
+ ui->progress_bar->setVisible(false);
+
+ ui->progress_bar->setMaximum(100);
+ ui->progress_bar->setMinimum(0);
+ ui->console_plaintextedit->setHidden(true);
+ ui->stop_push_button->setVisible(false);
+ _asked_to_stop = false;
+ // movie->start();
+ qDebug() << "WaitingMessageDialog::WaitingMessageDialog end";
}
WaitingMessageDialog::~WaitingMessageDialog()
{
- qDebug() << "WaitingMessageDialog::~WaitingMessageDialog";
- delete ui;
- qDebug() << "WaitingMessageDialog::~WaitingMessageDialog end";
+ qDebug() << "WaitingMessageDialog::~WaitingMessageDialog";
+ delete ui;
+ qDebug() << "WaitingMessageDialog::~WaitingMessageDialog end";
}
-void WaitingMessageDialog::toggledStopButton(bool pushed) {
- QMutexLocker mutex_locker(&_mutex);
- _asked_to_stop = true;
+void
+WaitingMessageDialog::toggledStopButton(bool pushed)
+{
+ QMutexLocker mutex_locker(&_mutex);
+ _asked_to_stop = true;
}
-bool WaitingMessageDialog::stopWorkerThread() {
- QMutexLocker mutex_locker(&_mutex);
- if (!ui->stop_push_button->isVisible()) {
- ui->stop_push_button->setChecked(false);
- ui->stop_push_button->setVisible(true);
- _asked_to_stop = false;
- return false;
+bool
+WaitingMessageDialog::stopWorkerThread()
+{
+ QMutexLocker mutex_locker(&_mutex);
+ if(!ui->stop_push_button->isVisible())
+ {
+ ui->stop_push_button->setChecked(false);
+ ui->stop_push_button->setVisible(true);
+ _asked_to_stop = false;
+ return false;
}
- return _asked_to_stop;
-
+ return _asked_to_stop;
}
-void WaitingMessageDialog::message(const QString & message) {
+void
+WaitingMessageDialog::message(const QString &message)
+{
- ui->progress_bar->setVisible(false);
- ui->message_label->setText(message);
+ ui->progress_bar->setVisible(false);
+ ui->message_label->setText(message);
}
-void WaitingMessageDialog::message(const QString & message, int progress_value) {
- qDebug() << "WaitingMessageDialog::message " << progress_value;
- ui->progress_bar->setVisible(true);
- ui->progress_bar->setValue(progress_value);
- ui->message_label->setText(message);
+void
+WaitingMessageDialog::message(const QString &message, int progress_value)
+{
+ qDebug() << "WaitingMessageDialog::message " << progress_value;
+ ui->progress_bar->setVisible(true);
+ ui->progress_bar->setValue(progress_value);
+ ui->message_label->setText(message);
}
-void WaitingMessageDialog::appendText(char * text) {
- ui->console_plaintextedit->setHidden(false);
- //ui->console_plaintextedit->appendText(text);
+void
+WaitingMessageDialog::appendText(char *text)
+{
+ ui->console_plaintextedit->setHidden(false);
+ // ui->console_plaintextedit->appendText(text);
- ui->console_plaintextedit->moveCursor (QTextCursor::End);
- ui->console_plaintextedit->insertPlainText (text);
+ ui->console_plaintextedit->moveCursor(QTextCursor::End);
+ ui->console_plaintextedit->insertPlainText(text);
}
-void WaitingMessageDialog::setText(const QString text) {
- ui->console_plaintextedit->setHidden(false);
- //ui->console_plaintextedit->appendText(text);
- ui->console_plaintextedit->setPlainText(text);
+void
+WaitingMessageDialog::setText(const QString text)
+{
+ ui->console_plaintextedit->setHidden(false);
+ // ui->console_plaintextedit->appendText(text);
+ ui->console_plaintextedit->setPlainText(text);
}
-void WaitingMessageDialog::hideEvent( QHideEvent* event ) {
- QWidget::hideEvent( event );
- qDebug() << "WaitingMessageDialog::hideEvent";
- _p_movie->stop();
- ui->console_plaintextedit->setHidden(true);
+void
+WaitingMessageDialog::hideEvent(QHideEvent *event)
+{
+ QWidget::hideEvent(event);
+ qDebug() << "WaitingMessageDialog::hideEvent";
+ _p_movie->stop();
+ ui->console_plaintextedit->setHidden(true);
}
-void WaitingMessageDialog::showEvent( QShowEvent* event ) {
- QWidget::showEvent( event );
- _p_movie->start();
- ui->stop_push_button->setChecked(false);
- ui->stop_push_button->setVisible(false);
- _asked_to_stop = false;
+void
+WaitingMessageDialog::showEvent(QShowEvent *event)
+{
+ QWidget::showEvent(event);
+ _p_movie->start();
+ ui->stop_push_button->setChecked(false);
+ ui->stop_push_button->setVisible(false);
+ _asked_to_stop = false;
}
diff --git a/src/gui/waiting_message_dialog/waitingmessagedialog.h b/src/gui/waiting_message_dialog/waitingmessagedialog.h
index ab9a471f6a3994b34413a4cf8ec499dd23582168..50a73da76796de26bf466165342ef5658bdad11c 100644
--- a/src/gui/waiting_message_dialog/waitingmessagedialog.h
+++ b/src/gui/waiting_message_dialog/waitingmessagedialog.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef WAITINGMESSAGEDIALOG_H
#define WAITINGMESSAGEDIALOG_H
@@ -31,40 +32,40 @@
#include "../widgets/automatic_filter_widget/automaticfilterwidget.h"
-namespace Ui {
-class WaitingMessageDialog;
+namespace Ui
+{
+ class WaitingMessageDialog;
}
class WaitingMessageDialog : public QDialog
{
- Q_OBJECT
-
-public:
- explicit WaitingMessageDialog(QWidget * parent);
- ~WaitingMessageDialog();
-
- void message(const QString & message);
- void message(const QString & message, int progress_value);
- void appendText(char * text);
- void setText(const QString text);
- void showEvent( QShowEvent* event );
- void hideEvent( QHideEvent* event );
-
- bool stopWorkerThread();
-
-private slots:
- void toggledStopButton(bool pushed);
-
-private:
- Ui::WaitingMessageDialog *ui;
- QMovie * _p_movie;
-
- bool _asked_to_stop = false;
-
-
- QMutex _mutex;
+ Q_OBJECT
+
+ public:
+ explicit WaitingMessageDialog(QWidget *parent);
+ ~WaitingMessageDialog();
+
+ void message(const QString &message);
+ void message(const QString &message, int progress_value);
+ void appendText(char *text);
+ void setText(const QString text);
+ void showEvent(QShowEvent *event);
+ void hideEvent(QHideEvent *event);
+
+ bool stopWorkerThread();
+
+ private slots:
+ void toggledStopButton(bool pushed);
+
+ private:
+ Ui::WaitingMessageDialog *ui;
+ QMovie *_p_movie;
+
+ bool _asked_to_stop = false;
+
+ QMutex _mutex;
};
#endif // WAITINGMESSAGEDIALOG_H
diff --git a/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.cpp b/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.cpp
index 3b8b1be26fb8b4fc189f2c4209886b2102ba62a6..e0202de5db129818c8ed968f0c2a627c6a533034 100644
--- a/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.cpp
+++ b/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "automaticfilterwidget.h"
@@ -29,77 +30,104 @@
#include <cmath>
-AutomaticFilterWidget::AutomaticFilterWidget(QWidget * parent):
- QWidget(parent),
- ui(new Ui::AutomaticFilterWidget)
+AutomaticFilterWidget::AutomaticFilterWidget(QWidget *parent)
+ : QWidget(parent), ui(new Ui::AutomaticFilterWidget)
{
- qDebug() << "AutomaticFilterWidget::AutomaticFilterWidget begin";
- ui->setupUi(this);
+ qDebug() << "AutomaticFilterWidget::AutomaticFilterWidget begin";
+ ui->setupUi(this);
- qDebug() << "AutomaticFilterWidget::AutomaticFilterWidget end";
+ qDebug() << "AutomaticFilterWidget::AutomaticFilterWidget end";
}
AutomaticFilterWidget::~AutomaticFilterWidget()
{
- qDebug() << "AutomaticFilterWidget::~AutomaticFilterWidget";
- delete ui;
- qDebug() << "AutomaticFilterWidget::~AutomaticFilterWidget end";
+ qDebug() << "AutomaticFilterWidget::~AutomaticFilterWidget";
+ delete ui;
+ qDebug() << "AutomaticFilterWidget::~AutomaticFilterWidget end";
}
-AutomaticFilterParameters AutomaticFilterWidget::getAutomaticFilterParameters() const {
- return _parameters;
+AutomaticFilterParameters
+AutomaticFilterWidget::getAutomaticFilterParameters() const
+{
+ return _parameters;
}
-void AutomaticFilterWidget::setAutomaticFilterParameters(const AutomaticFilterParameters & params) {
- qDebug() << "AutomaticFilterWidget::setAutomaticFilterParameters begin ";
- _parameters = params;
- _emit_changed = false;
- ui->peptide_evalue_spinbox->setValue(_parameters.getFilterPeptideEvalue());
- ui->protein_evalue_spinbox->setValue(_parameters.getFilterProteinEvalue());
- ui->peptide_number_spinbox->setValue(_parameters.getFilterMinimumPeptidePerMatch());
- //ui->protein_evalue_log_spinbox->setValue(std::log(_parameters.getFilterProteinEvalue()));
- ui->cross_sample_checkbox->setCheckState(Qt::Unchecked);
- if (_parameters.getFilterCrossSamplePeptideNumber()) ui->cross_sample_checkbox->setCheckState(Qt::Checked);
- _emit_changed = true;
- qDebug() << "AutomaticFilterWidget::setAutomaticFilterParameters end ";
+void
+AutomaticFilterWidget::setAutomaticFilterParameters(
+ const AutomaticFilterParameters ¶ms)
+{
+ qDebug() << "AutomaticFilterWidget::setAutomaticFilterParameters begin ";
+ _parameters = params;
+ _emit_changed = false;
+ ui->peptide_evalue_spinbox->setValue(_parameters.getFilterPeptideEvalue());
+ ui->protein_evalue_spinbox->setValue(_parameters.getFilterProteinEvalue());
+ ui->peptide_number_spinbox->setValue(
+ _parameters.getFilterMinimumPeptidePerMatch());
+ // ui->protein_evalue_log_spinbox->setValue(std::log(_parameters.getFilterProteinEvalue()));
+ ui->cross_sample_checkbox->setCheckState(Qt::Unchecked);
+ if(_parameters.getFilterCrossSamplePeptideNumber())
+ ui->cross_sample_checkbox->setCheckState(Qt::Checked);
+ _emit_changed = true;
+ qDebug() << "AutomaticFilterWidget::setAutomaticFilterParameters end ";
}
-void AutomaticFilterWidget::doCrossSample(bool is_cross_sample) {
- _parameters.setFilterCrossSamplePeptideNumber(is_cross_sample);
+void
+AutomaticFilterWidget::doCrossSample(bool is_cross_sample)
+{
+ _parameters.setFilterCrossSamplePeptideNumber(is_cross_sample);
- if (_emit_changed) emit automaticFilterParametersChanged(_parameters);
+ if(_emit_changed)
+ emit automaticFilterParametersChanged(_parameters);
}
-void AutomaticFilterWidget::doPeptideEvalue(double evalue) {
- _parameters.setFilterPeptideEvalue(evalue);
+void
+AutomaticFilterWidget::doPeptideEvalue(double evalue)
+{
+ _parameters.setFilterPeptideEvalue(evalue);
- if (_emit_changed) emit automaticFilterParametersChanged(_parameters);
+ if(_emit_changed)
+ emit automaticFilterParametersChanged(_parameters);
}
-void AutomaticFilterWidget::doProteinEvalue(double evalue) {
- if (_signal) {
- _parameters.setFilterProteinEvalue(evalue);
- _signal = false;
- ui->protein_evalue_log_spinbox->setValue(std::log10(_parameters.getFilterProteinEvalue()));
+void
+AutomaticFilterWidget::doProteinEvalue(double evalue)
+{
+ if(_signal)
+ {
+ _parameters.setFilterProteinEvalue(evalue);
+ _signal = false;
+ ui->protein_evalue_log_spinbox->setValue(
+ std::log10(_parameters.getFilterProteinEvalue()));
- if (_emit_changed) emit automaticFilterParametersChanged(_parameters);
+ if(_emit_changed)
+ emit automaticFilterParametersChanged(_parameters);
}
- else {
- _signal = true;
+ else
+ {
+ _signal = true;
}
}
-void AutomaticFilterWidget::doProteinLogEvalue(double evalue) {
- if (_signal) {
- _parameters.setFilterProteinEvalue(std::pow(10, evalue));
- _signal = false;
- ui->protein_evalue_spinbox->setValue(_parameters.getFilterProteinEvalue());
+void
+AutomaticFilterWidget::doProteinLogEvalue(double evalue)
+{
+ if(_signal)
+ {
+ _parameters.setFilterProteinEvalue(std::pow(10, evalue));
+ _signal = false;
+ ui->protein_evalue_spinbox->setValue(
+ _parameters.getFilterProteinEvalue());
- if (_emit_changed) emit automaticFilterParametersChanged(_parameters);
+ if(_emit_changed)
+ emit automaticFilterParametersChanged(_parameters);
}
- else {
- _signal = true;
+ else
+ {
+ _signal = true;
}
}
-void AutomaticFilterWidget::doPeptideNumber(int number) {
- _parameters.setFilterMinimumPeptidePerMatch((unsigned int) number);
- if (_emit_changed) emit automaticFilterParametersChanged(_parameters);
+void
+AutomaticFilterWidget::doPeptideNumber(int number)
+{
+ _parameters.setFilterMinimumPeptidePerMatch((unsigned int)number);
+ if(_emit_changed)
+ emit automaticFilterParametersChanged(_parameters);
}
diff --git a/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.h b/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.h
index 4b6e118d462a3551e09544ef029f4293297df0ca..a01b80525f1ec1fe1c66eb6068af61c41b67c56e 100644
--- a/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.h
+++ b/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef AUTOMATICFILTERWIDGET_H
#define AUTOMATICFILTERWIDGET_H
@@ -28,40 +29,40 @@
#include <QWidget>
-namespace Ui {
-class AutomaticFilterWidget;
+namespace Ui
+{
+ class AutomaticFilterWidget;
}
class AutomaticFilterWidget : public QWidget
{
- Q_OBJECT
+ Q_OBJECT
-public:
- explicit AutomaticFilterWidget(QWidget * parent);
- ~AutomaticFilterWidget();
+ public:
+ explicit AutomaticFilterWidget(QWidget *parent);
+ ~AutomaticFilterWidget();
- void setAutomaticFilterParameters(const AutomaticFilterParameters & params);
- AutomaticFilterParameters getAutomaticFilterParameters() const;
+ void setAutomaticFilterParameters(const AutomaticFilterParameters ¶ms);
+ AutomaticFilterParameters getAutomaticFilterParameters() const;
-public slots:
+ public slots:
-signals:
- void automaticFilterParametersChanged(AutomaticFilterParameters parameters);
-
-private slots:
- void doPeptideEvalue(double evalue);
- void doProteinEvalue(double evalue);
- void doProteinLogEvalue(double evalue);
- void doPeptideNumber(int number);
- void doCrossSample(bool is_cross_sample);
+ signals:
+ void automaticFilterParametersChanged(AutomaticFilterParameters parameters);
-private:
- Ui::AutomaticFilterWidget *ui;
- bool _signal = true;
- bool _emit_changed=true;
+ private slots:
+ void doPeptideEvalue(double evalue);
+ void doProteinEvalue(double evalue);
+ void doProteinLogEvalue(double evalue);
+ void doPeptideNumber(int number);
+ void doCrossSample(bool is_cross_sample);
- AutomaticFilterParameters _parameters;
+ private:
+ Ui::AutomaticFilterWidget *ui;
+ bool _signal = true;
+ bool _emit_changed = true;
+ AutomaticFilterParameters _parameters;
};
#endif // AUTOMATICFILTERWIDGET_H
diff --git a/src/gui/widgets/contaminant_widget/contaminantwidget.cpp b/src/gui/widgets/contaminant_widget/contaminantwidget.cpp
index 97b05057f938402594c443dc0c3158605a6713f6..2ab9d7847a202aa5bf775a582369784139795f95 100644
--- a/src/gui/widgets/contaminant_widget/contaminantwidget.cpp
+++ b/src/gui/widgets/contaminant_widget/contaminantwidget.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "contaminantwidget.h"
@@ -36,160 +37,206 @@
#include <QSettings>
#include <QFileDialog>
-ContaminantWidget::ContaminantWidget(QWidget * parent):
- QWidget(parent),
- ui(new Ui::ContaminantWidget)
+ContaminantWidget::ContaminantWidget(QWidget *parent)
+ : QWidget(parent), ui(new Ui::ContaminantWidget)
{
- qDebug() << "ContaminantWidget::ContaminantWidget begin";
- ui->setupUi(this);
- _emit_changed = false;
- _p_fasta_str_li = new QStandardItemModel();
- ui->contaminant_database_listview->setModel(_p_fasta_str_li);
- QItemSelectionModel * selection_model = ui->contaminant_database_listview->selectionModel();
- ui->contaminant_database_listview->setSelectionMode(QAbstractItemView::MultiSelection);
-
- doSelectContaminantSource();
- _emit_changed = true;
- qDebug() << "ContaminantWidget::ContaminantWidget end";
+ qDebug() << "ContaminantWidget::ContaminantWidget begin";
+ ui->setupUi(this);
+ _emit_changed = false;
+ _p_fasta_str_li = new QStandardItemModel();
+ ui->contaminant_database_listview->setModel(_p_fasta_str_li);
+ QItemSelectionModel *selection_model =
+ ui->contaminant_database_listview->selectionModel();
+ ui->contaminant_database_listview->setSelectionMode(
+ QAbstractItemView::MultiSelection);
+
+ doSelectContaminantSource();
+ _emit_changed = true;
+ qDebug() << "ContaminantWidget::ContaminantWidget end";
}
ContaminantWidget::~ContaminantWidget()
{
- qDebug() << "ContaminantWidget::~ContaminantWidget";
- delete ui;
- delete _p_fasta_str_li;
- qDebug() << "ContaminantWidget::~ContaminantWidget end";
+ qDebug() << "ContaminantWidget::~ContaminantWidget";
+ delete ui;
+ delete _p_fasta_str_li;
+ qDebug() << "ContaminantWidget::~ContaminantWidget end";
}
-void ContaminantWidget::setRegexpContaminantPattern(const QString & pattern) {
- _emit_changed = false;
- ui->contaminant_protein_regexp_line_edit->setText(pattern);
- _emit_changed = true;
+void
+ContaminantWidget::setRegexpContaminantPattern(const QString &pattern)
+{
+ _emit_changed = false;
+ ui->contaminant_protein_regexp_line_edit->setText(pattern);
+ _emit_changed = true;
}
-void ContaminantWidget::setFastaFileList(std::vector<FastaFileSp> fasta_file_list) {
-
- _p_fasta_str_li->removeRows(0, _p_fasta_str_li->rowCount());
- for (FastaFileSp fasta_file : fasta_file_list ) {
+void
+ContaminantWidget::setFastaFileList(std::vector<FastaFileSp> fasta_file_list)
+{
- QStandardItem *item;
- item = new QStandardItem(QString("%1").arg(fasta_file.get()->getFilename()));
- item->setEditable(false);
- item->setData(QVariant::fromValue(fasta_file), Qt::UserRole);
- _p_fasta_str_li->appendRow(item);
- //item->setData(QVariant(QString("%1").arg(fasta_file.get()->getAbsoluteFilePath())),Qt::UserRole);
+ _p_fasta_str_li->removeRows(0, _p_fasta_str_li->rowCount());
+ for(FastaFileSp fasta_file : fasta_file_list)
+ {
+
+ QStandardItem *item;
+ item =
+ new QStandardItem(QString("%1").arg(fasta_file.get()->getFilename()));
+ item->setEditable(false);
+ item->setData(QVariant::fromValue(fasta_file), Qt::UserRole);
+ _p_fasta_str_li->appendRow(item);
+ // item->setData(QVariant(QString("%1").arg(fasta_file.get()->getAbsoluteFilePath())),Qt::UserRole);
}
-
}
-void ContaminantWidget::getProjectContaminants(const Project * p_project) {
- _emit_changed = false;
- ui->contaminant_regexp_radiobutton->setChecked(true);
- ui->contaminant_protein_regexp_line_edit->setVisible(true);
- ui->contaminant_database_listview->setVisible(false);
- if (p_project->getProteinStore().getContaminantFastaFileList().size() > 0) {
- ui->contaminant_file_radiobutton->setChecked(true);
- ui->contaminant_protein_regexp_line_edit->setVisible(false);
- ui->contaminant_database_listview->setVisible(true);
+void
+ContaminantWidget::getProjectContaminants(const Project *p_project)
+{
+ _emit_changed = false;
+ ui->contaminant_regexp_radiobutton->setChecked(true);
+ ui->contaminant_protein_regexp_line_edit->setVisible(true);
+ ui->contaminant_database_listview->setVisible(false);
+ if(p_project->getProteinStore().getContaminantFastaFileList().size() > 0)
+ {
+ ui->contaminant_file_radiobutton->setChecked(true);
+ ui->contaminant_protein_regexp_line_edit->setVisible(false);
+ ui->contaminant_database_listview->setVisible(true);
}
- ui->contaminant_protein_regexp_line_edit->setText(p_project->getProteinStore().getRegexpContaminant().pattern());
+ ui->contaminant_protein_regexp_line_edit->setText(
+ p_project->getProteinStore().getRegexpContaminant().pattern());
- this->setFastaFileList( p_project->getFastaFileStore().getFastaFileList());
+ this->setFastaFileList(p_project->getFastaFileStore().getFastaFileList());
- ui->control_list_widget->setVisible(false);
- _no_project = false;
- _emit_changed = true;
+ ui->control_list_widget->setVisible(false);
+ _no_project = false;
+ _emit_changed = true;
}
-void ContaminantWidget::setProjectContaminants(Project * p_project) {
- qDebug() << "ContaminantWidget::setProjectContaminants begin";
- _emit_changed = false;
- if (ui->contaminant_file_radiobutton->isChecked()) {
- QModelIndexList index_list = ui->contaminant_database_listview->selectionModel()->selectedIndexes();
- p_project->getProteinStore().clearContaminants();
- if (index_list.size() > 0) {
- for (QModelIndex index :index_list) {
- if (index.data(Qt::UserRole).canConvert<FastaFileSp>()) {
- FastaFileSp p_fasta_file = index.data(Qt::UserRole).value<FastaFileSp>();
- p_fasta_file.get()->setContaminants(p_project->getProteinStore());
+void
+ContaminantWidget::setProjectContaminants(Project *p_project)
+{
+ qDebug() << "ContaminantWidget::setProjectContaminants begin";
+ _emit_changed = false;
+ if(ui->contaminant_file_radiobutton->isChecked())
+ {
+ QModelIndexList index_list =
+ ui->contaminant_database_listview->selectionModel()->selectedIndexes();
+ p_project->getProteinStore().clearContaminants();
+ if(index_list.size() > 0)
+ {
+ for(QModelIndex index : index_list)
+ {
+ if(index.data(Qt::UserRole).canConvert<FastaFileSp>())
+ {
+ FastaFileSp p_fasta_file =
+ index.data(Qt::UserRole).value<FastaFileSp>();
+ p_fasta_file.get()->setContaminants(
+ p_project->getProteinStore());
}
- else {
- throw pappso::PappsoException(QObject::tr("can not convert to FastaFile index.data().canConvert<FastaFile *>()"));
+ else
+ {
+ throw pappso::PappsoException(
+ QObject::tr("can not convert to FastaFile "
+ "index.data().canConvert<FastaFile *>()"));
}
}
}
- if (_no_project) {
- ui->control_list_widget->setVisible(true);
+ if(_no_project)
+ {
+ ui->control_list_widget->setVisible(true);
}
}
- else {
- p_project->getProteinStore().setRegexpContaminantPattern(ui->contaminant_protein_regexp_line_edit->text());
- ui->control_list_widget->setVisible(false);
+ else
+ {
+ p_project->getProteinStore().setRegexpContaminantPattern(
+ ui->contaminant_protein_regexp_line_edit->text());
+ ui->control_list_widget->setVisible(false);
}
- _emit_changed = true;
- qDebug() << "ContaminantWidget::setProjectContaminants end";
+ _emit_changed = true;
+ qDebug() << "ContaminantWidget::setProjectContaminants end";
}
-void ContaminantWidget::doChanged() {
- qDebug() << "ContaminantWidget::doChanged begin";
- if (_emit_changed) emit changed();
- qDebug() << "ContaminantWidget::doChanged end";
+void
+ContaminantWidget::doChanged()
+{
+ qDebug() << "ContaminantWidget::doChanged begin";
+ if(_emit_changed)
+ emit changed();
+ qDebug() << "ContaminantWidget::doChanged end";
}
-void ContaminantWidget::doSelectContaminantSource() {
- qDebug() << "ContaminantWidget::doSelectContaminantSource begin";
- ui->contaminant_database_listview->setVisible(false);
- ui->contaminant_protein_regexp_line_edit->setVisible(false);
- if (ui->contaminant_file_radiobutton->isChecked()) {
- ui->contaminant_database_listview->setVisible(true);
+void
+ContaminantWidget::doSelectContaminantSource()
+{
+ qDebug() << "ContaminantWidget::doSelectContaminantSource begin";
+ ui->contaminant_database_listview->setVisible(false);
+ ui->contaminant_protein_regexp_line_edit->setVisible(false);
+ if(ui->contaminant_file_radiobutton->isChecked())
+ {
+ ui->contaminant_database_listview->setVisible(true);
}
- else {
- ui->contaminant_protein_regexp_line_edit->setVisible(true);
+ else
+ {
+ ui->contaminant_protein_regexp_line_edit->setVisible(true);
}
- if (_emit_changed) emit changed();
- qDebug() << "ContaminantWidget::doSelectContaminantSource end";
+ if(_emit_changed)
+ emit changed();
+ qDebug() << "ContaminantWidget::doSelectContaminantSource end";
}
-void ContaminantWidget::doSelectFastaFile() {
- try {
- QSettings settings;
- QString default_fasta_location = settings.value("path/fastafiles_directory", "").toString();
-
- QStringList filenames = QFileDialog::getOpenFileNames(this,tr("FASTA files"),default_fasta_location,
- tr("FASTA files (*.fasta);;all files (*)") );
-
- if (filenames.size() > 0) {
- settings.setValue("path/fastafiles_directory", QFileInfo(filenames[0]).absolutePath());
+void
+ContaminantWidget::doSelectFastaFile()
+{
+ try
+ {
+ QSettings settings;
+ QString default_fasta_location =
+ settings.value("path/fastafiles_directory", "").toString();
+
+ QStringList filenames = QFileDialog::getOpenFileNames(
+ this, tr("FASTA files"), default_fasta_location,
+ tr("FASTA files (*.fasta);;all files (*)"));
+
+ if(filenames.size() > 0)
+ {
+ settings.setValue("path/fastafiles_directory",
+ QFileInfo(filenames[0]).absolutePath());
}
- std::vector<FastaFileSp> fasta_file_list;
- for (QString filename :filenames) {
- fasta_file_list.push_back(std::make_shared<FastaFile>(filename));
+ std::vector<FastaFileSp> fasta_file_list;
+ for(QString filename : filenames)
+ {
+ fasta_file_list.push_back(std::make_shared<FastaFile>(filename));
}
- for (FastaFileSp fasta_file : fasta_file_list ) {
+ for(FastaFileSp fasta_file : fasta_file_list)
+ {
- QStandardItem *item;
- item = new QStandardItem(QString("%1").arg(fasta_file.get()->getFilename()));
- item->setEditable(false);
- item->setData(QVariant::fromValue(fasta_file), Qt::UserRole);
- _p_fasta_str_li->appendRow(item);
- //item->setData(QVariant(QString("%1").arg(fasta_file.get()->getAbsoluteFilePath())),Qt::UserRole);
+ QStandardItem *item;
+ item = new QStandardItem(
+ QString("%1").arg(fasta_file.get()->getFilename()));
+ item->setEditable(false);
+ item->setData(QVariant::fromValue(fasta_file), Qt::UserRole);
+ _p_fasta_str_li->appendRow(item);
+ // item->setData(QVariant(QString("%1").arg(fasta_file.get()->getAbsoluteFilePath())),Qt::UserRole);
}
-
}
- catch (pappso::PappsoException & error) {
- //QMessageBox::warning(this,
- // tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
+ catch(pappso::PappsoException &error)
+ {
+ // QMessageBox::warning(this,
+ // tr("Error choosing identification result files :
+ // %1").arg(error.qwhat()), error);
}
}
-void ContaminantWidget::doClearList() {
- _p_fasta_str_li->removeRows( 0, _p_fasta_str_li->rowCount() );
+void
+ContaminantWidget::doClearList()
+{
+ _p_fasta_str_li->removeRows(0, _p_fasta_str_li->rowCount());
}
diff --git a/src/gui/widgets/contaminant_widget/contaminantwidget.h b/src/gui/widgets/contaminant_widget/contaminantwidget.h
index ef6c84a84497e451d44fab32c3175050f497b757..ffea09bd5da7ae97c8c5da086fb3b29eea72cae3 100644
--- a/src/gui/widgets/contaminant_widget/contaminantwidget.h
+++ b/src/gui/widgets/contaminant_widget/contaminantwidget.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef CONTAMINANTWIDGET_H
@@ -37,47 +38,47 @@
#include "../../../core/project.h"
-namespace Ui {
-class ContaminantWidget;
+namespace Ui
+{
+ class ContaminantWidget;
}
class ContaminantWidget : public QWidget
{
- Q_OBJECT
-
-public:
- explicit ContaminantWidget(QWidget * parent);
- ~ContaminantWidget();
-
-
- void setRegexpContaminantPattern(const QString & pattern);
-
- void setFastaFileList(std::vector<FastaFileSp> fasta_file_list);
-
- void setProjectContaminants(Project * p_project);
- void getProjectContaminants(const Project * p_project);
-
-public slots:
-
-signals:
- void changed();
-
-private slots:
- void doSelectContaminantSource();
- void doSelectFastaFile();
- void doClearList();
- void doChanged();
-
-
-private:
- Ui::ContaminantWidget *ui;
-
- bool _no_project = true;
-
- QStandardItemModel * _p_fasta_str_li;
-
- bool _emit_changed=true;
+ Q_OBJECT
+
+ public:
+ explicit ContaminantWidget(QWidget *parent);
+ ~ContaminantWidget();
+
+
+ void setRegexpContaminantPattern(const QString &pattern);
+
+ void setFastaFileList(std::vector<FastaFileSp> fasta_file_list);
+
+ void setProjectContaminants(Project *p_project);
+ void getProjectContaminants(const Project *p_project);
+
+ public slots:
+
+ signals:
+ void changed();
+
+ private slots:
+ void doSelectContaminantSource();
+ void doSelectFastaFile();
+ void doClearList();
+ void doChanged();
+
+
+ private:
+ Ui::ContaminantWidget *ui;
+
+ bool _no_project = true;
+
+ QStandardItemModel *_p_fasta_str_li;
+ bool _emit_changed = true;
};
#endif // CONTAMINANTWIDGET_H
diff --git a/src/gui/widgets/massitemdelegate.cpp b/src/gui/widgets/massitemdelegate.cpp
index fd11881ea6156bf59d99eb0b0153c9f3822bdd0b..c31acf57dff3f350d33c6b3d856744751b90cab7 100644
--- a/src/gui/widgets/massitemdelegate.cpp
+++ b/src/gui/widgets/massitemdelegate.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "massitemdelegate.h"
diff --git a/src/gui/widgets/massitemdelegate.h b/src/gui/widgets/massitemdelegate.h
index 80a20656baac5511e7246b74516b9649ad2e3655..1ee233834be08215c7381f9a172aaa5c279a13af 100644
--- a/src/gui/widgets/massitemdelegate.h
+++ b/src/gui/widgets/massitemdelegate.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef MASSITEMDELEGATE_H
#define MASSITEMDELEGATE_H
@@ -34,65 +35,75 @@
class MinuteItemDelegate : public QStyledItemDelegate
{
- Q_OBJECT
+ Q_OBJECT
-public:
+ public:
+ MinuteItemDelegate(QObject *parent = 0) : QStyledItemDelegate(parent)
+ {
+ }
- MinuteItemDelegate(QObject *parent = 0) : QStyledItemDelegate(parent) {}
-
- QString displayText(const QVariant & value, const QLocale & locale) const override
- {
- QString str = QString("%1'").arg(QString::number(value.toDouble(), 'f', 2));
- return str;
- }
+ QString
+ displayText(const QVariant &value, const QLocale &locale) const override
+ {
+ QString str = QString("%1'").arg(QString::number(value.toDouble(), 'f', 2));
+ return str;
+ }
};
class SecondItemDelegate : public QStyledItemDelegate
{
- Q_OBJECT
-
-public:
+ Q_OBJECT
- SecondItemDelegate(QObject *parent = 0) : QStyledItemDelegate(parent) {}
+ public:
+ SecondItemDelegate(QObject *parent = 0) : QStyledItemDelegate(parent)
+ {
+ }
- QString displayText(const QVariant & value, const QLocale & locale) const override
- {
- QString str = QString("%1\"").arg(QString::number(value.toDouble(), 'f', 2));
- return str;
- }
+ QString
+ displayText(const QVariant &value, const QLocale &locale) const override
+ {
+ QString str =
+ QString("%1\"").arg(QString::number(value.toDouble(), 'f', 2));
+ return str;
+ }
};
class PercentItemDelegate : public QStyledItemDelegate
{
- Q_OBJECT
+ Q_OBJECT
-public:
+ public:
+ PercentItemDelegate(QObject *parent = 0) : QStyledItemDelegate(parent)
+ {
+ }
- PercentItemDelegate(QObject *parent = 0) : QStyledItemDelegate(parent) {}
-
- QString displayText(const QVariant & value, const QLocale & locale) const override
- {
- QString str = QString("%1 %").arg(QString::number(value.toDouble()*100.0, 'f', 2));
- return str;
- }
+ QString
+ displayText(const QVariant &value, const QLocale &locale) const override
+ {
+ QString str =
+ QString("%1 %").arg(QString::number(value.toDouble() * 100.0, 'f', 2));
+ return str;
+ }
};
class MassItemDelegate : public QStyledItemDelegate
{
- Q_OBJECT
-
-public:
+ Q_OBJECT
- MassItemDelegate(QObject *parent = 0) : QStyledItemDelegate(parent) {}
+ public:
+ MassItemDelegate(QObject *parent = 0) : QStyledItemDelegate(parent)
+ {
+ }
- QString displayText(const QVariant & value, const QLocale & locale) const override
- {
- QString str = QString::number(value.toDouble(), 'f', 5);
- return str;
- }
+ QString
+ displayText(const QVariant &value, const QLocale &locale) const override
+ {
+ QString str = QString::number(value.toDouble(), 'f', 5);
+ return str;
+ }
};
#endif // MASSITEMDELEGATE_H
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index c09396e119b988b2a043002f8e9ce7c851263c55..904e2c5e65a80714f39b69448362611df61a1321 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "workerthread.h"
#include <odsstream/odsdocwriter.h>
@@ -46,392 +47,555 @@
#include "../core/tandem_run/tandemcondorprocess.h"
#include <QSettings>
-WorkerThread::WorkerThread(MainWindow * p_main_window)
+WorkerThread::WorkerThread(MainWindow *p_main_window)
{
- _p_main_window = p_main_window;
- qDebug() << "WorkerThread::WorkerThread begin MainWindow";
+ _p_main_window = p_main_window;
+ qDebug() << "WorkerThread::WorkerThread begin MainWindow";
- _p_work_monitor = new WorkMonitor();
+ _p_work_monitor = new WorkMonitor();
#if QT_VERSION >= 0x050000
- // Qt5 code
- //worker message
- connect(_p_work_monitor, &WorkMonitor::workerMessage, p_main_window,&MainWindow::doDisplayLoadingMessage);
- connect(_p_work_monitor, &WorkMonitor::workerMessagePercent, p_main_window,&MainWindow::doDisplayLoadingMessagePercent);
- connect(_p_work_monitor, &WorkMonitor::workerAppendText, p_main_window,&MainWindow::doWorkerAppendText);
- connect(_p_work_monitor, &WorkMonitor::workerSetText, p_main_window,&MainWindow::doWorkerSetText);
- connect(_p_work_monitor, &WorkMonitor::workerJobFinished, p_main_window,&MainWindow::doDisplayJobFinished);
-
- connect(p_main_window, &MainWindow::operateXpipFile, this,&WorkerThread::doXpipFileLoad);
- connect(p_main_window, &MainWindow::operateWritingXpipFile, this,&WorkerThread::doWritingXpipFile);
- connect(this, &WorkerThread::projectReady, p_main_window,&MainWindow::doProjectReady);
- connect(this, &WorkerThread::loadingResultsFinished, p_main_window,&MainWindow::doLoadingResultsReady);
-
- connect(p_main_window, &MainWindow::operateLoadingResults, this,&WorkerThread::doLoadingResults);
-
- connect(p_main_window, &MainWindow::operateRunningXtandem, this,&WorkerThread::doRunningXtandem);
- connect(this, &WorkerThread::loadingMessage, p_main_window,&MainWindow::doDisplayLoadingMessage);
- connect(this, &WorkerThread::projectNotReady, p_main_window,&MainWindow::doProjectNotReady);
-
- //grouping
- connect(p_main_window, &MainWindow::operateGrouping, this,&WorkerThread::doGrouping);
- connect(this, &WorkerThread::groupingFinished, p_main_window,&MainWindow::doGroupingFinished);
- //masschroq write
- connect(p_main_window, &MainWindow::operateWritingMassChroqFile, this,&WorkerThread::doWritingMassChroqFile);
- connect(p_main_window, &MainWindow::operateWritingMassChroqPrmFile, this,&WorkerThread::doWritingMassChroqPrmFile);
- connect(p_main_window, &MainWindow::operateWritingMcqrSpectralCountFile, this,&WorkerThread::doWritingMcqrSpectralCountFile);
- //protic write
- connect(p_main_window, &MainWindow::operateWritingProticFile, this,&WorkerThread::doWritingProticFile);
- //writing ODS file :
- connect(p_main_window, &MainWindow::operateWritingOdsFile, this,&WorkerThread::doWritingOdsFile);
- connect(this, &WorkerThread::operationFailed, p_main_window,&MainWindow::doOperationFailed);
- connect(this, &WorkerThread::operationFinished, p_main_window,&MainWindow::doOperationFinished);
+ // Qt5 code
+ // worker message
+ connect(_p_work_monitor, &WorkMonitor::workerMessage, p_main_window,
+ &MainWindow::doDisplayLoadingMessage);
+ connect(_p_work_monitor, &WorkMonitor::workerMessagePercent, p_main_window,
+ &MainWindow::doDisplayLoadingMessagePercent);
+ connect(_p_work_monitor, &WorkMonitor::workerAppendText, p_main_window,
+ &MainWindow::doWorkerAppendText);
+ connect(_p_work_monitor, &WorkMonitor::workerSetText, p_main_window,
+ &MainWindow::doWorkerSetText);
+ connect(_p_work_monitor, &WorkMonitor::workerJobFinished, p_main_window,
+ &MainWindow::doDisplayJobFinished);
+
+ connect(p_main_window, &MainWindow::operateXpipFile, this,
+ &WorkerThread::doXpipFileLoad);
+ connect(p_main_window, &MainWindow::operateWritingXpipFile, this,
+ &WorkerThread::doWritingXpipFile);
+ connect(this, &WorkerThread::projectReady, p_main_window,
+ &MainWindow::doProjectReady);
+ connect(this, &WorkerThread::loadingResultsFinished, p_main_window,
+ &MainWindow::doLoadingResultsReady);
+
+ connect(p_main_window, &MainWindow::operateLoadingResults, this,
+ &WorkerThread::doLoadingResults);
+
+ connect(p_main_window, &MainWindow::operateRunningXtandem, this,
+ &WorkerThread::doRunningXtandem);
+ connect(this, &WorkerThread::loadingMessage, p_main_window,
+ &MainWindow::doDisplayLoadingMessage);
+ connect(this, &WorkerThread::projectNotReady, p_main_window,
+ &MainWindow::doProjectNotReady);
+
+ // grouping
+ connect(p_main_window, &MainWindow::operateGrouping, this,
+ &WorkerThread::doGrouping);
+ connect(this, &WorkerThread::groupingFinished, p_main_window,
+ &MainWindow::doGroupingFinished);
+ // masschroq write
+ connect(p_main_window, &MainWindow::operateWritingMassChroqFile, this,
+ &WorkerThread::doWritingMassChroqFile);
+ connect(p_main_window, &MainWindow::operateWritingMassChroqPrmFile, this,
+ &WorkerThread::doWritingMassChroqPrmFile);
+ connect(p_main_window, &MainWindow::operateWritingMcqrSpectralCountFile, this,
+ &WorkerThread::doWritingMcqrSpectralCountFile);
+ // protic write
+ connect(p_main_window, &MainWindow::operateWritingProticFile, this,
+ &WorkerThread::doWritingProticFile);
+ // writing ODS file :
+ connect(p_main_window, &MainWindow::operateWritingOdsFile, this,
+ &WorkerThread::doWritingOdsFile);
+ connect(this, &WorkerThread::operationFailed, p_main_window,
+ &MainWindow::doOperationFailed);
+ connect(this, &WorkerThread::operationFinished, p_main_window,
+ &MainWindow::doOperationFinished);
#else
-// Qt4 code
- //worker message
- connect(_p_work_monitor, SIGNAL(workerMessage(QString)), p_main_window,SLOT(doDisplayLoadingMessage(QString)));
- connect(_p_work_monitor, SIGNAL(workerMessage(QString, int)), p_main_window,SLOT(doDisplayLoadingMessage(QString, int)));
- connect(_p_work_monitor, SIGNAL(workerAppendText(char *)), p_main_window,SLOT(doWorkerAppendText(char *)));
-
- connect(p_main_window, SIGNAL(operateXpipFile(QString)), this,SLOT(doXpipFileLoad(QString)));
- connect(this, SIGNAL(projectReady(ProjectSp)), p_main_window,SLOT(doProjectReady(ProjectSp)));
- connect(p_main_window, SIGNAL(operateLoadingResults(bool,AutomaticFilterParameters,QStringList)), this,SLOT(doLoadingResults(bool,AutomaticFilterParameters,QStringList)));
-
- connect(p_main_window, SIGNAL(operateRunningXtandem(TandemRunBatch)), this,SLOT(doRunningXtandem(TandemRunBatch)));
- connect(this, SIGNAL(loadingMessage(QString)), p_main_window,SLOT(doDisplayLoadingMessage(QString)));
- connect(this, SIGNAL(projectNotReady(QString)), p_main_window,SLOT(doProjectNotReady(QString)));
-
- //grouping
- connect(p_main_window, SIGNAL(operateGrouping(ProjectSp)), this,SLOT(doGrouping(ProjectSp)));
- connect(this, SIGNAL(groupingFinished()), p_main_window,SLOT(doGroupingFinished()));
- //masschroq write
- connect(p_main_window, SIGNAL(operateWritingMassChroqFile(QString, ProjectSp)), this,SLOT(doWritingMassChroqFile(QString, ProjectSp)));
- //protic write
- connect(p_main_window, SIGNAL(operateWritingProticFile(QString,ProjectSp)), this,SLOT(doWritingProticFile(QString,ProjectSp)));
- //writing ODS file :
- connect(p_main_window, SIGNAL(operateWritingOdsFile(QString, ProjectSp)), this,SLOT(doWritingOdsFile(QString, ProjectSp)));
- connect(this, SIGNAL(operationFailed(QString)), p_main_window,SLOT(doOperationFailed(QString)));
- connect(this, SIGNAL(operationFinished()), p_main_window,SLOT(doOperationFinished()));
+ // Qt4 code
+ // worker message
+ connect(_p_work_monitor, SIGNAL(workerMessage(QString)), p_main_window,
+ SLOT(doDisplayLoadingMessage(QString)));
+ connect(_p_work_monitor, SIGNAL(workerMessage(QString, int)), p_main_window,
+ SLOT(doDisplayLoadingMessage(QString, int)));
+ connect(_p_work_monitor, SIGNAL(workerAppendText(char *)), p_main_window,
+ SLOT(doWorkerAppendText(char *)));
+
+ connect(p_main_window, SIGNAL(operateXpipFile(QString)), this,
+ SLOT(doXpipFileLoad(QString)));
+ connect(this, SIGNAL(projectReady(ProjectSp)), p_main_window,
+ SLOT(doProjectReady(ProjectSp)));
+ connect(
+ p_main_window,
+ SIGNAL(operateLoadingResults(bool, AutomaticFilterParameters, QStringList)),
+ this, SLOT(doLoadingResults(bool, AutomaticFilterParameters, QStringList)));
+
+ connect(p_main_window, SIGNAL(operateRunningXtandem(TandemRunBatch)), this,
+ SLOT(doRunningXtandem(TandemRunBatch)));
+ connect(this, SIGNAL(loadingMessage(QString)), p_main_window,
+ SLOT(doDisplayLoadingMessage(QString)));
+ connect(this, SIGNAL(projectNotReady(QString)), p_main_window,
+ SLOT(doProjectNotReady(QString)));
+
+ // grouping
+ connect(p_main_window, SIGNAL(operateGrouping(ProjectSp)), this,
+ SLOT(doGrouping(ProjectSp)));
+ connect(this, SIGNAL(groupingFinished()), p_main_window,
+ SLOT(doGroupingFinished()));
+ // masschroq write
+ connect(p_main_window,
+ SIGNAL(operateWritingMassChroqFile(QString, ProjectSp)), this,
+ SLOT(doWritingMassChroqFile(QString, ProjectSp)));
+ // protic write
+ connect(p_main_window, SIGNAL(operateWritingProticFile(QString, ProjectSp)),
+ this, SLOT(doWritingProticFile(QString, ProjectSp)));
+ // writing ODS file :
+ connect(p_main_window, SIGNAL(operateWritingOdsFile(QString, ProjectSp)),
+ this, SLOT(doWritingOdsFile(QString, ProjectSp)));
+ connect(this, SIGNAL(operationFailed(QString)), p_main_window,
+ SLOT(doOperationFailed(QString)));
+ connect(this, SIGNAL(operationFinished()), p_main_window,
+ SLOT(doOperationFinished()));
#endif
- qDebug() << "WorkerThread::WorkerThread end MainWindow";
+ qDebug() << "WorkerThread::WorkerThread end MainWindow";
}
-WorkerThread::WorkerThread(ProjectWindow * p_project_window)
+WorkerThread::WorkerThread(ProjectWindow *p_project_window)
{
- qDebug() << "WorkerThread::WorkerThread begin ProjectWindow";
+ qDebug() << "WorkerThread::WorkerThread begin ProjectWindow";
- _p_work_monitor = new WorkMonitor();
+ _p_work_monitor = new WorkMonitor();
#if QT_VERSION >= 0x050000
- // Qt5 code
-
- //worker message
- connect(_p_work_monitor, &WorkMonitor::workerMessage, p_project_window,&ProjectWindow::doDisplayLoadingMessage);
- connect(_p_work_monitor, &WorkMonitor::workerMessagePercent, p_project_window,&ProjectWindow::doDisplayLoadingMessagePercent);
- connect(this, &WorkerThread::loadingMessage, p_project_window,&ProjectWindow::doDisplayLoadingMessage);
- //grouping
- connect(p_project_window, &ProjectWindow::operateGrouping, this,&WorkerThread::doGrouping);
- connect(this, &WorkerThread::groupingFinished, p_project_window,&ProjectWindow::doGroupingFinished);
-
-
- //PTM grouping on IdentificationGroup
- connect(p_project_window, &ProjectWindow::operatePtmGroupingOnIdentification, this,&WorkerThread::doPtmGroupingOnIdentification);
- connect(this, &WorkerThread::ptmGroupingOnIdentificationFinished, p_project_window,&ProjectWindow::refreshPtmGroup);
-
- //grouping on IdentificationGroup
- connect(p_project_window, &ProjectWindow::operateGroupingOnIdentification, this,&WorkerThread::doGroupingOnIdentification);
- connect(this, &WorkerThread::groupingOnIdentificationFinished, p_project_window,&ProjectWindow::refreshGroup);
-
- connect(this, &WorkerThread::operationFailed, p_project_window,&ProjectWindow::doOperationFailed);
- connect(this, &WorkerThread::operationFinished, p_project_window,&ProjectWindow::doOperationFinished);
+ // Qt5 code
+
+ // worker message
+ connect(_p_work_monitor, &WorkMonitor::workerMessage, p_project_window,
+ &ProjectWindow::doDisplayLoadingMessage);
+ connect(_p_work_monitor, &WorkMonitor::workerMessagePercent, p_project_window,
+ &ProjectWindow::doDisplayLoadingMessagePercent);
+ connect(this, &WorkerThread::loadingMessage, p_project_window,
+ &ProjectWindow::doDisplayLoadingMessage);
+ // grouping
+ connect(p_project_window, &ProjectWindow::operateGrouping, this,
+ &WorkerThread::doGrouping);
+ connect(this, &WorkerThread::groupingFinished, p_project_window,
+ &ProjectWindow::doGroupingFinished);
+
+
+ // PTM grouping on IdentificationGroup
+ connect(p_project_window, &ProjectWindow::operatePtmGroupingOnIdentification,
+ this, &WorkerThread::doPtmGroupingOnIdentification);
+ connect(this, &WorkerThread::ptmGroupingOnIdentificationFinished,
+ p_project_window, &ProjectWindow::refreshPtmGroup);
+
+ // grouping on IdentificationGroup
+ connect(p_project_window, &ProjectWindow::operateGroupingOnIdentification,
+ this, &WorkerThread::doGroupingOnIdentification);
+ connect(this, &WorkerThread::groupingOnIdentificationFinished,
+ p_project_window, &ProjectWindow::refreshGroup);
+
+ connect(this, &WorkerThread::operationFailed, p_project_window,
+ &ProjectWindow::doOperationFailed);
+ connect(this, &WorkerThread::operationFinished, p_project_window,
+ &ProjectWindow::doOperationFinished);
#else
-// Qt4 code
- qDebug() << "WorkerThread::WorkerThread Qt4 code";
-
- //worker message
- connect(_p_work_monitor, SIGNAL(workerMessage(QString)), p_project_window,SLOT(doDisplayLoadingMessage(QString)));
- connect(_p_work_monitor, SIGNAL(workerMessage(QString, int)), p_project_window,SLOT(doDisplayLoadingMessage(QString, int)));
-
- connect(this, SIGNAL(loadingMessage(QString)), p_project_window,SLOT(doDisplayLoadingMessage(QString)));
- //grouping
- connect(p_project_window, SIGNAL(operateGrouping(ProjectSp)), this,SLOT(doGrouping(ProjectSp)));
- connect(this, SIGNAL(groupingFinished()), p_project_window,SLOT(doGroupingFinished()));
-
-
- //PTM grouping on IdentificationGroup
- connect(p_project_window, SIGNAL(operatePtmGroupingOnIdentification(IdentificationGroup *)), this,SLOT(doPtmGroupingOnIdentification(IdentificationGroup *)));
- connect(this, SIGNAL(ptmGroupingOnIdentificationFinished(IdentificationGroup *)), p_project_window,SLOT(refreshPtmGroup(IdentificationGroup *)));
-
- //grouping on IdentificationGroup
- connect(p_project_window, SIGNAL(operateGroupingOnIdentification(IdentificationGroup *, GroupingType)), this,SLOT(doGroupingOnIdentification(IdentificationGroup *, GroupingType)));
- connect(this, SIGNAL(groupingOnIdentificationFinished(IdentificationGroup *)), p_project_window,SLOT(refreshGroup(IdentificationGroup *)));
-
- connect(this, SIGNAL(operationFailed(QString)), p_project_window,SLOT(doOperationFailed(QString)));
- connect(this, SIGNAL(operationFinished()), p_project_window,SLOT(doOperationFinished()));
+ // Qt4 code
+ qDebug() << "WorkerThread::WorkerThread Qt4 code";
+
+ // worker message
+ connect(_p_work_monitor, SIGNAL(workerMessage(QString)), p_project_window,
+ SLOT(doDisplayLoadingMessage(QString)));
+ connect(_p_work_monitor, SIGNAL(workerMessage(QString, int)),
+ p_project_window, SLOT(doDisplayLoadingMessage(QString, int)));
+
+ connect(this, SIGNAL(loadingMessage(QString)), p_project_window,
+ SLOT(doDisplayLoadingMessage(QString)));
+ // grouping
+ connect(p_project_window, SIGNAL(operateGrouping(ProjectSp)), this,
+ SLOT(doGrouping(ProjectSp)));
+ connect(this, SIGNAL(groupingFinished()), p_project_window,
+ SLOT(doGroupingFinished()));
+
+
+ // PTM grouping on IdentificationGroup
+ connect(p_project_window,
+ SIGNAL(operatePtmGroupingOnIdentification(IdentificationGroup *)),
+ this, SLOT(doPtmGroupingOnIdentification(IdentificationGroup *)));
+ connect(this,
+ SIGNAL(ptmGroupingOnIdentificationFinished(IdentificationGroup *)),
+ p_project_window, SLOT(refreshPtmGroup(IdentificationGroup *)));
+
+ // grouping on IdentificationGroup
+ connect(
+ p_project_window,
+ SIGNAL(
+ operateGroupingOnIdentification(IdentificationGroup *, GroupingType)),
+ this,
+ SLOT(doGroupingOnIdentification(IdentificationGroup *, GroupingType)));
+ connect(this, SIGNAL(groupingOnIdentificationFinished(IdentificationGroup *)),
+ p_project_window, SLOT(refreshGroup(IdentificationGroup *)));
+
+ connect(this, SIGNAL(operationFailed(QString)), p_project_window,
+ SLOT(doOperationFailed(QString)));
+ connect(this, SIGNAL(operationFinished()), p_project_window,
+ SLOT(doOperationFinished()));
#endif
- qDebug() << "WorkerThread::WorkerThread end ProjectWindow";
+ qDebug() << "WorkerThread::WorkerThread end ProjectWindow";
}
WorkerThread::~WorkerThread()
{
- qDebug() << "WorkerThread::WorkerThread destructor";
+ qDebug() << "WorkerThread::WorkerThread destructor";
}
-void WorkerThread::doXpipFileLoad(QString filename) {
- qDebug() << "WorkerThread::doXpipFileLoad begin "<< filename;
- try {
- QFileInfo new_xpip_file(filename);
- emit loadingMessage(tr("loading XPIP file"));
- qDebug() << "WorkerThread::doXpipFileLoad new_xpip_file "<< new_xpip_file.absoluteFilePath();
- XpipFile xpip_file(new_xpip_file);
- ProjectSp project_sp = xpip_file.getProjectSp(_p_work_monitor);
-
- emit projectReady(project_sp);
-
+void
+WorkerThread::doXpipFileLoad(QString filename)
+{
+ qDebug() << "WorkerThread::doXpipFileLoad begin " << filename;
+ try
+ {
+ QFileInfo new_xpip_file(filename);
+ emit loadingMessage(tr("loading XPIP file"));
+ qDebug() << "WorkerThread::doXpipFileLoad new_xpip_file "
+ << new_xpip_file.absoluteFilePath();
+ XpipFile xpip_file(new_xpip_file);
+ ProjectSp project_sp = xpip_file.getProjectSp(_p_work_monitor);
+
+ emit projectReady(project_sp);
}
- catch (pappso::PappsoException & error) {
- emit projectNotReady(tr("Error while reading XPIP file :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ emit projectNotReady(
+ tr("Error while reading XPIP file :\n%1").arg(error.qwhat()));
}
- qDebug() << "WorkerThread::doXpipFileLoad end";
+ qDebug() << "WorkerThread::doXpipFileLoad end";
}
-void WorkerThread::doPtmGroupingOnIdentification(IdentificationGroup * p_identification_group) {
- qDebug() << "WorkerThread::doPtmGroupingOnIdentification begin ";
- try {
- emit loadingMessage(tr("computing PTM islands"));
- try {
- p_identification_group->startPtmGrouping();
-
+void
+WorkerThread::doPtmGroupingOnIdentification(
+ IdentificationGroup *p_identification_group)
+{
+ qDebug() << "WorkerThread::doPtmGroupingOnIdentification begin ";
+ try
+ {
+ emit loadingMessage(tr("computing PTM islands"));
+ try
+ {
+ p_identification_group->startPtmGrouping();
}
- catch (pappso::PappsoException exception_pappso) {
- emit operationFailed(tr("Error computing PTM islands : %1").arg(exception_pappso.qwhat()));
+ catch(pappso::PappsoException exception_pappso)
+ {
+ emit operationFailed(tr("Error computing PTM islands : %1")
+ .arg(exception_pappso.qwhat()));
}
- catch (std::exception exception_std) {
- emit operationFailed(tr("Error computing PTM islands : %1").arg(exception_std.what()));
+ catch(std::exception exception_std)
+ {
+ emit operationFailed(
+ tr("Error computing PTM islands : %1").arg(exception_std.what()));
}
- emit loadingMessage(tr("computing PTM islands finished"));
- emit ptmGroupingOnIdentificationFinished(p_identification_group);
+ emit loadingMessage(tr("computing PTM islands finished"));
+ emit ptmGroupingOnIdentificationFinished(p_identification_group);
}
- catch (pappso::PappsoException & error) {
- emit operationFailed(tr("Error while computing PTM islands :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ emit operationFailed(
+ tr("Error while computing PTM islands :\n%1").arg(error.qwhat()));
}
- qDebug() << "WorkerThread::doPtmGroupingOnIdentification end ";
+ qDebug() << "WorkerThread::doPtmGroupingOnIdentification end ";
}
-void WorkerThread::doGroupingOnIdentification(IdentificationGroup * p_identification_group, GroupingType grouping_type) {
- qDebug() << "WorkerThread::doGroupingOnIdentification begin ";
- try {
- emit loadingMessage(tr("grouping proteins"));
- try {
- p_identification_group->startGrouping(grouping_type, _p_work_monitor);
-
+void
+WorkerThread::doGroupingOnIdentification(
+ IdentificationGroup *p_identification_group, GroupingType grouping_type)
+{
+ qDebug() << "WorkerThread::doGroupingOnIdentification begin ";
+ try
+ {
+ emit loadingMessage(tr("grouping proteins"));
+ try
+ {
+ p_identification_group->startGrouping(grouping_type, _p_work_monitor);
}
- catch (pappso::PappsoException exception_pappso) {
- emit operationFailed(tr("Error grouping identification : %1").arg(exception_pappso.qwhat()));
+ catch(pappso::PappsoException exception_pappso)
+ {
+ emit operationFailed(tr("Error grouping identification : %1")
+ .arg(exception_pappso.qwhat()));
}
- catch (std::exception exception_std) {
- emit operationFailed(tr("Error grouping identification : %1").arg(exception_std.what()));
+ catch(std::exception exception_std)
+ {
+ emit operationFailed(
+ tr("Error grouping identification : %1").arg(exception_std.what()));
}
- emit loadingMessage(tr("grouping proteins finished"));
- emit groupingOnIdentificationFinished(p_identification_group);
+ emit loadingMessage(tr("grouping proteins finished"));
+ emit groupingOnIdentificationFinished(p_identification_group);
}
- catch (pappso::PappsoException & error) {
- emit operationFailed(tr("Error while grouping :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ emit operationFailed(tr("Error while grouping :\n%1").arg(error.qwhat()));
}
- qDebug() << "WorkerThread::doGroupingOnIdentification end ";
+ qDebug() << "WorkerThread::doGroupingOnIdentification end ";
}
-void WorkerThread::doGrouping(ProjectSp project_sp) {
- qDebug() << "WorkerThread::doGrouping begin ";
- try {
- emit loadingMessage(tr("grouping proteins"));
- try {
- project_sp.get()->startGrouping(_p_work_monitor);
-
+void
+WorkerThread::doGrouping(ProjectSp project_sp)
+{
+ qDebug() << "WorkerThread::doGrouping begin ";
+ try
+ {
+ emit loadingMessage(tr("grouping proteins"));
+ try
+ {
+ project_sp.get()->startGrouping(_p_work_monitor);
}
- catch (pappso::PappsoException exception_pappso) {
- emit operationFailed(tr("Error grouping project : %1").arg(exception_pappso.qwhat()));
+ catch(pappso::PappsoException exception_pappso)
+ {
+ emit operationFailed(
+ tr("Error grouping project : %1").arg(exception_pappso.qwhat()));
}
- catch (std::exception exception_std) {
- emit operationFailed(tr("Error grouping project : %1").arg(exception_std.what()));
+ catch(std::exception exception_std)
+ {
+ emit operationFailed(
+ tr("Error grouping project : %1").arg(exception_std.what()));
}
- emit loadingMessage(tr("grouping proteins finished"));
- emit groupingFinished();
+ emit loadingMessage(tr("grouping proteins finished"));
+ emit groupingFinished();
}
- catch (pappso::PappsoException & error) {
- emit operationFailed(tr("Error while grouping :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ emit operationFailed(tr("Error while grouping :\n%1").arg(error.qwhat()));
}
- qDebug() << "WorkerThread::doGrouping end ";
+ qDebug() << "WorkerThread::doGrouping end ";
}
-void WorkerThread::doWritingXpipFile(QString filename, ProjectSp project_sp) {
+void
+WorkerThread::doWritingXpipFile(QString filename, ProjectSp project_sp)
+{
- try {
- emit loadingMessage(tr("writing XPIP file, please wait"));
- project_sp.get()->checkPsimodCompliance();
- Xpip xpip_file(filename);
- xpip_file.write(project_sp);
- xpip_file.close();
+ try
+ {
+ emit loadingMessage(tr("writing XPIP file, please wait"));
+ project_sp.get()->checkPsimodCompliance();
+ Xpip xpip_file(filename);
+ xpip_file.write(project_sp);
+ xpip_file.close();
- emit operationFinished();
+ emit operationFinished();
}
- catch (pappso::PappsoException & error) {
- emit operationFailed(tr("Error while writing XPIP file :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ emit operationFailed(
+ tr("Error while writing XPIP file :\n%1").arg(error.qwhat()));
}
}
-void WorkerThread::doWritingOdsFile(QString filename, ProjectSp project_sp) {
-
- try {
- emit loadingMessage(tr("writing ODS file, please wait"));
- OdsDocWriter writer(filename);
- OdsExport export_ods(project_sp.get());
- export_ods.write(&writer, _p_work_monitor);
- writer.close();
- emit operationFinished();
+void
+WorkerThread::doWritingOdsFile(QString filename, ProjectSp project_sp)
+{
+
+ try
+ {
+ emit loadingMessage(tr("writing ODS file, please wait"));
+ OdsDocWriter writer(filename);
+ OdsExport export_ods(project_sp.get());
+ export_ods.write(&writer, _p_work_monitor);
+ writer.close();
+ emit operationFinished();
}
- catch (pappso::PappsoException & error) {
- emit operationFailed(tr("Error while writing ODS file :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ emit operationFailed(
+ tr("Error while writing ODS file :\n%1").arg(error.qwhat()));
}
}
-void WorkerThread::doWritingMassChroqFile(QString filename, ProjectSp project_sp) {
+void
+WorkerThread::doWritingMassChroqFile(QString filename, ProjectSp project_sp)
+{
+
+ try
+ {
+ emit loadingMessage(tr("writing MassChroqML file, please wait"));
- try {
- emit loadingMessage(tr("writing MassChroqML file, please wait"));
-
- project_sp.get()->checkPsimodCompliance();
- MassChroQml output(filename);
- output.write(project_sp);
- output.close();
- emit operationFinished();
+ project_sp.get()->checkPsimodCompliance();
+ MassChroQml output(filename);
+ output.write(project_sp);
+ output.close();
+ emit operationFinished();
}
- catch (pappso::PappsoException & error) {
- emit operationFailed(tr("Error while writing MassChroqML file :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ emit operationFailed(
+ tr("Error while writing MassChroqML file :\n%1").arg(error.qwhat()));
}
}
-void WorkerThread::doWritingMassChroqPrmFile(QString filename, ProjectSp project_sp) {
+void
+WorkerThread::doWritingMassChroqPrmFile(QString filename, ProjectSp project_sp)
+{
+
+ try
+ {
+ emit loadingMessage(tr("writing MassChroqPRM file, please wait"));
- try {
- emit loadingMessage(tr("writing MassChroqPRM file, please wait"));
-
- project_sp.get()->checkPsimodCompliance();
- MassChroqPrm output(filename);
- output.write(project_sp);
- output.close();
- emit operationFinished();
+ project_sp.get()->checkPsimodCompliance();
+ MassChroqPrm output(filename);
+ output.write(project_sp);
+ output.close();
+ emit operationFinished();
}
- catch (pappso::PappsoException & error) {
- emit operationFailed(tr("Error while writing MassChroqPRM file :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ emit operationFailed(
+ tr("Error while writing MassChroqPRM file :\n%1").arg(error.qwhat()));
}
}
-void WorkerThread::doWritingProticFile(QString filename, ProjectSp project_sp) {
+void
+WorkerThread::doWritingProticFile(QString filename, ProjectSp project_sp)
+{
+
+ try
+ {
+ emit loadingMessage(tr("writing PROTICdbML file, please wait"));
- try {
- emit loadingMessage(tr("writing PROTICdbML file, please wait"));
-
- project_sp.get()->checkPsimodCompliance();
- ProticdbMl output(filename);
- output.write(project_sp);
- output.close();
- emit operationFinished();
+ project_sp.get()->checkPsimodCompliance();
+ ProticdbMl output(filename);
+ output.write(project_sp);
+ output.close();
+ emit operationFinished();
}
- catch (pappso::PappsoException & error) {
- emit operationFailed(tr("Error while writing PROTICdbML file :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ emit operationFailed(
+ tr("Error while writing PROTICdbML file :\n%1").arg(error.qwhat()));
}
}
-void WorkerThread::doWritingMcqrSpectralCountFile(QString filename, ProjectSp project_sp) {
- try {
- emit loadingMessage(tr("Writing %1 spectral count file for MassChroqR").arg(filename));
- QFile outFile;
- outFile.setFileName(filename);
- outFile.open(QIODevice::WriteOnly);
- QTextStream * p_outputStream = new QTextStream(&outFile);
- TsvOutputStream * p_writer = new TsvOutputStream(*p_outputStream);
- p_writer->setNoSheetName(true);
- McqrSpectralCount spectra_sheet(p_writer, project_sp.get());
- spectra_sheet.writeSheet();
-
- p_writer->close();
- delete p_writer;
- delete p_outputStream;
- outFile.close();
- emit operationFinished();
+void
+WorkerThread::doWritingMcqrSpectralCountFile(QString filename,
+ ProjectSp project_sp)
+{
+ try
+ {
+ emit loadingMessage(
+ tr("Writing %1 spectral count file for MassChroqR").arg(filename));
+ QFile outFile;
+ outFile.setFileName(filename);
+ outFile.open(QIODevice::WriteOnly);
+ QTextStream *p_outputStream = new QTextStream(&outFile);
+ TsvOutputStream *p_writer = new TsvOutputStream(*p_outputStream);
+ p_writer->setNoSheetName(true);
+ McqrSpectralCount spectra_sheet(p_writer, project_sp.get());
+ spectra_sheet.writeSheet();
+
+ p_writer->close();
+ delete p_writer;
+ delete p_outputStream;
+ outFile.close();
+ emit operationFinished();
}
- catch (OdsException & error) {
- emit operationFailed(tr("Error while writing spectral count file for MassChroqR :\n%1").arg(error.qwhat()));
+ catch(OdsException &error)
+ {
+ emit operationFailed(
+ tr("Error while writing spectral count file for MassChroqR :\n%1")
+ .arg(error.qwhat()));
}
- catch (pappso::PappsoException & errorb) {
- emit operationFailed(tr("Error while writing spectral count file for MassChroqR :\n%1").arg(errorb.qwhat()));
+ catch(pappso::PappsoException &errorb)
+ {
+ emit operationFailed(
+ tr("Error while writing spectral count file for MassChroqR :\n%1")
+ .arg(errorb.qwhat()));
}
}
-void WorkerThread::doLoadingResults(bool is_individual, AutomaticFilterParameters param, QStringList file_list) {
+void
+WorkerThread::doLoadingResults(bool is_individual,
+ AutomaticFilterParameters param,
+ QStringList file_list)
+{
- qDebug() << "WorkerThread::doLoadingResults begin ";
- try {
- if (file_list.size() == 0) {
- throw pappso::PappsoException(QObject::tr("file list is empty"));
+ qDebug() << "WorkerThread::doLoadingResults begin ";
+ try
+ {
+ if(file_list.size() == 0)
+ {
+ throw pappso::PappsoException(QObject::tr("file list is empty"));
}
- ProjectSp project_sp = Project().makeProjectSp();
- if (is_individual) {
- project_sp.get()->setProjectMode(ProjectMode::individual);
+ ProjectSp project_sp = Project().makeProjectSp();
+ if(is_individual)
+ {
+ project_sp.get()->setProjectMode(ProjectMode::individual);
}
- else {
- project_sp.get()->setProjectMode(ProjectMode::combined);
+ else
+ {
+ project_sp.get()->setProjectMode(ProjectMode::combined);
}
- _p_work_monitor->setProgressMaximumValue(file_list.size());
- int i=0;
- for (QString filename : file_list) {
- _p_work_monitor->message(tr("loading result file %1 (%2 on %3)").arg(filename).arg(i).arg(file_list.size()), i);
- project_sp.get()->readResultFile(filename);
- i++;
+ _p_work_monitor->setProgressMaximumValue(file_list.size());
+ int i = 0;
+ for(QString filename : file_list)
+ {
+ _p_work_monitor->message(tr("loading result file %1 (%2 on %3)")
+ .arg(filename)
+ .arg(i)
+ .arg(file_list.size()),
+ i);
+ project_sp.get()->readResultFile(filename);
+ i++;
}
- emit loadingMessage(tr("filtering proteins"));
- project_sp.get()->updateAutomaticFilters(param);
- qDebug() << "WorkerThread::doLoadingResults emit loadingResultsFinished(project_sp) ";
- emit loadingResultsFinished(project_sp);
-
+ emit loadingMessage(tr("filtering proteins"));
+ project_sp.get()->updateAutomaticFilters(param);
+ qDebug() << "WorkerThread::doLoadingResults emit "
+ "loadingResultsFinished(project_sp) ";
+ emit loadingResultsFinished(project_sp);
}
- catch (pappso::PappsoException & error) {
- qDebug() << "WorkerThread::doLoadingResults error ";
- emit projectNotReady(tr("Error while reading result files :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ qDebug() << "WorkerThread::doLoadingResults error ";
+ emit projectNotReady(
+ tr("Error while reading result files :\n%1").arg(error.qwhat()));
}
- qDebug() << "WorkerThread::doLoadingResults end ";
+ qDebug() << "WorkerThread::doLoadingResults end ";
}
-void WorkerThread::doRunningXtandem(TandemRunBatch tandem_run_batch) {
- qDebug() << "WorkerThread::doRunningXtandem begin ";
- try {
- emit loadingMessage(tr("Running X!Tandem, please wait"));
- qDebug() << "WorkerThread::doRunningXtandem tandem_run_batch " << tandem_run_batch._tandem_bin_path;
-
- QSettings settings;
- bool use_htcondor = settings.value("tandem/use_HTCondor", "false").toBool();
-
- if (use_htcondor) {
- TandemCondorProcess xt_process (_p_main_window ,_p_work_monitor, tandem_run_batch);
- xt_process.run();
+void
+WorkerThread::doRunningXtandem(TandemRunBatch tandem_run_batch)
+{
+ qDebug() << "WorkerThread::doRunningXtandem begin ";
+ try
+ {
+ emit loadingMessage(tr("Running X!Tandem, please wait"));
+ qDebug() << "WorkerThread::doRunningXtandem tandem_run_batch "
+ << tandem_run_batch._tandem_bin_path;
+
+ QSettings settings;
+ bool use_htcondor =
+ settings.value("tandem/use_HTCondor", "false").toBool();
+
+ if(use_htcondor)
+ {
+ TandemCondorProcess xt_process(_p_main_window, _p_work_monitor,
+ tandem_run_batch);
+ xt_process.run();
}
- else {
- TandemBatchProcess xt_process (_p_main_window ,_p_work_monitor, tandem_run_batch);
- xt_process.run();
+ else
+ {
+ TandemBatchProcess xt_process(_p_main_window, _p_work_monitor,
+ tandem_run_batch);
+ xt_process.run();
}
- emit operationFinished();
+ emit operationFinished();
}
- catch (pappso::PappsoException & error) {
- emit operationFailed(tr("Error while running X!Tandem job :\n%1").arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ emit operationFailed(
+ tr("Error while running X!Tandem job :\n%1").arg(error.qwhat()));
}
- qDebug() << "WorkerThread::doRunningXtandem end ";
+ qDebug() << "WorkerThread::doRunningXtandem end ";
}
diff --git a/src/gui/workerthread.h b/src/gui/workerthread.h
index c778e9572f57e7db6214ef5d993e9b85e6f111a2..ba40f8664aae6e0ea92176c53b765148abe33def 100644
--- a/src/gui/workerthread.h
+++ b/src/gui/workerthread.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef WORKERTHREAD_H
#define WORKERTHREAD_H
@@ -42,48 +43,51 @@ class ProjectWindow;
class WorkerThread : public QObject
{
- Q_OBJECT
+ Q_OBJECT
-public:
+ public:
+ WorkerThread(MainWindow *parent);
+ WorkerThread(ProjectWindow *parent);
+ ~WorkerThread();
- WorkerThread(MainWindow * parent);
- WorkerThread(ProjectWindow * parent);
- ~WorkerThread();
+ protected:
+ void closeEvent(QCloseEvent *event);
-protected:
+ public slots:
+ void doXpipFileLoad(QString filename);
+ void doLoadingResults(bool is_individual, AutomaticFilterParameters param,
+ QStringList file_list);
+ void doWritingXpipFile(QString filename, ProjectSp project_sp);
+ void doWritingOdsFile(QString filename, ProjectSp project_sp);
+ void doWritingMassChroqFile(QString filename, ProjectSp project_sp);
+ void doWritingMassChroqPrmFile(QString filename, ProjectSp project_sp);
+ void doWritingProticFile(QString filename, ProjectSp project_sp);
+ void doWritingMcqrSpectralCountFile(QString filename, ProjectSp project_sp);
+ void doGrouping(ProjectSp project_sp);
+ void doGroupingOnIdentification(IdentificationGroup *p_identification_group,
+ GroupingType grouping_type);
+ void
+ doPtmGroupingOnIdentification(IdentificationGroup *p_identification_group);
+ void doRunningXtandem(TandemRunBatch tandem_run_batch);
- void closeEvent(QCloseEvent *event);
-public slots:
- void doXpipFileLoad(QString filename);
- void doLoadingResults(bool is_individual, AutomaticFilterParameters param, QStringList file_list);
- void doWritingXpipFile(QString filename, ProjectSp project_sp);
- void doWritingOdsFile(QString filename, ProjectSp project_sp);
- void doWritingMassChroqFile(QString filename, ProjectSp project_sp);
- void doWritingMassChroqPrmFile(QString filename, ProjectSp project_sp);
- void doWritingProticFile(QString filename, ProjectSp project_sp);
- void doWritingMcqrSpectralCountFile(QString filename, ProjectSp project_sp);
- void doGrouping(ProjectSp project_sp);
- void doGroupingOnIdentification(IdentificationGroup * p_identification_group, GroupingType grouping_type);
- void doPtmGroupingOnIdentification(IdentificationGroup * p_identification_group);
- void doRunningXtandem(TandemRunBatch tandem_run_batch);
+ signals:
+ void loadingMessage(QString message);
+ void projectReady(ProjectSp project_sp);
+ void loadingResultsFinished(ProjectSp project_sp);
+ void projectNotReady(QString error);
+ void groupingFinished();
+ void
+ groupingOnIdentificationFinished(IdentificationGroup *p_identification_group);
+ void ptmGroupingOnIdentificationFinished(
+ IdentificationGroup *p_identification_group);
+ void operationFinished();
+ void operationFailed(QString error);
-
-signals:
- void loadingMessage(QString message);
- void projectReady(ProjectSp project_sp);
- void loadingResultsFinished(ProjectSp project_sp);
- void projectNotReady(QString error);
- void groupingFinished();
- void groupingOnIdentificationFinished(IdentificationGroup * p_identification_group);
- void ptmGroupingOnIdentificationFinished(IdentificationGroup * p_identification_group);
- void operationFinished();
- void operationFailed(QString error);
-
-private:
- WorkMonitor * _p_work_monitor;
- MainWindow * _p_main_window;
+ private:
+ WorkMonitor *_p_work_monitor;
+ MainWindow *_p_main_window;
};
#endif // WORKERTHREAD_H
diff --git a/src/gui/xic_view/xic_box/xicbox.cpp b/src/gui/xic_view/xic_box/xicbox.cpp
index d50674a6a5f38cbe262f71b4f41889255242c667..3fba0015823d580f69f774d0e4ae6a33058f0c6c 100644
--- a/src/gui/xic_view/xic_box/xicbox.cpp
+++ b/src/gui/xic_view/xic_box/xicbox.cpp
@@ -5,26 +5,27 @@
* \brief XIC box widget
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "xicbox.h"
#include "ui_xic_box.h"
@@ -36,436 +37,595 @@
#include <pappsomspp/exception/exceptionnotpossible.h>
-bool XicBoxNaturalIsotope::contains(const pappso::XicPeakSp & peak) const {
- for (const pappso::XicPeakSp & peak_i:detected_peak_list) {
- if (peak_i.get() == peak.get()) {
- return true;
+bool
+XicBoxNaturalIsotope::contains(const pappso::XicPeakSp &peak) const
+{
+ for(const pappso::XicPeakSp &peak_i : detected_peak_list)
+ {
+ if(peak_i.get() == peak.get())
+ {
+ return true;
}
}
- return false;
+ return false;
}
-class XicDetectionList: public pappso::XicDetectionSinkInterface {
-public:
- XicDetectionList () {
- _max_peak= nullptr;
- }
- void setPeptideEvidenceList(const std::vector<const PeptideEvidence *> & peptide_evidence_list) {
- for (const PeptideEvidence * p_evidence: peptide_evidence_list) {
- _rt_list.push_back(p_evidence->getRetentionTime());
- }
- }
- void setXicPeak (pappso::XicPeak & xic_peak) override {
- pappso::XicPeakSp peak_sp = xic_peak.makeXicPeakSp();
- _peak_list.push_back(peak_sp);
-
- for (pappso::pappso_double rt: _rt_list) {
- if (xic_peak.containsRt(rt)) {
- if ((_max_peak == nullptr) || (xic_peak.getArea() > _max_peak.get()->getArea())) {
- _max_peak = peak_sp;
- }
- }
- }
- };
- const pappso::XicPeakSp & getMatchedPeak() const {
- return _max_peak;
- }
- const std::vector<pappso::XicPeakSp> & getXicPeakList() const {
- return _peak_list;
- };
- void clear() {
- _peak_list.clear();
- _max_peak = nullptr;
- };
-private :
- unsigned int _count=0;
- std::vector<pappso::XicPeakSp> _peak_list;
- std::vector<pappso::pappso_double> _rt_list;
- pappso::XicPeakSp _max_peak;
+class XicDetectionList : public pappso::XicDetectionSinkInterface
+{
+ public:
+ XicDetectionList()
+ {
+ _max_peak = nullptr;
+ }
+ void
+ setPeptideEvidenceList(
+ const std::vector<const PeptideEvidence *> &peptide_evidence_list)
+ {
+ for(const PeptideEvidence *p_evidence : peptide_evidence_list)
+ {
+ _rt_list.push_back(p_evidence->getRetentionTime());
+ }
+ }
+ void
+ setXicPeak(pappso::XicPeak &xic_peak) override
+ {
+ pappso::XicPeakSp peak_sp = xic_peak.makeXicPeakSp();
+ _peak_list.push_back(peak_sp);
+
+ for(pappso::pappso_double rt : _rt_list)
+ {
+ if(xic_peak.containsRt(rt))
+ {
+ if((_max_peak == nullptr) ||
+ (xic_peak.getArea() > _max_peak.get()->getArea()))
+ {
+ _max_peak = peak_sp;
+ }
+ }
+ }
+ };
+ const pappso::XicPeakSp &
+ getMatchedPeak() const
+ {
+ return _max_peak;
+ }
+ const std::vector<pappso::XicPeakSp> &
+ getXicPeakList() const
+ {
+ return _peak_list;
+ };
+ void
+ clear()
+ {
+ _peak_list.clear();
+ _max_peak = nullptr;
+ };
+
+ private:
+ unsigned int _count = 0;
+ std::vector<pappso::XicPeakSp> _peak_list;
+ std::vector<pappso::pappso_double> _rt_list;
+ pappso::XicPeakSp _max_peak;
};
-
-XicBox::XicBox(XicWindow *parent):
- QWidget(parent),
- ui(new Ui::XicBox)
+XicBox::XicBox(XicWindow *parent) : QWidget(parent), ui(new Ui::XicBox)
{
- _p_xic_window = parent;
- ui->setupUi(this);
+ _p_xic_window = parent;
+ ui->setupUi(this);
- XicWorkerThread * p_worker = new XicWorkerThread();
- p_worker->moveToThread(&_xic_thread);
- _xic_thread.start();
+ XicWorkerThread *p_worker = new XicWorkerThread();
+ p_worker->moveToThread(&_xic_thread);
+ _xic_thread.start();
- //ui->histo_widget->setInteractions(QCP::iRangeDrag | QCP::iRangeZoom );
- //ui->xic_list_widget->setLayout(new QVBoxLayout(ui->xic_list_widget));
- ui->histo_widget->legend->setVisible(true);
+ // ui->histo_widget->setInteractions(QCP::iRangeDrag | QCP::iRangeZoom );
+ // ui->xic_list_widget->setLayout(new QVBoxLayout(ui->xic_list_widget));
+ ui->histo_widget->legend->setVisible(true);
- if (_p_xic_window->isRetentionTimeSeconds()) {
- ui->xic_widget->setRetentionTimeInSeconds();
+ if(_p_xic_window->isRetentionTimeSeconds())
+ {
+ ui->xic_widget->setRetentionTimeInSeconds();
}
- else {
- ui->xic_widget->setRetentionTimeInMinutes();
+ else
+ {
+ ui->xic_widget->setRetentionTimeInMinutes();
}
#if QT_VERSION >= 0x050000
- // Qt5 code
- connect(this, &XicBox::loadXic, p_worker, &XicWorkerThread::doXicLoad);
- connect(p_worker, &XicWorkerThread::xicLoaded,this, &XicBox::setXic);
- connect(p_worker, &XicWorkerThread::operationFailed, this, &XicBox::error);
-
-
- connect(this, &XicBox::computeIsotopeMassList, p_worker, &XicWorkerThread::doComputeIsotopeMassList);
- connect(p_worker, &XicWorkerThread::isotopeMassListComputed,this, &XicBox::setIsotopeMassList);
-
- connect(_p_xic_window, &XicWindow::reExtractXicNeeded,this, &XicBox::reExtractXic);
- connect(ui->xic_widget, &pappso::XicWidget::xicPeakListChanged,this, &XicBox::setXicPeakList);
- connect(ui->xic_widget, &pappso::XicWidget::clicked,this, &XicBox::onXicWidgetClick);
-
- connect(_p_xic_window, &XicWindow::rtUnitChangeNeeded,this, &XicBox::onRtUnitChanged);
+ // Qt5 code
+ connect(this, &XicBox::loadXic, p_worker, &XicWorkerThread::doXicLoad);
+ connect(p_worker, &XicWorkerThread::xicLoaded, this, &XicBox::setXic);
+ connect(p_worker, &XicWorkerThread::operationFailed, this, &XicBox::error);
+
+
+ connect(this, &XicBox::computeIsotopeMassList, p_worker,
+ &XicWorkerThread::doComputeIsotopeMassList);
+ connect(p_worker, &XicWorkerThread::isotopeMassListComputed, this,
+ &XicBox::setIsotopeMassList);
+
+ connect(_p_xic_window, &XicWindow::reExtractXicNeeded, this,
+ &XicBox::reExtractXic);
+ connect(ui->xic_widget, &pappso::XicWidget::xicPeakListChanged, this,
+ &XicBox::setXicPeakList);
+ connect(ui->xic_widget, &pappso::XicWidget::clicked, this,
+ &XicBox::onXicWidgetClick);
+
+ connect(_p_xic_window, &XicWindow::rtUnitChangeNeeded, this,
+ &XicBox::onRtUnitChanged);
#else
// Qt4 code
#endif
- QStringList msrun_list;
- for (MsRunSp msrun_sp : _p_xic_window->getProjectWindow()->getProjectP()->getMsRunStore().getMsRunList()) {
- msrun_list << msrun_sp.get()->getFilename();
- qDebug() << "ProteinListWindow::setIdentificationGroup " << msrun_sp.get()->getFilename();
+ QStringList msrun_list;
+ for(MsRunSp msrun_sp : _p_xic_window->getProjectWindow()
+ ->getProjectP()
+ ->getMsRunStore()
+ .getMsRunList())
+ {
+ msrun_list << msrun_sp.get()->getFilename();
+ qDebug() << "ProteinListWindow::setIdentificationGroup "
+ << msrun_sp.get()->getFilename();
}
- QCompleter *completer = new QCompleter(msrun_list, this);
- completer->setCaseSensitivity(Qt::CaseInsensitive);
-
- completer->setCompletionMode(QCompleter::PopupCompletion);
- completer->setModelSorting(QCompleter::CaseSensitivelySortedModel);
- completer->setFilterMode(Qt::MatchContains);
- ui->msrun_autocompletion->setCompleter(completer);
+ QCompleter *completer = new QCompleter(msrun_list, this);
+ completer->setCaseSensitivity(Qt::CaseInsensitive);
+ completer->setCompletionMode(QCompleter::PopupCompletion);
+ completer->setModelSorting(QCompleter::CaseSensitivelySortedModel);
+ completer->setFilterMode(Qt::MatchContains);
+ ui->msrun_autocompletion->setCompleter(completer);
}
XicBox::~XicBox()
{
- qDebug() << "XicBox::~XicBox";
- _xic_thread.quit();
- _xic_thread.wait();
+ qDebug() << "XicBox::~XicBox";
+ _xic_thread.quit();
+ _xic_thread.wait();
}
-void XicBox::onXicWidgetClick(double rt, double intensity) {
- qDebug() << __FILE__ << " " <<__FUNCTION__ << " " << __LINE__;
- ui->xic_widget->clearXicPeakBorders();
- std::vector <pappso::XicPeakSp> draw_peak_borders;
- for (XicBoxNaturalIsotope peak:_natural_isotope_list) {
- qDebug() << __FILE__ << " " <<__FUNCTION__ << " " << __LINE__;
- draw_peak_borders.push_back(peak.one_peak_sp);
- if (peak.one_peak_sp.get() != nullptr) {
- ui->xic_widget->drawXicPeakBorders(peak.one_peak_sp);
+void
+XicBox::onXicWidgetClick(double rt, double intensity)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ ui->xic_widget->clearXicPeakBorders();
+ std::vector<pappso::XicPeakSp> draw_peak_borders;
+ for(XicBoxNaturalIsotope peak : _natural_isotope_list)
+ {
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ draw_peak_borders.push_back(peak.one_peak_sp);
