diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index 0f21750d3a4793713edd73a124d765b42693dfe5..9ef578db626871d017589e5cc8cdedad9dbfbbed 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -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
+ ******************************************************************************/
#include "identificationdatasource.h"
#include "identificationxtandemfile.h"
@@ -30,144 +31,226 @@
IdentificationDataSource::IdentificationDataSource(const QString resource_name)
{
- _resource_name = resource_name;
+ _resource_name = resource_name;
}
-IdentificationDataSource::IdentificationDataSource(const IdentificationDataSource& other)
+IdentificationDataSource::IdentificationDataSource(
+ const IdentificationDataSource &other)
{
- _ms_run_sp = other._ms_run_sp;
- _resource_name = other._resource_name;
- _xml_id = other._xml_id;
- _version = other._version;
- _params = other._params;
- _param_stats = other._param_stats;
- _fastafile_list = other._fastafile_list;
+ _ms_run_sp = other._ms_run_sp;
+ _resource_name = other._resource_name;
+ _xml_id = other._xml_id;
+ _version = other._version;
+ _params = other._params;
+ _param_stats = other._param_stats;
+ _fastafile_list = other._fastafile_list;
- //PeptideEvidenceStore _peptide_evidence_store;
+ // PeptideEvidenceStore _peptide_evidence_store;
}
IdentificationDataSource::~IdentificationDataSource()
{
-
}
-const std::map<IdentificationEngineStatistics, QVariant> & IdentificationDataSource::getIdentificationEngineStatisticsMap() const {
- return _param_stats;
+const std::map<IdentificationEngineStatistics, QVariant> &
+IdentificationDataSource::getIdentificationEngineStatisticsMap() const
+{
+ return _param_stats;
}
-const std::map<IdentificationEngineParam, QVariant> & IdentificationDataSource::getIdentificationEngineParamMap() const {
- return _params;
+const std::map<IdentificationEngineParam, QVariant> &
+IdentificationDataSource::getIdentificationEngineParamMap() const
+{
+ return _params;
}
-const PeptideEvidenceStore & IdentificationDataSource::getPeptideEvidenceStore() const {
- return _peptide_evidence_store;
+const PeptideEvidenceStore &
+IdentificationDataSource::getPeptideEvidenceStore() const
+{
+ return _peptide_evidence_store;
}
-PeptideEvidenceStore & IdentificationDataSource::getPeptideEvidenceStore() {
- return _peptide_evidence_store;
+PeptideEvidenceStore &
+IdentificationDataSource::getPeptideEvidenceStore()
+{
+ return _peptide_evidence_store;
}
-void IdentificationDataSource::setXmlId(const QString xmlid) {
- _xml_id = xmlid;
+void
+IdentificationDataSource::setXmlId(const QString xmlid)
+{
+ _xml_id = xmlid;
}
-const QString & IdentificationDataSource::getXmlId() const {
- return _xml_id;
+const QString &
+IdentificationDataSource::getXmlId() const
+{
+ return _xml_id;
}
-bool IdentificationDataSource::operator==(const IdentificationDataSource& other) const
+bool
+IdentificationDataSource::
+operator==(const IdentificationDataSource &other) const
{
-
}
-const QString & IdentificationDataSource::getResourceName () const {
- return _resource_name;
+const QString &
+IdentificationDataSource::getResourceName() const
+{
+ return _resource_name;
}
-const QString IdentificationDataSource::getSampleName () const {
- return _ms_run_sp.get()->getSampleName();
+const QString
+IdentificationDataSource::getSampleName() const
+{
+ return _ms_run_sp.get()->getSampleName();
}
-void IdentificationDataSource::setMsRunSp (MsRunSp ms_run_sp) {
- _ms_run_sp = ms_run_sp;
+void
+IdentificationDataSource::setMsRunSp(MsRunSp ms_run_sp)
+{
+ _ms_run_sp = ms_run_sp;
}
-MsRunSp IdentificationDataSource::getMsRunSp () const {
- return (_ms_run_sp);
+MsRunSp
+IdentificationDataSource::getMsRunSp() const
+{
+ return (_ms_run_sp);
}
-void IdentificationDataSource::setIdentificationEngine(IdentificationEngine engine) {