+ if(peak.one_peak_sp.get() != nullptr)
+ {
+ ui->xic_widget->drawXicPeakBorders(peak.one_peak_sp);
}
}
- if (_peptide_evidence_list.size() == 0) {
- drawObservedAreaBars(draw_peak_borders);
+ if(_peptide_evidence_list.size() == 0)
+ {
+ drawObservedAreaBars(draw_peak_borders);
}
-
}
-void XicBox::remove() {
- _p_xic_window->removeXicBox(this);
+void
+XicBox::remove()
+{
+ _p_xic_window->removeXicBox(this);
}
-void XicBox::error(QString error_message) {
- QMessageBox::warning(this,
- tr("Error extracting XIC :"), error_message);
-
+void
+XicBox::error(QString error_message)
+{
+ QMessageBox::warning(this, tr("Error extracting XIC :"), error_message);
}
-void XicBox::extractXicInOtherMsRun() {
- qDebug() << "XicBox::extractXicInOtherMsRun begin";
- try {
- MsRunSp msrun_sp = _p_xic_window->getProjectWindow()->getProjectP()->getMsRunStore().getInstance(ui->msrun_autocompletion->text());
- _p_xic_window->addXicInMsRun(_p_peptide_evidence, msrun_sp);
+void
+XicBox::extractXicInOtherMsRun()
+{
+ qDebug() << "XicBox::extractXicInOtherMsRun begin";
+ try
+ {
+ MsRunSp msrun_sp = _p_xic_window->getProjectWindow()
+ ->getProjectP()
+ ->getMsRunStore()
+ .getInstance(ui->msrun_autocompletion->text());
+ _p_xic_window->addXicInMsRun(_p_peptide_evidence, msrun_sp);
}
- catch (pappso::ExceptionNotFound & error) {
- qDebug() << "XicBox::extractXicInOtherMsRun not found " << ui->msrun_autocompletion->text();
+ catch(pappso::ExceptionNotFound &error)
+ {
+ qDebug() << "XicBox::extractXicInOtherMsRun not found "
+ << ui->msrun_autocompletion->text();
}
}
-void XicBox::setPeptideEvidence(const PeptideEvidence * p_peptide_evidence) {
-
-
- _p_peptide_evidence = p_peptide_evidence;
- _msrun_sp = p_peptide_evidence->getIdentificationDataSource()->getMsRunSp();
-
- ui->peptide_label->setText(_p_peptide_evidence->getPeptideXtpSp().get()->toString());
- ui->msrun_label->setText(_p_peptide_evidence->getMsRunP()->getFilename());
- ui->charge_label->setText(QString("%1").arg(_p_peptide_evidence->getCharge()));
- ui->mz_label->setText(QString::number(_p_peptide_evidence->getTheoreticalMz(), 'f', 4));
-
- //get same xic peptide evidence (msrun, peptide, charge)
- //p_projet
- _peptide_evidence_list.clear();
- _p_xic_window->getProjectWindow()->getProjectP()->getSameXicPeptideEvidenceList(_peptide_evidence_list, _msrun_sp.get(),_p_peptide_evidence->getPeptideXtpSp().get(),_p_peptide_evidence->getCharge());
+void
+XicBox::setPeptideEvidence(const PeptideEvidence *p_peptide_evidence)
+{
- emit computeIsotopeMassList(_p_peptide_evidence->getPeptideXtpSp(), _p_peptide_evidence->getCharge(), _p_xic_window->getXicExtractPrecision(), 0.8);
+ _p_peptide_evidence = p_peptide_evidence;
+ _msrun_sp = p_peptide_evidence->getIdentificationDataSource()->getMsRunSp();
+
+ ui->peptide_label->setText(
+ _p_peptide_evidence->getPeptideXtpSp().get()->toString());
+ ui->msrun_label->setText(_p_peptide_evidence->getMsRunP()->getFilename());
+ ui->charge_label->setText(
+ QString("%1").arg(_p_peptide_evidence->getCharge()));
+ ui->mz_label->setText(
+ QString::number(_p_peptide_evidence->getTheoreticalMz(), 'f', 4));
+
+ // get same xic peptide evidence (msrun, peptide, charge)
+ // p_projet
+ _peptide_evidence_list.clear();
+ _p_xic_window->getProjectWindow()
+ ->getProjectP()
+ ->getSameXicPeptideEvidenceList(
+ _peptide_evidence_list, _msrun_sp.get(),
+ _p_peptide_evidence->getPeptideXtpSp().get(),
+ _p_peptide_evidence->getCharge());
+
+ emit computeIsotopeMassList(_p_peptide_evidence->getPeptideXtpSp(),
+ _p_peptide_evidence->getCharge(),
+ _p_xic_window->getXicExtractPrecision(), 0.8);
}
-void XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence * p_peptide_evidence, MsRunSp msrun_sp) {
- _p_peptide_evidence = p_peptide_evidence;
- _msrun_sp = msrun_sp;
-
- ui->peptide_label->setText(_p_peptide_evidence->getPeptideXtpSp().get()->toString());
- ui->msrun_label->setText(msrun_sp->getFilename());
- ui->charge_label->setText(QString("%1").arg(_p_peptide_evidence->getCharge()));
- ui->mz_label->setText(QString::number(_p_peptide_evidence->getTheoreticalMz(), 'f', 4));
-
- //get same xic peptide evidence (msrun, peptide, charge)
- //p_projet
- _peptide_evidence_list.clear();
-
- _p_xic_window->getProjectWindow()->getProjectP()->getSameXicPeptideEvidenceList(_peptide_evidence_list, _msrun_sp.get(),_p_peptide_evidence->getPeptideXtpSp().get(),_p_peptide_evidence->getCharge());
- //_p_xic_window->getProjectWindow()->getProjectP()->getSameXicPeptideEvidenceList(p_peptide_evidence, _peptide_evidence_list);
-
- emit computeIsotopeMassList(_p_peptide_evidence->getPeptideXtpSp(), _p_peptide_evidence->getCharge(), _p_xic_window->getXicExtractPrecision(), 0.8);
-
+void
+XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence *p_peptide_evidence,
+ MsRunSp msrun_sp)
+{
+ _p_peptide_evidence = p_peptide_evidence;
+ _msrun_sp = msrun_sp;
+
+ ui->peptide_label->setText(
+ _p_peptide_evidence->getPeptideXtpSp().get()->toString());
+ ui->msrun_label->setText(msrun_sp->getFilename());
+ ui->charge_label->setText(
+ QString("%1").arg(_p_peptide_evidence->getCharge()));
+ ui->mz_label->setText(
+ QString::number(_p_peptide_evidence->getTheoreticalMz(), 'f', 4));
+
+ // get same xic peptide evidence (msrun, peptide, charge)
+ // p_projet
+ _peptide_evidence_list.clear();
+
+ _p_xic_window->getProjectWindow()
+ ->getProjectP()
+ ->getSameXicPeptideEvidenceList(
+ _peptide_evidence_list, _msrun_sp.get(),
+ _p_peptide_evidence->getPeptideXtpSp().get(),
+ _p_peptide_evidence->getCharge());
+ //_p_xic_window->getProjectWindow()->getProjectP()->getSameXicPeptideEvidenceList(p_peptide_evidence,
+ //_peptide_evidence_list);
+
+ emit computeIsotopeMassList(_p_peptide_evidence->getPeptideXtpSp(),
+ _p_peptide_evidence->getCharge(),
+ _p_xic_window->getXicExtractPrecision(), 0.8);
}
-void XicBox::setXic(std::vector< pappso::XicSp> xic_sp_list) {
- qDebug() << "XicBox::setXic begin " << xic_sp_list.size();
- ui->xic_widget->clear();
- for (int i=0; i < xic_sp_list.size(); i++) {
- _natural_isotope_list[i].xic_sp = xic_sp_list[i];
+void
+XicBox::setXic(std::vector<pappso::XicSp> xic_sp_list)
+{
+ qDebug() << "XicBox::setXic begin " << xic_sp_list.size();
+ ui->xic_widget->clear();
+ for(int i = 0; i < xic_sp_list.size(); i++)
+ {
+ _natural_isotope_list[i].xic_sp = xic_sp_list[i];
}
- //pappso::XicWidget * xic_widget = new pappso::XicWidget(this);
- //ui->xic_list_widget->layout()->addWidget(xic_widget);
- for (XicBoxNaturalIsotope & xic_isotope :_natural_isotope_list) {
- //qDebug() << "XicBox::setXic xic " << xic_isotope.xic_sp.get();
- if (xic_isotope.xic_sp.get() == nullptr) {
- throw new pappso::PappsoException("Error in XicBox::setXic:\n xic_isotope.xic_sp.get() == nullptr");
+ // pappso::XicWidget * xic_widget = new pappso::XicWidget(this);
+ // ui->xic_list_widget->layout()->addWidget(xic_widget);
+ for(XicBoxNaturalIsotope &xic_isotope : _natural_isotope_list)
+ {
+ // qDebug() << "XicBox::setXic xic " << xic_isotope.xic_sp.get();
+ if(xic_isotope.xic_sp.get() == nullptr)
+ {
+ throw new pappso::PappsoException(
+ "Error in XicBox::setXic:\n xic_isotope.xic_sp.get() == nullptr");
}
- qDebug() << "XicBox::setXic xic_isotope.xic_sp.size() " << xic_isotope.xic_sp.get()->size();
- ui->xic_widget->addXicSp(xic_isotope.xic_sp);
- QString isotope_name = QString("+%1").arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber());
- if (xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank() > 1) {
- isotope_name = QString("+%1 [%2]").arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber()).arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank());
+ qDebug() << "XicBox::setXic xic_isotope.xic_sp.size() "
+ << xic_isotope.xic_sp.get()->size();
+ ui->xic_widget->addXicSp(xic_isotope.xic_sp);
+ QString isotope_name = QString("+%1").arg(
+ xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber());
+ if(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank() > 1)
+ {
+ isotope_name =
+ QString("+%1 [%2]")
+ .arg(xic_isotope.peptide_natural_isotope_sp.get()
+ ->getIsotopeNumber())
+ .arg(
+ xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank());
}
- isotope_name.append(QString(" (%1%)").arg((int) (xic_isotope.peptide_natural_isotope_sp.get()->getIntensityRatio()*100)));
- ui->xic_widget->setName(xic_isotope.xic_sp.get(), isotope_name);
-
- if (xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber() == 0) {
- for (const PeptideEvidence * peptide_evidence:_peptide_evidence_list) {
- qDebug() << "XicBox::setXic peptide_evidence " << peptide_evidence->getRetentionTime();
- ui->xic_widget->addMsMsEvent(xic_isotope.xic_sp.get(), peptide_evidence->getRetentionTime());
+ isotope_name.append(QString(" (%1%)").arg((
+ int)(xic_isotope.peptide_natural_isotope_sp.get()->getIntensityRatio() *
+ 100)));
+ ui->xic_widget->setName(xic_isotope.xic_sp.get(), isotope_name);
+
+ if(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber() == 0)
+ {
+ for(const PeptideEvidence *peptide_evidence : _peptide_evidence_list)
+ {
+ qDebug() << "XicBox::setXic peptide_evidence "
+ << peptide_evidence->getRetentionTime();
+ ui->xic_widget->addMsMsEvent(
+ xic_isotope.xic_sp.get(), peptide_evidence->getRetentionTime());
}
}
}
- qDebug() << "XicBox::setXic rescale" ;
+ qDebug() << "XicBox::setXic rescale";
- if (!_scaled) {
- ui->xic_widget->rescale();
- _scaled = true;
+ if(!_scaled)
+ {
+ ui->xic_widget->rescale();
+ _scaled = true;
}
- /*
- if (_isotope_mass_list.size() > _xic_widget_list.size()) {
- emit loadXic(_p_peptide_evidence->getMsRunP(), _isotope_mass_list[_xic_widget_list.size()].get()->getMz(), _p_xic_window->getXicExtractPrecision(), XicExtractMethod::max);
- }
- */
- XicDetectionList xic_list;
- xic_list.setPeptideEvidenceList(_peptide_evidence_list);
-
- std::vector <pappso::XicPeakSp> draw_peak_borders;
-
- for (XicBoxNaturalIsotope & xic_isotope :_natural_isotope_list) {
- try {
- xic_list.clear();
- _p_xic_window->xicDetect(*(xic_isotope.xic_sp.get()), &xic_list);
- xic_isotope.matched_peak_sp = xic_list.getMatchedPeak();
- xic_isotope.detected_peak_list = xic_list.getXicPeakList();
- ui->xic_widget->addXicPeakList(xic_isotope.xic_sp.get(), xic_list.getXicPeakList());
- draw_peak_borders.push_back(xic_isotope.matched_peak_sp);
+ /*
+ if (_isotope_mass_list.size() > _xic_widget_list.size()) {
+ emit loadXic(_p_peptide_evidence->getMsRunP(),
+ _isotope_mass_list[_xic_widget_list.size()].get()->getMz(),
+ _p_xic_window->getXicExtractPrecision(), XicExtractMethod::max);
+ }
+ */
+ XicDetectionList xic_list;
+ xic_list.setPeptideEvidenceList(_peptide_evidence_list);
+
+ std::vector<pappso::XicPeakSp> draw_peak_borders;
+
+ for(XicBoxNaturalIsotope &xic_isotope : _natural_isotope_list)
+ {
+ try
+ {
+ xic_list.clear();
+ _p_xic_window->xicDetect(*(xic_isotope.xic_sp.get()), &xic_list);
+ xic_isotope.matched_peak_sp = xic_list.getMatchedPeak();
+ xic_isotope.detected_peak_list = xic_list.getXicPeakList();
+ ui->xic_widget->addXicPeakList(xic_isotope.xic_sp.get(),
+ xic_list.getXicPeakList());
+ draw_peak_borders.push_back(xic_isotope.matched_peak_sp);
}
- catch (const pappso::ExceptionNotPossible & e) {
- qDebug() << e.qwhat();
+ catch(const pappso::ExceptionNotPossible &e)
+ {
+ qDebug() << e.qwhat();
}
}
- qDebug() << "XicBox::setXic plot" ;
- ui->xic_widget->plot();
- drawObservedAreaBars(draw_peak_borders);
+ qDebug() << "XicBox::setXic plot";
+ ui->xic_widget->plot();
+ drawObservedAreaBars(draw_peak_borders);
}
-void XicBox::drawObservedAreaBars(const std::vector<pappso::XicPeakSp> & observed_peak_to_draw_list) {
- if (_isotope_ratio_graph_observed_intensity == nullptr) {
- qDebug() << "XicBox::setXic plot new QCPBars" ;
- _isotope_ratio_graph_observed_intensity = new QCPBars(ui->histo_widget->xAxis, ui->histo_widget->yAxis2);
+void
+XicBox::drawObservedAreaBars(
+ const std::vector<pappso::XicPeakSp> &observed_peak_to_draw_list)
+{
+ if(_isotope_ratio_graph_observed_intensity == nullptr)
+ {
+ qDebug() << "XicBox::setXic plot new QCPBars";
+ _isotope_ratio_graph_observed_intensity =
+ new QCPBars(ui->histo_widget->xAxis, ui->histo_widget->yAxis2);
}
- else {
- qDebug() << "XicBox::setXic plot clearData" ;
- _isotope_ratio_graph_observed_intensity->clearData();
+ else
+ {
+ qDebug() << "XicBox::setXic plot clearData";
+ _isotope_ratio_graph_observed_intensity->clearData();
}
- _isotope_ratio_graph_observed_intensity->setName("XIC area");
- //ui->histo_widget->yAxis2->setLabel("intensity");
-
-
- QVector<double> observed_intensity_data;
- QVector<QString> labels;
-
- QVector<double> ticks;
- double sum = 0;
- int i = 0;
-
- qDebug() << "XicBox::setXic plot _isotope_mass_list" ;
- for (const XicBoxNaturalIsotope & xic_isotope : _natural_isotope_list) {
- pappso::XicPeakSp peak_to_draw;
- for (pappso::XicPeakSp observed_peak : observed_peak_to_draw_list) {
- if (xic_isotope.contains(observed_peak)) {
- peak_to_draw = observed_peak;
+ _isotope_ratio_graph_observed_intensity->setName("XIC area");
+ // ui->histo_widget->yAxis2->setLabel("intensity");
+
+
+ QVector<double> observed_intensity_data;
+ QVector<QString> labels;
+
+ QVector<double> ticks;
+ double sum = 0;
+ int i = 0;
+
+ qDebug() << "XicBox::setXic plot _isotope_mass_list";
+ for(const XicBoxNaturalIsotope &xic_isotope : _natural_isotope_list)
+ {
+ pappso::XicPeakSp peak_to_draw;
+ for(pappso::XicPeakSp observed_peak : observed_peak_to_draw_list)
+ {
+ if(xic_isotope.contains(observed_peak))
+ {
+ peak_to_draw = observed_peak;
}
}
- if (peak_to_draw.get() == nullptr) {
+ if(peak_to_draw.get() == nullptr)
+ {
}
- else {
- sum += peak_to_draw.get()->getArea();
- observed_intensity_data << peak_to_draw.get()->getArea();
- QString isotope_name = QString("+%1").arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber());
- if (xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank() > 1) {
- isotope_name = QString("+%1 [%2]").arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber()).arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank());
+ else
+ {
+ sum += peak_to_draw.get()->getArea();
+ observed_intensity_data << peak_to_draw.get()->getArea();
+ QString isotope_name = QString("+%1").arg(
+ xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber());
+ if(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank() > 1)
+ {
+ isotope_name =
+ QString("+%1 [%2]")
+ .arg(xic_isotope.peptide_natural_isotope_sp.get()
+ ->getIsotopeNumber())
+ .arg(xic_isotope.peptide_natural_isotope_sp.get()
+ ->getIsotopeRank());
}
- isotope_name.append(QString(" (%1%)").arg((int) (xic_isotope.peptide_natural_isotope_sp.get()->getIntensityRatio()*100)));
- labels << isotope_name;
- ticks << i;
+ isotope_name.append(QString(" (%1%)").arg(
+ (int)(xic_isotope.peptide_natural_isotope_sp.get()
+ ->getIntensityRatio() *
+ 100)));
+ labels << isotope_name;
+ ticks << i;
}
- i++;
+ i++;
}
- _isotope_ratio_graph_observed_intensity->setPen(QPen(QColor("red")));
- //_graph_peak_surface_list.back()->setScatterStyle(QCPScatterStyle::ssDot);
- // observed_intensity->setBrush(QBrush(QColor(170, 255, 0, 0)));
+ _isotope_ratio_graph_observed_intensity->setPen(QPen(QColor("red")));
+ //_graph_peak_surface_list.back()->setScatterStyle(QCPScatterStyle::ssDot);
+ // observed_intensity->setBrush(QBrush(QColor(170, 255, 0, 0)));
- if (ticks.size() > 0) {
- _isotope_ratio_graph_observed_intensity->setData(ticks, observed_intensity_data);
+ if(ticks.size() > 0)
+ {
+ _isotope_ratio_graph_observed_intensity->setData(ticks,
+ observed_intensity_data);
- ui->histo_widget->yAxis2->setVisible(true);
- ui->histo_widget->yAxis2->setRange(0, sum);
- ui->histo_widget->replot();
+ ui->histo_widget->yAxis2->setVisible(true);
+ ui->histo_widget->yAxis2->setRange(0, sum);
+ ui->histo_widget->replot();
}
- qDebug() << "XicBox::setXic end";
-
+ qDebug() << "XicBox::setXic end";
}
-void XicBox::setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list) {
+void
+XicBox::setIsotopeMassList(
+ std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list)
+{
- _natural_isotope_list.clear();
- std::vector<pappso::mz> mass_list;
- for (pappso::PeptideNaturalIsotopeAverageSp & natural_isotope_average: isotope_mass_list) {
- mass_list.push_back(natural_isotope_average.get()->getMz());
- _natural_isotope_list.push_back({nullptr, natural_isotope_average, nullptr, nullptr});
+ _natural_isotope_list.clear();
+ std::vector<pappso::mz> mass_list;
+ for(pappso::PeptideNaturalIsotopeAverageSp &natural_isotope_average :
+ isotope_mass_list)
+ {
+ mass_list.push_back(natural_isotope_average.get()->getMz());
+ _natural_isotope_list.push_back(
+ {nullptr, natural_isotope_average, nullptr, nullptr});
}
- emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(), pappso::XicExtractMethod::max);
-
- //histogram
- QCPBars * theoretical_ratio = new QCPBars(ui->histo_widget->xAxis, ui->histo_widget->yAxis);
- theoretical_ratio->setName("theoretical ratio");
- ui->histo_widget->xAxis->setLabel("isotopes");
- //ui->histo_widget->yAxis->setLabel("th. ratio");
-
- QVector<double> theoretical_ratio_data;
-
- QVector<double> ticks;
- QVector<QString> labels;
- int i = 0;
- double sum = 0;
- for (const XicBoxNaturalIsotope & xic_isotope: _natural_isotope_list) {
- sum += xic_isotope.peptide_natural_isotope_sp.get()->getIntensityRatio();
- theoretical_ratio_data << xic_isotope.peptide_natural_isotope_sp.get()->getIntensityRatio();
- QString isotope_name = QString("+%1").arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber());
- if (xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank() > 1) {
- isotope_name = QString("+%1 [%2]").arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber()).arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank());
+ emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(),
+ pappso::XicExtractMethod::max);
+
+ // histogram
+ QCPBars *theoretical_ratio =
+ new QCPBars(ui->histo_widget->xAxis, ui->histo_widget->yAxis);
+ theoretical_ratio->setName("theoretical ratio");
+ ui->histo_widget->xAxis->setLabel("isotopes");
+ // ui->histo_widget->yAxis->setLabel("th. ratio");
+
+ QVector<double> theoretical_ratio_data;
+
+ QVector<double> ticks;
+ QVector<QString> labels;
+ int i = 0;
+ double sum = 0;
+ for(const XicBoxNaturalIsotope &xic_isotope : _natural_isotope_list)
+ {
+ sum += xic_isotope.peptide_natural_isotope_sp.get()->getIntensityRatio();
+ theoretical_ratio_data
+ << xic_isotope.peptide_natural_isotope_sp.get()->getIntensityRatio();
+ QString isotope_name = QString("+%1").arg(
+ xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber());
+ if(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank() > 1)
+ {
+ isotope_name =
+ QString("+%1 [%2]")
+ .arg(xic_isotope.peptide_natural_isotope_sp.get()
+ ->getIsotopeNumber())
+ .arg(
+ xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank());
}
- isotope_name.append(QString(" (%1%)").arg((int) (xic_isotope.peptide_natural_isotope_sp.get()->getIntensityRatio()*100)));
- labels << isotope_name;
- ticks << i;
- i++;
+ isotope_name.append(QString(" (%1%)").arg((
+ int)(xic_isotope.peptide_natural_isotope_sp.get()->getIntensityRatio() *
+ 100)));
+ labels << isotope_name;
+ ticks << i;
+ i++;
}
- //QSharedPointer<QCPAxisTickerText> textTicker(new QCPAxisTickerText);
- //textTicker->addTicks(ticks, labels);
- //ui->histo_widget->xAxis->setTicker(textTicker);
- ui->histo_widget->xAxis->setTickLabelRotation(60);
- //ui->histo_widget->xAxis->setSubTicks(false);
- //ui->histo_widget->xAxis->setTickLength(0, 4);
- //ui->histo_widget->xAxis->setRange(0, 8);
+ // QSharedPointer<QCPAxisTickerText> textTicker(new QCPAxisTickerText);
+ // textTicker->addTicks(ticks, labels);
+ // ui->histo_widget->xAxis->setTicker(textTicker);
+ ui->histo_widget->xAxis->setTickLabelRotation(60);
+ // ui->histo_widget->xAxis->setSubTicks(false);
+ // ui->histo_widget->xAxis->setTickLength(0, 4);
+ // ui->histo_widget->xAxis->setRange(0, 8);
- ui->histo_widget->xAxis->setAutoTickStep(false); // <-- disable to use your own value
+ ui->histo_widget->xAxis->setAutoTickStep(
+ false); // <-- disable to use your own value
- ui->histo_widget->xAxis->setTickStep(1);
+ ui->histo_widget->xAxis->setTickStep(1);
- theoretical_ratio->setData(ticks, theoretical_ratio_data);
+ theoretical_ratio->setData(ticks, theoretical_ratio_data);
- ui->histo_widget->yAxis->setRange(0, sum);
- ui->histo_widget->xAxis->setRange(-0.8, _natural_isotope_list.size());
- ui->histo_widget->replot();
+ ui->histo_widget->yAxis->setRange(0, sum);
+ ui->histo_widget->xAxis->setRange(-0.8, _natural_isotope_list.size());
+ ui->histo_widget->replot();
}
-void XicBox::reExtractXic() {
- qDebug() << "XicBox::reExtractXic begin";
- ui->xic_widget->clear();
-
- std::vector<pappso::mz> mass_list;
- for (const XicBoxNaturalIsotope & xic_isotope: _natural_isotope_list) {
- mass_list.push_back(xic_isotope.peptide_natural_isotope_sp.get()->getMz());
+void
+XicBox::reExtractXic()
+{
+ qDebug() << "XicBox::reExtractXic begin";
+ ui->xic_widget->clear();
+
+ std::vector<pappso::mz> mass_list;
+ for(const XicBoxNaturalIsotope &xic_isotope : _natural_isotope_list)
+ {
+ mass_list.push_back(
+ xic_isotope.peptide_natural_isotope_sp.get()->getMz());
}
- emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(), pappso::XicExtractMethod::max);
- qDebug() << "XicBox::reExtractXic end";
+ emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(),
+ pappso::XicExtractMethod::max);
+ qDebug() << "XicBox::reExtractXic end";
}
-void XicBox::setRetentionTime(double rt) {
- qDebug() << "XicBox::setRetentionTime begin";
- ui->rt_label->setText(tr("rt=%1 (sec) rt=%2 (min)").arg(rt).arg(rt/60));
+void
+XicBox::setRetentionTime(double rt)
+{
+ qDebug() << "XicBox::setRetentionTime begin";
+ ui->rt_label->setText(tr("rt=%1 (sec) rt=%2 (min)").arg(rt).arg(rt / 60));
}
-void XicBox::setXicPeakList(std::vector<std::pair<pappso::XicSp, pappso::XicPeakSp>> xic_peak_list) {
- qDebug() << "XicBox::setXicPeakList begin";
- QString html ;
- for (XicBoxNaturalIsotope & xic_isotope: _natural_isotope_list) {
- xic_isotope.one_peak_sp = nullptr;
+void
+XicBox::setXicPeakList(
+ std::vector<std::pair<pappso::XicSp, pappso::XicPeakSp>> xic_peak_list)
+{
+ qDebug() << "XicBox::setXicPeakList begin";
+ QString html;
+ for(XicBoxNaturalIsotope &xic_isotope : _natural_isotope_list)
+ {
+ xic_isotope.one_peak_sp = nullptr;
}
- for (std::pair<pappso::XicSp, pappso::XicPeakSp> & pair_xic_peak: xic_peak_list) {
- for (XicBoxNaturalIsotope & xic_isotope: _natural_isotope_list) {
- if (xic_isotope.xic_sp.get() == pair_xic_peak.first.get()) {
- xic_isotope.one_peak_sp = pair_xic_peak.second;
+ for(std::pair<pappso::XicSp, pappso::XicPeakSp> &pair_xic_peak :
+ xic_peak_list)
+ {
+ for(XicBoxNaturalIsotope &xic_isotope : _natural_isotope_list)
+ {
+ if(xic_isotope.xic_sp.get() == pair_xic_peak.first.get())
+ {
+ xic_isotope.one_peak_sp = pair_xic_peak.second;
}
}
- html.append(tr("<p>%1<br/>area: %2<br/>rt begin: %3<br/>rt max: %4<br/>rt end: %5<br/></p>").arg(ui->xic_widget->getName(pair_xic_peak.first.get())).arg(pair_xic_peak.second.get()->getArea()).arg(pair_xic_peak.second.get()->getLeftBoundary().rt)
+ html.append(tr("<p>%1<br/>area: %2<br/>rt begin: %3<br/>rt max: "
+ "%4<br/>rt end: %5<br/></p>")
+ .arg(ui->xic_widget->getName(pair_xic_peak.first.get()))
+ .arg(pair_xic_peak.second.get()->getArea())
+ .arg(pair_xic_peak.second.get()->getLeftBoundary().rt)
.arg(pair_xic_peak.second.get()->getMaxXicElement().rt)
- .arg(pair_xic_peak.second.get()->getRightBoundary().rt)
- );
+ .arg(pair_xic_peak.second.get()->getRightBoundary().rt));
}
- ui->xic_widget->setToolTip(html);
- /*
- if (_popup_peak_info == nullptr) delete _popup_peak_info;
- _popup_peak_info = new QFrame( this ,Qt::Popup);
- //_popup_peak_info->setFrameStyle(Qt::WinPanel|Qt::Raised );
- _popup_peak_info->resize(150,100);
- _popup_peak_info->show();
- */
-
-
+ ui->xic_widget->setToolTip(html);
+ /*
+ if (_popup_peak_info == nullptr) delete _popup_peak_info;
+ _popup_peak_info = new QFrame( this ,Qt::Popup);
+ //_popup_peak_info->setFrameStyle(Qt::WinPanel|Qt::Raised );
+ _popup_peak_info->resize(150,100);
+ _popup_peak_info->show();
+ */
}
-void XicBox::onRtUnitChanged() {
- if (_p_xic_window->isRetentionTimeSeconds()) {
- ui->xic_widget->setRetentionTimeInSeconds();
+void
+XicBox::onRtUnitChanged()
+{
+ if(_p_xic_window->isRetentionTimeSeconds())
+ {
+ ui->xic_widget->setRetentionTimeInSeconds();
}
- else {
- ui->xic_widget->setRetentionTimeInMinutes();
+ else
+ {
+ ui->xic_widget->setRetentionTimeInMinutes();
}
}
diff --git a/src/gui/xic_view/xic_box/xicbox.h b/src/gui/xic_view/xic_box/xicbox.h
index 32bb2093333b4e052936521fa8de9c5e4ffa70b1..9225a6367cd2780e86c3c94fbb6585c520665b29 100644
--- a/src/gui/xic_view/xic_box/xicbox.h
+++ b/src/gui/xic_view/xic_box/xicbox.h
@@ -5,26 +5,27 @@
* \brief XIC box widget
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef XICBOX_H
#define XICBOX_H
@@ -38,65 +39,73 @@
#include <pappsomspp/peptide/peptidenaturalisotopelist.h>
#include <qcustomplot.h>
-namespace Ui {
-class XicBox;
+namespace Ui
+{
+ class XicBox;
}
-struct XicBoxNaturalIsotope {
-
- bool contains(const pappso::XicPeakSp & peak) const;
-
- pappso::XicSp xic_sp;
- pappso::PeptideNaturalIsotopeAverageSp peptide_natural_isotope_sp;
- pappso::XicPeakSp matched_peak_sp;
- pappso::XicPeakSp one_peak_sp;
- std::vector <pappso::XicPeakSp> detected_peak_list;
+struct XicBoxNaturalIsotope
+{
+
+ bool contains(const pappso::XicPeakSp &peak) const;
+
+ pappso::XicSp xic_sp;
+ pappso::PeptideNaturalIsotopeAverageSp peptide_natural_isotope_sp;
+ pappso::XicPeakSp matched_peak_sp;
+ pappso::XicPeakSp one_peak_sp;
+ std::vector<pappso::XicPeakSp> detected_peak_list;
};
-class XicBox: public QWidget
+class XicBox : public QWidget
{
- Q_OBJECT
-public:
-
- explicit XicBox(XicWindow * parent = 0);
- virtual ~XicBox();
- void setPeptideEvidence(const PeptideEvidence * p_peptide_evidence) ;
- void setPeptideEvidenceInMsRun(const PeptideEvidence * p_peptide_evidence, MsRunSp msrun_sp);
-
-signals :
- void loadXic(MsRunSp p_msrun, std::vector<pappso::mz> mz_list, pappso::PrecisionP precision, pappso::XicExtractMethod method);
- void computeIsotopeMassList(pappso::PeptideSp peptide_sp, unsigned int charge, pappso::PrecisionP precision, double minimum_isotope_pattern_ratio);
-private slots:
- void remove();
- void reExtractXic();
- void setXic(std::vector< pappso::XicSp> xic_sp_list);
- void setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list);
- void error(QString error_message);
- void extractXicInOtherMsRun();
- void setRetentionTime(double rt);
- void setXicPeakList(std::vector<std::pair<pappso::XicSp, pappso::XicPeakSp>> xic_peak_list);
- void onRtUnitChanged();
- void onXicWidgetClick(double rt, double intensity);
-
-private:
- void drawObservedAreaBars(const std::vector<pappso::XicPeakSp> & observed_peak_to_draw);
-
-private:
- Ui::XicBox *ui;
- QThread _xic_thread;
- XicWindow * _p_xic_window;
- const PeptideEvidence * _p_peptide_evidence;
- MsRunSp _msrun_sp;
- std::vector<const PeptideEvidence *> _peptide_evidence_list;
- std::vector<XicBoxNaturalIsotope> _natural_isotope_list;
- std::vector<pappso::XicWidget *> _xic_widget_list;
-
- QCPBars * _isotope_ratio_graph_observed_intensity= nullptr;
-
- bool _scaled = false;
-
- //QFrame * _popup_peak_info = nullptr;
+ Q_OBJECT
+ public:
+ explicit XicBox(XicWindow *parent = 0);
+ virtual ~XicBox();
+ void setPeptideEvidence(const PeptideEvidence *p_peptide_evidence);
+ void setPeptideEvidenceInMsRun(const PeptideEvidence *p_peptide_evidence,
+ MsRunSp msrun_sp);
+
+ signals:
+ void loadXic(MsRunSp p_msrun, std::vector<pappso::mz> mz_list,
+ pappso::PrecisionP precision, pappso::XicExtractMethod method);
+ void computeIsotopeMassList(pappso::PeptideSp peptide_sp, unsigned int charge,
+ pappso::PrecisionP precision,
+ double minimum_isotope_pattern_ratio);
+ private slots:
+ void remove();
+ void reExtractXic();
+ void setXic(std::vector<pappso::XicSp> xic_sp_list);
+ void setIsotopeMassList(
+ std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list);
+ void error(QString error_message);
+ void extractXicInOtherMsRun();
+ void setRetentionTime(double rt);
+ void setXicPeakList(
+ std::vector<std::pair<pappso::XicSp, pappso::XicPeakSp>> xic_peak_list);
+ void onRtUnitChanged();
+ void onXicWidgetClick(double rt, double intensity);
+
+ private:
+ void drawObservedAreaBars(
+ const std::vector<pappso::XicPeakSp> &observed_peak_to_draw);
+
+ private:
+ Ui::XicBox *ui;
+ QThread _xic_thread;
+ XicWindow *_p_xic_window;
+ const PeptideEvidence *_p_peptide_evidence;
+ MsRunSp _msrun_sp;
+ std::vector<const PeptideEvidence *> _peptide_evidence_list;
+ std::vector<XicBoxNaturalIsotope> _natural_isotope_list;
+ std::vector<pappso::XicWidget *> _xic_widget_list;
+
+ QCPBars *_isotope_ratio_graph_observed_intensity = nullptr;
+
+ bool _scaled = false;
+
+ // QFrame * _popup_peak_info = nullptr;
};
diff --git a/src/gui/xic_view/xic_widgets/zivydialog.cpp b/src/gui/xic_view/xic_widgets/zivydialog.cpp
index 5f4244c55cbb2bf2de6c34487af4ca8edc6ef788..5671bb6b37666f41517e09b3da647502c8700cc1 100644
--- a/src/gui/xic_view/xic_widgets/zivydialog.cpp
+++ b/src/gui/xic_view/xic_widgets/zivydialog.cpp
@@ -5,57 +5,63 @@
* \brief dialog window to edit Zivy quantification method
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "zivydialog.h"
#include <QVBoxLayout>
#include <QDebug>
-ZivyDialog::ZivyDialog(QWidget *parent) {
- _p_zivy_widget = new ZivyWidget(this);
- _p_button_box = new QDialogButtonBox(QDialogButtonBox::Ok
- | QDialogButtonBox::Cancel);
+ZivyDialog::ZivyDialog(QWidget *parent)
+{
+ _p_zivy_widget = new ZivyWidget(this);
+ _p_button_box =
+ new QDialogButtonBox(QDialogButtonBox::Ok | QDialogButtonBox::Cancel);
- connect(_p_button_box, &QDialogButtonBox::accepted, this, &QDialog::accept);
- connect(_p_button_box, &QDialogButtonBox::rejected, this, &QDialog::reject);
+ connect(_p_button_box, &QDialogButtonBox::accepted, this, &QDialog::accept);
+ connect(_p_button_box, &QDialogButtonBox::rejected, this, &QDialog::reject);
- QVBoxLayout *mainLayout = new QVBoxLayout;
- mainLayout->addWidget(_p_zivy_widget);
- mainLayout->addWidget(_p_button_box);
- setLayout(mainLayout);
+ QVBoxLayout *mainLayout = new QVBoxLayout;
+ mainLayout->addWidget(_p_zivy_widget);
+ mainLayout->addWidget(_p_button_box);
+ setLayout(mainLayout);
- setWindowTitle(tr("Edit parameters"));
+ setWindowTitle(tr("Edit parameters"));
}
ZivyDialog::~ZivyDialog()
{
- qDebug() << "ZivyDialog::~ZivyDialog";
+ qDebug() << "ZivyDialog::~ZivyDialog";
}
-void ZivyDialog::setZivyParams(const ZivyParams & params) {
- _p_zivy_widget->setZivyParams(params);
+void
+ZivyDialog::setZivyParams(const ZivyParams ¶ms)
+{
+ _p_zivy_widget->setZivyParams(params);
}
-const ZivyParams ZivyDialog::getZivyParams() const {
- return _p_zivy_widget->getZivyParams();
+const ZivyParams
+ZivyDialog::getZivyParams() const
+{
+ return _p_zivy_widget->getZivyParams();
}
diff --git a/src/gui/xic_view/xic_widgets/zivydialog.h b/src/gui/xic_view/xic_widgets/zivydialog.h
index 25c1625b46d9d1bd77d8a707e0133113ce4f5ac6..940a792c3e821d08de5572380d6434b31361ead0 100644
--- a/src/gui/xic_view/xic_widgets/zivydialog.h
+++ b/src/gui/xic_view/xic_widgets/zivydialog.h
@@ -5,26 +5,27 @@
* \brief dialog window to edit Zivy quantification method
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef ZIVYDIALOG_H
#define ZIVYDIALOG_H
@@ -35,19 +36,19 @@
class ZivyDialog : public QDialog
{
- Q_OBJECT
-
-public:
- explicit ZivyDialog(QWidget *parent = 0);
- virtual ~ZivyDialog();
-
-
- void setZivyParams(const ZivyParams & params);
- const ZivyParams getZivyParams() const;
-
-private:
- ZivyWidget * _p_zivy_widget;
- QDialogButtonBox * _p_button_box;
+ Q_OBJECT
+
+ public:
+ explicit ZivyDialog(QWidget *parent = 0);
+ virtual ~ZivyDialog();
+
+
+ void setZivyParams(const ZivyParams ¶ms);
+ const ZivyParams getZivyParams() const;
+
+ private:
+ ZivyWidget *_p_zivy_widget;
+ QDialogButtonBox *_p_button_box;
};
#endif // ZIVYDIALOG_H
diff --git a/src/gui/xic_view/xic_widgets/zivywidget.cpp b/src/gui/xic_view/xic_widgets/zivywidget.cpp
index e49e207e9af296e84ee8535e5904040d3174b21e..99e9d4c9c9994a43941b83e8a8f8fba876530359 100644
--- a/src/gui/xic_view/xic_widgets/zivywidget.cpp
+++ b/src/gui/xic_view/xic_widgets/zivywidget.cpp
@@ -5,97 +5,126 @@
* \brief Widget to edit Zivy quantification method
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "zivywidget.h"
#include "ui_zivy_widget.h"
#include <QDebug>
#include <QSettings>
-void ZivyParams::setDetectionParameters(pappso::XicDetectionZivy * detect_zivy) const {
- detect_zivy->setSmoothingHalfEdgeWindows(_smoothing_half_window);
- detect_zivy->setMinMaxHalfEdgeWindows(_minmax_half_window);
- detect_zivy->setMaxMinHalfEdgeWindows(_maxmin_half_window);
- detect_zivy->setDetectionThresholdOnMinmax(_minmax_threshold);
- detect_zivy->setDetectionThresholdOnMaxmin(_maxmin_threshold);
+void
+ZivyParams::setDetectionParameters(pappso::XicDetectionZivy *detect_zivy) const
+{
+ detect_zivy->setSmoothingHalfEdgeWindows(_smoothing_half_window);
+ detect_zivy->setMinMaxHalfEdgeWindows(_minmax_half_window);
+ detect_zivy->setMaxMinHalfEdgeWindows(_maxmin_half_window);
+ detect_zivy->setDetectionThresholdOnMinmax(_minmax_threshold);
+ detect_zivy->setDetectionThresholdOnMaxmin(_maxmin_threshold);
}
-void ZivyParams::saveSettings() const {
- QSettings settings;
- settings.setValue("xic/zivy_maxmin_threshold", QString("%1").arg(_maxmin_threshold));
- settings.setValue("xic/zivy_minmax_threshold", QString("%1").arg(_minmax_threshold));
- settings.setValue("xic/zivy_maxmin_half_window", QString("%1").arg(_maxmin_half_window));
- settings.setValue("xic/zivy_minmax_half_window", QString("%1").arg(_minmax_half_window));
- settings.setValue("xic/zivy_smoothing", QString("%1").arg(_smoothing_half_window));
+void
+ZivyParams::saveSettings() const
+{
+ QSettings settings;
+ settings.setValue("xic/zivy_maxmin_threshold",
+ QString("%1").arg(_maxmin_threshold));
+ settings.setValue("xic/zivy_minmax_threshold",
+ QString("%1").arg(_minmax_threshold));
+ settings.setValue("xic/zivy_maxmin_half_window",
+ QString("%1").arg(_maxmin_half_window));
+ settings.setValue("xic/zivy_minmax_half_window",
+ QString("%1").arg(_minmax_half_window));
+ settings.setValue("xic/zivy_smoothing",
+ QString("%1").arg(_smoothing_half_window));
}
-void ZivyParams::loadSettings() {
- QSettings settings;
- _maxmin_threshold = settings.value("xic/zivy_maxmin_threshold", QString("%1").arg(_maxmin_threshold)).toDouble();
- _minmax_threshold = settings.value("xic/zivy_minmax_threshold", QString("%1").arg(_minmax_threshold)).toDouble();
- _maxmin_half_window = settings.value("xic/zivy_maxmin_half_window", QString("%1").arg(_maxmin_half_window)).toInt();
- _minmax_half_window = settings.value("xic/zivy_minmax_half_window", QString("%1").arg(_minmax_half_window)).toInt();
- _smoothing_half_window = settings.value("xic/zivy_smoothing", QString("%1").arg(_smoothing_half_window)).toInt();
+void
+ZivyParams::loadSettings()
+{
+ QSettings settings;
+ _maxmin_threshold =
+ settings
+ .value("xic/zivy_maxmin_threshold", QString("%1").arg(_maxmin_threshold))
+ .toDouble();
+ _minmax_threshold =
+ settings
+ .value("xic/zivy_minmax_threshold", QString("%1").arg(_minmax_threshold))
+ .toDouble();
+ _maxmin_half_window = settings
+ .value("xic/zivy_maxmin_half_window",
+ QString("%1").arg(_maxmin_half_window))
+ .toInt();
+ _minmax_half_window = settings
+ .value("xic/zivy_minmax_half_window",
+ QString("%1").arg(_minmax_half_window))
+ .toInt();
+ _smoothing_half_window =
+ settings
+ .value("xic/zivy_smoothing", QString("%1").arg(_smoothing_half_window))
+ .toInt();
}
-ZivyWidget::ZivyWidget(QWidget *parent):
- QWidget(parent),
- ui(new Ui::ZivyWidget)
+ZivyWidget::ZivyWidget(QWidget *parent)
+ : QWidget(parent), ui(new Ui::ZivyWidget)
{
- ui->setupUi(this);
+ ui->setupUi(this);
#if QT_VERSION >= 0x050000
- // Qt5 code
+ // Qt5 code
#else
// Qt4 code
#endif
-
-
}
ZivyWidget::~ZivyWidget()
{
- qDebug() << "ZivyWidget::~ZivyWidget";
+ qDebug() << "ZivyWidget::~ZivyWidget";
}
-void ZivyWidget::setZivyParams(const ZivyParams & params) {
- ui->maxmin_spinbox->setValue(params._maxmin_half_window);
- ui->minmax_spinbox->setValue(params._minmax_half_window);
- ui->maxmin_threshold_spinbox->setValue(params._maxmin_threshold);
- ui->minmax_threshold_spinbox->setValue(params._minmax_threshold);
- ui->smoothing_spinbox->setValue(params._smoothing_half_window);
+void
+ZivyWidget::setZivyParams(const ZivyParams ¶ms)
+{
+ ui->maxmin_spinbox->setValue(params._maxmin_half_window);
+ ui->minmax_spinbox->setValue(params._minmax_half_window);
+ ui->maxmin_threshold_spinbox->setValue(params._maxmin_threshold);
+ ui->minmax_threshold_spinbox->setValue(params._minmax_threshold);
+ ui->smoothing_spinbox->setValue(params._smoothing_half_window);
}
-const ZivyParams ZivyWidget::getZivyParams() const {
- ZivyParams params;
+const ZivyParams
+ZivyWidget::getZivyParams() const
+{
+ ZivyParams params;
- params._maxmin_half_window = ui->maxmin_spinbox->value();
- params._minmax_half_window = ui->minmax_spinbox->value();
- params._maxmin_threshold = ui->maxmin_threshold_spinbox->value();
- params._minmax_threshold = ui->minmax_threshold_spinbox->value();
- params._smoothing_half_window = ui->smoothing_spinbox->value();
- return params;
+ params._maxmin_half_window = ui->maxmin_spinbox->value();
+ params._minmax_half_window = ui->minmax_spinbox->value();
+ params._maxmin_threshold = ui->maxmin_threshold_spinbox->value();
+ params._minmax_threshold = ui->minmax_threshold_spinbox->value();
+ params._smoothing_half_window = ui->smoothing_spinbox->value();
+ return params;
}
-void ZivyWidget::doSpinboxChanged (int value) {
- emit zivyChanged(getZivyParams());
-
+void
+ZivyWidget::doSpinboxChanged(int value)
+{
+ emit zivyChanged(getZivyParams());
}
diff --git a/src/gui/xic_view/xic_widgets/zivywidget.h b/src/gui/xic_view/xic_widgets/zivywidget.h
index a6f3bbf29013a993ae2b02cc0a2c6dd8e859fd61..a8e36d0a8b4feaa29394c3252b63e910f444107b 100644
--- a/src/gui/xic_view/xic_widgets/zivywidget.h
+++ b/src/gui/xic_view/xic_widgets/zivywidget.h
@@ -5,26 +5,27 @@
* \brief Widget to edit Zivy quantification method
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef ZIVYWIDGET_H
#define ZIVYWIDGET_H
@@ -32,43 +33,44 @@
#include <QWidget>
#include <pappsomspp/xic/detection/xicdetectionzivy.h>
-namespace Ui {
-class ZivyWidget;
+namespace Ui
+{
+ class ZivyWidget;
}
-struct ZivyParams {
- void setDetectionParameters(pappso::XicDetectionZivy * detect_zivy) const;
- void saveSettings() const;
- void loadSettings();
-
- unsigned int _maxmin_half_window = 3;
- unsigned int _minmax_half_window = 2;
- double _maxmin_threshold = 3000;
- double _minmax_threshold = 5000;
- unsigned int _smoothing_half_window = 1;
+struct ZivyParams
+{
+ void setDetectionParameters(pappso::XicDetectionZivy *detect_zivy) const;
+ void saveSettings() const;
+ void loadSettings();
+
+ unsigned int _maxmin_half_window = 3;
+ unsigned int _minmax_half_window = 2;
+ double _maxmin_threshold = 3000;
+ double _minmax_threshold = 5000;
+ unsigned int _smoothing_half_window = 1;
};
-class ZivyWidget: public QWidget
+class ZivyWidget : public QWidget
{
- Q_OBJECT
-public:
+ Q_OBJECT
+ public:
+ explicit ZivyWidget(QWidget *parent = 0);
+ virtual ~ZivyWidget();
+
+ void setZivyParams(const ZivyParams ¶ms);
+
+ const ZivyParams getZivyParams() const;
- explicit ZivyWidget(QWidget * parent = 0);
- virtual ~ZivyWidget();
-
- void setZivyParams(const ZivyParams & params);
-
- const ZivyParams getZivyParams() const;
+ signals:
+ void zivyChanged(ZivyParams zivy_params);
-signals :
- void zivyChanged(ZivyParams zivy_params);
+ protected slots:
+ void doSpinboxChanged(int value);
- protected
-slots :
- void doSpinboxChanged (int value);
-private:
- Ui::ZivyWidget *ui;
+ private:
+ Ui::ZivyWidget *ui;
};
#endif // ZIVYWIDGET_H
diff --git a/src/gui/xic_view/xicwindow.cpp b/src/gui/xic_view/xicwindow.cpp
index 2fea617297b6908631e0531a2cdbf01b03da4546..039383fa588d077b78c1d19b9965e533fea5d4cf 100644
--- a/src/gui/xic_view/xicwindow.cpp
+++ b/src/gui/xic_view/xicwindow.cpp
@@ -6,140 +6,165 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "xicwindow.h"
#include "ui_xic_window.h"
#include "../project_view/projectwindow.h"
#include "xic_box/xicbox.h"
-XicWindow::XicWindow(ProjectWindow *parent):
- QMainWindow(parent),
- ui(new Ui::XicWindow)
+XicWindow::XicWindow(ProjectWindow *parent)
+ : QMainWindow(parent), ui(new Ui::XicWindow)
{
- _project_window = parent;
+ _project_window = parent;
- ui->setupUi(this);
+ ui->setupUi(this);
- QSettings settings;
- QString precision_str = settings.value("xic/precision", "10 ppm").toString();
+ QSettings settings;
+ QString precision_str = settings.value("xic/precision", "10 ppm").toString();
- ui->xic_precision->setPrecision(pappso::Precision::fromString(precision_str));
+ ui->xic_precision->setPrecision(pappso::Precision::fromString(precision_str));
- ZivyParams zivy_params;
- zivy_params.loadSettings();
+ ZivyParams zivy_params;
+ zivy_params.loadSettings();
- zivy_params.setDetectionParameters(&_detect_zivy);
+ zivy_params.setDetectionParameters(&_detect_zivy);
- _p_zivy_dialog = new ZivyDialog(this);
- _p_zivy_dialog->setZivyParams(zivy_params);
+ _p_zivy_dialog = new ZivyDialog(this);
+ _p_zivy_dialog->setZivyParams(zivy_params);
-
- connect(_p_zivy_dialog, &ZivyDialog::accepted, this, &XicWindow::doAcceptedZivyDialog);
+ connect(_p_zivy_dialog, &ZivyDialog::accepted, this,
+ &XicWindow::doAcceptedZivyDialog);
#if QT_VERSION >= 0x050000
- // Qt5 code
+ // Qt5 code
#else
// Qt4 code
#endif
-
-
}
XicWindow::~XicWindow()
{
- qDebug() << "XicWindow::~XicWindow";
- delete _p_zivy_dialog;
+ qDebug() << "XicWindow::~XicWindow";
+ delete _p_zivy_dialog;
}
-void XicWindow::doEditZivyParams() {
- _p_zivy_dialog->show();
+void
+XicWindow::doEditZivyParams()
+{
+ _p_zivy_dialog->show();
}
-void XicWindow::clear() {
- QLayoutItem *wItem;
- while (wItem = ui->xic_vertical_layout->layout()->takeAt(0)) {
- wItem->widget()->setVisible(false);
- ui->xic_vertical_layout->layout()->removeWidget(wItem->widget());
- delete wItem->widget();
+void
+XicWindow::clear()
+{
+ QLayoutItem *wItem;
+ while(wItem = ui->xic_vertical_layout->layout()->takeAt(0))
+ {
+ wItem->widget()->setVisible(false);
+ ui->xic_vertical_layout->layout()->removeWidget(wItem->widget());
+ delete wItem->widget();
}
}
-ProjectWindow * XicWindow::getProjectWindow() {
- return _project_window;
+ProjectWindow *
+XicWindow::getProjectWindow()
+{
+ return _project_window;
}
-void XicWindow::addXic(const PeptideEvidence * p_peptide_evidence) {
- XicBox * p_box = new XicBox(this);
- p_box->setPeptideEvidence(p_peptide_evidence);
- ui->xic_vertical_layout->layout()->addWidget(p_box);
+void
+XicWindow::addXic(const PeptideEvidence *p_peptide_evidence)
+{
+ XicBox *p_box = new XicBox(this);
+ p_box->setPeptideEvidence(p_peptide_evidence);
+ ui->xic_vertical_layout->layout()->addWidget(p_box);
}
-void XicWindow::addXicInMsRun(const PeptideEvidence * p_peptide_evidence, MsRunSp msrun_sp) {
- XicBox * p_box = new XicBox(this);
- p_box->setPeptideEvidenceInMsRun(p_peptide_evidence, msrun_sp);
- ui->xic_vertical_layout->layout()->addWidget(p_box);
+void
+XicWindow::addXicInMsRun(const PeptideEvidence *p_peptide_evidence,
+ MsRunSp msrun_sp)
+{
+ XicBox *p_box = new XicBox(this);
+ p_box->setPeptideEvidenceInMsRun(p_peptide_evidence, msrun_sp);
+ ui->xic_vertical_layout->layout()->addWidget(p_box);
}
-void XicWindow::removeXicBox(XicBox * xic_box) {
- xic_box->setVisible(false);
- ui->xic_vertical_layout->layout()->removeWidget(xic_box);
- delete xic_box;
+void
+XicWindow::removeXicBox(XicBox *xic_box)
+{
+ xic_box->setVisible(false);
+ ui->xic_vertical_layout->layout()->removeWidget(xic_box);
+ delete xic_box;
}
-pappso::PrecisionP XicWindow::getXicExtractPrecision() const {
- return (ui->xic_precision->getPrecision());
+pappso::PrecisionP
+XicWindow::getXicExtractPrecision() const
+{
+ return (ui->xic_precision->getPrecision());
}
-void XicWindow::xicPrecisionChanged(pappso::PrecisionP precision) {
- qDebug() << "XicWindow::xicPrecisionChanged begin";
- qDebug() << "XicWindow::xicPrecisionChanged emit";
- emit reExtractXicNeeded();
- qDebug() << "XicWindow::xicPrecisionChanged end";
+void
+XicWindow::xicPrecisionChanged(pappso::PrecisionP precision)
+{
+ qDebug() << "XicWindow::xicPrecisionChanged begin";
+ qDebug() << "XicWindow::xicPrecisionChanged emit";
+ emit reExtractXicNeeded();
+ qDebug() << "XicWindow::xicPrecisionChanged end";
}
-void XicWindow::xicDetect(const pappso::Xic & xic,pappso::XicDetectionSinkInterface * sink) const {
- _detect_zivy.detect(xic, sink);
+void
+XicWindow::xicDetect(const pappso::Xic &xic,
+ pappso::XicDetectionSinkInterface *sink) const
+{
+ _detect_zivy.detect(xic, sink);
}
-void XicWindow::rtUnitChanged(QAbstractButton* button) {
- qDebug() << "XicWindow::rtUnitChanged begin";
- emit rtUnitChangeNeeded();
- qDebug() << "XicWindow::rtUnitChanged end";
+void
+XicWindow::rtUnitChanged(QAbstractButton *button)
+{
+ qDebug() << "XicWindow::rtUnitChanged begin";
+ emit rtUnitChangeNeeded();
+ qDebug() << "XicWindow::rtUnitChanged end";
}
-bool XicWindow::isRetentionTimeSeconds() const {
- if (ui->rt_sec_radiobutton->isChecked()) {
- return true;
+bool
+XicWindow::isRetentionTimeSeconds() const
+{
+ if(ui->rt_sec_radiobutton->isChecked())
+ {
+ return true;
}
- return false;
+ return false;
}
-void XicWindow::doAcceptedZivyDialog() {
- _p_zivy_dialog->getZivyParams().setDetectionParameters(&_detect_zivy);
- _p_zivy_dialog->getZivyParams().saveSettings();
- emit reExtractXicNeeded();
-
+void
+XicWindow::doAcceptedZivyDialog()
+{
+ _p_zivy_dialog->getZivyParams().setDetectionParameters(&_detect_zivy);
+ _p_zivy_dialog->getZivyParams().saveSettings();
+ emit reExtractXicNeeded();
}
diff --git a/src/gui/xic_view/xicwindow.h b/src/gui/xic_view/xicwindow.h
index 47e30679690f753e5667c7f2ce043e60cab18a49..1598c977b97cbbbfbe0e3ee6de41c3fc7a0abf0f 100644
--- a/src/gui/xic_view/xicwindow.h
+++ b/src/gui/xic_view/xicwindow.h
@@ -5,26 +5,27 @@
* \brief XIC window
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef XICWINDOW_H
#define XICWINDOW_H
@@ -40,56 +41,59 @@
class ProjectWindow;
-
-namespace Ui {
-class XicWindow;
+namespace Ui
+{
+ class XicWindow;
}
class XicBox;
-class XicWindow: public QMainWindow {
- Q_OBJECT
- friend XicBox;
-public:
-
- explicit XicWindow(ProjectWindow * parent = 0);
- ~XicWindow();
-
- void addXic(const PeptideEvidence * p_peptide_evidence);
- void addXicInMsRun(const PeptideEvidence * p_peptide_evidence, MsRunSp msrun_sp);
-
- pappso::PrecisionP getXicExtractPrecision() const;
-
- bool isRetentionTimeSeconds() const;
-
- void clear();
-public slots:
- void xicPrecisionChanged(pappso::PrecisionP precision);
- void rtUnitChanged(QAbstractButton* button);
-
- protected slots :
- void doEditZivyParams();
- void doAcceptedZivyDialog();
-
-signals :
- void reExtractXicNeeded();
- void rtUnitChangeNeeded();
-
-
-protected:
- ProjectWindow * getProjectWindow();
- void removeXicBox(XicBox * xic_box);
-
- void xicDetect(const pappso::Xic & xic,pappso::XicDetectionSinkInterface * sink) const;
-
-private:
- ProjectWindow * _project_window;
- Ui::XicWindow *ui;
-
- pappso::XicDetectionZivy _detect_zivy;
-
-
- ZivyDialog * _p_zivy_dialog;
+class XicWindow : public QMainWindow
+{
+ Q_OBJECT
+ friend XicBox;
+
+ public:
+ explicit XicWindow(ProjectWindow *parent = 0);
+ ~XicWindow();
+
+ void addXic(const PeptideEvidence *p_peptide_evidence);
+ void addXicInMsRun(const PeptideEvidence *p_peptide_evidence,
+ MsRunSp msrun_sp);
+
+ pappso::PrecisionP getXicExtractPrecision() const;
+
+ bool isRetentionTimeSeconds() const;
+
+ void clear();
+ public slots:
+ void xicPrecisionChanged(pappso::PrecisionP precision);
+ void rtUnitChanged(QAbstractButton *button);
+
+ protected slots:
+ void doEditZivyParams();
+ void doAcceptedZivyDialog();
+
+ signals:
+ void reExtractXicNeeded();
+ void rtUnitChangeNeeded();
+
+
+ protected:
+ ProjectWindow *getProjectWindow();
+ void removeXicBox(XicBox *xic_box);
+
+ void xicDetect(const pappso::Xic &xic,
+ pappso::XicDetectionSinkInterface *sink) const;
+
+ private:
+ ProjectWindow *_project_window;
+ Ui::XicWindow *ui;
+
+ pappso::XicDetectionZivy _detect_zivy;
+
+
+ ZivyDialog *_p_zivy_dialog;
};
#endif // XICWINDOW_H
diff --git a/src/gui/xic_view/xicworkerthread.h b/src/gui/xic_view/xicworkerthread.h
index 36f4cce343057365ba16b01e7425fe9d8b9b07f6..ec0428b4f40a98603a4a05c784e13863aac5ac2b 100644
--- a/src/gui/xic_view/xicworkerthread.h
+++ b/src/gui/xic_view/xicworkerthread.h
@@ -5,52 +5,56 @@
* \brief XIC worker
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef XICWORKERTHREAD_H
#define XICWORKERTHREAD_H
#include <pappsomspp/peptide/peptidenaturalisotopelist.h>
-#include<QObject>
+#include <QObject>
#include "../../core/msrun.h"
#include <pappsomspp/xic/xic.h>
#include <pappsomspp/xicextractor/msrunxicextractor.h>
class XicWorkerThread : public QObject
{
- Q_OBJECT
-public:
+ Q_OBJECT
+ public:
+ public slots:
+ void doXicLoad(MsRunSp p_msrun, std::vector<pappso::mz> mz_list,
+ pappso::PrecisionP precision, pappso::XicExtractMethod method);
+ void doComputeIsotopeMassList(pappso::PeptideSp peptide_sp,
+ unsigned int charge,
+ pappso::PrecisionP precision,
+ double minimum_isotope_pattern_ratio);
-public slots:
- void doXicLoad(MsRunSp p_msrun, std::vector<pappso::mz> mz_list, pappso::PrecisionP precision, pappso::XicExtractMethod method);
- void doComputeIsotopeMassList(pappso::PeptideSp peptide_sp, unsigned int charge, pappso::PrecisionP precision, double minimum_isotope_pattern_ratio);
-
-signals:
- void xicLoaded(std::vector<pappso::XicSp> xic_sp_list);
- void isotopeMassListComputed(std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list);
- void operationFailed(QString error);
-
-private:
- std::vector<pappso::MsRunXicExtractorSp> _extractor_list;
+ signals:
+ void xicLoaded(std::vector<pappso::XicSp> xic_sp_list);
+ void isotopeMassListComputed(
+ std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list);
+ void operationFailed(QString error);
+ private:
+ std::vector<pappso::MsRunXicExtractorSp> _extractor_list;
};
#endif // XICWORKERTHREAD_H
diff --git a/src/input/condorqxmlsaxhandler.cpp b/src/input/condorqxmlsaxhandler.cpp
index 74242691edaec3d678628e1215ef5c016e238e85..0b7081d3794435b5d0297cdc249768636bedc0be 100644
--- a/src/input/condorqxmlsaxhandler.cpp
+++ b/src/input/condorqxmlsaxhandler.cpp
@@ -7,227 +7,297 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "condorqxmlsaxhandler.h"
#include "../core/tandem_run/tandemcondorprocess.h"
#include <pappsomspp/pappsoexception.h>
-CondorQxmlSaxHandler::CondorQxmlSaxHandler(TandemCondorProcess * tandem_condor_process) {
- _is_empty = true;
- _tandem_condor_process = tandem_condor_process;
+CondorQxmlSaxHandler::CondorQxmlSaxHandler(
+ TandemCondorProcess *tandem_condor_process)
+{
+ _is_empty = true;
+ _tandem_condor_process = tandem_condor_process;
}
-CondorQxmlSaxHandler::~CondorQxmlSaxHandler() {
+CondorQxmlSaxHandler::~CondorQxmlSaxHandler()
+{
}
+bool
+CondorQxmlSaxHandler::startElement(const QString &namespaceURI,
+ const QString &localName,
+ const QString &qName,
+ const QXmlAttributes &attributes)
+{
+ qDebug() << "CondorQxmlSaxHandler::startElement begin" << namespaceURI << " "
+ << localName << " " << qName;
+ _tag_stack.push_back(qName);
+ bool is_ok = true;
-bool CondorQxmlSaxHandler::startElement(const QString & namespaceURI, const QString & localName,
- const QString & qName, const QXmlAttributes & attributes) {
- qDebug()<< "CondorQxmlSaxHandler::startElement begin" << namespaceURI << " " << localName << " " << qName ;
- _tag_stack.push_back(qName);
- bool is_ok = true;
+ try
+ {
+ // startElement_group
- try {
- //startElement_group
-
- if (qName == "c") {
- is_ok = startElement_c(attributes);
- } else if (qName == "a") {
- is_ok = startElement_a(attributes);
+ if(qName == "c")
+ {
+ is_ok = startElement_c(attributes);
+ }
+ else if(qName == "a")
+ {
+ is_ok = startElement_a(attributes);
}
- _current_text.clear();
+ _current_text.clear();
}
- catch (pappso::PappsoException exception_pappso) {
- _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::startElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
- return false;
+ catch(pappso::PappsoException exception_pappso)
+ {
+ _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::startElement tag "
+ "%1, PAPPSO exception:\n%2")
+ .arg(qName)
+ .arg(exception_pappso.qwhat());
+ return false;
}
- catch (std::exception exception_std) {
- _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::startElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
- return false;
+ catch(std::exception exception_std)
+ {
+ _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::startElement tag "
+ "%1, std exception:\n%2")
+ .arg(qName)
+ .arg(exception_std.what());
+ return false;
}
- return is_ok;
+ return is_ok;
}
-bool CondorQxmlSaxHandler::endElement(const QString & namespaceURI, const QString & localName,
- const QString & qName) {
+bool
+CondorQxmlSaxHandler::endElement(const QString &namespaceURI,
+ const QString &localName, const QString &qName)
+{
- bool is_ok = true;
- // endElement_peptide_list
- try {
+ bool is_ok = true;
+ // endElement_peptide_list
+ try
+ {
- if (qName == "a")
+ if(qName == "a")
{
- is_ok = endElement_a();
+ is_ok = endElement_a();
}
- else if (qName == "c") {
- is_ok = endElement_c();
+ else if(qName == "c")
+ {
+ is_ok = endElement_c();
}
- else if (qName == "i") {
- is_ok = endElement_i();
+ else if(qName == "i")
+ {
+ is_ok = endElement_i();
}
- else if (qName == "s") {
- is_ok = endElement_s();
+ else if(qName == "s")
+ {
+ is_ok = endElement_s();
}
-
}
- catch (pappso::PappsoException exception_pappso) {
- _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::endElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
- return false;
+ catch(pappso::PappsoException exception_pappso)
+ {
+ _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::endElement tag "
+ "%1, PAPPSO exception:\n%2")
+ .arg(qName)
+ .arg(exception_pappso.qwhat());
+ return false;
}
- catch (std::exception exception_std) {
- _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::endElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
- return false;
+ catch(std::exception exception_std)
+ {
+ _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::endElement tag "
+ "%1, std exception:\n%2")
+ .arg(qName)
+ .arg(exception_std.what());
+ return false;
}
- _current_text.clear();
- _tag_stack.pop_back();
+ _current_text.clear();
+ _tag_stack.pop_back();
- return is_ok;
+ return is_ok;
}
-bool CondorQxmlSaxHandler::error(const QXmlParseException &exception) {
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
- exception.message());
+bool
+CondorQxmlSaxHandler::error(const QXmlParseException &exception)
+{
+ _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+ "%3")
+ .arg(exception.lineNumber())
+ .arg(exception.columnNumber())
+ .arg(exception.message());
- return false;
+ return false;
}
-bool CondorQxmlSaxHandler::fatalError(const QXmlParseException &exception) {
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
- exception.message());
- return false;
+bool
+CondorQxmlSaxHandler::fatalError(const QXmlParseException &exception)
+{
+ _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+ "%3")
+ .arg(exception.lineNumber())
+ .arg(exception.columnNumber())
+ .arg(exception.message());
+ return false;
}
-QString CondorQxmlSaxHandler::errorString() const {
- return _errorStr;
+QString
+CondorQxmlSaxHandler::errorString() const
+{
+ return _errorStr;
}
-bool CondorQxmlSaxHandler::endDocument() {
+bool
+CondorQxmlSaxHandler::endDocument()
+{
- unsigned int really_completed_jobs = 0;
- if (_is_empty) {
- really_completed_jobs = _tandem_condor_process->getCondorJobSize();
- } else {
- int total_jobs = 0;
- for (std::int8_t i=0; i < 10; i++) {
- total_jobs += _count_status[i];
+ unsigned int really_completed_jobs = 0;
+ if(_is_empty)
+ {
+ really_completed_jobs = _tandem_condor_process->getCondorJobSize();
+ }
+ else
+ {
+ int total_jobs = 0;
+ for(std::int8_t i = 0; i < 10; i++)
+ {
+ total_jobs += _count_status[i];
}
- int diff_jobs = _tandem_condor_process->getCondorJobSize()
- - total_jobs;
- really_completed_jobs = _count_status[(std::int8_t) CondorJobStatus::Completed] + diff_jobs;
+ int diff_jobs = _tandem_condor_process->getCondorJobSize() - total_jobs;
+ really_completed_jobs =
+ _count_status[(std::int8_t)CondorJobStatus::Completed] + diff_jobs;
}
- _count_status[(std::int8_t) CondorJobStatus::Completed] = really_completed_jobs;
+ _count_status[(std::int8_t)CondorJobStatus::Completed] =
+ really_completed_jobs;
- _tandem_condor_process->setCondorJobStatus(_count_status);
- /*
- xtandemCondorAnalysis.setJobCompleted(junexpanded, jidle, jrunning,
- jremoved, reallyCompletedJobs, jheld, jsubmission_error);
+ _tandem_condor_process->setCondorJobStatus(_count_status);
+ /*
+ xtandemCondorAnalysis.setJobCompleted(junexpanded, jidle, jrunning,
+ jremoved, reallyCompletedJobs, jheld, jsubmission_error);
- */
+ */
- return true;
+ return true;
}
-bool CondorQxmlSaxHandler::startDocument() {
- for (std::int8_t i=0; i < 10; i++) {
- _count_status[i] = 0;
+bool
+CondorQxmlSaxHandler::startDocument()
+{
+ for(std::int8_t i = 0; i < 10; i++)
+ {
+ _count_status[i] = 0;
}
- _is_empty = true;
- return true;
+ _is_empty = true;
+ return true;
}
-bool CondorQxmlSaxHandler::characters(const QString &str) {
- _current_text += str;
- return true;
+bool
+CondorQxmlSaxHandler::characters(const QString &str)
+{
+ _current_text += str;
+ return true;
}
-bool CondorQxmlSaxHandler::startElement_c(QXmlAttributes attributes) {
-
-// <c>
-// <a n="ProcId"><i>0</i></a>
- _condor_job_status = CondorJobStatus::Unexpanded;
- _current_proc_id = 0;
- _is_empty = false;
- _current_remote_host = "";
- _current_last_remote_host = "";
- return true;
-
+bool
+CondorQxmlSaxHandler::startElement_c(QXmlAttributes attributes)
+{
+
+ // <c>
+ // <a n="ProcId"><i>0</i></a>
+ _condor_job_status = CondorJobStatus::Unexpanded;
+ _current_proc_id = 0;
+ _is_empty = false;
+ _current_remote_host = "";
+ _current_last_remote_host = "";
+ return true;
}
-bool CondorQxmlSaxHandler::startElement_a(QXmlAttributes attributes) {
- // logger.debug("startElementgroup begin");
- // <group label="performance parameters" type="parameters">
- _in_name = attributes.value("n");
- return true;
-
+bool
+CondorQxmlSaxHandler::startElement_a(QXmlAttributes attributes)
+{
+ // logger.debug("startElementgroup begin");
+ // <group label="performance parameters" type="parameters">
+ _in_name = attributes.value("n");
+ return true;
}
-bool CondorQxmlSaxHandler::endElement_a() {
- _in_name = "";
- return true;
+bool
+CondorQxmlSaxHandler::endElement_a()
+{
+ _in_name = "";
+ return true;
}
-bool CondorQxmlSaxHandler::endElement_i() {
- if (_in_name == "ProcId") {
- _current_proc_id = _current_text.toInt();
- } else if (_in_name == "JobStatus") {
- // <a n="JobStatus"><i>2</i></a>
- _condor_job_status = static_cast<CondorJobStatus>(_current_text.toInt());
- // logger.debug(currentProcId);
+bool
+CondorQxmlSaxHandler::endElement_i()
+{
+ if(_in_name == "ProcId")
+ {
+ _current_proc_id = _current_text.toInt();
+ }
+ else if(_in_name == "JobStatus")
+ {
+ // <a n="JobStatus"><i>2</i></a>
+ _condor_job_status = static_cast<CondorJobStatus>(_current_text.toInt());
+ // logger.debug(currentProcId);
}
- return true;
+ return true;
}
-bool CondorQxmlSaxHandler::endElement_s() {
- if (_in_name == "RemoteHost") {
- // <a n="RemoteHost"><s>slot1@proteus3</s></a>
- _current_remote_host = _current_text;
- } else if ( _in_name == "LastRemoteHost") {
- // <a n="LastRemoteHost"><s>slot1@proteus4</s></a>
- _current_last_remote_host = _current_text;
+bool
+CondorQxmlSaxHandler::endElement_s()
+{
+ if(_in_name == "RemoteHost")
+ {
+ // <a n="RemoteHost"><s>slot1@proteus3</s></a>
+ _current_remote_host = _current_text;
}
- return true;
-
+ else if(_in_name == "LastRemoteHost")
+ {
+ // <a n="LastRemoteHost"><s>slot1@proteus4</s></a>
+ _current_last_remote_host = _current_text;
+ }
+ return true;
}
-bool CondorQxmlSaxHandler::endElement_c() {
- /*
- * 0 Unexpanded U 1 Idle I 2 Running R 3 Removed X 4 Completed C 5 Held
- * H 6 Submission_err E
- */
- _count_status[(std::int8_t) _condor_job_status] += 1;
-
- qDebug() << "currentRemoteHost:" << _current_remote_host <<
- " currentLastRemoteHost" << _current_last_remote_host << " "
- << (std::int8_t)_condor_job_status;
- return true;
+bool
+CondorQxmlSaxHandler::endElement_c()
+{
+ /*
+ * 0 Unexpanded U 1 Idle I 2 Running R 3 Removed X 4 Completed C 5 Held
+ * H 6 Submission_err E
+ */
+ _count_status[(std::int8_t)_condor_job_status] += 1;
+
+ qDebug() << "currentRemoteHost:" << _current_remote_host
+ << " currentLastRemoteHost" << _current_last_remote_host << " "
+ << (std::int8_t)_condor_job_status;
+ return true;
}
/*
@@ -243,7 +313,7 @@ import fr.inra.pappso.xtandempipeline.thread.XtandemCondorAnalysis;
public class HandlerHTCondorQueue extends SaxBaseHandler {
private static final Logger logger = Logger
- .getLogger(HandlerHTCondorQueue.class);
+ .getLogger(HandlerHTCondorQueue.class);
private Object inName;
private Integer currentProcId;
private Integer currentJobStatus;
@@ -260,14 +330,14 @@ private XtandemCondorAnalysis xtandemCondorAnalysis;
private boolean empty = true;
public HandlerHTCondorQueue(XtandemCondorAnalysis xtandemCondorAnalysis)
- throws MSMSException {
- super();
- this.xtandemCondorAnalysis = xtandemCondorAnalysis;
+ throws MSMSException {
+ super();
+ this.xtandemCondorAnalysis = xtandemCondorAnalysis;
}
@Override
public void startDocument() throws SAXException {
- this.empty = true;
+ this.empty = true;
}
diff --git a/src/input/condorqxmlsaxhandler.h b/src/input/condorqxmlsaxhandler.h
index dd946473b291d18a697f382681ff8dea937ca294..4fd269c619fbc50a0cead5d997c9ec4688816fe6 100644
--- a/src/input/condorqxmlsaxhandler.h
+++ b/src/input/condorqxmlsaxhandler.h
@@ -7,26 +7,27 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef CONDORQXMLSAXHANDLER_H
#define CONDORQXMLSAXHANDLER_H
@@ -37,63 +38,63 @@ class TandemCondorProcess;
/** \def CondorJobStatus
* */
-enum class CondorJobStatus: std::int8_t {
- Unexpanded =0, ///< 0 Unexpanded U
- Idle =1, ///< 1 Idle I
- Running=2, ///< 2 Running R
- Removed=3, ///< 3 Removed X
- Completed=4, ///< 4 Completed C
- Held=5, ///< 5 Held H
- Submission_err=6 ///< 6 Submission_err E
+enum class CondorJobStatus : std::int8_t
+{
+ Unexpanded = 0, ///< 0 Unexpanded U
+ Idle = 1, ///< 1 Idle I
+ Running = 2, ///< 2 Running R
+ Removed = 3, ///< 3 Removed X
+ Completed = 4, ///< 4 Completed C
+ Held = 5, ///< 5 Held H
+ Submission_err = 6 ///< 6 Submission_err E
};
-class CondorQxmlSaxHandler: public QXmlDefaultHandler
+class CondorQxmlSaxHandler : public QXmlDefaultHandler
{
-public:
- CondorQxmlSaxHandler(TandemCondorProcess * tandem_condor_process);
- ~CondorQxmlSaxHandler();
-
- bool startElement(const QString & namespaceURI, const QString & localName,
- const QString & qName, const QXmlAttributes & attributes);
-
- bool endElement(const QString & namespaceURI, const QString & localName,
- const QString & qName);
-
- bool startDocument();
-
- bool endDocument();
-
- bool characters(const QString &str);
-
- bool fatalError(const QXmlParseException &exception);
- bool error(const QXmlParseException &exception);
-
- QString errorString() const;
-
-private:
- bool startElement_c(QXmlAttributes attributes);
- bool startElement_a(QXmlAttributes attributes);
- bool endElement_c();
- bool endElement_a();
- bool endElement_i();
- bool endElement_s();
-
-private:
- TandemCondorProcess * _tandem_condor_process;
-
- std::vector<QString> _tag_stack;
- QString _errorStr;
- QString _current_text;
-
- QString _in_name;
- CondorJobStatus _condor_job_status;
- unsigned int _current_proc_id;
- QString _current_remote_host;
- QString _current_last_remote_host;
-
- std::int8_t _count_status[10];
- bool _is_empty;
+ public:
+ CondorQxmlSaxHandler(TandemCondorProcess *tandem_condor_process);
+ ~CondorQxmlSaxHandler();
+
+ bool startElement(const QString &namespaceURI, const QString &localName,
+ const QString &qName, const QXmlAttributes &attributes);
+
+ bool endElement(const QString &namespaceURI, const QString &localName,
+ const QString &qName);
+
+ bool startDocument();
+
+ bool endDocument();
+
+ bool characters(const QString &str);
+
+ bool fatalError(const QXmlParseException &exception);
+ bool error(const QXmlParseException &exception);
+
+ QString errorString() const;
+
+ private:
+ bool startElement_c(QXmlAttributes attributes);
+ bool startElement_a(QXmlAttributes attributes);
+ bool endElement_c();
+ bool endElement_a();
+ bool endElement_i();
+ bool endElement_s();
+
+ private:
+ TandemCondorProcess *_tandem_condor_process;
+
+ std::vector<QString> _tag_stack;
+ QString _errorStr;
+ QString _current_text;
+
+ QString _in_name;
+ CondorJobStatus _condor_job_status;
+ unsigned int _current_proc_id;
+ QString _current_remote_host;
+ QString _current_last_remote_host;
+ std::int8_t _count_status[10];
+ bool _is_empty;
};
#endif // CONDORQXMLSAXHANDLER_H
diff --git a/src/input/identificationpwizreader.h b/src/input/identificationpwizreader.h
index 0ff1f4266cbc04b75488427a4fb7dee50f37b91c..4738d65f668345c032277e8bbcc3090786ad65f6 100644
--- a/src/input/identificationpwizreader.h
+++ b/src/input/identificationpwizreader.h
@@ -46,7 +46,7 @@ namespace pwiz
{
class IdentDataFile;
}
-}
+} // namespace pwiz
class IdentificationPwizReader
{
diff --git a/src/input/mascot/mascotdatparser.cpp b/src/input/mascot/mascotdatparser.cpp
index bd1ee45add8cf6333f85f7fe4457451ba16c62af..1fde28eaf9217af05778419f962f0147087358e5 100644
--- a/src/input/mascot/mascotdatparser.cpp
+++ b/src/input/mascot/mascotdatparser.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "mascotdatparser.h"
#include "mimeparser.h"
@@ -36,572 +37,759 @@
#include "../../core/proteinmatch.h"
#include "../../core/peptideevidence.h"
-MascotDatParser::MascotDatParser(Project * p_project, IdentificationGroup * p_identification_group,
- IdentificationDataSource * p_identification_data_source) {
- _p_project = p_project;
- _p_identification_group = p_identification_group;
- _p_identification_data_source = p_identification_data_source;
-
- _regexp_header_line.setPattern("^([A-Z,a-z,0-9,_]+)=(.*)$");
+MascotDatParser::MascotDatParser(
+ Project *p_project, IdentificationGroup *p_identification_group,
+ IdentificationDataSource *p_identification_data_source)
+{
+ _p_project = p_project;
+ _p_identification_group = p_identification_group;
+ _p_identification_data_source = p_identification_data_source;
+ _regexp_header_line.setPattern("^([A-Z,a-z,0-9,_]+)=(.*)$");
}
-MascotDatParser::~MascotDatParser() {
+MascotDatParser::~MascotDatParser()
+{
}
-void MascotDatParser::parse(QIODevice * in_stream) {
- qDebug() << "MascotDatParser::parse begin";
- MimeParser mime_parser(in_stream);
- mime_parser.open();
-
- for(bool more=mime_parser.goToFirstFile(); more; more=mime_parser.goToNextFile()) {
- qDebug() << "MascotDatParser::parse mimetype=" << mime_parser.getCurrentMimeType() << " filename=" << mime_parser.getCurrentFileName();
-
- if (mime_parser.getCurrentFileName() == "proteins") {
- while(!mime_parser.getCurrentTextStream().atEnd()) {
- parseProteinLine( mime_parser.getCurrentTextStream().readLine());
+void
+MascotDatParser::parse(QIODevice *in_stream)
+{
+ qDebug() << "MascotDatParser::parse begin";
+ MimeParser mime_parser(in_stream);
+ mime_parser.open();
+
+ for(bool more = mime_parser.goToFirstFile(); more;
+ more = mime_parser.goToNextFile())
+ {
+ qDebug() << "MascotDatParser::parse mimetype="
+ << mime_parser.getCurrentMimeType()
+ << " filename=" << mime_parser.getCurrentFileName();
+
+ if(mime_parser.getCurrentFileName() == "proteins")
+ {
+ while(!mime_parser.getCurrentTextStream().atEnd())
+ {
+ parseProteinLine(mime_parser.getCurrentTextStream().readLine());
}
}
- else if (mime_parser.getCurrentFileName() == "header") {
- while(!mime_parser.getCurrentTextStream().atEnd()) {
- parseHeaderLine( mime_parser.getCurrentTextStream().readLine());
+ else if(mime_parser.getCurrentFileName() == "header")
+ {
+ while(!mime_parser.getCurrentTextStream().atEnd())
+ {
+ parseHeaderLine(mime_parser.getCurrentTextStream().readLine());
}
}
- else if (mime_parser.getCurrentFileName() == "masses") {
- while(!mime_parser.getCurrentTextStream().atEnd()) {
- parseMassesLine( mime_parser.getCurrentTextStream().readLine());
+ else if(mime_parser.getCurrentFileName() == "masses")
+ {
+ while(!mime_parser.getCurrentTextStream().atEnd())
+ {
+ parseMassesLine(mime_parser.getCurrentTextStream().readLine());
}
-
}
- else if (mime_parser.getCurrentFileName() == "summary") {
- while(!mime_parser.getCurrentTextStream().atEnd()) {
- parseSummaryLine( mime_parser.getCurrentTextStream().readLine());
+ else if(mime_parser.getCurrentFileName() == "summary")
+ {
+ while(!mime_parser.getCurrentTextStream().atEnd())
+ {
+ parseSummaryLine(mime_parser.getCurrentTextStream().readLine());
}
}
- else if (mime_parser.getCurrentFileName() == "peptides") {
- while(!mime_parser.getCurrentTextStream().atEnd()) {
- parsePeptidesLine( mime_parser.getCurrentTextStream().readLine());
+ else if(mime_parser.getCurrentFileName() == "peptides")
+ {
+ while(!mime_parser.getCurrentTextStream().atEnd())
+ {
+ parsePeptidesLine(mime_parser.getCurrentTextStream().readLine());
}
- saveAndClearPeptide();
+ saveAndClearPeptide();
}
- else if (mime_parser.getCurrentFileName() == "decoy_summary") {
- _is_decoy_section = true;
- while(!mime_parser.getCurrentTextStream().atEnd()) {
- parseSummaryLine( mime_parser.getCurrentTextStream().readLine());
+ else if(mime_parser.getCurrentFileName() == "decoy_summary")
+ {
+ _is_decoy_section = true;
+ while(!mime_parser.getCurrentTextStream().atEnd())
+ {
+ parseSummaryLine(mime_parser.getCurrentTextStream().readLine());
}
- _is_decoy_section = false;
+ _is_decoy_section = false;
}
- else if (mime_parser.getCurrentFileName() == "decoy_peptides") {
- _is_decoy_section = true;
- while(!mime_parser.getCurrentTextStream().atEnd()) {
- parsePeptidesLine( mime_parser.getCurrentTextStream().readLine());
+ else if(mime_parser.getCurrentFileName() == "decoy_peptides")
+ {
+ _is_decoy_section = true;
+ while(!mime_parser.getCurrentTextStream().atEnd())
+ {
+ parsePeptidesLine(mime_parser.getCurrentTextStream().readLine());
}
- saveAndClearPeptide();
- _is_decoy_section = false;
+ saveAndClearPeptide();
+ _is_decoy_section = false;
}
- else if (mime_parser.getCurrentFileName().startsWith("query")) {
- _current_query_index = mime_parser.getCurrentFileName().mid(5).toUInt();
- while(!mime_parser.getCurrentTextStream().atEnd()) {
- parseQueryLine( mime_parser.getCurrentTextStream().readLine());
+ else if(mime_parser.getCurrentFileName().startsWith("query"))
+ {
+ _current_query_index =
+ mime_parser.getCurrentFileName().mid(5).toUInt();
+ while(!mime_parser.getCurrentTextStream().atEnd())
+ {
+ parseQueryLine(mime_parser.getCurrentTextStream().readLine());
}
- saveQuery();
+ saveQuery();
}
-
}
- mime_parser.close();
- qDebug() << "MascotDatParser::parse end";
+ mime_parser.close();
+ qDebug() << "MascotDatParser::parse end";
}
-void MascotDatParser::parseMassesLine(const QString & masses_line) {
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " " << masses_line;
- if (_regexp_header_line.exactMatch(masses_line)) {
- QStringList header_list = _regexp_header_line.capturedTexts();
-
-// C_term=17.002740
-//N_term=1.007825
-//delta1=15.994915,Oxidation (M)
- if (header_list[1].startsWith("delta")) {
- _delta_modification_list.push_back(MascotModification());
- unsigned index = header_list[1].mid(5).toUInt();
- QStringList delta_mod_list = header_list[2].split(",");
- pappso::pappso_double mass = delta_mod_list[0].toDouble();
- if (delta_mod_list[1] == "Oxidation (M)") {
- _delta_modification_list[index-1].modification = pappso::AaModification::getInstance("MOD:00719");
- _delta_modification_list[index-1].residue = 'M';
+void
+MascotDatParser::parseMassesLine(const QString &masses_line)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << masses_line;
+ if(_regexp_header_line.exactMatch(masses_line))
+ {
+ QStringList header_list = _regexp_header_line.capturedTexts();
+
+ // C_term=17.002740
+ // N_term=1.007825
+ // delta1=15.994915,Oxidation (M)
+ if(header_list[1].startsWith("delta"))
+ {
+ _delta_modification_list.push_back(MascotModification());
+ unsigned index = header_list[1].mid(5).toUInt();
+ QStringList delta_mod_list = header_list[2].split(",");
+ pappso::pappso_double mass = delta_mod_list[0].toDouble();
+ if(delta_mod_list[1] == "Oxidation (M)")
+ {
+ _delta_modification_list[index - 1].modification =
+ pappso::AaModification::getInstance("MOD:00719");
+ _delta_modification_list[index - 1].residue = 'M';
}
- else {
- _delta_modification_list[index-1].modification = pappso::AaModification::getInstanceCustomizedMod(mass);
+ else
+ {
+ _delta_modification_list[index - 1].modification =
+ pappso::AaModification::getInstanceCustomizedMod(mass);
}
- //_number_of_residues = header_list[5].toUInt();
+ //_number_of_residues = header_list[5].toUInt();
}
-//FixedModResidues1=C
- else if (header_list[1].startsWith("FixedModResidues")) {
- unsigned index = header_list[1].mid(16).toUInt();
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " " << index;
- _fixed_modification_list[index-1].residue = header_list[2].at(0);
+ // FixedModResidues1=C
+ else if(header_list[1].startsWith("FixedModResidues"))
+ {
+ unsigned index = header_list[1].mid(16).toUInt();
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << index;
+ _fixed_modification_list[index - 1].residue = header_list[2].at(0);
}
-//NeutralLoss1=0.000000
-//NeutralLoss1_master=63.998285
-//FixedMod1=57.021464,Carbamidomethyl (C)
- else if (header_list[1].startsWith("FixedMod")) {
- unsigned index = header_list[1].mid(8).toUInt();
- _fixed_modification_list.push_back(MascotModification());
- QStringList fixed_mod_list = header_list[2].split(",");
- pappso::pappso_double mass = fixed_mod_list[0].toDouble();
- //_number_of_residues = header_list[2].toUInt();
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " " << header_list[2];
-
- if (fixed_mod_list[1] == "Carbamidomethyl (C)") {
- _fixed_modification_list[index-1].modification = pappso::AaModification::getInstance("MOD:00397");
- _fixed_modification_list[index-1].residue = 'C';
+ // NeutralLoss1=0.000000
+ // NeutralLoss1_master=63.998285
+ // FixedMod1=57.021464,Carbamidomethyl (C)
+ else if(header_list[1].startsWith("FixedMod"))
+ {
+ unsigned index = header_list[1].mid(8).toUInt();
+ _fixed_modification_list.push_back(MascotModification());
+ QStringList fixed_mod_list = header_list[2].split(",");
+ pappso::pappso_double mass = fixed_mod_list[0].toDouble();
+ //_number_of_residues = header_list[2].toUInt();
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << header_list[2];
+
+ if(fixed_mod_list[1] == "Carbamidomethyl (C)")