- _engine = engine;
+void
+IdentificationDataSource::setIdentificationEngine(IdentificationEngine engine)
+{
+ _engine = engine;
}
-IdentificationEngine IdentificationDataSource::getIdentificationEngine() const {
- return _engine;
+IdentificationEngine
+IdentificationDataSource::getIdentificationEngine() const
+{
+ return _engine;
}
-const QString IdentificationDataSource::getIdentificationEngineName() const {
- QString name = "unknown";
- switch (_engine) {
- case IdentificationEngine::XTandem :
+const QString
+IdentificationDataSource::getIdentificationEngineName() const
+{
+ QString name = "unknown";
+ switch(_engine)
+ {
+ case IdentificationEngine::XTandem:
name = "X!Tandem";
break;
- case IdentificationEngine::peptider :
+ case IdentificationEngine::peptider:
name = "peptider";
break;
}
- return name;
+ return name;
}
-const QString& IdentificationDataSource::getIdentificationEngineVersion() const {
- return _version;
+const QString &
+IdentificationDataSource::getIdentificationEngineVersion() const
+{
+ return _version;
}
-void IdentificationDataSource::setIdentificationEngineVersion(const QString& version) {
- _version = version;
+void
+IdentificationDataSource::setIdentificationEngineVersion(const QString &version)
+{
+ _version = version;
}
-void IdentificationDataSource::setIdentificationEngineParam(IdentificationEngineParam param, const QVariant& value) {
- _params.insert(std::pair<IdentificationEngineParam, QVariant>(param, value));
+void
+IdentificationDataSource::setIdentificationEngineParam(
+ IdentificationEngineParam param, const QVariant &value)
+{
+ _params.insert(std::pair<IdentificationEngineParam, QVariant>(param, value));
}
-const QVariant IdentificationDataSource::getIdentificationEngineParam(IdentificationEngineParam param) const {
- try {
- return _params.at(param);
+const QVariant
+IdentificationDataSource::getIdentificationEngineParam(
+ IdentificationEngineParam param) const
+{
+ try
+ {
+ return _params.at(param);
}
- catch (std::out_of_range) {
- return QVariant();
+ catch(std::out_of_range)
+ {
+ return QVariant();
}
}
-void IdentificationDataSource::setIdentificationEngineStatistics(IdentificationEngineStatistics param, const QVariant& value) {
- _param_stats.insert(std::pair<IdentificationEngineStatistics, QVariant>(param, value));
+void
+IdentificationDataSource::setIdentificationEngineStatistics(
+ IdentificationEngineStatistics param, const QVariant &value)
+{
+ _param_stats.insert(
+ std::pair<IdentificationEngineStatistics, QVariant>(param, value));
}
-const QVariant IdentificationDataSource::getIdentificationEngineStatistics(IdentificationEngineStatistics param) const {
- try {
- return _param_stats.at(param);
+const QVariant
+IdentificationDataSource::getIdentificationEngineStatistics(
+ IdentificationEngineStatistics param) const
+{
+ try
+ {
+ return _param_stats.at(param);
}
- catch (std::out_of_range) {
- return QVariant();
+ catch(std::out_of_range)
+ {
+ return QVariant();
}
}
-pappso::SpectrumSp IdentificationDataSource::getSpectrumSp(unsigned int scan_number) const {
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ ;
- if (_ms_run_sp.get()->getMzFormat() == pappso::MzFormat::MGF) {
- scan_number = scan_number-1;
+pappso::SpectrumSp
+IdentificationDataSource::getSpectrumSp(unsigned int scan_number) const
+{
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ if(_ms_run_sp.get()->getMzFormat() == pappso::MzFormat::MGF)
+ {
+ scan_number = scan_number - 1;
}
- if (_ms_run_sp.get()->findMsRunFile() == false) {
- throw pappso::ExceptionNotFound(QObject::tr("mz data \"%1\" file not found").arg(_ms_run_sp.get()->getFilename()));
+ pappso::MsRunReaderSp msrun_reader_sp = _ms_run_sp.get()->getMsRunReaderSp();
+
+ if(msrun_reader_sp == nullptr)
+ {