+ {
+ _fixed_modification_list[index - 1].modification =
+ pappso::AaModification::getInstance("MOD:00397");
+ _fixed_modification_list[index - 1].residue = 'C';
}
- else {
- _fixed_modification_list[index-1].modification = pappso::AaModification::getInstanceCustomizedMod(mass);
+ else
+ {
+ _fixed_modification_list[index - 1].modification =
+ pappso::AaModification::getInstanceCustomizedMod(mass);
}
}
}
- else {
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " QREGEXP does not work on " << masses_line;
+ else
+ {
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
+ << " QREGEXP does not work on " << masses_line;
}
-
-
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " " << _fixed_modification_list.size();
-}
-void MascotDatParser::parseProteinLine(const QString & protein_line) {
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " " << protein_line;
- ProteinXtpSp sp_xtp_protein;
- //02::"tr|A0A0D9SF80|A0A0D9SF80_HUMAN"=55120.88,"General transcription factor II-I repeat domain-containing protein 2A OS=Homo sapiens GN=GTF2IRD2B PE=4 SV=1"
- QRegExp regexp_protein("^(.*)::\"(.*)\"=([0-9]+\\.[0-9]+),\"(.*)\"$");
- if (regexp_protein.exactMatch(protein_line)) {
- QStringList protein_list = regexp_protein.capturedTexts();
- FastaFileSp fasta_file_sp = _fasta_file_list[protein_list[1].toUInt()-1];
- _current_protein.setAccession(protein_list[2]);
- _current_protein.setDescription(protein_list[4]);
- _current_protein.setFastaFileP(fasta_file_sp.get());
-
- sp_xtp_protein = _current_protein.makeProteinXtpSp();
- sp_xtp_protein = _p_project->getProteinStore().getInstance(sp_xtp_protein);
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << _fixed_modification_list.size();
+}
+
+void
+MascotDatParser::parseProteinLine(const QString &protein_line)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << protein_line;
+ ProteinXtpSp sp_xtp_protein;
+ // 02::"tr|A0A0D9SF80|A0A0D9SF80_HUMAN"=55120.88,"General transcription factor
+ // II-I repeat domain-containing protein 2A OS=Homo sapiens GN=GTF2IRD2B PE=4
+ // SV=1"
+ QRegExp regexp_protein("^(.*)::\"(.*)\"=([0-9]+\\.[0-9]+),\"(.*)\"$");
+ if(regexp_protein.exactMatch(protein_line))
+ {
+ QStringList protein_list = regexp_protein.capturedTexts();
+ FastaFileSp fasta_file_sp =
+ _fasta_file_list[protein_list[1].toUInt() - 1];
+ _current_protein.setAccession(protein_list[2]);
+ _current_protein.setDescription(protein_list[4]);
+ _current_protein.setFastaFileP(fasta_file_sp.get());
+
+ sp_xtp_protein = _current_protein.makeProteinXtpSp();
+ sp_xtp_protein =
+ _p_project->getProteinStore().getInstance(sp_xtp_protein);
}
- else {
- QRegExp regexp_proteinb("^\"(.*)\"=([0-9]+\\.[0-9]+),\"(.*)\"$");
- if (regexp_proteinb.exactMatch(protein_line)) {
- QStringList protein_list = regexp_proteinb.capturedTexts();
- FastaFileSp fasta_file_sp = _fasta_file_list[0];
-
- _current_protein.setAccession(protein_list[1]);
- _current_protein.setDescription(protein_list[3]);
- _current_protein.setFastaFileP(fasta_file_sp.get());
-
- sp_xtp_protein = _current_protein.makeProteinXtpSp();
- sp_xtp_protein = _p_project->getProteinStore().getInstance(sp_xtp_protein);
+ else
+ {
+ QRegExp regexp_proteinb("^\"(.*)\"=([0-9]+\\.[0-9]+),\"(.*)\"$");
+ if(regexp_proteinb.exactMatch(protein_line))
+ {
+ QStringList protein_list = regexp_proteinb.capturedTexts();
+ FastaFileSp fasta_file_sp = _fasta_file_list[0];
+
+ _current_protein.setAccession(protein_list[1]);
+ _current_protein.setDescription(protein_list[3]);
+ _current_protein.setFastaFileP(fasta_file_sp.get());
+
+ sp_xtp_protein = _current_protein.makeProteinXtpSp();
+ sp_xtp_protein =
+ _p_project->getProteinStore().getInstance(sp_xtp_protein);
}
- else {
- qDebug() << "MascotDatParser::parseProteinLine error " << protein_line;
+ else
+ {
+ qDebug() << "MascotDatParser::parseProteinLine error "
+ << protein_line;
}
}
}
-void MascotDatParser::parseHeaderLine(const QString & header_line) {
- if (_regexp_header_line.exactMatch(header_line)) {
- QStringList header_list = _regexp_header_line.capturedTexts();
-//sequences=73998
-//sequences_after_tax=73998
-//residues=24900901
- if (header_list[1].startsWith("residues")) {
- qDebug() << "queries=" << header_list[2];
- _number_of_residues = header_list[2].toUInt();
+void
+MascotDatParser::parseHeaderLine(const QString &header_line)
+{
+ if(_regexp_header_line.exactMatch(header_line))
+ {
+ QStringList header_list = _regexp_header_line.capturedTexts();
+ // sequences=73998
+ // sequences_after_tax=73998
+ // residues=24900901
+ if(header_list[1].startsWith("residues"))
+ {
+ qDebug() << "queries=" << header_list[2];
+ _number_of_residues = header_list[2].toUInt();
}
-//distribution=64847,0,1,576,2254,1934,1417,984,683,419,238,192,113,89,74,46,23,32,28,21,11,3,2,3,3,2,1,1,0,0,0,0,0,0,1
-//decoy_type=1
-//distribution_decoy=65162,0,1,552,2259,1891,1422,957,601,376,192,159,126,73,56,64,26,27,22,14,6,4,1,1,3,2,1
-//exec_time=484
-//date=1517587671
-//time=17:07:51
-//queries=54084
- else if (header_list[1].startsWith("queries")) {
- qDebug() << "queries=" << header_list[2];
- _number_of_queries = header_list[2].toUInt();
- _query_peptide_results.resize(_number_of_queries);
- _summary_list.resize(_number_of_queries);
- _decoy_query_peptide_results.resize(_number_of_queries);
- _decoy_summary_list.resize(_number_of_queries);
+ // distribution=64847,0,1,576,2254,1934,1417,984,683,419,238,192,113,89,74,46,23,32,28,21,11,3,2,3,3,2,1,1,0,0,0,0,0,0,1
+ // decoy_type=1
+ // distribution_decoy=65162,0,1,552,2259,1891,1422,957,601,376,192,159,126,73,56,64,26,27,22,14,6,4,1,1,3,2,1
+ // exec_time=484
+ // date=1517587671
+ // time=17:07:51
+ // queries=54084
+ else if(header_list[1].startsWith("queries"))
+ {
+ qDebug() << "queries=" << header_list[2];
+ _number_of_queries = header_list[2].toUInt();
+ _query_peptide_results.resize(_number_of_queries);
+ _summary_list.resize(_number_of_queries);
+ _decoy_query_peptide_results.resize(_number_of_queries);
+ _decoy_summary_list.resize(_number_of_queries);
}
-//min_peaks_for_homology=6
-//max_hits=50
-//version=2.5.0
- else if (header_list[1] == "version") {
- _p_identification_data_source->setIdentificationEngineVersion(header_list[2]);
+ // min_peaks_for_homology=6
+ // max_hits=50
+ // version=2.5.0
+ else if(header_list[1] == "version")
+ {
+ _p_identification_data_source->setIdentificationEngineVersion(
+ header_list[2]);
}
-//fastafile=C:/inetpub/mascot/sequence/ECOLI_INRA/current/ECOLI_INRA_1.fasta
- else if (header_list[1].startsWith("fastafile")) {
- qDebug() << "fastafile=" << header_list[2];
- _fasta_file_list.push_back( _p_project->getFastaFileStore().getInstance(FastaFile(header_list[2])));
-
- _p_identification_data_source->addFastaFile(_fasta_file_list.back());
+ // fastafile=C:/inetpub/mascot/sequence/ECOLI_INRA/current/ECOLI_INRA_1.fasta
+ else if(header_list[1].startsWith("fastafile"))
+ {
+ qDebug() << "fastafile=" << header_list[2];
+ _fasta_file_list.push_back(
+ _p_project->getFastaFileStore().getInstance(
+ FastaFile(header_list[2])));
+
+ _p_identification_data_source->addFastaFile(_fasta_file_list.back());
}
-//release=ECOLI_INRA_1.fasta
-//sequences1=4305
-//sequences_after_tax1=4305
-//residues1=1356026
-//fastafile2=C:/inetpub/mascot/sequence/HUMAN_INRA/current/HUMAN_INRA_1.fasta
-//release2=HUMAN_INRA_1.fasta
-//sequences2=69693
-//sequences_after_tax2=69693
-//residues2=23544875
-//taskid=151758718701
+ // release=ECOLI_INRA_1.fasta
+ // sequences1=4305
+ // sequences_after_tax1=4305
+ // residues1=1356026
+ // fastafile2=C:/inetpub/mascot/sequence/HUMAN_INRA/current/HUMAN_INRA_1.fasta
+ // release2=HUMAN_INRA_1.fasta
+ // sequences2=69693
+ // sequences_after_tax2=69693
+ // residues2=23544875
+ // taskid=151758718701
}
}
-void MascotDatParser::parsePeptidesLine(const QString & peptide_line) {
- try {
- if (_regexp_header_line.exactMatch(peptide_line)) {
- QStringList header_list = _regexp_header_line.capturedTexts();
- QString index = header_list[1];
- QString value = header_list[2];
- QStringList index_list = index.split("_");
- if (index_list.size() == 3) {
- if (index_list[2] == "db") {
- saveAndClearPeptide();
- //q1_p1_db=02
- while (value.size() > 0) {
- QString fasta_str = value.mid(0,2);
- _current_peptide.fasta_file_list.push_back(_fasta_file_list.at(fasta_str.toInt()-1));
- value = value.mid(2);
+void
+MascotDatParser::parsePeptidesLine(const QString &peptide_line)
+{
+ try
+ {
+ if(_regexp_header_line.exactMatch(peptide_line))
+ {
+ QStringList header_list = _regexp_header_line.capturedTexts();
+ QString index = header_list[1];
+ QString value = header_list[2];
+ QStringList index_list = index.split("_");
+ if(index_list.size() == 3)
+ {
+ if(index_list[2] == "db")
+ {
+ saveAndClearPeptide();
+ // q1_p1_db=02
+ while(value.size() > 0)
+ {
+ QString fasta_str = value.mid(0, 2);
+ _current_peptide.fasta_file_list.push_back(
+ _fasta_file_list.at(fasta_str.toInt() - 1));
+ value = value.mid(2);
}
}
- //q856_p9_subst=1,X,W
- else if (index_list[2] == "subst") {
- _current_peptide.subst = value;
+ // q856_p9_subst=1,X,W
+ else if(index_list[2] == "subst")
+ {
+ _current_peptide.subst = value;
}
}
- else if (index_list.size() == 2) {
- if (value == "-1") {
- //no result for this query
+ else if(index_list.size() == 2)
+ {
+ if(value == "-1")
+ {
+ // no result for this query
}
- else {
-
- QString query_index = index_list[0];
- _current_peptide.query_index = query_index.mid(1).toUInt();
- QString peptide_index = index_list[1];
- _current_peptide.peptide_index = peptide_index.mid(1).toUInt();
- //q1_p1=0,597.302322,0.997884,2,GAWHK,9,0000000,7.97,0000012000000000000,0,0;"sp|O95006|OR2F2_HUMAN":0:299:303:1
- int position = value.indexOf(";\"", 0);
- QString peptide_string = value.mid(0, position);
- //qDebug() << "peptide_string=" << peptide_string;
-
- _current_peptide.peptide_string_list = peptide_string.split(",");
-
-
-
- QString protein_string = value.mid(position+2);
- //qDebug() << "protein_string=" << protein_string;
- //"sp|Q9Y2I7|FYV1_HUMAN":0:670:675:2,"tr|E9PDH4|E9PDH4_HUMAN":0:614:619:2
- _current_peptide.protein_string_list = protein_string.split(",\"");
+ else
+ {
+
+ QString query_index = index_list[0];
+ _current_peptide.query_index = query_index.mid(1).toUInt();
+ QString peptide_index = index_list[1];
+ _current_peptide.peptide_index =
+ peptide_index.mid(1).toUInt();
+ // q1_p1=0,597.302322,0.997884,2,GAWHK,9,0000000,7.97,0000012000000000000,0,0;"sp|O95006|OR2F2_HUMAN":0:299:303:1
+ int position = value.indexOf(";\"", 0);
+ QString peptide_string = value.mid(0, position);
+ // qDebug() << "peptide_string=" << peptide_string;
+
+ _current_peptide.peptide_string_list =
+ peptide_string.split(",");
+
+
+ QString protein_string = value.mid(position + 2);
+ // qDebug() << "protein_string=" << protein_string;
+ //"sp|Q9Y2I7|FYV1_HUMAN":0:670:675:2,"tr|E9PDH4|E9PDH4_HUMAN":0:614:619:2
+ _current_peptide.protein_string_list =
+ protein_string.split(",\"");
}
-
-
}
- /*
- q1_p1_db=02
- q1_p1=0,597.302322,0.997884,2,GAWHK,9,0000000,7.97,0000012000000000000,0,0;"sp|O95006|OR2F2_HUMAN":0:299:303:1
- q1_p1_terms=K,L
- q1_p2_db=02
- q1_p2=1,598.296219,0.003987,2,KEEPP,11,0000000,1.32,0002000000000000000,0,0;"tr|E9PNM8|E9PNM8_HUMAN":0:134:138:1
- q1_p2_terms=R,-
- q2_p1_db=02
- q2_p1=1,598.380234,-0.000316,3,KAGVPK,13,00000000,17.13,0002011000000000000,0,0;"tr|H7C1P9|H7C1P9_HUMAN":0:945:950:2
- q2_p1_terms=K,K
- q2_p2_db=0202
- q2_p2=1,598.380234,-0.000316,2,KQPVK,9,0000000,9.54,0002011000000000000,0,0;"sp|P33527|MRP1_HUMAN":0:270:274:1,"tr|I3L4X2|I3L4X2_HUMAN":0:169:173:1
- q2_p2_terms=R,V:R,V
- q2_p3_db=02
- q2_p3=1,598.380234,-0.000316,2,KAVPGK,13,00000000,7.03,0002001000000000000,0,0;"sp|Q13061|TRDN_HUMAN":0:440:445:2
- q2_p3_terms=K,K
- q2_p4_db=0202
- q2_p4=1,598.380234,-0.000316,2,IPGGKK,14,00000000,1.26,0002001000000000000,0,0;"sp|Q9Y2I7|FYV1_HUMAN":0:670:675:2,"tr|E9PDH4|E9PDH4_HUMAN":0:614:619:2
- q2_p4_terms=K,F:K,F
- */
-
-
- /*
- q856_p9_db=0202
- q856_p9=0,685.427521,-0.000117,3,XLLVR,12,0000000,13.68,0000002000000000000,0,0;"tr|V9GY00|V9GY00_HUMAN":0:1:5:1,"tr|H7C3C3|H7C3C3_HUMAN":0:1:5:1
- q856_p9_terms=-,L:-,V
- q856_p9_subst=1,X,W
- */
-
+ /*
+ q1_p1_db=02
+ q1_p1=0,597.302322,0.997884,2,GAWHK,9,0000000,7.97,0000012000000000000,0,0;"sp|O95006|OR2F2_HUMAN":0:299:303:1
+ q1_p1_terms=K,L
+ q1_p2_db=02
+ q1_p2=1,598.296219,0.003987,2,KEEPP,11,0000000,1.32,0002000000000000000,0,0;"tr|E9PNM8|E9PNM8_HUMAN":0:134:138:1
+ q1_p2_terms=R,-
+ q2_p1_db=02
+ q2_p1=1,598.380234,-0.000316,3,KAGVPK,13,00000000,17.13,0002011000000000000,0,0;"tr|H7C1P9|H7C1P9_HUMAN":0:945:950:2
+ q2_p1_terms=K,K
+ q2_p2_db=0202
+ q2_p2=1,598.380234,-0.000316,2,KQPVK,9,0000000,9.54,0002011000000000000,0,0;"sp|P33527|MRP1_HUMAN":0:270:274:1,"tr|I3L4X2|I3L4X2_HUMAN":0:169:173:1
+ q2_p2_terms=R,V:R,V
+ q2_p3_db=02
+ q2_p3=1,598.380234,-0.000316,2,KAVPGK,13,00000000,7.03,0002001000000000000,0,0;"sp|Q13061|TRDN_HUMAN":0:440:445:2
+ q2_p3_terms=K,K
+ q2_p4_db=0202
+ q2_p4=1,598.380234,-0.000316,2,IPGGKK,14,00000000,1.26,0002001000000000000,0,0;"sp|Q9Y2I7|FYV1_HUMAN":0:670:675:2,"tr|E9PDH4|E9PDH4_HUMAN":0:614:619:2
+ q2_p4_terms=K,F:K,F
+ */
+
+
+ /*
+ q856_p9_db=0202
+ q856_p9=0,685.427521,-0.000117,3,XLLVR,12,0000000,13.68,0000002000000000000,0,0;"tr|V9GY00|V9GY00_HUMAN":0:1:5:1,"tr|H7C3C3|H7C3C3_HUMAN":0:1:5:1
+ q856_p9_terms=-,L:-,V
+ q856_p9_subst=1,X,W
+ */
}
}
- catch (pappso::PappsoException exception_pappso) {
- _error_str = QObject::tr("ERROR in MascotDatParser::parsePeptidesLine %1, PAPPSO exception:\n%2").arg(peptide_line).arg(exception_pappso.qwhat());
- qDebug() << _error_str;
- throw pappso::PappsoException(_error_str);
+ catch(pappso::PappsoException exception_pappso)
+ {
+ _error_str = QObject::tr("ERROR in MascotDatParser::parsePeptidesLine "
+ "%1, PAPPSO exception:\n%2")
+ .arg(peptide_line)
+ .arg(exception_pappso.qwhat());
+ qDebug() << _error_str;
+ throw pappso::PappsoException(_error_str);
}
- catch (std::exception exception_std) {
- _error_str = QObject::tr("ERROR in MascotDatParser::parsePeptidesLine %1, std exception:\n%2").arg(peptide_line).arg(exception_std.what());
- qDebug() << _error_str;
- throw pappso::PappsoException(_error_str);
+ catch(std::exception exception_std)
+ {
+ _error_str =
+ QObject::tr(
+ "ERROR in MascotDatParser::parsePeptidesLine %1, std exception:\n%2")
+ .arg(peptide_line)
+ .arg(exception_std.what());
+ qDebug() << _error_str;
+ throw pappso::PappsoException(_error_str);
}
}
-void MascotDatParser::parseQueryLine(const QString & query_line) {
- try {
- if (_regexp_header_line.exactMatch(query_line)) {
- QStringList header_list = _regexp_header_line.capturedTexts();
- QString index = header_list[1];
- QString value = header_list[2];
+void
+MascotDatParser::parseQueryLine(const QString &query_line)
+{
+ try
+ {
+ if(_regexp_header_line.exactMatch(query_line))
+ {
+ QStringList header_list = _regexp_header_line.capturedTexts();
+ QString index = header_list[1];
+ QString value = header_list[2];
- //title=FULL%20ISSLGSVGAGIVAVKK%20N22213%20%20%20QEP1_SpikeIn_230914_1_3ng_270914%2e35282%2e35282%2e2
- if (index == "title") {
- _current_query.title = value;
+ // title=FULL%20ISSLGSVGAGIVAVKK%20N22213%20%20%20QEP1_SpikeIn_230914_1_3ng_270914%2e35282%2e35282%2e2
+ if(index == "title")
+ {
+ _current_query.title = value;
}
- //rtinseconds=5703.84
- else if (index == "rtinseconds") {
- _current_query.rt = value.toDouble();
+ // rtinseconds=5703.84
+ else if(index == "rtinseconds")
+ {
+ _current_query.rt = value.toDouble();
}
- //index=44035
- else if (index == "index") {
- _current_query.query_index = value.toUInt();
+ // index=44035
+ else if(index == "index")
+ {
+ _current_query.query_index = value.toUInt();
}
- //charge=2+
- else if (index == "charge") {
- _current_query.charge = value.mid(0,value.size()-1).toUInt();
+ // charge=2+
+ else if(index == "charge")
+ {
+ _current_query.charge = value.mid(0, value.size() - 1).toUInt();
}
}
- /*
- mass_min=129.102051
- mass_max=1198.751099
- int_min=2327
- int_max=6.845e+005
- num_vals=44
- num_used1=-1
- Ions1=129.102051:1.111e+005,275.207306:9.008e+004,374.275299:9.717e+004,514.825623:1.929e+004,599.878906:1.472e+005,714.431519:1.356e+004,815.466003:9643,924.570435:4428,1028.645630:1.257e+005,1085.665527:6.845e+005,1198.751099:1.858e+005,147.112656:7.954e+004,261.159271:4.327e+004,357.248169:2.192e+004,506.312775:3319,543.336548:1.083e+005,655.376465:9786,1011.625977:1.747e+004,1068.641602:9.804e+004,1181.725342:2.712e+004,130.086014:3.602e+004,257.197388:1.455e+004,357.212097:3960,591.370056:2.454e+004,972.547058:3819,1069.647583:4.457e+004,201.123077:1.566e+004,299.171783:1.421e+004,534.825562:1.036e+004,1087.671631:2.374e+004,173.128418:1.512e+004,244.129089:1.052e+004,590.873291:8065,1067.656006:2.235e+004,228.133957:1.35e+004,258.180115:3194,534.333374:3635,1096.635376:1.549e+004,200.139084:1.026e+004,535.328552:3006,1070.637085:4813,183.112442:9925,131.080994:4806,211.108139:2327
-
- */
+ /*
+ mass_min=129.102051
+ mass_max=1198.751099
+ int_min=2327
+ int_max=6.845e+005
+ num_vals=44
+ num_used1=-1
+ Ions1=129.102051:1.111e+005,275.207306:9.008e+004,374.275299:9.717e+004,514.825623:1.929e+004,599.878906:1.472e+005,714.431519:1.356e+004,815.466003:9643,924.570435:4428,1028.645630:1.257e+005,1085.665527:6.845e+005,1198.751099:1.858e+005,147.112656:7.954e+004,261.159271:4.327e+004,357.248169:2.192e+004,506.312775:3319,543.336548:1.083e+005,655.376465:9786,1011.625977:1.747e+004,1068.641602:9.804e+004,1181.725342:2.712e+004,130.086014:3.602e+004,257.197388:1.455e+004,357.212097:3960,591.370056:2.454e+004,972.547058:3819,1069.647583:4.457e+004,201.123077:1.566e+004,299.171783:1.421e+004,534.825562:1.036e+004,1087.671631:2.374e+004,173.128418:1.512e+004,244.129089:1.052e+004,590.873291:8065,1067.656006:2.235e+004,228.133957:1.35e+004,258.180115:3194,534.333374:3635,1096.635376:1.549e+004,200.139084:1.026e+004,535.328552:3006,1070.637085:4813,183.112442:9925,131.080994:4806,211.108139:2327
+
+ */
}
- catch (pappso::PappsoException exception_pappso) {
- _error_str = QObject::tr("ERROR in MascotDatParser::parseQueryLine %1, PAPPSO exception:\n%2").arg(query_line).arg(exception_pappso.qwhat());
- qDebug() << _error_str;
- throw pappso::PappsoException(_error_str);
+ catch(pappso::PappsoException exception_pappso)
+ {
+ _error_str =
+ QObject::tr(
+ "ERROR in MascotDatParser::parseQueryLine %1, PAPPSO exception:\n%2")
+ .arg(query_line)
+ .arg(exception_pappso.qwhat());
+ qDebug() << _error_str;
+ throw pappso::PappsoException(_error_str);
}
- catch (std::exception exception_std) {
- _error_str = QObject::tr("ERROR in MascotDatParser::parseQueryLine %1, std exception:\n%2").arg(query_line).arg(exception_std.what());
- qDebug() << _error_str;
- throw pappso::PappsoException(_error_str);
+ catch(std::exception exception_std)
+ {
+ _error_str =
+ QObject::tr(
+ "ERROR in MascotDatParser::parseQueryLine %1, std exception:\n%2")
+ .arg(query_line)
+ .arg(exception_std.what());
+ qDebug() << _error_str;
+ throw pappso::PappsoException(_error_str);
}
}
-void MascotDatParser::parseSummaryLine(const QString & summary_line) {
- std::vector<SummaryLine> * p_summary_list = & _summary_list;
- if (_is_decoy_section) {
- p_summary_list = & _decoy_summary_list;
+void
+MascotDatParser::parseSummaryLine(const QString &summary_line)
+{
+ std::vector<SummaryLine> *p_summary_list = &_summary_list;
+ if(_is_decoy_section)
+ {
+ p_summary_list = &_decoy_summary_list;
}
- if (_regexp_header_line.exactMatch(summary_line)) {
- QStringList header_list = _regexp_header_line.capturedTexts();
- QString index = header_list[1];
- QString value = header_list[2];
-
-
- //qmass1=598.300206
- if (index.startsWith("qmass")) {
- unsigned int query_index = index.mid(5).toUInt();
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " " << query_index << " " << index;
- //_current_query.title = value;
- (*p_summary_list)[query_index-1].exp_mass=value.toDouble();
+ if(_regexp_header_line.exactMatch(summary_line))
+ {
+ QStringList header_list = _regexp_header_line.capturedTexts();
+ QString index = header_list[1];
+ QString value = header_list[2];
+
+
+ // qmass1=598.300206
+ if(index.startsWith("qmass"))
+ {
+ unsigned int query_index = index.mid(5).toUInt();
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << query_index << " " << index;
+ //_current_query.title = value;
+ (*p_summary_list)[query_index - 1].exp_mass = value.toDouble();
}
- //qexp1=300.157379,2+
-//qintensity1=2054822.6250
-//qmatch1=73
- else if (index.startsWith("qmatch")) {
- unsigned int query_index = index.mid(6).toUInt();
- //_current_query.title = value;
- (*p_summary_list)[query_index-1].match=value.toDouble();
+ // qexp1=300.157379,2+
+ // qintensity1=2054822.6250
+ // qmatch1=73
+ else if(index.startsWith("qmatch"))
+ {
+ unsigned int query_index = index.mid(6).toUInt();
+ //_current_query.title = value;
+ (*p_summary_list)[query_index - 1].match = value.toDouble();
}
-//qplughole1=14.820890
- else if (index.startsWith("qplughole")) {
- unsigned int query_index = index.mid(9).toUInt();
- //_current_query.title = value;
- (*p_summary_list)[query_index-1].plug_hole=value.toDouble();
+ // qplughole1=14.820890
+ else if(index.startsWith("qplughole"))
+ {
+ unsigned int query_index = index.mid(9).toUInt();
+ //_current_query.title = value;
+ (*p_summary_list)[query_index - 1].plug_hole = value.toDouble();
}
-
}
}
-void MascotDatParser::saveAndClearPeptide() {
- //qDebug() << "MascotDatParser::saveAndClearPeptide begin";
- if (_current_peptide.query_index > 0) {
- // save
- if (_is_decoy_section) {
- _decoy_query_peptide_results[_current_peptide.query_index-1].push_back(_current_peptide);
+void
+MascotDatParser::saveAndClearPeptide()
+{
+ // qDebug() << "MascotDatParser::saveAndClearPeptide begin";
+ if(_current_peptide.query_index > 0)
+ {
+ // save
+ if(_is_decoy_section)
+ {
+ _decoy_query_peptide_results[_current_peptide.query_index - 1]
+ .push_back(_current_peptide);
}
- else {
- _query_peptide_results[_current_peptide.query_index-1].push_back(_current_peptide);
+ else
+ {
+ _query_peptide_results[_current_peptide.query_index - 1].push_back(
+ _current_peptide);
}
}
- //new peptide query clear
- _current_peptide.peptide_string_list.clear();
- _current_peptide.fasta_file_list.clear();
- _current_peptide.query_index = 0;
- _current_peptide.subst = "";
- //qDebug() << "MascotDatParser::saveAndClearPeptide end";
+ // new peptide query clear
+ _current_peptide.peptide_string_list.clear();
+ _current_peptide.fasta_file_list.clear();
+ _current_peptide.query_index = 0;
+ _current_peptide.subst = "";
+ // qDebug() << "MascotDatParser::saveAndClearPeptide end";
}
-void MascotDatParser::saveQuery() {
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- if (_current_query.query_index > 0) {
- std::vector< PeptideLine> peptide_list = _query_peptide_results[_current_query.query_index-1];
- savePeptideList(peptide_list, false);
- peptide_list = _decoy_query_peptide_results[_current_query.query_index-1];
- savePeptideList(peptide_list, true);
+void
+MascotDatParser::saveQuery()
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ if(_current_query.query_index > 0)
+ {
+ std::vector<PeptideLine> peptide_list =
+ _query_peptide_results[_current_query.query_index - 1];
+ savePeptideList(peptide_list, false);
+ peptide_list =
+ _decoy_query_peptide_results[_current_query.query_index - 1];
+ savePeptideList(peptide_list, true);
}
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-void MascotDatParser::savePeptideList(std::vector< PeptideLine> & peptide_list, bool is_decoy) {
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
-
- PeptideEvidence peptide_evidence(_p_identification_data_source->getMsRunSp().get(),_current_query.query_index);
- peptide_evidence.setCharge(_current_query.charge);
- peptide_evidence.setChecked(true);
- peptide_evidence.setExperimentalMass(_summary_list[_current_query.query_index-1].exp_mass);
- peptide_evidence.setRetentionTime(_current_query.rt);
-
- peptide_evidence.setIdentificationDataSource( _p_identification_data_source);
- //parse and save
- for(PeptideLine & peptide_line:peptide_list) {
-
- /*
- *
- 0 setMissedCleavages(Integer.parseInt(st.nextToken()));
- 1 setPeptideMr(Double.parseDouble(st.nextToken()));
- 2 setDeltaMass(Double.parseDouble(st.nextToken()));
- 3 setNumberOfIonsMatched(Integer.parseInt(st.nextToken()));
- 4 setSequence(st.nextToken());
- 5 setPeaksUsedFromIons1(Integer.parseInt(st.nextToken()));
- 6 setVariableModificationsArray(st.nextToken());
- 7 setIonsScore(Double.parseDouble(st.nextToken()));
- 8 parseIonSeries(st.nextToken());
- 9 setPeaksUsedFromIons2(Integer.parseInt(st.nextToken()));
- 10 setPeaksUsedFromIons3(Integer.parseInt(st.nextToken()));
- */
- pappso::pappso_double ion_score = peptide_line.peptide_string_list.at(7).toDouble();
- peptide_evidence.setParam(PeptideEvidenceParam::mascot_score, QVariant(ion_score));
-
- if (is_decoy) {
- peptide_evidence.setEvalue(getEvalue(ion_score, _decoy_summary_list.at(_current_query.query_index-1), 0.05));
+void
+MascotDatParser::savePeptideList(std::vector<PeptideLine> &peptide_list,
+ bool is_decoy)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+
+ PeptideEvidence peptide_evidence(
+ _p_identification_data_source->getMsRunSp().get(),
+ _current_query.query_index);
+ peptide_evidence.setCharge(_current_query.charge);
+ peptide_evidence.setChecked(true);
+ peptide_evidence.setExperimentalMass(
+ _summary_list[_current_query.query_index - 1].exp_mass);
+ peptide_evidence.setRetentionTime(_current_query.rt);
+
+ peptide_evidence.setIdentificationDataSource(_p_identification_data_source);
+ // parse and save
+ for(PeptideLine &peptide_line : peptide_list)
+ {
+
+ /*
+ *
+ 0 setMissedCleavages(Integer.parseInt(st.nextToken()));
+ 1 setPeptideMr(Double.parseDouble(st.nextToken()));
+ 2 setDeltaMass(Double.parseDouble(st.nextToken()));
+ 3 setNumberOfIonsMatched(Integer.parseInt(st.nextToken()));
+ 4 setSequence(st.nextToken());
+ 5 setPeaksUsedFromIons1(Integer.parseInt(st.nextToken()));
+ 6 setVariableModificationsArray(st.nextToken());
+ 7 setIonsScore(Double.parseDouble(st.nextToken()));
+ 8 parseIonSeries(st.nextToken());
+ 9 setPeaksUsedFromIons2(Integer.parseInt(st.nextToken()));
+ 10 setPeaksUsedFromIons3(Integer.parseInt(st.nextToken()));
+ */
+ pappso::pappso_double ion_score =
+ peptide_line.peptide_string_list.at(7).toDouble();
+ peptide_evidence.setParam(PeptideEvidenceParam::mascot_score,
+ QVariant(ion_score));
+
+ if(is_decoy)
+ {
+ peptide_evidence.setEvalue(getEvalue(
+ ion_score, _decoy_summary_list.at(_current_query.query_index - 1),
+ 0.05));
}
- else {
- peptide_evidence.setEvalue(getEvalue(ion_score, _summary_list.at(_current_query.query_index-1), 0.05));
+ else
+ {
+ peptide_evidence.setEvalue(getEvalue(
+ ion_score, _summary_list.at(_current_query.query_index - 1), 0.05));
}
- peptide_evidence.setParam(PeptideEvidenceParam::mascot_expectation_value, QVariant(peptide_evidence.getEvalue()));
-
- QString peptide_str =peptide_line.peptide_string_list.at(4);
- if (!peptide_line.subst.isEmpty()) {
- //q856_p9_subst=1,X,W
- //q24379_p2_subst=1,B,D,8,B,D
- QStringList subst_list = peptide_line.subst.split(",");
- for (unsigned int i=0; i < subst_list.size(); i+=3) {
- peptide_str = peptide_str.replace(subst_list.at(0+i).toInt()-1,1,subst_list.at(2+i));
+ peptide_evidence.setParam(PeptideEvidenceParam::mascot_expectation_value,
+ QVariant(peptide_evidence.getEvalue()));
+
+ QString peptide_str = peptide_line.peptide_string_list.at(4);
+ if(!peptide_line.subst.isEmpty())
+ {
+ // q856_p9_subst=1,X,W
+ // q24379_p2_subst=1,B,D,8,B,D
+ QStringList subst_list = peptide_line.subst.split(",");
+ for(unsigned int i = 0; i < subst_list.size(); i += 3)
+ {
+ peptide_str = peptide_str.replace(
+ subst_list.at(0 + i).toInt() - 1, 1, subst_list.at(2 + i));
}
}
- PeptideXtpSp peptide_sp;
- peptide_sp = PeptideXtp(peptide_str).makePeptideXtpSp();
-
- //variable modifications :
- setVariableModifications(peptide_sp, peptide_line.peptide_string_list.at(6));
-
- //fixed modifications :
- for (unsigned int i=0; i < peptide_str.size(); i++) {
- for (MascotModification mascot_modif :_fixed_modification_list) {
- if (peptide_str.at(i) == mascot_modif.residue) {
- peptide_sp.get()->addAaModification(mascot_modif.modification, i);
+ PeptideXtpSp peptide_sp;
+ peptide_sp = PeptideXtp(peptide_str).makePeptideXtpSp();
+
+ // variable modifications :
+ setVariableModifications(peptide_sp,
+ peptide_line.peptide_string_list.at(6));
+
+ // fixed modifications :
+ for(unsigned int i = 0; i < peptide_str.size(); i++)
+ {
+ for(MascotModification mascot_modif : _fixed_modification_list)
+ {
+ if(peptide_str.at(i) == mascot_modif.residue)
+ {
+ peptide_sp.get()->addAaModification(mascot_modif.modification,
+ i);
}
}
}
- peptide_evidence.setPeptideXtpSp(_p_project->getPeptideStore().getInstance(peptide_sp));
+ peptide_evidence.setPeptideXtpSp(
+ _p_project->getPeptideStore().getInstance(peptide_sp));
- //qDebug() << __FILE__ << " " << __FUNCTION__<< " peptide=" << peptide_str << " evalue=" << peptide_evidence.getEvalue() << " ionscore=" << ion_score;
+ // qDebug() << __FILE__ << " " << __FUNCTION__<< " peptide=" <<
+ // peptide_str << " evalue=" << peptide_evidence.getEvalue() << "
+ // ionscore=" << ion_score;
- if (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) {
- throw pappso::PappsoException(QObject::tr("ERROR (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) %1").arg(peptide_line.protein_string_list.join(",\"")));
+ if(peptide_line.protein_string_list.size() !=
+ peptide_line.fasta_file_list.size())
+ {
+ throw pappso::PappsoException(
+ QObject::tr("ERROR (peptide_line.protein_string_list.size() != "
+ "peptide_line.fasta_file_list.size()) %1")
+ .arg(peptide_line.protein_string_list.join(",\"")));
}
- unsigned int i=0;
- foreach (const QString &str, peptide_line.protein_string_list) {
- //sp|O95006|OR2F2_HUMAN":0:299:303:1
- int position = str.indexOf("\"", 0);
- QString accession = str.mid(0, position);
- if (is_decoy) {
- accession = QString("%1|reversed").arg(accession);
+ unsigned int i = 0;
+ foreach(const QString &str, peptide_line.protein_string_list)
+ {
+ // sp|O95006|OR2F2_HUMAN":0:299:303:1
+ int position = str.indexOf("\"", 0);
+ QString accession = str.mid(0, position);
+ if(is_decoy)
+ {
+ accession = QString("%1|reversed").arg(accession);
}
- //qDebug() << "accession=" << accession;
- QStringList position_list = str.mid(position+2).split(":");
- if (position_list.size() != 4) {
- throw pappso::PappsoException(QObject::tr("ERROR position_list.size() != 4 %1").arg(str));
+ // qDebug() << "accession=" << accession;
+ QStringList position_list = str.mid(position + 2).split(":");
+ if(position_list.size() != 4)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("ERROR position_list.size() != 4 %1").arg(str));
}
- unsigned int start = position_list.at(1).toUInt()-1;
- unsigned int stop = position_list.at(2).toUInt()-1;
- //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- ProteinXtp protein;
- protein.setAccession(accession);
- protein.setFastaFileP(peptide_line.fasta_file_list[i].get());
- if (is_decoy) {
- protein.setIsDecoy(true);
+ unsigned int start = position_list.at(1).toUInt() - 1;
+ unsigned int stop = position_list.at(2).toUInt() - 1;
+ // qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+ ProteinXtp protein;
+ protein.setAccession(accession);
+ protein.setFastaFileP(peptide_line.fasta_file_list[i].get());
+ if(is_decoy)
+ {
+ protein.setIsDecoy(true);
}
- ProteinMatch * p_protein_match = _p_identification_group->getProteinMatchInstance(accession);
- if (p_protein_match == nullptr) {
- throw pappso::PappsoException(QObject::tr("ERROR (p_protein_match == nullptr) %1").arg(str));
+ ProteinMatch *p_protein_match =
+ _p_identification_group->getProteinMatchInstance(accession);
+ if(p_protein_match == nullptr)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("ERROR (p_protein_match == nullptr) %1").arg(str));
}
- //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- ProteinXtpSp sp_xtp_protein = protein.makeProteinXtpSp();
- p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
- p_protein_match->setChecked(true);
-
- PeptideMatch peptide_match;
- peptide_match.setStart(start);
- peptide_match.setPeptideEvidenceSp(_p_identification_data_source->getPeptideEvidenceStore().getInstance(&peptide_evidence));
-
- p_protein_match->addPeptideMatch(peptide_match);
- i++;
+ // qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+ ProteinXtpSp sp_xtp_protein = protein.makeProteinXtpSp();
+ p_protein_match->setProteinXtpSp(
+ _p_project->getProteinStore().getInstance(sp_xtp_protein));
+ p_protein_match->setChecked(true);
+
+ PeptideMatch peptide_match;
+ peptide_match.setStart(start);
+ peptide_match.setPeptideEvidenceSp(
+ _p_identification_data_source->getPeptideEvidenceStore()
+ .getInstance(&peptide_evidence));
+
+ p_protein_match->addPeptideMatch(peptide_match);
+ i++;
}
}
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-pappso::pappso_double MascotDatParser::getEvalue(pappso::pappso_double ion_score, SummaryLine & summary_line, pappso::pappso_double confidence_interval) const {
- pappso::pappso_double identity_threshold = (pappso::pappso_double)10.0 * std::log(summary_line.match / (confidence_interval * (pappso::pappso_double)20.0)) / log((pappso::pappso_double)10);;
- return (confidence_interval * pow((pappso::pappso_double)10, ((identity_threshold - ion_score) / (pappso::pappso_double)10)));
+pappso::pappso_double
+MascotDatParser::getEvalue(pappso::pappso_double ion_score,
+ SummaryLine &summary_line,
+ pappso::pappso_double confidence_interval) const
+{
+ pappso::pappso_double identity_threshold =
+ (pappso::pappso_double)10.0 *
+ std::log(summary_line.match /
+ (confidence_interval * (pappso::pappso_double)20.0)) /
+ log((pappso::pappso_double)10);
+ ;
+ return (confidence_interval *
+ pow((pappso::pappso_double)10,
+ ((identity_threshold - ion_score) / (pappso::pappso_double)10)));
}
-pappso::pappso_double MascotDatParser::getEvalueExperimental(pappso::pappso_double ion_score, SummaryLine & summary_line, pappso::pappso_double confidence_interval) const {
- // Evalue experimental Homology threshold (QPlughole value from .dat file).
- pappso::pappso_double eval = (ion_score - summary_line.plug_hole) / (pappso::pappso_double)10;
- eval = confidence_interval / pow((pappso::pappso_double)10, eval);
+pappso::pappso_double
+MascotDatParser::getEvalueExperimental(
+ pappso::pappso_double ion_score, SummaryLine &summary_line,
+ pappso::pappso_double confidence_interval) const
+{
+ // Evalue experimental Homology threshold (QPlughole value from .dat file).
+ pappso::pappso_double eval =
+ (ion_score - summary_line.plug_hole) / (pappso::pappso_double)10;
+ eval = confidence_interval / pow((pappso::pappso_double)10, eval);
}
-void MascotDatParser::setVariableModifications(PeptideXtpSp & peptide_sp, QString variable_modifications_string) {
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- //
- for (unsigned int i=0; i < variable_modifications_string.size() ; i++) {
- if (variable_modifications_string.mid(i,1).toUInt() > 0) {
- MascotModification mascot_modification = _delta_modification_list[variable_modifications_string.mid(i,1).toUInt()-1];
- peptide_sp.get()->addAaModification(mascot_modification.modification, i-1);
+void
+MascotDatParser::setVariableModifications(PeptideXtpSp &peptide_sp,
+ QString variable_modifications_string)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ //
+ for(unsigned int i = 0; i < variable_modifications_string.size(); i++)
+ {
+ if(variable_modifications_string.mid(i, 1).toUInt() > 0)
+ {
+ MascotModification mascot_modification = _delta_modification_list
+ [variable_modifications_string.mid(i, 1).toUInt() - 1];
+ peptide_sp.get()->addAaModification(mascot_modification.modification,
+ i - 1);
}
}
}
diff --git a/src/input/mascot/mascotdatparser.h b/src/input/mascot/mascotdatparser.h
index 6c345406a4689da4b3a69e44df91f2513a21124f..bd170cc00018859dab0e19e6621ec318c195ecd3 100644
--- a/src/input/mascot/mascotdatparser.h
+++ b/src/input/mascot/mascotdatparser.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef MASCOTDATPARSER_H
#define MASCOTDATPARSER_H
@@ -34,83 +35,91 @@
class MascotDatParser
{
-public:
- MascotDatParser(Project * p_project, IdentificationGroup * p_identification_group,
- IdentificationDataSource * p_identification_data_source);
- virtual ~MascotDatParser();
- void parse(QIODevice * in_stream);
-private:
- void parseProteinLine(const QString & protein_line);
- void parseHeaderLine(const QString & protein_line);
- void parsePeptidesLine(const QString & peptide_line);
- void parseQueryLine(const QString & query_line);
- void parseSummaryLine(const QString & summary_line);
- void parseMassesLine(const QString & masses_line);
- void saveQuery();
- void saveAndClearPeptide();
- void setVariableModifications(PeptideXtpSp & peptide_sp, QString variable_modifications_string);
-
-
-
- struct MascotModification {
- pappso::AaModificationP modification;
- QChar residue;
- };
-
-
- struct PeptideLine {
- unsigned int query_index=0;
- unsigned int peptide_index=0;
- QString subst;
- QStringList peptide_string_list;
- QStringList protein_string_list;
- std::vector<FastaFileSp> fasta_file_list;
- };
- struct QueryLine {
- unsigned int query_index=0;
- unsigned int charge=0;
- pappso::pappso_double rt=0;
- QString title;
- };
- struct SummaryLine {
- pappso::pappso_double match=0; //qmatch, identity threshold
- pappso::pappso_double exp_mass=0;
- pappso::pappso_double plug_hole=0; //qplughole, homology threshold
- };
- void savePeptideList(std::vector< PeptideLine> & peptide_list, bool is_decoy);
- pappso::pappso_double getEvalue(pappso::pappso_double ion_score, SummaryLine & summary_line, pappso::pappso_double confidence_interval = 0.05) const;
- pappso::pappso_double getEvalueExperimental(pappso::pappso_double ion_score, SummaryLine & summary_line, pappso::pappso_double confidence_interval = 0.05) const;
-
-private:
- Project * _p_project;
- IdentificationGroup * _p_identification_group;
- IdentificationDataSource * _p_identification_data_source;
-
-
- ProteinXtp _current_protein;
- std::vector<FastaFileSp> _fasta_file_list;
-
-
-
- QRegExp _regexp_header_line;
- unsigned int _number_of_queries=0;
- unsigned int _number_of_residues=0;
- unsigned int _current_query_index=0;
- QString _error_str;
- bool _is_decoy_section = false;
-
- PeptideLine _current_peptide;
- QueryLine _current_query;
-
- std::vector<std::vector<PeptideLine>> _query_peptide_results;
- std::vector<SummaryLine> _summary_list;
- std::vector<std::vector<PeptideLine>> _decoy_query_peptide_results;
- std::vector<SummaryLine> _decoy_summary_list;
-
- std::vector<MascotModification> _delta_modification_list;
- std::vector<MascotModification> _fixed_modification_list;
-
-
+ public:
+ MascotDatParser(Project *p_project,
+ IdentificationGroup *p_identification_group,
+ IdentificationDataSource *p_identification_data_source);
+ virtual ~MascotDatParser();
+ void parse(QIODevice *in_stream);
+
+ private:
+ void parseProteinLine(const QString &protein_line);
+ void parseHeaderLine(const QString &protein_line);
+ void parsePeptidesLine(const QString &peptide_line);
+ void parseQueryLine(const QString &query_line);
+ void parseSummaryLine(const QString &summary_line);
+ void parseMassesLine(const QString &masses_line);
+ void saveQuery();
+ void saveAndClearPeptide();
+ void setVariableModifications(PeptideXtpSp &peptide_sp,
+ QString variable_modifications_string);
+
+
+ struct MascotModification
+ {
+ pappso::AaModificationP modification;
+ QChar residue;
+ };
+
+
+ struct PeptideLine
+ {
+ unsigned int query_index = 0;
+ unsigned int peptide_index = 0;
+ QString subst;
+ QStringList peptide_string_list;
+ QStringList protein_string_list;
+ std::vector<FastaFileSp> fasta_file_list;
+ };
+ struct QueryLine
+ {
+ unsigned int query_index = 0;
+ unsigned int charge = 0;
+ pappso::pappso_double rt = 0;
+ QString title;
+ };
+ struct SummaryLine
+ {
+ pappso::pappso_double match = 0; // qmatch, identity threshold
+ pappso::pappso_double exp_mass = 0;
+ pappso::pappso_double plug_hole = 0; // qplughole, homology threshold
+ };
+ void savePeptideList(std::vector<PeptideLine> &peptide_list, bool is_decoy);
+ pappso::pappso_double
+ getEvalue(pappso::pappso_double ion_score, SummaryLine &summary_line,
+ pappso::pappso_double confidence_interval = 0.05) const;
+ pappso::pappso_double
+ getEvalueExperimental(pappso::pappso_double ion_score,
+ SummaryLine &summary_line,
+ pappso::pappso_double confidence_interval = 0.05) const;
+
+ private:
+ Project *_p_project;
+ IdentificationGroup *_p_identification_group;
+ IdentificationDataSource *_p_identification_data_source;
+
+
+ ProteinXtp _current_protein;
+ std::vector<FastaFileSp> _fasta_file_list;
+
+
+ QRegExp _regexp_header_line;
+ unsigned int _number_of_queries = 0;
+ unsigned int _number_of_residues = 0;
+ unsigned int _current_query_index = 0;
+ QString _error_str;
+ bool _is_decoy_section = false;
+
+ PeptideLine _current_peptide;
+ QueryLine _current_query;
+
+ std::vector<std::vector<PeptideLine>> _query_peptide_results;
+ std::vector<SummaryLine> _summary_list;
+ std::vector<std::vector<PeptideLine>> _decoy_query_peptide_results;
+ std::vector<SummaryLine> _decoy_summary_list;
+
+ std::vector<MascotModification> _delta_modification_list;
+ std::vector<MascotModification> _fixed_modification_list;
};
#endif // MASCOTDATPARSER_H
diff --git a/src/input/mascot/mimeparser.cpp b/src/input/mascot/mimeparser.cpp
index 2b566bd0ed61a38ce1295e3d7a75a9474c6abe62..9afe6a3e3f869e02d905c83efdf20bb67e76abc3 100644
--- a/src/input/mascot/mimeparser.cpp
+++ b/src/input/mascot/mimeparser.cpp
@@ -6,151 +6,188 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "mimeparser.h"
#include <QRegExp>
#include <QDebug>
#include <pappsomspp/pappsoexception.h>
-MimeParser::MimeParser(QIODevice * p_inputstream) {
- _p_inputstream = p_inputstream;
+MimeParser::MimeParser(QIODevice *p_inputstream)
+{
+ _p_inputstream = p_inputstream;
}
-MimeParser::~MimeParser() {
- close();
+MimeParser::~MimeParser()
+{
+ close();
}
-bool MimeParser::open() {
- qDebug() << "MimeParser::open begin";
- if (_p_inputstream->open(QIODevice::ReadOnly)) {
- _real_in = new QTextStream(_p_inputstream);
+bool
+MimeParser::open()
+{
+ qDebug() << "MimeParser::open begin";
+ if(_p_inputstream->open(QIODevice::ReadOnly))
+ {
+ _real_in = new QTextStream(_p_inputstream);
}
- else {
- throw pappso::PappsoException(QObject::tr("Error opening mime QIODevice"));
+ else
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error opening mime QIODevice"));
}
- qDebug() << "MimeParser::open end";
-
+ qDebug() << "MimeParser::open end";
}
-bool MimeParser::close() {
- qDebug() << "MimeParser::close begin";
+bool
+MimeParser::close()
+{
+ qDebug() << "MimeParser::close begin";
- _priv_file_string = "";
- if (_p_current_file_content != nullptr) {
- delete _p_current_file_content;
- _p_current_file_content = nullptr;
+ _priv_file_string = "";
+ if(_p_current_file_content != nullptr)
+ {
+ delete _p_current_file_content;
+ _p_current_file_content = nullptr;
}
- qDebug() << "MimeParser::close delete _real_in";
- if (_real_in !=nullptr) {
- delete _real_in;
- _real_in =nullptr;
+ qDebug() << "MimeParser::close delete _real_in";
+ if(_real_in != nullptr)
+ {
+ delete _real_in;
+ _real_in = nullptr;
}
- qDebug() << "MimeParser::close delete _p_inputstream";
- if (_p_inputstream !=nullptr) {
- _p_inputstream->close();
- //delete _p_inputstream;
- _p_inputstream =nullptr;
+ qDebug() << "MimeParser::close delete _p_inputstream";
+ if(_p_inputstream != nullptr)
+ {
+ _p_inputstream->close();
+ // delete _p_inputstream;
+ _p_inputstream = nullptr;
}
- qDebug() << "MimeParser::close end";
+ qDebug() << "MimeParser::close end";
}
-bool MimeParser::goToFirstFile() {
- qDebug() << "MimeParser::goToFirstFile begin";
+bool
+MimeParser::goToFirstFile()
+{
+ qDebug() << "MimeParser::goToFirstFile begin";
- /*
- MIME-Version: 1.0 (Generated by Mascot version 1.0)
- Content-Type: multipart/mixed; boundary=gc0p4Jq0M2Yt08jU534c0p
+ /*
+ MIME-Version: 1.0 (Generated by Mascot version 1.0)
+ Content-Type: multipart/mixed; boundary=gc0p4Jq0M2Yt08jU534c0p
- --gc0p4Jq0M2Yt08jU534c0p
- Content-Type: application/x-Mascot; name="parameters"
- */
- QRegExp regexp_boundary("^Content-Type:\\smultipart/mixed;\\sboundary=(.*)$");
+ --gc0p4Jq0M2Yt08jU534c0p
+ Content-Type: application/x-Mascot; name="parameters"
+ */
+ QRegExp regexp_boundary("^Content-Type:\\smultipart/mixed;\\sboundary=(.*)$");
- while(!_real_in->atEnd()) {
- QString line = _real_in->readLine();
- qDebug() << "MimeParser::goToFirstFile line=" << line;
- if (regexp_boundary.exactMatch(line)) {
- QStringList boundary_list = regexp_boundary.capturedTexts();
- _boundary = QString("--%1").arg(boundary_list[1]);
- break;
+ while(!_real_in->atEnd())
+ {
+ QString line = _real_in->readLine();
+ qDebug() << "MimeParser::goToFirstFile line=" << line;
+ if(regexp_boundary.exactMatch(line))
+ {
+ QStringList boundary_list = regexp_boundary.capturedTexts();
+ _boundary = QString("--%1").arg(boundary_list[1]);
+ break;
}
}
- if (_boundary.isEmpty()) {
- qDebug() << "MimeParser::goToFirstFile _boundary.isEmpty";
- return false;
+ if(_boundary.isEmpty())
+ {
+ qDebug() << "MimeParser::goToFirstFile _boundary.isEmpty";
+ return false;
}
- while(!_real_in->atEnd()) {
- QString line = _real_in->readLine();
- if (line == _boundary) break;
+ while(!_real_in->atEnd())
+ {
+ QString line = _real_in->readLine();
+ if(line == _boundary)
+ break;
}
- qDebug() << "MimeParser::goToFirstFile end";
- return readFile();
+ qDebug() << "MimeParser::goToFirstFile end";
+ return readFile();
}
-bool MimeParser::readFile() {
- qDebug() << "MimeParser::readFile begin";
- _current_mime_type = "";
- _current_file_name = "";
- _priv_file_string = "";
+bool
+MimeParser::readFile()
+{
+ qDebug() << "MimeParser::readFile begin";
+ _current_mime_type = "";
+ _current_file_name = "";
+ _priv_file_string = "";
- if (_p_current_file_content != nullptr) {
- delete _p_current_file_content;
+ if(_p_current_file_content != nullptr)
+ {
+ delete _p_current_file_content;
}
- _p_current_file_content = new QTextStream(&_priv_file_string);
+ _p_current_file_content = new QTextStream(&_priv_file_string);
- QString line = _real_in->readLine();
- if (line.isEmpty()) return false;
- //Content-Type: application/x-Mascot; name="masses"
- QRegExp regexp_mimetype("^Content-Type:\\s(.*);\\sname=\"(.*)\"$");
- if (regexp_mimetype.exactMatch(line)) {
- QStringList mimetype_list = regexp_mimetype.capturedTexts();
- _current_mime_type = mimetype_list[1];
- _current_file_name = mimetype_list[2];
+ QString line = _real_in->readLine();
+ if(line.isEmpty())
+ return false;
+ // Content-Type: application/x-Mascot; name="masses"
+ QRegExp regexp_mimetype("^Content-Type:\\s(.*);\\sname=\"(.*)\"$");
+ if(regexp_mimetype.exactMatch(line))
+ {
+ QStringList mimetype_list = regexp_mimetype.capturedTexts();
+ _current_mime_type = mimetype_list[1];
+ _current_file_name = mimetype_list[2];
}
- else {
- return false;
+ else
+ {
+ return false;
}
- _real_in->readLine();
- while(!_real_in->atEnd()) {
- QString line = _real_in->readLine();
- if (line == _boundary) break;
- *_p_current_file_content << line << endl;
+ _real_in->readLine();
+ while(!_real_in->atEnd())
+ {
+ QString line = _real_in->readLine();
+ if(line == _boundary)
+ break;
+ *_p_current_file_content << line << endl;
}
- qDebug() << "MimeParser::readFile end";
- return true;
+ qDebug() << "MimeParser::readFile end";
+ return true;
}
-bool MimeParser::goToNextFile() {
- return readFile();
+bool
+MimeParser::goToNextFile()
+{
+ return readFile();
}
-const QString & MimeParser::getCurrentMimeType() const {
- return _current_mime_type;
+const QString &
+MimeParser::getCurrentMimeType() const
+{
+ return _current_mime_type;
}
-const QString & MimeParser::getCurrentFileName() const {
- return _current_file_name;
+const QString &
+MimeParser::getCurrentFileName() const
+{
+ return _current_file_name;
}
-QTextStream & MimeParser::getCurrentTextStream() {
- if (_p_current_file_content == nullptr) {
- throw pappso::PappsoException(QObject::tr("Error current file content empty"));
+QTextStream &
+MimeParser::getCurrentTextStream()
+{
+ if(_p_current_file_content == nullptr)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error current file content empty"));
}
- _p_current_file_content->reset();
- return *_p_current_file_content;
+ _p_current_file_content->reset();
+ return *_p_current_file_content;
}
diff --git a/src/input/mascot/mimeparser.h b/src/input/mascot/mimeparser.h
index 2c792abf47f40178a3f4548c40bcebc7483c0d15..3dccec594cdddddb02a0474a5bf696db613a7859 100644
--- a/src/input/mascot/mimeparser.h
+++ b/src/input/mascot/mimeparser.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef MIMEPARSER_H
#define MIMEPARSER_H
@@ -35,28 +36,28 @@
class MimeParser
{
-public:
- MimeParser(QIODevice * p_inputstream);
- virtual ~MimeParser();
- bool open();
- bool close();
- bool goToFirstFile();
- bool goToNextFile();
- const QString & getCurrentMimeType() const;
- const QString & getCurrentFileName() const;
- QTextStream & getCurrentTextStream();
-
-private:
- bool readFile();
-
-private:
- QString _current_file_name;
- QString _current_mime_type;
- QIODevice * _p_inputstream = nullptr;
- QTextStream * _real_in = nullptr;
- QString _boundary;
- QTextStream * _p_current_file_content = nullptr;
- QString _priv_file_string;
+ public:
+ MimeParser(QIODevice *p_inputstream);
+ virtual ~MimeParser();
+ bool open();
+ bool close();
+ bool goToFirstFile();
+ bool goToNextFile();
+ const QString &getCurrentMimeType() const;
+ const QString &getCurrentFileName() const;
+ QTextStream &getCurrentTextStream();
+
+ private:
+ bool readFile();
+
+ private:
+ QString _current_file_name;
+ QString _current_mime_type;
+ QIODevice *_p_inputstream = nullptr;
+ QTextStream *_real_in = nullptr;
+ QString _boundary;
+ QTextStream *_p_current_file_content = nullptr;
+ QString _priv_file_string;
};
#endif // MIMEPARSER_H
diff --git a/src/input/pepxmlsaxhandler.cpp b/src/input/pepxmlsaxhandler.cpp
index bb5a0e0f63b1ed407a82d5a80b6acaf9dc414158..a5667416dce071bf755a0d835443d84697590d83 100644
--- a/src/input/pepxmlsaxhandler.cpp
+++ b/src/input/pepxmlsaxhandler.cpp
@@ -326,7 +326,7 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
//<alternative_protein protein="sp|P46784|RS10B_YEAST" protein_descr="40S
// ribosomal protein S10-B OS=Saccharomyces cerevisiae (strain ATCC 204508
-// \
+// \
//S288c) GN=RPS10B PE=1 SV=1" num_tol_term="2" peptide_prev_aa="K"
// peptide_next_aa="N"/>
bool
diff --git a/src/input/pepxmlsaxhandler.h b/src/input/pepxmlsaxhandler.h
index 19e8bb619fd279f76f2420c8f0fd82ebf106038f..8856408c83d1c7cec5d1c68b4ff8b009174f1f18 100644
--- a/src/input/pepxmlsaxhandler.h
+++ b/src/input/pepxmlsaxhandler.h
@@ -77,7 +77,7 @@ class PepXmlSaxHandler : public QXmlDefaultHandler
bool startElement_search_score(QXmlAttributes attributes);
bool startElement_mod_aminoacid_mass(QXmlAttributes attributes);
bool startElement_modification_info(QXmlAttributes attributes);
-
+
bool endElement_search_hit();
bool endElement_modification_info();
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 386b829f39162d0ba6af8e514a735ac42d0f7aa9..b80e79862d71de02db0e0b6248c77aa05a9a81d6 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -1,24 +1,25 @@
/*******************************************************************************
-* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "xpipsaxhandler.h"
#include <pappsomspp/exception/exceptionnotfound.h>
@@ -26,406 +27,575 @@
#include "../utils/peptidestore.h"
#include "../utils/proteinstore.h"
-XpipSaxHandler::XpipSaxHandler(WorkMonitorInterface * p_monitor, Project * p_project):_p_project(p_project)
+XpipSaxHandler::XpipSaxHandler(WorkMonitorInterface *p_monitor,
+ Project *p_project)
+ : _p_project(p_project)
{
- qDebug() << "XpipSaxHandler::XpipSaxHandler begin" ;
- _p_monitor = p_monitor;
- qDebug() << "XpipSaxHandler::XpipSaxHandler end" ;
+ qDebug() << "XpipSaxHandler::XpipSaxHandler begin";
+ _p_monitor = p_monitor;
+ qDebug() << "XpipSaxHandler::XpipSaxHandler end";
}
XpipSaxHandler::~XpipSaxHandler()
{
-
}
-bool XpipSaxHandler::isJavaXpip() const {
- return _is_java_xpip;
+bool
+XpipSaxHandler::isJavaXpip() const
+{
+ return _is_java_xpip;
}
-bool XpipSaxHandler::startElement(const QString & namespaceURI, const QString & localName,
- const QString & qName, const QXmlAttributes & attributes) {
- qDebug()<< "XpipSaxHandler::startElement begin" << namespaceURI << " " << localName << " " << qName ;
- _tag_stack.push_back(qName);
- bool is_ok = true;
+bool
+XpipSaxHandler::startElement(const QString &namespaceURI,
+ const QString &localName, const QString &qName,
+ const QXmlAttributes &attributes)
+{
+ qDebug() << "XpipSaxHandler::startElement begin" << namespaceURI << " "
+ << localName << " " << qName;
+ _tag_stack.push_back(qName);
+ bool is_ok = true;
- try {
+ try
+ {
- if (_tag_stack.size() == 1) {
- _is_java_xpip = true;
- if (qName != "xtandem_pipeline") {
- _is_java_xpip = false;
- throw pappso::ExceptionNotFound(QObject::tr("ERROR this file is not an xpip file %1").arg(qName));
- }
- } else
- //startElement_group
- if (qName == "match") {
- is_ok = startElement_match(attributes);
- } else if (qName == "protein") {
- is_ok = startElement_protein(attributes);
- } else if (qName == "identification") {
- is_ok = startElement_identification(attributes);
- }
- //<sample value="P6_08_10"/>
- else if (qName == "sample") {
- is_ok = startElement_sample(attributes);
- } else if (qName == "peptide") {
- is_ok = startElement_peptide(attributes);
- } else if (qName == "modifs_mass") {
- is_ok = startElement_modifs_mass(attributes);
- } else if (qName == "modif") {
- is_ok = startElement_modif(attributes);
- } else if (qName == "filter_params") {
- is_ok = startElement_filter_params(attributes);
- } else if (qName == "information") {
- is_ok = startElement_information(attributes);
+ if(_tag_stack.size() == 1)
+ {
+ _is_java_xpip = true;
+ if(qName != "xtandem_pipeline")
+ {
+ _is_java_xpip = false;
+ throw pappso::ExceptionNotFound(
+ QObject::tr("ERROR this file is not an xpip file %1")
+ .arg(qName));
}
+ }
+ else
+ // startElement_group
+ if(qName == "match")
+ {
+ is_ok = startElement_match(attributes);
+ }
+ else if(qName == "protein")
+ {
+ is_ok = startElement_protein(attributes);
+ }
+ else if(qName == "identification")
+ {
+ is_ok = startElement_identification(attributes);
+ }
+ //<sample value="P6_08_10"/>
+ else if(qName == "sample")
+ {
+ is_ok = startElement_sample(attributes);
+ }
+ else if(qName == "peptide")
+ {
+ is_ok = startElement_peptide(attributes);
+ }
+ else if(qName == "modifs_mass")
+ {
+ is_ok = startElement_modifs_mass(attributes);
+ }
+ else if(qName == "modif")
+ {
+ is_ok = startElement_modif(attributes);
+ }
+ else if(qName == "filter_params")
+ {
+ is_ok = startElement_filter_params(attributes);
+ }
+ else if(qName == "information")
+ {
+ is_ok = startElement_information(attributes);
+ }
- _current_text.clear();
+ _current_text.clear();
}
- catch (pappso::PappsoException exception_pappso) {
- _errorStr = QObject::tr("ERROR in XpipSaxHandler::startElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
- return false;
+ catch(pappso::PappsoException exception_pappso)
+ {
+ _errorStr =
+ QObject::tr(
+ "ERROR in XpipSaxHandler::startElement tag %1, PAPPSO exception:\n%2")
+ .arg(qName)
+ .arg(exception_pappso.qwhat());
+ return false;
}
- catch (std::exception exception_std) {
- _errorStr = QObject::tr("ERROR in XpipSaxHandler::startElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
- return false;
+ catch(std::exception exception_std)
+ {
+ _errorStr =
+ QObject::tr(
+ "ERROR in XpipSaxHandler::startElement tag %1, std exception:\n%2")
+ .arg(qName)
+ .arg(exception_std.what());
+ return false;
}
- return is_ok;
+ return is_ok;
}
-bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & localName,
- const QString & qName) {
+bool
+XpipSaxHandler::endElement(const QString &namespaceURI,
+ const QString &localName, const QString &qName)
+{
- bool is_ok = true;
- // endElement_peptide_list
- try {
- if (qName == "protein")
+ bool is_ok = true;
+ // endElement_peptide_list
+ try
+ {
+ if(qName == "protein")
{
- is_ok = endElement_protein();
+ is_ok = endElement_protein();
}
- else if (qName == "identification") {
- is_ok = endElement_identification();
+ else if(qName == "identification")
+ {
+ is_ok = endElement_identification();
}
- else if (qName == "peptide") {
- is_ok = endElement_peptide();
+ else if(qName == "peptide")
+ {
+ is_ok = endElement_peptide();
}
- else if (qName == "sequence") {
- is_ok = endElement_sequence();
+ else if(qName == "sequence")
+ {
+ is_ok = endElement_sequence();
}
- else if (qName == "match") {
- is_ok = endElement_match();
+ else if(qName == "match")
+ {
+ is_ok = endElement_match();
}
- // end of detection_moulon
- // else if ((_tag_stack.size() > 1) &&
- // (_tag_stack[_tag_stack.size() - 2] == "detection_moulon"))
+ // end of detection_moulon
+ // else if ((_tag_stack.size() > 1) &&
+ // (_tag_stack[_tag_stack.size() - 2] == "detection_moulon"))
}
- catch (pappso::PappsoException exception_pappso) {
- _errorStr = QObject::tr("ERROR in XpipSaxHandler::endElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
- return false;
+ catch(pappso::PappsoException exception_pappso)
+ {
+ _errorStr =
+ QObject::tr(
+ "ERROR in XpipSaxHandler::endElement tag %1, PAPPSO exception:\n%2")
+ .arg(qName)
+ .arg(exception_pappso.qwhat());
+ return false;
}
- catch (std::exception exception_std) {
- _errorStr = QObject::tr("ERROR in XpipSaxHandler::endElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
- return false;
+ catch(std::exception exception_std)
+ {
+ _errorStr =
+ QObject::tr(
+ "ERROR in XpipSaxHandler::endElement tag %1, std exception:\n%2")
+ .arg(qName)
+ .arg(exception_std.what());
+ return false;
}
- _current_text.clear();
- _tag_stack.pop_back();
+ _current_text.clear();
+ _tag_stack.pop_back();
- return is_ok;
+ return is_ok;
}
-bool XpipSaxHandler::startElement_identification(QXmlAttributes attributes) {
+bool
+XpipSaxHandler::startElement_identification(QXmlAttributes attributes)
+{
- qDebug() << "startElement_identification ";
- _map_massstr_aamod.clear();
- _current_identification_group_p = _p_project->newIdentificationGroup();
- qDebug() << "startElement_identification end" ;
- return true;
+ qDebug() << "startElement_identification ";
+ _map_massstr_aamod.clear();
+ _current_identification_group_p = _p_project->newIdentificationGroup();
+ qDebug() << "startElement_identification end";
+ return true;
}
-bool XpipSaxHandler::startElement_filter_params(QXmlAttributes attributes) {
+bool
+XpipSaxHandler::startElement_filter_params(QXmlAttributes attributes)
+{
-//<filter_params pep_evalue="0.01" prot_evalue="-2.0" pep_number="1" filter_to_all="false" database_filter="contaminants_standarts.fasta"/>
- qDebug() << "startElement_filter_params ";
- _automatic_filter_parameters.setFilterPeptideEvalue( attributes.value("pep_evalue").simplified().toDouble());
- _automatic_filter_parameters.setFilterProteinEvalue( std::pow ((double) 10.0,attributes.value("prot_evalue").simplified().toDouble()));
- _automatic_filter_parameters.setFilterMinimumPeptidePerMatch( attributes.value("pep_number").simplified().toUInt());
- _automatic_filter_parameters.setFilterCrossSamplePeptideNumber(false);
- if (attributes.value("filter_to_all").simplified() == "true") {
- _automatic_filter_parameters.setFilterCrossSamplePeptideNumber(true);
+ //<filter_params pep_evalue="0.01" prot_evalue="-2.0" pep_number="1"
+ //filter_to_all="false" database_filter="contaminants_standarts.fasta"/>
+ qDebug() << "startElement_filter_params ";
+ _automatic_filter_parameters.setFilterPeptideEvalue(
+ attributes.value("pep_evalue").simplified().toDouble());
+ _automatic_filter_parameters.setFilterProteinEvalue(std::pow(
+ (double)10.0, attributes.value("prot_evalue").simplified().toDouble()));
+ _automatic_filter_parameters.setFilterMinimumPeptidePerMatch(
+ attributes.value("pep_number").simplified().toUInt());
+ _automatic_filter_parameters.setFilterCrossSamplePeptideNumber(false);
+ if(attributes.value("filter_to_all").simplified() == "true")
+ {
+ _automatic_filter_parameters.setFilterCrossSamplePeptideNumber(true);
}
- _p_project->getFastaFileStore().getInstance(FastaFile(attributes.value("database_filter")));
- qDebug() << "startElement_filter_params end" ;
- return true;
+ _p_project->getFastaFileStore().getInstance(
+ FastaFile(attributes.value("database_filter")));
+ qDebug() << "startElement_filter_params end";
+ return true;
}
-bool XpipSaxHandler::startElement_information(QXmlAttributes attributes) {
+bool
+XpipSaxHandler::startElement_information(QXmlAttributes attributes)
+{
-//<information Data_Type="indiv" match_number="223"/>
- qDebug() << "startElement_information ";
- _p_project->setProjectMode(ProjectMode::combined);
- if (attributes.value("Data_Type").simplified() == "indiv") {
- _p_project->setProjectMode(ProjectMode::individual);
+ //<information Data_Type="indiv" match_number="223"/>
+ qDebug() << "startElement_information ";
+ _p_project->setProjectMode(ProjectMode::combined);
+ if(attributes.value("Data_Type").simplified() == "indiv")
+ {
+ _p_project->setProjectMode(ProjectMode::individual);
}
- _total_protein_match = attributes.value("match_number").toUInt();
+ _total_protein_match = attributes.value("match_number").toUInt();
- _p_monitor->setProgressMaximumValue(_total_protein_match);
- qDebug() << "startElement_information end" ;
- return true;
+ _p_monitor->setProgressMaximumValue(_total_protein_match);
+ qDebug() << "startElement_information end";
+ return true;
}
-bool XpipSaxHandler::startElement_modifs_mass(QXmlAttributes attributes) {
-
- /*
- <modifs_list_mass><modifs_mass modvalue="-18.01056"/>
- <modifs_mass modvalue="-17.02655"/>
- <modifs_mass modvalue="15.99491"/>
- <modifs_mass modvalue="42.01057"/>
- <modifs_mass modvalue="42.01056"/>
- <modifs_mass modvalue="57.02146"/>
- </modifs_list_mass>
- */
- qDebug() << "startElement_modifs_mass ";
- QString mass_str(attributes.value("modvalue").simplified());
- pappso::mz mass = mass_str.toDouble();
-
- pappso::AaModificationP mod = getAaModificationP(mass);
-
- _map_massstr_aamod[mass_str] = mod;
- qDebug() << "startElement_modifs_mass end" ;
- return true;
+bool
+XpipSaxHandler::startElement_modifs_mass(QXmlAttributes attributes)
+{
+
+ /*
+ <modifs_list_mass><modifs_mass modvalue="-18.01056"/>
+ <modifs_mass modvalue="-17.02655"/>
+ <modifs_mass modvalue="15.99491"/>
+ <modifs_mass modvalue="42.01057"/>
+ <modifs_mass modvalue="42.01056"/>
+ <modifs_mass modvalue="57.02146"/>
+ </modifs_list_mass>
+ */
+ qDebug() << "startElement_modifs_mass ";
+ QString mass_str(attributes.value("modvalue").simplified());
+ pappso::mz mass = mass_str.toDouble();
+
+ pappso::AaModificationP mod = getAaModificationP(mass);
+
+ _map_massstr_aamod[mass_str] = mod;
+ qDebug() << "startElement_modifs_mass end";
+ return true;
}
//<sample value="P6_21_23"/>
-bool XpipSaxHandler::startElement_sample(QXmlAttributes attributes) {
+bool
+XpipSaxHandler::startElement_sample(QXmlAttributes attributes)
+{
- qDebug() << "startElement_sample ";
+ qDebug() << "startElement_sample ";
- MsRunSp ms_run = _p_project->getMsRunStore().getInstance(attributes.value("value").simplified());
- ms_run.get()->setFilename(attributes.value("value").simplified());
- //_current_identification_group_p->addMsRunSp(ms_run);
- qDebug() << "startElement_sample end" ;
- return true;
+ MsRunSp ms_run = _p_project->getMsRunStore().getInstance(
+ attributes.value("value").simplified());
+ ms_run.get()->setFilename(attributes.value("value").simplified());
+ //_current_identification_group_p->addMsRunSp(ms_run);
+ qDebug() << "startElement_sample end";
+ return true;
}
-bool XpipSaxHandler::startElement_match(QXmlAttributes attributes) {
+bool
+XpipSaxHandler::startElement_match(QXmlAttributes attributes)
+{
- qDebug() << "startElement_match ";
- /*
- * <match_list><match validate="true">
- */
- _p_protein_match = new ProteinMatch();
- _p_protein_match->setChecked(false);
- if (attributes.value("validate").simplified().toLower() == "true") {
- _p_protein_match->setChecked(true);
+ qDebug() << "startElement_match ";
+ /*
+ * <match_list><match validate="true">
+ */
+ _p_protein_match = new ProteinMatch();
+ _p_protein_match->setChecked(false);
+ if(attributes.value("validate").simplified().toLower() == "true")
+ {
+ _p_protein_match->setChecked(true);
}
- qDebug() << "startElement_match end" ;
- return true;
+ qDebug() << "startElement_match end";
+ return true;
}
-bool XpipSaxHandler::startElement_protein(QXmlAttributes attributes) {
-
- qDebug() << "startElement_protein ";
- /*
- * <protein peptide_number="268" evalue="-432.77353" URL="Genome_Z_mays_5a.fasta"
- * description="GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC 4.1.1.31)
- * seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01; parent_gene=GRMZM2G083841">
- <protein_evalue evalue="-399.36093" sample="20120906_balliau_extract_1_A02_urzb-1"/>
- <protein_evalue evalue="-384.54382" sample="20120906_balliau_extract_1_A01_urnb-1"/>
- <sequence>MASTKAPGPGEKHHSIDAQLRQLVPGKVSEDDKLIEYDALLVDRFLNILQDLHGPSLREFVQECYEVSADYEGKGDTTKLGELGAKLTGLAPADAILVASSILHMLNLANLAEEVQIAHRRRNSKLKKGGFADEGSATTESDIEETLKRLVSEVGKSPEEVFEALKNQTVDLVFTAHPTQSARRSLLQKNARIRNCLTQLNAKDITDDDKQELDEALQREIQAAFRTDEIRRAQPTPQDEMRYGMSYIHETVWKGVPKFLRRVDTALKNIGINERLPYNVSLIRFSSWMGGDRDGNPRVTPEVTRDVCLLARMMAANLYIDQIEELMFELSMWRCNDELRVRAEELHSSSGSKVTKYYIEFWKQIPPNEPYRVILGHVRDKLYNTRERARHLLASGVSEISAESSFTSIEEFLEPLELCYKSLCDCGDKAIADGSLLDLLRQVFTFGLSLVKLDIRQESERHTDVIDAITTHLGIGSYREWPEDKRQEWLLSELRGKRPLLPPDLPQTDEIADVIGAFHVLAELPPDSFGPYIISMATAPSDVLAVELLQRECGVRQPLPVVPLFERLADLQSAPASVERLFSVDWYMDRIKGKQQVMVGYSDSGKDAGRLSAAWQLYRAQEEMAQVAKRYGVKLTLFHGRGGTVGRGGGPTHLAILSQPPDTINGSIRVTVQGEVIEFCFGEEHLCFQTLQRFTAATLEHGMHPPVSPKPEWRKLMDEMAVVATEEYRSVVVKEARFVEYFRSATPETEYGRMNIGSRPAKRRPGGGITTLRAIPWIFSWTQTRFHLPVWLGVGAAFKFAIDKDVRNFQVLKEMYNEWPFFRVTLDLLEMVFAKGDPGIAGLYDELLVAEELKPFGKQLRDKYVETQQLLLQIAGHKDILEGDPFLKQGLVLRNPYITTLNVFQAYTLKRIRDPNFKVTPQPPLSKEFADENKPAGLVKLNPASEYPPGLEDTLILTMKGIAAGMQNTG</sequence>
- </protein>
- */
- _current_protein.setCompleteDescription(attributes.value("description"));
- _current_fasta_file_sp = _p_project->getFastaFileStore().getInstance(FastaFile(attributes.value("URL")));
- _current_protein.setFastaFileP(_current_fasta_file_sp.get());
- qDebug() << "startElement_protein end" ;
- return true;
+bool
+XpipSaxHandler::startElement_protein(QXmlAttributes attributes)
+{
+
+ qDebug() << "startElement_protein ";
+ /*
+ * <protein peptide_number="268" evalue="-432.77353"
+ URL="Genome_Z_mays_5a.fasta"
+ * description="GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1
+ (PEPCase 1)(PEPC 1)(EC 4.1.1.31)
+ * seq=translation; coord=9:61296279..61301686:1;
+ parent_transcript=GRMZM2G083841_T01; parent_gene=GRMZM2G083841">
+ <protein_evalue evalue="-399.36093"
+ sample="20120906_balliau_extract_1_A02_urzb-1"/> <protein_evalue
+ evalue="-384.54382" sample="20120906_balliau_extract_1_A01_urnb-1"/>
+ <sequence>MASTKAPGPGEKHHSIDAQLRQLVPGKVSEDDKLIEYDALLVDRFLNILQDLHGPSLREFVQECYEVSADYEGKGDTTKLGELGAKLTGLAPADAILVASSILHMLNLANLAEEVQIAHRRRNSKLKKGGFADEGSATTESDIEETLKRLVSEVGKSPEEVFEALKNQTVDLVFTAHPTQSARRSLLQKNARIRNCLTQLNAKDITDDDKQELDEALQREIQAAFRTDEIRRAQPTPQDEMRYGMSYIHETVWKGVPKFLRRVDTALKNIGINERLPYNVSLIRFSSWMGGDRDGNPRVTPEVTRDVCLLARMMAANLYIDQIEELMFELSMWRCNDELRVRAEELHSSSGSKVTKYYIEFWKQIPPNEPYRVILGHVRDKLYNTRERARHLLASGVSEISAESSFTSIEEFLEPLELCYKSLCDCGDKAIADGSLLDLLRQVFTFGLSLVKLDIRQESERHTDVIDAITTHLGIGSYREWPEDKRQEWLLSELRGKRPLLPPDLPQTDEIADVIGAFHVLAELPPDSFGPYIISMATAPSDVLAVELLQRECGVRQPLPVVPLFERLADLQSAPASVERLFSVDWYMDRIKGKQQVMVGYSDSGKDAGRLSAAWQLYRAQEEMAQVAKRYGVKLTLFHGRGGTVGRGGGPTHLAILSQPPDTINGSIRVTVQGEVIEFCFGEEHLCFQTLQRFTAATLEHGMHPPVSPKPEWRKLMDEMAVVATEEYRSVVVKEARFVEYFRSATPETEYGRMNIGSRPAKRRPGGGITTLRAIPWIFSWTQTRFHLPVWLGVGAAFKFAIDKDVRNFQVLKEMYNEWPFFRVTLDLLEMVFAKGDPGIAGLYDELLVAEELKPFGKQLRDKYVETQQLLLQIAGHKDILEGDPFLKQGLVLRNPYITTLNVFQAYTLKRIRDPNFKVTPQPPLSKEFADENKPAGLVKLNPASEYPPGLEDTLILTMKGIAAGMQNTG</sequence>
+ </protein>
+ */
+ _current_protein.setCompleteDescription(attributes.value("description"));
+ _current_fasta_file_sp = _p_project->getFastaFileStore().getInstance(
+ FastaFile(attributes.value("URL")));
+ _current_protein.setFastaFileP(_current_fasta_file_sp.get());
+ qDebug() << "startElement_protein end";
+ return true;
}
-bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
-
-//<peptide sample="20120208_Blein_rep4_1_B03_DW21-4-26-328"
- //sample_file="/gorgone/pappso/moulon/users/Melisande/test-param-masschroq/20120208_Blein_rep4_1_B03_DW21-4-26-328.xml"
- //scan="2589" scan_in_xtandem="2589" RT="603" mhplus_obser="873.5401" mhplus_theo="873.5408" deltamass="-7.0E-4"
- //sequence="IATAIEKK" pre="NPAR" post="AADA" start="331" stop="338" charge="2" evalue="9.2E-4" hypercorr="35.2" validate="true">
-//<modifs></modifs></peptide>
-
- //<modifs><modif aa="M" modvalue="15.99491" posi="17" posi_in_prot="49"/>
-//</modifs>
- qDebug() << "startElement_peptide ";
- _current_peptide_sp = PeptideXtp(attributes.value("sequence").simplified()).makePeptideXtpSp();
- MsRunSp ms_run_id = _p_project->getMsRunStore().getInstance(attributes.value("sample").simplified());
- _p_peptide_evidence = new PeptideEvidence(ms_run_id.get(), attributes.value("scan").simplified().toUInt());
- _p_peptide_evidence->setRetentionTime(attributes.value("RT").simplified().toDouble());
- _p_peptide_evidence->setEvalue(attributes.value("evalue").simplified().toDouble());
- pappso::pappso_double exp_mass = attributes.value("mhplus_obser").simplified().toDouble() - pappso::MHPLUS;
- _p_peptide_evidence->setExperimentalMass(exp_mass);
- _current_peptide_match.setStart(attributes.value("start").simplified().toUInt()-1);
- _p_peptide_evidence->setCharge(attributes.value("charge").simplified().toUInt());
- _p_peptide_evidence->setParam(PeptideEvidenceParam::tandem_hyperscore, QVariant( attributes.value("hypercorr").toDouble()));
-
- IdentificationDataSource* p_identification_data_source = _p_project->getIdentificationDataSourceStore().getInstance(attributes.value("sample_file").simplified()).get();
- _p_peptide_evidence->setIdentificationDataSource( p_identification_data_source);
- if (p_identification_data_source->getMsRunSp().get() == nullptr) {
- p_identification_data_source->setMsRunSp(ms_run_id);
+bool
+XpipSaxHandler::startElement_peptide(QXmlAttributes attributes)
+{
+
+ //<peptide sample="20120208_Blein_rep4_1_B03_DW21-4-26-328"
+ // sample_file="/gorgone/pappso/moulon/users/Melisande/test-param-masschroq/20120208_Blein_rep4_1_B03_DW21-4-26-328.xml"
+ // scan="2589" scan_in_xtandem="2589" RT="603" mhplus_obser="873.5401"
+ // mhplus_theo="873.5408" deltamass="-7.0E-4" sequence="IATAIEKK" pre="NPAR"
+ // post="AADA" start="331" stop="338" charge="2" evalue="9.2E-4"
+ // hypercorr="35.2" validate="true">
+ //<modifs></modifs></peptide>
+
+ //<modifs><modif aa="M" modvalue="15.99491" posi="17" posi_in_prot="49"/>
+ //</modifs>
+ qDebug() << "startElement_peptide ";
+ _current_peptide_sp =
+ PeptideXtp(attributes.value("sequence").simplified()).makePeptideXtpSp();
+ MsRunSp ms_run_id = _p_project->getMsRunStore().getInstance(
+ attributes.value("sample").simplified());
+ _p_peptide_evidence = new PeptideEvidence(
+ ms_run_id.get(), attributes.value("scan").simplified().toUInt());
+ _p_peptide_evidence->setRetentionTime(
+ attributes.value("RT").simplified().toDouble());
+ _p_peptide_evidence->setEvalue(
+ attributes.value("evalue").simplified().toDouble());
+ pappso::pappso_double exp_mass =
+ attributes.value("mhplus_obser").simplified().toDouble() - pappso::MHPLUS;
+ _p_peptide_evidence->setExperimentalMass(exp_mass);
+ _current_peptide_match.setStart(
+ attributes.value("start").simplified().toUInt() - 1);
+ _p_peptide_evidence->setCharge(
+ attributes.value("charge").simplified().toUInt());
+ _p_peptide_evidence->setParam(
+ PeptideEvidenceParam::tandem_hyperscore,
+ QVariant(attributes.value("hypercorr").toDouble()));
+
+ IdentificationDataSource *p_identification_data_source =
+ _p_project->getIdentificationDataSourceStore()
+ .getInstance(attributes.value("sample_file").simplified())
+ .get();
+ _p_peptide_evidence->setIdentificationDataSource(
+ p_identification_data_source);
+ if(p_identification_data_source->getMsRunSp().get() == nullptr)
+ {
+ p_identification_data_source->setMsRunSp(ms_run_id);
}
- if (p_identification_data_source->getMsRunSp().get() != ms_run_id.get()) {
- throw pappso::PappsoException(QObject::tr("p_identification_data_source->getMsRunSp().get() != ms_run_id.get()"));
+ if(p_identification_data_source->getMsRunSp().get() != ms_run_id.get())
+ {
+ throw pappso::PappsoException(QObject::tr(
+ "p_identification_data_source->getMsRunSp().get() != ms_run_id.get()"));
}
- _current_identification_group_p->addIdentificationDataSourceP(p_identification_data_source);
- p_identification_data_source->addFastaFile(_current_fasta_file_sp);
- _p_peptide_evidence->setChecked(false);
- if (attributes.value("validate").simplified().toLower() == "true") {
- _p_peptide_evidence->setChecked(true);
+ _current_identification_group_p->addIdentificationDataSourceP(
+ p_identification_data_source);
+ p_identification_data_source->addFastaFile(_current_fasta_file_sp);
+ _p_peptide_evidence->setChecked(false);
+ if(attributes.value("validate").simplified().toLower() == "true")
+ {
+ _p_peptide_evidence->setChecked(true);
}
- qDebug() << "startElement_peptide end" ;
- return true;
+ qDebug() << "startElement_peptide end";
+ return true;
}
-bool XpipSaxHandler::startElement_modif(QXmlAttributes attributes) {
+bool
+XpipSaxHandler::startElement_modif(QXmlAttributes attributes)
+{
- //<modifs><modif aa="M" modvalue="15.99491" posi="17" posi_in_prot="49"/>
- qDebug() << "startElement_modif ";
- pappso::AaModificationP modif = _map_massstr_aamod[attributes.value("modvalue").simplified()];
- unsigned int position = attributes.value("posi").simplified().toUInt();
- _current_peptide_sp.get()->addAaModification(modif, position-1);
- qDebug() << "startElement_modif end" ;
- return true;
+ //<modifs><modif aa="M" modvalue="15.99491" posi="17" posi_in_prot="49"/>
+ qDebug() << "startElement_modif ";
+ pappso::AaModificationP modif =
+ _map_massstr_aamod[attributes.value("modvalue").simplified()];
+ unsigned int position = attributes.value("posi").simplified().toUInt();
+ _current_peptide_sp.get()->addAaModification(modif, position - 1);
+ qDebug() << "startElement_modif end";
+ return true;
}
-bool XpipSaxHandler::endElement_peptide() {
- qDebug() << "endElement_peptide ";
- PeptideXtpSp peptide_const = PeptideXtp(*(_current_peptide_sp.get())).makePeptideXtpSp();
- peptide_const = _p_project->getPeptideStore().getInstance(peptide_const);
- _p_peptide_evidence->setPeptideXtpSp(peptide_const);
- _current_peptide_match.setPeptideEvidenceSp(_p_peptide_evidence->getIdentificationDataSource()->getPeptideEvidenceStore().getInstance(_p_peptide_evidence));
- _p_protein_match->addPeptideMatch(_current_peptide_match);
- delete _p_peptide_evidence;
- return true;
+bool
+XpipSaxHandler::endElement_peptide()
+{
+ qDebug() << "endElement_peptide ";
+ PeptideXtpSp peptide_const =
+ PeptideXtp(*(_current_peptide_sp.get())).makePeptideXtpSp();
+ peptide_const = _p_project->getPeptideStore().getInstance(peptide_const);
+ _p_peptide_evidence->setPeptideXtpSp(peptide_const);
+ _current_peptide_match.setPeptideEvidenceSp(
+ _p_peptide_evidence->getIdentificationDataSource()
+ ->getPeptideEvidenceStore()
+ .getInstance(_p_peptide_evidence));
+ _p_protein_match->addPeptideMatch(_current_peptide_match);
+ delete _p_peptide_evidence;
+ return true;
}
-bool XpipSaxHandler::endElement_sequence() {
- //if ((_tag_stack.size() > 1) && (_tag_stack[_tag_stack.size() - 1] == "protein")) {
-
- //._sequence.replace(QRegExp("\\*"), "")).removeTranslationStop()
- _current_protein.setSequence(_current_text);
- //}
- //else {
- // XtandemHyperscore hyperscore(_curent_spectrum, _current_peptide_sp, _precision, _ion_list, _max_charge,_refine_spectrum_synthesis);
- //}
- return true;
+bool
+XpipSaxHandler::endElement_sequence()
+{
+ // if ((_tag_stack.size() > 1) && (_tag_stack[_tag_stack.size() - 1] ==
+ // "protein")) {
+
+ //._sequence.replace(QRegExp("\\*"), "")).removeTranslationStop()
+ _current_protein.setSequence(_current_text);
+ //}
+ // else {
+ // XtandemHyperscore hyperscore(_curent_spectrum, _current_peptide_sp,
+ // _precision, _ion_list, _max_charge,_refine_spectrum_synthesis);
+ //}
+ return true;
}
-bool XpipSaxHandler::endElement_protein() {
+bool
+XpipSaxHandler::endElement_protein()
+{
- ProteinXtpSp sp_xtp_protein = _current_protein.makeProteinXtpSp();
+ ProteinXtpSp sp_xtp_protein = _current_protein.makeProteinXtpSp();
- _p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
+ _p_protein_match->setProteinXtpSp(
+ _p_project->getProteinStore().getInstance(sp_xtp_protein));
- return true;
+ return true;
}
-bool XpipSaxHandler::endElement_identification() {
+bool
+XpipSaxHandler::endElement_identification()
+{
- return true;
+ return true;
}
-bool XpipSaxHandler::endElement_match() {
- _count_protein_match++;
- _p_monitor->message(QObject::tr("reading match %1").arg(_count_protein_match), _count_protein_match);
- _current_identification_group_p->addProteinMatch(_p_protein_match);
- _p_protein_match = nullptr;
- return true;
+bool
+XpipSaxHandler::endElement_match()
+{
+ _count_protein_match++;
+ _p_monitor->message(QObject::tr("reading match %1").arg(_count_protein_match),
+ _count_protein_match);
+ _current_identification_group_p->addProteinMatch(_p_protein_match);
+ _p_protein_match = nullptr;
+ return true;
}
-bool XpipSaxHandler::error(const QXmlParseException &exception) {
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
- exception.message());
+bool
+XpipSaxHandler::error(const QXmlParseException &exception)
+{
+ _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+ "%3")
+ .arg(exception.lineNumber())
+ .arg(exception.columnNumber())
+ .arg(exception.message());
- return false;
+ return false;
}
-bool XpipSaxHandler::fatalError(const QXmlParseException &exception) {
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
- exception.message());
- return false;
+bool
+XpipSaxHandler::fatalError(const QXmlParseException &exception)
+{
+ _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+ "%3")
+ .arg(exception.lineNumber())
+ .arg(exception.columnNumber())
+ .arg(exception.message());
+ return false;
}
-QString XpipSaxHandler::errorString() const {
- return _errorStr;
+QString
+XpipSaxHandler::errorString() const
+{
+ return _errorStr;
}
-bool XpipSaxHandler::endDocument() {
- //_p_project->getProteinStore().setRegexpDecoyPattern(_p_project->getProteinStore().getRegexpDecoy().pattern());
- _p_project->updateAutomaticFilters(_automatic_filter_parameters);
- return true;
+bool
+XpipSaxHandler::endDocument()
+{
+ //_p_project->getProteinStore().setRegexpDecoyPattern(_p_project->getProteinStore().getRegexpDecoy().pattern());
+ _p_project->updateAutomaticFilters(_automatic_filter_parameters);
+ return true;
}
-bool XpipSaxHandler::startDocument() {
- _count_protein_match=0;
- return true;
+bool
+XpipSaxHandler::startDocument()
+{
+ _count_protein_match = 0;
+ return true;
}
-bool XpipSaxHandler::characters(const QString &str) {
- _current_text += str;
- return true;
+bool
+XpipSaxHandler::characters(const QString &str)
+{
+ _current_text += str;
+ return true;
}
-pappso::AaModificationP XpipSaxHandler::getAaModificationP(pappso::mz mass) const {
- pappso::PrecisionP precision = pappso::Precision::getDaltonInstance(0.01);
+pappso::AaModificationP
+XpipSaxHandler::getAaModificationP(pappso::mz mass) const
+{
+ pappso::PrecisionP precision = pappso::Precision::getDaltonInstance(0.01);
- pappso::AaModificationP oxidation = pappso::AaModification::getInstance("MOD:00719");
- if (pappso::MassRange(oxidation->getMass(),precision).contains(mass)) {
- return oxidation;
+ pappso::AaModificationP oxidation =
+ pappso::AaModification::getInstance("MOD:00719");
+ if(pappso::MassRange(oxidation->getMass(), precision).contains(mass))
+ {
+ return oxidation;
}
- pappso::AaModificationP iodoacetamide = pappso::AaModification::getInstance("MOD:00397");
- if (pappso::MassRange(iodoacetamide->getMass(),precision).contains(mass)) {
- return iodoacetamide;
+ pappso::AaModificationP iodoacetamide =
+ pappso::AaModification::getInstance("MOD:00397");
+ if(pappso::MassRange(iodoacetamide->getMass(), precision).contains(mass))
+ {
+ return iodoacetamide;
}
- pappso::AaModificationP acetylated = pappso::AaModification::getInstance("MOD:00408");
- if (pappso::MassRange(acetylated->getMass(),precision).contains(mass)) {
- return acetylated;
+ pappso::AaModificationP acetylated =
+ pappso::AaModification::getInstance("MOD:00408");
+ if(pappso::MassRange(acetylated->getMass(), precision).contains(mass))
+ {
+ return acetylated;
}
- pappso::AaModificationP phosphorylated = pappso::AaModification::getInstance("MOD:00696");
- if (pappso::MassRange(phosphorylated->getMass(),precision).contains(mass)) {
- return phosphorylated;
+ pappso::AaModificationP phosphorylated =
+ pappso::AaModification::getInstance("MOD:00696");
+ if(pappso::MassRange(phosphorylated->getMass(), precision).contains(mass))
+ {
+ return phosphorylated;
}
- pappso::AaModificationP ammonia = pappso::AaModification::getInstance("MOD:01160");
- if (pappso::MassRange(ammonia->getMass(),precision).contains(mass)) {
- return ammonia;
+ pappso::AaModificationP ammonia =
+ pappso::AaModification::getInstance("MOD:01160");
+ if(pappso::MassRange(ammonia->getMass(), precision).contains(mass))
+ {
+ return ammonia;
}
- pappso::AaModificationP dehydrated = pappso::AaModification::getInstance("MOD:00704");
- if (pappso::MassRange(dehydrated->getMass(),precision).contains(mass)) {
- return dehydrated;
+ pappso::AaModificationP dehydrated =
+ pappso::AaModification::getInstance("MOD:00704");
+ if(pappso::MassRange(dehydrated->getMass(), precision).contains(mass))
+ {
+ return dehydrated;
}
- pappso::AaModificationP dimethylated = pappso::AaModification::getInstance("MOD:00429");
- if (pappso::MassRange(dimethylated->getMass(),precision).contains(mass)) {
- return dimethylated;
+ pappso::AaModificationP dimethylated =
+ pappso::AaModification::getInstance("MOD:00429");
+ if(pappso::MassRange(dimethylated->getMass(), precision).contains(mass))
+ {
+ return dimethylated;
}
- pappso::AaModificationP dimethylated_medium = pappso::AaModification::getInstance("MOD:00552");
- if (pappso::MassRange(dimethylated_medium->getMass(),precision).contains(mass)) {
- return dimethylated_medium;
+ pappso::AaModificationP dimethylated_medium =
+ pappso::AaModification::getInstance("MOD:00552");
+ if(pappso::MassRange(dimethylated_medium->getMass(), precision)
+ .contains(mass))
+ {
+ return dimethylated_medium;
}
- pappso::AaModificationP dimethylated_heavy = pappso::AaModification::getInstance("MOD:00638");
- if (pappso::MassRange(dimethylated_heavy->getMass(),precision).contains(mass)) {
- return dimethylated_heavy;
+ pappso::AaModificationP dimethylated_heavy =
+ pappso::AaModification::getInstance("MOD:00638");
+ if(pappso::MassRange(dimethylated_heavy->getMass(), precision).contains(mass))
+ {
+ return dimethylated_heavy;
}
- pappso::AaModificationP DimethylpyrroleAdduct = pappso::AaModification::getInstance("MOD:00628");
- if (pappso::MassRange(DimethylpyrroleAdduct->getMass(),precision).contains(mass)) {
- return DimethylpyrroleAdduct;
+ pappso::AaModificationP DimethylpyrroleAdduct =
+ pappso::AaModification::getInstance("MOD:00628");
+ if(pappso::MassRange(DimethylpyrroleAdduct->getMass(), precision)
+ .contains(mass))
+ {
+ return DimethylpyrroleAdduct;
}
- // modification not found, creating customized mod :
- return pappso::AaModification::getInstanceCustomizedMod(mass);
+ // modification not found, creating customized mod :
+ return pappso::AaModification::getInstanceCustomizedMod(mass);
- throw pappso::ExceptionNotFound(QObject::tr("XpipSaxHandler::getAaModificationP => modification not found for mass %1").arg(mass));
+ throw pappso::ExceptionNotFound(
+ QObject::tr("XpipSaxHandler::getAaModificationP => modification not found "
+ "for mass %1")
+ .arg(mass));
}
-
-
diff --git a/src/input/xpipsaxhandler.h b/src/input/xpipsaxhandler.h
index e5187702f63bd862b77d5cc978a5bc615812290a..fdb335a17cb62e970ed5d29ae3d93e5c8612ec87 100644
--- a/src/input/xpipsaxhandler.h
+++ b/src/input/xpipsaxhandler.h
@@ -1,24 +1,25 @@
/*******************************************************************************
-* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef XPIPSAXHANDLER_H
#define XPIPSAXHANDLER_H
@@ -32,70 +33,70 @@
#include "../core/proteinmatch.h"
#include "../utils/workmonitor.h"
-class XpipSaxHandler: public QXmlDefaultHandler
+class XpipSaxHandler : public QXmlDefaultHandler
{
-public:
- XpipSaxHandler(WorkMonitorInterface * p_monitor, Project * p_project);
- ~XpipSaxHandler();
-
- bool startElement(const QString & namespaceURI, const QString & localName,
- const QString & qName, const QXmlAttributes & attributes);
-
- bool endElement(const QString & namespaceURI, const QString & localName,
- const QString & qName);
-
- bool startDocument();
-
- bool endDocument();
-
- bool characters(const QString &str);
-
- bool fatalError(const QXmlParseException &exception);
- bool error(const QXmlParseException &exception);
-
- QString errorString() const;
- bool isJavaXpip() const;
-
-
-private:
- bool startElement_filter_params(QXmlAttributes attributes);
- bool startElement_information(QXmlAttributes attributes);
- bool startElement_identification(QXmlAttributes attributes);
- bool startElement_match(QXmlAttributes attributes);
- bool startElement_peptide(QXmlAttributes attributes);
- bool startElement_protein(QXmlAttributes attributes);
- bool startElement_sample(QXmlAttributes attributes);
- bool startElement_modifs_mass(QXmlAttributes attributes);
- bool startElement_modif(QXmlAttributes attributes);
- bool endElement_identification();
- bool endElement_sequence();
- bool endElement_protein();
- bool endElement_peptide();
- bool endElement_match();
-
- pappso::AaModificationP getAaModificationP(pappso::mz mass) const;
-
-private:
- WorkMonitorInterface * _p_monitor;
- std::vector<QString> _tag_stack;
- QString _errorStr;
- QString _current_text;
- AutomaticFilterParameters _automatic_filter_parameters;
-
- Project * _p_project;
- ProteinMatch * _p_protein_match;
- PeptideEvidence * _p_peptide_evidence;
- PeptideMatch _current_peptide_match;
- ProteinXtp _current_protein;
- PeptideXtpSp _current_peptide_sp;
- IdentificationGroup * _current_identification_group_p;
- FastaFileSp _current_fasta_file_sp;
-
- QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
- uint _count_protein_match=0;
- uint _total_protein_match;
-
- bool _is_java_xpip = false;
+ public:
+ XpipSaxHandler(WorkMonitorInterface *p_monitor, Project *p_project);
+ ~XpipSaxHandler();
+
+ bool startElement(const QString &namespaceURI, const QString &localName,
+ const QString &qName, const QXmlAttributes &attributes);
+
+ bool endElement(const QString &namespaceURI, const QString &localName,
+ const QString &qName);
+
+ bool startDocument();
+
+ bool endDocument();
+
+ bool characters(const QString &str);
+
+ bool fatalError(const QXmlParseException &exception);
+ bool error(const QXmlParseException &exception);
+
+ QString errorString() const;
+ bool isJavaXpip() const;
+
+
+ private:
+ bool startElement_filter_params(QXmlAttributes attributes);
+ bool startElement_information(QXmlAttributes attributes);
+ bool startElement_identification(QXmlAttributes attributes);
+ bool startElement_match(QXmlAttributes attributes);
+ bool startElement_peptide(QXmlAttributes attributes);
+ bool startElement_protein(QXmlAttributes attributes);
+ bool startElement_sample(QXmlAttributes attributes);
+ bool startElement_modifs_mass(QXmlAttributes attributes);
+ bool startElement_modif(QXmlAttributes attributes);
+ bool endElement_identification();
+ bool endElement_sequence();
+ bool endElement_protein();
+ bool endElement_peptide();
+ bool endElement_match();
+
+ pappso::AaModificationP getAaModificationP(pappso::mz mass) const;
+
+ private:
+ WorkMonitorInterface *_p_monitor;
+ std::vector<QString> _tag_stack;
+ QString _errorStr;
+ QString _current_text;
+ AutomaticFilterParameters _automatic_filter_parameters;
+
+ Project *_p_project;
+ ProteinMatch *_p_protein_match;
+ PeptideEvidence *_p_peptide_evidence;
+ PeptideMatch _current_peptide_match;
+ ProteinXtp _current_protein;
+ PeptideXtpSp _current_peptide_sp;
+ IdentificationGroup *_current_identification_group_p;
+ FastaFileSp _current_fasta_file_sp;
+
+ QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
+ uint _count_protein_match = 0;
+ uint _total_protein_match;
+
+ bool _is_java_xpip = false;
};
#endif // XTANDEMRESULTSHANDLER_H
diff --git a/src/input/xtandemparamsaxhandler.cpp b/src/input/xtandemparamsaxhandler.cpp
index 06e44a24258b5f4e20dc39f545f6214bde652c53..08b9feed0efd9aa3ac6fa1b0126c0fa6ed2a75e7 100644
--- a/src/input/xtandemparamsaxhandler.cpp
+++ b/src/input/xtandemparamsaxhandler.cpp
@@ -6,164 +6,225 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "xtandemparamsaxhandler.h"
#include <pappsomspp/pappsoexception.h>
#include <QDebug>
-XtandemParamSaxHandler::XtandemParamSaxHandler(TandemParameters * p_tandem_parameters) {
- _p_tandem_parameters = p_tandem_parameters;
+XtandemParamSaxHandler::XtandemParamSaxHandler(
+ TandemParameters *p_tandem_parameters)
+{
+ _p_tandem_parameters = p_tandem_parameters;
- //<note type="input" label="output, xsl path">tandem-style.xsl</note>
- _p_tandem_parameters->setParamLabelValue("output, xsl path", "tandem-style.xsl");
- //<note type="input" label="output, mzid">no</note>
- _p_tandem_parameters->setParamLabelValue("output, mzid", "no");
+ //<note type="input" label="output, xsl path">tandem-style.xsl</note>
+ _p_tandem_parameters->setParamLabelValue("output, xsl path",
+ "tandem-style.xsl");
+ //<note type="input" label="output, mzid">no</note>
+ _p_tandem_parameters->setParamLabelValue("output, mzid", "no");
}
-XtandemParamSaxHandler::~XtandemParamSaxHandler() {
+XtandemParamSaxHandler::~XtandemParamSaxHandler()
+{
}
-
-bool XtandemParamSaxHandler::startElement(const QString & namespaceURI, const QString & localName,
- const QString & qName, const QXmlAttributes & attributes) {
- //qDebug()<< "XtandemParamSaxHandler::startElement begin" << namespaceURI << " " << localName << " " << qName ;
- _tag_stack.push_back(qName);
- bool is_ok = true;
-
- try {
- //<bioml label="example api document">
- if (_tag_stack.size() == 1) {
- if (qName != "bioml") {
- _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::startElement root tag %1 is not <bioml>").arg(qName);
- return false;
+bool
+XtandemParamSaxHandler::startElement(const QString &namespaceURI,
+ const QString &localName,
+ const QString &qName,
+ const QXmlAttributes &attributes)
+{
+ // qDebug()<< "XtandemParamSaxHandler::startElement begin" << namespaceURI <<
+ // " " << localName << " " << qName ;
+ _tag_stack.push_back(qName);
+ bool is_ok = true;
+
+ try
+ {
+ //<bioml label="example api document">
+ if(_tag_stack.size() == 1)
+ {
+ if(qName != "bioml")
+ {
+ _errorStr =
+ QObject::tr("ERROR in XtandemParamSaxHandler::startElement "
+ "root tag %1 is not <bioml>")
+ .arg(qName);
+ return false;
}
}
- //startElement_group
+ // startElement_group
- if (qName == "note") {
- is_ok = startElement_note(attributes);
+ if(qName == "note")
+ {
+ is_ok = startElement_note(attributes);
}
- _current_text.clear();
+ _current_text.clear();
}
- catch (pappso::PappsoException exception_pappso) {
- _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::startElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
- return false;
+ catch(pappso::PappsoException exception_pappso)
+ {
+ _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::startElement "
+ "tag %1, PAPPSO exception:\n%2")
+ .arg(qName)
+ .arg(exception_pappso.qwhat());
+ return false;
}
- catch (std::exception exception_std) {
- _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::startElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
- return false;
+ catch(std::exception exception_std)
+ {
+ _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::startElement "
+ "tag %1, std exception:\n%2")
+ .arg(qName)
+ .arg(exception_std.what());
+ return false;
}
- return is_ok;
+ return is_ok;
}
-bool XtandemParamSaxHandler::endElement(const QString & namespaceURI, const QString & localName,
- const QString & qName) {
+bool
+XtandemParamSaxHandler::endElement(const QString &namespaceURI,
+ const QString &localName,
+ const QString &qName)
+{
- bool is_ok = true;
- // endElement_peptide_list
- try {
+ bool is_ok = true;
+ // endElement_peptide_list
+ try
+ {
- if (qName == "note")
+ if(qName == "note")
{
- is_ok = endElement_note();
+ is_ok = endElement_note();
}
-
}
- catch (pappso::PappsoException exception_pappso) {
- _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::endElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
- return false;
+ catch(pappso::PappsoException exception_pappso)
+ {
+ _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::endElement tag "
+ "%1, PAPPSO exception:\n%2")
+ .arg(qName)
+ .arg(exception_pappso.qwhat());
+ return false;
}
- catch (std::exception exception_std) {
- _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::endElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
- return false;
+ catch(std::exception exception_std)
+ {
+ _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::endElement tag "
+ "%1, std exception:\n%2")
+ .arg(qName)
+ .arg(exception_std.what());
+ return false;
}
- _current_text.clear();
- _tag_stack.pop_back();
+ _current_text.clear();
+ _tag_stack.pop_back();
- return is_ok;
+ return is_ok;
}
-bool XtandemParamSaxHandler::error(const QXmlParseException &exception) {
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
- exception.message());
- qDebug() << "XtandemParamSaxHandler::error " << _errorStr;
- return false;
+bool
+XtandemParamSaxHandler::error(const QXmlParseException &exception)
+{
+ _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+ "%3")
+ .arg(exception.lineNumber())
+ .arg(exception.columnNumber())
+ .arg(exception.message());
+ qDebug() << "XtandemParamSaxHandler::error " << _errorStr;
+ return false;
}
-bool XtandemParamSaxHandler::fatalError(const QXmlParseException &exception) {
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
- exception.message());
- qDebug() << "XtandemParamSaxHandler::fatalError " << _errorStr;
- return false;
+bool
+XtandemParamSaxHandler::fatalError(const QXmlParseException &exception)
+{
+ _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+ "%3")
+ .arg(exception.lineNumber())
+ .arg(exception.columnNumber())
+ .arg(exception.message());
+ qDebug() << "XtandemParamSaxHandler::fatalError " << _errorStr;
+ return false;
}
-QString XtandemParamSaxHandler::errorString() const {
- return _errorStr;
+QString
+XtandemParamSaxHandler::errorString() const
+{
+ return _errorStr;
}
-bool XtandemParamSaxHandler::endDocument() {
+bool
+XtandemParamSaxHandler::endDocument()
+{
- return true;
+ return true;
}
-bool XtandemParamSaxHandler::startDocument() {
- /*<?xml version="1.0" encoding="UTF-8"?>
- <bioml label="example api document">
- <note type="input" label="spectrum, parent monoisotopic mass error units">ppm</note>
- <note type="input" label="spectrum, parent monoisotopic mass error minus">10</note>
- */
- return true;
+bool
+XtandemParamSaxHandler::startDocument()
+{
+ /*<?xml version="1.0" encoding="UTF-8"?>
+ <bioml label="example api document">
+ <note type="input" label="spectrum, parent monoisotopic mass error
+ units">ppm</note> <note type="input" label="spectrum, parent monoisotopic mass
+ error minus">10</note>
+ */
+ return true;
}
-bool XtandemParamSaxHandler::characters(const QString &str) {
- _current_text += str;
- return true;
+bool
+XtandemParamSaxHandler::characters(const QString &str)
+{
+ _current_text += str;
+ return true;
}
-bool XtandemParamSaxHandler::startElement_note(QXmlAttributes attributes) {
- //qDebug() << "XtandemParamSaxHandler::startElement_note begin " << attributes.value("type");
- _current_label = "";
+bool
+XtandemParamSaxHandler::startElement_note(QXmlAttributes attributes)
+{
+ // qDebug() << "XtandemParamSaxHandler::startElement_note begin " <<
+ // attributes.value("type");
+ _current_label = "";
- if (attributes.value("type") == "input") {
- _current_label = attributes.value("label");
+ if(attributes.value("type") == "input")
+ {
+ _current_label = attributes.value("label");
}
- // qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " << _current_label;
- return true;
-
+ // qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " <<
+ // _current_label;
+ return true;
}
-bool XtandemParamSaxHandler::endElement_note() {
-// qDebug() << "XtandemParamSaxHandler::endElement_note begin " << _current_label << " " << _current_text.simplified();
- if (!_current_label.isEmpty()) {
- _p_tandem_parameters->setParamLabelValue( _current_label, _current_text.simplified());
+bool
+XtandemParamSaxHandler::endElement_note()
+{
+ // qDebug() << "XtandemParamSaxHandler::endElement_note begin " <<
+ // _current_label << " " << _current_text.simplified();
+ if(!_current_label.isEmpty())
+ {
+ _p_tandem_parameters->setParamLabelValue(_current_label,
+ _current_text.simplified());
}
- return true;
+ return true;
}
diff --git a/src/input/xtandemparamsaxhandler.h b/src/input/xtandemparamsaxhandler.h
index 88791ee5984a3b76cb06a1a13db8140d4a29befe..398f516ca4c03dd9551c99d7c9a6e5d7df30939f 100644
--- a/src/input/xtandemparamsaxhandler.h
+++ b/src/input/xtandemparamsaxhandler.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef XTANDEMPARAMSAXHANDLER_H
#define XTANDEMPARAMSAXHANDLER_H
@@ -34,42 +35,41 @@
#include <vector>
#include "../core/tandem_run/tandemparameters.h"
-class XtandemParamSaxHandler: public QXmlDefaultHandler
+class XtandemParamSaxHandler : public QXmlDefaultHandler
{
-public:
- XtandemParamSaxHandler(TandemParameters * p_tandem_parameters);
- ~XtandemParamSaxHandler();
-
- bool startElement(const QString & namespaceURI, const QString & localName,
- const QString & qName, const QXmlAttributes & attributes);
+ public:
+ XtandemParamSaxHandler(TandemParameters *p_tandem_parameters);
+ ~XtandemParamSaxHandler();
- bool endElement(const QString & namespaceURI, const QString & localName,
- const QString & qName);
+ bool startElement(const QString &namespaceURI, const QString &localName,
+ const QString &qName, const QXmlAttributes &attributes);
- bool startDocument();
+ bool endElement(const QString &namespaceURI, const QString &localName,
+ const QString &qName);
- bool endDocument();
+ bool startDocument();
- bool characters(const QString &str);
+ bool endDocument();
- bool fatalError(const QXmlParseException &exception);
- bool error(const QXmlParseException &exception);
+ bool characters(const QString &str);
- QString errorString() const;
-
-private:
- bool startElement_note(QXmlAttributes attributes);
- bool endElement_note();
+ bool fatalError(const QXmlParseException &exception);
+ bool error(const QXmlParseException &exception);
-private:
- TandemParameters * _p_tandem_parameters;
-
- std::vector<QString> _tag_stack;
- QString _errorStr;
- QString _current_text;
-
- QString _current_label;
+ QString errorString() const;
+ private:
+ bool startElement_note(QXmlAttributes attributes);
+ bool endElement_note();
+
+ private:
+ TandemParameters *_p_tandem_parameters;
+
+ std::vector<QString> _tag_stack;
+ QString _errorStr;
+ QString _current_text;
+
+ QString _current_label;
};
#endif // XTANDEMPARAMSAXHANDLER_H
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index a7fd35aeaa14ef6abbe8273ac312f1f256359e47..57b17071e31ba50749e20ec2597256a1b0d68f92 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -165,9 +165,9 @@ bool
XtandemSaxHandler::startElement_group(QXmlAttributes attrs)
{
//<group id="1976" mh="1120.529471" z="2" rt="PT667.022S" expect="9.7e-04"
- //label="GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase
- //1)(PEPC 1)(EC..." type="model" sumI="5.34" maxI="35986.9" fI="359.869"
- //act="0" >
+ // label="GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase
+ // 1)(PEPC 1)(EC..." type="model" sumI="5.34" maxI="35986.9" fI="359.869"
+ // act="0" >
bool is_ok = true;
// logger.debug("startElementgroup begin");
// <group label="performance parameters" type="parameters">
@@ -190,8 +190,8 @@ bool
XtandemSaxHandler::startElement_note(QXmlAttributes attributes)
{
//<note label="description">GRMZM2G083841_P01 P04711 Phosphoenolpyruvate
- //carboxylase 1 (PEPCase 1)(PEPC 1)(EC //4.1.1.31) seq=translation;
- //coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01;
+ // carboxylase 1 (PEPCase 1)(PEPC 1)(EC //4.1.1.31) seq=translation;
+ // coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01;
////parent_gene=GRMZM2G083841</note>
bool is_ok = true;
_current_note_label = attributes.value("label");
@@ -212,7 +212,7 @@ XtandemSaxHandler::startElement_file(QXmlAttributes attributes)
{
bool is_ok = true;
//<file type="peptide"
- //URL="/gorgone/pappso/formation/TD/Database/Genome_Z_mays_5a.fasta"/>
+ // URL="/gorgone/pappso/formation/TD/Database/Genome_Z_mays_5a.fasta"/>
if(attributes.value("type") == "peptide")
{
// prot_.setDatabase(identification_.getDatabaseSet().getInstance(
@@ -238,7 +238,8 @@ XtandemSaxHandler::startElement_domain(QXmlAttributes attributes)
{
// mh="1120.529471"
//<domain id="1976.1.1" start="620" end="629" expect="9.7e-04" mh="1120.5307"
- //delta="-0.0012" hyperscore="29.9" nextscore="10.2" y_score="10.4" y_ions="7"
+ // delta="-0.0012" hyperscore="29.9" nextscore="10.2" y_score="10.4"
+ // y_ions="7"
// b_score="11.2" b_ions="3" pre="QLYR" post="RYGV" seq="AQEEMAQVAK"
// missed_cleavages="0"> qDebug() << "startElement_domain ";
bool is_ok = true;
@@ -430,13 +431,14 @@ bool
XtandemSaxHandler::startElement_protein(QXmlAttributes attributes)
{
//<protein expect="-704.6" id="1976.1" uid="195701" label="GRMZM2G083841_P01
- //P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC..."
- //sumI="9.36" >
+ // P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC..."
+ // sumI="9.36" >
bool is_ok = true;
// the protein label could be truncated => we must wait for the <note
- // label="description">sp|P11413|G6PD_HUMAN Glucose-6-phosphate 1-dehydrogenase
- // OS=Homo sapiens GN=G6PD PE=1 SV=4</note> to get the real protein
+ // label="description">sp|P11413|G6PD_HUMAN Glucose-6-phosphate
+ // 1-dehydrogenase OS=Homo sapiens GN=G6PD PE=1 SV=4</note> to get the real
+ // protein
_p_protein_match = nullptr;
// qDebug() << "startElement_protein end" ;
return is_ok;
@@ -447,8 +449,8 @@ bool
XtandemSaxHandler::endElement_note()
{
//<note label="description">GRMZM2G083841_P01 P04711 Phosphoenolpyruvate
- //carboxylase 1 (PEPCase 1)(PEPC 1)(EC //4.1.1.31) seq=translation;
- //coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01;
+ // carboxylase 1 (PEPCase 1)(PEPC 1)(EC //4.1.1.31) seq=translation;
+ // coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01;
////parent_gene=GRMZM2G083841</note>
bool is_ok = true;
if(_is_protein_description)
@@ -495,7 +497,7 @@ XtandemSaxHandler::endElement_note()
//<group label="input parameters" type="parameters">
//<note type="input" label="list path, default
- //parameters">/gorgone/pappso/tmp/temp_condor_job8533994640337729751189420695540169/QExactive_analysis_FDR_nosemi.xml</note>
+ // parameters">/gorgone/pappso/tmp/temp_condor_job8533994640337729751189420695540169/QExactive_analysis_FDR_nosemi.xml</note>
if(_current_note_label == "list path, default parameters")
{
_p_identification_data_source->setIdentificationEngineParam(
@@ -579,7 +581,7 @@ XtandemSaxHandler::endElement_note()
monoisotopic mass isotope error">yes</note>
*/
//<note type="input" label="spectrum,
- //path">/gorgone/pappso/formation/TD/mzXML/20120906_balliau_extract_1_A02_urzb-1.mzXML</note>
+ // path">/gorgone/pappso/formation/TD/mzXML/20120906_balliau_extract_1_A02_urzb-1.mzXML</note>
if(_current_note_label == "spectrum, path")
{
diff --git a/src/input/xtpxpipsaxhandler.cpp b/src/input/xtpxpipsaxhandler.cpp
index db9234736a8be2eb7f596ef5518d67861d5a2e6b..d577fd393c8f94d1baf0ad5cd725c305c84f116a 100644
--- a/src/input/xtpxpipsaxhandler.cpp
+++ b/src/input/xtpxpipsaxhandler.cpp
@@ -504,8 +504,8 @@ bool
XtpXpipSaxHandler::startElement_identification_source(QXmlAttributes attributes)
{
//<identification_source id="identa0" msrun_id="sampa0"
- //path="/espace/bio/tandem/20120906_balliau_extract_1_A01_urnb-1.xml"
- //engine="1" version="2017.2.1.4" fasta_ids="fastaa0">
+ // path="/espace/bio/tandem/20120906_balliau_extract_1_A01_urnb-1.xml"
+ // engine="1" version="2017.2.1.4" fasta_ids="fastaa0">
qDebug() << "startElement_identification_source ";
@@ -542,7 +542,7 @@ bool
XtpXpipSaxHandler::startElement_msrun(QXmlAttributes attributes)
{
//<msrun id="sampa0" name="20120906_balliau_extract_1_A01_urnb-1" format="0"
- //path="20120906_balliau_extract_1_A01_urnb-1"/>
+ // path="20120906_balliau_extract_1_A01_urnb-1"/>
qDebug() << "startElement_msrun ";
diff --git a/src/input/xtpxpipsaxhandler.h b/src/input/xtpxpipsaxhandler.h
index ed62a4f0eb4f597aa6976dd4e447c228d0dadc08..29f8767953cd2be02758081304c1080004e956a7 100644
--- a/src/input/xtpxpipsaxhandler.h
+++ b/src/input/xtpxpipsaxhandler.h
@@ -7,26 +7,27 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef XTPXPIPSAXHANDLER_H
#define XTPXPIPSAXHANDLER_H
@@ -40,104 +41,104 @@
#include "../core/proteinmatch.h"
#include "../utils/workmonitor.h"
-class XtpXpipSaxHandler: public QXmlDefaultHandler
+class XtpXpipSaxHandler : public QXmlDefaultHandler
{
-public:
- XtpXpipSaxHandler(WorkMonitorInterface * p_monitor, Project * p_project);
- ~XtpXpipSaxHandler();
-
- bool startElement(const QString & namespaceURI, const QString & localName,
- const QString & qName, const QXmlAttributes & attributes);
-
- bool endElement(const QString & namespaceURI, const QString & localName,
- const QString & qName);
-
- bool startDocument();
-
- bool endDocument();
-
- bool characters(const QString &str);
-
- bool fatalError(const QXmlParseException &exception);
- bool error(const QXmlParseException &exception);
-
- QString errorString() const;
- bool isXtpXpip() const;
-
-
-private:
- bool startElement_filter_params(QXmlAttributes attributes);
- bool startElement_description(QXmlAttributes attributes);
- bool startElement_fasta_file(QXmlAttributes attributes);
- bool startElement_protein_match(QXmlAttributes attributes);
- bool startElement_peptide_match(QXmlAttributes attributes);
- bool startElement_peptide(QXmlAttributes attributes);
- bool startElement_peptide_evidence(QXmlAttributes attributes);
- bool startElement_peptide_evidence_list(QXmlAttributes attributes);
- bool startElement_protein(QXmlAttributes attributes);
- bool startElement_msrun(QXmlAttributes attributes);
- bool startElement_identification_source(QXmlAttributes attributes);
- bool startElement_identification_group(QXmlAttributes attributes);
-
- bool startElement_modification(QXmlAttributes attributes);
- bool startElement_mod(QXmlAttributes attributes);
- bool startElement_param(QXmlAttributes attributes);
- bool startElement_stat(QXmlAttributes attributes);
- bool startElement_counts(QXmlAttributes attributes);
- bool startElement_label_method(QXmlAttributes attributes);
- bool startElement_contaminants(QXmlAttributes attributes);
- bool startElement_decoys(QXmlAttributes attributes);
-
- //bool endElement_identification();
- bool endElement_sequence();
- bool endElement_msrun();
- bool endElement_protein();
- bool endElement_peptide();
- bool endElement_protein_match();
- bool endElement_peptide_evidence();
- bool endElement_peptide_evidence_list();
- bool endElement_identification_group();
- bool endElement_identification_source();
-
-private:
- WorkMonitorInterface * _p_monitor;
- std::vector<QString> _tag_stack;
- QString _errorStr;
- QString _current_text;
- AutomaticFilterParameters _automatic_filter_parameters;
-
- Project * _p_project;
- ProteinMatch * _p_protein_match;
- PeptideEvidence * _p_peptide_evidence;
- IdentificationGroup * _current_identification_group_p;
-
- std::map<QString, pappso::AaModificationP> _map_modifs;
- std::map<QString, FastaFileSp> _map_fasta_files;
- std::map<QString, ProteinXtpSp> _map_proteins;
- std::map<QString, MsRunSp> _map_msruns;
- std::map<QString, IdentificationDataSourceSp> _map_ident_sources;
- std::map<QString, PeptideEvidenceSp> _map_peptide_evidences;
- PeptideEvidenceSp _sp_current_peptide_evidence;
- ProteinXtpSp _sp_current_protein;
- PeptideXtpSp _current_peptide_sp;
- IdentificationDataSourceSp _sp_current_identification_source;
- LabelingMethodSp _sp_labeling_method;
- MsRunSp _sp_msrun;
- std::map<QString, PeptideXtpSp> _map_peptides;
- bool _is_xtpcpp_xpip = false;
- QString _current_id;
-
-
- std::size_t _count_proteins=0;
- std::size_t _count_peptides=0;
- std::size_t _count_peptide_evidences=0;
- std::size_t _count_protein_matches=0;
- std::size_t _count_total=0;
- std::size_t _total_proteins;
- std::size_t _total_peptides;
- std::size_t _total_peptide_evidences;
- std::size_t _total_protein_matches;
- std::size_t _total;
+ public:
+ XtpXpipSaxHandler(WorkMonitorInterface *p_monitor, Project *p_project);
+ ~XtpXpipSaxHandler();
+
+ bool startElement(const QString &namespaceURI, const QString &localName,
+ const QString &qName, const QXmlAttributes &attributes);
+
+ bool endElement(const QString &namespaceURI, const QString &localName,
+ const QString &qName);
+
+ bool startDocument();
+
+ bool endDocument();
+
+ bool characters(const QString &str);
+
+ bool fatalError(const QXmlParseException &exception);
+ bool error(const QXmlParseException &exception);
+
+ QString errorString() const;
+ bool isXtpXpip() const;
+
+
+ private:
+ bool startElement_filter_params(QXmlAttributes attributes);
+ bool startElement_description(QXmlAttributes attributes);
+ bool startElement_fasta_file(QXmlAttributes attributes);
+ bool startElement_protein_match(QXmlAttributes attributes);
+ bool startElement_peptide_match(QXmlAttributes attributes);
+ bool startElement_peptide(QXmlAttributes attributes);
+ bool startElement_peptide_evidence(QXmlAttributes attributes);
+ bool startElement_peptide_evidence_list(QXmlAttributes attributes);
+ bool startElement_protein(QXmlAttributes attributes);
+ bool startElement_msrun(QXmlAttributes attributes);
+ bool startElement_identification_source(QXmlAttributes attributes);
+ bool startElement_identification_group(QXmlAttributes attributes);
+
+ bool startElement_modification(QXmlAttributes attributes);
+ bool startElement_mod(QXmlAttributes attributes);
+ bool startElement_param(QXmlAttributes attributes);
+ bool startElement_stat(QXmlAttributes attributes);
+ bool startElement_counts(QXmlAttributes attributes);
+ bool startElement_label_method(QXmlAttributes attributes);
+ bool startElement_contaminants(QXmlAttributes attributes);
+ bool startElement_decoys(QXmlAttributes attributes);
+
+ // bool endElement_identification();
+ bool endElement_sequence();
+ bool endElement_msrun();
+ bool endElement_protein();
+ bool endElement_peptide();
+ bool endElement_protein_match();
+ bool endElement_peptide_evidence();
+ bool endElement_peptide_evidence_list();
+ bool endElement_identification_group();
+ bool endElement_identification_source();
+
+ private:
+ WorkMonitorInterface *_p_monitor;
+ std::vector<QString> _tag_stack;
+ QString _errorStr;
+ QString _current_text;
+ AutomaticFilterParameters _automatic_filter_parameters;
+
+ Project *_p_project;
+ ProteinMatch *_p_protein_match;
+ PeptideEvidence *_p_peptide_evidence;
+ IdentificationGroup *_current_identification_group_p;
+
+ std::map<QString, pappso::AaModificationP> _map_modifs;
+ std::map<QString, FastaFileSp> _map_fasta_files;
+ std::map<QString, ProteinXtpSp> _map_proteins;
+ std::map<QString, MsRunSp> _map_msruns;
+ std::map<QString, IdentificationDataSourceSp> _map_ident_sources;
+ std::map<QString, PeptideEvidenceSp> _map_peptide_evidences;
+ PeptideEvidenceSp _sp_current_peptide_evidence;
+ ProteinXtpSp _sp_current_protein;
+ PeptideXtpSp _current_peptide_sp;
+ IdentificationDataSourceSp _sp_current_identification_source;
+ LabelingMethodSp _sp_labeling_method;
+ MsRunSp _sp_msrun;
+ std::map<QString, PeptideXtpSp> _map_peptides;
+ bool _is_xtpcpp_xpip = false;
+ QString _current_id;
+
+
+ std::size_t _count_proteins = 0;
+ std::size_t _count_peptides = 0;
+ std::size_t _count_peptide_evidences = 0;
+ std::size_t _count_protein_matches = 0;
+ std::size_t _count_total = 0;
+ std::size_t _total_proteins;
+ std::size_t _total_peptides;
+ std::size_t _total_peptide_evidences;
+ std::size_t _total_protein_matches;
+ std::size_t _total;
};
#endif // XTPXPIPSAXHANDLER_H
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index f993f7359f4d45d8711d96caa52f07ebcea3b1e6..570c75c25039639920dcc88a24c57ecfdc551b64 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "masschroqml.h"
#include <pappsomspp/pappsoexception.h>
@@ -35,486 +36,598 @@
#include <QStringList>
#include <QSettings>
-struct McqObserved {
- bool operator ==(const McqObserved &other) const {
- return (msrun==other.msrun && scan==other.scan && charge==other.charge);
- };
- const MsRun * msrun;
- unsigned int scan;
- unsigned int charge;
+struct McqObserved
+{
+ bool
+ operator==(const McqObserved &other) const
+ {
+ return (msrun == other.msrun && scan == other.scan &&
+ charge == other.charge);
+ };
+ const MsRun *msrun;
+ unsigned int scan;
+ unsigned int charge;
};
-struct McqPeptide {
- QString id;
- QStringList mods;
- QStringList prot_ids;
- QString seq;
- const pappso::Peptide * native_peptide;
- std::vector<McqObserved> observed_in;
+struct McqPeptide
+{
+ QString id;
+ QStringList mods;
+ QStringList prot_ids;
+ QString seq;
+ const pappso::Peptide *native_peptide;
+ std::vector<McqObserved> observed_in;
};
-struct McqPsimod {
- unsigned int at;
- QString accession;
+struct McqPsimod
+{
+ unsigned int at;
+ QString accession;
};
-MassChroQml::MassChroQml(const QString & out_filename)
+MassChroQml::MassChroQml(const QString &out_filename)
{
- //_p_digestion_pipeline = p_digestion_pipeline;
+ //_p_digestion_pipeline = p_digestion_pipeline;
- //_mzidentml = "http://psidev.info/psi/pi/mzIdentML/1.1";
- QString complete_out_filename = out_filename;
- _output_file = new QFile(complete_out_filename);
+ //_mzidentml = "http://psidev.info/psi/pi/mzIdentML/1.1";
+ QString complete_out_filename = out_filename;
+ _output_file = new QFile(complete_out_filename);
- if (_output_file->open(QIODevice::WriteOnly))
+ if(_output_file->open(QIODevice::WriteOnly))
{
- _output_stream = new QXmlStreamWriter();
- _output_stream->setDevice(_output_file);
- } else
+ _output_stream = new QXmlStreamWriter();
+ _output_stream->setDevice(_output_file);
+ }
+ else
{
- throw pappso::PappsoException(QObject::tr("error : cannot open the MassChroqML output file : %1\n").arg(out_filename));
+ throw pappso::PappsoException(
+ QObject::tr("error : cannot open the MassChroqML output file : %1\n")
+ .arg(out_filename));
}
- _output_stream->setAutoFormatting(true);
- _output_stream->writeStartDocument("1.0");
-
- _detect_zivy.loadSettings();
+ _output_stream->setAutoFormatting(true);
+ _output_stream->writeStartDocument("1.0");
+ _detect_zivy.loadSettings();
}
MassChroQml::~MassChroQml()
{
- delete _output_file;
- delete _output_stream;
+ delete _output_file;
+ delete _output_stream;
}
-void MassChroQml::close() {
- _output_stream->writeEndDocument();
- _output_file->close();
+void
+MassChroQml::close()
+{
+ _output_stream->writeEndDocument();
+ _output_file->close();
}
-void MassChroQml::write(ProjectSp sp_project) {
+void
+MassChroQml::write(ProjectSp sp_project)
+{
- _sp_project = sp_project;
- if (_sp_project.get() == nullptr) {
- throw pappso::PappsoException(QObject::tr("Error writing MassChroqML file :\n project is empty"));
+ _sp_project = sp_project;
+ if(_sp_project.get() == nullptr)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error writing MassChroqML file :\n project is empty"));
}
- //<masschroq>
- _output_stream->writeStartElement("masschroq");
- _output_stream->writeAttribute("type","input");
- _output_stream->writeAttribute("version","2.2");
- //_output_stream->writeAttribute("creationDate", QDateTime::currentDateTime().toString( Qt::ISODate));
- //_output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance","xsi");
- //_output_stream->writeAttribute("xmlns","http://pappso.inra.fr/xsd/masschroqml/2.2");
- //_output_stream->writeAttribute("http://www.w3.org/2001/XMLSchema-instance","schemaLocation","http://pappso.inra.fr/xsd/masschroqml/2.2 http://pappso.inra.fr/xsd/masschroq-2.2.xsd");
-
- // <rawdata><!-- time_values_dir="directory" to read retention time corrections-->
- _output_stream->writeStartElement("rawdata");
- _output_stream->writeComment("time_values_dir=\"directory\" to read retention time corrections");
-
- std::vector<MsRunSp> msrun_list = _sp_project.get()->getMsRunStore().getMsRunList();
- for (MsRunSp & msrun : msrun_list) {
-
- //<data_file id="samp0" format="mzxml" path="bsa1.mzXML" type="centroid" />
- _output_stream->writeStartElement("data_file");
- _output_stream->writeAttribute("id",msrun.get()->getXmlId());
- if(msrun.get()->getMzFormat() == pappso::MzFormat::mzXML) {
- _output_stream->writeAttribute("format","mzxml");
+ //<masschroq>
+ _output_stream->writeStartElement("masschroq");
+ _output_stream->writeAttribute("type", "input");
+ _output_stream->writeAttribute("version", "2.2");
+ //_output_stream->writeAttribute("creationDate",
+ //QDateTime::currentDateTime().toString( Qt::ISODate));
+ //_output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance","xsi");
+ //_output_stream->writeAttribute("xmlns","http://pappso.inra.fr/xsd/masschroqml/2.2");
+ //_output_stream->writeAttribute("http://www.w3.org/2001/XMLSchema-instance","schemaLocation","http://pappso.inra.fr/xsd/masschroqml/2.2
+ //http://pappso.inra.fr/xsd/masschroq-2.2.xsd");
+
+ // <rawdata><!-- time_values_dir="directory" to read retention time
+ // corrections-->
+ _output_stream->writeStartElement("rawdata");
+ _output_stream->writeComment(
+ "time_values_dir=\"directory\" to read retention time corrections");
+
+ std::vector<MsRunSp> msrun_list =
+ _sp_project.get()->getMsRunStore().getMsRunList();
+ for(MsRunSp &msrun : msrun_list)
+ {
+
+ //<data_file id="samp0" format="mzxml" path="bsa1.mzXML" type="centroid"
+ ///>
+ _output_stream->writeStartElement("data_file");
+ _output_stream->writeAttribute("id", msrun.get()->getXmlId());
+ if(msrun.get()->getMzFormat() == pappso::MzFormat::mzXML)
+ {
+ _output_stream->writeAttribute("format", "mzxml");
}
- _output_stream->writeAttribute("path",msrun.get()->getFilename());
- _output_stream->writeAttribute("type","centroid");
- // <data_file id="samp1" format="mzxml" path="bsa2.mzXML" type="profile" />
- _output_stream->writeEndElement();
+ _output_stream->writeAttribute("path", msrun.get()->getFilename());
+ _output_stream->writeAttribute("type", "centroid");
+ // <data_file id="samp1" format="mzxml" path="bsa2.mzXML" type="profile"
+ // />
+ _output_stream->writeEndElement();
}
- // <data_file id="samp2" format="mzml" path="/home/user/bsa3.mzml" type="profile" />
-//<data_file id="samp3" format="mzml" path="/home/user/bsa4.mzml" type="profile" />
- // _output_stream.writeEndElement();
- // </rawdata>
- _output_stream->writeEndElement();
-
-
- writeGroups();
- writeProteinList();
- writePeptideList();
- writeIsotopeLabelList();
- writeAlignments();
- writeQuantificationMethods();
- _output_stream->writeStartElement("quantification");
- writeQuantificationResults();
- writeQuantificationTraces();
- writeQuantify();
- _output_stream->writeEndElement();
-
-
- _output_stream->writeEndDocument();
+ // <data_file id="samp2" format="mzml" path="/home/user/bsa3.mzml"
+ // type="profile" />
+ //<data_file id="samp3" format="mzml" path="/home/user/bsa4.mzml"
+ //type="profile" />
+ // _output_stream.writeEndElement();
+ // </rawdata>
+ _output_stream->writeEndElement();
+
+
+ writeGroups();
+ writeProteinList();
+ writePeptideList();
+ writeIsotopeLabelList();
+ writeAlignments();
+ writeQuantificationMethods();
+ _output_stream->writeStartElement("quantification");
+ writeQuantificationResults();
+ writeQuantificationTraces();
+ writeQuantify();
+ _output_stream->writeEndElement();
+
+
+ _output_stream->writeEndDocument();
}
-
-void MassChroQml::writeQuantificationResults() {
- //<quantification_results>
- _output_stream->writeStartElement("quantification_results");
- //<quantification_result output_file="result1"
- // format="tsv" />
- _output_stream->writeStartElement("quantification_result");
- _output_stream->writeAttribute("output_file","result1");
- _output_stream->writeAttribute("format","tsv");
- _output_stream->writeEndElement();
- //<quantification_result output_file="result2"
- // format="ods" />
- _output_stream->writeComment("<quantification_result output_file=\"result2\" format=\"ods\" />");
- //<compar_result output_file="compar"
- // format="ods" />
-
- _output_stream->writeStartElement("compar_result");
- _output_stream->writeAttribute("output_file","result1");
- _output_stream->writeAttribute("format","ods");
- _output_stream->writeEndElement();
- //</quantification_results>
- _output_stream->writeEndElement();
+void
+MassChroQml::writeQuantificationResults()
+{
+ //<quantification_results>
+ _output_stream->writeStartElement("quantification_results");
+ //<quantification_result output_file="result1"
+ // format="tsv" />
+ _output_stream->writeStartElement("quantification_result");
+ _output_stream->writeAttribute("output_file", "result1");
+ _output_stream->writeAttribute("format", "tsv");
+ _output_stream->writeEndElement();
+ //<quantification_result output_file="result2"
+ // format="ods" />
+ _output_stream->writeComment(
+ "<quantification_result output_file=\"result2\" format=\"ods\" />");
+ //<compar_result output_file="compar"
+ // format="ods" />
+
+ _output_stream->writeStartElement("compar_result");
+ _output_stream->writeAttribute("output_file", "result1");
+ _output_stream->writeAttribute("format", "ods");
+ _output_stream->writeEndElement();
+ //</quantification_results>
+ _output_stream->writeEndElement();
}
-void MassChroQml::writeQuantificationTraces() {
- //<quantification_traces>
-
- _output_stream->writeStartElement("quantification_traces");
- //<peptide_traces peptide_ids="pep0 pep1" output_dir="pep_traces"
- // format="tsv" />
- _output_stream->writeComment("<peptide_traces peptide_ids=\"pep0 pep1\" output_dir=\"pep_traces\" format=\"tsv\" />");
- /*
- <all_xics_traces output_dir="all_xics_traces" format="tsv" />
- <mz_traces mz_values="634.635 449.754 552.234" output_dir="mz_traces"
- format="tsv" />
- <mzrt_traces output_dir="mzrt_traces" format="tsv">
- <mzrt_values>
- <mzrt_value mz="732.317" rt="230.712" />
- <mzrt_value mz="575.256" rt="254.788" />
- </mzrt_values>
- </mzrt_traces>*/
- //</quantification_traces>
-
- _output_stream->writeEndElement();
+void
+MassChroQml::writeQuantificationTraces()
+{
+ //<quantification_traces>
+
+ _output_stream->writeStartElement("quantification_traces");
+ //<peptide_traces peptide_ids="pep0 pep1" output_dir="pep_traces"
+ // format="tsv" />
+ _output_stream->writeComment("<peptide_traces peptide_ids=\"pep0 pep1\" "
+ "output_dir=\"pep_traces\" format=\"tsv\" />");
+ /*
+ <all_xics_traces output_dir="all_xics_traces" format="tsv" />
+ <mz_traces mz_values="634.635 449.754 552.234" output_dir="mz_traces"
+ format="tsv" />
+ <mzrt_traces output_dir="mzrt_traces" format="tsv">
+ <mzrt_values>
+ <mzrt_value mz="732.317" rt="230.712" />
+ <mzrt_value mz="575.256" rt="254.788" />
+ </mzrt_values>
+ </mzrt_traces>*/
+ //</quantification_traces>
+
+ _output_stream->writeEndElement();
}
-void MassChroQml::writeQuantify() {
- //<quantify id="q1" withingroup="G1" quantification_method_id="my_qzivy">
- _output_stream->writeStartElement("quantify");
- _output_stream->writeAttribute("id","q1");
- _output_stream->writeAttribute("withingroup","fractiona1");
- _output_stream->writeAttribute("quantification_method_id","quant1");
- //<peptides_in_peptide_list mode="real_or_mean" />
- //</quantify>
- //<quantify id="q2" withingroup="G2" quantification_method_id="my_moulon">
- //<peptides_in_peptide_list mode="post_matching"
- // isotope_label_refs="iso1 iso2" />
-
- _output_stream->writeStartElement("peptides_in_peptide_list");
- _output_stream->writeAttribute("mode","post_matching");
- _output_stream->writeAttribute("ni_min_abundance","0.8");
- if (_sp_project.get()->getLabelingMethodSp().get() != nullptr) {
- QStringList isotope_label_ref;
- for (const Label * p_label :_sp_project.get()->getLabelingMethodSp().get()->getLabelList()) {
- isotope_label_ref << p_label->getXmlId();
+void
+MassChroQml::writeQuantify()
+{
+ //<quantify id="q1" withingroup="G1" quantification_method_id="my_qzivy">
+ _output_stream->writeStartElement("quantify");
+ _output_stream->writeAttribute("id", "q1");
+ _output_stream->writeAttribute("withingroup", "fractiona1");
+ _output_stream->writeAttribute("quantification_method_id", "quant1");
+ //<peptides_in_peptide_list mode="real_or_mean" />
+ //</quantify>
+ //<quantify id="q2" withingroup="G2" quantification_method_id="my_moulon">
+ //<peptides_in_peptide_list mode="post_matching"
+ // isotope_label_refs="iso1 iso2" />
+
+ _output_stream->writeStartElement("peptides_in_peptide_list");
+ _output_stream->writeAttribute("mode", "post_matching");
+ _output_stream->writeAttribute("ni_min_abundance", "0.8");
+ if(_sp_project.get()->getLabelingMethodSp().get() != nullptr)
+ {
+ QStringList isotope_label_ref;
+ for(const Label *p_label :
+ _sp_project.get()->getLabelingMethodSp().get()->getLabelList())
+ {
+ isotope_label_ref << p_label->getXmlId();
}
- _output_stream->writeAttribute("isotope_label_refs",isotope_label_ref.join(" "));
+ _output_stream->writeAttribute("isotope_label_refs",
+ isotope_label_ref.join(" "));
}
- _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
- _output_stream->writeComment("<mz_list>732.317 449.754 552.234 464.251 381.577 569.771 575.256</mz_list>");
- _output_stream->writeComment("<mzrt_list>\n <mzrt mz=\"732.317\" rt=\"230.712\" />\n <mzrt mz=\"575.256\" rt=\"254.788\" />\n </mzrt_list>");
+ _output_stream->writeComment("<mz_list>732.317 449.754 552.234 464.251 "
+ "381.577 569.771 575.256</mz_list>");
+ _output_stream->writeComment(
+ "<mzrt_list>\n <mzrt mz=\"732.317\" rt=\"230.712\" />\n <mzrt "
+ "mz=\"575.256\" rt=\"254.788\" />\n </mzrt_list>");
- //</quantify>
- _output_stream->writeEndElement();
+ //</quantify>
+ _output_stream->writeEndElement();
}
-void MassChroQml::writeQuantificationMethods() {
- //<quantification_methods>
- _output_stream->writeStartElement("quantification_methods");
- //<quantification_method id="my_qzivy">
- _output_stream->writeStartElement("quantification_method");
- _output_stream->writeAttribute("id","quant1");
- //<xic_extraction xic_type="sum">
- _output_stream->writeStartElement("xic_extraction");
- _output_stream->writeAttribute("xic_type","max");
- _output_stream->writeComment("max : XIC on BasePeak; sum : XIC on TIC");
- //<ppm_range min="10" max="10"/><!--For XIC extraction on Da use: mz_range-->
-
-
- _output_stream->writeComment("For XIC extraction on Da use: mz_range");
- _output_stream->writeStartElement("ppm_range");
- _output_stream->writeAttribute("min","10");
- _output_stream->writeAttribute("max","10");
- _output_stream->writeEndElement();
- //</xic_extraction>
- _output_stream->writeEndElement();
- //<xic_filters>
- _output_stream->writeStartElement("xic_filters");
- //<anti_spike half="5"/>
- _output_stream->writeStartElement("anti_spike");
- _output_stream->writeAttribute("half","5");
- _output_stream->writeEndElement();
- //<background half_mediane="5" half_min_max="20"/>
- _output_stream->writeComment("<background half_mediane=\"5\" half_min_max=\"20\"/>");
- //</xic_filters>
- _output_stream->writeEndElement();
- //<peak_detection>
-
- _output_stream->writeStartElement("peak_detection");
- //<detection_zivy>
- _output_stream->writeStartElement("detection_zivy");
- //<mean_filter_half_edge>1</mean_filter_half_edge>
- _output_stream->writeStartElement("mean_filter_half_edge");
- _output_stream->writeCharacters(QString("%1").arg(_detect_zivy._smoothing_half_window));
- _output_stream->writeEndElement();
- //<minmax_half_edge>3</minmax_half_edge>
- _output_stream->writeStartElement("minmax_half_edge");
- _output_stream->writeCharacters(QString("%1").arg(_detect_zivy._minmax_half_window));
- _output_stream->writeEndElement();
- //<maxmin_half_edge>2</maxmin_half_edge>
- _output_stream->writeStartElement("maxmin_half_edge");
- _output_stream->writeCharacters(QString("%1").arg(_detect_zivy._maxmin_half_window));
- _output_stream->writeEndElement();
- //<detection_threshold_on_max>5000</detection_threshold_on_max>
- _output_stream->writeStartElement("detection_threshold_on_max");
- _output_stream->writeCharacters(QString("%1").arg(_detect_zivy._minmax_threshold));
- _output_stream->writeEndElement();
- //<detection_threshold_on_min>3000</detection_threshold_on_min>
- _output_stream->writeStartElement("detection_threshold_on_min");
- _output_stream->writeCharacters(QString("%1").arg(_detect_zivy._maxmin_threshold));
- _output_stream->writeEndElement();
- //</detection_zivy>
- _output_stream->writeEndElement();
- //</peak_detection>
-
- _output_stream->writeEndElement();
- //</quantification_method>
- _output_stream->writeEndElement();
- //</quantification_methods>
- _output_stream->writeEndElement();
+void
+MassChroQml::writeQuantificationMethods()
+{
+ //<quantification_methods>
+ _output_stream->writeStartElement("quantification_methods");
+ //<quantification_method id="my_qzivy">
+ _output_stream->writeStartElement("quantification_method");
+ _output_stream->writeAttribute("id", "quant1");
+ //<xic_extraction xic_type="sum">
+ _output_stream->writeStartElement("xic_extraction");
+ _output_stream->writeAttribute("xic_type", "max");
+ _output_stream->writeComment("max : XIC on BasePeak; sum : XIC on TIC");
+ //<ppm_range min="10" max="10"/><!--For XIC extraction on Da use: mz_range-->
+
+
+ _output_stream->writeComment("For XIC extraction on Da use: mz_range");
+ _output_stream->writeStartElement("ppm_range");
+ _output_stream->writeAttribute("min", "10");
+ _output_stream->writeAttribute("max", "10");
+ _output_stream->writeEndElement();
+ //</xic_extraction>
+ _output_stream->writeEndElement();
+ //<xic_filters>
+ _output_stream->writeStartElement("xic_filters");
+ //<anti_spike half="5"/>
+ _output_stream->writeStartElement("anti_spike");
+ _output_stream->writeAttribute("half", "5");
+ _output_stream->writeEndElement();
+ //<background half_mediane="5" half_min_max="20"/>
+ _output_stream->writeComment(
+ "<background half_mediane=\"5\" half_min_max=\"20\"/>");
+ //</xic_filters>
+ _output_stream->writeEndElement();
+ //<peak_detection>
+
+ _output_stream->writeStartElement("peak_detection");
+ //<detection_zivy>
+ _output_stream->writeStartElement("detection_zivy");
+ //<mean_filter_half_edge>1</mean_filter_half_edge>
+ _output_stream->writeStartElement("mean_filter_half_edge");
+ _output_stream->writeCharacters(
+ QString("%1").arg(_detect_zivy._smoothing_half_window));
+ _output_stream->writeEndElement();
+ //<minmax_half_edge>3</minmax_half_edge>
+ _output_stream->writeStartElement("minmax_half_edge");
+ _output_stream->writeCharacters(
+ QString("%1").arg(_detect_zivy._minmax_half_window));
+ _output_stream->writeEndElement();
+ //<maxmin_half_edge>2</maxmin_half_edge>
+ _output_stream->writeStartElement("maxmin_half_edge");
+ _output_stream->writeCharacters(
+ QString("%1").arg(_detect_zivy._maxmin_half_window));
+ _output_stream->writeEndElement();
+ //<detection_threshold_on_max>5000</detection_threshold_on_max>
+ _output_stream->writeStartElement("detection_threshold_on_max");
+ _output_stream->writeCharacters(
+ QString("%1").arg(_detect_zivy._minmax_threshold));
+ _output_stream->writeEndElement();
+ //<detection_threshold_on_min>3000</detection_threshold_on_min>
+ _output_stream->writeStartElement("detection_threshold_on_min");
+ _output_stream->writeCharacters(
+ QString("%1").arg(_detect_zivy._maxmin_threshold));
+ _output_stream->writeEndElement();
+ //</detection_zivy>
+ _output_stream->writeEndElement();
+ //</peak_detection>
+
+ _output_stream->writeEndElement();
+ //</quantification_method>
+ _output_stream->writeEndElement();
+ //</quantification_methods>
+ _output_stream->writeEndElement();
}
-void MassChroQml::writeAlignments() {
- //<alignments>
- _output_stream->writeStartElement("alignments");
- //<alignment_methods>
- _output_stream->writeStartElement("alignment_methods");
- //<alignment_method id="my_ms2">
- _output_stream->writeStartElement("alignment_method");
- _output_stream->writeAttribute("id","my_ms2");
-
- //<ms2><!-- write_time_values_output_dir="directory" to write retention time corrections -->
-
- _output_stream->writeStartElement("ms2");
- _output_stream->writeComment("write_time_values_output_dir=\"directory\" to write retention time corrections");
- //<ms2_tendency_halfwindow>10</ms2_tendency_halfwindow>
- _output_stream->writeStartElement("ms2_tendency_halfwindow");
- _output_stream->writeCharacters("10");
- _output_stream->writeEndElement();
- //<ms2_smoothing_halfwindow>5</ms2_smoothing_halfwindow>
-
- _output_stream->writeStartElement("ms2_smoothing_halfwindow");
- _output_stream->writeCharacters("15");
- _output_stream->writeEndElement();
- //<ms1_smoothing_halfwindow>3</ms1_smoothing_halfwindow>
-
- _output_stream->writeStartElement("ms1_smoothing_halfwindow");
- _output_stream->writeCharacters("0");
- _output_stream->writeEndElement();
- //</ms2>
- _output_stream->writeEndElement();
- //</alignment_method>
- _output_stream->writeEndElement();
- _output_stream->writeComment("<alignment_method id=\"my_obiwarp\"> \n<obiwarp>\n <lmat_precision>1</lmat_precision>\n <mz_start>500</mz_start>\n <mz_stop>1200</mz_stop>\n </obiwarp>\n </alignment_method>");
- //</alignment_methods>
- _output_stream->writeEndElement();
- //<align group_id="G1" method_id="my_ms2" reference_data_id="samp0" />
- //<align group_id="G2" method_id="my_obiwarp" reference_data_id="samp2" />
- _output_stream->writeStartElement("align");
- _output_stream->writeAttribute("group_id","fractiona1");
- _output_stream->writeAttribute("method_id","my_ms2");
- _output_stream->writeAttribute("reference_data_id","msruna1");
- _output_stream->writeEndElement();
- //</alignments>
- _output_stream->writeEndElement();
+void
+MassChroQml::writeAlignments()
+{
+ //<alignments>
+ _output_stream->writeStartElement("alignments");
+ //<alignment_methods>
+ _output_stream->writeStartElement("alignment_methods");
+ //<alignment_method id="my_ms2">
+ _output_stream->writeStartElement("alignment_method");
+ _output_stream->writeAttribute("id", "my_ms2");
+
+ //<ms2><!-- write_time_values_output_dir="directory" to write retention time
+ //corrections -->
+
+ _output_stream->writeStartElement("ms2");
+ _output_stream->writeComment("write_time_values_output_dir=\"directory\" to "
+ "write retention time corrections");
+ //<ms2_tendency_halfwindow>10</ms2_tendency_halfwindow>
+ _output_stream->writeStartElement("ms2_tendency_halfwindow");
+ _output_stream->writeCharacters("10");
+ _output_stream->writeEndElement();
+ //<ms2_smoothing_halfwindow>5</ms2_smoothing_halfwindow>
+
+ _output_stream->writeStartElement("ms2_smoothing_halfwindow");
+ _output_stream->writeCharacters("15");
+ _output_stream->writeEndElement();
+ //<ms1_smoothing_halfwindow>3</ms1_smoothing_halfwindow>
+
+ _output_stream->writeStartElement("ms1_smoothing_halfwindow");
+ _output_stream->writeCharacters("0");
+ _output_stream->writeEndElement();
+ //</ms2>
+ _output_stream->writeEndElement();
+ //</alignment_method>
+ _output_stream->writeEndElement();
+ _output_stream->writeComment(
+ "<alignment_method id=\"my_obiwarp\"> \n<obiwarp>\n "
+ "<lmat_precision>1</lmat_precision>\n <mz_start>500</mz_start>\n "
+ " <mz_stop>1200</mz_stop>\n </obiwarp>\n "
+ "</alignment_method>");
+ //</alignment_methods>
+ _output_stream->writeEndElement();
+ //<align group_id="G1" method_id="my_ms2" reference_data_id="samp0" />
+ //<align group_id="G2" method_id="my_obiwarp" reference_data_id="samp2" />
+ _output_stream->writeStartElement("align");
+ _output_stream->writeAttribute("group_id", "fractiona1");
+ _output_stream->writeAttribute("method_id", "my_ms2");
+ _output_stream->writeAttribute("reference_data_id", "msruna1");
+ _output_stream->writeEndElement();
+ //</alignments>
+ _output_stream->writeEndElement();
}
-void MassChroQml::writeIsotopeLabelList() {
- LabelingMethod * p_labeling_method = _sp_project.get()->getLabelingMethodSp().get();
- if (p_labeling_method != nullptr) {
- //<isotope_label_list>
- p_labeling_method->writeMassChroqMl(_output_stream);
+void
+MassChroQml::writeIsotopeLabelList()
+{
+ LabelingMethod *p_labeling_method =
+ _sp_project.get()->getLabelingMethodSp().get();
+ if(p_labeling_method != nullptr)
+ {
+ //<isotope_label_list>
+ p_labeling_method->writeMassChroqMl(_output_stream);
}
}
-void MassChroQml::writePeptideList() {
-//<peptide_list>
- _output_stream->writeStartElement("peptide_list");
- const std::map<unsigned int, GroupingGroupSp> & group_store = _p_identification_group->getGroupStore().getGroupMap();
+void
+MassChroQml::writePeptideList()
+{
+ //<peptide_list>
+ _output_stream->writeStartElement("peptide_list");
+ const std::map<unsigned int, GroupingGroupSp> &group_store =
+ _p_identification_group->getGroupStore().getGroupMap();
- for (auto & group_pair :group_store) {
- writePeptideListInGroup(group_pair.second.get());
+ for(auto &group_pair : group_store)
+ {
+ writePeptideListInGroup(group_pair.second.get());
}
- //</peptide_list>
- _output_stream->writeEndElement();
+ //</peptide_list>
+ _output_stream->writeEndElement();
}
-void MassChroQml::writePeptideListInGroup(const GroupingGroup * p_group) {
-
- const std::vector<std::pair<unsigned int, const PeptideEvidence *>> & sg_peptide_evidence_list = p_group->getPairSgNumberPeptideEvidenceList();
- std::vector<McqPeptide> mcq_peptide_list;
-
- for (auto & sg_peptide_pair :sg_peptide_evidence_list) {
- unsigned int sg_number = sg_peptide_pair.first;
- const PeptideEvidence * peptide_evidence = sg_peptide_pair.second;
-
- McqPeptide mcq_peptide;
- mcq_peptide.id = peptide_evidence->getGrpPeptideSp().get()->getGroupingId();
- mcq_peptide.mods << peptide_evidence->getPeptideXtpSp().get()->getModifString();
- mcq_peptide.prot_ids << p_group->getProteinGroupingIdOfSubgroup(sg_number);
- mcq_peptide.seq = peptide_evidence->getPeptideXtpSp().get()->getSequence();
- mcq_peptide.native_peptide = peptide_evidence->getPeptideXtpSp().get()->getNativePeptideP();
- McqObserved observed = {peptide_evidence->getMsRunP(),peptide_evidence->getScan(),peptide_evidence->getCharge() };
- mcq_peptide.observed_in.push_back(observed);
- mcq_peptide_list.push_back(mcq_peptide);
+void
+MassChroQml::writePeptideListInGroup(const GroupingGroup *p_group)
+{
+ const std::vector<std::pair<unsigned int, const PeptideEvidence *>>
+ &sg_peptide_evidence_list = p_group->getPairSgNumberPeptideEvidenceList();
+ std::vector<McqPeptide> mcq_peptide_list;
+ for(auto &sg_peptide_pair : sg_peptide_evidence_list)
+ {
+ unsigned int sg_number = sg_peptide_pair.first;
+ const PeptideEvidence *peptide_evidence = sg_peptide_pair.second;
+
+ McqPeptide mcq_peptide;
+ mcq_peptide.id =
+ peptide_evidence->getGrpPeptideSp().get()->getGroupingId();
+ mcq_peptide.mods
+ << peptide_evidence->getPeptideXtpSp().get()->getModifString();
+ mcq_peptide.prot_ids << p_group->getProteinGroupingIdOfSubgroup(
+ sg_number);
+ mcq_peptide.seq =
+ peptide_evidence->getPeptideXtpSp().get()->getSequence();
+ mcq_peptide.native_peptide =
+ peptide_evidence->getPeptideXtpSp().get()->getNativePeptideP();
+ McqObserved observed = {peptide_evidence->getMsRunP(),
+ peptide_evidence->getScan(),
+ peptide_evidence->getCharge()};
+ mcq_peptide.observed_in.push_back(observed);
+ mcq_peptide_list.push_back(mcq_peptide);
}
- //sort list
- std::sort(mcq_peptide_list.begin(),mcq_peptide_list.end(),[](const McqPeptide & first, const McqPeptide & second) {
- return (first.id < second.id) ;
- });
+ // sort list
+ std::sort(mcq_peptide_list.begin(), mcq_peptide_list.end(),
+ [](const McqPeptide &first, const McqPeptide &second) {
+ return (first.id < second.id);
+ });
- std::vector<McqPeptide> cumul_mcq_peptide_list;
- if (mcq_peptide_list.size() > 0) {
- McqPeptide cumul = mcq_peptide_list[0];
- for (McqPeptide & mcq_peptide : mcq_peptide_list) {
- if (cumul.id == mcq_peptide.id) {
+ std::vector<McqPeptide> cumul_mcq_peptide_list;
+ if(mcq_peptide_list.size() > 0)
+ {
+ McqPeptide cumul = mcq_peptide_list[0];
+ for(McqPeptide &mcq_peptide : mcq_peptide_list)
+ {
+ if(cumul.id == mcq_peptide.id)
+ {
- cumul.observed_in.push_back(mcq_peptide.observed_in[0]);
+ cumul.observed_in.push_back(mcq_peptide.observed_in[0]);
- if (!cumul.prot_ids.contains(mcq_peptide.prot_ids[0])) {
- cumul.prot_ids << mcq_peptide.prot_ids[0];
+ if(!cumul.prot_ids.contains(mcq_peptide.prot_ids[0]))
+ {
+ cumul.prot_ids << mcq_peptide.prot_ids[0];
}
- if (!cumul.mods.contains(mcq_peptide.mods[0])) {
- cumul.mods << mcq_peptide.mods[0];
+ if(!cumul.mods.contains(mcq_peptide.mods[0]))
+ {
+ cumul.mods << mcq_peptide.mods[0];
}
}
- else {
- cumul_mcq_peptide_list.push_back(cumul);
- cumul = mcq_peptide;
+ else
+ {
+ cumul_mcq_peptide_list.push_back(cumul);
+ cumul = mcq_peptide;
}
}
- cumul_mcq_peptide_list.push_back(cumul);
+ cumul_mcq_peptide_list.push_back(cumul);
}
- for (McqPeptide mcq_peptide : cumul_mcq_peptide_list) {
- //<peptide id="pep0" mh="1463.626" mods="114.08" prot_ids="P1.1"
- // seq="TCVADESHAGCEK">
- _output_stream->writeStartElement("peptide");
- _output_stream->writeAttribute("id",mcq_peptide.id);
- _output_stream->writeAttribute("mods",mcq_peptide.mods.join("|"));
- _output_stream->writeAttribute("prot_ids",mcq_peptide.prot_ids.join(" "));
- _output_stream->writeAttribute("mh",QString::number(mcq_peptide.native_peptide->getMz(1), 'f', 10));
- _output_stream->writeAttribute("seq",mcq_peptide.seq);
-
- //<modifications><!-- this tag is optional but gives an exact mass computation -->
- std::vector<McqPsimod> mod_list;
- unsigned int pos=1;
- for (const pappso::Aa & aa: *(mcq_peptide.native_peptide)) {
- const std::list<pappso::AaModificationP> aa_mod_list = aa.getModificationList();
- for (pappso::AaModificationP mod : aa_mod_list) {
- if (!mod->isInternal()) {
- McqPsimod psimod;
- psimod.accession = mod->getAccession();
- psimod.at = pos;
- mod_list.push_back(psimod);
+ for(McqPeptide mcq_peptide : cumul_mcq_peptide_list)
+ {
+ //<peptide id="pep0" mh="1463.626" mods="114.08" prot_ids="P1.1"
+ // seq="TCVADESHAGCEK">
+ _output_stream->writeStartElement("peptide");
+ _output_stream->writeAttribute("id", mcq_peptide.id);
+ _output_stream->writeAttribute("mods", mcq_peptide.mods.join("|"));
+ _output_stream->writeAttribute("prot_ids",
+ mcq_peptide.prot_ids.join(" "));
+ _output_stream->writeAttribute(
+ "mh", QString::number(mcq_peptide.native_peptide->getMz(1), 'f', 10));
+ _output_stream->writeAttribute("seq", mcq_peptide.seq);
+
+ //<modifications><!-- this tag is optional but gives an exact mass
+ //computation -->
+ std::vector<McqPsimod> mod_list;
+ unsigned int pos = 1;
+ for(const pappso::Aa &aa : *(mcq_peptide.native_peptide))
+ {
+ const std::list<pappso::AaModificationP> aa_mod_list =
+ aa.getModificationList();
+ for(pappso::AaModificationP mod : aa_mod_list)
+ {
+ if(!mod->isInternal())
+ {
+ McqPsimod psimod;
+ psimod.accession = mod->getAccession();
+ psimod.at = pos;
+ mod_list.push_back(psimod);
}
}
- pos++;
+ pos++;
}
- if (mod_list.size() > 0) {
- _output_stream->writeStartElement("modifications");
- for (McqPsimod & psimod :mod_list) {
- //<psimod at="2" acc="MOD:00397"></psimod>
- _output_stream->writeStartElement("psimod");
- _output_stream->writeAttribute("at",QString("%1").arg(psimod.at));
- _output_stream->writeAttribute("acc",psimod.accession);
- //<psimod at="11" acc="MOD:00397"></psimod>
- _output_stream->writeEndElement();
+ if(mod_list.size() > 0)
+ {
+ _output_stream->writeStartElement("modifications");
+ for(McqPsimod &psimod : mod_list)
+ {
+ //<psimod at="2" acc="MOD:00397"></psimod>
+ _output_stream->writeStartElement("psimod");
+ _output_stream->writeAttribute("at",
+ QString("%1").arg(psimod.at));
+ _output_stream->writeAttribute("acc", psimod.accession);
+ //<psimod at="11" acc="MOD:00397"></psimod>
+ _output_stream->writeEndElement();
}
- //</modifications>
- _output_stream->writeEndElement();
+ //</modifications>
+ _output_stream->writeEndElement();
}
- //<observed_in data="samp0" scan="655" z="2" />
- std::sort(mcq_peptide.observed_in.begin(), mcq_peptide.observed_in.end(),[](const McqObserved & first, const McqObserved & second) {
- return std::tie(first.charge, first.scan, first.msrun) < std::tie(second.charge, second.scan, second.msrun);
- });
- auto last = std::unique(mcq_peptide.observed_in.begin(), mcq_peptide.observed_in.end());
- mcq_peptide.observed_in.erase(last, mcq_peptide.observed_in.end());
-
- for (McqObserved observed_in : mcq_peptide.observed_in) {
- _output_stream->writeStartElement("observed_in");
- _output_stream->writeAttribute("data",observed_in.msrun->getXmlId());
- _output_stream->writeAttribute("scan",QString("%1").arg(observed_in.scan));
- _output_stream->writeAttribute("z",QString("%1").arg(observed_in.charge));
- _output_stream->writeEndElement();
+ //<observed_in data="samp0" scan="655" z="2" />
+ std::sort(mcq_peptide.observed_in.begin(), mcq_peptide.observed_in.end(),
+ [](const McqObserved &first, const McqObserved &second) {
+ return std::tie(first.charge, first.scan, first.msrun) <
+ std::tie(second.charge, second.scan, second.msrun);
+ });
+ auto last = std::unique(mcq_peptide.observed_in.begin(),
+ mcq_peptide.observed_in.end());
+ mcq_peptide.observed_in.erase(last, mcq_peptide.observed_in.end());
+
+ for(McqObserved observed_in : mcq_peptide.observed_in)
+ {
+ _output_stream->writeStartElement("observed_in");
+ _output_stream->writeAttribute("data", observed_in.msrun->getXmlId());
+ _output_stream->writeAttribute("scan",
+ QString("%1").arg(observed_in.scan));
+ _output_stream->writeAttribute("z",
+ QString("%1").arg(observed_in.charge));
+ _output_stream->writeEndElement();
}
- //<observed_in data="samp1" scan="798" z="2" />*/
- //</peptide>
- _output_stream->writeEndElement();
+ //<observed_in data="samp1" scan="798" z="2" />*/
+ //</peptide>
+ _output_stream->writeEndElement();
}
}
-void MassChroQml::writeGroups() {
-//<groups>
- _output_stream->writeStartElement("groups");
- //<group data_ids="samp0 samp1" id="G1" />
- _output_stream->writeStartElement("group");
- _output_stream->writeAttribute("id",QString("fractiona1"));
- std::vector<MsRunSp> msrun_list = _sp_project.get()->getMsRunStore().getMsRunList();
- QStringList list;
- for (MsRunSp & msrun : msrun_list) {
- list << msrun.get()->getXmlId();
+void
+MassChroQml::writeGroups()
+{
+ //<groups>
+ _output_stream->writeStartElement("groups");
+ //<group data_ids="samp0 samp1" id="G1" />
+ _output_stream->writeStartElement("group");
+ _output_stream->writeAttribute("id", QString("fractiona1"));
+ std::vector<MsRunSp> msrun_list =
+ _sp_project.get()->getMsRunStore().getMsRunList();
+ QStringList list;
+ for(MsRunSp &msrun : msrun_list)
+ {
+ list << msrun.get()->getXmlId();
}
- _output_stream->writeAttribute("data_ids",list.join(" "));
- _output_stream->writeEndElement();
- //<group data_ids="samp2 samp3" id="G2" />
-// </groups>
- _output_stream->writeEndElement();
+ _output_stream->writeAttribute("data_ids", list.join(" "));
+ _output_stream->writeEndElement();
+ //<group data_ids="samp2 samp3" id="G2" />
+ // </groups>
+ _output_stream->writeEndElement();
}
-void MassChroQml::writeProteinList() {
-//<protein_list>
- _output_stream->writeStartElement("protein_list");
- std::vector<IdentificationGroup *> identification_list = _sp_project.get()->getIdentificationGroupList();
- if (identification_list.size() == 0) {
- throw pappso::PappsoException(QObject::tr("Error writing MassChroqML file :\n no protein list"));
+void
+MassChroQml::writeProteinList()
+{
+ //<protein_list>
+ _output_stream->writeStartElement("protein_list");
+ std::vector<IdentificationGroup *> identification_list =
+ _sp_project.get()->getIdentificationGroupList();
+ if(identification_list.size() == 0)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error writing MassChroqML file :\n no protein list"));
}
- if (identification_list.size() > 1) {
- throw pappso::PappsoException(QObject::tr("Error writing MassChroqML file :\n only available in combine mode"));
+ if(identification_list.size() > 1)
+ {
+ throw pappso::PappsoException(QObject::tr(
+ "Error writing MassChroqML file :\n only available in combine mode"));
}
- _p_identification_group = identification_list[0];
- for (ProteinMatch * p_protein_match :_p_identification_group->getProteinMatchList()) {
- if (!p_protein_match->isGrouped()) continue;
- //<protein desc="conta|P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
- // id="P1.1" />
- pappso::GrpProteinSp grp_protein = p_protein_match->getGrpProteinSp();
- if (grp_protein.get()->getRank() == 1) {
- _output_stream->writeStartElement("protein");
- _output_stream->writeAttribute("id",grp_protein.get()->getGroupingId());
- QStringList list;
- list << p_protein_match->getProteinXtpSp().get()->getAccession();
- list << p_protein_match->getProteinXtpSp().get()->getDescription();
- _output_stream->writeAttribute("desc",list.join(" "));
- //<protein desc="conta|P02770|ALBU_RAT SERUM ALBUMIN PRECURSOR."