+ if(_ms_run_sp.get()->findMsRunFile() == false)
+ {
+ throw pappso::ExceptionNotFound(
+ QObject::tr("mz data \"%1\" file not found")
+ .arg(_ms_run_sp.get()->getFilename()));
+ }
}
-
- //qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << _ms_run_sp.get()->getMsRunReaderSp().get()->getSpectrumListSize();
- pappso::SpectrumSp spectrum_sp = _ms_run_sp.get()->getMsRunReaderSp().get()->getSpectrumSp(scan_number);
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ ;
- return spectrum_sp;
+ msrun_reader_sp = _ms_run_sp.get()->getMsRunReaderSp();
+ if(msrun_reader_sp == nullptr)
+ {
+ throw pappso::ExceptionNotFound(
+ QObject::tr("mz data \"%1\" file not found")
+ .arg(_ms_run_sp.get()->getFilename()));
+ }
+
+
+ // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ <<
+ // _ms_run_sp.get()->getMsRunReaderSp().get()->getSpectrumListSize();
+ pappso::SpectrumSp spectrum_sp =
+ msrun_reader_sp.get()->getSpectrumSp(scan_number);
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ return spectrum_sp;
}
-void IdentificationDataSource::addFastaFile (FastaFileSp file) {
- _fastafile_list.push_back(file);
+void
+IdentificationDataSource::addFastaFile(FastaFileSp file)
+{
+ _fastafile_list.push_back(file);
}
-const std::vector<FastaFileSp> & IdentificationDataSource::getFastaFileList() const {
- qDebug()<< "IdentificationDataSource::getFastaFileList begin" << _fastafile_list.size();
- return _fastafile_list;
+const std::vector<FastaFileSp> &
+IdentificationDataSource::getFastaFileList() const
+{
+ qDebug() << "IdentificationDataSource::getFastaFileList begin"
+ << _fastafile_list.size();
+ return _fastafile_list;
}
-const bool IdentificationDataSource::isValid(const PeptideEvidence * p_peptide_evidence, const AutomaticFilterParameters & automatic_filter_parameters) const {
-
- if (p_peptide_evidence->getEvalue() <= automatic_filter_parameters.getFilterPeptideEvalue()) {
- return true;
+const bool
+IdentificationDataSource::isValid(
+ const PeptideEvidence *p_peptide_evidence,
+ const AutomaticFilterParameters &automatic_filter_parameters) const
+{
+
+ if(p_peptide_evidence->getEvalue() <=
+ automatic_filter_parameters.getFilterPeptideEvalue())
+ {
+ return true;
}
- return false;
+ return false;
}
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 666e75c8194577803f8a329e43b5f56e03c9385f..ef5736adff4de3aa6544b5821218f9969e75df30 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.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 "identificationgroup.h"
#include "project.h"
@@ -27,317 +28,460 @@
#include <pappsomspp/pappsoexception.h>
-IdentificationGroup::IdentificationGroup(Project * project)
+IdentificationGroup::IdentificationGroup(Project *project)
{
- _p_project = project;
+ _p_project = project;
}
IdentificationGroup::~IdentificationGroup()
{
- auto it = _protein_match_list.begin();
- while (it != _protein_match_list.end()) {
- delete (*it);
- it++;
+ auto it = _protein_match_list.begin();
+ while(it != _protein_match_list.end())
+ {
+ delete(*it);
+ it++;
}
}
-const PtmGroupingExperiment * IdentificationGroup::getPtmGroupingExperiment() const {
- return _p_grp_ptm_experiment;
+const PtmGroupingExperiment *
+IdentificationGroup::getPtmGroupingExperiment() const
+{
+ return _p_grp_ptm_experiment;
}
-const GroupStore & IdentificationGroup::getGroupStore() const {
- return _group_store;
+const GroupStore &
+IdentificationGroup::getGroupStore() const
+{
+ return _group_store;
}
-pappso::pappso_double IdentificationGroup::computeProtoNsafSum(const MsRun * p_msrun_id ) const {
- pappso::pappso_double nsaf_sum = 0;
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->getValidationState() >= ValidationState::grouped) {
- nsaf_sum += p_protein_match->getProtoNsaf(p_msrun_id);
+pappso::pappso_double
+IdentificationGroup::computeProtoNsafSum(const MsRun *p_msrun_id) const
+{
+ pappso::pappso_double nsaf_sum = 0;
+ for(auto &p_protein_match : _protein_match_list)
+ {
+ if(p_protein_match->getValidationState() >= ValidationState::grouped)
+ {
+ nsaf_sum += p_protein_match->getProtoNsaf(p_msrun_id);
}
}
- return nsaf_sum;
+ return nsaf_sum;
}
-unsigned int IdentificationGroup::countPeptideMass(ValidationState state) const {
+unsigned int
+IdentificationGroup::countPeptideMass(ValidationState state) const
+{
- std::vector<pappso::GrpPeptide *> count_peptide_mass;
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->getValidationState() >= state) {
- p_protein_match->countPeptideMass(count_peptide_mass, state);
+ std::vector<pappso::GrpPeptide *> count_peptide_mass;
+ for(auto &p_protein_match : _protein_match_list)
+ {
+ if(p_protein_match->getValidationState() >= state)
+ {
+ p_protein_match->countPeptideMass(count_peptide_mass, state);
}
}
- std::sort(count_peptide_mass.begin(), count_peptide_mass.end());
- auto last = std::unique(count_peptide_mass.begin(),count_peptide_mass.end());
- return std::distance(count_peptide_mass.begin(),last);
+ std::sort(count_peptide_mass.begin(), count_peptide_mass.end());
+ auto last = std::unique(count_peptide_mass.begin(), count_peptide_mass.end());
+ return std::distance(count_peptide_mass.begin(), last);
}
-unsigned int IdentificationGroup::countPeptideMassSample(ValidationState state) const {
+unsigned int
+IdentificationGroup::countPeptideMassSample(ValidationState state) const
+{
- std::vector<std::size_t> count_peptide_mass_sample;
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->getValidationState() >= state) {
- p_protein_match->countPeptideMassSample(count_peptide_mass_sample, state);
+ std::vector<std::size_t> count_peptide_mass_sample;
+ for(auto &p_protein_match : _protein_match_list)
+ {
+ if(p_protein_match->getValidationState() >= state)
+ {
+ p_protein_match->countPeptideMassSample(count_peptide_mass_sample,
+ state);
}
}
- std::sort(count_peptide_mass_sample.begin(), count_peptide_mass_sample.end());
- auto last = std::unique(count_peptide_mass_sample.begin(),count_peptide_mass_sample.end());
- return std::distance(count_peptide_mass_sample.begin(),last);
+ std::sort(count_peptide_mass_sample.begin(), count_peptide_mass_sample.end());
+ auto last = std::unique(count_peptide_mass_sample.begin(),
+ count_peptide_mass_sample.end());
+ return std::distance(count_peptide_mass_sample.begin(), last);
}
-unsigned int IdentificationGroup::countDecoyPeptideMassSample(ValidationState state) const {
- std::vector<std::size_t> count_peptide_mass_sample;
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
- if (p_protein_match->getValidationState() >= state) {
- p_protein_match->countPeptideMassSample(count_peptide_mass_sample, state);
+unsigned int
+IdentificationGroup::countDecoyPeptideMassSample(ValidationState state) const
+{
+ std::vector<std::size_t> count_peptide_mass_sample;
+ for(auto &p_protein_match : _protein_match_list)
+ {
+ if(p_protein_match->getProteinXtpSp().get()->isDecoy())
+ {
+ if(p_protein_match->getValidationState() >= state)
+ {
+ p_protein_match->countPeptideMassSample(count_peptide_mass_sample,
+ state);
}
}
}
- std::sort(count_peptide_mass_sample.begin(), count_peptide_mass_sample.end());
- auto last = std::unique(count_peptide_mass_sample.begin(),count_peptide_mass_sample.end());
- return std::distance(count_peptide_mass_sample.begin(),last);
+ std::sort(count_peptide_mass_sample.begin(), count_peptide_mass_sample.end());
+ auto last = std::unique(count_peptide_mass_sample.begin(),
+ count_peptide_mass_sample.end());
+ return std::distance(count_peptide_mass_sample.begin(), last);
}
-unsigned int IdentificationGroup::countDecoyProteinMatch(ValidationState state) const {
- return std::count_if (_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)) {