- // id="P1.2" />
- _output_stream->writeEndElement();
+ _p_identification_group = identification_list[0];
+ for(ProteinMatch *p_protein_match :
+ _p_identification_group->getProteinMatchList())
+ {
+ if(!p_protein_match->isGrouped())
+ continue;
+ //<protein desc="conta|P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
+ // id="P1.1" />
+ pappso::GrpProteinSp grp_protein = p_protein_match->getGrpProteinSp();
+ if(grp_protein.get()->getRank() == 1)
+ {
+ _output_stream->writeStartElement("protein");
+ _output_stream->writeAttribute("id",
+ grp_protein.get()->getGroupingId());
+ QStringList list;
+ list << p_protein_match->getProteinXtpSp().get()->getAccession();
+ list << p_protein_match->getProteinXtpSp().get()->getDescription();
+ _output_stream->writeAttribute("desc", list.join(" "));
+ //<protein desc="conta|P02770|ALBU_RAT SERUM ALBUMIN PRECURSOR."
+ // id="P1.2" />
+ _output_stream->writeEndElement();
}
}
- //</protein_list>
- _output_stream->writeEndElement();
+ //</protein_list>
+ _output_stream->writeEndElement();
}
diff --git a/src/output/masschroqml.h b/src/output/masschroqml.h
index d46ce93ff91add2ee3b4e251f30f6087dca594b6..bfe3226901c8ec903f263a647736617322c770d7 100644
--- a/src/output/masschroqml.h
+++ b/src/output/masschroqml.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef MASSCHROQML_H
#define MASSCHROQML_H
@@ -40,30 +41,31 @@
class MassChroQml
{
- public:
- MassChroQml(const QString & out_filename);
- ~MassChroQml();
+ public:
+ MassChroQml(const QString &out_filename);
+ ~MassChroQml();
- void write(ProjectSp sp_project);
- void close();
-private:
- void writeGroups();
- void writeProteinList();
- void writePeptideList();
- void writePeptideListInGroup(const GroupingGroup * p_group);
- void writeIsotopeLabelList();
- void writeAlignments();
- void writeQuantificationMethods();
- void writeQuantificationResults();
- void writeQuantificationTraces();
- void writeQuantify();
-
-private :
- QFile * _output_file;
- QXmlStreamWriter * _output_stream;
- ProjectSp _sp_project;
- IdentificationGroup * _p_identification_group;
- ZivyParams _detect_zivy;
+ void write(ProjectSp sp_project);
+ void close();
+
+ private:
+ void writeGroups();
+ void writeProteinList();
+ void writePeptideList();
+ void writePeptideListInGroup(const GroupingGroup *p_group);
+ void writeIsotopeLabelList();
+ void writeAlignments();
+ void writeQuantificationMethods();
+ void writeQuantificationResults();
+ void writeQuantificationTraces();
+ void writeQuantify();
+
+ private:
+ QFile *_output_file;
+ QXmlStreamWriter *_output_stream;
+ ProjectSp _sp_project;
+ IdentificationGroup *_p_identification_group;
+ ZivyParams _detect_zivy;
};
#endif // MASSCHROQML_H
diff --git a/src/output/masschroqprm.cpp b/src/output/masschroqprm.cpp
index 8f5c272c972aae4183616952d27229a0107d21be..3bd5d50f0de3cdda761445b1e6642e1985a0b187 100644
--- a/src/output/masschroqprm.cpp
+++ b/src/output/masschroqprm.cpp
@@ -6,159 +6,199 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "masschroqprm.h"
#include <pappsomspp/pappsoexception.h>
#include <pappsomspp/utils.h>
-MassChroqPrm::MassChroqPrm(const QString & out_filename) {
- //_p_digestion_pipeline = p_digestion_pipeline;
+MassChroqPrm::MassChroqPrm(const QString &out_filename)
+{
+ //_p_digestion_pipeline = p_digestion_pipeline;
- //_mzidentml = "http://psidev.info/psi/pi/mzIdentML/1.1";
- QString complete_out_filename = out_filename;
- _output_file = new QFile(complete_out_filename);
+ //_mzidentml = "http://psidev.info/psi/pi/mzIdentML/1.1";
+ QString complete_out_filename = out_filename;
+ _output_file = new QFile(complete_out_filename);
- if (_output_file->open(QIODevice::WriteOnly))
+ if(_output_file->open(QIODevice::WriteOnly))
{
- _output_stream = new QXmlStreamWriter();
- _output_stream->setDevice(_output_file);
- } else
+ _output_stream = new QXmlStreamWriter();
+ _output_stream->setDevice(_output_file);
+ }
+ else
{
- throw pappso::PappsoException(QObject::tr("error : cannot open the MassChroqPRM output file : %1\n").arg(out_filename));
+ throw pappso::PappsoException(
+ QObject::tr("error : cannot open the MassChroqPRM output file : %1\n")
+ .arg(out_filename));
}
- _output_stream->setAutoFormatting(true);
- _output_stream->writeStartDocument("1.0");
-
-
+ _output_stream->setAutoFormatting(true);
+ _output_stream->writeStartDocument("1.0");
}
MassChroqPrm::~MassChroqPrm()
{
- delete _output_file;
- delete _output_stream;
+ delete _output_file;
+ delete _output_stream;
}
-void MassChroqPrm::close() {
- _output_stream->writeEndDocument();
- _output_file->close();
+void
+MassChroqPrm::close()
+{
+ _output_stream->writeEndDocument();
+ _output_file->close();
}
-void MassChroqPrm::write(ProjectSp sp_project) {
+void
+MassChroqPrm::write(ProjectSp sp_project)
+{
- _sp_project = sp_project;
- if (_sp_project.get() == nullptr) {
- throw pappso::PappsoException(QObject::tr("Error writing MassChroqPRM file :\n project is empty"));
+ _sp_project = sp_project;
+ if(_sp_project.get() == nullptr)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error writing MassChroqPRM file :\n project is empty"));
}
- //<masschroq>
- _output_stream->writeStartElement("masschroqprm");
- /*
- *
- <parameters>
- <parentIonMassTolerance>
- <daltonPrecision value="1.5"/>
- </parentIonMassTolerance>
- <fragmentIonMassTolerance>
- <daltonPrecision value="0.02"/>
- </fragmentIonMassTolerance>
- </parameters>
- */
- _output_stream->writeStartElement("parameters");
- _output_stream->writeStartElement("parentIonMassTolerance");
- _output_stream->writeComment("choose dalton or ppm mass precision to select parent ions based on the precursor mass of each MS/MS spectrum");
- _output_stream->writeStartElement("ppmPrecision");
- _output_stream->writeAttribute("value", "10");
- _output_stream->writeEndElement();
- _output_stream->writeEndElement();
- _output_stream->writeStartElement("fragmentIonMassTolerance");
- _output_stream->writeComment("choose dalton or ppm mass precision to MS/MS fragment ion observed mass with theoretical mass");
- _output_stream->writeStartElement("daltonPrecision");
- _output_stream->writeAttribute("value", "0.02");
- _output_stream->writeEndElement();
- _output_stream->writeEndElement();
- _output_stream->writeEndElement();
-
- writePeptides();
+ //<masschroq>
+ _output_stream->writeStartElement("masschroqprm");
+ /*
+ *
+ <parameters>
+ <parentIonMassTolerance>
+ <daltonPrecision value="1.5"/>
+ </parentIonMassTolerance>
+ <fragmentIonMassTolerance>
+ <daltonPrecision value="0.02"/>
+ </fragmentIonMassTolerance>
+ </parameters>
+ */
+ _output_stream->writeStartElement("parameters");
+ _output_stream->writeStartElement("parentIonMassTolerance");
+ _output_stream->writeComment(
+ "choose dalton or ppm mass precision to select parent ions based on the "
+ "precursor mass of each MS/MS spectrum");
+ _output_stream->writeStartElement("ppmPrecision");
+ _output_stream->writeAttribute("value", "10");
+ _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
+ _output_stream->writeStartElement("fragmentIonMassTolerance");
+ _output_stream->writeComment(
+ "choose dalton or ppm mass precision to MS/MS fragment ion observed mass "
+ "with theoretical mass");
+ _output_stream->writeStartElement("daltonPrecision");
+ _output_stream->writeAttribute("value", "0.02");
+ _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
+
+ writePeptides();
}
-void MassChroqPrm::writePeptides() {
-
- /*
- *
- *
- * <peptide seq="TCVADESHAGCEK" id="p1"> <psimod at="2"
- * acc="MOD:00397"/> <psimod at="11" acc="MOD:00397"/> </peptide>
- */
- try {
-
- _output_stream->writeStartElement("peptideList");
-
- for (IdentificationDataSourceSp identification_data_source_sp :_sp_project.get()->getIdentificationDataSourceStore().getIdentificationDataSourceList()) {
- for (const PeptideEvidenceSp & peptide_evidence_sp: identification_data_source_sp.get()->getPeptideEvidenceStore().getPeptideEvidenceList()) {
- const pappso::GrpPeptide * p_grp_peptide =peptide_evidence_sp.get()->getGrpPeptideSp().get();
-
- if (p_grp_peptide != nullptr) {
- std::set<const pappso::GrpPeptide *> _already_writed;
- if (_already_writed.find(p_grp_peptide) == _already_writed.end()) {
- _already_writed.insert(p_grp_peptide);
- PeptideXtp * p_peptide = peptide_evidence_sp.get()->getPeptideXtpSp().get();
- _output_stream->writeStartElement("peptide");
- _output_stream->writeAttribute("id",p_grp_peptide->getGroupingId());
- _output_stream->writeAttribute("seq", p_peptide->getSequence());
-
-
- unsigned int i=0;
- for (const pappso::Aa & amino_acid: *p_peptide) {
-
- std::list<pappso::AaModificationP> aa_modif_list = amino_acid.getModificationList();
+void
+MassChroqPrm::writePeptides()
+{
+ /*
+ *
+ *
+ * <peptide seq="TCVADESHAGCEK" id="p1"> <psimod at="2"
+ * acc="MOD:00397"/> <psimod at="11" acc="MOD:00397"/> </peptide>
+ */
+ try
+ {
- for (auto && aa_modif : aa_modif_list) {
- if (!aa_modif->isInternal()) {
- _output_stream->writeStartElement("psimod");
- _output_stream->writeAttribute("acc", aa_modif->getAccession());
- _output_stream->writeAttribute("at", QString ("%1").arg(i));
- _output_stream->writeEndElement();// mod
+ _output_stream->writeStartElement("peptideList");
+
+ for(IdentificationDataSourceSp identification_data_source_sp :
+ _sp_project.get()
+ ->getIdentificationDataSourceStore()
+ .getIdentificationDataSourceList())
+ {
+ for(const PeptideEvidenceSp &peptide_evidence_sp :
+ identification_data_source_sp.get()
+ ->getPeptideEvidenceStore()
+ .getPeptideEvidenceList())
+ {
+ const pappso::GrpPeptide *p_grp_peptide =
+ peptide_evidence_sp.get()->getGrpPeptideSp().get();
+
+ if(p_grp_peptide != nullptr)
+ {
+ std::set<const pappso::GrpPeptide *> _already_writed;
+ if(_already_writed.find(p_grp_peptide) ==
+ _already_writed.end())
+ {
+ _already_writed.insert(p_grp_peptide);
+ PeptideXtp *p_peptide =
+ peptide_evidence_sp.get()->getPeptideXtpSp().get();
+ _output_stream->writeStartElement("peptide");
+ _output_stream->writeAttribute(
+ "id", p_grp_peptide->getGroupingId());
+ _output_stream->writeAttribute("seq",
+ p_peptide->getSequence());
+
+
+ unsigned int i = 0;
+ for(const pappso::Aa &amino_acid : *p_peptide)
+ {
+
+ std::list<pappso::AaModificationP> aa_modif_list =
+ amino_acid.getModificationList();
+
+
+ for(auto &&aa_modif : aa_modif_list)
+ {
+ if(!aa_modif->isInternal())
+ {
+ _output_stream->writeStartElement("psimod");
+ _output_stream->writeAttribute(
+ "acc", aa_modif->getAccession());
+ _output_stream->writeAttribute(
+ "at", QString("%1").arg(i));
+ _output_stream->writeEndElement(); // mod
}
}
- i++;
+ i++;
}
- _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
}
}
}
}
- //peptideList
- _output_stream->writeEndElement();
+ // peptideList
+ _output_stream->writeEndElement();
}
- catch (pappso::PappsoException &error)
+ catch(pappso::PappsoException &error)
{
- throw pappso::PappsoException(QObject::tr("Error in MassChroqPrm::writePeptides :\n%1").arg(error.qwhat()));
+ throw pappso::PappsoException(
+ QObject::tr("Error in MassChroqPrm::writePeptides :\n%1")
+ .arg(error.qwhat()));
}
- catch (std::exception &error)
+ catch(std::exception &error)
{
- throw pappso::PappsoException(QObject::tr("Error in MassChroqPrm::writePeptides stdex :\n%1").arg(error.what()));
+ throw pappso::PappsoException(
+ QObject::tr("Error in MassChroqPrm::writePeptides stdex :\n%1")
+ .arg(error.what()));
}
-
}
diff --git a/src/output/masschroqprm.h b/src/output/masschroqprm.h
index bc2e8e04c05ac89d4840c18626ee031482e68d0c..f3081a5e612c9dce09a4b852457dc83f47947996 100644
--- a/src/output/masschroqprm.h
+++ b/src/output/masschroqprm.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef MASSCHROQPRM_H
#define MASSCHROQPRM_H
@@ -38,20 +39,21 @@
class MassChroqPrm
{
- public:
- MassChroqPrm(const QString & out_filename);
- ~MassChroqPrm();
-
- void write(ProjectSp sp_project);
- void close();
-private:
- void writePeptides();
-
-private :
- QFile * _output_file;
- QXmlStreamWriter * _output_stream;
- ProjectSp _sp_project;
- IdentificationGroup * _p_identification_group;
+ public:
+ MassChroqPrm(const QString &out_filename);
+ ~MassChroqPrm();
+
+ void write(ProjectSp sp_project);
+ void close();
+
+ private:
+ void writePeptides();
+
+ private:
+ QFile *_output_file;
+ QXmlStreamWriter *_output_stream;
+ ProjectSp _sp_project;
+ IdentificationGroup *_p_identification_group;
};
#endif // MASSCHROQPRM_H
diff --git a/src/output/mcqr/mcqrscpeptide.cpp b/src/output/mcqr/mcqrscpeptide.cpp
index 1557a21e97d1d4829a5baa902b1c04fe023cc49c..e63951cc2beb35bcbb7ce8481b43b3771d03b25f 100644
--- a/src/output/mcqr/mcqrscpeptide.cpp
+++ b/src/output/mcqr/mcqrscpeptide.cpp
@@ -6,143 +6,195 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "mcqrscpeptide.h"
#include <pappsomspp/pappsoexception.h>
-bool ScPeptideLabel::operator<(const ScPeptideLabel& other) const {
- return tie(_p_grp_peptide, _p_label) < tie(other._p_grp_peptide, other._p_label) ;
+bool
+ScPeptideLabel::operator<(const ScPeptideLabel &other) const
+{
+ return tie(_p_grp_peptide, _p_label) <
+ tie(other._p_grp_peptide, other._p_label);
}
-McqRscPeptide::McqRscPeptide (CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
- _p_writer = p_writer;
+McqRscPeptide::McqRscPeptide(CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : _p_project(p_project)
+{
+ _p_writer = p_writer;
}
-void McqRscPeptide::writeSheet () {
- _p_writer->writeSheet("peptide_sc");
-
- std::vector<IdentificationGroup *> identification_list = _p_project->getIdentificationGroupList();
- if (identification_list.size() > 1) {
- throw pappso::PappsoException(QObject::tr("error : cannot write MassChroqR spectral count file in individual mode"));
+void
+McqRscPeptide::writeSheet()
+{
+ _p_writer->writeSheet("peptide_sc");
+
+ std::vector<IdentificationGroup *> identification_list =
+ _p_project->getIdentificationGroupList();
+ if(identification_list.size() > 1)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("error : cannot write MassChroqR spectral count file in "
+ "individual mode"));
}
- for (IdentificationGroup * p_ident:identification_list) {
- //writeHeaders(p_ident);
- writeIdentificationGroup(p_ident);
+ for(IdentificationGroup *p_ident : identification_list)
+ {
+ // writeHeaders(p_ident);
+ writeIdentificationGroup(p_ident);
}
}
-void McqRscPeptide::writeHeaders(IdentificationGroup * p_ident) {
-
-//ProteinID, msrun, msrunfile, accession, description, q
- _p_writer->writeCell("peptide");
- _p_writer->writeCell("label");
- _p_writer->writeCell("msrun");
- _p_writer->writeCell("msrunfile");
- //_p_writer->writeCell("sequence");
- _p_writer->writeCell("sc");
- //_p_writer->writeCell(p_protein_match->countSampleScan(state, p_msrun));
+void
+McqRscPeptide::writeHeaders(IdentificationGroup *p_ident)
+{
+ // ProteinID, msrun, msrunfile, accession, description, q
+ _p_writer->writeCell("peptide");
+ _p_writer->writeCell("label");
+ _p_writer->writeCell("msrun");
+ _p_writer->writeCell("msrunfile");
+ //_p_writer->writeCell("sequence");
+ _p_writer->writeCell("sc");
+ //_p_writer->writeCell(p_protein_match->countSampleScan(state, p_msrun));
}
+void
+McqRscPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
+{
+ ValidationState validation_state = ValidationState::grouped;
-void McqRscPeptide::writeIdentificationGroup(IdentificationGroup * p_ident) {
- ValidationState validation_state = ValidationState::grouped;
+ std::vector<MsRunSp> ms_run_sp_list = p_ident->getMsRunSpList();
+ writeHeaders(p_ident);
+ for(const std::pair<unsigned int, GroupingGroupSp> &group_pair :
+ p_ident->getGroupStore().getGroupMap())
+ {
- std::vector<MsRunSp> ms_run_sp_list = p_ident->getMsRunSpList();
- writeHeaders(p_ident);
- for (const std::pair<unsigned int, GroupingGroupSp> & group_pair : p_ident->getGroupStore().getGroupMap()) {
+ std::vector<const ProteinMatch *> protein_match_list =
+ group_pair.second.get()->getProteinMatchList();
- std::vector<const ProteinMatch *> protein_match_list = group_pair.second.get()->getProteinMatchList();
+ std::sort(protein_match_list.begin(), protein_match_list.end(),
+ [](const ProteinMatch *a, const ProteinMatch *b) {
+ return a->getGrpProteinSp().get()->getSubGroupNumber() <
+ b->getGrpProteinSp().get()->getSubGroupNumber();
+ });
- std::sort(protein_match_list.begin(), protein_match_list.end(),
- [](const ProteinMatch * a, const ProteinMatch * b)
+ for(auto &protein_match : protein_match_list)
{
- return a->getGrpProteinSp().get()->getSubGroupNumber() < b->getGrpProteinSp().get()->getSubGroupNumber();
- });
- for (auto & protein_match:protein_match_list) {
-
- //count number of scan fore each GrpPeptide
- std::map<ScPeptideLabel, std::size_t> count_scan_zero;
- for (const PeptideMatch & peptide_match:protein_match->getPeptideMatchList(validation_state) ) {
- count_scan_zero.insert ( std::pair<ScPeptideLabel, std::size_t>({peptide_match.getPeptideEvidence()->getGrpPeptideSp().get(), peptide_match.getPeptideEvidence()->getPeptideXtpSp()->getLabel()},0) );
+ // count number of scan fore each GrpPeptide
+ std::map<ScPeptideLabel, std::size_t> count_scan_zero;
+ for(const PeptideMatch &peptide_match :
+ protein_match->getPeptideMatchList(validation_state))
+ {
+ count_scan_zero.insert(std::pair<ScPeptideLabel, std::size_t>(
+ {peptide_match.getPeptideEvidence()->getGrpPeptideSp().get(),
+ peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ ->getLabel()},
+ 0));
}
- for (auto & msrun_sp : ms_run_sp_list) {
- std::vector<PeptideMatch> peptide_match_in_msrun = protein_match->getPeptideMatchList(validation_state, msrun_sp.get());
- writePeptidesInMsrun(msrun_sp.get(), peptide_match_in_msrun, count_scan_zero);
+ for(auto &msrun_sp : ms_run_sp_list)
+ {
+ std::vector<PeptideMatch> peptide_match_in_msrun =
+ protein_match->getPeptideMatchList(validation_state,
+ msrun_sp.get());
+ writePeptidesInMsrun(msrun_sp.get(), peptide_match_in_msrun,
+ count_scan_zero);
}
}
-
}
- _p_writer->writeLine();
+ _p_writer->writeLine();
}
-void McqRscPeptide::writePeptidesInMsrun(const MsRun * p_msrun,const std::vector<PeptideMatch> & peptide_match_in_msrun, const std::map<ScPeptideLabel, std::size_t> & count_scan_zero) {
- try {
+void
+McqRscPeptide::writePeptidesInMsrun(
+ const MsRun *p_msrun, const std::vector<PeptideMatch> &peptide_match_in_msrun,
+ const std::map<ScPeptideLabel, std::size_t> &count_scan_zero)
+{
+ try
+ {
- qDebug() << "McqRscPeptide::writePeptidesInMsrun begin" ;
- //count number of scan fore each GrpPeptide
- std::map<ScPeptideLabel, std::size_t> count_scan(count_scan_zero);
+ qDebug() << "McqRscPeptide::writePeptidesInMsrun begin";
+ // count number of scan fore each GrpPeptide
+ std::map<ScPeptideLabel, std::size_t> count_scan(count_scan_zero);
- for (const PeptideMatch & peptide_match:peptide_match_in_msrun) {
- std::pair<std::map<ScPeptideLabel, std::size_t>::iterator,bool> ret;
- ret = count_scan.insert ( std::pair<ScPeptideLabel, std::size_t>({peptide_match.getPeptideEvidence()->getGrpPeptideSp().get(),peptide_match.getPeptideEvidence()->getPeptideXtpSp()->getLabel()},0) );
- if (ret.second==false) {
- //already exists
- ret.first->second++;
+ for(const PeptideMatch &peptide_match : peptide_match_in_msrun)
+ {
+ std::pair<std::map<ScPeptideLabel, std::size_t>::iterator, bool> ret;
+ ret = count_scan.insert(std::pair<ScPeptideLabel, std::size_t>(
+ {peptide_match.getPeptideEvidence()->getGrpPeptideSp().get(),
+ peptide_match.getPeptideEvidence()->getPeptideXtpSp()->getLabel()},
+ 0));
+ if(ret.second == false)
+ {
+ // already exists
+ ret.first->second++;
}
- else {
- //error : it should exists
- throw pappso::PappsoException(QObject::tr("error in %1 %2 %3").arg(__FILE__).arg(__FUNCTION__).arg(__LINE__));
+ else
+ {
+ // error : it should exists
+ throw pappso::PappsoException(QObject::tr("error in %1 %2 %3")
+ .arg(__FILE__)
+ .arg(__FUNCTION__)
+ .arg(__LINE__));
}
}
- for (const std::pair<ScPeptideLabel, std::size_t> & pair_count :count_scan) {
- _p_writer->writeLine();
+ for(const std::pair<ScPeptideLabel, std::size_t> &pair_count : count_scan)
+ {
+ _p_writer->writeLine();
- _p_writer->writeCell(pair_count.first._p_grp_peptide->getGroupingId());
- if (pair_count.first._p_label == nullptr) {
- _p_writer->writeEmptyCell();
+ _p_writer->writeCell(
+ pair_count.first._p_grp_peptide->getGroupingId());
+ if(pair_count.first._p_label == nullptr)
+ {
+ _p_writer->writeEmptyCell();
}
- else {
- _p_writer->writeCell(pair_count.first._p_label->getXmlId());
+ else
+ {
+ _p_writer->writeCell(pair_count.first._p_label->getXmlId());
}
-
- _p_writer->writeCell(p_msrun->getXmlId());
- _p_writer->writeCell(p_msrun->getSampleName());
- //_p_writer->writeCell(pair.first->getSequence());
- _p_writer->writeCell((unsigned int) pair_count.second);
+
+ _p_writer->writeCell(p_msrun->getXmlId());
+ _p_writer->writeCell(p_msrun->getSampleName());
+ //_p_writer->writeCell(pair.first->getSequence());
+ _p_writer->writeCell((unsigned int)pair_count.second);
}
- qDebug() << "McqRscPeptide::writePeptidesInMsrun end" ;
+ qDebug() << "McqRscPeptide::writePeptidesInMsrun end";
}
- catch (pappso::PappsoException error) {
- throw pappso::PappsoException(QObject::tr("Error writing scan count in msrun %1 :\n%2").arg(p_msrun->getXmlId()).arg(error.qwhat()));
+ catch(pappso::PappsoException error)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error writing scan count in msrun %1 :\n%2")
+ .arg(p_msrun->getXmlId())
+ .arg(error.qwhat()));
}
}
diff --git a/src/output/mcqr/mcqrscpeptide.h b/src/output/mcqr/mcqrscpeptide.h
index ea42e19968b215da8e3d6aab0b3b231fe68f4991..ca774b80710d7fd491fe02cb0c22e739debe800b 100644
--- a/src/output/mcqr/mcqrscpeptide.h
+++ b/src/output/mcqr/mcqrscpeptide.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef MCQRSCPEPTIDE_H
#define MCQRSCPEPTIDE_H
@@ -35,27 +36,32 @@
#include <pappsomspp/grouping/grppeptide.h>
-struct ScPeptideLabel {
- bool operator<(const ScPeptideLabel& other) const;
-
- const pappso::GrpPeptide * _p_grp_peptide=nullptr;
- const Label * _p_label=nullptr;
+struct ScPeptideLabel
+{
+ bool operator<(const ScPeptideLabel &other) const;
+
+ const pappso::GrpPeptide *_p_grp_peptide = nullptr;
+ const Label *_p_label = nullptr;
};
class McqRscPeptide
{
-public :
- McqRscPeptide (CalcWriterInterface * p_writer, const Project * p_project);
-
- void writeSheet();
-private :
- void writeIdentificationGroup(IdentificationGroup * p_ident);
- void writeHeaders(IdentificationGroup * p_ident);
- void writePeptidesInMsrun(const MsRun * p_msrun,const std::vector<PeptideMatch> & peptide_match_in_msrun, const std::map<ScPeptideLabel, std::size_t> & count_scan_zero);
-
-private :
- const Project * _p_project;
- CalcWriterInterface * _p_writer;
+ public:
+ McqRscPeptide(CalcWriterInterface *p_writer, const Project *p_project);
+
+ void writeSheet();
+
+ private:
+ void writeIdentificationGroup(IdentificationGroup *p_ident);
+ void writeHeaders(IdentificationGroup *p_ident);
+ void writePeptidesInMsrun(
+ const MsRun *p_msrun,
+ const std::vector<PeptideMatch> &peptide_match_in_msrun,
+ const std::map<ScPeptideLabel, std::size_t> &count_scan_zero);
+
+ private:
+ const Project *_p_project;
+ CalcWriterInterface *_p_writer;
};
#endif // MCQRSCPEPTIDE_H
diff --git a/src/output/mcqr/mcqrscprotein.cpp b/src/output/mcqr/mcqrscprotein.cpp
index 03fcd5cd3bf854c7c961c1dbc4c27633c515774c..b77b4830c2fe473ac7351abeb13bdd746bd55c36 100644
--- a/src/output/mcqr/mcqrscprotein.cpp
+++ b/src/output/mcqr/mcqrscprotein.cpp
@@ -6,115 +6,144 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "mcqrscprotein.h"
#include <pappsomspp/pappsoexception.h>
-
-McqRscProtein::McqRscProtein (CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
- _p_writer = p_writer;
+McqRscProtein::McqRscProtein(CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : _p_project(p_project)
+{
+ _p_writer = p_writer;
}
-void McqRscProtein::writeSheet () {
- _p_writer->writeSheet("protein_sc");
-
- std::vector<IdentificationGroup *> identification_list = _p_project->getIdentificationGroupList();
- if (identification_list.size() > 1) {
- throw pappso::PappsoException(QObject::tr("error : cannot write MassChroqR spectral count file in individual mode"));
+void
+McqRscProtein::writeSheet()
+{
+ _p_writer->writeSheet("protein_sc");
+
+ std::vector<IdentificationGroup *> identification_list =
+ _p_project->getIdentificationGroupList();
+ if(identification_list.size() > 1)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("error : cannot write MassChroqR spectral count file in "
+ "individual mode"));
}
- for (IdentificationGroup * p_ident:identification_list) {
- //writeHeaders(p_ident);
- writeIdentificationGroup(p_ident);
+ for(IdentificationGroup *p_ident : identification_list)
+ {
+ // writeHeaders(p_ident);
+ writeIdentificationGroup(p_ident);
}
}
-void McqRscProtein::writeHeaders(IdentificationGroup * p_ident) {
-
-//ProteinID, msrun, msrunfile, accession, description, q
- _p_writer->writeCell("peptide");
- _p_writer->writeCell("protein");
- _p_writer->writeCell("accession");
- _p_writer->writeCell("description");
- //_p_writer->writeCell(p_protein_match->countSampleScan(state, p_msrun));
+void
+McqRscProtein::writeHeaders(IdentificationGroup *p_ident)
+{
+ // ProteinID, msrun, msrunfile, accession, description, q
+ _p_writer->writeCell("peptide");
+ _p_writer->writeCell("protein");
+ _p_writer->writeCell("accession");
+ _p_writer->writeCell("description");
+ //_p_writer->writeCell(p_protein_match->countSampleScan(state, p_msrun));
}
+void
+McqRscProtein::writeIdentificationGroup(IdentificationGroup *p_ident)
+{
-void McqRscProtein::writeIdentificationGroup(IdentificationGroup * p_ident) {
+ _ms_run_sp_list = p_ident->getMsRunSpList();
+ writeHeaders(p_ident);
+ for(const std::pair<unsigned int, GroupingGroupSp> &group_pair :
+ p_ident->getGroupStore().getGroupMap())
+ {
- _ms_run_sp_list = p_ident->getMsRunSpList();
- writeHeaders(p_ident);
- for (const std::pair<unsigned int, GroupingGroupSp> & group_pair : p_ident->getGroupStore().getGroupMap()) {
+ std::vector<const ProteinMatch *> protein_match_list =
+ group_pair.second.get()->getProteinMatchList();
- std::vector<const ProteinMatch *> protein_match_list = group_pair.second.get()->getProteinMatchList();
+ std::sort(protein_match_list.begin(), protein_match_list.end(),
+ [](const ProteinMatch *a, const ProteinMatch *b) {
+ return a->getGrpProteinSp().get()->getSubGroupNumber() <
+ b->getGrpProteinSp().get()->getSubGroupNumber();
+ });
- std::sort(protein_match_list.begin(), protein_match_list.end(),
- [](const ProteinMatch * a, const ProteinMatch * b)
+ for(auto &protein_match : protein_match_list)
{
- return a->getGrpProteinSp().get()->getSubGroupNumber() < b->getGrpProteinSp().get()->getSubGroupNumber();
- });
-
- for (auto & protein_match:protein_match_list) {
- writeOneProtein(group_pair.second.get(), protein_match);
+ writeOneProtein(group_pair.second.get(), protein_match);
}
-
}
- _p_writer->writeLine();
+ _p_writer->writeLine();
}
-void McqRscProtein::writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match) {
- try {
+void
+McqRscProtein::writeOneProtein(const GroupingGroup *p_group,
+ const ProteinMatch *p_protein_match)
+{
+ try
+ {
- qDebug() << "McqRscProtein::writeOneProtein begin" ;
- ValidationState validation_state = ValidationState::grouped;
+ qDebug() << "McqRscProtein::writeOneProtein begin";
+ ValidationState validation_state = ValidationState::grouped;
- pappso::GrpProtein * p_grp_protein = p_protein_match->getGrpProteinSp().get();
+ pappso::GrpProtein *p_grp_protein =
+ p_protein_match->getGrpProteinSp().get();
- ProteinXtp * p_protein = p_protein_match->getProteinXtpSp().get();
+ ProteinXtp *p_protein = p_protein_match->getProteinXtpSp().get();
- //for (MsRunSp & msrun_sp : _ms_run_sp_list) {
- std::set<QString> peptide_list;
- for (PeptideMatch & peptide_match : p_protein_match->getPeptideMatchList(validation_state)) {
- peptide_list.insert( peptide_match.getPeptideEvidence()->getGrpPeptideSp().get()->getGroupingId());
+ // for (MsRunSp & msrun_sp : _ms_run_sp_list) {
+ std::set<QString> peptide_list;
+ for(PeptideMatch &peptide_match :
+ p_protein_match->getPeptideMatchList(validation_state))
+ {
+ peptide_list.insert(peptide_match.getPeptideEvidence()
+ ->getGrpPeptideSp()
+ .get()
+ ->getGroupingId());
}
-
- for (const QString & peptide_str :peptide_list) {
- _p_writer->writeLine();
-
- _p_writer->writeCell(peptide_str);
- _p_writer->writeCell(p_grp_protein->getGroupingId());
- _p_writer->writeCell(p_protein->getAccession());
- _p_writer->writeCell(p_protein->getDescription());
+
+ for(const QString &peptide_str : peptide_list)
+ {
+ _p_writer->writeLine();
+
+ _p_writer->writeCell(peptide_str);
+ _p_writer->writeCell(p_grp_protein->getGroupingId());
+ _p_writer->writeCell(p_protein->getAccession());
+ _p_writer->writeCell(p_protein->getDescription());
}
- qDebug() << "McqRscProtein::writeOneProtein end" ;
+ qDebug() << "McqRscProtein::writeOneProtein end";
}
- catch (pappso::PappsoException error) {
- throw pappso::PappsoException(QObject::tr("Error writing protein %1 :\n%2").arg(p_protein_match->getProteinXtpSp().get()->getAccession()).arg(error.qwhat()));
+ catch(pappso::PappsoException error)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error writing protein %1 :\n%2")
+ .arg(p_protein_match->getProteinXtpSp().get()->getAccession())
+ .arg(error.qwhat()));
}
}
-
diff --git a/src/output/mcqr/mcqrscprotein.h b/src/output/mcqr/mcqrscprotein.h
index 259a6393a91d648e078b7571cb8bc3708b3f1bb4..947e85819b277f6f049bee7a53382f10ecf4763e 100644
--- a/src/output/mcqr/mcqrscprotein.h
+++ b/src/output/mcqr/mcqrscprotein.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef MCQRSCPROTEIN_H
#define MCQRSCPROTEIN_H
@@ -35,19 +36,21 @@
class McqRscProtein
{
-public :
- McqRscProtein (CalcWriterInterface * p_writer, const Project * p_project);
-
- void writeSheet();
-private :
- void writeIdentificationGroup(IdentificationGroup * p_ident);
- void writeHeaders(IdentificationGroup * p_ident);
- void writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match);
-
-private :
- const Project * _p_project;
- CalcWriterInterface * _p_writer;
- std::vector<MsRunSp> _ms_run_sp_list;
+ public:
+ McqRscProtein(CalcWriterInterface *p_writer, const Project *p_project);
+
+ void writeSheet();
+
+ private:
+ void writeIdentificationGroup(IdentificationGroup *p_ident);
+ void writeHeaders(IdentificationGroup *p_ident);
+ void writeOneProtein(const GroupingGroup *p_group,
+ const ProteinMatch *p_protein_match);
+
+ private:
+ const Project *_p_project;
+ CalcWriterInterface *_p_writer;
+ std::vector<MsRunSp> _ms_run_sp_list;
};
#endif // MCQRSCPROTEIN_H
diff --git a/src/output/mcqrspectralcount.cpp b/src/output/mcqrspectralcount.cpp
index 3e5b1377422138daeca754781e733bb9333c0dad..c1593519933ed0b14593319b30378e3d4fc16057 100644
--- a/src/output/mcqrspectralcount.cpp
+++ b/src/output/mcqrspectralcount.cpp
@@ -6,121 +6,147 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "mcqrspectralcount.h"
#include <pappsomspp/pappsoexception.h>
-
-McqrSpectralCount::McqrSpectralCount (CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
- _p_writer = p_writer;
+McqrSpectralCount::McqrSpectralCount(CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : _p_project(p_project)
+{
+ _p_writer = p_writer;
}
-void McqrSpectralCount::writeSheet () {
- _p_writer->writeSheet("MassChroqR spectral counting");
-
- std::vector<IdentificationGroup *> identification_list = _p_project->getIdentificationGroupList();
- if (identification_list.size() > 1) {
- throw pappso::PappsoException(QObject::tr("error : cannot write MassChroqR spectral count file in individual mode"));
+void
+McqrSpectralCount::writeSheet()
+{
+ _p_writer->writeSheet("MassChroqR spectral counting");
+
+ std::vector<IdentificationGroup *> identification_list =
+ _p_project->getIdentificationGroupList();
+ if(identification_list.size() > 1)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("error : cannot write MassChroqR spectral count file in "
+ "individual mode"));
}
- for (IdentificationGroup * p_ident:identification_list) {
- //writeHeaders(p_ident);
- writeIdentificationGroup(p_ident);
+ for(IdentificationGroup *p_ident : identification_list)
+ {
+ // writeHeaders(p_ident);
+ writeIdentificationGroup(p_ident);
}
}
-void McqrSpectralCount::writeHeaders(IdentificationGroup * p_ident) {
-
-//ProteinID, msrun, msrunfile, accession, description, q
- _p_writer->writeCell("protein");
- _p_writer->writeCell("msrun");
- _p_writer->writeCell("msrunfile");
- _p_writer->writeCell("accession");
- _p_writer->writeCell("description");
- _p_writer->writeCell("sc");
- //_p_writer->writeCell(p_protein_match->countSampleScan(state, p_msrun));
+void
+McqrSpectralCount::writeHeaders(IdentificationGroup *p_ident)
+{
+ // ProteinID, msrun, msrunfile, accession, description, q
+ _p_writer->writeCell("protein");
+ _p_writer->writeCell("msrun");
+ _p_writer->writeCell("msrunfile");
+ _p_writer->writeCell("accession");
+ _p_writer->writeCell("description");
+ _p_writer->writeCell("sc");
+ //_p_writer->writeCell(p_protein_match->countSampleScan(state, p_msrun));
}
+void
+McqrSpectralCount::writeIdentificationGroup(IdentificationGroup *p_ident)
+{
-void McqrSpectralCount::writeIdentificationGroup(IdentificationGroup * p_ident) {
+ _ms_run_sp_list = p_ident->getMsRunSpList();
+ writeHeaders(p_ident);
+ for(const std::pair<unsigned int, GroupingGroupSp> &group_pair :
+ p_ident->getGroupStore().getGroupMap())
+ {
- _ms_run_sp_list = p_ident->getMsRunSpList();
- writeHeaders(p_ident);
- for (const std::pair<unsigned int, GroupingGroupSp> & group_pair : p_ident->getGroupStore().getGroupMap()) {
+ std::vector<const ProteinMatch *> protein_match_list =
+ group_pair.second.get()->getProteinMatchList();
- std::vector<const ProteinMatch *> protein_match_list = group_pair.second.get()->getProteinMatchList();
+ std::sort(protein_match_list.begin(), protein_match_list.end(),
+ [](const ProteinMatch *a, const ProteinMatch *b) {
+ return a->getGrpProteinSp().get()->getSubGroupNumber() <
+ b->getGrpProteinSp().get()->getSubGroupNumber();
+ });
- std::sort(protein_match_list.begin(), protein_match_list.end(),
- [](const ProteinMatch * a, const ProteinMatch * b)
+ for(auto &protein_match : protein_match_list)
{
- return a->getGrpProteinSp().get()->getSubGroupNumber() < b->getGrpProteinSp().get()->getSubGroupNumber();
- });
-
- for (auto & protein_match:protein_match_list) {
- writeOneProtein(group_pair.second.get(), protein_match);
+ writeOneProtein(group_pair.second.get(), protein_match);
}
-
}
- _p_writer->writeLine();
+ _p_writer->writeLine();
}
-void McqrSpectralCount::writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match) {
- try {
+void
+McqrSpectralCount::writeOneProtein(const GroupingGroup *p_group,
+ const ProteinMatch *p_protein_match)
+{
+ try
+ {
- qDebug() << "McqrSpectralCount::writeOneProtein begin" ;
- ValidationState validation_state = ValidationState::validAndChecked;
+ qDebug() << "McqrSpectralCount::writeOneProtein begin";
+ ValidationState validation_state = ValidationState::validAndChecked;
- pappso::GrpProtein * p_grp_protein = p_protein_match->getGrpProteinSp().get();
+ pappso::GrpProtein *p_grp_protein =
+ p_protein_match->getGrpProteinSp().get();
- ProteinXtp * p_protein = p_protein_match->getProteinXtpSp().get();
+ ProteinXtp *p_protein = p_protein_match->getProteinXtpSp().get();
- for (MsRunSp & msrun_sp : _ms_run_sp_list) {
- _p_writer->writeLine();
-
- _p_writer->writeCell(p_grp_protein->getGroupingId());
-
- _p_writer->writeCell(msrun_sp.get()->getXmlId());
- _p_writer->writeCell(msrun_sp.get()->getFilename());
-
- //const std::list<DbXref> & dbxref_list = p_protein->getDbxrefList();
- //if (dbxref_list.size() == 0) {
- _p_writer->writeCell(p_protein->getAccession());
- //}
- //else {
- // _p_writer->writeCell(dbxref_list.front().getUrl(), p_protein->getAccession());
- //}
- _p_writer->writeCell(p_protein->getDescription());
- _p_writer->writeCell(p_protein_match->countSampleScan(validation_state, msrun_sp.get()));
+ for(MsRunSp &msrun_sp : _ms_run_sp_list)
+ {
+ _p_writer->writeLine();
+
+ _p_writer->writeCell(p_grp_protein->getGroupingId());
+
+ _p_writer->writeCell(msrun_sp.get()->getXmlId());
+ _p_writer->writeCell(msrun_sp.get()->getFilename());
+
+ // const std::list<DbXref> & dbxref_list = p_protein->getDbxrefList();
+ // if (dbxref_list.size() == 0) {
+ _p_writer->writeCell(p_protein->getAccession());
+ //}
+ // else {
+ // _p_writer->writeCell(dbxref_list.front().getUrl(),
+ // p_protein->getAccession());
+ //}
+ _p_writer->writeCell(p_protein->getDescription());
+ _p_writer->writeCell(
+ p_protein_match->countSampleScan(validation_state, msrun_sp.get()));
}
- qDebug() << "McqrSpectralCount::writeOneProtein end" ;
+ qDebug() << "McqrSpectralCount::writeOneProtein end";
}
- catch (pappso::PappsoException error) {
- throw pappso::PappsoException(QObject::tr("Error writing protein %1 :\n%2").arg(p_protein_match->getProteinXtpSp().get()->getAccession()).arg(error.qwhat()));
+ catch(pappso::PappsoException error)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error writing protein %1 :\n%2")
+ .arg(p_protein_match->getProteinXtpSp().get()->getAccession())
+ .arg(error.qwhat()));
}
}
-
diff --git a/src/output/mcqrspectralcount.h b/src/output/mcqrspectralcount.h
index 1a3d6c3ed2b2e45d68eaefc32e8a555403c10ba6..a59c71c151660b6f1679ef49543d759eeef48975 100644
--- a/src/output/mcqrspectralcount.h
+++ b/src/output/mcqrspectralcount.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef MCQRSPECTRALCOUNT_H
#define MCQRSPECTRALCOUNT_H
@@ -35,19 +36,21 @@
class McqrSpectralCount
{
-public :
- McqrSpectralCount (CalcWriterInterface * p_writer, const Project * p_project);
-
- void writeSheet();
-private :
- void writeIdentificationGroup(IdentificationGroup * p_ident);
- void writeHeaders(IdentificationGroup * p_ident);
- void writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match);
-
-private :
- const Project * _p_project;
- CalcWriterInterface * _p_writer;
- std::vector<MsRunSp> _ms_run_sp_list;
+ public:
+ McqrSpectralCount(CalcWriterInterface *p_writer, const Project *p_project);
+
+ void writeSheet();
+
+ private:
+ void writeIdentificationGroup(IdentificationGroup *p_ident);
+ void writeHeaders(IdentificationGroup *p_ident);
+ void writeOneProtein(const GroupingGroup *p_group,
+ const ProteinMatch *p_protein_match);
+
+ private:
+ const Project *_p_project;
+ CalcWriterInterface *_p_writer;
+ std::vector<MsRunSp> _ms_run_sp_list;
};
#endif // MCQRSPECTRALCOUNT_H
diff --git a/src/output/ods/comparbasesheet.h b/src/output/ods/comparbasesheet.h
index c0fc4f4606ddfac6069730a396cb967ee5198f86..3881628e66b680bd6abdb750b626cc6852d80db3 100644
--- a/src/output/ods/comparbasesheet.h
+++ b/src/output/ods/comparbasesheet.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef COMPARBASESHEET_H
#define COMPARBASESHEET_H
@@ -37,29 +38,34 @@
class ComparBaseSheet
{
-public :
- ComparBaseSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
-private :
- void writeIdentificationGroup(IdentificationGroup * p_ident);
- void writeHeaders(IdentificationGroup * p_ident);
-public :
- void writeSheet();
-protected :
- virtual void writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun)=0;
- void writeProteinMatch(const ProteinMatch * p_protein_match);
+ public:
+ ComparBaseSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project);
+ private:
+ void writeIdentificationGroup(IdentificationGroup *p_ident);
+ void writeHeaders(IdentificationGroup *p_ident);
-protected :
- OdsExport * _p_ods_export;
- const Project * _p_project;
- CalcWriterInterface * _p_writer;
- std::vector<MsRunSp> _msrun_list;
- QString _title_sheet;
-
- QString _first_cell_coordinate;
-
- IdentificationGroup * _p_current_identification_group;
-
+ public:
+ void writeSheet();
+
+ protected:
+ virtual void writeComparValue(const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun) = 0;
+ void writeProteinMatch(const ProteinMatch *p_protein_match);
+
+
+ protected:
+ OdsExport *_p_ods_export;
+ const Project *_p_project;
+ CalcWriterInterface *_p_writer;
+ std::vector<MsRunSp> _msrun_list;
+ QString _title_sheet;
+
+ QString _first_cell_coordinate;
+
+ IdentificationGroup *_p_current_identification_group;
};
#endif // COMPARBASESHEET_H
diff --git a/src/output/ods/comparspecificspectrasheet.cpp b/src/output/ods/comparspecificspectrasheet.cpp
index 0e041c3bad25fe95777f5f6f520a1bbe37cf8911..3dfde052324db8093fad2e4b51b4f6b73eebce10 100644
--- a/src/output/ods/comparspecificspectrasheet.cpp
+++ b/src/output/ods/comparspecificspectrasheet.cpp
@@ -6,48 +6,71 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "comparspecificspectrasheet.h"
-ComparSpecificSpectraSheet::ComparSpecificSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): ComparBaseSheet(p_ods_export, p_writer, p_project) {
- _title_sheet = "compar specific spectra";
+ComparSpecificSpectraSheet::ComparSpecificSpectraSheet(
+ OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : ComparBaseSheet(p_ods_export, p_writer, p_project)
+{
+ _title_sheet = "compar specific spectra";
}
-void ComparSpecificSpectraSheet::writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) {
- qDebug() << "ComparSpecificSpectraSheet::writeComparValue begin";
- _p_writer->writeCell((unsigned int) p_protein_match->getGroupingGroupSp().get()->countSpecificSampleScan(p_protein_match, state, p_msrun));
- qDebug() << "ComparSpecificSpectraSheet::writeComparValue end";
+void
+ComparSpecificSpectraSheet::writeComparValue(
+ const ProteinMatch *p_protein_match, ValidationState state,
+ const MsRun *p_msrun)
+{
+ qDebug() << "ComparSpecificSpectraSheet::writeComparValue begin";
+ _p_writer->writeCell(
+ (unsigned int)p_protein_match->getGroupingGroupSp()
+ .get()
+ ->countSpecificSampleScan(p_protein_match, state, p_msrun));
+ qDebug() << "ComparSpecificSpectraSheet::writeComparValue end";
}
-ComparSpecificSequenceSheet::ComparSpecificSequenceSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): ComparBaseSheet(p_ods_export, p_writer, p_project) {
- _title_sheet = "compar specific unique sequence";
+ComparSpecificSequenceSheet::ComparSpecificSequenceSheet(
+ OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : ComparBaseSheet(p_ods_export, p_writer, p_project)
+{
+ _title_sheet = "compar specific unique sequence";
}
-void ComparSpecificSequenceSheet::writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) {
- qDebug() << "ComparSpecificSequenceSheet::writeComparValue begin";
- _p_writer->writeCell((unsigned int) p_protein_match->getGroupingGroupSp().get()->countSpecificSequenceLi(p_protein_match, state, p_msrun));
- qDebug() << "ComparSpecificSequenceSheet::writeComparValue end";
+void
+ComparSpecificSequenceSheet::writeComparValue(
+ const ProteinMatch *p_protein_match, ValidationState state,
+ const MsRun *p_msrun)
+{
+ qDebug() << "ComparSpecificSequenceSheet::writeComparValue begin";
+ _p_writer->writeCell(
+ (unsigned int)p_protein_match->getGroupingGroupSp()
+ .get()
+ ->countSpecificSequenceLi(p_protein_match, state, p_msrun));
+ qDebug() << "ComparSpecificSequenceSheet::writeComparValue end";
}
diff --git a/src/output/ods/comparspecificspectrasheet.h b/src/output/ods/comparspecificspectrasheet.h
index eeab2ee9e0eaf21061585e9213c15d5836358548..c94310ea54ac6c2a4b50ff8ee1971c494572c711 100644
--- a/src/output/ods/comparspecificspectrasheet.h
+++ b/src/output/ods/comparspecificspectrasheet.h
@@ -6,46 +6,56 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef COMPARSPECIFICSPECTRASHEET_H
#define COMPARSPECIFICSPECTRASHEET_H
#include "comparbasesheet.h"
-class ComparSpecificSpectraSheet: public ComparBaseSheet
+class ComparSpecificSpectraSheet : public ComparBaseSheet
{
-public :
- ComparSpecificSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
-protected :
- virtual void writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) override;
+ public:
+ ComparSpecificSpectraSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project);
+
+ protected:
+ virtual void writeComparValue(const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun) override;
};
-class ComparSpecificSequenceSheet:public ComparBaseSheet
+class ComparSpecificSequenceSheet : public ComparBaseSheet
{
-public :
- ComparSpecificSequenceSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
+ public:
+ ComparSpecificSequenceSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project);
-protected :
- virtual void writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) override;
+ protected:
+ virtual void writeComparValue(const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun) override;
};
#endif // COMPARSPECIFICSPECTRASHEET_H
diff --git a/src/output/ods/comparspectrasheet.cpp b/src/output/ods/comparspectrasheet.cpp
index fb5c82395e5f2ee707045df58a5bc76b953964ba..a5fbc14db572b510a4fc277234e58b9921a306b5 100644
--- a/src/output/ods/comparspectrasheet.cpp
+++ b/src/output/ods/comparspectrasheet.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "comparspectrasheet.h"
@@ -34,64 +35,107 @@
#include <QDebug>
-ComparSpectraSheet::ComparSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): ComparBaseSheet(p_ods_export, p_writer, p_project) {
- _title_sheet = "compar spectra";
+ComparSpectraSheet::ComparSpectraSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : ComparBaseSheet(p_ods_export, p_writer, p_project)
+{
+ _title_sheet = "compar spectra";
}
-void ComparSpectraSheet::writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) {
- qDebug() << "ComparSpectraSheet::writeComparValue begin";
- _p_writer->writeCell(p_protein_match->countSampleScan(state, p_msrun));
- qDebug() << "ComparSpectraSheet::writeComparValue end";
+void
+ComparSpectraSheet::writeComparValue(const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun)
+{
+ qDebug() << "ComparSpectraSheet::writeComparValue begin";
+ _p_writer->writeCell(p_protein_match->countSampleScan(state, p_msrun));
+ qDebug() << "ComparSpectraSheet::writeComparValue end";
}
-ComparSequenceSheet::ComparSequenceSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): ComparBaseSheet(p_ods_export, p_writer, p_project) {
- _title_sheet = "compar unique sequence";
+ComparSequenceSheet::ComparSequenceSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : ComparBaseSheet(p_ods_export, p_writer, p_project)
+{
+ _title_sheet = "compar unique sequence";
}
-void ComparSequenceSheet::writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) {
- qDebug() << "ComparSequenceSheet::writeComparValue begin";
- _p_writer->writeCell((unsigned int) p_protein_match->countSequenceLi(state, p_msrun));
- qDebug() << "ComparSequenceSheet::writeComparValue end";
+void
+ComparSequenceSheet::writeComparValue(const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun)
+{
+ qDebug() << "ComparSequenceSheet::writeComparValue begin";
+ _p_writer->writeCell(
+ (unsigned int)p_protein_match->countSequenceLi(state, p_msrun));
+ qDebug() << "ComparSequenceSheet::writeComparValue end";
}
-ComparPaiSheet::ComparPaiSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): ComparBaseSheet(p_ods_export, p_writer, p_project) {
- _title_sheet = "compar PAI";
+ComparPaiSheet::ComparPaiSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : ComparBaseSheet(p_ods_export, p_writer, p_project)
+{
+ _title_sheet = "compar PAI";
}
-void ComparPaiSheet::writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) {
- qDebug() << "ComparPaiSheet::writeComparValue begin";
- _p_writer->writeCell(p_protein_match->getPAI(p_msrun));
- qDebug() << "ComparPaiSheet::writeComparValue end";
+void
+ComparPaiSheet::writeComparValue(const ProteinMatch *p_protein_match,
+ ValidationState state, const MsRun *p_msrun)
+{
+ qDebug() << "ComparPaiSheet::writeComparValue begin";
+ _p_writer->writeCell(p_protein_match->getPAI(p_msrun));
+ qDebug() << "ComparPaiSheet::writeComparValue end";
}
-ComparEmpaiSheet::ComparEmpaiSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): ComparBaseSheet(p_ods_export, p_writer, p_project) {
- _title_sheet = "compar emPAI";
+ComparEmpaiSheet::ComparEmpaiSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : ComparBaseSheet(p_ods_export, p_writer, p_project)
+{
+ _title_sheet = "compar emPAI";
}
-void ComparEmpaiSheet::writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) {
- qDebug() << "ComparEmpaiSheet::writeComparValue begin";
- _p_writer->writeCell(p_protein_match->getEmPAI(p_msrun));
- qDebug() << "ComparEmpaiSheet::writeComparValue end";
+void
+ComparEmpaiSheet::writeComparValue(const ProteinMatch *p_protein_match,
+ ValidationState state, const MsRun *p_msrun)
+{
+ qDebug() << "ComparEmpaiSheet::writeComparValue begin";
+ _p_writer->writeCell(p_protein_match->getEmPAI(p_msrun));
+ qDebug() << "ComparEmpaiSheet::writeComparValue end";
}
-ComparNsafSheet::ComparNsafSheet(OdsExport* p_ods_export, CalcWriterInterface* p_writer, const Project* p_project): ComparBaseSheet(p_ods_export, p_writer, p_project) {
- _title_sheet = "compar NSAF";
+ComparNsafSheet::ComparNsafSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : ComparBaseSheet(p_ods_export, p_writer, p_project)
+{
+ _title_sheet = "compar NSAF";
}
-void ComparNsafSheet::writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) {
- qDebug() << "ComparNsafSheet::writeComparValue begin";
- pappso::pappso_double proto_nsaf_sum=0;
- std::pair<std::map<const MsRun *,pappso::pappso_double>::iterator,bool> ret = _map_proto_nsaf_sum_by_msrun.insert(std::pair<const MsRun *,pappso::pappso_double>(p_msrun,0));
- if (ret.second==false) {
- //"element 'z' already existed";
- proto_nsaf_sum = ret.first->second;
- }
- else {
- proto_nsaf_sum = _p_current_identification_group->computeProtoNsafSum(p_msrun);
+void
+ComparNsafSheet::writeComparValue(const ProteinMatch *p_protein_match,
+ ValidationState state, const MsRun *p_msrun)
+{
+ qDebug() << "ComparNsafSheet::writeComparValue begin";
+ pappso::pappso_double proto_nsaf_sum = 0;
+ std::pair<std::map<const MsRun *, pappso::pappso_double>::iterator, bool>
+ ret = _map_proto_nsaf_sum_by_msrun.insert(
+ std::pair<const MsRun *, pappso::pappso_double>(p_msrun, 0));
+ if(ret.second == false)
+ {
+ //"element 'z' already existed";
+ proto_nsaf_sum = ret.first->second;
+ }
+ else
+ {
+ proto_nsaf_sum =
+ _p_current_identification_group->computeProtoNsafSum(p_msrun);
ret.first->second = proto_nsaf_sum;
- }
+ }
- _p_writer->writeCell(p_protein_match->getNsaf(proto_nsaf_sum,p_msrun));
- qDebug() << "ComparNsafSheet::writeComparValue end";
+ _p_writer->writeCell(p_protein_match->getNsaf(proto_nsaf_sum, p_msrun));
+ qDebug() << "ComparNsafSheet::writeComparValue end";
}
diff --git a/src/output/ods/comparspectrasheet.h b/src/output/ods/comparspectrasheet.h
index 29653e279fafad17320b4b59449e39f27ff7220a..ced41c2a2d5c7311178b6abb0ac6892cf9b0685d 100644
--- a/src/output/ods/comparspectrasheet.h
+++ b/src/output/ods/comparspectrasheet.h
@@ -6,79 +6,95 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef COMPARSPECTRASHEET_H
#define COMPARSPECTRASHEET_H
#include "comparbasesheet.h"
-class ComparSpectraSheet:public ComparBaseSheet
+class ComparSpectraSheet : public ComparBaseSheet
{
-public :
- ComparSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
+ public:
+ ComparSpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project);
-protected :
- virtual void writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) override;
+ protected:
+ virtual void writeComparValue(const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun) override;
};
-class ComparSequenceSheet:public ComparBaseSheet
+class ComparSequenceSheet : public ComparBaseSheet
{
-public :
- ComparSequenceSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
+ public:
+ ComparSequenceSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project);
-protected :
- virtual void writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) override;
+ protected:
+ virtual void writeComparValue(const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun) override;
};
-class ComparPaiSheet:public ComparBaseSheet
+class ComparPaiSheet : public ComparBaseSheet
{
-public :
- ComparPaiSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
+ public:
+ ComparPaiSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project);
-protected :
- virtual void writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) override;
+ protected:
+ virtual void writeComparValue(const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun) override;
};
-class ComparEmpaiSheet:public ComparBaseSheet
+class ComparEmpaiSheet : public ComparBaseSheet
{
-public :
- ComparEmpaiSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
+ public:
+ ComparEmpaiSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project);
-protected :
- virtual void writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) override;
+ protected:
+ virtual void writeComparValue(const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun) override;
};
-class ComparNsafSheet:public ComparBaseSheet
+class ComparNsafSheet : public ComparBaseSheet
{
-public :
- ComparNsafSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
-
-protected :
- virtual void writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) override;
-private:
-
- std::map<const MsRun *, pappso::pappso_double> _map_proto_nsaf_sum_by_msrun;
+ public:
+ ComparNsafSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project);
+
+ protected:
+ virtual void writeComparValue(const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun) override;
+
+ private:
+ std::map<const MsRun *, pappso::pappso_double> _map_proto_nsaf_sum_by_msrun;
};
#endif // COMPARSPECTRASHEET_H
diff --git a/src/output/ods/groupingsheet.cpp b/src/output/ods/groupingsheet.cpp
index e3ca9d302f5afdde5d7e849e85059681f12a836d..4b7d3095aedc65059c172acb502e5f924e6653a1 100644
--- a/src/output/ods/groupingsheet.cpp
+++ b/src/output/ods/groupingsheet.cpp
@@ -6,90 +6,111 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "groupingsheet.h"
-GroupingSheet::GroupingSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
- _p_writer = p_writer;
- _p_ods_export = p_ods_export;
- p_writer->writeSheet("groups");
+GroupingSheet::GroupingSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : _p_project(p_project)
+{
+ _p_writer = p_writer;
+ _p_ods_export = p_ods_export;
+ p_writer->writeSheet("groups");
-
- OdsTableSettings table_settings;
- table_settings.setVerticalSplit(1);
- _p_writer->setCurrentOdsTableSettings(table_settings);
- writeHeaders();
+ OdsTableSettings table_settings;
+ table_settings.setVerticalSplit(1);
+ _p_writer->setCurrentOdsTableSettings(table_settings);
- std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
- for (IdentificationGroup * p_ident:identification_list) {
- //writeHeaders(p_ident);
- writeIdentificationGroup(p_ident);
+ writeHeaders();
+
+ std::vector<IdentificationGroup *> identification_list =
+ p_project->getIdentificationGroupList();
+ for(IdentificationGroup *p_ident : identification_list)
+ {
+ // writeHeaders(p_ident);
+ writeIdentificationGroup(p_ident);
}
}
-void GroupingSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
- _p_writer->writeLine();
- if (_p_project->getProjectMode() == ProjectMode::individual) {
- _p_writer->writeCell(p_ident->getMsRunSpList().at(0).get()->getSampleName());
+void
+GroupingSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
+{
+ _p_writer->writeLine();
+ if(_p_project->getProjectMode() == ProjectMode::individual)
+ {
+ _p_writer->writeCell(
+ p_ident->getMsRunSpList().at(0).get()->getSampleName());
}
- _p_writer->writeCell((unsigned int) p_ident->countGroup());
- _p_writer->writeCell((unsigned int) p_ident->countSubGroup());
- _p_writer->writeCell(p_ident->countProteinMatch(ValidationState::grouped));
- _p_writer->writeCell(p_ident->countPeptideMass(ValidationState::grouped));
- _p_writer->writeCell(p_ident->countPeptideMatch(ValidationState::grouped));
- //_p_writer->writeCell(p_ident->countSequence(ValidationState::grouped));
- _p_writer->writeCell(p_ident->countPeptideMassSample(ValidationState::grouped));
- _p_writer->writeCell(p_ident->getProteinFdr(ValidationState::valid));
- _p_writer->writeCell(p_ident->getPeptideMassFdr(ValidationState::valid));
+ _p_writer->writeCell((unsigned int)p_ident->countGroup());
+ _p_writer->writeCell((unsigned int)p_ident->countSubGroup());
+ _p_writer->writeCell(p_ident->countProteinMatch(ValidationState::grouped));
+ _p_writer->writeCell(p_ident->countPeptideMass(ValidationState::grouped));
+ _p_writer->writeCell(p_ident->countPeptideMatch(ValidationState::grouped));
+ //_p_writer->writeCell(p_ident->countSequence(ValidationState::grouped));
+ _p_writer->writeCell(
+ p_ident->countPeptideMassSample(ValidationState::grouped));
+ _p_writer->writeCell(p_ident->getProteinFdr(ValidationState::valid));
+ _p_writer->writeCell(p_ident->getPeptideMassFdr(ValidationState::valid));
}
-void GroupingSheet::writeHeaders() {
- // groups, subgroups, proteins, psm, sequence, peptide/mass, pep FDR, prot FDR
+void
+GroupingSheet::writeHeaders()
+{
+ // groups, subgroups, proteins, psm, sequence, peptide/mass, pep FDR, prot FDR
- _p_writer->writeLine();
- if (_p_project->getProjectMode() == ProjectMode::individual) {
- _p_writer->writeCell("sample");
+ _p_writer->writeLine();
+ if(_p_project->getProjectMode() == ProjectMode::individual)
+ {
+ _p_writer->writeCell("sample");
}
- _p_writer->setCellAnnotation("number of groups");
- _p_writer->writeCell("groups");
- _p_writer->setCellAnnotation("number of subgroups");
- _p_writer->writeCell("subgroups");
- _p_writer->setCellAnnotation("number of grouped proteins");
- _p_writer->writeCell("proteins");
- _p_writer->setCellAnnotation("number of distinct grouped peptides in the whole experiment");
- _p_writer->writeCell("peptides");
- _p_writer->setCellAnnotation("number of peptide hits : each grouped peptide spectrum match given by the identification engine");
- _p_writer->writeCell("psm");
- //_p_writer->writeCell("sequences");
- _p_writer->setCellAnnotation("number of unique combinations : grouped peptide sequence+modifications+sample name");
- _p_writer->writeCell("peptide/mass/sample");
- _p_writer->setCellAnnotation("FDR at the protein level (number of decoy valid proteins / totale number of valid proteins)");
- _p_writer->writeCell("prot FDR");
- _p_writer->setCellAnnotation("FDR at the peptide level (number of decoy valid peptides / totale number of valid peptides)");
- _p_writer->writeCell("pep FDR");
-
-
+ _p_writer->setCellAnnotation("number of groups");
+ _p_writer->writeCell("groups");
+ _p_writer->setCellAnnotation("number of subgroups");
+ _p_writer->writeCell("subgroups");
+ _p_writer->setCellAnnotation("number of grouped proteins");
+ _p_writer->writeCell("proteins");
+ _p_writer->setCellAnnotation(
+ "number of distinct grouped peptides in the whole experiment");
+ _p_writer->writeCell("peptides");
+ _p_writer->setCellAnnotation(
+ "number of peptide hits : each grouped peptide spectrum match given by the "
+ "identification engine");
+ _p_writer->writeCell("psm");
+ //_p_writer->writeCell("sequences");
+ _p_writer->setCellAnnotation("number of unique combinations : grouped "
+ "peptide sequence+modifications+sample name");
+ _p_writer->writeCell("peptide/mass/sample");
+ _p_writer->setCellAnnotation(
+ "FDR at the protein level (number of decoy valid proteins / totale number "
+ "of valid proteins)");
+ _p_writer->writeCell("prot FDR");
+ _p_writer->setCellAnnotation(
+ "FDR at the peptide level (number of decoy valid peptides / totale number "
+ "of valid peptides)");
+ _p_writer->writeCell("pep FDR");
}
diff --git a/src/output/ods/groupingsheet.h b/src/output/ods/groupingsheet.h
index d73bbc86b15a14f8bb4dc952f4c9a3150c16aee3..9202bc4fd7b64a0bcebd3537502c0ea891849218 100644
--- a/src/output/ods/groupingsheet.h
+++ b/src/output/ods/groupingsheet.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef GROUPINGSHEET_H
#define GROUPINGSHEET_H
@@ -36,17 +37,18 @@
class GroupingSheet
{
-public :
- GroupingSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
-private:
-
- void writeIdentificationGroup(IdentificationGroup * p_ident);
- void writeHeaders();
-
-private :
- OdsExport * _p_ods_export;
- const Project * _p_project;
- CalcWriterInterface * _p_writer;
+ public:
+ GroupingSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project);
+
+ private:
+ void writeIdentificationGroup(IdentificationGroup *p_ident);
+ void writeHeaders();
+
+ private:
+ OdsExport *_p_ods_export;
+ const Project *_p_project;
+ CalcWriterInterface *_p_writer;
};
#endif // GROUPINGSHEET_H
diff --git a/src/output/ods/infosheet.h b/src/output/ods/infosheet.h
index 313399d5b25cc5a88cc495bd01e17ff877704d07..e3ec4d4200dc6ff9ebbca015bf0989fd05f5fd13 100644
--- a/src/output/ods/infosheet.h
+++ b/src/output/ods/infosheet.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef INFOSHEET_H
#define INFOSHEET_H
@@ -37,13 +38,14 @@
class InfoSheet
{
-public :
- InfoSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
+ public:
+ InfoSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project);
-private :
- OdsExport * _p_ods_export;
- const Project * _p_project;
- CalcWriterInterface * _p_writer;
+ private:
+ OdsExport *_p_ods_export;
+ const Project *_p_project;
+ CalcWriterInterface *_p_writer;
};
#endif // INFOSHEET_H
diff --git a/src/output/ods/odsexport.h b/src/output/ods/odsexport.h
index 52564aa37221eaf04d60a9290a81fd5a675fa287..9c0294d1de0a975c20f08b6f7d539b1c6a850421 100644
--- a/src/output/ods/odsexport.h
+++ b/src/output/ods/odsexport.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef ODSEXPORT_H
#define ODSEXPORT_H
@@ -36,17 +37,17 @@
class OdsExport
{
-public:
- OdsExport(const Project * project);
-
- void write(CalcWriterInterface * p_writer, WorkMonitorInterface * p_monitor);
-
- void setEvenOrOddStyle(unsigned int number, CalcWriterInterface * p_writer);
-
-private:
- const Project * _p_project;
- OdsTableCellStyleRef _even_style;
- OdsTableCellStyleRef _odd_style;
+ public:
+ OdsExport(const Project *project);
+
+ void write(CalcWriterInterface *p_writer, WorkMonitorInterface *p_monitor);
+
+ void setEvenOrOddStyle(unsigned int number, CalcWriterInterface *p_writer);
+
+ private:
+ const Project *_p_project;
+ OdsTableCellStyleRef _even_style;
+ OdsTableCellStyleRef _odd_style;
};
#endif // ODSEXPORT_H
diff --git a/src/output/ods/peptidepossheet.cpp b/src/output/ods/peptidepossheet.cpp
index d9f17a9f8ea1860fc42704c0ea759a79c6ae96a2..65279b1c72b8a7ec6b526b0836e99e916477a3a0 100644
--- a/src/output/ods/peptidepossheet.cpp
+++ b/src/output/ods/peptidepossheet.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "peptidepossheet.h"
#include <tuple>
@@ -33,156 +34,200 @@
#include <QDebug>
-PeptidePosSheet::PeptidePosSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
- _p_ods_export = p_ods_export;
- _p_writer = p_writer;
- p_writer->writeSheet("peptide pos");
-
- OdsTableSettings table_settings;
- table_settings.setVerticalSplit(1);
- _p_writer->setCurrentOdsTableSettings(table_settings);
-
- std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
- for (IdentificationGroup * p_ident:identification_list) {
- //writeHeaders(p_ident);
- writeIdentificationGroup(p_ident);
+PeptidePosSheet::PeptidePosSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : _p_project(p_project)
+{
+ _p_ods_export = p_ods_export;
+ _p_writer = p_writer;
+ p_writer->writeSheet("peptide pos");
+
+ OdsTableSettings table_settings;
+ table_settings.setVerticalSplit(1);
+ _p_writer->setCurrentOdsTableSettings(table_settings);
+
+ std::vector<IdentificationGroup *> identification_list =
+ p_project->getIdentificationGroupList();
+ for(IdentificationGroup *p_ident : identification_list)
+ {
+ // writeHeaders(p_ident);
+ writeIdentificationGroup(p_ident);
}
}
-void PeptidePosSheet::writeHeaders(IdentificationGroup * p_ident) {
- // Peptide ID Protein ID accession description Sequence Modifs Start Stop MH+ theo
+void
+PeptidePosSheet::writeHeaders(IdentificationGroup *p_ident)
+{
+ // Peptide ID Protein ID accession description Sequence Modifs Start Stop MH+
+ // theo
- //MS Sample : 20120906_balliau_extract_1_A01_urnb-1
- const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
- if (msrun_list.size() == 1) {
- _p_writer->writeCell("sample");
- _p_writer->writeLine();
- _p_writer->writeCell(msrun_list[0].get()->getSampleName());
- _p_writer->writeLine();
+ // MS Sample : 20120906_balliau_extract_1_A01_urnb-1
+ const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
+ if(msrun_list.size() == 1)
+ {
+ _p_writer->writeCell("sample");
+ _p_writer->writeLine();
+ _p_writer->writeCell(msrun_list[0].get()->getSampleName());
+ _p_writer->writeLine();
}
- _p_writer->writeLine();
- _p_writer->writeCell("Group ID");
- _p_writer->writeCell("Subgroup ID");
- //_p_writer->setCellAnnotation("MS sample name (MS run)");
- _p_writer->writeCell("Protein ID");
- _p_writer->writeCell("accession");
- _p_writer->writeCell("description");
- _p_writer->writeCell("Peptide ID");
- _p_writer->writeCell("Sequence");
- _p_writer->writeCell("Modifs");
- _p_writer->writeCell("Start");
- _p_writer->writeCell("Stop");
- _p_writer->writeCell("MH+ theo");
-
-
+ _p_writer->writeLine();
+ _p_writer->writeCell("Group ID");
+ _p_writer->writeCell("Subgroup ID");
+ //_p_writer->setCellAnnotation("MS sample name (MS run)");
+ _p_writer->writeCell("Protein ID");
+ _p_writer->writeCell("accession");
+ _p_writer->writeCell("description");
+ _p_writer->writeCell("Peptide ID");
+ _p_writer->writeCell("Sequence");
+ _p_writer->writeCell("Modifs");
+ _p_writer->writeCell("Start");
+ _p_writer->writeCell("Stop");
+ _p_writer->writeCell("MH+ theo");
}
-void PeptidePosSheet::writeBestPeptideMatch(const ProteinMatch * p_protein_match,const PeptideMatch & peptide_match) {
-
- _p_writer->writeLine();
- const PeptideEvidence * p_peptide_evidence = peptide_match.getPeptideEvidence();
-
-
- unsigned int group_number = p_protein_match->getGrpProteinSp().get()->getGroupNumber();
- unsigned int subgroup_number = p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
- unsigned int rank_number = p_protein_match->getGrpProteinSp().get()->getRank();
-
- _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
- _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(group_number));
- _p_ods_export->setEvenOrOddStyle(subgroup_number, _p_writer);
- _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(subgroup_number));
- _p_ods_export->setEvenOrOddStyle(rank_number, _p_writer);
- _p_writer->writeCell(p_protein_match->getGrpProteinSp().get()->getGroupingId());
- _p_writer->clearTableCellStyleRef();
- _p_writer->writeCell(p_protein_match->getProteinXtpSp().get()->getAccession());
- _p_writer->writeCell(p_protein_match->getProteinXtpSp().get()->getDescription());
- _p_writer->writeCell(p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
- _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getSequence());
- _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
- _p_writer->writeCell(peptide_match.getStart()+1);
- _p_writer->writeCell(peptide_match.getStart()+p_peptide_evidence->getPeptideXtpSp().get()->getSequence().size());
- _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getMz(1));
-
-
+void
+PeptidePosSheet::writeBestPeptideMatch(const ProteinMatch *p_protein_match,
+ const PeptideMatch &peptide_match)
+{
+
+ _p_writer->writeLine();
+ const PeptideEvidence *p_peptide_evidence =
+ peptide_match.getPeptideEvidence();
+
+
+ unsigned int group_number =
+ p_protein_match->getGrpProteinSp().get()->getGroupNumber();
+ unsigned int subgroup_number =
+ p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
+ unsigned int rank_number =
+ p_protein_match->getGrpProteinSp().get()->getRank();
+
+ _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
+ _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(group_number));
+ _p_ods_export->setEvenOrOddStyle(subgroup_number, _p_writer);
+ _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(subgroup_number));
+ _p_ods_export->setEvenOrOddStyle(rank_number, _p_writer);
+ _p_writer->writeCell(
+ p_protein_match->getGrpProteinSp().get()->getGroupingId());
+ _p_writer->clearTableCellStyleRef();
+ _p_writer->writeCell(
+ p_protein_match->getProteinXtpSp().get()->getAccession());
+ _p_writer->writeCell(
+ p_protein_match->getProteinXtpSp().get()->getDescription());
+ _p_writer->writeCell(
+ p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
+ _p_writer->writeCell(
+ p_peptide_evidence->getPeptideXtpSp().get()->getSequence());
+ _p_writer->writeCell(
+ p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
+ _p_writer->writeCell(peptide_match.getStart() + 1);
+ _p_writer->writeCell(
+ peptide_match.getStart() +
+ p_peptide_evidence->getPeptideXtpSp().get()->getSequence().size());
+ _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getMz(1));
}
-void PeptidePosSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
- qDebug() << "PeptidePosSheet::writeIdentificationGroup begin";
- writeHeaders(p_ident);
+void
+PeptidePosSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
+{
+ qDebug() << "PeptidePosSheet::writeIdentificationGroup begin";
+ writeHeaders(p_ident);
- std::vector<ProteinMatch *> protein_match_list;
+ std::vector<ProteinMatch *> protein_match_list;
- for (ProteinMatch * p_protein_match: p_ident->getProteinMatchList()) {
- if (p_protein_match->getValidationState() < ValidationState::grouped) continue;
- protein_match_list.push_back(p_protein_match);
+ for(ProteinMatch *p_protein_match : p_ident->getProteinMatchList())
+ {
+ if(p_protein_match->getValidationState() < ValidationState::grouped)
+ continue;
+ protein_match_list.push_back(p_protein_match);
}
- std::sort(protein_match_list.begin(), protein_match_list.end(),
- [](const ProteinMatch * a, const ProteinMatch * b)
- {
- unsigned int agroup = a->getGrpProteinSp().get()->getGroupNumber();
- unsigned int asubgroup = a->getGrpProteinSp().get()->getSubGroupNumber();
- unsigned int arank = a->getGrpProteinSp().get()->getRank();
- unsigned int bgroup = b->getGrpProteinSp().get()->getGroupNumber();
- unsigned int bsubgroup = b->getGrpProteinSp().get()->getSubGroupNumber();
- unsigned int brank = b->getGrpProteinSp().get()->getRank();
- return std::tie(agroup, asubgroup, arank) < std::tie(bgroup, bsubgroup, brank);
- });
+ std::sort(
+ protein_match_list.begin(), protein_match_list.end(),
+ [](const ProteinMatch *a, const ProteinMatch *b) {
+ unsigned int agroup = a->getGrpProteinSp().get()->getGroupNumber();
+ unsigned int asubgroup = a->getGrpProteinSp().get()->getSubGroupNumber();
+ unsigned int arank = a->getGrpProteinSp().get()->getRank();
+ unsigned int bgroup = b->getGrpProteinSp().get()->getGroupNumber();
+ unsigned int bsubgroup = b->getGrpProteinSp().get()->getSubGroupNumber();
+ unsigned int brank = b->getGrpProteinSp().get()->getRank();
+ return std::tie(agroup, asubgroup, arank) <
+ std::tie(bgroup, bsubgroup, brank);
+ });
- for (ProteinMatch * p_protein_match : protein_match_list) {
+ for(ProteinMatch *p_protein_match : protein_match_list)
+ {
- std::vector<PeptideMatch> peptide_match_list;
+ std::vector<PeptideMatch> peptide_match_list;
- for (auto & peptide_match: p_protein_match->getPeptideMatchList()) {
- if (peptide_match.getPeptideEvidence()->getValidationState() < ValidationState::grouped) continue;
- peptide_match_list.push_back(peptide_match);
+ for(auto &peptide_match : p_protein_match->getPeptideMatchList())
+ {
+ if(peptide_match.getPeptideEvidence()->getValidationState() <
+ ValidationState::grouped)
+ continue;
+ peptide_match_list.push_back(peptide_match);
}
- std::sort(peptide_match_list.begin(), peptide_match_list.end(),
- [](const PeptideMatch & a, const PeptideMatch & b)
+ std::sort(peptide_match_list.begin(), peptide_match_list.end(),
+ [](const PeptideMatch &a, const PeptideMatch &b) {
+ unsigned int arank =
+ a.getPeptideEvidence()->getGrpPeptideSp().get()->getRank();
+ unsigned int aposition = a.getStart();
+ unsigned int brank =
+ b.getPeptideEvidence()->getGrpPeptideSp().get()->getRank();
+ unsigned int bposition = b.getStart();
+ return std::tie(arank, aposition) <
+ std::tie(brank, bposition);
+ });
+
+ const PeptideMatch *p_best_peptide_match = nullptr;
+
+ for(auto &peptide_match : peptide_match_list)
{
- unsigned int arank = a.getPeptideEvidence()->getGrpPeptideSp().get()->getRank();
- unsigned int aposition = a.getStart();
- unsigned int brank = b.getPeptideEvidence()->getGrpPeptideSp().get()->getRank();
- unsigned int bposition = b.getStart();
- return std::tie(arank, aposition) < std::tie(brank, bposition);
- });
-
- const PeptideMatch * p_best_peptide_match = nullptr;
-
- for (auto & peptide_match:peptide_match_list) {
- if (p_best_peptide_match == nullptr) {
- p_best_peptide_match = &peptide_match;
+ if(p_best_peptide_match == nullptr)
+ {
+ p_best_peptide_match = &peptide_match;
}
- //change spectra :
- unsigned int arank = p_best_peptide_match->getPeptideEvidence()->getGrpPeptideSp().get()->getRank();
- unsigned int aposition = p_best_peptide_match->getStart();
- unsigned int brank = peptide_match.getPeptideEvidence()->getGrpPeptideSp().get()->getRank();
- unsigned int bposition = peptide_match.getStart();
-
- if (std::tie(arank, aposition) != std::tie(brank, bposition)) {
- //write p_best_peptide_match
- writeBestPeptideMatch(p_protein_match, *p_best_peptide_match);
- p_best_peptide_match = &peptide_match;
+ // change spectra :
+ unsigned int arank = p_best_peptide_match->getPeptideEvidence()
+ ->getGrpPeptideSp()
+ .get()
+ ->getRank();
+ unsigned int aposition = p_best_peptide_match->getStart();
+ unsigned int brank = peptide_match.getPeptideEvidence()
+ ->getGrpPeptideSp()
+ .get()
+ ->getRank();
+ unsigned int bposition = peptide_match.getStart();
+
+ if(std::tie(arank, aposition) != std::tie(brank, bposition))
+ {
+ // write p_best_peptide_match
+ writeBestPeptideMatch(p_protein_match, *p_best_peptide_match);
+ p_best_peptide_match = &peptide_match;
}
- else {
- if (p_best_peptide_match->getPeptideEvidence()->getEvalue()> peptide_match.getPeptideEvidence()->getEvalue()) {
- p_best_peptide_match = &peptide_match;
+ else
+ {
+ if(p_best_peptide_match->getPeptideEvidence()->getEvalue() >
+ peptide_match.getPeptideEvidence()->getEvalue())
+ {
+ p_best_peptide_match = &peptide_match;
}
}
}
- if (p_best_peptide_match != nullptr) {
- writeBestPeptideMatch(p_protein_match, *p_best_peptide_match);
-
+ if(p_best_peptide_match != nullptr)
+ {
+ writeBestPeptideMatch(p_protein_match, *p_best_peptide_match);
}
}
- _p_writer->writeLine();
- _p_writer->writeLine();
- qDebug() << "PeptidePosSheet::writeIdentificationGroup end";
+ _p_writer->writeLine();
+ _p_writer->writeLine();
+ qDebug() << "PeptidePosSheet::writeIdentificationGroup end";
}
diff --git a/src/output/ods/peptidepossheet.h b/src/output/ods/peptidepossheet.h
index 0e9d47c286dcddd3ffee8aa868a5768d7e672ea8..a7b32bf8cfc34ea6a970f7abc372fb21d37ceaf1 100644
--- a/src/output/ods/peptidepossheet.h
+++ b/src/output/ods/peptidepossheet.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PEPTIDEPOSSHEET_H
@@ -39,17 +40,20 @@
class PeptidePosSheet
{
-public :
- PeptidePosSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
-private :
- void writeIdentificationGroup(IdentificationGroup * p_ident);
- void writeHeaders(IdentificationGroup * p_ident);
- void writeBestPeptideMatch(const ProteinMatch * p_protein_match, const PeptideMatch & peptide_match);
-
-private :
- OdsExport * _p_ods_export;
- const Project * _p_project;
- CalcWriterInterface * _p_writer;
+ public:
+ PeptidePosSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project);
+
+ private:
+ void writeIdentificationGroup(IdentificationGroup *p_ident);
+ void writeHeaders(IdentificationGroup *p_ident);
+ void writeBestPeptideMatch(const ProteinMatch *p_protein_match,
+ const PeptideMatch &peptide_match);
+
+ private:
+ OdsExport *_p_ods_export;
+ const Project *_p_project;
+ CalcWriterInterface *_p_writer;
};
#endif // PEPTIDEPOSSHEET_H
diff --git a/src/output/ods/peptidesheet.cpp b/src/output/ods/peptidesheet.cpp
index 7010c69fb1ad94a968ddbb80b9e729bbc8019341..847e6d7ef94c9efa222fb0479063f0f930298c43 100644
--- a/src/output/ods/peptidesheet.cpp
+++ b/src/output/ods/peptidesheet.cpp
@@ -6,142 +6,176 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "peptidesheet.h"
#include <pappsomspp/utils.h>
-PeptideSheet::PeptideSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
- _p_ods_export = p_ods_export;
- _p_writer = p_writer;
- p_writer->writeSheet("peptides");
-
- OdsTableSettings table_settings;
- table_settings.setVerticalSplit(1);
- _p_writer->setCurrentOdsTableSettings(table_settings);
-
- std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
- for (IdentificationGroup * p_ident:identification_list) {
- //writeHeaders(p_ident);
- writeIdentificationGroup(p_ident);
+PeptideSheet::PeptideSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : _p_project(p_project)
+{
+ _p_ods_export = p_ods_export;
+ _p_writer = p_writer;
+ p_writer->writeSheet("peptides");
+
+ OdsTableSettings table_settings;
+ table_settings.setVerticalSplit(1);
+ _p_writer->setCurrentOdsTableSettings(table_settings);
+
+ std::vector<IdentificationGroup *> identification_list =
+ p_project->getIdentificationGroupList();
+ for(IdentificationGroup *p_ident : identification_list)
+ {
+ // writeHeaders(p_ident);
+ writeIdentificationGroup(p_ident);
}
}
-void PeptideSheet::writeHeaders(IdentificationGroup * p_ident) {
- // Group ID Peptide ID SequenceLI Modifs Charge MH+ theo Number of subgroups Subgroup ids Number of spectra
- //MS Sample : 20120906_balliau_extract_1_A01_urnb-1
- const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
- if (msrun_list.size() == 1) {
- _p_writer->writeCell("sample");
- _p_writer->writeLine();
- _p_writer->writeCell(msrun_list[0].get()->getSampleName());
- _p_writer->writeLine();
+void
+PeptideSheet::writeHeaders(IdentificationGroup *p_ident)
+{
+ // Group ID Peptide ID SequenceLI Modifs Charge MH+ theo Number of subgroups
+ // Subgroup ids Number of spectra
+ // MS Sample : 20120906_balliau_extract_1_A01_urnb-1
+ const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
+ if(msrun_list.size() == 1)
+ {
+ _p_writer->writeCell("sample");
+ _p_writer->writeLine();
+ _p_writer->writeCell(msrun_list[0].get()->getSampleName());
+ _p_writer->writeLine();
}
- _p_writer->writeLine();
- _p_writer->writeCell("Group ID");
- _p_writer->writeCell("Peptide ID");
- _p_writer->setCellAnnotation("peptide sequence where all leucine are turned into isoleucine");
- _p_writer->writeCell("SequenceLI");
- _p_writer->writeCell("Modifs");
- _p_writer->setCellAnnotation("the charge associated to the best peptide Evalue for this sequenceLI");
- _p_writer->writeCell("Charge");
- _p_writer->setCellAnnotation("theoretical mh");
- _p_writer->writeCell("MH+ theo");
- _p_writer->writeCell("Number of subgroups");
- _p_writer->writeCell("Subgroup ids");
- _p_writer->setCellAnnotation("number of scans associated to this peptide");
- _p_writer->writeCell("Number of spectra");
-
-
+ _p_writer->writeLine();
+ _p_writer->writeCell("Group ID");
+ _p_writer->writeCell("Peptide ID");
+ _p_writer->setCellAnnotation(
+ "peptide sequence where all leucine are turned into isoleucine");
+ _p_writer->writeCell("SequenceLI");
+ _p_writer->writeCell("Modifs");
+ _p_writer->setCellAnnotation(
+ "the charge associated to the best peptide Evalue for this sequenceLI");
+ _p_writer->writeCell("Charge");
+ _p_writer->setCellAnnotation("theoretical mh");
+ _p_writer->writeCell("MH+ theo");
+ _p_writer->writeCell("Number of subgroups");
+ _p_writer->writeCell("Subgroup ids");
+ _p_writer->setCellAnnotation("number of scans associated to this peptide");
+ _p_writer->writeCell("Number of spectra");
}
-void PeptideSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
+void
+PeptideSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
+{
- writeHeaders(p_ident);
- for (const std::pair<unsigned int, GroupingGroupSp> & group_pair : p_ident->getGroupStore().getGroupMap()) {
+ writeHeaders(p_ident);
+ for(const std::pair<unsigned int, GroupingGroupSp> &group_pair :
+ p_ident->getGroupStore().getGroupMap())
+ {
- std::vector<const PeptideEvidence *> peptide_evidence_list = group_pair.second.get()->getPeptideEvidenceList();
+ std::vector<const PeptideEvidence *> peptide_evidence_list =
+ group_pair.second.get()->getPeptideEvidenceList();
- std::sort(peptide_evidence_list.begin(), peptide_evidence_list.end(),
- [](const PeptideEvidence * a, const PeptideEvidence * b)
- {
- return a->getGrpPeptideSp().get()->getRank() < b->getGrpPeptideSp().get()->getRank();
- });
+ std::sort(peptide_evidence_list.begin(), peptide_evidence_list.end(),
+ [](const PeptideEvidence *a, const PeptideEvidence *b) {
+ return a->getGrpPeptideSp().get()->getRank() <
+ b->getGrpPeptideSp().get()->getRank();
+ });
- const PeptideEvidence * p_best_peptide_evidence = nullptr;
- _sample_scan_list.clear();
+ const PeptideEvidence *p_best_peptide_evidence = nullptr;
+ _sample_scan_list.clear();
- for (auto & peptide_evidence: peptide_evidence_list) {
- if (p_best_peptide_evidence == nullptr) {
- p_best_peptide_evidence = peptide_evidence;
+ for(auto &peptide_evidence : peptide_evidence_list)
+ {
+ if(p_best_peptide_evidence == nullptr)
+ {
+ p_best_peptide_evidence = peptide_evidence;
}
- if (p_best_peptide_evidence->getGrpPeptideSp().get() != peptide_evidence->getGrpPeptideSp().get()) {
- //write p_best_peptide_match
- writeBestPeptideEvidence(group_pair.second.get(), p_best_peptide_evidence);
- p_best_peptide_evidence = peptide_evidence;
+ if(p_best_peptide_evidence->getGrpPeptideSp().get() !=
+ peptide_evidence->getGrpPeptideSp().get())
+ {
+ // write p_best_peptide_match
+ writeBestPeptideEvidence(group_pair.second.get(),
+ p_best_peptide_evidence);
+ p_best_peptide_evidence = peptide_evidence;
}
- else {
- if (p_best_peptide_evidence->getEvalue()> peptide_evidence->getEvalue()) {
- p_best_peptide_evidence = peptide_evidence;
+ else
+ {
+ if(p_best_peptide_evidence->getEvalue() >
+ peptide_evidence->getEvalue())
+ {
+ p_best_peptide_evidence = peptide_evidence;
}
}
- _sample_scan_list.push_back(peptide_evidence->getHashSampleScan());
+ _sample_scan_list.push_back(peptide_evidence->getHashSampleScan());
}
- if (p_best_peptide_evidence != nullptr) {
- writeBestPeptideEvidence(group_pair.second.get(), p_best_peptide_evidence);
+ if(p_best_peptide_evidence != nullptr)
+ {
+ writeBestPeptideEvidence(group_pair.second.get(),
+ p_best_peptide_evidence);
}
}
- _p_writer->writeLine();
- _p_writer->writeLine();
+ _p_writer->writeLine();
+ _p_writer->writeLine();
}
-void PeptideSheet::writeBestPeptideEvidence(const GroupingGroup * p_group,const PeptideEvidence * p_peptide_evidence) {
-
- std::sort(_sample_scan_list.begin(), _sample_scan_list.end());
- auto last = std::unique(_sample_scan_list.begin(), _sample_scan_list.end());
- _sample_scan_list.erase(last, _sample_scan_list.end());
-
- _p_writer->writeLine();
-
-
- unsigned int group_number = p_peptide_evidence->getGrpPeptideSp().get()->getGroupNumber();
-
- _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
- _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(group_number));
- _p_writer->clearTableCellStyleRef();
- _p_writer->writeCell(p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
- _p_writer->writeCell(p_peptide_evidence->getGrpPeptideSp().get()->getSequence());
- _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
- _p_writer->writeCell(p_peptide_evidence->getCharge());
- _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getNativePeptideP()->getMz(1));
- QStringList sg_list = p_group->getSubgroupIdList(p_peptide_evidence);
- _p_writer->writeCell((unsigned int) sg_list.size());
- _p_writer->writeCell(sg_list.join(" "));
- _p_writer->writeCell((unsigned int) _sample_scan_list.size());
-
- _sample_scan_list.clear();
+void
+PeptideSheet::writeBestPeptideEvidence(
+ const GroupingGroup *p_group, const PeptideEvidence *p_peptide_evidence)
+{
+
+ std::sort(_sample_scan_list.begin(), _sample_scan_list.end());
+ auto last = std::unique(_sample_scan_list.begin(), _sample_scan_list.end());
+ _sample_scan_list.erase(last, _sample_scan_list.end());
+
+ _p_writer->writeLine();
+
+
+ unsigned int group_number =
+ p_peptide_evidence->getGrpPeptideSp().get()->getGroupNumber();
+
+ _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
+ _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(group_number));
+ _p_writer->clearTableCellStyleRef();
+ _p_writer->writeCell(
+ p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
+ _p_writer->writeCell(
+ p_peptide_evidence->getGrpPeptideSp().get()->getSequence());
+ _p_writer->writeCell(
+ p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
+ _p_writer->writeCell(p_peptide_evidence->getCharge());
+ _p_writer->writeCell(
+ p_peptide_evidence->getPeptideXtpSp().get()->getNativePeptideP()->getMz(1));
+ QStringList sg_list = p_group->getSubgroupIdList(p_peptide_evidence);
+ _p_writer->writeCell((unsigned int)sg_list.size());
+ _p_writer->writeCell(sg_list.join(" "));
+ _p_writer->writeCell((unsigned int)_sample_scan_list.size());
+
+ _sample_scan_list.clear();
}
diff --git a/src/output/ods/peptidesheet.h b/src/output/ods/peptidesheet.h
index 8820e7e1b67c003dbed65375ec523bf24e5e808a..7db49c459755b1ee2c01ea27459fa19d643ae125 100644
--- a/src/output/ods/peptidesheet.h
+++ b/src/output/ods/peptidesheet.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PEPTIDESHEET_H
#define PEPTIDESHEET_H
@@ -37,18 +38,21 @@
class PeptideSheet
{
-public :
- PeptideSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
-private :
- void writeIdentificationGroup(IdentificationGroup * p_ident);
- void writeHeaders(IdentificationGroup * p_ident);
- void writeBestPeptideEvidence(const GroupingGroup * p_group, const PeptideEvidence * p_peptide_evidence);
-
-private :
- OdsExport * _p_ods_export;
- const Project * _p_project;
- CalcWriterInterface * _p_writer;
- std::vector<size_t> _sample_scan_list;
+ public:
+ PeptideSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project);
+
+ private:
+ void writeIdentificationGroup(IdentificationGroup *p_ident);
+ void writeHeaders(IdentificationGroup *p_ident);
+ void writeBestPeptideEvidence(const GroupingGroup *p_group,
+ const PeptideEvidence *p_peptide_evidence);
+
+ private:
+ OdsExport *_p_ods_export;
+ const Project *_p_project;
+ CalcWriterInterface *_p_writer;
+ std::vector<size_t> _sample_scan_list;
};
diff --git a/src/output/ods/proteinsheet.cpp b/src/output/ods/proteinsheet.cpp
index 0bc93d1e1fcfbb45e206a68ccddcdbe2692b81a6..5a67f8ef9b5f3a65d2ddf5e739c5a5b86f78af59 100644
--- a/src/output/ods/proteinsheet.cpp
+++ b/src/output/ods/proteinsheet.cpp
@@ -84,12 +84,13 @@ ProteinSheet::writeHeaders(IdentificationGroup *p_ident)
_p_writer->writeCell("Group ID");
_p_writer->setCellAnnotation("subgroup number");
_p_writer->writeCell("Sub-group ID");
-
- _p_writer->setCellAnnotation(ProteinTableModel::getDescription(ProteinListColumn::protein_grouping_id));
+
+ _p_writer->setCellAnnotation(
+ ProteinTableModel::getDescription(ProteinListColumn::protein_grouping_id));
_p_writer->writeCell("Protein ID");
- //writeCellHeader(ProteinListColumn::protein_grouping_id);
+ // writeCellHeader(ProteinListColumn::protein_grouping_id);
//_p_writer->setCellAnnotation("unique protein identifier within this grouping
- //experiment"); _p_writer->writeCell("Protein ID");
+ // experiment"); _p_writer->writeCell("Protein ID");
writeCellHeader(ProteinListColumn::accession);
writeCellHeader(ProteinListColumn::description);
@@ -103,7 +104,7 @@ ProteinSheet::writeHeaders(IdentificationGroup *p_ident)
writeCellHeader(ProteinListColumn::spectrum);
//_p_writer->setCellAnnotation("number of scans (spectra) attributed to this
- //protein");
+ // protein");
// _p_writer->writeCell("Spectra");
writeCellHeader(ProteinListColumn::specific_spectrum);
diff --git a/src/output/ods/ptm/ptmislandsheet.cpp b/src/output/ods/ptm/ptmislandsheet.cpp
index 6aa43fa81731455e8badc5936dc3f1f26c9ad0a3..70fa50a757927289128db809bb12ede2da74f14f 100644
--- a/src/output/ods/ptm/ptmislandsheet.cpp
+++ b/src/output/ods/ptm/ptmislandsheet.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmislandsheet.h"
@@ -33,149 +34,197 @@
#include <pappsomspp/utils.h>
#include <pappsomspp/pappsoexception.h>
-PtmIslandSheet::PtmIslandSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
- qDebug() << "PtmIslandSheet::PtmIslandSheet begin" ;
- _p_writer = p_writer;
- _p_ods_export = p_ods_export;
- p_writer->writeSheet("PTM islands");
-
- std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
- for (IdentificationGroup * p_ident:identification_list) {
- //writeHeaders(p_ident);
- writeIdentificationGroup(p_ident);
+PtmIslandSheet::PtmIslandSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : _p_project(p_project)
+{
+ qDebug() << "PtmIslandSheet::PtmIslandSheet begin";
+ _p_writer = p_writer;
+ _p_ods_export = p_ods_export;
+ p_writer->writeSheet("PTM islands");
+
+ std::vector<IdentificationGroup *> identification_list =
+ p_project->getIdentificationGroupList();
+ for(IdentificationGroup *p_ident : identification_list)
+ {
+ // writeHeaders(p_ident);
+ writeIdentificationGroup(p_ident);
}
- qDebug() << "PtmIslandSheet::PtmIslandSheet end" ;
+ qDebug() << "PtmIslandSheet::PtmIslandSheet end";
}
-void PtmIslandSheet::writeCellHeader(PtmIslandListColumn column) {
- qDebug() << "PtmIslandSheet::writeCellHeader begin " << (std::int8_t) column;
- _p_writer->setCellAnnotation(PtmIslandTableModel::getDescription(column));
- _p_writer->writeCell(PtmIslandTableModel::getTitle(column));
- qDebug() << "PtmIslandSheet::writeCellHeader end" ;
+void
+PtmIslandSheet::writeCellHeader(PtmIslandListColumn column)
+{
+ qDebug() << "PtmIslandSheet::writeCellHeader begin " << (std::int8_t)column;
+ _p_writer->setCellAnnotation(PtmIslandTableModel::getDescription(column));
+ _p_writer->writeCell(PtmIslandTableModel::getTitle(column));
+ qDebug() << "PtmIslandSheet::writeCellHeader end";
}
-void PtmIslandSheet::writeHeaders(IdentificationGroup * p_ident) {
-
- //ptm
-
-//Group ID Sub-group ID PhosphoIsland ID Description MW Phosphosites positions Spectra Uniques number of proteins sharing these phosphosites
-//a1 a1.a1 a1.a1.a1 AT1G01100.1 | Symbols: | 60S acidic ribosomal protein family | chr1:50284-50954 REVERSE LENGTH=112 11,1000003814697 102 435 3 6
- qDebug() << "PtmIslandSheet::writeHeaders begin" ;
- const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
- if (msrun_list.size() == 1) {
- _p_writer->writeCell("sample");
- _p_writer->writeLine();
- _p_writer->writeCell(msrun_list[0].get()->getSampleName());
- _p_writer->writeLine();
- }
- _p_writer->writeLine();
-
- _p_writer->setCellAnnotation("PTM group number");
- _p_writer->writeCell("PTM group ID");
- _p_writer->setCellAnnotation("PTM subgroup number");
- _p_writer->writeCell("PTM sub-group ID");
- writeCellHeader(PtmIslandListColumn::ptm_island_id);
- //_p_writer->PtmIslandListColumn("unique protein identifier within this grouping experiment");
- //_p_writer->writeCell("Protein ID");
-
- writeCellHeader(PtmIslandListColumn::accession);
- writeCellHeader(PtmIslandListColumn::description);
- _p_writer->setCellAnnotation("computed molecular weight for this protein (sum of amino acid masses)");
- _p_writer->writeCell("MW");
- writeCellHeader(PtmIslandListColumn::ptm_position_list);
-
- writeCellHeader(PtmIslandListColumn::spectrum);
- //_p_writer->setCellAnnotation("number of scans (spectra) attributed to this protein");
- // _p_writer->writeCell("Spectra");
- writeCellHeader(PtmIslandListColumn::sequence);
+void
+PtmIslandSheet::writeHeaders(IdentificationGroup *p_ident)
+{
- _p_writer->setCellAnnotation("Number of proteins sharing this PTM island");
- _p_writer->writeCell("Number of proteins");
-
- qDebug() << "PtmIslandSheet::writeHeaders end" ;
+ // ptm
+ // Group ID Sub-group ID PhosphoIsland ID Description MW Phosphosites
+ // positions Spectra Uniques number of proteins sharing these phosphosites a1
+ // a1.a1 a1.a1.a1 AT1G01100.1 | Symbols: | 60S acidic ribosomal protein
+ // family | chr1:50284-50954 REVERSE LENGTH=112 11,1000003814697 102 435 3 6
+ qDebug() << "PtmIslandSheet::writeHeaders begin";
+ const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
+ if(msrun_list.size() == 1)
+ {
+ _p_writer->writeCell("sample");
+ _p_writer->writeLine();
+ _p_writer->writeCell(msrun_list[0].get()->getSampleName());
+ _p_writer->writeLine();
+ }
+ _p_writer->writeLine();
+
+ _p_writer->setCellAnnotation("PTM group number");
+ _p_writer->writeCell("PTM group ID");
+ _p_writer->setCellAnnotation("PTM subgroup number");
+ _p_writer->writeCell("PTM sub-group ID");
+ writeCellHeader(PtmIslandListColumn::ptm_island_id);
+ //_p_writer->PtmIslandListColumn("unique protein identifier within this
+ //grouping experiment"); _p_writer->writeCell("Protein ID");
+
+ writeCellHeader(PtmIslandListColumn::accession);
+ writeCellHeader(PtmIslandListColumn::description);
+ _p_writer->setCellAnnotation(
+ "computed molecular weight for this protein (sum of amino acid masses)");
+ _p_writer->writeCell("MW");
+ writeCellHeader(PtmIslandListColumn::ptm_position_list);
+
+ writeCellHeader(PtmIslandListColumn::spectrum);
+ //_p_writer->setCellAnnotation("number of scans (spectra) attributed to this
+ //protein");
+ // _p_writer->writeCell("Spectra");
+ writeCellHeader(PtmIslandListColumn::sequence);
+
+ _p_writer->setCellAnnotation("Number of proteins sharing this PTM island");
+ _p_writer->writeCell("Number of proteins");
+
+ qDebug() << "PtmIslandSheet::writeHeaders end";
}
-void PtmIslandSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
+void
+PtmIslandSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
+{
- qDebug() << "PtmIslandSheet::writeIdentificationGroup begin" ;
- _p_ptm_grouping_experiment = p_ident->getPtmGroupingExperiment();
- if (_p_ptm_grouping_experiment == nullptr) {
- throw pappso::PappsoException(QObject::tr("Error writing PTM island :\n_p_ptm_grouping_experiment = nullptr"));
+ qDebug() << "PtmIslandSheet::writeIdentificationGroup begin";
+ _p_ptm_grouping_experiment = p_ident->getPtmGroupingExperiment();
+ if(_p_ptm_grouping_experiment == nullptr)
+ {
+ throw pappso::PappsoException(QObject::tr(
+ "Error writing PTM island :\n_p_ptm_grouping_experiment = nullptr"));
}
- writeHeaders(p_ident);
+ writeHeaders(p_ident);
- qDebug() << "PtmIslandSheet::writeIdentificationGroup getPtmIslandList" ;
- std::vector<PtmIslandSp> ptm_island_list;
- for (auto ptm_island_sp : _p_ptm_grouping_experiment->getPtmIslandList() ) {
- qDebug() << "PtmIslandSheet::writeIdentificationGroup getPtmIslandList copy" ;
- ptm_island_list.push_back(ptm_island_sp);
+ qDebug() << "PtmIslandSheet::writeIdentificationGroup getPtmIslandList";
+ std::vector<PtmIslandSp> ptm_island_list;
+ for(auto ptm_island_sp : _p_ptm_grouping_experiment->getPtmIslandList())
+ {
+ qDebug()
+ << "PtmIslandSheet::writeIdentificationGroup getPtmIslandList copy";
+ ptm_island_list.push_back(ptm_island_sp);
}
- qDebug() << "PtmIslandSheet::writeIdentificationGroup sort" ;
- std::sort(ptm_island_list.begin(), ptm_island_list.end(),
- [](PtmIslandSp & a, PtmIslandSp & b)
+ qDebug() << "PtmIslandSheet::writeIdentificationGroup sort";
+ std::sort(ptm_island_list.begin(), ptm_island_list.end(),
+ [](PtmIslandSp &a, PtmIslandSp &b) {
+ return a.get()->getGroupingId() < b.get()->getGroupingId();
+ });
+
+ qDebug() << "PtmIslandSheet::writeIdentificationGroup 2";
+ for(auto &ptm_island : ptm_island_list)
{
- return a.get()->getGroupingId() < b.get()->getGroupingId();
- });
-
- qDebug() << "PtmIslandSheet::writeIdentificationGroup 2" ;
- for (auto & ptm_island:ptm_island_list) {
- writeOnePtmIsland(ptm_island);
+ writeOnePtmIsland(ptm_island);
}
- _p_writer->writeLine();
- qDebug() << "PtmIslandSheet::writeIdentificationGroup end" ;
+ _p_writer->writeLine();
+ qDebug() << "PtmIslandSheet::writeIdentificationGroup end";
}
-void PtmIslandSheet::writeOnePtmIsland(PtmIslandSp & sp_ptm_island) {
- try {
- _p_writer->writeLine();
-
- qDebug() << "PtmIslandSheet::writeOnePtmIsland begin" ;
- ValidationState validation_state = ValidationState::validAndChecked;
-
- //pappso::GrpProtein * p_grp_protein = p_protein_match->getGrpProteinSp().get();
-
- ProteinXtp * p_protein = sp_ptm_island.get()->getProteinMatch()->getProteinXtpSp().get();
-
- const PtmIslandSubgroup * p_ptm_island_subgroup = sp_ptm_island.get()->getPtmIslandSubroup();
- const PtmIslandGroup * p_ptm_island_group = p_ptm_island_subgroup->getPtmIslandGroup();
- unsigned int group_number = p_ptm_island_group->getGroupNumber();
- unsigned int subgroup_number = p_ptm_island_subgroup->getSubgroupNumber();
-
- _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
- _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(group_number));
- _p_ods_export->setEvenOrOddStyle(subgroup_number, _p_writer);
- _p_writer->writeCell(QString("%1.%2").arg(pappso::Utils::getLexicalOrderedString(group_number)).arg(pappso::Utils::getLexicalOrderedString(subgroup_number)));
- _p_writer->clearTableCellStyleRef();
- _p_writer->writeCell(sp_ptm_island.get()->getGroupingId());
- const std::list<DbXref> & dbxref_list = p_protein->getDbxrefList();
- if (dbxref_list.size() == 0) {
- _p_writer->writeCell(p_protein->getAccession());
+void
+PtmIslandSheet::writeOnePtmIsland(PtmIslandSp &sp_ptm_island)
+{
+ try
+ {
+ _p_writer->writeLine();
+
+ qDebug() << "PtmIslandSheet::writeOnePtmIsland begin";
+ ValidationState validation_state = ValidationState::validAndChecked;
+
+ // pappso::GrpProtein * p_grp_protein =
+ // p_protein_match->getGrpProteinSp().get();
+
+ ProteinXtp *p_protein =
+ sp_ptm_island.get()->getProteinMatch()->getProteinXtpSp().get();
+
+ const PtmIslandSubgroup *p_ptm_island_subgroup =
+ sp_ptm_island.get()->getPtmIslandSubroup();
+ const PtmIslandGroup *p_ptm_island_group =
+ p_ptm_island_subgroup->getPtmIslandGroup();
+ unsigned int group_number = p_ptm_island_group->getGroupNumber();
+ unsigned int subgroup_number = p_ptm_island_subgroup->getSubgroupNumber();
+
+ _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
+ _p_writer->writeCell(
+ pappso::Utils::getLexicalOrderedString(group_number));
+ _p_ods_export->setEvenOrOddStyle(subgroup_number, _p_writer);
+ _p_writer->writeCell(
+ QString("%1.%2")
+ .arg(pappso::Utils::getLexicalOrderedString(group_number))
+ .arg(pappso::Utils::getLexicalOrderedString(subgroup_number)));
+ _p_writer->clearTableCellStyleRef();
+ _p_writer->writeCell(sp_ptm_island.get()->getGroupingId());
+ const std::list<DbXref> &dbxref_list = p_protein->getDbxrefList();
+ if(dbxref_list.size() == 0)
+ {
+ _p_writer->writeCell(p_protein->getAccession());
}
- else {
- _p_writer->writeCell(dbxref_list.front().getUrl(), p_protein->getAccession());
+ else
+ {
+ _p_writer->writeCell(dbxref_list.front().getUrl(),
+ p_protein->getAccession());
}
- _p_writer->writeCell(p_protein->getDescription());
- _p_writer->writeCell(p_protein->getMass());
+ _p_writer->writeCell(p_protein->getDescription());
+ _p_writer->writeCell(p_protein->getMass());
- QStringList position_list;
- for (unsigned int position : sp_ptm_island.get()->getPositionList()) {
- position_list << QString("%1").arg(position+1);
+ QStringList position_list;
+ for(unsigned int position : sp_ptm_island.get()->getPositionList())
+ {
+ position_list << QString("%1").arg(position + 1);
}
- _p_writer->writeCell(position_list.join(" "));
- // _p_writer->writeCell("Spectra");
- _p_writer->writeCell((unsigned int) sp_ptm_island.get()->getPtmIslandSubroup()->countSampleScan());
- // _p_writer->writeCell("Uniques");
- _p_writer->writeCell((unsigned int) sp_ptm_island.get()->countSequence());
- _p_writer->writeCell((unsigned int) sp_ptm_island.get()->getPtmIslandSubroup()->getPtmIslandList().size());
-
-
- qDebug() << "ProteinSheet::writeOneProtein end" ;
+ _p_writer->writeCell(position_list.join(" "));
+ // _p_writer->writeCell("Spectra");
+ _p_writer->writeCell((unsigned int)sp_ptm_island.get()
+ ->getPtmIslandSubroup()
+ ->countSampleScan());
+ // _p_writer->writeCell("Uniques");
+ _p_writer->writeCell((unsigned int)sp_ptm_island.get()->countSequence());
+ _p_writer->writeCell((unsigned int)sp_ptm_island.get()
+ ->getPtmIslandSubroup()
+ ->getPtmIslandList()
+ .size());
+
+
+ qDebug() << "ProteinSheet::writeOneProtein end";
}
- catch (pappso::PappsoException error) {
- throw pappso::PappsoException(QObject::tr("Error writing PTM island of protein %1 :\n%2").arg(sp_ptm_island.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession()).arg(error.qwhat()));
+ catch(pappso::PappsoException error)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error writing PTM island of protein %1 :\n%2")
+ .arg(sp_ptm_island.get()
+ ->getProteinMatch()
+ ->getProteinXtpSp()
+ .get()
+ ->getAccession())
+ .arg(error.qwhat()));
}
}
diff --git a/src/output/ods/ptm/ptmislandsheet.h b/src/output/ods/ptm/ptmislandsheet.h
index 247d650f3bf1dc4efa425a52ad04d3796821e072..b9e9071fd792d0f03e6d77670e9c0efd38cdf9f8 100644
--- a/src/output/ods/ptm/ptmislandsheet.h
+++ b/src/output/ods/ptm/ptmislandsheet.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMISLANDSHEET_H
#define PTMISLANDSHEET_H
@@ -38,20 +39,23 @@
class PtmIslandSheet
{
-public :
- PtmIslandSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
-private :
- void writeIdentificationGroup(IdentificationGroup * p_ident);
- void writeHeaders(IdentificationGroup * p_ident);
- void writeOnePtmIsland(PtmIslandSp & sp_ptm_island);
-
-protected:
- void writeCellHeader(PtmIslandListColumn column);
-private :
- OdsExport * _p_ods_export;
- const Project * _p_project;
- CalcWriterInterface * _p_writer;
- const PtmGroupingExperiment * _p_ptm_grouping_experiment;
+ public:
+ PtmIslandSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project);
+
+ private:
+ void writeIdentificationGroup(IdentificationGroup *p_ident);
+ void writeHeaders(IdentificationGroup *p_ident);
+ void writeOnePtmIsland(PtmIslandSp &sp_ptm_island);
+
+ protected:
+ void writeCellHeader(PtmIslandListColumn column);
+
+ private:
+ OdsExport *_p_ods_export;
+ const Project *_p_project;
+ CalcWriterInterface *_p_writer;
+ const PtmGroupingExperiment *_p_ptm_grouping_experiment;
};
#endif // PTMISLANDSHEET_H
diff --git a/src/output/ods/ptm/ptmspectrasheet.cpp b/src/output/ods/ptm/ptmspectrasheet.cpp
index c1ecba40e626557cda654551b003cebadd51d908..015382f70db4356ce90424dea7ce6b79fcb73e16 100644
--- a/src/output/ods/ptm/ptmspectrasheet.cpp
+++ b/src/output/ods/ptm/ptmspectrasheet.cpp
@@ -6,267 +6,331 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "ptmspectrasheet.h"
#include <tuple>
#include <pappsomspp/utils.h>
-PtmSpectraSheet::PtmSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project, const QString & sheet_name): _p_project(p_project) {
- _p_ods_export = p_ods_export;
- _p_writer = p_writer;
- p_writer->writeSheet(sheet_name);
-
- OdsTableSettings table_settings;
- table_settings.setVerticalSplit(1);
- _p_writer->setCurrentOdsTableSettings(table_settings);
-
- std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
- for (IdentificationGroup * p_ident:identification_list) {
- //writeHeaders(p_ident);
- writeIdentificationGroup(p_ident);
+PtmSpectraSheet::PtmSpectraSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project,
+ const QString &sheet_name)
+ : _p_project(p_project)
+{
+ _p_ods_export = p_ods_export;
+ _p_writer = p_writer;
+ p_writer->writeSheet(sheet_name);
+
+ OdsTableSettings table_settings;
+ table_settings.setVerticalSplit(1);
+ _p_writer->setCurrentOdsTableSettings(table_settings);
+
+ std::vector<IdentificationGroup *> identification_list =
+ p_project->getIdentificationGroupList();
+ for(IdentificationGroup *p_ident : identification_list)
+ {
+ // writeHeaders(p_ident);
+ writeIdentificationGroup(p_ident);
}
}
-PtmSpectraSheet::PtmSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): PtmSpectraSheet(p_ods_export, p_writer, p_project, QString("PTM spectra")) {
+PtmSpectraSheet::PtmSpectraSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : PtmSpectraSheet(p_ods_export, p_writer, p_project, QString("PTM spectra"))
+{
}
-void PtmSpectraSheet::writeCellHeader(PeptideListColumn column) {
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- _p_writer->setCellAnnotation(PeptideTableModel::getDescription(column));
- _p_writer->writeCell(PeptideTableModel::getTitle(column));
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+void
+PtmSpectraSheet::writeCellHeader(PeptideListColumn column)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _p_writer->setCellAnnotation(PeptideTableModel::getDescription(column));
+ _p_writer->writeCell(PeptideTableModel::getTitle(column));
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-void PtmSpectraSheet::writeHeaders(IdentificationGroup * p_ident) {
- // Group ID Sub-group ID Phosphopeptide ID Sample Scan Rt Sequence (top) Modifs (top) Best position in peptide All observed positions in phosphopeptide Number of phosphoislands Phosphoislands Ids Best e-value Charge MH+ Obs MH+ theo DeltaMH+ Delta-ppm
+void
+PtmSpectraSheet::writeHeaders(IdentificationGroup *p_ident)
+{
+ // Group ID Sub-group ID Phosphopeptide ID Sample Scan Rt Sequence (top)
+ // Modifs (top) Best position in peptide All observed positions in
+ // phosphopeptide Number of phosphoislands Phosphoislands Ids Best e-value
+ // Charge MH+ Obs MH+ theo DeltaMH+ Delta-ppm
- //MS Sample : 20120906_balliau_extract_1_A01_urnb-1
- const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
- if (msrun_list.size() == 1) {
- _p_writer->writeCell("sample");
- _p_writer->writeLine();
- _p_writer->writeCell(msrun_list[0].get()->getSampleName());
- _p_writer->writeLine();
+ // MS Sample : 20120906_balliau_extract_1_A01_urnb-1
+ const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
+ if(msrun_list.size() == 1)
+ {
+ _p_writer->writeCell("sample");
+ _p_writer->writeLine();
+ _p_writer->writeCell(msrun_list[0].get()->getSampleName());
+ _p_writer->writeLine();
}
- _p_writer->writeLine();
+ _p_writer->writeLine();
- // Group ID
- _p_writer->writeCell("group ID");
+ // Group ID
+ _p_writer->writeCell("group ID");
- // Sub-group ID
+ // Sub-group ID
- // Phosphopeptide ID
- writeCellHeader(PeptideListColumn::peptide_grouping_id);
+ // Phosphopeptide ID
+ writeCellHeader(PeptideListColumn::peptide_grouping_id);
- // Modifs (top) Best position in peptide All observed positions in phosphopeptide Number of phosphoislands Phosphoislands Ids Best e-value Charge MH+ Obs MH+ theo DeltaMH+ Delta-ppm
+ // Modifs (top) Best position in peptide All observed positions in
+ // phosphopeptide Number of phosphoislands Phosphoislands Ids Best e-value
+ // Charge MH+ Obs MH+ theo DeltaMH+ Delta-ppm
- // Sample
- writeCellHeader(PeptideListColumn::sample);
+ // Sample
+ writeCellHeader(PeptideListColumn::sample);
- // Scan
- writeCellHeader(PeptideListColumn::scan);
+ // Scan
+ writeCellHeader(PeptideListColumn::scan);
- // Rt
- writeCellHeader(PeptideListColumn::rt);
+ // Rt
+ writeCellHeader(PeptideListColumn::rt);
- writeCellHeader(PeptideListColumn::charge);
+ writeCellHeader(PeptideListColumn::charge);
- writeCellHeader(PeptideListColumn::experimental_mz);
+ writeCellHeader(PeptideListColumn::experimental_mz);
- // Sequence (top)
- _p_writer->setCellAnnotation("peptide sequence (best match)");
- _p_writer->writeCell("sequence (top)");
+ // Sequence (top)
+ _p_writer->setCellAnnotation("peptide sequence (best match)");
+ _p_writer->writeCell("sequence (top)");
- // Modifs (top)
- _p_writer->setCellAnnotation("peptide modification list (best match)");
- _p_writer->writeCell("modifs (top)");
+ // Modifs (top)
+ _p_writer->setCellAnnotation("peptide modification list (best match)");
+ _p_writer->writeCell("modifs (top)");
- if (_p_project->getLabelingMethodSp().get() != nullptr) {
- _p_writer->setCellAnnotation("peptide label (best match)");
- _p_writer->writeCell("Label (top)");
+ if(_p_project->getLabelingMethodSp().get() != nullptr)
+ {
+ _p_writer->setCellAnnotation("peptide label (best match)");
+ _p_writer->writeCell("Label (top)");
}
- // Best position in peptide
- _p_writer->setCellAnnotation("best PTM positions for this sample/scan");
- _p_writer->writeCell("best positions in peptide");
+ // Best position in peptide
+ _p_writer->setCellAnnotation("best PTM positions for this sample/scan");
+ _p_writer->writeCell("best positions in peptide");
- // All observed positions in phosphopeptide
- _p_writer->setCellAnnotation("All observed positions for this sample/scan");
- _p_writer->writeCell("all positions in peptide");
+ // All observed positions in phosphopeptide
+ _p_writer->setCellAnnotation("All observed positions for this sample/scan");
+ _p_writer->writeCell("all positions in peptide");
- // Number of phosphoislands
- _p_writer->setCellAnnotation("Number of phosphoislands share this sample/scan");
- _p_writer->writeCell("number of phosphoislands");
+ // Number of phosphoislands
+ _p_writer->setCellAnnotation(
+ "Number of phosphoislands share this sample/scan");
+ _p_writer->writeCell("number of phosphoislands");
- // Phosphoislands Ids
- _p_writer->setCellAnnotation("Phosphoislands id list");
- _p_writer->writeCell("phosphoislands");
+ // Phosphoislands Ids
+ _p_writer->setCellAnnotation("Phosphoislands id list");
+ _p_writer->writeCell("phosphoislands");
- // Best e-value
- _p_writer->writeCell("best E-value");
+ // Best e-value
+ _p_writer->writeCell("best E-value");
- _p_writer->writeCell("best hyperscore");
+ _p_writer->writeCell("best hyperscore");
- // MH+ Obs
- writeCellHeader(PeptideListColumn::experimental_mhplus);
+ // MH+ Obs
+ writeCellHeader(PeptideListColumn::experimental_mhplus);
- // MH+ theo
- writeCellHeader(PeptideListColumn::theoretical_mhplus);
-
- // DeltaMH+
- writeCellHeader(PeptideListColumn::delta_mhplus);
-
- // Delta-ppm
- writeCellHeader(PeptideListColumn::delta_ppm);
+ // MH+ theo
+ writeCellHeader(PeptideListColumn::theoretical_mhplus);
+ // DeltaMH+
+ writeCellHeader(PeptideListColumn::delta_mhplus);
+ // Delta-ppm
+ writeCellHeader(PeptideListColumn::delta_ppm);
}
-void PtmSpectraSheet::writeBestPeptideEvidence(const PtmSampleScan & ptm_sample_scan , std::set<const PtmIsland *> & ptmisland_occurence_list) {
-
- _p_writer->writeLine();
-
- const PeptideEvidence * p_peptide_evidence = ptm_sample_scan.getRepresentativePeptideMatch().getPeptideEvidence();
-
- unsigned int group_number = p_peptide_evidence->getGrpPeptideSp().get()->getGroupNumber();
- unsigned int rank_number = p_peptide_evidence->getGrpPeptideSp().get()->getRank();
-
- _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
- _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(group_number));
- _p_ods_export->setEvenOrOddStyle(rank_number, _p_writer);
- _p_writer->writeCell(p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
- _p_writer->clearTableCellStyleRef();
- _p_writer->writeCell(p_peptide_evidence->getMsRunP()->getSampleName());
- _p_writer->writeCell(p_peptide_evidence->getScan());
- _p_writer->writeCell(p_peptide_evidence->getRetentionTime());
- _p_writer->writeCell(p_peptide_evidence->getCharge());
- _p_writer->writeCell(p_peptide_evidence->getExperimentalMz());
- _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getSequence());
- _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
- if (_p_project->getLabelingMethodSp().get() != nullptr) {
- const Label * p_label = p_peptide_evidence->getPeptideXtpSp().get()->getLabel();
- if (p_label != nullptr) {
- _p_writer->writeCell(p_label->getXmlId());
+void
+PtmSpectraSheet::writeBestPeptideEvidence(
+ const PtmSampleScan &ptm_sample_scan,
+ std::set<const PtmIsland *> &ptmisland_occurence_list)
+{
+
+ _p_writer->writeLine();
+
+ const PeptideEvidence *p_peptide_evidence =
+ ptm_sample_scan.getRepresentativePeptideMatch().getPeptideEvidence();
+
+ unsigned int group_number =
+ p_peptide_evidence->getGrpPeptideSp().get()->getGroupNumber();
+ unsigned int rank_number =
+ p_peptide_evidence->getGrpPeptideSp().get()->getRank();
+
+ _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
+ _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(group_number));
+ _p_ods_export->setEvenOrOddStyle(rank_number, _p_writer);
+ _p_writer->writeCell(
+ p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
+ _p_writer->clearTableCellStyleRef();
+ _p_writer->writeCell(p_peptide_evidence->getMsRunP()->getSampleName());
+ _p_writer->writeCell(p_peptide_evidence->getScan());
+ _p_writer->writeCell(p_peptide_evidence->getRetentionTime());
+ _p_writer->writeCell(p_peptide_evidence->getCharge());
+ _p_writer->writeCell(p_peptide_evidence->getExperimentalMz());
+ _p_writer->writeCell(
+ p_peptide_evidence->getPeptideXtpSp().get()->getSequence());
+ _p_writer->writeCell(
+ p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
+ if(_p_project->getLabelingMethodSp().get() != nullptr)
+ {
+ const Label *p_label =
+ p_peptide_evidence->getPeptideXtpSp().get()->getLabel();
+ if(p_label != nullptr)
+ {
+ _p_writer->writeCell(p_label->getXmlId());
}
- else {
- _p_writer->writeEmptyCell();
+ else
+ {
+ _p_writer->writeEmptyCell();
}
}
- QStringList position_list;
- for (unsigned int position :ptm_sample_scan.getBestPtmPositionList(_p_ptm_grouping_experiment)) {
- position_list << QString("%1").arg(position+1);
+ QStringList position_list;
+ for(unsigned int position :
+ ptm_sample_scan.getBestPtmPositionList(_p_ptm_grouping_experiment))
+ {
+ position_list << QString("%1").arg(position + 1);
}
- _p_writer->writeCell(position_list.join(" "));
-
- position_list.clear();
- //return _ptm_sample_scan_list.at(row).get()->getObservedPtmPositionList();
- for (unsigned int position :ptm_sample_scan.getObservedPtmPositionList(_p_ptm_grouping_experiment)) {
- position_list << QString("%1").arg(position+1);
+ _p_writer->writeCell(position_list.join(" "));
+
+ position_list.clear();
+ // return _ptm_sample_scan_list.at(row).get()->getObservedPtmPositionList();
+ for(unsigned int position :
+ ptm_sample_scan.getObservedPtmPositionList(_p_ptm_grouping_experiment))
+ {
+ position_list << QString("%1").arg(position + 1);
}
- _p_writer->writeCell(position_list.join(" "));
-
- _p_writer->writeCell((unsigned int) ptmisland_occurence_list.size());
- position_list.clear();
- //return _ptm_sample_scan_list.at(row).get()->getObservedPtmPositionList();
- for (const PtmIsland * ptm_island:ptmisland_occurence_list) {
- position_list << ptm_island->getGroupingId();
+ _p_writer->writeCell(position_list.join(" "));
+
+ _p_writer->writeCell((unsigned int)ptmisland_occurence_list.size());
+ position_list.clear();
+ // return _ptm_sample_scan_list.at(row).get()->getObservedPtmPositionList();
+ for(const PtmIsland *ptm_island : ptmisland_occurence_list)
+ {
+ position_list << ptm_island->getGroupingId();
}
- _p_writer->writeCell(position_list.join(" "));
-
- _p_writer->writeCell(p_peptide_evidence->getEvalue());
- _p_writer->writeCell(p_peptide_evidence->getParam(PeptideEvidenceParam::tandem_hyperscore).toDouble());
-
- _p_writer->writeCell(p_peptide_evidence->getExperimentalMass()+pappso::MHPLUS);
- _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getMz(1));
- _p_writer->writeCell(p_peptide_evidence->getDeltaMass());
- _p_writer->writeCell(p_peptide_evidence->getPpmDeltaMass());
-
-
+ _p_writer->writeCell(position_list.join(" "));
+
+ _p_writer->writeCell(p_peptide_evidence->getEvalue());
+ _p_writer->writeCell(
+ p_peptide_evidence->getParam(PeptideEvidenceParam::tandem_hyperscore)
+ .toDouble());
+
+ _p_writer->writeCell(p_peptide_evidence->getExperimentalMass() +
+ pappso::MHPLUS);
+ _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getMz(1));
+ _p_writer->writeCell(p_peptide_evidence->getDeltaMass());
+ _p_writer->writeCell(p_peptide_evidence->getPpmDeltaMass());
}
-void PtmSpectraSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- _p_ptm_grouping_experiment = p_ident->getPtmGroupingExperiment();
-
- writeHeaders(p_ident);
- for (const PtmIslandSubgroupSp & ptm_island_subgroup_sp : _p_ptm_grouping_experiment->getPtmIslandSubgroupList() ) {
- writePtmIslandSubgroupSp(ptm_island_subgroup_sp);
+void
+PtmSpectraSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _p_ptm_grouping_experiment = p_ident->getPtmGroupingExperiment();
+
+ writeHeaders(p_ident);
+ for(const PtmIslandSubgroupSp &ptm_island_subgroup_sp :
+ _p_ptm_grouping_experiment->getPtmIslandSubgroupList())
+ {
+ writePtmIslandSubgroupSp(ptm_island_subgroup_sp);
}
- _p_writer->writeLine();
- _p_writer->writeLine();
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+ _p_writer->writeLine();
+ _p_writer->writeLine();
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-void PtmSpectraSheet::writePtmIslandSubgroupSp(const PtmIslandSubgroupSp & ptm_island_subgroup_sp) {
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- struct PtmSampleScanOccurence {
- PtmSampleScan ptm_sample_scan;
- std::set<const PtmIsland *> ptmisland_occurence_list;
- };
- std::vector<PtmSampleScanOccurence> ptm_sample_scan_occurence_list;
-
- for (PtmIslandSp ptm_island_sp :ptm_island_subgroup_sp.get()->getPtmIslandList()) {
-
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- for (PeptideMatch peptide_match: ptm_island_sp.get()->getPeptideMatchList()) {
-
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- std::vector<PtmSampleScanOccurence>::iterator it_ptm = ptm_sample_scan_occurence_list.begin();
- std::vector<PtmSampleScanOccurence>::iterator it_ptm_end = ptm_sample_scan_occurence_list.end();
- while ((it_ptm != it_ptm_end) && (it_ptm->ptm_sample_scan.add(peptide_match) == false)) {
- //peptide added
- it_ptm++;
+void
+PtmSpectraSheet::writePtmIslandSubgroupSp(
+ const PtmIslandSubgroupSp &ptm_island_subgroup_sp)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ struct PtmSampleScanOccurence
+ {
+ PtmSampleScan ptm_sample_scan;
+ std::set<const PtmIsland *> ptmisland_occurence_list;
+ };
+ std::vector<PtmSampleScanOccurence> ptm_sample_scan_occurence_list;
+
+ for(PtmIslandSp ptm_island_sp :
+ ptm_island_subgroup_sp.get()->getPtmIslandList())
+ {
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ for(PeptideMatch peptide_match :
+ ptm_island_sp.get()->getPeptideMatchList())
+ {
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ std::vector<PtmSampleScanOccurence>::iterator it_ptm =
+ ptm_sample_scan_occurence_list.begin();
+ std::vector<PtmSampleScanOccurence>::iterator it_ptm_end =
+ ptm_sample_scan_occurence_list.end();
+ while((it_ptm != it_ptm_end) &&
+ (it_ptm->ptm_sample_scan.add(peptide_match) == false))
+ {
+ // peptide added
+ it_ptm++;
}
- if (it_ptm == it_ptm_end) {
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- //peptide NOT added
- PtmSampleScanOccurence new_occurence = {PtmSampleScan(peptide_match),std::set<const PtmIsland *>()};
- new_occurence.ptmisland_occurence_list.insert(ptm_island_sp.get());
- ptm_sample_scan_occurence_list.push_back(new_occurence);
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+ if(it_ptm == it_ptm_end)
+ {
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ // peptide NOT added
+ PtmSampleScanOccurence new_occurence = {
+ PtmSampleScan(peptide_match), std::set<const PtmIsland *>()};
+ new_occurence.ptmisland_occurence_list.insert(
+ ptm_island_sp.get());
+ ptm_sample_scan_occurence_list.push_back(new_occurence);
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
- else {
- //peptide added
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- it_ptm->ptmisland_occurence_list.insert(ptm_island_sp.get());
+ else
+ {
+ // peptide added
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ it_ptm->ptmisland_occurence_list.insert(ptm_island_sp.get());
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
}
}
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- for (PtmSampleScanOccurence & occurence: ptm_sample_scan_occurence_list) {
- writeBestPeptideEvidence(occurence.ptm_sample_scan, occurence.ptmisland_occurence_list);
+ for(PtmSampleScanOccurence &occurence : ptm_sample_scan_occurence_list)
+ {
+ writeBestPeptideEvidence(occurence.ptm_sample_scan,
+ occurence.ptmisland_occurence_list);
}
- qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
diff --git a/src/output/ods/ptm/ptmspectrasheet.h b/src/output/ods/ptm/ptmspectrasheet.h
index 444aa68d45bca1a974845e95b8096170d100769c..6b589c045e6ee0e065899167e3416511a66a29ed 100644
--- a/src/output/ods/ptm/ptmspectrasheet.h
+++ b/src/output/ods/ptm/ptmspectrasheet.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PTMSPECTRASHEET_H
#define PTMSPECTRASHEET_H
@@ -38,22 +39,28 @@
class PtmSpectraSheet
{
-public :
- PtmSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
-
-protected :
- PtmSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project, const QString & sheet_name);
- virtual void writeIdentificationGroup(IdentificationGroup * p_ident);
- void writeHeaders(IdentificationGroup * p_ident);
- void writeBestPeptideEvidence(const PtmSampleScan & ptm_sample_scan , std::set<const PtmIsland *> & ptmisland_occurence_list);
- void writeCellHeader(PeptideListColumn column);
-
- void writePtmIslandSubgroupSp(const PtmIslandSubgroupSp & ptm_island_subgroup_sp);
-protected :
- OdsExport * _p_ods_export;
- const PtmGroupingExperiment * _p_ptm_grouping_experiment;
- const Project * _p_project;
- CalcWriterInterface * _p_writer;
+ public:
+ PtmSpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project);
+
+ protected:
+ PtmSpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project, const QString &sheet_name);
+ virtual void writeIdentificationGroup(IdentificationGroup *p_ident);
+ void writeHeaders(IdentificationGroup *p_ident);
+ void writeBestPeptideEvidence(
+ const PtmSampleScan &ptm_sample_scan,
+ std::set<const PtmIsland *> &ptmisland_occurence_list);
+ void writeCellHeader(PeptideListColumn column);
+
+ void
+ writePtmIslandSubgroupSp(const PtmIslandSubgroupSp &ptm_island_subgroup_sp);
+
+ protected:
+ OdsExport *_p_ods_export;
+ const PtmGroupingExperiment *_p_ptm_grouping_experiment;
+ const Project *_p_project;
+ CalcWriterInterface *_p_writer;
};
#endif // PTMSPECTRASHEET_H
diff --git a/src/output/ods/samplesheet.cpp b/src/output/ods/samplesheet.cpp
index c90b0bd6842cc01f85e74a2033e3e181ffd907a1..5a579ef90de84a13f12e78fe8b78109b9f77a41c 100644
--- a/src/output/ods/samplesheet.cpp
+++ b/src/output/ods/samplesheet.cpp
@@ -274,7 +274,7 @@ SampleSheet::writeIdentificationDataSource(
{
_p_writer->writeCell(var_sample.toInt());
}
-
+
var_sample =
msrun_sp.get()->getMsRunStatistics(MsRunStatistics::tic_spectra_ms1);
if(var_sample.isNull())
diff --git a/src/output/ods/samplesheet.h b/src/output/ods/samplesheet.h
index 345d1629e356d9b77134489f4fcc51c71dd846a9..12677f5f2186c78196fda60434185f57c15b0f59 100644
--- a/src/output/ods/samplesheet.h
+++ b/src/output/ods/samplesheet.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef SAMPLESHEET_H
#define SAMPLESHEET_H
@@ -36,17 +37,20 @@
class SampleSheet
{
-public :
- SampleSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
+ public:
+ SampleSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project);
-private:
- void writeHeaders();
- void writeIdentificationDataSource(IdentificationDataSource * p_ident_data_source);
-private :
- OdsExport * _p_ods_export;
- const Project * _p_project;
- CalcWriterInterface * _p_writer;
- bool _msrun_statistics = true;
+ private:
+ void writeHeaders();
+ void
+ writeIdentificationDataSource(IdentificationDataSource *p_ident_data_source);
+
+ private:
+ OdsExport *_p_ods_export;
+ const Project *_p_project;
+ CalcWriterInterface *_p_writer;
+ bool _msrun_statistics = true;
};
#endif // SAMPLESHEET_H
diff --git a/src/output/ods/simplesheet.cpp b/src/output/ods/simplesheet.cpp
index 7f4517be5c3b9c8cb21107d7dca0e05f8655c454..a6f96f101b038fe0cc80605f80ece98f67ccb496 100644
--- a/src/output/ods/simplesheet.cpp
+++ b/src/output/ods/simplesheet.cpp
@@ -6,60 +6,70 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "simplesheet.h"
#include "../../core/identificationgroup.h"
-SimpleSheet::SimpleSheet (CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
- _p_writer = p_writer;
- p_writer->writeSheet("simple");
-
- std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
-
- for (IdentificationGroup * p_ident:identification_list) {
- writeIdentificationGroup(p_ident);
+SimpleSheet::SimpleSheet(CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : _p_project(p_project)
+{
+ _p_writer = p_writer;
+ p_writer->writeSheet("simple");
+
+ std::vector<IdentificationGroup *> identification_list =
+ p_project->getIdentificationGroupList();
+
+ for(IdentificationGroup *p_ident : identification_list)
+ {
+ writeIdentificationGroup(p_ident);
}
}
-void SimpleSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
-
- //_p_writer->writeSheet("simple");
- const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
- _p_writer->writeCell("protein");
- _p_writer->writeLine();
- _p_writer->writeEmptyCell();
- _p_writer->writeCell("peptide");
- _p_writer->writeLine();
- if (msrun_list.size() == 1) {
- _p_writer->writeCell("sample");
- _p_writer->writeLine();
- _p_writer->writeCell(msrun_list[0].get()->getSampleName());
- _p_writer->writeLine();
+void
+SimpleSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
+{
+
+ //_p_writer->writeSheet("simple");
+ const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
+ _p_writer->writeCell("protein");
+ _p_writer->writeLine();
+ _p_writer->writeEmptyCell();
+ _p_writer->writeCell("peptide");
+ _p_writer->writeLine();
+ if(msrun_list.size() == 1)
+ {
+ _p_writer->writeCell("sample");
+ _p_writer->writeLine();
+ _p_writer->writeCell(msrun_list[0].get()->getSampleName());
+ _p_writer->writeLine();
}
-
- for (ProteinMatch * p_protein_match :p_ident->getProteinMatchList()) {
- _p_writer->writeCell(p_protein_match->getProteinXtpSp().get()->getAccession());
- _p_writer->writeLine();
+
+ for(ProteinMatch *p_protein_match : p_ident->getProteinMatchList())
+ {
+ _p_writer->writeCell(
+ p_protein_match->getProteinXtpSp().get()->getAccession());
+ _p_writer->writeLine();
}
-
}
diff --git a/src/output/ods/simplesheet.h b/src/output/ods/simplesheet.h
index 447172b7352706d712097cd0d97b8de07f32be11..2d3b98ebb10adea1da7849ebed05d45ba5cae26e 100644
--- a/src/output/ods/simplesheet.h
+++ b/src/output/ods/simplesheet.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef SIMPLESHEET_H
#define SIMPLESHEET_H
@@ -36,13 +37,15 @@
class SimpleSheet
{
- public :
- SimpleSheet (CalcWriterInterface * p_writer, const Project * p_project);
-private :
- void writeIdentificationGroup(IdentificationGroup * p_ident);
-private :
- const Project * _p_project;
- CalcWriterInterface * _p_writer;
+ public:
+ SimpleSheet(CalcWriterInterface *p_writer, const Project *p_project);
+
+ private:
+ void writeIdentificationGroup(IdentificationGroup *p_ident);
+
+ private:
+ const Project *_p_project;
+ CalcWriterInterface *_p_writer;
};
#endif // SIMPLESHEET_H
diff --git a/src/output/ods/spectrasheet.cpp b/src/output/ods/spectrasheet.cpp
index e75b4e0c3d9f1ef78776e04e3f73903d75fed82d..c56f6b1e61b55e562cf25551ebf94aa8a9bcd2dd 100644
--- a/src/output/ods/spectrasheet.cpp
+++ b/src/output/ods/spectrasheet.cpp
@@ -6,177 +6,227 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "spectrasheet.h"
#include <tuple>
#include <pappsomspp/utils.h>
-SpectraSheet::SpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project, const QString & sheet_name): _p_project(p_project) {
- _p_ods_export = p_ods_export;
- _p_writer = p_writer;
- p_writer->writeSheet(sheet_name);
-
- OdsTableSettings table_settings;
- table_settings.setVerticalSplit(1);
- _p_writer->setCurrentOdsTableSettings(table_settings);
-
- std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
- for (IdentificationGroup * p_ident:identification_list) {
- //writeHeaders(p_ident);
- writeIdentificationGroup(p_ident);
+SpectraSheet::SpectraSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project, const QString &sheet_name)
+ : _p_project(p_project)
+{
+ _p_ods_export = p_ods_export;
+ _p_writer = p_writer;
+ p_writer->writeSheet(sheet_name);
+
+ OdsTableSettings table_settings;
+ table_settings.setVerticalSplit(1);
+ _p_writer->setCurrentOdsTableSettings(table_settings);
+
+ std::vector<IdentificationGroup *> identification_list =
+ p_project->getIdentificationGroupList();
+ for(IdentificationGroup *p_ident : identification_list)
+ {
+ // writeHeaders(p_ident);
+ writeIdentificationGroup(p_ident);
}
}
-SpectraSheet::SpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): SpectraSheet(p_ods_export, p_writer, p_project, QString("spectra")) {
+SpectraSheet::SpectraSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project)
+ : SpectraSheet(p_ods_export, p_writer, p_project, QString("spectra"))
+{
}
-void SpectraSheet::writeCellHeader(PeptideListColumn column) {
- qDebug() << "SpectraSheet::writeCellHeader begin " << (std::int8_t) column;
- _p_writer->setCellAnnotation(PeptideTableModel::getDescription(column));
- _p_writer->writeCell(PeptideTableModel::getTitle(column));
- qDebug() << "SpectraSheet::writeCellHeader end" ;
+void
+SpectraSheet::writeCellHeader(PeptideListColumn column)
+{
+ qDebug() << "SpectraSheet::writeCellHeader begin " << (std::int8_t)column;
+ _p_writer->setCellAnnotation(PeptideTableModel::getDescription(column));
+ _p_writer->writeCell(PeptideTableModel::getTitle(column));
+ qDebug() << "SpectraSheet::writeCellHeader end";
}
-void SpectraSheet::writeHeaders(IdentificationGroup * p_ident) {
- // Group ID Peptide ID Sample Scan Rt (minutes) Sequence (top) Modifs (top) Number of subgroups Sub-groups Ids Best E-value Best hyperscore m/z Obs Charge MH+ Obs MH+ theo DeltaMH+ Delta-ppm
-
- //MS Sample : 20120906_balliau_extract_1_A01_urnb-1
- const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
- if (msrun_list.size() == 1) {
- _p_writer->writeCell("sample");
- _p_writer->writeLine();
- _p_writer->writeCell(msrun_list[0].get()->getSampleName());
- _p_writer->writeLine();
+void
+SpectraSheet::writeHeaders(IdentificationGroup *p_ident)
+{
+ // Group ID Peptide ID Sample Scan Rt (minutes) Sequence (top) Modifs (top)
+ // Number of subgroups Sub-groups Ids Best E-value Best hyperscore m/z Obs
+ // Charge MH+ Obs MH+ theo DeltaMH+ Delta-ppm
+
+ // MS Sample : 20120906_balliau_extract_1_A01_urnb-1
+ const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
+ if(msrun_list.size() == 1)
+ {
+ _p_writer->writeCell("sample");
+ _p_writer->writeLine();
+ _p_writer->writeCell(msrun_list[0].get()->getSampleName());
+ _p_writer->writeLine();
}
- _p_writer->writeLine();
- _p_writer->writeCell("Group ID");
- _p_writer->writeCell("Peptide ID");
-
- writeCellHeader(PeptideListColumn::sample);
- writeCellHeader(PeptideListColumn::scan);
- writeCellHeader(PeptideListColumn::rt);
- writeCellHeader(PeptideListColumn::experimental_mz);
- _p_writer->setCellAnnotation("peptide sequence (best match)");
- _p_writer->writeCell("Sequence (top)");
- _p_writer->setCellAnnotation("peptide charge (best match)");
- _p_writer->writeCell("Charge (top)");
- _p_writer->setCellAnnotation("peptide modifications (best match)");
- _p_writer->writeCell("Modifs (top)");
- if (_p_project->getLabelingMethodSp().get() != nullptr) {
- _p_writer->setCellAnnotation("peptide label (best match)");
- _p_writer->writeCell("Label (top)");
+ _p_writer->writeLine();
+ _p_writer->writeCell("Group ID");
+ _p_writer->writeCell("Peptide ID");
+
+ writeCellHeader(PeptideListColumn::sample);
+ writeCellHeader(PeptideListColumn::scan);
+ writeCellHeader(PeptideListColumn::rt);
+ writeCellHeader(PeptideListColumn::experimental_mz);
+ _p_writer->setCellAnnotation("peptide sequence (best match)");
+ _p_writer->writeCell("Sequence (top)");
+ _p_writer->setCellAnnotation("peptide charge (best match)");
+ _p_writer->writeCell("Charge (top)");
+ _p_writer->setCellAnnotation("peptide modifications (best match)");
+ _p_writer->writeCell("Modifs (top)");
+ if(_p_project->getLabelingMethodSp().get() != nullptr)
+ {
+ _p_writer->setCellAnnotation("peptide label (best match)");
+ _p_writer->writeCell("Label (top)");
}
- _p_writer->writeCell("Best E-value");
- _p_writer->writeCell("Best hyperscore");
- writeCellHeader(PeptideListColumn::delta_mhplus);
-
-
+ _p_writer->writeCell("Best E-value");
+ _p_writer->writeCell("Best hyperscore");
+ writeCellHeader(PeptideListColumn::delta_mhplus);
}
-void SpectraSheet::writeBestPeptideEvidence(const GroupingGroup * p_group,const PeptideEvidence * p_peptide_evidence) {
-
- _p_writer->writeLine();
-
- unsigned int group_number = p_peptide_evidence->getGrpPeptideSp().get()->getGroupNumber();
- unsigned int rank_number = p_peptide_evidence->getGrpPeptideSp().get()->getRank();
-
- _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
- _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(group_number));
- _p_ods_export->setEvenOrOddStyle(rank_number, _p_writer);
- _p_writer->writeCell(p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
- _p_writer->clearTableCellStyleRef();
- _p_writer->writeCell(p_peptide_evidence->getMsRunP()->getSampleName());
- _p_writer->writeCell(p_peptide_evidence->getScan());
- _p_writer->writeCell(p_peptide_evidence->getRetentionTime());
- _p_writer->writeCell(p_peptide_evidence->getExperimentalMz());
- _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getSequence());
- _p_writer->writeCell(p_peptide_evidence->getCharge());
- _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
- if (_p_project->getLabelingMethodSp().get() != nullptr) {
- const Label * p_label = p_peptide_evidence->getPeptideXtpSp().get()->getLabel();
- if (p_label != nullptr) {
- _p_writer->writeCell(p_label->getXmlId());
+void
+SpectraSheet::writeBestPeptideEvidence(
+ const GroupingGroup *p_group, const PeptideEvidence *p_peptide_evidence)
+{
+
+ _p_writer->writeLine();
+
+ unsigned int group_number =
+ p_peptide_evidence->getGrpPeptideSp().get()->getGroupNumber();
+ unsigned int rank_number =
+ p_peptide_evidence->getGrpPeptideSp().get()->getRank();
+
+ _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
+ _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(group_number));
+ _p_ods_export->setEvenOrOddStyle(rank_number, _p_writer);
+ _p_writer->writeCell(
+ p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
+ _p_writer->clearTableCellStyleRef();
+ _p_writer->writeCell(p_peptide_evidence->getMsRunP()->getSampleName());
+ _p_writer->writeCell(p_peptide_evidence->getScan());
+ _p_writer->writeCell(p_peptide_evidence->getRetentionTime());
+ _p_writer->writeCell(p_peptide_evidence->getExperimentalMz());
+ _p_writer->writeCell(
+ p_peptide_evidence->getPeptideXtpSp().get()->getSequence());
+ _p_writer->writeCell(p_peptide_evidence->getCharge());
+ _p_writer->writeCell(
+ p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
+ if(_p_project->getLabelingMethodSp().get() != nullptr)
+ {
+ const Label *p_label =
+ p_peptide_evidence->getPeptideXtpSp().get()->getLabel();
+ if(p_label != nullptr)
+ {
+ _p_writer->writeCell(p_label->getXmlId());
}
- else {
- _p_writer->writeEmptyCell();
+ else
+ {
+ _p_writer->writeEmptyCell();
}
}
- _p_writer->writeCell(p_peptide_evidence->getEvalue());
- _p_writer->writeCell(p_peptide_evidence->getParam(PeptideEvidenceParam::tandem_hyperscore).toDouble());
- _p_writer->writeCell(p_peptide_evidence->getDeltaMass());
-
-
+ _p_writer->writeCell(p_peptide_evidence->getEvalue());
+ _p_writer->writeCell(
+ p_peptide_evidence->getParam(PeptideEvidenceParam::tandem_hyperscore)
+ .toDouble());
+ _p_writer->writeCell(p_peptide_evidence->getDeltaMass());
}
-void SpectraSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
-
- writeHeaders(p_ident);
- for (const std::pair<unsigned int, GroupingGroupSp> & group_pair : p_ident->getGroupStore().getGroupMap()) {
-
- std::vector<const PeptideEvidence *> peptide_evidence_list = group_pair.second.get()->getPeptideEvidenceList();
-
- std::sort(peptide_evidence_list.begin(), peptide_evidence_list.end(),
- [](const PeptideEvidence * a, const PeptideEvidence * b)
- {
- unsigned int arank = a->getGrpPeptideSp().get()->getRank();
- unsigned int ascan = a->getScan();
- unsigned int brank = b->getGrpPeptideSp().get()->getRank();
- unsigned int bscan = b->getScan();
- return std::tie(arank, a->getMsRunP()->getSampleName(), ascan) < std::tie(brank, b->getMsRunP()->getSampleName(), bscan);
+void
+SpectraSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
+{
+
+ writeHeaders(p_ident);
+ for(const std::pair<unsigned int, GroupingGroupSp> &group_pair :
+ p_ident->getGroupStore().getGroupMap())
+ {
+
+ std::vector<const PeptideEvidence *> peptide_evidence_list =
+ group_pair.second.get()->getPeptideEvidenceList();
+
+ std::sort(
+ peptide_evidence_list.begin(), peptide_evidence_list.end(),
+ [](const PeptideEvidence *a, const PeptideEvidence *b) {
+ unsigned int arank = a->getGrpPeptideSp().get()->getRank();
+ unsigned int ascan = a->getScan();
+ unsigned int brank = b->getGrpPeptideSp().get()->getRank();
+ unsigned int bscan = b->getScan();
+ return std::tie(arank, a->getMsRunP()->getSampleName(), ascan) <
+ std::tie(brank, b->getMsRunP()->getSampleName(), bscan);
});
- const PeptideEvidence * p_best_peptide_evidence = nullptr;
+ const PeptideEvidence *p_best_peptide_evidence = nullptr;
- for (auto & peptide_evidence:peptide_evidence_list) {
- if (p_best_peptide_evidence == nullptr) {
- p_best_peptide_evidence = peptide_evidence;
+ for(auto &peptide_evidence : peptide_evidence_list)
+ {
+ if(p_best_peptide_evidence == nullptr)
+ {
+ p_best_peptide_evidence = peptide_evidence;
}
- //change spectra :
- unsigned int arank = p_best_peptide_evidence->getGrpPeptideSp().get()->getRank();
- unsigned int ascan = p_best_peptide_evidence->getScan();
- unsigned int brank = peptide_evidence->getGrpPeptideSp().get()->getRank();
- unsigned int bscan = peptide_evidence->getScan();
-
- if (std::tie(arank, p_best_peptide_evidence->getMsRunP()->getSampleName(), ascan) != std::tie(brank, peptide_evidence->getMsRunP()->getSampleName(), bscan)) {
- //write p_best_peptide_match
- writeBestPeptideEvidence(group_pair.second.get(), p_best_peptide_evidence);
- p_best_peptide_evidence = peptide_evidence;
+ // change spectra :
+ unsigned int arank =
+ p_best_peptide_evidence->getGrpPeptideSp().get()->getRank();
+ unsigned int ascan = p_best_peptide_evidence->getScan();
+ unsigned int brank =
+ peptide_evidence->getGrpPeptideSp().get()->getRank();
+ unsigned int bscan = peptide_evidence->getScan();
+
+ if(std::tie(arank,
+ p_best_peptide_evidence->getMsRunP()->getSampleName(),
+ ascan) !=
+ std::tie(brank, peptide_evidence->getMsRunP()->getSampleName(),
+ bscan))
+ {
+ // write p_best_peptide_match
+ writeBestPeptideEvidence(group_pair.second.get(),
+ p_best_peptide_evidence);
+ p_best_peptide_evidence = peptide_evidence;
}
- else {
- if (p_best_peptide_evidence->getEvalue()> peptide_evidence->getEvalue()) {
- p_best_peptide_evidence = peptide_evidence;
+ else
+ {
+ if(p_best_peptide_evidence->getEvalue() >
+ peptide_evidence->getEvalue())
+ {
+ p_best_peptide_evidence = peptide_evidence;
}
}
}
- if (p_best_peptide_evidence != nullptr) {
- writeBestPeptideEvidence(group_pair.second.get(), p_best_peptide_evidence);
+ if(p_best_peptide_evidence != nullptr)
+ {
+ writeBestPeptideEvidence(group_pair.second.get(),
+ p_best_peptide_evidence);
}
}
- _p_writer->writeLine();
- _p_writer->writeLine();
+ _p_writer->writeLine();
+ _p_writer->writeLine();
}
diff --git a/src/output/ods/spectrasheet.h b/src/output/ods/spectrasheet.h
index 356798d31819bc8bb042ac9763b4b1038bd968e1..5035d45aed2ce9f09695a7d67b70fa3c7d4dc20c 100644
--- a/src/output/ods/spectrasheet.h
+++ b/src/output/ods/spectrasheet.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef SPECTRASHEET_H
#define SPECTRASHEET_H
@@ -38,20 +39,23 @@
class SpectraSheet
{
-public :
- SpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
-protected :
- SpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project, const QString & sheet_name);
- virtual void writeIdentificationGroup(IdentificationGroup * p_ident);
- void writeHeaders(IdentificationGroup * p_ident);
- void writeBestPeptideEvidence(const GroupingGroup * p_group, const PeptideEvidence * p_peptide_evidence);
- void writeCellHeader(PeptideListColumn column);
+ public:
+ SpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project);
-protected :
- OdsExport * _p_ods_export;
- const Project * _p_project;
- CalcWriterInterface * _p_writer;
+ protected:
+ SpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ const Project *p_project, const QString &sheet_name);
+ virtual void writeIdentificationGroup(IdentificationGroup *p_ident);
+ void writeHeaders(IdentificationGroup *p_ident);
+ void writeBestPeptideEvidence(const GroupingGroup *p_group,
+ const PeptideEvidence *p_peptide_evidence);
+ void writeCellHeader(PeptideListColumn column);
+
+ protected:
+ OdsExport *_p_ods_export;
+ const Project *_p_project;
+ CalcWriterInterface *_p_writer;
};
#endif // SPECTRASHEET_H
-
diff --git a/src/output/proticdbml.cpp b/src/output/proticdbml.cpp
index c2a59cc76b6d238b48348fcbe78ef00f842b1782..9648842e50dfa7cc8c35759fd263e4d518ceff97 100644
--- a/src/output/proticdbml.cpp
+++ b/src/output/proticdbml.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "proticdbml.h"
#include <pappsomspp/pappsoexception.h>
@@ -36,705 +37,940 @@
#include "../config.h"
#include "../utils/utils.h"
-ProticdbMl::ProticdbMl(const QString & out_filename)
+ProticdbMl::ProticdbMl(const QString &out_filename)
{
- //_p_digestion_pipeline = p_digestion_pipeline;
+ //_p_digestion_pipeline = p_digestion_pipeline;
- //_mzidentml = "http://psidev.info/psi/pi/mzIdentML/1.1";
- QString complete_out_filename = out_filename;
- _output_file = new QFile(complete_out_filename);
+ //_mzidentml = "http://psidev.info/psi/pi/mzIdentML/1.1";
+ QString complete_out_filename = out_filename;
+ _output_file = new QFile(complete_out_filename);
- if (_output_file->open(QIODevice::WriteOnly))
+ if(_output_file->open(QIODevice::WriteOnly))
{
- _output_stream = new QXmlStreamWriter();
- _output_stream->setDevice(_output_file);
- } else
+ _output_stream = new QXmlStreamWriter();
+ _output_stream->setDevice(_output_file);
+ }
+ else
{
- throw pappso::PappsoException(QObject::tr("error : cannot open the PROTICdbML output file : %1\n").arg(out_filename));
+ throw pappso::PappsoException(
+ QObject::tr("error : cannot open the PROTICdbML output file : %1\n")
+ .arg(out_filename));
}
- _output_stream->setAutoFormatting(true);
- _output_stream->writeStartDocument("1.0");
-
-
+ _output_stream->setAutoFormatting(true);
+ _output_stream->writeStartDocument("1.0");
}
ProticdbMl::~ProticdbMl()
{
- delete _output_file;
- delete _output_stream;
+ delete _output_file;
+ delete _output_stream;
}
-void ProticdbMl::close() {
- _output_stream->writeEndDocument();
- _output_file->close();
+void
+ProticdbMl::close()
+{
+ _output_stream->writeEndDocument();
+ _output_file->close();
- qDebug() << "ProticdbMl::close end duration = " << _duracel.elapsed() << "ms";
+ qDebug() << "ProticdbMl::close end duration = " << _duracel.elapsed() << "ms";
}
+void
+ProticdbMl::write(ProjectSp sp_project)
+{
-void ProticdbMl::write(ProjectSp sp_project) {
-
- qDebug() << "ProticdbMl::write begin";
- _duracel.start();
- _sp_project = sp_project;
- if (_sp_project.get() == nullptr) {
- throw pappso::PappsoException(QObject::tr("Error writing PROTICdbML file :\n project is empty"));
+ qDebug() << "ProticdbMl::write begin";
+ _duracel.start();
+ _sp_project = sp_project;
+ if(_sp_project.get() == nullptr)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error writing PROTICdbML file :\n project is empty"));
}
- _output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance","xsi");
- // writer.setDefaultNamespace(namespaceURI);
- _output_stream->writeStartElement("PROTICdb");
- //_output_stream->writeAttribute("xmlns","http://pappso.inra.fr/xsd/masschroqml/2.2");
- //_output_stream->writeAttribute("http://www.w3.org/2001/XMLSchema-instance","schemaLocation","http://pappso.inra.fr/xsd/masschroqml/2.2 http://pappso.inra.fr/xsd/masschroq-2.2.xsd");
+ _output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance",
+ "xsi");
+ // writer.setDefaultNamespace(namespaceURI);
+ _output_stream->writeStartElement("PROTICdb");
+ //_output_stream->writeAttribute("xmlns","http://pappso.inra.fr/xsd/masschroqml/2.2");
+ //_output_stream->writeAttribute("http://www.w3.org/2001/XMLSchema-instance","schemaLocation","http://pappso.inra.fr/xsd/masschroqml/2.2
+ //http://pappso.inra.fr/xsd/masschroq-2.2.xsd");
- //writer.writeAttribute(xmlnsxsi, "noNamespaceSchemaLocation", xsischemaLocation);
+ // writer.writeAttribute(xmlnsxsi, "noNamespaceSchemaLocation",
+ // xsischemaLocation);
- _output_stream->writeAttribute("version", "1.0");
+ _output_stream->writeAttribute("version", "1.0");
- _output_stream->writeAttribute("type", "MSidentificationResults");
+ _output_stream->writeAttribute("type", "MSidentificationResults");
- writeIdentMethod();
- _output_stream->writeStartElement("sequences");
- for (IdentificationGroup * p_ident_group : sp_project.get()->getIdentificationGroupList()) {
+ writeIdentMethod();
+ _output_stream->writeStartElement("sequences");
+ for(IdentificationGroup *p_ident_group :
+ sp_project.get()->getIdentificationGroupList())
+ {
- for (ProteinMatch * p_protein_match: p_ident_group->getProteinMatchList()) {
- writeSequence(p_protein_match);
+ for(ProteinMatch *p_protein_match : p_ident_group->getProteinMatchList())
+ {
+ writeSequence(p_protein_match);
}
}
- //</sequences>
- _output_stream->writeEndElement();
-
- writeProject();
+ //</sequences>
+ _output_stream->writeEndElement();
+ writeProject();
}
-void ProticdbMl::writeSequence(ProteinMatch * p_protein_match) {
- qDebug() << "ProticdbMl::writeSequence begin";
- if (p_protein_match->getValidationState() != ValidationState::grouped) return;
- pappso::GrpProtein * p_grp_protein = p_protein_match->getGrpProteinSp().get();
-
- if (_map_accession2xmlid.find(p_grp_protein->getAccession()) == _map_accession2xmlid.end()) {
- //not found
-
- QString id = QString("seq%1").arg(_map_accession2xmlid.size());
- _output_stream->writeStartElement("sequence");
- _output_stream->writeAttribute("id", id);
- QString display_id = QString("%1 %2").arg(p_grp_protein->getAccession()).arg(p_protein_match->getProteinXtpSp().get()->getDescription());
- _output_stream->writeAttribute("display_id", display_id.left(60));
- // <dbxref key="AT5G16390"
- // dbname="AGI_LocusCode"></dbxref>
- //if (prot.get_dbxref_type().equals("no") == false) {
- for (const DbXref & dbxref :p_protein_match->getProteinXtpSp().get()->getDbxrefList()) {
- _output_stream->writeStartElement("dbxref");
- _output_stream->writeAttribute("dbname", Utils::getDatabaseName(dbxref.database));
- _output_stream->writeAttribute("key",
- dbxref.accession);
- _output_stream->writeEndElement();// dbxref
- }
- _output_stream->writeStartElement("description");
- _output_stream->writeCharacters(p_protein_match->getProteinXtpSp().get()->getDescription());
- _output_stream->writeEndElement();// description
- _output_stream->writeStartElement("seq");
- _output_stream->writeCharacters(p_protein_match->getProteinXtpSp().get()->getSequence());
- _output_stream->writeEndElement();// seq
-
- _output_stream->writeEndElement();// sequence
-
- _map_accession2xmlid.insert(std::pair<QString, QString>(p_grp_protein->getAccession(), id));
+void
+ProticdbMl::writeSequence(ProteinMatch *p_protein_match)
+{
+ qDebug() << "ProticdbMl::writeSequence begin";
+ if(p_protein_match->getValidationState() != ValidationState::grouped)
+ return;
+ pappso::GrpProtein *p_grp_protein = p_protein_match->getGrpProteinSp().get();
+ if(_map_accession2xmlid.find(p_grp_protein->getAccession()) ==
+ _map_accession2xmlid.end())
+ {
+ // not found
+
+ QString id = QString("seq%1").arg(_map_accession2xmlid.size());
+ _output_stream->writeStartElement("sequence");
+ _output_stream->writeAttribute("id", id);
+ QString display_id =
+ QString("%1 %2")
+ .arg(p_grp_protein->getAccession())
+ .arg(p_protein_match->getProteinXtpSp().get()->getDescription());
+ _output_stream->writeAttribute("display_id", display_id.left(60));
+ // <dbxref key="AT5G16390"
+ // dbname="AGI_LocusCode"></dbxref>
+ // if (prot.get_dbxref_type().equals("no") == false) {
+ for(const DbXref &dbxref :
+ p_protein_match->getProteinXtpSp().get()->getDbxrefList())
+ {
+ _output_stream->writeStartElement("dbxref");
+ _output_stream->writeAttribute(
+ "dbname", Utils::getDatabaseName(dbxref.database));
+ _output_stream->writeAttribute("key", dbxref.accession);
+ _output_stream->writeEndElement(); // dbxref
+ }
+ _output_stream->writeStartElement("description");
+ _output_stream->writeCharacters(
+ p_protein_match->getProteinXtpSp().get()->getDescription());
+ _output_stream->writeEndElement(); // description
+ _output_stream->writeStartElement("seq");
+ _output_stream->writeCharacters(
+ p_protein_match->getProteinXtpSp().get()->getSequence());
+ _output_stream->writeEndElement(); // seq
+
+ _output_stream->writeEndElement(); // sequence
+
+ _map_accession2xmlid.insert(
+ std::pair<QString, QString>(p_grp_protein->getAccession(), id));
}
- qDebug() << "ProticdbMl::writeSequence end";
+ qDebug() << "ProticdbMl::writeSequence end";
}
-void ProticdbMl::writeProject() {
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- _output_stream->writeStartElement("project");
- _output_stream->writeAttribute("name", "");
- _output_stream->writeAttribute("id", "p1");
- // ajout des echantillons_msrun
- writeSamples();
- writeMsRuns();
-
- _output_stream->writeStartElement("identificationRuns");
-
- for (IdentificationGroup * p_identification : _sp_project.get()->getIdentificationGroupList()) {
- _output_stream->writeStartElement("identificationRun");
- // ajout d'une mnip d'identification
- writeIdentificationRun(p_identification);
+void
+ProticdbMl::writeProject()
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _output_stream->writeStartElement("project");
+ _output_stream->writeAttribute("name", "");
+ _output_stream->writeAttribute("id", "p1");
+ // ajout des echantillons_msrun
+ writeSamples();
+ writeMsRuns();
+
+ _output_stream->writeStartElement("identificationRuns");
+
+ for(IdentificationGroup *p_identification :
+ _sp_project.get()->getIdentificationGroupList())
+ {
+ _output_stream->writeStartElement("identificationRun");
+ // ajout d'une mnip d'identification
+ writeIdentificationRun(p_identification);
- // ajout des petides
- writepeptideHits(p_identification);
+ // ajout des petides
+ writepeptideHits(p_identification);
- // ajout des mathces
- writeMatchs(p_identification);
+ // ajout des mathces
+ writeMatchs(p_identification);
- _output_stream->writeEndElement();// identificationRun
+ _output_stream->writeEndElement(); // identificationRun
}
- _output_stream->writeEndElement();// identificationRuns
- _output_stream->writeEndElement();// project
+ _output_stream->writeEndElement(); // identificationRuns
+ _output_stream->writeEndElement(); // project
- _output_stream->writeEndDocument();
+ _output_stream->writeEndDocument();
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-void ProticdbMl::writeIdentMethod() {
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- // Ajout des méthodes
- _output_stream->writeStartElement("identMeth");
- _output_stream->writeAttribute("name", "");
- _output_stream->writeAttribute("id", "m1");
- _output_stream->writeEndElement();
-
- // Ajout des base de données
- _output_stream->writeStartElement("customDb");
- _output_stream->writeAttribute("name", "");
- _output_stream->writeAttribute("id", "customdb0");
- _output_stream->writeEndElement();
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
-
-
+void
+ProticdbMl::writeIdentMethod()
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ // Ajout des méthodes
+ _output_stream->writeStartElement("identMeth");
+ _output_stream->writeAttribute("name", "");
+ _output_stream->writeAttribute("id", "m1");
+ _output_stream->writeEndElement();
+
+ // Ajout des base de données
+ _output_stream->writeStartElement("customDb");
+ _output_stream->writeAttribute("name", "");
+ _output_stream->writeAttribute("id", "customdb0");
+ _output_stream->writeEndElement();
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-void ProticdbMl::writeSamples() {
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- _output_stream->writeStartElement("samples");
- for (MsRunSp msrun_sp : _sp_project.get()->getMsRunStore().getMsRunList()) {
- _output_stream->writeStartElement("sample");
- QString id_samp = "bsamp" + pappso::Utils::getLexicalOrderedString(_sample_to_id.size());
- QString id_msrun = msrun_sp.get()->getXmlId();
- QString name = msrun_sp.get()->getSampleName();
- // balise sample
- _output_stream->writeAttribute("name", name);
- _output_stream->writeAttribute("id", id_samp);
- _output_stream->writeEmptyElement("description");
- _sample_to_id.insert(std::pair<QString, QString>( name, id_samp));
-
- // Element spectrumList = doc.createElement("spectrumList");
- // msRun.appendChild(spectrumList);
-
- //msrun_to_id.put(samp.getSampleName(), id_msrun);
- _output_stream->writeEndElement();// sample
-
+void
+ProticdbMl::writeSamples()
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _output_stream->writeStartElement("samples");
+ for(MsRunSp msrun_sp : _sp_project.get()->getMsRunStore().getMsRunList())
+ {
+ _output_stream->writeStartElement("sample");
+ QString id_samp =
+ "bsamp" + pappso::Utils::getLexicalOrderedString(_sample_to_id.size());
+ QString id_msrun = msrun_sp.get()->getXmlId();
+ QString name = msrun_sp.get()->getSampleName();
+ // balise sample
+ _output_stream->writeAttribute("name", name);
+ _output_stream->writeAttribute("id", id_samp);
+ _output_stream->writeEmptyElement("description");
+ _sample_to_id.insert(std::pair<QString, QString>(name, id_samp));
+
+ // Element spectrumList = doc.createElement("spectrumList");
+ // msRun.appendChild(spectrumList);
+
+ // msrun_to_id.put(samp.getSampleName(), id_msrun);
+ _output_stream->writeEndElement(); // sample
}
- _output_stream->writeEndElement();// samples
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _output_stream->writeEndElement(); // samples
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-void ProticdbMl::writeMsRuns() {
-
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- _output_stream->writeStartElement("msRuns");
- for (MsRunSp msrun_sp : _sp_project.get()->getMsRunStore().getMsRunList()) {
+void
+ProticdbMl::writeMsRuns()
+{
- QString name = msrun_sp.get()->getSampleName();
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _output_stream->writeStartElement("msRuns");
+ for(MsRunSp msrun_sp : _sp_project.get()->getMsRunStore().getMsRunList())
+ {
- QString id_samp = _sample_to_id.at(name);
+ QString name = msrun_sp.get()->getSampleName();
- // Element spectrumList = doc.createElement("spectrumList");
- // msRun.appendChild(spectrumList);
+ QString id_samp = _sample_to_id.at(name);
- QString id_msrun = msrun_sp.get()->getXmlId();
+ // Element spectrumList = doc.createElement("spectrumList");
+ // msRun.appendChild(spectrumList);
- // balise MsRun
- _output_stream->writeStartElement("msRun");
- _output_stream->writeAttribute("sample_id", id_samp);
- _output_stream->writeAttribute("id", id_msrun);
+ QString id_msrun = msrun_sp.get()->getXmlId();
- _output_stream->writeStartElement("description");
- _output_stream->writeStartElement("admin");
- // writer.writeStartElement("contact");
- // writer.writeStartElement("email");
- // writer.writeCharacters("valot@moulon.inra.fr");
- // writer.writeEndElement();// email
+ // balise MsRun
+ _output_stream->writeStartElement("msRun");
+ _output_stream->writeAttribute("sample_id", id_samp);
+ _output_stream->writeAttribute("id", id_msrun);
- // writer.writeStartElement("name");
- // writer.writeCharacters("Valot Benoit");
- // writer.writeEndElement();// name
- // writer.writeEndElement();// contact
+ _output_stream->writeStartElement("description");
+ _output_stream->writeStartElement("admin");
+ // writer.writeStartElement("contact");
+ // writer.writeStartElement("email");
+ // writer.writeCharacters("valot@moulon.inra.fr");
+ // writer.writeEndElement();// email
- _output_stream->writeStartElement("sourceFile");
- _output_stream->writeStartElement("nameOfFile");
- _output_stream->writeCharacters(name + ".RAW");
- _output_stream->writeEndElement();// nameOfFile
- _output_stream->writeEndElement();// sourceFile
+ // writer.writeStartElement("name");
+ // writer.writeCharacters("Valot Benoit");
+ // writer.writeEndElement();// name
+ // writer.writeEndElement();// contact
- _output_stream->writeStartElement("sampleName");
- _output_stream->writeCharacters(name);
- _output_stream->writeEndElement();// sampleName
- _output_stream->writeEndElement();// admin
- _output_stream->writeEndElement();// description
+ _output_stream->writeStartElement("sourceFile");
+ _output_stream->writeStartElement("nameOfFile");
+ _output_stream->writeCharacters(name + ".RAW");
+ _output_stream->writeEndElement(); // nameOfFile
+ _output_stream->writeEndElement(); // sourceFile
- _output_stream->writeEndElement();// msRun
+ _output_stream->writeStartElement("sampleName");
+ _output_stream->writeCharacters(name);
+ _output_stream->writeEndElement(); // sampleName
+ _output_stream->writeEndElement(); // admin
+ _output_stream->writeEndElement(); // description
+ _output_stream->writeEndElement(); // msRun
}
- _output_stream->writeEndElement();// msRuns
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _output_stream->writeEndElement(); // msRuns
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-void ProticdbMl::writeIdentificationDataSource(IdentificationDataSource * p_identification_data_source) {
+void
+ProticdbMl::writeIdentificationDataSource(
+ IdentificationDataSource *p_identification_data_source)
+{
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- _output_stream->writeStartElement("dataProcessing");
- _output_stream->writeStartElement("software");
- _output_stream->writeStartElement("name");
- if (p_identification_data_source->getIdentificationEngine() == IdentificationEngine::XTandem) {
- _output_stream->writeAttribute("acc", "PROTICdbO:0000283");
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _output_stream->writeStartElement("dataProcessing");
+ _output_stream->writeStartElement("software");
+ _output_stream->writeStartElement("name");
+ if(p_identification_data_source->getIdentificationEngine() ==
+ IdentificationEngine::XTandem)
+ {
+ _output_stream->writeAttribute("acc", "PROTICdbO:0000283");
}
- _output_stream->writeCharacters(p_identification_data_source->getIdentificationEngineName());
-
- _output_stream->writeEndElement();// name
- _output_stream->writeStartElement("version");
- _output_stream->writeCharacters(p_identification_data_source->getIdentificationEngineVersion());
- _output_stream->writeEndElement();// version
- _output_stream->writeEndElement();// software
- _output_stream->writeStartElement("processingMethod");
- // mzXml source file name
- writeCvParam("PROTICdbO:0000343",p_identification_data_source->getMsRunSp().get()->getFilename(),
- "MS/MS data source file name");
- if (p_identification_data_source->getIdentificationEngine() == IdentificationEngine::XTandem) {
- // model file name
- writeCvParam("PROTICdbO:0000342", p_identification_data_source->getIdentificationEngineParam(IdentificationEngineParam::tandem_param).toString(),
- "X!tandem xml model file name");
- // xtandem result file name
- writeCvParam("PROTICdbO:0000341", p_identification_data_source->getResourceName(),
- "X!tandem xml result file name");
+ _output_stream->writeCharacters(
+ p_identification_data_source->getIdentificationEngineName());
+
+ _output_stream->writeEndElement(); // name
+ _output_stream->writeStartElement("version");
+ _output_stream->writeCharacters(
+ p_identification_data_source->getIdentificationEngineVersion());
+ _output_stream->writeEndElement(); // version
+ _output_stream->writeEndElement(); // software
+ _output_stream->writeStartElement("processingMethod");
+ // mzXml source file name
+ writeCvParam("PROTICdbO:0000343",
+ p_identification_data_source->getMsRunSp().get()->getFilename(),
+ "MS/MS data source file name");
+ if(p_identification_data_source->getIdentificationEngine() ==
+ IdentificationEngine::XTandem)
+ {
+ // model file name
+ writeCvParam("PROTICdbO:0000342",
+ p_identification_data_source
+ ->getIdentificationEngineParam(
+ IdentificationEngineParam::tandem_param)
+ .toString(),
+ "X!tandem xml model file name");
+ // xtandem result file name
+ writeCvParam("PROTICdbO:0000341",
+ p_identification_data_source->getResourceName(),
+ "X!tandem xml result file name");
}
- _output_stream->writeEndElement();// processingMethod
- _output_stream->writeEndElement();// dataProcessing
- /*
- _output_stream->writeStartElement("dataProcessing");
- _output_stream->writeStartElement("software");
- _output_stream->writeStartElement("name");
- _output_stream->writeAttribute("acc", "PROTICdbO:0000283");
- _output_stream->writeCharacters("X!Tandem");
- _output_stream->writeEndElement();// name
- _output_stream->writeStartElement("version");
- _output_stream->writeCharacters(XtandemPipelineSession.getInstance()
- .getConfig().getXtandemVersion());
- _output_stream->writeEndElement();// version
- _output_stream->writeEndElement();// software
- _output_stream->writeStartElement("processingMethod");
- _output_stream->writeEndElement();// processingMethod
- _output_stream->writeEndElement();// dataProcessing
- */
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _output_stream->writeEndElement(); // processingMethod
+ _output_stream->writeEndElement(); // dataProcessing
+ /*
+ _output_stream->writeStartElement("dataProcessing");
+ _output_stream->writeStartElement("software");
+ _output_stream->writeStartElement("name");
+ _output_stream->writeAttribute("acc", "PROTICdbO:0000283");
+ _output_stream->writeCharacters("X!Tandem");
+ _output_stream->writeEndElement();// name
+ _output_stream->writeStartElement("version");
+ _output_stream->writeCharacters(XtandemPipelineSession.getInstance()
+ .getConfig().getXtandemVersion());
+ _output_stream->writeEndElement();// version
+ _output_stream->writeEndElement();// software
+ _output_stream->writeStartElement("processingMethod");
+ _output_stream->writeEndElement();// processingMethod
+ _output_stream->writeEndElement();// dataProcessing
+ */
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-void ProticdbMl::writeIdentificationRun(IdentificationGroup * p_identification) {
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- _output_stream->writeAttribute("ident_method_id", "m1");
- _output_stream->writeAttribute("customdb_id", "customdb0");
-
- _output_stream->writeStartElement("description");
- _output_stream->writeStartElement("admin");
- // writer.writeStartElement("contact");
- // writer.writeStartElement("email");
- // writer.writeCharacters("valot@moulon.inra.fr");
- // writer.writeEndElement();// email
-
- // writer.writeStartElement("name");
- // writer.writeCharacters("Valot Benoit");
- // writer.writeEndElement();// name
- // writer.writeEndElement();// contact
- /*
- this.xpipFile = XtandemPipelineSession.getInstance()
- .getCurrentXpipFile();
-
- _output_stream->writeStartElement("sourceFile");
- _output_stream->writeStartElement("nameOfFile");
- // TODO
- // get the loaded xpip file name
- _output_stream->writeCharacters(this.xpipFile.getName());
- _output_stream->writeEndElement();// nameOfFile
- _output_stream->writeStartElement("pathToFile");
- _output_stream->writeCharacters(this.xpipFile.getAbsolutePath());
- _output_stream->writeEndElement();// pathToFile
- _output_stream->writeStartElement("fileType");
- _output_stream->writeCharacters("XPIP file");
- _output_stream->writeEndElement();// fileType
- _output_stream->writeEndElement();// sourceFile
- */
- _output_stream->writeEndElement();// admin
-
- // if we can retrieve original informations in xml xtandem results
- //
- for (IdentificationDataSource * p_identification_data_source : p_identification->getIdentificationDataSourceList()) {
- writeIdentificationDataSource(p_identification_data_source);
+void
+ProticdbMl::writeIdentificationRun(IdentificationGroup *p_identification)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _output_stream->writeAttribute("ident_method_id", "m1");
+ _output_stream->writeAttribute("customdb_id", "customdb0");
+
+ _output_stream->writeStartElement("description");
+ _output_stream->writeStartElement("admin");
+ // writer.writeStartElement("contact");
+ // writer.writeStartElement("email");
+ // writer.writeCharacters("valot@moulon.inra.fr");
+ // writer.writeEndElement();// email
+
+ // writer.writeStartElement("name");
+ // writer.writeCharacters("Valot Benoit");
+ // writer.writeEndElement();// name
+ // writer.writeEndElement();// contact
+ /*
+ this.xpipFile = XtandemPipelineSession.getInstance()
+ .getCurrentXpipFile();
+
+ _output_stream->writeStartElement("sourceFile");
+ _output_stream->writeStartElement("nameOfFile");
+ // TODO
+ // get the loaded xpip file name
+ _output_stream->writeCharacters(this.xpipFile.getName());
+ _output_stream->writeEndElement();// nameOfFile
+ _output_stream->writeStartElement("pathToFile");
+ _output_stream->writeCharacters(this.xpipFile.getAbsolutePath());
+ _output_stream->writeEndElement();// pathToFile
+ _output_stream->writeStartElement("fileType");
+ _output_stream->writeCharacters("XPIP file");
+ _output_stream->writeEndElement();// fileType
+ _output_stream->writeEndElement();// sourceFile
+ */
+ _output_stream->writeEndElement(); // admin
+
+ // if we can retrieve original informations in xml xtandem results
+ //
+ for(IdentificationDataSource *p_identification_data_source :
+ p_identification->getIdentificationDataSourceList())
+ {
+ writeIdentificationDataSource(p_identification_data_source);
}
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
-
-// id: PROTICdbO:0000316
-// name: X!TandemPipeline
-
- _output_stream->writeStartElement("dataProcessing");
- _output_stream->writeStartElement("software");
- _output_stream->writeStartElement("name");
- _output_stream->writeAttribute("acc", "PROTICdbO:0000316");
- _output_stream->writeCharacters("X!TandemPipeline");
- _output_stream->writeEndElement();// name
- _output_stream->writeStartElement("version");
- _output_stream->writeCharacters(XTPCPP_VERSION);
- _output_stream->writeEndElement();// version
- _output_stream->writeEndElement();// software
- _output_stream->writeStartElement("processingMethod");
-// cvParams
-
- writeCvParam("PROTICdbO:0000323", QString("%1").arg(_sp_project.get()->getAutomaticFilterParameters().getFilterProteinEvalue()),
- "X!TandemPipeline filter on protein evalue (log)");
-
-// indi
-// combine
-// phospho
- if (_sp_project.get()->getProjectMode() == ProjectMode::combined) {
- writeCvParam("PROTICdbO:0000320", "combine", "");
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+
+ // id: PROTICdbO:0000316
+ // name: X!TandemPipeline
+
+ _output_stream->writeStartElement("dataProcessing");
+ _output_stream->writeStartElement("software");
+ _output_stream->writeStartElement("name");
+ _output_stream->writeAttribute("acc", "PROTICdbO:0000316");
+ _output_stream->writeCharacters("X!TandemPipeline");
+ _output_stream->writeEndElement(); // name
+ _output_stream->writeStartElement("version");
+ _output_stream->writeCharacters(XTPCPP_VERSION);
+ _output_stream->writeEndElement(); // version
+ _output_stream->writeEndElement(); // software
+ _output_stream->writeStartElement("processingMethod");
+ // cvParams
+
+ writeCvParam("PROTICdbO:0000323",
+ QString("%1").arg(_sp_project.get()
+ ->getAutomaticFilterParameters()
+ .getFilterProteinEvalue()),
+ "X!TandemPipeline filter on protein evalue (log)");
+
+ // indi
+ // combine
+ // phospho
+ if(_sp_project.get()->getProjectMode() == ProjectMode::combined)
+ {
+ writeCvParam("PROTICdbO:0000320", "combine", "");
}
- else {
- writeCvParam("PROTICdbO:0000319", "indiv", "");
+ else
+ {
+ writeCvParam("PROTICdbO:0000319", "indiv", "");
}
- //if (xtpExperimentType.equals("phospho")) {
- // this.writeCvParam("PROTICdbO:0000321", xtpExperimentType, "");
- //}
-
- writeCvParam("PROTICdbO:0000325", QString("%1").arg(_sp_project.get()->getAutomaticFilterParameters().getFilterMinimumPeptidePerMatch()),
- "X!TandemPipeline filter on minimal number of peptide per protein");
-
- writeCvParam("PROTICdbO:0000324", QString("%1").arg(_sp_project.get()->getAutomaticFilterParameters().getFilterPeptideEvalue()),
- "X!TandemPipeline filter on peptide evalue");
-
-// TODO write database filter
-// this.writeCvParam("PROTICdbO:0000324", ""
-// +
-// XtandemPipelineSession.getInstance().getConfig().get_database_filter(),
-// "X!TandemPipeline filter on peptide evalue");
-
- _output_stream->writeEndElement();// processingMethod
-
- _output_stream->writeEndElement();// dataProcessing
-
- _output_stream->writeEndElement();// description
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ // if (xtpExperimentType.equals("phospho")) {
+ // this.writeCvParam("PROTICdbO:0000321", xtpExperimentType, "");
+ //}
+
+ writeCvParam(
+ "PROTICdbO:0000325",
+ QString("%1").arg(_sp_project.get()
+ ->getAutomaticFilterParameters()
+ .getFilterMinimumPeptidePerMatch()),
+ "X!TandemPipeline filter on minimal number of peptide per protein");
+
+ writeCvParam("PROTICdbO:0000324",
+ QString("%1").arg(_sp_project.get()
+ ->getAutomaticFilterParameters()
+ .getFilterPeptideEvalue()),
+ "X!TandemPipeline filter on peptide evalue");
+
+ // TODO write database filter
+ // this.writeCvParam("PROTICdbO:0000324", ""
+ // +
+ // XtandemPipelineSession.getInstance().getConfig().get_database_filter(),
+ // "X!TandemPipeline filter on peptide evalue");
+
+ _output_stream->writeEndElement(); // processingMethod
+
+ _output_stream->writeEndElement(); // dataProcessing
+
+ _output_stream->writeEndElement(); // description
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-void ProticdbMl::writepeptideHits(IdentificationGroup * p_identification) {
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- _output_stream->writeStartElement("peptideHits");
- for (std::pair <unsigned int, GroupingGroupSp > group_pair : p_identification->getGroupStore().getGroupMap()) {
- writepeptideHitsbyGroup(group_pair.second.get());
+void
+ProticdbMl::writepeptideHits(IdentificationGroup *p_identification)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _output_stream->writeStartElement("peptideHits");
+ for(std::pair<unsigned int, GroupingGroupSp> group_pair :
+ p_identification->getGroupStore().getGroupMap())
+ {
+ writepeptideHitsbyGroup(group_pair.second.get());
}
- _output_stream->writeEndElement();// "peptideHits");
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _output_stream->writeEndElement(); // "peptideHits");
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-QString getProticPeptideHitKey(const PeptideEvidence * p_peptide_evidence) {
- return (QString ("%1 %2 %3").arg(p_peptide_evidence->getHashSampleScan()).arg(p_peptide_evidence->getPeptideXtpSp().get()->toAbsoluteString()).arg(p_peptide_evidence->getIdentificationDataSource()->getResourceName()));
+QString
+getProticPeptideHitKey(const PeptideEvidence *p_peptide_evidence)
+{
+ return (
+ QString("%1 %2 %3")
+ .arg(p_peptide_evidence->getHashSampleScan())
+ .arg(p_peptide_evidence->getPeptideXtpSp().get()->toAbsoluteString())
+ .arg(
+ p_peptide_evidence->getIdentificationDataSource()->getResourceName()));
}
-struct ProticPeptideHit {
- bool operator ==(const ProticPeptideHit &other) const {
- return (key == other.key);
- };
- /** key = getProticPeptideHitKey
- * */
- QString key;
- PeptideMatch peptide_match;
+struct ProticPeptideHit
+{
+ bool
+ operator==(const ProticPeptideHit &other) const
+ {
+ return (key == other.key);
+ };
+ /** key = getProticPeptideHitKey
+ * */
+ QString key;
+ PeptideMatch peptide_match;
};
-void ProticdbMl::writepeptideHitsbyGroup(GroupingGroup * p_group) {
+void
+ProticdbMl::writepeptideHitsbyGroup(GroupingGroup *p_group)
+{
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- std::vector <ProticPeptideHit> protic_peptide_hit_list;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ std::vector<ProticPeptideHit> protic_peptide_hit_list;
- for (const ProteinMatch* p_protein_match : p_group->getProteinMatchList()) {
- for (const PeptideMatch & peptide_match : p_protein_match->getPeptideMatchList(ValidationState::grouped)) {
- ProticPeptideHit protic_peptide_hit = {getProticPeptideHitKey(peptide_match.getPeptideEvidence()), peptide_match};
- protic_peptide_hit_list.push_back(protic_peptide_hit);
+ for(const ProteinMatch *p_protein_match : p_group->getProteinMatchList())
+ {
+ for(const PeptideMatch &peptide_match :
+ p_protein_match->getPeptideMatchList(ValidationState::grouped))
+ {
+ ProticPeptideHit protic_peptide_hit = {
+ getProticPeptideHitKey(peptide_match.getPeptideEvidence()),
+ peptide_match};
+ protic_peptide_hit_list.push_back(protic_peptide_hit);
}
}
- std::sort(protic_peptide_hit_list.begin(),protic_peptide_hit_list.end(),[](const ProticPeptideHit & first, const ProticPeptideHit & second) {
- return (first.key < second.key) ;
- });
- auto last = std::unique(protic_peptide_hit_list.begin(), protic_peptide_hit_list.end());
- protic_peptide_hit_list.erase(last, protic_peptide_hit_list.end());
-
- for (ProticPeptideHit & protic_peptide_hit :protic_peptide_hit_list) {
- QString xml_id = QString("pep%1").arg(_peptidekey_to_id.size()+1);
- writePeptideHit(xml_id, protic_peptide_hit);
- _peptidekey_to_id.insert(std::pair<QString, QString>(protic_peptide_hit.key, xml_id));
+ std::sort(protic_peptide_hit_list.begin(), protic_peptide_hit_list.end(),
+ [](const ProticPeptideHit &first, const ProticPeptideHit &second) {
+ return (first.key < second.key);
+ });
+ auto last =
+ std::unique(protic_peptide_hit_list.begin(), protic_peptide_hit_list.end());
+ protic_peptide_hit_list.erase(last, protic_peptide_hit_list.end());
+
+ for(ProticPeptideHit &protic_peptide_hit : protic_peptide_hit_list)
+ {
+ QString xml_id = QString("pep%1").arg(_peptidekey_to_id.size() + 1);
+ writePeptideHit(xml_id, protic_peptide_hit);
+ _peptidekey_to_id.insert(
+ std::pair<QString, QString>(protic_peptide_hit.key, xml_id));
}
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
+void
+ProticdbMl::writePeptideHit(QString xml_id,
+ ProticPeptideHit &protic_peptide_hit)
+{
-void ProticdbMl::writePeptideHit(QString xml_id, ProticPeptideHit & protic_peptide_hit) {
-
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- if (protic_peptide_hit.peptide_match.getPeptideEvidence() == nullptr) {
- throw pappso::PappsoException(QObject::tr("Error protic_peptide_hit.peptide_match->getPeptideEvidence() == nullptr : \n%1 %2 %3").arg(__FILE__)
- .arg(__FUNCTION__)
- .arg(__LINE__)
- );
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ if(protic_peptide_hit.peptide_match.getPeptideEvidence() == nullptr)
+ {
+ throw pappso::PappsoException(
+ QObject::tr(
+ "Error protic_peptide_hit.peptide_match->getPeptideEvidence() == "
+ "nullptr : \n%1 %2 %3")
+ .arg(__FILE__)
+ .arg(__FUNCTION__)
+ .arg(__LINE__));
}
- if (protic_peptide_hit.peptide_match.getPeptideEvidence()->getPeptideXtpSp().get() == nullptr) {
- throw pappso::PappsoException(QObject::tr("Error protic_peptide_hit.peptide_match->getPeptideEvidence()->getPeptideXtpSp().get() == nullptr : \n%1 %2 %3").arg(__FILE__)
- .arg(__FUNCTION__)
- .arg(__LINE__)
- );
+ if(protic_peptide_hit.peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get() == nullptr)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error "
+ "protic_peptide_hit.peptide_match->getPeptideEvidence()->"
+ "getPeptideXtpSp().get() == nullptr : \n%1 %2 %3")
+ .arg(__FILE__)
+ .arg(__FUNCTION__)
+ .arg(__LINE__));
}
- // param par default
- _output_stream->writeStartElement("peptideHit");
- _output_stream->writeAttribute("calc_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getMass()));
- _output_stream->writeAttribute("exp_mz", Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()->getExperimentalMz()));
- _output_stream->writeAttribute("delta", Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()->getDeltaMass()));
- _output_stream->writeAttribute("exp_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()->getExperimentalMass()));
- _output_stream->writeAttribute("acq_number", QString ("%1").arg(protic_peptide_hit.peptide_match.getPeptideEvidence()->getScan()));
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- _output_stream->writeAttribute("ms_run_id", protic_peptide_hit.peptide_match.getPeptideEvidence()->getMsRunP()->getXmlId());
- _output_stream->writeAttribute("id", xml_id);
- _output_stream->writeAttribute("exp_z", QString ("%1").arg(protic_peptide_hit.peptide_match.getPeptideEvidence()->getCharge()));
-
- writeCvParam("PROTICdbO:0000339",protic_peptide_hit.peptide_match.getPeptideEvidence()->getGrpPeptideSp().get()->getGroupingId(),
- "peptide mass id");
- /*
- if (xtpExperimentType.equals("phospho")) {
- this.writeCvParam("PROTICdbO:0000349",
- Utils.getPappsoPhosphoPeptideMassId(group, peptideMass),
- "phosphopeptide mass id");
- }
- */
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- // pep.getMsRun().
- IdentificationEngine identification_engine = protic_peptide_hit.peptide_match.getPeptideEvidence()->getIdentificationDataSource()->getIdentificationEngine();
- if (identification_engine == IdentificationEngine::XTandem) {
- // cvparam specifique xtandem
-
- writeCvParam("PROTICdbO:0000287", Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()->getEvalue()),
- "xtandem peptide evalue");
-
- writeCvParam("PROTICdbO:0000288", Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()->getParam(PeptideEvidenceParam::tandem_hyperscore).toDouble()),
- "xtandem peptide hyperscore");
+ // param par default
+ _output_stream->writeStartElement("peptideHit");
+ _output_stream->writeAttribute(
+ "calc_mr",
+ Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getMass()));
+ _output_stream->writeAttribute(
+ "exp_mz",
+ Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()
+ ->getExperimentalMz()));
+ _output_stream->writeAttribute(
+ "delta",
+ Utils::getXmlDouble(
+ protic_peptide_hit.peptide_match.getPeptideEvidence()->getDeltaMass()));
+ _output_stream->writeAttribute(
+ "exp_mr",
+ Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()
+ ->getExperimentalMass()));
+ _output_stream->writeAttribute(
+ "acq_number",
+ QString("%1").arg(
+ protic_peptide_hit.peptide_match.getPeptideEvidence()->getScan()));
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _output_stream->writeAttribute(
+ "ms_run_id", protic_peptide_hit.peptide_match.getPeptideEvidence()
+ ->getMsRunP()
+ ->getXmlId());
+ _output_stream->writeAttribute("id", xml_id);
+ _output_stream->writeAttribute(
+ "exp_z",
+ QString("%1").arg(
+ protic_peptide_hit.peptide_match.getPeptideEvidence()->getCharge()));
+
+ writeCvParam("PROTICdbO:0000339",
+ protic_peptide_hit.peptide_match.getPeptideEvidence()
+ ->getGrpPeptideSp()
+ .get()
+ ->getGroupingId(),
+ "peptide mass id");
+ /*
+ if (xtpExperimentType.equals("phospho")) {
+ this.writeCvParam("PROTICdbO:0000349",
+ Utils.getPappsoPhosphoPeptideMassId(group,
+ peptideMass), "phosphopeptide mass id");
+ }
+ */
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ // pep.getMsRun().
+ IdentificationEngine identification_engine =
+ protic_peptide_hit.peptide_match.getPeptideEvidence()
+ ->getIdentificationDataSource()
+ ->getIdentificationEngine();
+ if(identification_engine == IdentificationEngine::XTandem)
+ {
+ // cvparam specifique xtandem
+
+ writeCvParam(
+ "PROTICdbO:0000287",
+ Utils::getXmlDouble(
+ protic_peptide_hit.peptide_match.getPeptideEvidence()->getEvalue()),
+ "xtandem peptide evalue");
+
+ writeCvParam("PROTICdbO:0000288",
+ Utils::getXmlDouble(
+ protic_peptide_hit.peptide_match.getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::tandem_hyperscore)
+ .toDouble()),
+ "xtandem peptide hyperscore");
}
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- writeCvParam("PROTICdbO:0000289",QString ("%1").arg(protic_peptide_hit.peptide_match.getPeptideEvidence()->getRetentionTime()),
- "xtandem peptide retention time");
-
- // sequences avec les modifs
- _output_stream->writeStartElement("pepSeq");
- _output_stream->writeStartElement("peptide");
- _output_stream->writeCharacters(protic_peptide_hit.peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequence());
- _output_stream->writeEndElement();// peptide
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- if (!protic_peptide_hit.peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getModifString().isEmpty()) {
- writePtms(protic_peptide_hit.peptide_match.getPeptideEvidence()->getPeptideXtpSp().get());
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ writeCvParam(
+ "PROTICdbO:0000289",
+ QString("%1").arg(protic_peptide_hit.peptide_match.getPeptideEvidence()
+ ->getRetentionTime()),
+ "xtandem peptide retention time");
+
+ // sequences avec les modifs
+ _output_stream->writeStartElement("pepSeq");
+ _output_stream->writeStartElement("peptide");
+ _output_stream->writeCharacters(
+ protic_peptide_hit.peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getSequence());
+ _output_stream->writeEndElement(); // peptide
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ if(!protic_peptide_hit.peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getModifString()
+ .isEmpty())
+ {
+ writePtms(protic_peptide_hit.peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get());
}
- _output_stream->writeEndElement();// pepSeq
- _output_stream->writeEndElement();// peptideHit
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _output_stream->writeEndElement(); // pepSeq
+ _output_stream->writeEndElement(); // peptideHit
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-void ProticdbMl::writePtms(PeptideXtp * p_peptide) {
- _output_stream->writeStartElement("ptms");
- QStringList modif_list;
- unsigned int i=1;
- for (const pappso::Aa & amino_acid: *p_peptide) {
- std::list<pappso::AaModificationP> aa_modif_list = amino_acid.getModificationList();
- QStringList aamodif;
- for (auto && aa_modif : aa_modif_list) {
- if (!aa_modif->isInternal()) {
- aamodif << QString::number(aa_modif->getMass(), 'f', 2);
- _output_stream->writeStartElement("ptm");
- _output_stream->writeAttribute("diff_mono", Utils::getXmlDouble(aa_modif->getMass()));
- _output_stream->writeAttribute("position", QString ("%1").arg(i));
- _output_stream->writeAttribute("aa", QString(amino_acid.getLetter()));
- _output_stream->writeEndElement();// ptm
+void
+ProticdbMl::writePtms(PeptideXtp *p_peptide)
+{
+ _output_stream->writeStartElement("ptms");
+ QStringList modif_list;
+ unsigned int i = 1;
+ for(const pappso::Aa &amino_acid : *p_peptide)
+ {
+ std::list<pappso::AaModificationP> aa_modif_list =
+ amino_acid.getModificationList();
+ QStringList aamodif;
+ for(auto &&aa_modif : aa_modif_list)
+ {
+ if(!aa_modif->isInternal())
+ {
+ aamodif << QString::number(aa_modif->getMass(), 'f', 2);
+ _output_stream->writeStartElement("ptm");
+ _output_stream->writeAttribute(
+ "diff_mono", Utils::getXmlDouble(aa_modif->getMass()));
+ _output_stream->writeAttribute("position", QString("%1").arg(i));
+ _output_stream->writeAttribute("aa",
+ QString(amino_acid.getLetter()));
+ _output_stream->writeEndElement(); // ptm
}
}
- i++;
+ i++;
}
- _output_stream->writeEndElement();// ptms
+ _output_stream->writeEndElement(); // ptms
}
-void ProticdbMl::writeMatchs(IdentificationGroup * p_identification) {
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+void
+ProticdbMl::writeMatchs(IdentificationGroup *p_identification)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- _output_stream->writeStartElement("matchs");
- for (std::pair <unsigned int, GroupingGroupSp > group_pair : p_identification->getGroupStore().getGroupMap()) {
- //for (Group group : identification.getGrouping().getGroupList()) {
- std::vector<const ProteinMatch *> protein_match_list = group_pair.second.get()->getProteinMatchList();
- //sort protein match by subgroup
- std::sort(protein_match_list.begin(), protein_match_list.end(),
- [](const ProteinMatch * a, const ProteinMatch * b)
+ _output_stream->writeStartElement("matchs");
+ for(std::pair<unsigned int, GroupingGroupSp> group_pair :
+ p_identification->getGroupStore().getGroupMap())
+ {
+ // for (Group group : identification.getGrouping().getGroupList()) {
+ std::vector<const ProteinMatch *> protein_match_list =
+ group_pair.second.get()->getProteinMatchList();
+ // sort protein match by subgroup
+ std::sort(protein_match_list.begin(), protein_match_list.end(),
+ [](const ProteinMatch *a, const ProteinMatch *b) {
+ return a->getGrpProteinSp().get()->getSubGroupNumber() <
+ b->getGrpProteinSp().get()->getSubGroupNumber();
+ });
+
+ std::vector<const ProteinMatch *> protein_match_subgroup_list;
+ for(const ProteinMatch *p_protein_match : protein_match_list)
{
- return a->getGrpProteinSp().get()->getSubGroupNumber() < b->getGrpProteinSp().get()->getSubGroupNumber();
- });
-
- std::vector<const ProteinMatch *> protein_match_subgroup_list;
- for (const ProteinMatch * p_protein_match: protein_match_list) {
- if (protein_match_subgroup_list.size() == 0) {
- protein_match_subgroup_list.push_back(p_protein_match);
+ if(protein_match_subgroup_list.size() == 0)
+ {
+ protein_match_subgroup_list.push_back(p_protein_match);
}
- else {
- if (protein_match_subgroup_list[0]->getGrpProteinSp().get()->getSubGroupNumber() != p_protein_match->getGrpProteinSp().get()->getSubGroupNumber()) {
- writeMatch(protein_match_subgroup_list);
- protein_match_subgroup_list.clear();
- protein_match_subgroup_list.push_back(p_protein_match);
+ else
+ {
+ if(protein_match_subgroup_list[0]
+ ->getGrpProteinSp()
+ .get()
+ ->getSubGroupNumber() !=
+ p_protein_match->getGrpProteinSp().get()->getSubGroupNumber())
+ {
+ writeMatch(protein_match_subgroup_list);
+ protein_match_subgroup_list.clear();
+ protein_match_subgroup_list.push_back(p_protein_match);
}
- else {
- protein_match_subgroup_list.push_back(p_protein_match);
+ else
+ {
+ protein_match_subgroup_list.push_back(p_protein_match);
}
}
}
- writeMatch(protein_match_subgroup_list);
+ writeMatch(protein_match_subgroup_list);
}
- _output_stream->writeEndElement();// "matchs");
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _output_stream->writeEndElement(); // "matchs");
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
-const QString & ProticdbMl::getPeptideXmlId(const PeptideMatch* p_peptide_match) const {
- QString peptide_key = getProticPeptideHitKey(p_peptide_match->getPeptideEvidence());
- auto it = _peptidekey_to_id.find(peptide_key);
- if (it == _peptidekey_to_id.end()) {
- throw pappso::PappsoException(QObject::tr("Error peptide key %1 not found for peptide match %2 sample=%3 scan=%4 start=%5").arg(peptide_key)
- .arg(p_peptide_match->getPeptideEvidence()->getPeptideXtpSp().get()->toString())
- .arg(p_peptide_match->getPeptideEvidence()->getMsRunP()->getXmlId())
- .arg(p_peptide_match->getPeptideEvidence()->getScan())
- .arg(p_peptide_match->getStart())
- );
+const QString &
+ProticdbMl::getPeptideXmlId(const PeptideMatch *p_peptide_match) const
+{
+ QString peptide_key =
+ getProticPeptideHitKey(p_peptide_match->getPeptideEvidence());
+ auto it = _peptidekey_to_id.find(peptide_key);
+ if(it == _peptidekey_to_id.end())
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error peptide key %1 not found for peptide match %2 "
+ "sample=%3 scan=%4 start=%5")
+ .arg(peptide_key)
+ .arg(p_peptide_match->getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->toString())
+ .arg(p_peptide_match->getPeptideEvidence()->getMsRunP()->getXmlId())
+ .arg(p_peptide_match->getPeptideEvidence()->getScan())
+ .arg(p_peptide_match->getStart()));
}
- return it->second;
-
+ return it->second;
}
-const QString & ProticdbMl::getProteinXmlId(const ProteinMatch* p_protein_match) const {
- auto it = _map_accession2xmlid.find(p_protein_match->getProteinXtpSp().get()->getAccession());
- if (it == _map_accession2xmlid.end()) {
- throw pappso::PappsoException(QObject::tr("Error protein accession %1 not found for protein %2")
- .arg(p_protein_match->getProteinXtpSp().get()->getAccession())
- .arg(p_protein_match->getProteinXtpSp().get()->getAccession()));
+const QString &
+ProticdbMl::getProteinXmlId(const ProteinMatch *p_protein_match) const
+{
+ auto it = _map_accession2xmlid.find(
+ p_protein_match->getProteinXtpSp().get()->getAccession());
+ if(it == _map_accession2xmlid.end())
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error protein accession %1 not found for protein %2")
+ .arg(p_protein_match->getProteinXtpSp().get()->getAccession())
+ .arg(p_protein_match->getProteinXtpSp().get()->getAccession()));
}
- return it->second;
+ return it->second;
}
-void ProticdbMl::writeMatch(std::vector<const ProteinMatch *> & protein_match_sg_list) {
- try {
- if (protein_match_sg_list.size() == 0) return;
- //for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
- _output_stream->writeStartElement("match");
-
- // samples
- QStringList sample_name_list;
- for (const PeptideMatch & peptide_match: protein_match_sg_list[0]->getPeptideMatchList(ValidationState::grouped)) {
- sample_name_list << peptide_match.getPeptideEvidence()->getMsRunP()->getSampleName();
+void
+ProticdbMl::writeMatch(std::vector<const ProteinMatch *> &protein_match_sg_list)
+{
+ try
+ {
+ if(protein_match_sg_list.size() == 0)
+ return;
+ // for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
+ _output_stream->writeStartElement("match");
+
+ // samples
+ QStringList sample_name_list;
+ for(const PeptideMatch &peptide_match :
+ protein_match_sg_list[0]->getPeptideMatchList(
+ ValidationState::grouped))
+ {
+ sample_name_list
+ << peptide_match.getPeptideEvidence()->getMsRunP()->getSampleName();
}
- sample_name_list = sample_name_list.toSet().toList();
- for (QString sample_name :sample_name_list) {
- _output_stream->writeStartElement("matchSample");
- _output_stream->writeAttribute(
- "sample_id",_sample_to_id[sample_name]);
- _output_stream->writeAttribute("name", sample_name);
- _output_stream->writeEndElement();// "matchSample");
+ sample_name_list = sample_name_list.toSet().toList();
+ for(QString sample_name : sample_name_list)
+ {
+ _output_stream->writeStartElement("matchSample");
+ _output_stream->writeAttribute("sample_id",
+ _sample_to_id[sample_name]);
+ _output_stream->writeAttribute("name", sample_name);
+ _output_stream->writeEndElement(); // "matchSample");
}
- // proteins
- for (const ProteinMatch * p_protein_match: protein_match_sg_list) {
- _output_stream->writeStartElement("proteinHit");
- _output_stream->writeAttribute("sequence_id",QString("%1 %2").arg(p_protein_match->getProteinXtpSp().get()->getAccession()).arg(p_protein_match->getProteinXtpSp().get()->getDescription()));
- // proteinHit.setAttribute("score", "");
- _output_stream->writeAttribute("rank", QString("%1").arg(p_protein_match->getGrpProteinSp().get()->getRank()));
-
- // //cvparam
- writeCvParam("PROTICdbO:0000284",QString("%1").arg(p_protein_match->getProteinXtpSp().get()->getMass()),
- "MW computation");
- // evalue
- writeCvParam("PROTICdbO:0000291", Utils::getXmlDouble(p_protein_match->getLogEvalue())
- , "Xtandem log evalue");
-
- // coverage
- writeCvParam(
- "PROTICdbO:0000285", Utils::getXmlDouble(p_protein_match->getCoverage()),
- "protein coverage");
-
- // [Term]
- // id: PROTICdbO:0000335
- // name: X!TandemPipeline PAI
- writeCvParam("PROTICdbO:0000335",Utils::getXmlDouble(p_protein_match->getPAI()), "PAI");
-
- // [Term]
- // id: PROTICdbO:0000337
- // name: protein group number
- writeCvParam("PROTICdbO:0000337",p_protein_match->getGrpProteinSp().get()->getGroupingId(), "grouping number");
-
- _output_stream->writeEndElement();// "proteinHit");
+ // proteins
+ for(const ProteinMatch *p_protein_match : protein_match_sg_list)
+ {
+ _output_stream->writeStartElement("proteinHit");
+ _output_stream->writeAttribute(
+ "sequence_id",
+ QString("%1 %2")
+ .arg(p_protein_match->getProteinXtpSp().get()->getAccession())
+ .arg(p_protein_match->getProteinXtpSp().get()->getDescription()));
+ // proteinHit.setAttribute("score", "");
+ _output_stream->writeAttribute(
+ "rank", QString("%1").arg(
+ p_protein_match->getGrpProteinSp().get()->getRank()));
+
+ // //cvparam
+ writeCvParam("PROTICdbO:0000284",
+ QString("%1").arg(
+ p_protein_match->getProteinXtpSp().get()->getMass()),
+ "MW computation");
+ // evalue
+ writeCvParam("PROTICdbO:0000291",
+ Utils::getXmlDouble(p_protein_match->getLogEvalue()),
+ "Xtandem log evalue");
+
+ // coverage
+ writeCvParam("PROTICdbO:0000285",
+ Utils::getXmlDouble(p_protein_match->getCoverage()),
+ "protein coverage");
+
+ // [Term]
+ // id: PROTICdbO:0000335
+ // name: X!TandemPipeline PAI
+ writeCvParam("PROTICdbO:0000335",
+ Utils::getXmlDouble(p_protein_match->getPAI()), "PAI");
+
+ // [Term]
+ // id: PROTICdbO:0000337
+ // name: protein group number
+ writeCvParam(
+ "PROTICdbO:0000337",
+ p_protein_match->getGrpProteinSp().get()->getGroupingId(),
+ "grouping number");
+
+ _output_stream->writeEndElement(); // "proteinHit");
}
- for (const ProteinMatch * p_protein_match: protein_match_sg_list) {
- //peptides
- for (const PeptideMatch & peptide_match: p_protein_match->getPeptideMatchList(ValidationState::grouped)) {
- // peptidesHitRef
- QString peptide_xml_id = getPeptideXmlId(&peptide_match);
-
- _output_stream->writeStartElement("peptideHitRef");
- _output_stream->writeAttribute("peptide_hit_id", peptide_xml_id);
-
- _output_stream->writeStartElement("fromSeq");
- _output_stream->writeAttribute(
- "seq_id", getProteinXmlId(p_protein_match));
- _output_stream->writeAttribute("start", QString("%1").arg(peptide_match.getStart()+1));
- _output_stream->writeAttribute("stop", QString("%1").arg(peptide_match.getStop()+1));
- QString residue_before_nter = "-";
- if (peptide_match.getStart() > 0) {
- residue_before_nter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(peptide_match.getStart()-1,1);
+ for(const ProteinMatch *p_protein_match : protein_match_sg_list)
+ {
+ // peptides
+ for(const PeptideMatch &peptide_match :
+ p_protein_match->getPeptideMatchList(ValidationState::grouped))
+ {
+ // peptidesHitRef
+ QString peptide_xml_id = getPeptideXmlId(&peptide_match);
+
+ _output_stream->writeStartElement("peptideHitRef");
+ _output_stream->writeAttribute("peptide_hit_id", peptide_xml_id);
+
+ _output_stream->writeStartElement("fromSeq");
+ _output_stream->writeAttribute("seq_id",
+ getProteinXmlId(p_protein_match));
+ _output_stream->writeAttribute(
+ "start", QString("%1").arg(peptide_match.getStart() + 1));
+ _output_stream->writeAttribute(
+ "stop", QString("%1").arg(peptide_match.getStop() + 1));
+ QString residue_before_nter = "-";
+ if(peptide_match.getStart() > 0)
+ {
+ residue_before_nter =
+ p_protein_match->getProteinXtpSp().get()->getSequence().mid(
+ peptide_match.getStart() - 1, 1);
}
- _output_stream->writeAttribute("residue_before_nter", residue_before_nter);
- QString residue_after_cter = "-";
- if (peptide_match.getStop() < (p_protein_match->getProteinXtpSp().get()->getSequence().size()-1)) {
- residue_after_cter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(peptide_match.getStop(),1);
+ _output_stream->writeAttribute("residue_before_nter",
+ residue_before_nter);
+ QString residue_after_cter = "-";
+ if(peptide_match.getStop() < (p_protein_match->getProteinXtpSp()
+ .get()
+ ->getSequence()
+ .size() -
+ 1))
+ {
+ residue_after_cter =
+ p_protein_match->getProteinXtpSp().get()->getSequence().mid(
+ peptide_match.getStop(), 1);
}
- _output_stream->writeAttribute("residue_after_cter", residue_after_cter);
+ _output_stream->writeAttribute("residue_after_cter",
+ residue_after_cter);
- _output_stream->writeEndElement();// fromSeq
- _output_stream->writeEndElement();// peptideHitRef
+ _output_stream->writeEndElement(); // fromSeq
+ _output_stream->writeEndElement(); // peptideHitRef
}
-
}
- _output_stream->writeEndElement();// "match");
+ _output_stream->writeEndElement(); // "match");
}
- catch (pappso::PappsoException &error)
+ catch(pappso::PappsoException &error)
{
- throw pappso::PappsoException(QObject::tr("Error in ProticdbMl::writeMatch :\n%1").arg(error.qwhat()));
+ throw pappso::PappsoException(
+ QObject::tr("Error in ProticdbMl::writeMatch :\n%1")
+ .arg(error.qwhat()));
}
- catch (std::exception &error)
+ catch(std::exception &error)
{
- throw pappso::PappsoException(QObject::tr("Error in ProticdbMl::writeMatch stdex :\n%1").arg(error.what()));
+ throw pappso::PappsoException(
+ QObject::tr("Error in ProticdbMl::writeMatch stdex :\n%1")
+ .arg(error.what()));
}
}
-void ProticdbMl::writeOboModif(pappso::AaModificationP mod) {
- _output_stream->writeStartElement("cvParam");
- _output_stream->writeAttribute("name", mod->getName());
- _output_stream->writeAttribute("cvLabel", "MOD");
- _output_stream->writeAttribute("accession", mod->getAccession());
- _output_stream->writeEndElement();// cvParam
+void
+ProticdbMl::writeOboModif(pappso::AaModificationP mod)
+{
+ _output_stream->writeStartElement("cvParam");
+ _output_stream->writeAttribute("name", mod->getName());
+ _output_stream->writeAttribute("cvLabel", "MOD");
+ _output_stream->writeAttribute("accession", mod->getAccession());
+ _output_stream->writeEndElement(); // cvParam
}
-void ProticdbMl::writeCvParam(QString acc, QString value, QString description) {
- _output_stream->writeStartElement("cvParam");
+void
+ProticdbMl::writeCvParam(QString acc, QString value, QString description)
+{
+ _output_stream->writeStartElement("cvParam");
- _output_stream->writeAttribute("value",value);
- if (description.isEmpty()) {
- _output_stream->writeAttribute("name", "N.A.");
- } else {
- _output_stream->writeAttribute("name", description);
+ _output_stream->writeAttribute("value", value);
+ if(description.isEmpty())
+ {
+ _output_stream->writeAttribute("name", "N.A.");
}
- _output_stream->writeAttribute("cvLabel", "PROTICdbO");
- _output_stream->writeAttribute("accession", acc);
- _output_stream->writeEndElement();// cvParam
-
+ else
+ {
+ _output_stream->writeAttribute("name", description);
+ }
+ _output_stream->writeAttribute("cvLabel", "PROTICdbO");
+ _output_stream->writeAttribute("accession", acc);
+ _output_stream->writeEndElement(); // cvParam
}
-
diff --git a/src/output/proticdbml.h b/src/output/proticdbml.h
index df91fcb066716e9b917ae34249b4e16e98585b00..6292e320f1a25057bd2684d4d466773aa890d5e6 100644
--- a/src/output/proticdbml.h
+++ b/src/output/proticdbml.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PROTICDBML_H
#define PROTICDBML_H
@@ -42,42 +43,43 @@ struct ProticPeptideHit;
class ProticdbMl
{
- public:
- ProticdbMl(const QString & out_filename);
- ~ProticdbMl();
+ public:
+ ProticdbMl(const QString &out_filename);
+ ~ProticdbMl();
- void write(ProjectSp sp_project);
- void close();
-
-private :
- void writeOboModif(pappso::AaModificationP mod);
- void writeCvParam(QString acc, QString value, QString description);
- void writeSequence(ProteinMatch * p_protein_match);
- void writeProject();
- void writeIdentMethod();
- void writeSamples();
- void writeMsRuns();
- void writeIdentificationRun(IdentificationGroup * p_identification);
- void writeIdentificationDataSource(IdentificationDataSource * p_identification_data_source);
- void writepeptideHits(IdentificationGroup * p_identification);
- void writepeptideHitsbyGroup(GroupingGroup * p_group);
- void writePeptideHit(QString xml_id, ProticPeptideHit & protic_peptide_hit);
- void writePtms(PeptideXtp * p_peptide);
- void writeMatchs(IdentificationGroup * p_identification);
- void writeMatch(std::vector<const ProteinMatch *> & protein_match_sg_list);
-
- const QString & getPeptideXmlId(const PeptideMatch* p_peptide_match) const;
- const QString & getProteinXmlId(const ProteinMatch* p_protein_match) const;
-
-private :
- QFile * _output_file;
- QXmlStreamWriter * _output_stream;
- ProjectSp _sp_project;
- IdentificationGroup * _p_identification_group;
- QTime _duracel;
- std::map<QString, QString> _map_accession2xmlid;
- std::map<QString, QString> _sample_to_id;
- std::map<QString, QString> _peptidekey_to_id;
+ void write(ProjectSp sp_project);
+ void close();
+
+ private:
+ void writeOboModif(pappso::AaModificationP mod);
+ void writeCvParam(QString acc, QString value, QString description);
+ void writeSequence(ProteinMatch *p_protein_match);
+ void writeProject();
+ void writeIdentMethod();
+ void writeSamples();
+ void writeMsRuns();
+ void writeIdentificationRun(IdentificationGroup *p_identification);
+ void writeIdentificationDataSource(
+ IdentificationDataSource *p_identification_data_source);
+ void writepeptideHits(IdentificationGroup *p_identification);
+ void writepeptideHitsbyGroup(GroupingGroup *p_group);
+ void writePeptideHit(QString xml_id, ProticPeptideHit &protic_peptide_hit);
+ void writePtms(PeptideXtp *p_peptide);
+ void writeMatchs(IdentificationGroup *p_identification);
+ void writeMatch(std::vector<const ProteinMatch *> &protein_match_sg_list);
+
+ const QString &getPeptideXmlId(const PeptideMatch *p_peptide_match) const;
+ const QString &getProteinXmlId(const ProteinMatch *p_protein_match) const;
+
+ private:
+ QFile *_output_file;
+ QXmlStreamWriter *_output_stream;
+ ProjectSp _sp_project;
+ IdentificationGroup *_p_identification_group;
+ QTime _duracel;
+ std::map<QString, QString> _map_accession2xmlid;
+ std::map<QString, QString> _sample_to_id;
+ std::map<QString, QString> _peptidekey_to_id;
};
#endif // PROTICDBML_H
diff --git a/src/output/xpip.cpp b/src/output/xpip.cpp
index 5a7761cd36823433091b8773036c945394123e2c..5cc8afa9675d6b9261797efd1a75a53fa1dcd04b 100644
--- a/src/output/xpip.cpp
+++ b/src/output/xpip.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "xpip.h"
#include "../config.h"
@@ -34,490 +35,672 @@
#include <pappsomspp/utils.h>
#include <QDebug>
-Xpip::Xpip(const QString & out_filename)
+Xpip::Xpip(const QString &out_filename)
{
- //_p_digestion_pipeline = p_digestion_pipeline;
+ //_p_digestion_pipeline = p_digestion_pipeline;
- //_mzidentml = "http://psidev.info/psi/pi/mzIdentML/1.1";
- QString complete_out_filename = out_filename;
- _output_file = new QFile(complete_out_filename);
+ //_mzidentml = "http://psidev.info/psi/pi/mzIdentML/1.1";
+ QString complete_out_filename = out_filename;
+ _output_file = new QFile(complete_out_filename);
- if (_output_file->open(QIODevice::WriteOnly))
+ if(_output_file->open(QIODevice::WriteOnly))
{
- _output_stream = new QXmlStreamWriter();
- _output_stream->setDevice(_output_file);
- } else
+ _output_stream = new QXmlStreamWriter();
+ _output_stream->setDevice(_output_file);
+ }
+ else
{
- throw pappso::PappsoException(QObject::tr("error : cannot open the XPIP output file : %1\n").arg(out_filename));
+ throw pappso::PappsoException(
+ QObject::tr("error : cannot open the XPIP output file : %1\n")
+ .arg(out_filename));
}
- _output_stream->setAutoFormatting(true);
- _output_stream->writeStartDocument("1.0");
-
-
+ _output_stream->setAutoFormatting(true);
+ _output_stream->writeStartDocument("1.0");
}
Xpip::~Xpip()
{
- delete _output_file;
- delete _output_stream;
+ delete _output_file;
+ delete _output_stream;
}
-void Xpip::close() {
- _output_file->close();
+void
+Xpip::close()
+{
+ _output_file->close();
}
-void Xpip::write(ProjectSp sp_project) {
+void
+Xpip::write(ProjectSp sp_project)
+{
- _sp_project = sp_project;
- if (_sp_project.get() == nullptr) {
- throw pappso::PappsoException(QObject::tr("Error writing XPIP :\n project is empty"));
+ _sp_project = sp_project;
+ if(_sp_project.get() == nullptr)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error writing XPIP :\n project is empty"));
}
-//<xtandem_pipeline version="3.3.5">
- _output_stream->writeStartElement("xpip");
- _output_stream->writeAttribute("version","4.0");
- //_output_stream->writeAttribute("creationDate", QDateTime::currentDateTime().toString( Qt::ISODate));
- _output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance","xsi");
- //_output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance","xsi");
- _output_stream->writeAttribute("xmlns","http://pappso.inra.fr/xsd/xpip/4.0");
- //xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd"
- _output_stream->writeAttribute("http://www.w3.org/2001/XMLSchema-instance","schemaLocation","http://pappso.inra.fr/xsd/xpip/4.0 http://pappso.inra.fr/xsd/xpip-4.0.xsd");
-
-
- //<information Data_Type="combi" match_number="6807"/>
- // _output_stream->writeStartElement("information");
- // _output_stream->writeAttribute("Data_Type","combi");
- // _output_stream->writeEndElement();
- writeDescription();
- writeCounts();
-
- //<filter_params pep_evalue="0.01" prot_evalue="-2.0" pep_number="2" filter_to_all="false" database_filter="/gorgone/pappso/jouy/raw/2013_Orbitrap/2013_07_04_Chanat/contaminants_standarts.fasta"/>
- //const AutomaticFilterParameters & getAutomaticFilterParameters() const;
- writeFilterParameters(_sp_project.get()->getAutomaticFilterParameters());
- writeFastaFileList(_sp_project.get()->getFastaFileStore());
-
- _output_stream->writeStartElement("contaminants");
- std::vector<const FastaFile *> conta_file_list = _sp_project.get()->getProteinStore().getContaminantFastaFileList();
- _output_stream->writeAttribute("regexp",_sp_project.get()->getProteinStore().getRegexpContaminant().pattern());
- QStringList fasta_list;
- for (const FastaFile * fasta_file : conta_file_list) {
- fasta_list << fasta_file->getXmlId();
+ //<xtandem_pipeline version="3.3.5">
+ _output_stream->writeStartElement("xpip");
+ _output_stream->writeAttribute("version", "4.0");
+ //_output_stream->writeAttribute("creationDate",
+ //QDateTime::currentDateTime().toString( Qt::ISODate));
+ _output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance",
+ "xsi");
+ //_output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance","xsi");
+ _output_stream->writeAttribute("xmlns", "http://pappso.inra.fr/xsd/xpip/4.0");
+ // xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1
+ // http://www.psidev.info/files/mzIdentML1.1.0.xsd"
+ _output_stream->writeAttribute("http://www.w3.org/2001/XMLSchema-instance",
+ "schemaLocation",
+ "http://pappso.inra.fr/xsd/xpip/4.0 "
+ "http://pappso.inra.fr/xsd/xpip-4.0.xsd");
+
+
+ //<information Data_Type="combi" match_number="6807"/>
+ // _output_stream->writeStartElement("information");
+ // _output_stream->writeAttribute("Data_Type","combi");
+ // _output_stream->writeEndElement();
+ writeDescription();
+ writeCounts();
+
+ //<filter_params pep_evalue="0.01" prot_evalue="-2.0" pep_number="2"
+ //filter_to_all="false"
+ //database_filter="/gorgone/pappso/jouy/raw/2013_Orbitrap/2013_07_04_Chanat/contaminants_standarts.fasta"/>
+ // const AutomaticFilterParameters & getAutomaticFilterParameters() const;
+ writeFilterParameters(_sp_project.get()->getAutomaticFilterParameters());
+ writeFastaFileList(_sp_project.get()->getFastaFileStore());
+
+ _output_stream->writeStartElement("contaminants");
+ std::vector<const FastaFile *> conta_file_list =
+ _sp_project.get()->getProteinStore().getContaminantFastaFileList();
+ _output_stream->writeAttribute(
+ "regexp",
+ _sp_project.get()->getProteinStore().getRegexpContaminant().pattern());
+ QStringList fasta_list;
+ for(const FastaFile *fasta_file : conta_file_list)
+ {
+ fasta_list << fasta_file->getXmlId();
}
- _output_stream->writeAttribute("fasta_id",fasta_list.join(" "));
- _output_stream->writeEndElement();
-
- _output_stream->writeStartElement("decoys");
- std::vector<const FastaFile *> decoy_file_list = _sp_project.get()->getProteinStore().getDecoyFastaFileList();
- _output_stream->writeAttribute("regexp",_sp_project.get()->getProteinStore().getRegexpDecoy().pattern());
- QStringList fasta_conta_list;
- for (const FastaFile * fasta_file : conta_file_list) {
- fasta_conta_list << fasta_file->getXmlId();
+ _output_stream->writeAttribute("fasta_id", fasta_list.join(" "));
+ _output_stream->writeEndElement();
+
+ _output_stream->writeStartElement("decoys");
+ std::vector<const FastaFile *> decoy_file_list =
+ _sp_project.get()->getProteinStore().getDecoyFastaFileList();
+ _output_stream->writeAttribute(
+ "regexp", _sp_project.get()->getProteinStore().getRegexpDecoy().pattern());
+ QStringList fasta_conta_list;
+ for(const FastaFile *fasta_file : conta_file_list)
+ {
+ fasta_conta_list << fasta_file->getXmlId();
}
- _output_stream->writeAttribute("fasta_id",fasta_conta_list.join(" "));
- _output_stream->writeEndElement();
+ _output_stream->writeAttribute("fasta_id", fasta_conta_list.join(" "));
+ _output_stream->writeEndElement();
- writeMsrunList(_sp_project.get()->getMsRunStore());
- writeIdentificationDataSourceList(_sp_project.get()->getIdentificationDataSourceStore());
+ writeMsrunList(_sp_project.get()->getMsRunStore());
+ writeIdentificationDataSourceList(
+ _sp_project.get()->getIdentificationDataSourceStore());
- writeProteinList();
- writePeptideList();
+ writeProteinList();
+ writePeptideList();
- writeIdentificationGroupList();
- _output_stream->writeEndDocument();
+ writeIdentificationGroupList();
+ _output_stream->writeEndDocument();
}
-void Xpip::writeDoubleAttribute(const QString & attribute, pappso::pappso_double value) {
- _output_stream->writeAttribute(attribute,QString::number(value, 'g', 10));
-
+void
+Xpip::writeDoubleAttribute(const QString &attribute,
+ pappso::pappso_double value)
+{
+ _output_stream->writeAttribute(attribute, QString::number(value, 'g', 10));
}
-void Xpip::writeBooleanAttribute(const QString & attribute, bool value) {
- if (value) {
- _output_stream->writeAttribute(attribute,"true");
+void
+Xpip::writeBooleanAttribute(const QString &attribute, bool value)
+{
+ if(value)
+ {
+ _output_stream->writeAttribute(attribute, "true");
}
- else {
- _output_stream->writeAttribute(attribute,"false");
+ else
+ {
+ _output_stream->writeAttribute(attribute, "false");
}
-
}
-void Xpip::writeFilterParameters(const AutomaticFilterParameters & filters) {
- qDebug() << "Xpip::writeFilterParameters begin";
- _output_stream->writeStartElement("filter_params");
- writeDoubleAttribute("pep_evalue",filters.getFilterPeptideEvalue());
- writeDoubleAttribute("prot_evalue",filters.getFilterProteinEvalue());
- _output_stream->writeAttribute("pep_number",QString("%1").arg(filters.getFilterMinimumPeptidePerMatch()));
- writeBooleanAttribute("cross_sample",filters.getFilterCrossSamplePeptideNumber());
- _output_stream->writeEndElement();
- qDebug() << "Xpip::writeFilterParameters end";
+void
+Xpip::writeFilterParameters(const AutomaticFilterParameters &filters)
+{
+ qDebug() << "Xpip::writeFilterParameters begin";
+ _output_stream->writeStartElement("filter_params");
+ writeDoubleAttribute("pep_evalue", filters.getFilterPeptideEvalue());
+ writeDoubleAttribute("prot_evalue", filters.getFilterProteinEvalue());
+ _output_stream->writeAttribute(
+ "pep_number", QString("%1").arg(filters.getFilterMinimumPeptidePerMatch()));
+ writeBooleanAttribute("cross_sample",
+ filters.getFilterCrossSamplePeptideNumber());
+ _output_stream->writeEndElement();
+ qDebug() << "Xpip::writeFilterParameters end";
}
-void Xpip::writeDescription() {
+void
+Xpip::writeDescription()
+{
- _output_stream->writeStartElement("description");
- _output_stream->writeAttribute("version",XTPCPP_VERSION);
- _output_stream->writeAttribute("grouping","peptidemass");
- if (_sp_project.get()->getProjectMode() == ProjectMode::combined) {
- writeBooleanAttribute("combine",true);
+ _output_stream->writeStartElement("description");
+ _output_stream->writeAttribute("version", XTPCPP_VERSION);
+ _output_stream->writeAttribute("grouping", "peptidemass");
+ if(_sp_project.get()->getProjectMode() == ProjectMode::combined)
+ {
+ writeBooleanAttribute("combine", true);
}
- else {
- writeBooleanAttribute("combine",false);
+ else
+ {
+ writeBooleanAttribute("combine", false);
}
- _output_stream->writeAttribute("date",QDateTime::currentDateTime().toString( Qt::ISODate));
- _output_stream->writeEndElement();
+ _output_stream->writeAttribute(
+ "date", QDateTime::currentDateTime().toString(Qt::ISODate));
+ _output_stream->writeEndElement();
}
-void Xpip::writeCounts() {
+void
+Xpip::writeCounts()
+{
- _output_stream->writeStartElement("counts");
- _output_stream->writeAttribute("proteins",QString("%1").arg(_sp_project.get()->getProteinStore().size()));
- _output_stream->writeAttribute("peptides",QString("%1").arg(_sp_project.get()->getPeptideStore().size()));
+ _output_stream->writeStartElement("counts");
+ _output_stream->writeAttribute(
+ "proteins", QString("%1").arg(_sp_project.get()->getProteinStore().size()));
+ _output_stream->writeAttribute(
+ "peptides", QString("%1").arg(_sp_project.get()->getPeptideStore().size()));
- std::size_t count_peptide_evidences=0;
- std::size_t count_protein_matches=0;
- for (const IdentificationGroup * p_group : _sp_project.get()->getIdentificationGroupList()) {
- for (const IdentificationDataSource * p_id_source : p_group->getIdentificationDataSourceList()) {
- count_peptide_evidences += p_id_source->getPeptideEvidenceStore().size();
+ std::size_t count_peptide_evidences = 0;
+ std::size_t count_protein_matches = 0;
+ for(const IdentificationGroup *p_group :
+ _sp_project.get()->getIdentificationGroupList())
+ {
+ for(const IdentificationDataSource *p_id_source :
+ p_group->getIdentificationDataSourceList())
+ {
+ count_peptide_evidences +=
+ p_id_source->getPeptideEvidenceStore().size();
}
- count_protein_matches += p_group->getProteinMatchList().size();
+ count_protein_matches += p_group->getProteinMatchList().size();
}
- _output_stream->writeAttribute("peptide_evidences",QString("%1").arg(count_peptide_evidences));
- _output_stream->writeAttribute("protein_matches",QString("%1").arg(count_protein_matches));
- _output_stream->writeEndElement();
+ _output_stream->writeAttribute("peptide_evidences",
+ QString("%1").arg(count_peptide_evidences));
+ _output_stream->writeAttribute("protein_matches",
+ QString("%1").arg(count_protein_matches));
+ _output_stream->writeEndElement();
}
-void Xpip::writeIdentificationDataSourceList(const IdentificationDataSourceStore & ident_store) {
-
- _output_stream->writeStartElement("identification_source_list");
- for (const IdentificationDataSourceSp ident_source_sp : ident_store.getIdentificationDataSourceList()) {
- _output_stream->writeStartElement("identification_source");
- _output_stream->writeAttribute("id",ident_source_sp.get()->getXmlId());
- _output_stream->writeAttribute("msrun_id",ident_source_sp.get()->getMsRunSp().get()->getXmlId());
- //_output_stream->writeAttribute("format",QString("%1").arg(static_cast<std::int8_t>(ident_source_sp.get()->getIdentFormat())));
- _output_stream->writeAttribute("path",ident_source_sp.get()->getResourceName());
-
- _output_stream->writeAttribute("engine",QString("%1").arg(static_cast<std::int8_t>(ident_source_sp.get()->getIdentificationEngine())));
- _output_stream->writeAttribute("version",ident_source_sp.get()->getIdentificationEngineVersion());
+void
+Xpip::writeIdentificationDataSourceList(
+ const IdentificationDataSourceStore &ident_store)
+{
- QStringList fasta_file_id;
- for (FastaFileSp fasta_file :ident_source_sp.get()->getFastaFileList()) {
- fasta_file_id << fasta_file.get()->getXmlId();
+ _output_stream->writeStartElement("identification_source_list");
+ for(const IdentificationDataSourceSp ident_source_sp :
+ ident_store.getIdentificationDataSourceList())
+ {
+ _output_stream->writeStartElement("identification_source");
+ _output_stream->writeAttribute("id", ident_source_sp.get()->getXmlId());
+ _output_stream->writeAttribute(
+ "msrun_id", ident_source_sp.get()->getMsRunSp().get()->getXmlId());
+ //_output_stream->writeAttribute("format",QString("%1").arg(static_cast<std::int8_t>(ident_source_sp.get()->getIdentFormat())));
+ _output_stream->writeAttribute("path",
+ ident_source_sp.get()->getResourceName());
+
+ _output_stream->writeAttribute(
+ "engine", QString("%1").arg(static_cast<std::int8_t>(
+ ident_source_sp.get()->getIdentificationEngine())));
+ _output_stream->writeAttribute(
+ "version", ident_source_sp.get()->getIdentificationEngineVersion());
+
+ QStringList fasta_file_id;
+ for(FastaFileSp fasta_file : ident_source_sp.get()->getFastaFileList())
+ {
+ fasta_file_id << fasta_file.get()->getXmlId();
}
- _output_stream->writeAttribute("fasta_ids",fasta_file_id.join(" "));
-
- const std::map<IdentificationEngineParam, QVariant> params = ident_source_sp.get()->getIdentificationEngineParamMap();
- if (params.size() > 0) {
- _output_stream->writeStartElement("params");
- for (const std::pair<IdentificationEngineParam, QVariant> stat_pair: params) {
- _output_stream->writeStartElement("param");
- _output_stream->writeAttribute("key",QString("%1").arg(static_cast<std::int8_t>(stat_pair.first)));
- _output_stream->writeAttribute("value",stat_pair.second.toString());
- _output_stream->writeEndElement();
+ _output_stream->writeAttribute("fasta_ids", fasta_file_id.join(" "));
+
+ const std::map<IdentificationEngineParam, QVariant> params =
+ ident_source_sp.get()->getIdentificationEngineParamMap();
+ if(params.size() > 0)
+ {
+ _output_stream->writeStartElement("params");
+ for(const std::pair<IdentificationEngineParam, QVariant> stat_pair :
+ params)
+ {
+ _output_stream->writeStartElement("param");
+ _output_stream->writeAttribute(
+ "key",
+ QString("%1").arg(static_cast<std::int8_t>(stat_pair.first)));
+ _output_stream->writeAttribute("value",
+ stat_pair.second.toString());
+ _output_stream->writeEndElement();
}
- _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
}
- const std::map<IdentificationEngineStatistics, QVariant> stats = ident_source_sp.get()->getIdentificationEngineStatisticsMap();
- if (stats.size() > 0) {
- _output_stream->writeStartElement("stats");
- for (const std::pair<IdentificationEngineStatistics, QVariant> stat_pair: stats) {
- _output_stream->writeStartElement("stat");
- _output_stream->writeAttribute("key",QString("%1").arg(static_cast<std::int8_t>(stat_pair.first)));
- _output_stream->writeAttribute("value",stat_pair.second.toString());
- _output_stream->writeEndElement();
+ const std::map<IdentificationEngineStatistics, QVariant> stats =
+ ident_source_sp.get()->getIdentificationEngineStatisticsMap();
+ if(stats.size() > 0)
+ {
+ _output_stream->writeStartElement("stats");
+ for(const std::pair<IdentificationEngineStatistics, QVariant>
+ stat_pair : stats)
+ {
+ _output_stream->writeStartElement("stat");
+ _output_stream->writeAttribute(
+ "key",
+ QString("%1").arg(static_cast<std::int8_t>(stat_pair.first)));
+ _output_stream->writeAttribute("value",
+ stat_pair.second.toString());
+ _output_stream->writeEndElement();
}
- _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
}
- _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
}
- _output_stream->writeEndElement();
-
+ _output_stream->writeEndElement();
}
-void Xpip::writeMsrunList(const MsRunStore & msrun_store) {
-
- _output_stream->writeStartElement("msrun_list");
- for (const MsRunSp msrun_sp : msrun_store.getMsRunList()) {
- _output_stream->writeStartElement("msrun");
- _output_stream->writeAttribute("id",msrun_sp.get()->getXmlId());
- _output_stream->writeAttribute("name",msrun_sp.get()->getSampleName());
- _output_stream->writeAttribute("format",QString("%1").arg(static_cast<std::int8_t>(msrun_sp.get()->getMzFormat())));
- QFileInfo mz_info(msrun_sp.get()->getFilename());
- if (mz_info.exists()) {
- _output_stream->writeAttribute("path",msrun_sp.get()->getFilename());
+void
+Xpip::writeMsrunList(const MsRunStore &msrun_store)
+{
+
+ _output_stream->writeStartElement("msrun_list");
+ for(const MsRunSp msrun_sp : msrun_store.getMsRunList())
+ {
+ _output_stream->writeStartElement("msrun");
+ _output_stream->writeAttribute("id", msrun_sp.get()->getXmlId());
+ _output_stream->writeAttribute("name", msrun_sp.get()->getSampleName());
+ _output_stream->writeAttribute(
+ "format", QString("%1").arg(
+ static_cast<std::int8_t>(msrun_sp.get()->getMzFormat())));
+ QFileInfo mz_info(msrun_sp.get()->getFilename());
+ if(mz_info.exists())
+ {
+ _output_stream->writeAttribute("path", msrun_sp.get()->getFilename());
}
- else {
- _output_stream->writeAttribute("path",mz_info.completeBaseName());
+ else
+ {
+ _output_stream->writeAttribute("path", mz_info.completeBaseName());
}
- const std::map<MsRunStatistics, QVariant> stats = msrun_sp.get()->getMsRunStatisticsMap();
- if (stats.size() > 0) {
- _output_stream->writeStartElement("stats");
- for (const std::pair<MsRunStatistics, QVariant> stat_pair: stats) {
- _output_stream->writeStartElement("stat");
- _output_stream->writeAttribute("key",QString("%1").arg(static_cast<std::int8_t>(stat_pair.first)));
- _output_stream->writeAttribute("value",stat_pair.second.toString());
- _output_stream->writeEndElement();
+ const std::map<MsRunStatistics, QVariant> stats =
+ msrun_sp.get()->getMsRunStatisticsMap();
+ if(stats.size() > 0)
+ {
+ _output_stream->writeStartElement("stats");
+ for(const std::pair<MsRunStatistics, QVariant> stat_pair : stats)
+ {
+ _output_stream->writeStartElement("stat");
+ _output_stream->writeAttribute(
+ "key",
+ QString("%1").arg(static_cast<std::int8_t>(stat_pair.first)));
+ _output_stream->writeAttribute("value",
+ stat_pair.second.toString());
+ _output_stream->writeEndElement();
}
- _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
}
- _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
}
- _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
}
-void Xpip::writeFastaFileList(const FastaFileStore & fasta_store) {
- qDebug() << "Xpip::writeFastaFileList begin";
- _output_stream->writeStartElement("fasta_file_list");
- for (FastaFileSp fasta_file_sp : fasta_store.getFastaFileList()) {
- _output_stream->writeStartElement("fasta_file");
- _output_stream->writeAttribute("id",fasta_file_sp.get()->getXmlId());
- _output_stream->writeAttribute("path",fasta_file_sp.get()->getAbsoluteFilePath());
+void
+Xpip::writeFastaFileList(const FastaFileStore &fasta_store)
+{
+ qDebug() << "Xpip::writeFastaFileList begin";
+ _output_stream->writeStartElement("fasta_file_list");
+ for(FastaFileSp fasta_file_sp : fasta_store.getFastaFileList())
+ {
+ _output_stream->writeStartElement("fasta_file");
+ _output_stream->writeAttribute("id", fasta_file_sp.get()->getXmlId());
+ _output_stream->writeAttribute(
+ "path", fasta_file_sp.get()->getAbsoluteFilePath());
- _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
}
- _output_stream->writeEndElement();
- qDebug() << "Xpip::writeFastaFileList end";
+ _output_stream->writeEndElement();
+ qDebug() << "Xpip::writeFastaFileList end";
}
-void Xpip::writeProteinList() {
- qDebug() << "Xpip::writeProteinList begin";
- _output_stream->writeStartElement("protein_list");
- const ProteinStore & protein_store = _sp_project.get()->getProteinStore();
- for (std::pair<QString, ProteinXtpSp> protein_pair : protein_store.getProteinMap()) {
- const ProteinXtp * p_protein = protein_pair.second.get();
- _output_stream->writeStartElement("protein");
- if (p_protein->getFastaFileP() == nullptr) {
- throw pappso::PappsoException(QObject::tr("Error writing XPIP file :\n FastaFile pointer is null for protein accession %1").arg(p_protein->getAccession()));
+void
+Xpip::writeProteinList()
+{
+ qDebug() << "Xpip::writeProteinList begin";
+ _output_stream->writeStartElement("protein_list");
+ const ProteinStore &protein_store = _sp_project.get()->getProteinStore();
+ for(std::pair<QString, ProteinXtpSp> protein_pair :
+ protein_store.getProteinMap())
+ {
+ const ProteinXtp *p_protein = protein_pair.second.get();
+ _output_stream->writeStartElement("protein");
+ if(p_protein->getFastaFileP() == nullptr)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error writing XPIP file :\n FastaFile pointer is null "
+ "for protein accession %1")
+ .arg(p_protein->getAccession()));
}
- _output_stream->writeAttribute("fasta_id",p_protein->getFastaFileP()->getXmlId());
- _output_stream->writeAttribute("acc",p_protein->getAccession());
- _output_stream->writeAttribute("description",p_protein->getDescription());
-
- if (p_protein->isDecoy()) {
- _output_stream->writeAttribute("is_decoy","true");
+ _output_stream->writeAttribute("fasta_id",
+ p_protein->getFastaFileP()->getXmlId());
+ _output_stream->writeAttribute("acc", p_protein->getAccession());
+ _output_stream->writeAttribute("description",
+ p_protein->getDescription());
+
+ if(p_protein->isDecoy())
+ {
+ _output_stream->writeAttribute("is_decoy", "true");
}
- else {
- _output_stream->writeAttribute("is_decoy","false");
+ else
+ {
+ _output_stream->writeAttribute("is_decoy", "false");
}
- if (p_protein->isContaminant()) {
- _output_stream->writeAttribute("is_contaminant","true");
+ if(p_protein->isContaminant())
+ {
+ _output_stream->writeAttribute("is_contaminant", "true");
}
- else {
- _output_stream->writeAttribute("is_contaminant","false");
+ else
+ {
+ _output_stream->writeAttribute("is_contaminant", "false");
}
- _output_stream->writeStartElement("sequence");
- _output_stream->writeCharacters(p_protein->getSequence());
- _output_stream->writeEndElement();
-
- for (DbXref db_xref : p_protein->getDbxrefList()) {
- _output_stream->writeStartElement("dbxref");
- _output_stream->writeAttribute("acc",db_xref.accession);
- _output_stream->writeAttribute("database",QString("%1").arg(static_cast<std::int8_t>(db_xref.database)));
- _output_stream->writeEndElement();
+ _output_stream->writeStartElement("sequence");
+ _output_stream->writeCharacters(p_protein->getSequence());
+ _output_stream->writeEndElement();
+
+ for(DbXref db_xref : p_protein->getDbxrefList())
+ {
+ _output_stream->writeStartElement("dbxref");
+ _output_stream->writeAttribute("acc", db_xref.accession);
+ _output_stream->writeAttribute(
+ "database",
+ QString("%1").arg(static_cast<std::int8_t>(db_xref.database)));
+ _output_stream->writeEndElement();
}
- _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
}
- _output_stream->writeEndElement();
- qDebug() << "Xpip::writeProteinList end";
+ _output_stream->writeEndElement();
+ qDebug() << "Xpip::writeProteinList end";
}
-QString Xpip::getPeptideId(std::size_t crc_peptide) const {
- return QString("p%1").arg(pappso::Utils::getLexicalOrderedString(crc_peptide));
+QString
+Xpip::getPeptideId(std::size_t crc_peptide) const
+{
+ return QString("p%1").arg(
+ pappso::Utils::getLexicalOrderedString(crc_peptide));
}
-void Xpip::writeLabelingMethod() {
- qDebug() << "Xpip::writeLabelingMethod begin";
-
- LabelingMethod * p_labeling_method = _sp_project.get()->getLabelingMethodSp().get();
- if (p_labeling_method == nullptr) return;
- _output_stream->writeStartElement("label_method");
- _output_stream->writeAttribute("id",p_labeling_method->getXmlId());
-
- _output_stream->writeStartElement("label_list");
- for (const Label * p_label : p_labeling_method->getLabelList()) {
- _output_stream->writeStartElement("label");
- _output_stream->writeAttribute("id", p_label->getXmlId());
- for (const LabelModification label_modification : p_label->getLabelModifictionList()) {
- _output_stream->writeStartElement("label_modification");
- _output_stream->writeAttribute("at", label_modification.at);
- _output_stream->writeAttribute("mod", label_modification.modification->getAccession());
- _output_stream->writeEndElement();// label_modification
+void
+Xpip::writeLabelingMethod()
+{
+ qDebug() << "Xpip::writeLabelingMethod begin";
+
+ LabelingMethod *p_labeling_method =
+ _sp_project.get()->getLabelingMethodSp().get();
+ if(p_labeling_method == nullptr)
+ return;
+ _output_stream->writeStartElement("label_method");
+ _output_stream->writeAttribute("id", p_labeling_method->getXmlId());
+
+ _output_stream->writeStartElement("label_list");
+ for(const Label *p_label : p_labeling_method->getLabelList())
+ {
+ _output_stream->writeStartElement("label");
+ _output_stream->writeAttribute("id", p_label->getXmlId());
+ for(const LabelModification label_modification :
+ p_label->getLabelModifictionList())
+ {
+ _output_stream->writeStartElement("label_modification");
+ _output_stream->writeAttribute("at", label_modification.at);
+ _output_stream->writeAttribute(
+ "mod", label_modification.modification->getAccession());
+ _output_stream->writeEndElement(); // label_modification
}
- _output_stream->writeEndElement();// label
+ _output_stream->writeEndElement(); // label
}
- _output_stream->writeEndElement();// label_list
+ _output_stream->writeEndElement(); // label_list
- _output_stream->writeEndElement();// label_method
- qDebug() << "Xpip::writeLabelingMethod end";
+ _output_stream->writeEndElement(); // label_method
+ qDebug() << "Xpip::writeLabelingMethod end";
}
-void Xpip::writePeptideList() {
- qDebug() << "Xpip::writePeptideList begin";
- _output_stream->writeStartElement("peptide_list");
-
- writeLabelingMethod();
-
- const PeptideStore & peptide_store = _sp_project.get()->getPeptideStore();
- _output_stream->writeStartElement("modification_list");
- for (pappso::AaModificationP mod_p : peptide_store.getModificationCollection()) {
- QString id = QString("mod%1").arg(pappso::Utils::getLexicalOrderedString(_map_modifications.size()+1));
- _map_modifications.insert(std::pair<pappso::AaModificationP, QString>(mod_p, id));
- _output_stream->writeStartElement("modification");
- _output_stream->writeAttribute("id", id);
- _output_stream->writeAttribute("mod", mod_p->getAccession());
- _output_stream->writeEndElement();// modification
+void
+Xpip::writePeptideList()
+{
+ qDebug() << "Xpip::writePeptideList begin";
+ _output_stream->writeStartElement("peptide_list");
+
+ writeLabelingMethod();
+
+ const PeptideStore &peptide_store = _sp_project.get()->getPeptideStore();
+ _output_stream->writeStartElement("modification_list");
+ for(pappso::AaModificationP mod_p : peptide_store.getModificationCollection())
+ {
+ QString id = QString("mod%1").arg(
+ pappso::Utils::getLexicalOrderedString(_map_modifications.size() + 1));
+ _map_modifications.insert(
+ std::pair<pappso::AaModificationP, QString>(mod_p, id));
+ _output_stream->writeStartElement("modification");
+ _output_stream->writeAttribute("id", id);
+ _output_stream->writeAttribute("mod", mod_p->getAccession());
+ _output_stream->writeEndElement(); // modification
}
- _output_stream->writeEndElement();// modification_list
-
- for (std::pair<std::size_t, PeptideXtpSp> peptide_pair : peptide_store.getPeptideMap()) {
- const PeptideXtp * p_peptide = peptide_pair.second.get();
- _output_stream->writeStartElement("peptide");
- QString idp = QString("p%1").arg(pappso::Utils::getLexicalOrderedString(_map_peptides.size()+1));
- _map_peptides.insert(std::pair<const PeptideXtp *, QString>(p_peptide, idp));
- _output_stream->writeAttribute("id",idp);
- _output_stream->writeAttribute("seq",p_peptide->getSequence());
-
- const Label * p_label = p_peptide->getLabel();
- if (p_label != nullptr) {
- _output_stream->writeAttribute("label_id",p_label->getXmlId());
+ _output_stream->writeEndElement(); // modification_list
+
+ for(std::pair<std::size_t, PeptideXtpSp> peptide_pair :
+ peptide_store.getPeptideMap())
+ {
+ const PeptideXtp *p_peptide = peptide_pair.second.get();
+ _output_stream->writeStartElement("peptide");
+ QString idp = QString("p%1").arg(
+ pappso::Utils::getLexicalOrderedString(_map_peptides.size() + 1));
+ _map_peptides.insert(
+ std::pair<const PeptideXtp *, QString>(p_peptide, idp));
+ _output_stream->writeAttribute("id", idp);
+ _output_stream->writeAttribute("seq", p_peptide->getSequence());
+
+ const Label *p_label = p_peptide->getLabel();
+ if(p_label != nullptr)
+ {
+ _output_stream->writeAttribute("label_id", p_label->getXmlId());
}
- unsigned int i=0;
- for (const pappso::Aa & amino_acid: *p_peptide) {
+ unsigned int i = 0;
+ for(const pappso::Aa &amino_acid : *p_peptide)
+ {
- std::list<pappso::AaModificationP> aa_modif_list = amino_acid.getModificationList();
+ std::list<pappso::AaModificationP> aa_modif_list =
+ amino_acid.getModificationList();
- for (auto && aa_modif : aa_modif_list) {
- if (!aa_modif->isInternal()) {
- _output_stream->writeStartElement("mod");
- _output_stream->writeAttribute("ref", _map_modifications.at(aa_modif));
- _output_stream->writeAttribute("position", QString ("%1").arg(i));
- _output_stream->writeAttribute("aa", QString(amino_acid.getLetter()));
- _output_stream->writeEndElement();// mod
+ for(auto &&aa_modif : aa_modif_list)
+ {
+ if(!aa_modif->isInternal())
+ {
+ _output_stream->writeStartElement("mod");
+ _output_stream->writeAttribute(
+ "ref", _map_modifications.at(aa_modif));
+ _output_stream->writeAttribute("position",
+ QString("%1").arg(i));
+ _output_stream->writeAttribute(
+ "aa", QString(amino_acid.getLetter()));
+ _output_stream->writeEndElement(); // mod
}
}
- i++;
+ i++;
}
- _output_stream->writeEndElement();// peptide
+ _output_stream->writeEndElement(); // peptide
}
- _output_stream->writeEndElement(); //peptide_list
- qDebug() << "Xpip::writePeptideList end";
+ _output_stream->writeEndElement(); // peptide_list
+ qDebug() << "Xpip::writePeptideList end";
}
-void Xpip::writeIdentificationGroupList() {
- qDebug() << "Xpip::writeIdentificationGroupList begin";
- _output_stream->writeStartElement("identification_group_list");
- for (const IdentificationGroup * p_identification_group : _sp_project.get()->getIdentificationGroupList()) {
- //std::vector<ProteinMatch *> & getProteinMatchList()
- writeIdentificationGroup(p_identification_group);
+void
+Xpip::writeIdentificationGroupList()
+{
+ qDebug() << "Xpip::writeIdentificationGroupList begin";
+ _output_stream->writeStartElement("identification_group_list");
+ for(const IdentificationGroup *p_identification_group :
+ _sp_project.get()->getIdentificationGroupList())
+ {
+ // std::vector<ProteinMatch *> & getProteinMatchList()
+ writeIdentificationGroup(p_identification_group);
}
- _output_stream->writeEndElement(); //identification_group_list
- qDebug() << "Xpip::writeIdentificationGroupList end";
+ _output_stream->writeEndElement(); // identification_group_list
+ qDebug() << "Xpip::writeIdentificationGroupList end";
}
-void Xpip::writePeptideEvidence(const PeptideEvidence * p_peptide_evidence) {
- qDebug() << "Xpip::writePeptideEvidence begin";
+void
+Xpip::writePeptideEvidence(const PeptideEvidence *p_peptide_evidence)
+{
+ qDebug() << "Xpip::writePeptideEvidence begin";
- _output_stream->writeStartElement("peptide_evidence");
- QString idp = QString("pe%1").arg(pappso::Utils::getLexicalOrderedString(_map_peptide_evidences.size()+1));
- _map_peptide_evidences.insert(std::pair<const PeptideEvidence *, QString>(p_peptide_evidence, idp));
- _output_stream->writeAttribute("id",idp);
+ _output_stream->writeStartElement("peptide_evidence");
+ QString idp = QString("pe%1").arg(
+ pappso::Utils::getLexicalOrderedString(_map_peptide_evidences.size() + 1));
+ _map_peptide_evidences.insert(
+ std::pair<const PeptideEvidence *, QString>(p_peptide_evidence, idp));
+ _output_stream->writeAttribute("id", idp);
- //_output_stream->writeAttribute("ms_id",p_peptide_match->getMsRunP()->getXmlId());
- try {
- _output_stream->writeAttribute("peptide_id",_map_peptides.at( p_peptide_evidence->getPeptideXtpSp().get()));
+ //_output_stream->writeAttribute("ms_id",p_peptide_match->getMsRunP()->getXmlId());
+ try
+ {
+ _output_stream->writeAttribute(
+ "peptide_id",
+ _map_peptides.at(p_peptide_evidence->getPeptideXtpSp().get()));
}
- catch (out_of_range exception_std) {
- throw pappso::PappsoException(QObject::tr("ERROR in Xpip::writePeptideEvidence peptide %1 not found in map :\n%2").arg(p_peptide_evidence->getPeptideXtpSp().get()->toAbsoluteString()).arg(exception_std.what()));
+ catch(out_of_range exception_std)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("ERROR in Xpip::writePeptideEvidence peptide %1 not found "
+ "in map :\n%2")
+ .arg(p_peptide_evidence->getPeptideXtpSp().get()->toAbsoluteString())
+ .arg(exception_std.what()));
}
- qDebug() << "Xpip::writePeptideEvidence scan";
- _output_stream->writeAttribute("scan",QString("%1").arg(p_peptide_evidence->getScan()));
- writeDoubleAttribute("rt",p_peptide_evidence->getRetentionTime());
- _output_stream->writeAttribute("eng",QString("%1").arg((unsigned int) p_peptide_evidence->getIdentificationEngine()));
- writeDoubleAttribute("evalue",p_peptide_evidence->getEvalue());
- writeDoubleAttribute("exp_mass",p_peptide_evidence->getExperimentalMass());
- _output_stream->writeAttribute("charge",QString("%1").arg(p_peptide_evidence->getCharge()));
-
- if (p_peptide_evidence->isChecked()) {
- _output_stream->writeAttribute("checked","true");
+ qDebug() << "Xpip::writePeptideEvidence scan";
+ _output_stream->writeAttribute(
+ "scan", QString("%1").arg(p_peptide_evidence->getScan()));
+ writeDoubleAttribute("rt", p_peptide_evidence->getRetentionTime());
+ _output_stream->writeAttribute(
+ "eng", QString("%1").arg(
+ (unsigned int)p_peptide_evidence->getIdentificationEngine()));
+ writeDoubleAttribute("evalue", p_peptide_evidence->getEvalue());
+ writeDoubleAttribute("exp_mass", p_peptide_evidence->getExperimentalMass());
+ _output_stream->writeAttribute(
+ "charge", QString("%1").arg(p_peptide_evidence->getCharge()));
+
+ if(p_peptide_evidence->isChecked())
+ {
+ _output_stream->writeAttribute("checked", "true");
}
- else {
- _output_stream->writeAttribute("checked","false");
+ else
+ {
+ _output_stream->writeAttribute("checked", "false");
}
- qDebug() << "Xpip::writePeptideEvidence getParamList";
- const std::map<PeptideEvidenceParam, QVariant> & params = p_peptide_evidence->getParamList();
+ qDebug() << "Xpip::writePeptideEvidence getParamList";
+ const std::map<PeptideEvidenceParam, QVariant> ¶ms =
+ p_peptide_evidence->getParamList();
- //if (params.size() > 0) {
- // _output_stream->writeStartElement("stats");
- for (const std::pair<PeptideEvidenceParam, QVariant> param_pair: params) {
- _output_stream->writeStartElement("param");
- _output_stream->writeAttribute("key",QString("%1").arg(static_cast<std::int8_t>(param_pair.first)));
- _output_stream->writeAttribute("value",param_pair.second.toString());
- _output_stream->writeEndElement();
+ // if (params.size() > 0) {
+ // _output_stream->writeStartElement("stats");
+ for(const std::pair<PeptideEvidenceParam, QVariant> param_pair : params)
+ {
+ _output_stream->writeStartElement("param");
+ _output_stream->writeAttribute(
+ "key", QString("%1").arg(static_cast<std::int8_t>(param_pair.first)));
+ _output_stream->writeAttribute("value", param_pair.second.toString());
+ _output_stream->writeEndElement();
}
- // _output_stream->writeEndElement();
- _output_stream->writeEndElement(); //peptide_evidence
- qDebug() << "Xpip::writePeptideEvidence end";
+ // _output_stream->writeEndElement();
+ _output_stream->writeEndElement(); // peptide_evidence
+ qDebug() << "Xpip::writePeptideEvidence end";
}
-void Xpip::writePeptideEvidenceList(const IdentificationDataSource * p_ident_data_source) {
- qDebug() << "Xpip::writePeptideEvidenceList begin";
+void
+Xpip::writePeptideEvidenceList(
+ const IdentificationDataSource *p_ident_data_source)
+{
+ qDebug() << "Xpip::writePeptideEvidenceList begin";
- _output_stream->writeStartElement("peptide_evidence_list");
- _output_stream->writeAttribute("ident_source_id",p_ident_data_source->getXmlId());
+ _output_stream->writeStartElement("peptide_evidence_list");
+ _output_stream->writeAttribute("ident_source_id",
+ p_ident_data_source->getXmlId());
- for (const PeptideEvidenceSp & sp_peptide_evidence:p_ident_data_source->getPeptideEvidenceStore().getPeptideEvidenceList()) {
- writePeptideEvidence(sp_peptide_evidence.get());
+ for(const PeptideEvidenceSp &sp_peptide_evidence :
+ p_ident_data_source->getPeptideEvidenceStore().getPeptideEvidenceList())
+ {
+ writePeptideEvidence(sp_peptide_evidence.get());
}
- _output_stream->writeEndElement(); //peptide_evidence_list
- qDebug() << "Xpip::writePeptideEvidenceList end";
+ _output_stream->writeEndElement(); // peptide_evidence_list
+ qDebug() << "Xpip::writePeptideEvidenceList end";
}
-void Xpip::writeIdentificationGroup(const IdentificationGroup * p_identification_group) {
- qDebug() << "Xpip::writeIdentificationGroup begin";
- _output_stream->writeStartElement("identification_group");
- //QStringList id_list;
- for ( const IdentificationDataSource * ident_data_source : p_identification_group->getIdentificationDataSourceList()) {
- //id_list << ident_data_source->getXmlId();
- writePeptideEvidenceList(ident_data_source);
+void
+Xpip::writeIdentificationGroup(
+ const IdentificationGroup *p_identification_group)
+{
+ qDebug() << "Xpip::writeIdentificationGroup begin";
+ _output_stream->writeStartElement("identification_group");
+ // QStringList id_list;
+ for(const IdentificationDataSource *ident_data_source :
+ p_identification_group->getIdentificationDataSourceList())
+ {
+ // id_list << ident_data_source->getXmlId();
+ writePeptideEvidenceList(ident_data_source);
}
- _output_stream->writeStartElement("protein_match_list");
- for (const ProteinMatch * p_protein_match : p_identification_group->getProteinMatchList()) {
- //std::vector<ProteinMatch *> & getProteinMatchList()
- _output_stream->writeStartElement("protein_match");
- _output_stream->writeAttribute("acc", p_protein_match->getProteinXtpSp().get()->getAccession());
- if (p_protein_match->isChecked()) {
- _output_stream->writeAttribute("checked","true");
+ _output_stream->writeStartElement("protein_match_list");
+ for(const ProteinMatch *p_protein_match :
+ p_identification_group->getProteinMatchList())
+ {
+ // std::vector<ProteinMatch *> & getProteinMatchList()
+ _output_stream->writeStartElement("protein_match");
+ _output_stream->writeAttribute(
+ "acc", p_protein_match->getProteinXtpSp().get()->getAccession());
+ if(p_protein_match->isChecked())
+ {
+ _output_stream->writeAttribute("checked", "true");
}
- else {
- _output_stream->writeAttribute("checked","false");
+ else
+ {
+ _output_stream->writeAttribute("checked", "false");
}
- for (const PeptideMatch & peptide_match : p_protein_match->getPeptideMatchList()) {
- writePeptideMatch(peptide_match);
+ for(const PeptideMatch &peptide_match :
+ p_protein_match->getPeptideMatchList())
+ {
+ writePeptideMatch(peptide_match);
}
- _output_stream->writeEndElement();// protein_match
+ _output_stream->writeEndElement(); // protein_match
}
- _output_stream->writeEndElement(); //protein_match_list
- _output_stream->writeEndElement(); //identification_group
- qDebug() << "Xpip::writeIdentificationGroup end";
+ _output_stream->writeEndElement(); // protein_match_list
+ _output_stream->writeEndElement(); // identification_group
+ qDebug() << "Xpip::writeIdentificationGroup end";
}
-void Xpip::writePeptideMatch(const PeptideMatch & peptide_match) {
- qDebug() << "Xpip::writePeptideMatch begin";
- _output_stream->writeStartElement("peptide_match");
- _output_stream->writeAttribute("peptide_evidence_id",_map_peptide_evidences.at( peptide_match.getPeptideEvidence()));
- _output_stream->writeAttribute("start",QString("%1").arg(peptide_match.getStart()));
-
- _output_stream->writeEndElement(); //protein_match_list
- qDebug() << "Xpip::writePeptideMatch end";
+void
+Xpip::writePeptideMatch(const PeptideMatch &peptide_match)
+{
+ qDebug() << "Xpip::writePeptideMatch begin";
+ _output_stream->writeStartElement("peptide_match");
+ _output_stream->writeAttribute(
+ "peptide_evidence_id",
+ _map_peptide_evidences.at(peptide_match.getPeptideEvidence()));
+ _output_stream->writeAttribute("start",
+ QString("%1").arg(peptide_match.getStart()));
+
+ _output_stream->writeEndElement(); // protein_match_list
+ qDebug() << "Xpip::writePeptideMatch end";
}
diff --git a/src/output/xpip.h b/src/output/xpip.h
index f378379e5e91f52f1d4fe1b4bca80021d2e1601c..e44d9afa7cc12789dc5bca695dedfeb04ebf2a33 100644
--- a/src/output/xpip.h
+++ b/src/output/xpip.h
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef XPIP_H
#define XPIP_H
@@ -37,44 +38,47 @@
class Xpip
{
-public:
- Xpip(const QString & out_filename);
- ~Xpip();
+ public:
+ Xpip(const QString &out_filename);
+ ~Xpip();
- void write(ProjectSp sp_project);
- void close();
+ void write(ProjectSp sp_project);
+ void close();
-private :
- void writeFilterParameters(const AutomaticFilterParameters & filters);
- void writeDescription();
- void writeCounts();
+ private:
+ void writeFilterParameters(const AutomaticFilterParameters &filters);
+ void writeDescription();
+ void writeCounts();
- void writeMsrunList(const MsRunStore & msrun_store);
- void writeIdentificationDataSourceList(const IdentificationDataSourceStore & ident_store);
- void writeFastaFileList(const FastaFileStore & fasta_store);
- void writeDoubleAttribute(const QString & attribute, pappso::pappso_double value);
- void writeBooleanAttribute(const QString & attribute, bool value);
-
- void writeProteinList();
- void writePeptideList();
- void writeLabelingMethod();
- void writeIdentificationGroupList();
- void writeIdentificationGroup(const IdentificationGroup * p_identification_group);
- void writePeptideEvidenceList(const IdentificationDataSource * p_ident_data_source);
- void writePeptideMatch(const PeptideMatch & peptide_match);
- void writePeptideEvidence(const PeptideEvidence * p_peptide_evidence);
+ void writeMsrunList(const MsRunStore &msrun_store);
+ void writeIdentificationDataSourceList(
+ const IdentificationDataSourceStore &ident_store);
+ void writeFastaFileList(const FastaFileStore &fasta_store);
+ void writeDoubleAttribute(const QString &attribute,
+ pappso::pappso_double value);
+ void writeBooleanAttribute(const QString &attribute, bool value);
- QString getPeptideId(std::size_t crc_peptide) const;
+ void writeProteinList();
+ void writePeptideList();
+ void writeLabelingMethod();
+ void writeIdentificationGroupList();
+ void
+ writeIdentificationGroup(const IdentificationGroup *p_identification_group);
+ void
+ writePeptideEvidenceList(const IdentificationDataSource *p_ident_data_source);
+ void writePeptideMatch(const PeptideMatch &peptide_match);
+ void writePeptideEvidence(const PeptideEvidence *p_peptide_evidence);
-private :
- QFile * _output_file;
- QXmlStreamWriter * _output_stream;
- ProjectSp _sp_project;
-
- std::map<pappso::AaModificationP, QString> _map_modifications;
- std::map<const PeptideXtp *, QString> _map_peptides;
- std::map<const PeptideEvidence *, QString> _map_peptide_evidences;
+ QString getPeptideId(std::size_t crc_peptide) const;
+ private:
+ QFile *_output_file;
+ QXmlStreamWriter *_output_stream;
+ ProjectSp _sp_project;
+
+ std::map<pappso::AaModificationP, QString> _map_modifications;
+ std::map<const PeptideXtp *, QString> _map_peptides;
+ std::map<const PeptideEvidence *, QString> _map_peptide_evidences;
};
#endif // XPIP_H
diff --git a/src/utils/fastafilestore.cpp b/src/utils/fastafilestore.cpp
index 617b2998300ea89c0fc0c5ba81278f714ac9cbbb..040024de05ac0eb518a939815fe4b7e84d649bf8 100644
--- a/src/utils/fastafilestore.cpp
+++ b/src/utils/fastafilestore.cpp
@@ -7,64 +7,74 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "fastafilestore.h"
#include <pappsomspp/utils.h>
#include <QDebug>
FastaFileStore::FastaFileStore()
{
-
}
FastaFileStore::~FastaFileStore()
{
-
}
-FastaFileSp FastaFileStore::getInstance(const FastaFile & location) {
- qDebug() << "FastaFileStore::getInstance() begin ";
- qDebug() << "FastaFileStore::getInstance() begin "<< location.getAbsoluteFilePath();
- std::vector<FastaFileSp>::iterator it = _map_fastafile.begin();
- std::vector<FastaFileSp>::iterator itend = _map_fastafile.end();
- while (it != itend) {
- if (it->get()->getFilename() == location.getFilename()) {
+FastaFileSp
+FastaFileStore::getInstance(const FastaFile &location)
+{
+ qDebug() << "FastaFileStore::getInstance() begin ";
+ qDebug() << "FastaFileStore::getInstance() begin "
+ << location.getAbsoluteFilePath();
+ std::vector<FastaFileSp>::iterator it = _map_fastafile.begin();
+ std::vector<FastaFileSp>::iterator itend = _map_fastafile.end();
+ while(it != itend)
+ {
+ if(it->get()->getFilename() == location.getFilename())
+ {
- qDebug() << "FastaFileStore::getInstance() end b "<< it->get()->getFilename();
- return *it;
+ qDebug() << "FastaFileStore::getInstance() end b "
+ << it->get()->getFilename();
+ return *it;
}
- it++;
+ it++;
}
- FastaFileSp fastafile_sp = std::make_shared<FastaFile>(location);
+ FastaFileSp fastafile_sp = std::make_shared<FastaFile>(location);
- fastafile_sp.get()->setXmlId(QString("fasta%1").arg(pappso::Utils::getLexicalOrderedString(_map_fastafile.size())));
- _map_fastafile.push_back(fastafile_sp);
- qDebug() << "FastaFileStore::getFastaFileList() end a " << _map_fastafile.size();
- return fastafile_sp;
+ fastafile_sp.get()->setXmlId(QString("fasta%1").arg(
+ pappso::Utils::getLexicalOrderedString(_map_fastafile.size())));
+ _map_fastafile.push_back(fastafile_sp);
+ qDebug() << "FastaFileStore::getFastaFileList() end a "
+ << _map_fastafile.size();
+ return fastafile_sp;
}
-const std::vector<FastaFileSp> & FastaFileStore::getFastaFileList() const {
- qDebug() << "FastaFileStore::getFastaFileList() begin" ;
- qDebug() << "FastaFileStore::getFastaFileList() begin" << _map_fastafile.size();
- return _map_fastafile;
+const std::vector<FastaFileSp> &
+FastaFileStore::getFastaFileList() const
+{
+ qDebug() << "FastaFileStore::getFastaFileList() begin";
+ qDebug() << "FastaFileStore::getFastaFileList() begin"
+ << _map_fastafile.size();
+ return _map_fastafile;
}
diff --git a/src/utils/fastafilestore.h b/src/utils/fastafilestore.h
index af3e877b3d5b9c1ed3be2d13722969a66be30d06..1a6e2387dbeac56221d2378406e8805d6150fd22 100644
--- a/src/utils/fastafilestore.h
+++ b/src/utils/fastafilestore.h
@@ -7,26 +7,27 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef FASTAFILESTORE_H
#define FASTAFILESTORE_H
@@ -36,15 +37,16 @@
class FastaFileStore
{
-public:
- FastaFileStore();
- ~FastaFileStore();
-
- FastaFileSp getInstance(const FastaFile & fastafile);
-
- const std::vector<FastaFileSp> & getFastaFileList() const;
-private:
- std::vector<FastaFileSp> _map_fastafile;
+ public:
+ FastaFileStore();
+ ~FastaFileStore();
+
+ FastaFileSp getInstance(const FastaFile &fastafile);
+
+ const std::vector<FastaFileSp> &getFastaFileList() const;
+
+ private:
+ std::vector<FastaFileSp> _map_fastafile;
};
diff --git a/src/utils/groupstore.cpp b/src/utils/groupstore.cpp
index 6371c5fc29486d0a68a67fe4c3663dc7e2b90d32..e16ab3b3ebc577d9c83ae807890b35d44bd014be 100644
--- a/src/utils/groupstore.cpp
+++ b/src/utils/groupstore.cpp
@@ -7,73 +7,87 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "groupstore.h"
GroupStore::GroupStore()
{
-
}
GroupStore::~GroupStore()
{
-
}
-void GroupStore::clear() {
- _map_group.clear();
+void
+GroupStore::clear()
+{
+ _map_group.clear();
}
-std::size_t GroupStore::countGroup() const {
- return _map_group.size();
+std::size_t
+GroupStore::countGroup() const
+{
+ return _map_group.size();
}
-std::size_t GroupStore::countSubGroup() const {
-
- unsigned int count = 0;
- for (auto && pair_group :_map_group) {
+std::size_t
+GroupStore::countSubGroup() const
+{
+
+ unsigned int count = 0;
+ for(auto &&pair_group : _map_group)
+ {
count += pair_group.second->getNumberOfSubgroups();
}
- return count;
+ return count;
}
- const std::map<unsigned int, GroupingGroupSp> & GroupStore::getGroupMap() const {
- return _map_group;
- }
+const std::map<unsigned int, GroupingGroupSp> &
+GroupStore::getGroupMap() const
+{
+ return _map_group;
+}
-GroupingGroupSp GroupStore::getInstance(unsigned int group_number) {
+GroupingGroupSp
+GroupStore::getInstance(unsigned int group_number)
+{
- GroupingGroupSp sp_group;
- if (group_number > 0) {
- std::map< unsigned int, GroupingGroupSp>::iterator it = _map_group.find(group_number);
- if (it != _map_group.end()) {
- sp_group = it->second;
+ GroupingGroupSp sp_group;
+ if(group_number > 0)
+ {
+ std::map<unsigned int, GroupingGroupSp>::iterator it =
+ _map_group.find(group_number);
+ if(it != _map_group.end())
+ {
+ sp_group = it->second;
}
- else {
- sp_group = std::make_shared<GroupingGroup>();
- _map_group.insert(std::pair<unsigned int, GroupingGroupSp>(group_number,sp_group));
+ else
+ {
+ sp_group = std::make_shared<GroupingGroup>();
+ _map_group.insert(
+ std::pair<unsigned int, GroupingGroupSp>(group_number, sp_group));
}
}
- return (sp_group);
-
+ return (sp_group);
}
diff --git a/src/utils/groupstore.h b/src/utils/groupstore.h
index 98db1ce5408f9f7c607098d7e18e25664234a5ef..7132ac4e5f2dbf8411bea80080ee4f06bfc1d2e4 100644
--- a/src/utils/groupstore.h
+++ b/src/utils/groupstore.h
@@ -7,26 +7,27 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "../grouping/groupinggroup.h"
@@ -37,17 +38,18 @@
class GroupStore
{
-public:
- GroupStore();
- ~GroupStore();
- GroupingGroupSp getInstance(unsigned int group_number);
- const std::map<unsigned int, GroupingGroupSp> & getGroupMap() const;
-
- void clear();
- std::size_t countGroup() const;
- std::size_t countSubGroup() const;
-private :
- std::map<unsigned int, GroupingGroupSp> _map_group;
+ public:
+ GroupStore();
+ ~GroupStore();
+ GroupingGroupSp getInstance(unsigned int group_number);
+ const std::map<unsigned int, GroupingGroupSp> &getGroupMap() const;
+
+ void clear();
+ std::size_t countGroup() const;
+ std::size_t countSubGroup() const;
+
+ private:
+ std::map<unsigned int, GroupingGroupSp> _map_group;
};
#endif // GROUPSTORE_H
diff --git a/src/utils/identificationdatasourcestore.cpp b/src/utils/identificationdatasourcestore.cpp
index 51705b31c08445d7f19c84cce6131124e5674c3e..1f7df966988b33650162ed22313df5d36f2212d6 100644
--- a/src/utils/identificationdatasourcestore.cpp
+++ b/src/utils/identificationdatasourcestore.cpp
@@ -2,31 +2,33 @@
* \file utils/identificationdatasourcestore.cpp
* \date 5/4/2017
* \author Olivier Langella
- * \brief store unique version of identification data sources (output files from identification engines)
+ * \brief store unique version of identification data sources (output files from
+ * identification engines)
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "identificationdatasourcestore.h"
#include "../core/identification_sources/identificationxtandemfile.h"
@@ -38,97 +40,153 @@
IdentificationDataSourceStore::IdentificationDataSourceStore()
{
-
}
IdentificationDataSourceStore::~IdentificationDataSourceStore()
{
-
}
-IdentificationDataSourceSp IdentificationDataSourceStore::getInstance(const QString & location, IdentificationEngine engine) {
- qDebug() << "IdentificationDataSourceStore::getInstance begin " << location;
- std::map< QString, IdentificationDataSourceSp >::iterator it = _map_identification_data_sources.find(location);
- if (it != _map_identification_data_sources.end()) {
- qDebug() << "IdentificationDataSourceStore::getInstance found " << location;
- return it->second;
+IdentificationDataSourceSp
+IdentificationDataSourceStore::getInstance(const QString &location,
+ IdentificationEngine engine)
+{
+ qDebug() << "IdentificationDataSourceStore::getInstance begin " << location;
+ std::map<QString, IdentificationDataSourceSp>::iterator it =
+ _map_identification_data_sources.find(location);
+ if(it != _map_identification_data_sources.end())
+ {
+ qDebug() << "IdentificationDataSourceStore::getInstance found "
+ << location;
+ return it->second;
}
- else {
- QFileInfo location_file(location);
- QString ext = location_file.suffix();
- qDebug() << "IdentificationDataSourceStore::getInstance coucou 1 ";
- //QString sample_name = location_file.baseName();
- IdentificationDataSourceSp p_identfile = nullptr;
- if (ext.toLower() == "xml") {
- //X!Tandem result file
- p_identfile = std::make_shared<IdentificationXtandemFile>(location_file);
- } else if (ext.toLower() == "pep") {
- //pep xml file
- p_identfile = std::make_shared<IdentificationPwizFile>(location_file);
- } else {
- p_identfile = std::make_shared<IdentificationPwizFile>(location_file);
+ else
+ {
+ QFileInfo location_file(location);
+ QString ext = location_file.suffix();
+ qDebug() << "IdentificationDataSourceStore::getInstance coucou 1 ";
+ // QString sample_name = location_file.baseName();
+ IdentificationDataSourceSp p_identfile = nullptr;
+ if(ext.toLower() == "xml")
+ {
+ // X!Tandem result file
+ p_identfile =
+ std::make_shared<IdentificationXtandemFile>(location_file);
}
- if (p_identfile == nullptr) {
- throw pappso::PappsoException(QObject::tr("Identification resource %1 not recognized (null pointer)").arg(location));
+ else if(ext.toLower() == "pep")
+ {
+ // pep xml file
+ p_identfile = std::make_shared<IdentificationPwizFile>(location_file);
}
- qDebug() << "IdentificationDataSourceStore::getInstance coucou 2 ";
- p_identfile.get()->setXmlId(QString("ident%1").arg(pappso::Utils::getLexicalOrderedString(_map_identification_data_sources.size())));
- p_identfile.get()->setIdentificationEngine(engine);
- _map_identification_data_sources.insert(std::pair< QString, IdentificationDataSourceSp >(location, p_identfile));
- _map_identification_data_sources.insert(std::pair< QString, IdentificationDataSourceSp >(location_file.absoluteFilePath(), p_identfile));
- qDebug() << "IdentificationDataSourceStore::getInstance inserted " << location;
- return p_identfile;
+ else
+ {
+ p_identfile = std::make_shared<IdentificationPwizFile>(location_file);
+ }
+ if(p_identfile == nullptr)
+ {
+ throw pappso::PappsoException(
+ QObject::tr(
+ "Identification resource %1 not recognized (null pointer)")
+ .arg(location));
+ }
+ qDebug() << "IdentificationDataSourceStore::getInstance coucou 2 ";
+ p_identfile.get()->setXmlId(
+ QString("ident%1").arg(pappso::Utils::getLexicalOrderedString(
+ _map_identification_data_sources.size())));
+ p_identfile.get()->setIdentificationEngine(engine);
+ _map_identification_data_sources.insert(
+ std::pair<QString, IdentificationDataSourceSp>(location, p_identfile));
+ _map_identification_data_sources.insert(
+ std::pair<QString, IdentificationDataSourceSp>(
+ location_file.absoluteFilePath(), p_identfile));
+ qDebug() << "IdentificationDataSourceStore::getInstance inserted "
+ << location;
+ return p_identfile;
}
- throw pappso::PappsoException(QObject::tr("Identification resource %1 not recognized").arg(location));
+ throw pappso::PappsoException(
+ QObject::tr("Identification resource %1 not recognized").arg(location));
}
-IdentificationDataSourceSp IdentificationDataSourceStore::getInstance(const QString & location) {
- qDebug() << "IdentificationDataSourceStore::getInstance begin " << location;
- qDebug() << " " << _map_identification_data_sources.size();
- std::map< QString, IdentificationDataSourceSp >::iterator it = _map_identification_data_sources.find(location);
- if (it != _map_identification_data_sources.end()) {
- return it->second;
+IdentificationDataSourceSp
+IdentificationDataSourceStore::getInstance(const QString &location)
+{
+ qDebug() << "IdentificationDataSourceStore::getInstance begin " << location;
+ qDebug() << " " << _map_identification_data_sources.size();
+ std::map<QString, IdentificationDataSourceSp>::iterator it =
+ _map_identification_data_sources.find(location);
+ if(it != _map_identification_data_sources.end())
+ {
+ return it->second;
}
- else {
- QFileInfo location_file(location);
- QString ext = location_file.completeSuffix();
- //QString sample_name = location_file.baseName();
- IdentificationDataSourceSp p_identfile = nullptr;
- if (ext.toLower() == "xml") {
- //X!Tandem result file
- p_identfile = std::make_shared<IdentificationXtandemFile>(location_file);
- } else if (ext.toLower() == "pep") {
- //pep xml file
- p_identfile = std::make_shared<IdentificationPepXmlFile>(location_file);
- } else if (ext.toLower() == "pep.xml") {
- //pep xml file
- p_identfile = std::make_shared<IdentificationPepXmlFile>(location_file);
- } else if (ext.toLower() == "pepxml") {
- //pep xml file
- p_identfile = std::make_shared<IdentificationPepXmlFile>(location_file);
- } else if (ext.toLower() == "dat") {
- //MASCOT dat file
- p_identfile = std::make_shared<IdentificationMascotDatFile>(location_file);
- } else {
- p_identfile = std::make_shared<IdentificationPwizFile>(location_file);
+ else
+ {
+ QFileInfo location_file(location);
+ QString ext = location_file.completeSuffix();
+ // QString sample_name = location_file.baseName();
+ IdentificationDataSourceSp p_identfile = nullptr;
+ if(ext.toLower() == "xml")
+ {
+ // X!Tandem result file
+ p_identfile =
+ std::make_shared<IdentificationXtandemFile>(location_file);
}
- if (p_identfile == nullptr) {
- throw pappso::PappsoException(QObject::tr("Identification resource %1 not recognized (null pointer)").arg(location));
+ else if(ext.toLower() == "pep")
+ {
+ // pep xml file
+ p_identfile =
+ std::make_shared<IdentificationPepXmlFile>(location_file);
}
- p_identfile.get()->setXmlId(QString("ident%1").arg(pappso::Utils::getLexicalOrderedString(_map_identification_data_sources.size())));
+ else if(ext.toLower() == "pep.xml")
+ {
+ // pep xml file
+ p_identfile =
+ std::make_shared<IdentificationPepXmlFile>(location_file);
+ }
+ else if(ext.toLower() == "pepxml")
+ {
+ // pep xml file
+ p_identfile =
+ std::make_shared<IdentificationPepXmlFile>(location_file);
+ }
+ else if(ext.toLower() == "dat")
+ {
+ // MASCOT dat file
+ p_identfile =
+ std::make_shared<IdentificationMascotDatFile>(location_file);
+ }
+ else
+ {
+ p_identfile = std::make_shared<IdentificationPwizFile>(location_file);
+ }
+ if(p_identfile == nullptr)
+ {
+ throw pappso::PappsoException(
+ QObject::tr(
+ "Identification resource %1 not recognized (null pointer)")
+ .arg(location));
+ }
+ p_identfile.get()->setXmlId(
+ QString("ident%1").arg(pappso::Utils::getLexicalOrderedString(
+ _map_identification_data_sources.size())));
- _map_identification_data_sources.insert(std::pair< QString, IdentificationDataSourceSp >(location, p_identfile));
- _map_identification_data_sources.insert(std::pair< QString, IdentificationDataSourceSp >(location_file.absoluteFilePath(), p_identfile));
- return p_identfile;
+ _map_identification_data_sources.insert(
+ std::pair<QString, IdentificationDataSourceSp>(location, p_identfile));
+ _map_identification_data_sources.insert(
+ std::pair<QString, IdentificationDataSourceSp>(
+ location_file.absoluteFilePath(), p_identfile));
+ return p_identfile;
}
- throw pappso::PappsoException(QObject::tr("Identification resource %1 not recognized").arg(location));
+ throw pappso::PappsoException(
+ QObject::tr("Identification resource %1 not recognized").arg(location));
}
-std::vector<IdentificationDataSourceSp> IdentificationDataSourceStore::getIdentificationDataSourceList() const {
- std::vector<IdentificationDataSourceSp> idsource_list;
- for (auto & msrun_pair :_map_identification_data_sources) {
- idsource_list.push_back(msrun_pair.second);
+std::vector<IdentificationDataSourceSp>
+IdentificationDataSourceStore::getIdentificationDataSourceList() const
+{
+ std::vector<IdentificationDataSourceSp> idsource_list;
+ for(auto &msrun_pair : _map_identification_data_sources)
+ {
+ idsource_list.push_back(msrun_pair.second);
}
- return idsource_list;
+ return idsource_list;
}
diff --git a/src/utils/identificationdatasourcestore.h b/src/utils/identificationdatasourcestore.h
index a84b06a83c997fa73e55b29e5c190817f3db78b7..b59e667ae4a57ce83e6772fcbd770382c7940b2d 100644
--- a/src/utils/identificationdatasourcestore.h
+++ b/src/utils/identificationdatasourcestore.h
@@ -2,31 +2,33 @@
* \file utils/identificationdatasourcestore.h
* \date 5/4/2017
* \author Olivier Langella
- * \brief store unique version of identification data sources (output files from identification engines)
+ * \brief store unique version of identification data sources (output files from
+ * identification engines)
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef IDENTIFICATIONDATASOURCESTORE_H
#define IDENTIFICATIONDATASOURCESTORE_H
@@ -38,15 +40,19 @@
class IdentificationDataSourceStore
{
-public:
- IdentificationDataSourceStore();
- ~IdentificationDataSourceStore();
- IdentificationDataSourceSp getInstance(const QString & location);
- IdentificationDataSourceSp getInstance(const QString & location, IdentificationEngine engine);
-
- std::vector<IdentificationDataSourceSp> getIdentificationDataSourceList() const;
-private :
- std::map<QString, IdentificationDataSourceSp> _map_identification_data_sources;
+ public:
+ IdentificationDataSourceStore();
+ ~IdentificationDataSourceStore();
+ IdentificationDataSourceSp getInstance(const QString &location);
+ IdentificationDataSourceSp getInstance(const QString &location,
+ IdentificationEngine engine);
+
+ std::vector<IdentificationDataSourceSp>
+ getIdentificationDataSourceList() const;
+
+ private:
+ std::map<QString, IdentificationDataSourceSp>
+ _map_identification_data_sources;
};
#endif // IDENTIFICATIONDATASOURCESTORE_H
diff --git a/src/utils/msrunstatisticshandler.cpp b/src/utils/msrunstatisticshandler.cpp
index a73714ccf99753db25a9adff946fe9fe17ee1ceb..cd1c3d0d8373689872bb198c2bdbaa634436f9f3 100644
--- a/src/utils/msrunstatisticshandler.cpp
+++ b/src/utils/msrunstatisticshandler.cpp
@@ -78,7 +78,8 @@ MsRunStatisticsHandler::getMsLevelTic(unsigned int ms_level) const
return 0;
if(ms_level > _tic_ms_level_spectrum.size())
return 0;
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << _tic_ms_level_spectrum[ms_level - 1];
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
+ << _tic_ms_level_spectrum[ms_level - 1];
return (_tic_ms_level_spectrum[ms_level - 1]);
}
diff --git a/src/utils/msrunstatisticshandler.h b/src/utils/msrunstatisticshandler.h
index ae57c462c4203ad4a76c46acbdccf27c9c920a2d..c0a645ef67d06e47d595783e7fbd8852b8ecc8a7 100644
--- a/src/utils/msrunstatisticshandler.h
+++ b/src/utils/msrunstatisticshandler.h
@@ -2,28 +2,29 @@
* \file utils/msrunstatisticshandler.h
* \date 12/08/2018
* \author Olivier Langella
- * \brief handler on MZ data file to read all spectrums and make basic statistics
+ * \brief handler on MZ data file to read all spectrums and make basic
+ * statistics
*/
/*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ ******************************************************************************/
#pragma once
diff --git a/src/utils/msrunstore.h b/src/utils/msrunstore.h
index 48391de8c890b8e26df4b6aa47a20bacc7900526..e0853179a944d34dab9ff0e289cfb4976386ad08 100644
--- a/src/utils/msrunstore.h
+++ b/src/utils/msrunstore.h
@@ -7,26 +7,27 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef MSRUNSTORE_H
#define MSRUNSTORE_H
@@ -38,16 +39,17 @@
class MsRunStore
{
-public:
- MsRunStore();
- ~MsRunStore();
-
- MsRunSp getInstance(const QString & location);
- MsRunSp getInstance(const MsRun * p_msrun);
-
- const std::vector<MsRunSp> & getMsRunList() const;
-private:
- std::vector<MsRunSp> _map_msrun;
+ public:
+ MsRunStore();
+ ~MsRunStore();
+
+ MsRunSp getInstance(const QString &location);
+ MsRunSp getInstance(const MsRun *p_msrun);
+
+ const std::vector<MsRunSp> &getMsRunList() const;
+
+ private:
+ std::vector<MsRunSp> _map_msrun;
};
#endif // MSRUNSTORE_H
diff --git a/src/utils/peptideevidencestore.cpp b/src/utils/peptideevidencestore.cpp
index e2ebd231eeb952b92a583fd0c155efe0b17e06d2..a99100907b1a2bb2535c079b58b4673194b294d4 100644
--- a/src/utils/peptideevidencestore.cpp
+++ b/src/utils/peptideevidencestore.cpp
@@ -6,101 +6,139 @@
*/
-
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "peptideevidencestore.h"
#include <QDebug>
#include <pappsomspp/pappsoexception.h>
#include "../core/peptideevidence.h"
-std::shared_ptr<PeptideEvidence> & PeptideEvidenceStore::recordInstance(const PeptideEvidence * p_peptide_evidence) {
- _peptide_evidence_list.push_back(p_peptide_evidence->makePeptideEvidenceSp());
-
- //qDebug() << "PeptideEvidenceStore::getInstance end " << find_it->second.get()->getScan() << " size=" << _multimap_scan_evidence.size();
- return _peptide_evidence_list.back();
+std::shared_ptr<PeptideEvidence> &
+PeptideEvidenceStore::recordInstance(const PeptideEvidence *p_peptide_evidence)
+{
+ _peptide_evidence_list.push_back(p_peptide_evidence->makePeptideEvidenceSp());
+
+ // qDebug() << "PeptideEvidenceStore::getInstance end " <<
+ // find_it->second.get()->getScan() << " size=" <<
+ // _multimap_scan_evidence.size();
+ return _peptide_evidence_list.back();
}
-std::shared_ptr<PeptideEvidence> & PeptideEvidenceStore::getInstance(const PeptideEvidence * p_peptide_evidence) {
- //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " scan=" << p_peptide_evidence->getScan();
- //qDebug() << "PeptideEvidenceStore::getInstance begin" ;
- std::multimap<unsigned int ,PeptideEvidenceSp>::iterator it = _multimap_scan_evidence.find(p_peptide_evidence->getScan());
- std::multimap<unsigned int ,PeptideEvidenceSp>::iterator find_it = _multimap_scan_evidence.end();
-
-
- while ((find_it == _multimap_scan_evidence.end()) && (it->first == p_peptide_evidence->getScan()) && (it != find_it)) {
- if (it->second.get()->getPeptideXtpSp().get() == p_peptide_evidence->getPeptideXtpSp().get()) {
- //it is the same peptide
- find_it = it;
+std::shared_ptr<PeptideEvidence> &
+PeptideEvidenceStore::getInstance(const PeptideEvidence *p_peptide_evidence)
+{
+ // qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " scan="
+ // << p_peptide_evidence->getScan(); qDebug() <<
+ // "PeptideEvidenceStore::getInstance begin" ;
+ std::multimap<unsigned int, PeptideEvidenceSp>::iterator it =
+ _multimap_scan_evidence.find(p_peptide_evidence->getScan());
+ std::multimap<unsigned int, PeptideEvidenceSp>::iterator find_it =
+ _multimap_scan_evidence.end();
+
+
+ while((find_it == _multimap_scan_evidence.end()) &&
+ (it->first == p_peptide_evidence->getScan()) && (it != find_it))
+ {
+ if(it->second.get()->getPeptideXtpSp().get() ==
+ p_peptide_evidence->getPeptideXtpSp().get())
+ {
+ // it is the same peptide
+ find_it = it;
}
- else {
- //throw pappso::PappsoException(QObject::tr("PeptideEvidenceStore::getInstance multiple peptide for scan %1").arg(p_peptide_evidence->getScan()));
+ else
+ {
+ // throw
+ // pappso::PappsoException(QObject::tr("PeptideEvidenceStore::getInstance
+ // multiple peptide for scan %1").arg(p_peptide_evidence->getScan()));
}
- it++;
+ it++;
}
- if (find_it == _multimap_scan_evidence.end()) {
- // insert it
- find_it = _multimap_scan_evidence.insert(std::pair<unsigned int , PeptideEvidenceSp>(p_peptide_evidence->getScan(), p_peptide_evidence->makePeptideEvidenceSp()));
- _peptide_evidence_list.push_back(find_it->second);
+ if(find_it == _multimap_scan_evidence.end())
+ {
+ // insert it
+ find_it = _multimap_scan_evidence.insert(
+ std::pair<unsigned int, PeptideEvidenceSp>(
+ p_peptide_evidence->getScan(),
+ p_peptide_evidence->makePeptideEvidenceSp()));
+ _peptide_evidence_list.push_back(find_it->second);
}
- //qDebug() << "PeptideEvidenceStore::getInstance end " << find_it->second.get()->getScan() << " size=" << _multimap_scan_evidence.size();
- //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- return find_it->second;
-
+ // qDebug() << "PeptideEvidenceStore::getInstance end " <<
+ // find_it->second.get()->getScan() << " size=" <<
+ // _multimap_scan_evidence.size(); qDebug() << __FILE__ << " " <<
+ // __FUNCTION__<< " " << __LINE__;
+ return find_it->second;
}
-std::size_t PeptideEvidenceStore::size() const {
- return _peptide_evidence_list.size();
+std::size_t
+PeptideEvidenceStore::size() const
+{
+ return _peptide_evidence_list.size();
}
-void PeptideEvidenceStore::clearMap() {
- qDebug() << "PeptideEvidenceStore::clearMap begin" ;
- _multimap_scan_evidence.clear();
- qDebug() << "PeptideEvidenceStore::clearMap end" ;
-
+void
+PeptideEvidenceStore::clearMap()
+{
+ qDebug() << "PeptideEvidenceStore::clearMap begin";
+ _multimap_scan_evidence.clear();
+ qDebug() << "PeptideEvidenceStore::clearMap end";
}
-void PeptideEvidenceStore::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
- qDebug() << "PeptideEvidenceStore::updateAutomaticFilters begin" ;
- for (PeptideEvidenceSp & peptide_evidence_sp:_peptide_evidence_list) {
- peptide_evidence_sp.get()->updateAutomaticFilters(automatic_filter_parameters);
+void
+PeptideEvidenceStore::updateAutomaticFilters(
+ const AutomaticFilterParameters &automatic_filter_parameters)
+{
+ qDebug() << "PeptideEvidenceStore::updateAutomaticFilters begin";
+ for(PeptideEvidenceSp &peptide_evidence_sp : _peptide_evidence_list)
+ {
+ peptide_evidence_sp.get()->updateAutomaticFilters(
+ automatic_filter_parameters);
}
- qDebug() << "PeptideEvidenceStore::updateAutomaticFilters end" ;
-
+ qDebug() << "PeptideEvidenceStore::updateAutomaticFilters end";
}
-const std::vector<std::shared_ptr<PeptideEvidence>> & PeptideEvidenceStore::getPeptideEvidenceList() const {
- return _peptide_evidence_list;
+const std::vector<std::shared_ptr<PeptideEvidence>> &
+PeptideEvidenceStore::getPeptideEvidenceList() const
+{
+ return _peptide_evidence_list;
}
-void PeptideEvidenceStore::getSameXicPeptideEvidenceList(std::vector<const PeptideEvidence *> & peptide_evidence_list, const MsRun * p_msrun, const PeptideXtp * p_peptide, unsigned int charge) const {
- for (const PeptideEvidenceSp & peptide_evidence_sp:_peptide_evidence_list) {
- if (p_msrun != peptide_evidence_sp.get()->getMsRunP()) continue;
- else if (p_peptide != peptide_evidence_sp.get()->getPeptideXtpSp().get()) continue;
- else if (charge != peptide_evidence_sp.get()->getCharge()) continue;
- peptide_evidence_list.push_back(peptide_evidence_sp.get());
+void
+PeptideEvidenceStore::getSameXicPeptideEvidenceList(
+ std::vector<const PeptideEvidence *> &peptide_evidence_list,
+ const MsRun *p_msrun, const PeptideXtp *p_peptide, unsigned int charge) const
+{
+ for(const PeptideEvidenceSp &peptide_evidence_sp : _peptide_evidence_list)
+ {
+ if(p_msrun != peptide_evidence_sp.get()->getMsRunP())
+ continue;
+ else if(p_peptide != peptide_evidence_sp.get()->getPeptideXtpSp().get())
+ continue;
+ else if(charge != peptide_evidence_sp.get()->getCharge())
+ continue;
+ peptide_evidence_list.push_back(peptide_evidence_sp.get());
}
}
diff --git a/src/utils/peptideevidencestore.h b/src/utils/peptideevidencestore.h
index 1ae1889c3778f7f611744407a651d9d9d6854a7d..515cc660572c66a501881799e863a5ca19134e5b 100644
--- a/src/utils/peptideevidencestore.h
+++ b/src/utils/peptideevidencestore.h
@@ -7,26 +7,27 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PEPTIDEEVIDENCESTORE_H
#define PEPTIDEEVIDENCESTORE_H
@@ -42,33 +43,41 @@ class PeptideEvidence;
class PeptideEvidenceStore
{
-public:
- /** @brief directly register an instance of peptide evidence : no duplication check
- */
- std::shared_ptr<PeptideEvidence> & recordInstance(const PeptideEvidence * p_peptide_evidence);
- /** @brief register an instance of peptide evidence : duplication check
- */
- std::shared_ptr<PeptideEvidence> & getInstance(const PeptideEvidence * p_peptide_evidence);
- void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
-
- const std::vector<std::shared_ptr<PeptideEvidence>> & getPeptideEvidenceList() const;
- std::size_t size() const;
- void clearMap();
-
-
-
- /** @brief look for a peptide in the same XIC
- * @param peptide_evidence_list the peptide evidence list to build
- * @param p_msrun MSrun to look for
- * @param p_peptide peptide to look for
- * @param charge charge to look for
- */
- void getSameXicPeptideEvidenceList(std::vector<const PeptideEvidence *> & peptide_evidence_list, const MsRun * p_msrun, const PeptideXtp * p_peptide, unsigned int charge) const;
+ public:
+ /** @brief directly register an instance of peptide evidence : no duplication
+ * check
+ */
+ std::shared_ptr<PeptideEvidence> &
+ recordInstance(const PeptideEvidence *p_peptide_evidence);
+ /** @brief register an instance of peptide evidence : duplication check
+ */
+ std::shared_ptr<PeptideEvidence> &
+ getInstance(const PeptideEvidence *p_peptide_evidence);
+ void updateAutomaticFilters(
+ const AutomaticFilterParameters &automatic_filter_parameters);
-private:
- std::vector<std::shared_ptr<PeptideEvidence>> _peptide_evidence_list;
-
- std::multimap<unsigned int ,std::shared_ptr<PeptideEvidence>> _multimap_scan_evidence;
+ const std::vector<std::shared_ptr<PeptideEvidence>> &
+ getPeptideEvidenceList() const;
+ std::size_t size() const;
+ void clearMap();
+
+
+ /** @brief look for a peptide in the same XIC
+ * @param peptide_evidence_list the peptide evidence list to build
+ * @param p_msrun MSrun to look for
+ * @param p_peptide peptide to look for
+ * @param charge charge to look for
+ */
+ void getSameXicPeptideEvidenceList(
+ std::vector<const PeptideEvidence *> &peptide_evidence_list,
+ const MsRun *p_msrun, const PeptideXtp *p_peptide,
+ unsigned int charge) const;
+
+ private:
+ std::vector<std::shared_ptr<PeptideEvidence>> _peptide_evidence_list;
+
+ std::multimap<unsigned int, std::shared_ptr<PeptideEvidence>>
+ _multimap_scan_evidence;
};
#endif // PEPTIDEEVIDENCESTORE_H
diff --git a/src/utils/peptidestore.cpp b/src/utils/peptidestore.cpp
index 9156c44f4897df6ace4eaecefd68c995e9e5a5e6..f22a1e6c6bfac334a15cb051cbd786d426ad65f9 100644
--- a/src/utils/peptidestore.cpp
+++ b/src/utils/peptidestore.cpp
@@ -24,7 +24,8 @@
* along with peptider. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
- * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
******************************************************************************/
#include "peptidestore.h"
@@ -33,81 +34,113 @@
PeptideStore::PeptideStore()
{
-
}
PeptideStore::~PeptideStore()
{
-
}
-PeptideXtpSp & PeptideStore::getInstance(PeptideXtpSp & peptide_in) {
- std::size_t sequence_crc = _hash_fn ( peptide_in.get()->toAbsoluteString().toStdString());
-
- //QByteArray source = peptide_in.get()->getLiAbsoluteString().toUtf8();
- //quint16 sequence_li_crc = qChecksum(source.data(), source.length());
-
- std::pair<std::unordered_map< std::size_t, PeptideXtpSp>::iterator,bool> ret = _map_crc_peptide_list.insert(std::pair<std::size_t, PeptideXtpSp>(sequence_crc,peptide_in));
- if (ret.second) {
- //if new peptide in store
-
- for (auto && aa : *(ret.first->second.get())) {
- std::list<pappso::AaModificationP> mod_list = aa.getModificationList();
- _modification_collection.insert(mod_list.begin(), mod_list.end());
+PeptideXtpSp &
+PeptideStore::getInstance(PeptideXtpSp &peptide_in)
+{
+ std::size_t sequence_crc =
+ _hash_fn(peptide_in.get()->toAbsoluteString().toStdString());
+
+ // QByteArray source = peptide_in.get()->getLiAbsoluteString().toUtf8();
+ // quint16 sequence_li_crc = qChecksum(source.data(), source.length());
+
+ std::pair<std::unordered_map<std::size_t, PeptideXtpSp>::iterator, bool> ret =
+ _map_crc_peptide_list.insert(
+ std::pair<std::size_t, PeptideXtpSp>(sequence_crc, peptide_in));
+ if(ret.second)
+ {
+ // if new peptide in store
+
+ for(auto &&aa : *(ret.first->second.get()))
+ {
+ std::list<pappso::AaModificationP> mod_list =
+ aa.getModificationList();
+ _modification_collection.insert(mod_list.begin(), mod_list.end());
}
}
- return ret.first->second;
-
+ return ret.first->second;
}
-std::size_t PeptideStore::size() const {
- return _map_crc_peptide_list.size();
+std::size_t
+PeptideStore::size() const
+{
+ return _map_crc_peptide_list.size();
}
-bool PeptideStore::replaceModification(pappso::AaModificationP oldmod, pappso::AaModificationP newmod) {
- for (std::pair<std::size_t, PeptideXtpSp> pair_peptide:_map_crc_peptide_list) {
- PeptideXtpSp peptide_xtp = pair_peptide.second;
- peptide_xtp.get()->replaceAaModification(oldmod, newmod);
+bool
+PeptideStore::replaceModification(pappso::AaModificationP oldmod,
+ pappso::AaModificationP newmod)
+{
+ for(std::pair<std::size_t, PeptideXtpSp> pair_peptide : _map_crc_peptide_list)
+ {
+ PeptideXtpSp peptide_xtp = pair_peptide.second;
+ peptide_xtp.get()->replaceAaModification(oldmod, newmod);
}
- _modification_collection.erase(oldmod);
- _modification_collection.insert(newmod);
-
+ _modification_collection.erase(oldmod);
+ _modification_collection.insert(newmod);
}
-void PeptideStore::clearLabelingMethod() {
- for (std::pair<std::size_t, PeptideXtpSp> pair_peptide:_map_crc_peptide_list) {
- PeptideXtpSp peptide_xtp = pair_peptide.second;
- peptide_xtp.get()->clearLabel();
+void
+PeptideStore::clearLabelingMethod()
+{
+ for(std::pair<std::size_t, PeptideXtpSp> pair_peptide : _map_crc_peptide_list)
+ {
+ PeptideXtpSp peptide_xtp = pair_peptide.second;
+ peptide_xtp.get()->clearLabel();
}
}
-const std::set<pappso::AaModificationP> & PeptideStore::getModificationCollection() const {
- return _modification_collection;
+const std::set<pappso::AaModificationP> &
+PeptideStore::getModificationCollection() const
+{
+ return _modification_collection;
}
-bool PeptideStore::checkPsimodCompliance() const {
- for (pappso::AaModificationP modification :_modification_collection) {
- if (modification->isInternal()) {
+bool
+PeptideStore::checkPsimodCompliance() const
+{
+ for(pappso::AaModificationP modification : _modification_collection)
+ {
+ if(modification->isInternal())
+ {
}
- else {
- if (modification->getAccession().startsWith("MOD:")) {
+ else
+ {
+ if(modification->getAccession().startsWith("MOD:"))
+ {
}
- else {
- throw pappso::PappsoException(QObject::tr("Modification %1 is not a PSIMOD accession. Please go into the edit=>modifications menu to replace modifications masses by PSIMOD accessions").arg(modification->getAccession()));
+ else
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Modification %1 is not a PSIMOD accession. Please "
+ "go into the edit=>modifications menu to replace "
+ "modifications masses by PSIMOD accessions")
+ .arg(modification->getAccession()));
}
}
}
- return true;
+ return true;
}
-void PeptideStore::setLabelingMethodSp(LabelingMethodSp labeling_method_sp) {
- if (_labeling_method_sp != nullptr) {
- clearLabelingMethod();
+void
+PeptideStore::setLabelingMethodSp(LabelingMethodSp labeling_method_sp)
+{
+ if(_labeling_method_sp != nullptr)
+ {
+ clearLabelingMethod();
}
- _labeling_method_sp = labeling_method_sp;
- for (std::pair<std::size_t, PeptideXtpSp> pair_peptide:_map_crc_peptide_list) {
- PeptideXtpSp peptide_xtp = pair_peptide.second;
- peptide_xtp.get()->applyLabelingMethod(labeling_method_sp);
+ _labeling_method_sp = labeling_method_sp;
+ for(std::pair<std::size_t, PeptideXtpSp> pair_peptide : _map_crc_peptide_list)
+ {
+ PeptideXtpSp peptide_xtp = pair_peptide.second;
+ peptide_xtp.get()->applyLabelingMethod(labeling_method_sp);
}
}
-const std::unordered_map<std::size_t, PeptideXtpSp> & PeptideStore::getPeptideMap() const {
- return _map_crc_peptide_list;
+const std::unordered_map<std::size_t, PeptideXtpSp> &
+PeptideStore::getPeptideMap() const
+{
+ return _map_crc_peptide_list;
}
diff --git a/src/utils/peptidestore.h b/src/utils/peptidestore.h
index 53862e9f7e65ab6521b4aafb4d6347c0f1b2c590..55faba9da51d7122ecbf31859996f2d8d407cd2e 100644
--- a/src/utils/peptidestore.h
+++ b/src/utils/peptidestore.h
@@ -24,7 +24,8 @@
* along with peptider. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
- * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
******************************************************************************/
#ifndef PEPTIDESTORE_H
@@ -37,39 +38,40 @@
class PeptideStore
{
-public:
- PeptideStore();
- ~PeptideStore();
-
- PeptideXtpSp & getInstance(PeptideXtpSp & peptide_in);
+ public:
+ PeptideStore();
+ ~PeptideStore();
- /** @brief check that modifications are coded with PSI MOD accessions
- */
- bool checkPsimodCompliance() const;
+ PeptideXtpSp &getInstance(PeptideXtpSp &peptide_in);
- const std::set<pappso::AaModificationP> & getModificationCollection() const;
+ /** @brief check that modifications are coded with PSI MOD accessions
+ */
+ bool checkPsimodCompliance() const;
- /** @brief replaces all occurences of a given modification by another one
- */
- bool replaceModification(pappso::AaModificationP oldmod, pappso::AaModificationP newmod);
+ const std::set<pappso::AaModificationP> &getModificationCollection() const;
- /** @brief apply labeling method to all peptide match
- * */
- void setLabelingMethodSp(LabelingMethodSp labeling_method_sp);
-
- const std::unordered_map<std::size_t, PeptideXtpSp> & getPeptideMap() const;
- std::size_t size() const;
-private:
- /** @brief reset labeling method
- * */
- void clearLabelingMethod();
+ /** @brief replaces all occurences of a given modification by another one
+ */
+ bool replaceModification(pappso::AaModificationP oldmod,
+ pappso::AaModificationP newmod);
-private :
+ /** @brief apply labeling method to all peptide match
+ * */
+ void setLabelingMethodSp(LabelingMethodSp labeling_method_sp);
- LabelingMethodSp _labeling_method_sp;
- std::hash<std::string> _hash_fn;
- std::unordered_map<std::size_t, PeptideXtpSp> _map_crc_peptide_list;
- std::set<pappso::AaModificationP> _modification_collection;
+ const std::unordered_map<std::size_t, PeptideXtpSp> &getPeptideMap() const;
+ std::size_t size() const;
+
+ private:
+ /** @brief reset labeling method
+ * */
+ void clearLabelingMethod();
+
+ private:
+ LabelingMethodSp _labeling_method_sp;
+ std::hash<std::string> _hash_fn;
+ std::unordered_map<std::size_t, PeptideXtpSp> _map_crc_peptide_list;
+ std::set<pappso::AaModificationP> _modification_collection;
};
#endif // PEPTIDESTORE_H
diff --git a/src/utils/proteinstore.cpp b/src/utils/proteinstore.cpp
index 98195342ea2c701c162c278cd2f36fda17c74785..9d4a3b8222877059fd4d866c2c1445fd8282aa62 100644
--- a/src/utils/proteinstore.cpp
+++ b/src/utils/proteinstore.cpp
@@ -6,26 +6,27 @@
*/
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "proteinstore.h"
#include "../files/fastafile.h"
@@ -35,120 +36,172 @@
ProteinStore::ProteinStore()
{
- QSettings settings;
-
- _regexp_contaminant.setPattern(settings.value("automatic_filter/contaminant_regexp","^conta\\|").toString());
- _regexp_decoy.setPattern(settings.value("automatic_filter/decoy_regexp",".*\\|reversed$").toString());
-
+ QSettings settings;
+ _regexp_contaminant.setPattern(
+ settings.value("automatic_filter/contaminant_regexp", "^conta\\|")
+ .toString());
+ _regexp_decoy.setPattern(
+ settings.value("automatic_filter/decoy_regexp", ".*\\|reversed$")
+ .toString());
}
ProteinStore::~ProteinStore()
{
-
}
-std::size_t ProteinStore::size() const {
- return _map_accession_protein_list.size();
+std::size_t
+ProteinStore::size() const
+{
+ return _map_accession_protein_list.size();
}
-const std::vector<const FastaFile *> & ProteinStore::getContaminantFastaFileList() const {
- return _fasta_contaminant_list;
+const std::vector<const FastaFile *> &
+ProteinStore::getContaminantFastaFileList() const
+{
+ return _fasta_contaminant_list;
}
-const std::vector<const FastaFile *> & ProteinStore::getDecoyFastaFileList() const {
- return _fasta_decoy_list;
+const std::vector<const FastaFile *> &
+ProteinStore::getDecoyFastaFileList() const
+{
+ return _fasta_decoy_list;
}
-QRegExp ProteinStore::getRegexpContaminant() const {
- return (_regexp_contaminant);
+QRegExp
+ProteinStore::getRegexpContaminant() const
+{
+ return (_regexp_contaminant);
}
-void ProteinStore::setRegexpContaminantPattern(const QString & pattern) {
- _regexp_contaminant.setPattern(pattern);
+void
+ProteinStore::setRegexpContaminantPattern(const QString &pattern)
+{
+ _regexp_contaminant.setPattern(pattern);
- for (std::pair<const QString, ProteinXtpSp> & acc_protein :_map_accession_protein_list) {
- setProteinInformations(acc_protein.second);
+ for(std::pair<const QString, ProteinXtpSp> &acc_protein :
+ _map_accession_protein_list)
+ {
+ setProteinInformations(acc_protein.second);
}
- QSettings settings;
- settings.setValue("automatic_filter/contaminant_regexp", pattern);
+ QSettings settings;
+ settings.setValue("automatic_filter/contaminant_regexp", pattern);
}
-QRegExp ProteinStore::getRegexpDecoy() const {
- return (_regexp_decoy);
+QRegExp
+ProteinStore::getRegexpDecoy() const
+{
+ return (_regexp_decoy);
}
-const std::map<QString, ProteinXtpSp> & ProteinStore::getProteinMap() const {
- return _map_accession_protein_list;
+const std::map<QString, ProteinXtpSp> &
+ProteinStore::getProteinMap() const
+{
+ return _map_accession_protein_list;
}
-void ProteinStore::setRegexpDecoyPattern(const QString & pattern) {
- _regexp_decoy.setPattern(pattern);
+void
+ProteinStore::setRegexpDecoyPattern(const QString &pattern)
+{
+ _regexp_decoy.setPattern(pattern);
- for (std::pair<const QString, ProteinXtpSp> & acc_protein :_map_accession_protein_list) {
- setProteinInformations(acc_protein.second);
+ for(std::pair<const QString, ProteinXtpSp> &acc_protein :
+ _map_accession_protein_list)
+ {
+ setProteinInformations(acc_protein.second);
}
- QSettings settings;
- settings.setValue("automatic_filter/decoy_regexp", pattern);
-
+ QSettings settings;
+ settings.setValue("automatic_filter/decoy_regexp", pattern);
}
-void ProteinStore::clearDecoys() {
- _fasta_decoy_list.clear();
- for (std::pair<const QString, ProteinXtpSp> & acc_protein :_map_accession_protein_list) {
- acc_protein.second.get()->setIsDecoy(false);
+void
+ProteinStore::clearDecoys()
+{
+ _fasta_decoy_list.clear();
+ for(std::pair<const QString, ProteinXtpSp> &acc_protein :
+ _map_accession_protein_list)
+ {
+ acc_protein.second.get()->setIsDecoy(false);
}
}
-void ProteinStore::clearContaminants() {
- _fasta_contaminant_list.clear();
- for (std::pair<const QString, ProteinXtpSp> & acc_protein :_map_accession_protein_list) {
- acc_protein.second.get()->setIsContaminant(false);
+void
+ProteinStore::clearContaminants()
+{
+ _fasta_contaminant_list.clear();
+ for(std::pair<const QString, ProteinXtpSp> &acc_protein :
+ _map_accession_protein_list)
+ {
+ acc_protein.second.get()->setIsContaminant(false);
}
}
-void ProteinStore::addContaminantFastaFile(const FastaFile * p_fasta_file) {
- _fasta_contaminant_list.push_back(p_fasta_file);
+void
+ProteinStore::addContaminantFastaFile(const FastaFile *p_fasta_file)
+{
+ _fasta_contaminant_list.push_back(p_fasta_file);
}
-void ProteinStore::addDecoyFastaFile(const FastaFile * p_fasta_file) {
- _fasta_decoy_list.push_back(p_fasta_file);
+void
+ProteinStore::addDecoyFastaFile(const FastaFile *p_fasta_file)
+{
+ _fasta_decoy_list.push_back(p_fasta_file);
}
-void ProteinStore::setDecoyAccession(QString accession) {
- std::map<QString, ProteinXtpSp>::iterator it = _map_accession_protein_list.find(accession);
- if (it != _map_accession_protein_list.end()) {
- it->second.get()->setIsDecoy(true);
+void
+ProteinStore::setDecoyAccession(QString accession)
+{
+ std::map<QString, ProteinXtpSp>::iterator it =
+ _map_accession_protein_list.find(accession);
+ if(it != _map_accession_protein_list.end())
+ {
+ it->second.get()->setIsDecoy(true);
}
}
-void ProteinStore::setContaminantAccession(QString accession) {
- std::map<QString, ProteinXtpSp>::iterator it = _map_accession_protein_list.find(accession);
- if (it != _map_accession_protein_list.end()) {
- it->second.get()->setIsContaminant(true);
+void
+ProteinStore::setContaminantAccession(QString accession)
+{
+ std::map<QString, ProteinXtpSp>::iterator it =
+ _map_accession_protein_list.find(accession);
+ if(it != _map_accession_protein_list.end())
+ {
+ it->second.get()->setIsContaminant(true);
}
}
-ProteinXtpSp & ProteinStore::getInstance(ProteinXtpSp & protein_in) {
+ProteinXtpSp &
+ProteinStore::getInstance(ProteinXtpSp &protein_in)
+{
- std::pair<std::map< QString, ProteinXtpSp>::iterator,bool> ret = _map_accession_protein_list.insert(std::pair<QString, ProteinXtpSp>(protein_in.get()->getAccession(),protein_in));
+ std::pair<std::map<QString, ProteinXtpSp>::iterator, bool> ret =
+ _map_accession_protein_list.insert(std::pair<QString, ProteinXtpSp>(
+ protein_in.get()->getAccession(), protein_in));
- if (ret.second) {
- //the protein is new in the store, update content
- setProteinInformations(ret.first->second);
+ if(ret.second)
+ {
+ // the protein is new in the store, update content
+ setProteinInformations(ret.first->second);
- if (ret.first->second.get()->getDbxrefList().size() == 0) {
- ret.first->second.get()->parseAccession2dbxref();
+ if(ret.first->second.get()->getDbxrefList().size() == 0)
+ {
+ ret.first->second.get()->parseAccession2dbxref();
}
}
- return (ret.first->second);
-
+ return (ret.first->second);
}
-void ProteinStore::setProteinInformations(ProteinXtpSp & protein_in) {
- //qDebug() << "ProteinStore::setProteinInformations begin" << peptide_in.get()->getSequence();
- protein_in.get()->setIsContaminant(false);
- protein_in.get()->setIsDecoy(false);
- QString accession = protein_in.get()->getAccession();
-
- if ((!_regexp_contaminant.isEmpty()) && (_regexp_contaminant.indexIn(accession, 0)>-1)) {
- //qDebug() << "ProteinStore::setProteinInformations is contaminant " << accession;
- protein_in.get()->setIsContaminant(true);
+void
+ProteinStore::setProteinInformations(ProteinXtpSp &protein_in)
+{
+ // qDebug() << "ProteinStore::setProteinInformations begin" <<
+ // peptide_in.get()->getSequence();
+ protein_in.get()->setIsContaminant(false);
+ protein_in.get()->setIsDecoy(false);
+ QString accession = protein_in.get()->getAccession();
+
+ if((!_regexp_contaminant.isEmpty()) &&
+ (_regexp_contaminant.indexIn(accession, 0) > -1))
+ {
+ // qDebug() << "ProteinStore::setProteinInformations is contaminant " <<
+ // accession;
+ protein_in.get()->setIsContaminant(true);
}
- if ((!_regexp_decoy.isEmpty()) && (_regexp_decoy.indexIn(accession, 0)>-1) ) {
- protein_in.get()->setIsDecoy(true);
+ if((!_regexp_decoy.isEmpty()) && (_regexp_decoy.indexIn(accession, 0) > -1))
+ {
+ protein_in.get()->setIsDecoy(true);
}
- //qDebug() << "ProteinStore::setProteinInformations end";
+ // qDebug() << "ProteinStore::setProteinInformations end";
}
diff --git a/src/utils/proteinstore.h b/src/utils/proteinstore.h
index 9a6e1541896144a71131147fcfb89ba93a212328..4d84a4c41cfb717976c2afdfacda93f1910882ae 100644
--- a/src/utils/proteinstore.h
+++ b/src/utils/proteinstore.h
@@ -7,26 +7,27 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PROTEINSTORE_H
@@ -43,52 +44,51 @@ class FastaFile;
class ProteinStore
{
-public:
- ProteinStore();
- ~ProteinStore();
-
- ProteinXtpSp & getInstance(ProteinXtpSp & protein_in);
-
- void setRegexpDecoyPattern(const QString & pattern);
-
- QRegExp getRegexpDecoy() const;
-
- void setRegexpContaminantPattern(const QString & pattern);
-
- QRegExp getRegexpContaminant() const;
-
- void addContaminantFastaFile(const FastaFile * p_fasta_file);
- void addDecoyFastaFile(const FastaFile * p_fasta_file);
-
- const std::vector<const FastaFile *> & getContaminantFastaFileList() const;
- const std::vector<const FastaFile *> & getDecoyFastaFileList() const;
-
-
- void clearContaminants();
- void clearDecoys();
-
- void setContaminantAccession(QString accession);
- void setDecoyAccession(QString accession);
- std::size_t size() const;
-
- const std::map<QString, ProteinXtpSp> & getProteinMap() const;
-
-private :
- void setProteinInformations(ProteinXtpSp & protein_in);
-private :
-
- std::map<QString, ProteinXtpSp> _map_accession_protein_list;
-
- /** \brief decoy Fasta file liste */
- std::vector<const FastaFile *> _fasta_decoy_list;
- /** \brief contaminant Fasta file liste */
- std::vector<const FastaFile *> _fasta_contaminant_list;
-
- /** \brief recognize decoy accession */
- QRegExp _regexp_decoy;
- /** \brief recognize contaminant accession */
- QRegExp _regexp_contaminant;
+ public:
+ ProteinStore();
+ ~ProteinStore();
+ ProteinXtpSp &getInstance(ProteinXtpSp &protein_in);
+
+ void setRegexpDecoyPattern(const QString &pattern);
+
+ QRegExp getRegexpDecoy() const;
+
+ void setRegexpContaminantPattern(const QString &pattern);
+
+ QRegExp getRegexpContaminant() const;
+
+ void addContaminantFastaFile(const FastaFile *p_fasta_file);
+ void addDecoyFastaFile(const FastaFile *p_fasta_file);
+
+ const std::vector<const FastaFile *> &getContaminantFastaFileList() const;
+ const std::vector<const FastaFile *> &getDecoyFastaFileList() const;
+
+
+ void clearContaminants();
+ void clearDecoys();
+
+ void setContaminantAccession(QString accession);
+ void setDecoyAccession(QString accession);
+ std::size_t size() const;
+
+ const std::map<QString, ProteinXtpSp> &getProteinMap() const;
+
+ private:
+ void setProteinInformations(ProteinXtpSp &protein_in);
+
+ private:
+ std::map<QString, ProteinXtpSp> _map_accession_protein_list;
+
+ /** \brief decoy Fasta file liste */
+ std::vector<const FastaFile *> _fasta_decoy_list;
+ /** \brief contaminant Fasta file liste */
+ std::vector<const FastaFile *> _fasta_contaminant_list;
+
+ /** \brief recognize decoy accession */
+ QRegExp _regexp_decoy;
+ /** \brief recognize contaminant accession */
+ QRegExp _regexp_contaminant;
};
#endif // PROTEINSTORE_H
diff --git a/src/utils/types.h b/src/utils/types.h
index c80ad03ccc3679b4368284fdef4e1973eeaec38f..91f06ca306b7d68dd635afc5021ce5ac49796bce 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -73,20 +73,22 @@ enum class PeptideEvidenceParam : std::int8_t
3, ///< PSI-MS MS:1001172 mascot:expectation value 2.42102904673618e-006
peptide_prophet_probability = 4, ///< no PSI MS description
peptide_inter_prophet_probability = 5, ///< no PSI MS description
- omssa_evalue = 6, ///< MS:1001328 "OMSSA E-value." [PSI:PI]
- omssa_pvalue = 7, ///< MS:1001329 "OMSSA p-value." [PSI:PI]
- msgfplus_raw = 8, ///< MS:1002049 "MS-GF raw score." [PSI:PI]
- msgfplus_denovo = 9, ///< MS:1002050 "MS-GF de novo score." [PSI:PI]
- msgfplus_energy = 10, ///< MS:1002051 "MS-GF energy score." [PSI:PI]
+ omssa_evalue = 6, ///< MS:1001328 "OMSSA E-value." [PSI:PI]
+ omssa_pvalue = 7, ///< MS:1001329 "OMSSA p-value." [PSI:PI]
+ msgfplus_raw = 8, ///< MS:1002049 "MS-GF raw score." [PSI:PI]
+ msgfplus_denovo = 9, ///< MS:1002050 "MS-GF de novo score." [PSI:PI]
+ msgfplus_energy = 10, ///< MS:1002051 "MS-GF energy score." [PSI:PI]
msgfplus_SpecEValue = 11, ///< MS:1002052 "MS-GF spectral E-value." [PSI:PI]
- msgfplus_EValue = 12, ///< MS:1002053 "MS-GF E-value." [PSI:PI]
+ msgfplus_EValue = 12, ///< MS:1002053 "MS-GF E-value." [PSI:PI]
msgfplus_isotope_error = 13, ///< MS-GF isotope error
- comet_xcorr = 14, ///< MS:1002252 "The Comet result 'XCorr'." [PSI:PI]
+ comet_xcorr = 14, ///< MS:1002252 "The Comet result 'XCorr'." [PSI:PI]
comet_deltacn = 15, ///< MS:1002253 "The Comet result 'DeltaCn'." [PSI:PI]
- comet_deltacnstar = 16, ///< MS:1002254 "The Comet result 'DeltaCnStar'." [PSI:PI]
+ comet_deltacnstar =
+ 16, ///< MS:1002254 "The Comet result 'DeltaCnStar'." [PSI:PI]
comet_spscore = 17, ///< MS:1002255 "The Comet result 'SpScore'." [PSI:PI]
- comet_sprank = 18, ///< MS:1002256 "The Comet result 'SpRank'." [PSI:PI]
- comet_expectation_value = 19, ///< MS:1002257 "The Comet result 'Expectation value'." [PSI:PI]
+ comet_sprank = 18, ///< MS:1002256 "The Comet result 'SpRank'." [PSI:PI]
+ comet_expectation_value =
+ 19, ///< MS:1002257 "The Comet result 'Expectation value'." [PSI:PI]
};
@@ -124,9 +126,9 @@ enum class MsRunStatistics : std::int8_t
total_spectra_ms1 = 2, ///< total number of MS1 spectra
total_spectra_ms2 = 3, ///< total number of MS2 spectra
total_spectra_ms3 = 4, ///< total number of MS3 spectra
- tic_spectra_ms1 = 5, ///< total ion current in MS1 spectra
- tic_spectra_ms2 = 6, ///< total ion current in MS2 spectra
- tic_spectra_ms3 = 7, ///< total ion current in MS3 spectra
+ tic_spectra_ms1 = 5, ///< total ion current in MS1 spectra
+ tic_spectra_ms2 = 6, ///< total ion current in MS2 spectra
+ tic_spectra_ms3 = 7, ///< total ion current in MS3 spectra
};
diff --git a/src/utils/workmonitor.cpp b/src/utils/workmonitor.cpp
index e1294423fc6874952f7669b2d6c003234d9829ef..c80a0a2e647a552f8fd84e1b7bfab05770fdd8c3 100644
--- a/src/utils/workmonitor.cpp
+++ b/src/utils/workmonitor.cpp
@@ -7,64 +7,81 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "workmonitor.h"
#include <QDebug>
-WorkMonitor::WorkMonitor() {
- _max_value = 100;
- _timer_duration = 200;
- _time.restart();
+WorkMonitor::WorkMonitor()
+{
+ _max_value = 100;
+ _timer_duration = 200;
+ _time.restart();
}
-void WorkMonitor::finished(const QString & message) {
- emit workerJobFinished(message);
+void
+WorkMonitor::finished(const QString &message)
+{
+ emit workerJobFinished(message);
}
-void WorkMonitor::message(const QString & message) {
- if (_time.elapsed() > _timer_duration) {
- _time.currentTime();
- emit workerMessage(message);
+void
+WorkMonitor::message(const QString &message)
+{
+ if(_time.elapsed() > _timer_duration)
+ {
+ _time.currentTime();
+ emit workerMessage(message);
}
}
-void WorkMonitor::message(const QString & message, int value) {
- qDebug() << "WorkMonitor::message " << value << " " << _max_value << " " << (value/_max_value)*100;
- if (_time.elapsed() > _timer_duration) {
- int percent = ((float)value/(float)_max_value)*(float)100;
+void
+WorkMonitor::message(const QString &message, int value)
+{
+ qDebug() << "WorkMonitor::message " << value << " " << _max_value << " "
+ << (value / _max_value) * 100;
+ if(_time.elapsed() > _timer_duration)
+ {
+ int percent = ((float)value / (float)_max_value) * (float)100;
- _time.restart();
- emit workerMessagePercent(message,percent);
+ _time.restart();
+ emit workerMessagePercent(message, percent);
}
}
-void WorkMonitor::setProgressMaximumValue(int max_value) {
- //qDebug() << "WorkMonitor::setProgressMaximumValue " << max_value;
- _max_value = max_value;
+void
+WorkMonitor::setProgressMaximumValue(int max_value)
+{
+ // qDebug() << "WorkMonitor::setProgressMaximumValue " << max_value;
+ _max_value = max_value;
}
-void WorkMonitor::appendText(char * p_char) {
- //qDebug() << "WorkMonitor::setProgressMaximumValue " << max_value;
- emit workerAppendText(p_char);
+void
+WorkMonitor::appendText(char *p_char)
+{
+ // qDebug() << "WorkMonitor::setProgressMaximumValue " << max_value;
+ emit workerAppendText(p_char);
}
-void WorkMonitor::setText(const QString text) {
- emit workerSetText(text);
+void
+WorkMonitor::setText(const QString text)
+{
+ emit workerSetText(text);
}
diff --git a/src/utils/workmonitor.h b/src/utils/workmonitor.h
index 4c45540e5a384dbd156b7134927becf011587573..73818ac8b13ec67759b619409c23920a22efaa5d 100644
--- a/src/utils/workmonitor.h
+++ b/src/utils/workmonitor.h
@@ -7,26 +7,27 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef WORKMONITOR_H
#define WORKMONITOR_H
@@ -36,38 +37,38 @@
class WorkMonitorInterface
{
-public:
- virtual void finished(const QString & message) = 0;
- virtual void message(const QString & message) = 0;
- virtual void message(const QString & message, int value) = 0;
- virtual void setProgressMaximumValue(int max_value) = 0;
- virtual void appendText(char * p_char) =0;
- virtual void setText(const QString text)=0;
+ public:
+ virtual void finished(const QString &message) = 0;
+ virtual void message(const QString &message) = 0;
+ virtual void message(const QString &message, int value) = 0;
+ virtual void setProgressMaximumValue(int max_value) = 0;
+ virtual void appendText(char *p_char) = 0;
+ virtual void setText(const QString text) = 0;
};
-class WorkMonitor: public QObject, public WorkMonitorInterface
+class WorkMonitor : public QObject, public WorkMonitorInterface
{
- Q_OBJECT
-public:
- WorkMonitor();
- void finished(const QString & message) override;
- void message(const QString & message) override;
- void message(const QString & message, int value) override;
- void setProgressMaximumValue(int max_value) override;
- void appendText(char * p_char) override;
- void setText(const QString text) override;
+ Q_OBJECT
+ public:
+ WorkMonitor();
+ void finished(const QString &message) override;
+ void message(const QString &message) override;
+ void message(const QString &message, int value) override;
+ void setProgressMaximumValue(int max_value) override;
+ void appendText(char *p_char) override;
+ void setText(const QString text) override;
-signals:
- void workerJobFinished(QString message);
- void workerMessage(QString message);
- void workerMessagePercent(QString message, int value);
- void workerAppendText(char * p_char);
- void workerSetText(QString text);
+ signals:
+ void workerJobFinished(QString message);
+ void workerMessage(QString message);
+ void workerMessagePercent(QString message, int value);
+ void workerAppendText(char *p_char);
+ void workerSetText(QString text);
-private :
- QTime _time;
- int _max_value;
- int _timer_duration;
+ private:
+ QTime _time;
+ int _max_value;
+ int _timer_duration;
};
#endif // WORKMONITOR_H