- return true;
+unsigned int
+IdentificationGroup::countDecoyProteinMatch(ValidationState state) const
+{
+ return std::count_if(
+ _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))
+ {
+ return true;
}
- else {
- return false;
+ else
+ {
+ return false;
}
});
}
-unsigned int IdentificationGroup::countPeptideEvidence(ValidationState state) const {
- std::set<const PeptideEvidence *> peptide_evidence_set;
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->getValidationState() >= state) {
- p_protein_match->collectPeptideEvidences(peptide_evidence_set,state);
+unsigned int
+IdentificationGroup::countPeptideEvidence(ValidationState state) const
+{
+ std::set<const PeptideEvidence *> peptide_evidence_set;
+ for(auto &p_protein_match : _protein_match_list)
+ {
+ if(p_protein_match->getValidationState() >= state)
+ {
+ p_protein_match->collectPeptideEvidences(peptide_evidence_set, state);
}
}
- return peptide_evidence_set.size();
+ return peptide_evidence_set.size();
}
-unsigned int IdentificationGroup::countDecoyPeptideEvidence(ValidationState state) const {
- std::set<const PeptideEvidence *> peptide_evidence_set;
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->getValidationState() >= state) {
- if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
- p_protein_match->collectPeptideEvidences(peptide_evidence_set,state);
+unsigned int
+IdentificationGroup::countDecoyPeptideEvidence(ValidationState state) const
+{
+ std::set<const PeptideEvidence *> peptide_evidence_set;
+ for(auto &p_protein_match : _protein_match_list)
+ {
+ if(p_protein_match->getValidationState() >= state)
+ {
+ if(p_protein_match->getProteinXtpSp().get()->isDecoy())
+ {
+ p_protein_match->collectPeptideEvidences(peptide_evidence_set,
+ state);
}
}
}
- return peptide_evidence_set.size();
+ return peptide_evidence_set.size();
}
-unsigned int IdentificationGroup::countPeptideMatch(ValidationState state) const {
- unsigned int i=0;
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->getValidationState() >= state) {
- i+=p_protein_match->countPeptideMatch(state);
+unsigned int
+IdentificationGroup::countPeptideMatch(ValidationState state) const
+{
+ unsigned int i = 0;
+ for(auto &p_protein_match : _protein_match_list)
+ {
+ if(p_protein_match->getValidationState() >= state)
+ {
+ i += p_protein_match->countPeptideMatch(state);
}
}
- return i;
+ return i;
}
-unsigned int IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const {
- unsigned int i=0;
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->getValidationState() >= state) {
- if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
- i+=p_protein_match->countPeptideMatch(state);
+unsigned int
+IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const
+{
+ unsigned int i = 0;
+ for(auto &p_protein_match : _protein_match_list)
+ {
+ if(p_protein_match->getValidationState() >= state)
+ {
+ if(p_protein_match->getProteinXtpSp().get()->isDecoy())
+ {
+ i += p_protein_match->countPeptideMatch(state);
}
}
}
- return i;
+ return i;
}
-unsigned int IdentificationGroup::countProteinMatch(ValidationState state) const {
- return std::count_if (_protein_match_list.begin(), _protein_match_list.end(), [state](const ProteinMatch * p_protein_match) {
- if (p_protein_match->getValidationState() >= state) {
- return true;
- }
- else {
- return false;
- }
- });
-}
-
-void IdentificationGroup::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
- qDebug() << "IdentificationGroup::updateAutomaticFilters begin" ;
- for (IdentificationDataSource * p_identification_source_list:_id_source_list) {
- p_identification_source_list->getPeptideEvidenceStore().updateAutomaticFilters(automatic_filter_parameters);
- }
-
- qDebug() << "IdentificationGroup::updateAutomaticFilters begin p_protein_match" ;
- for (auto & p_protein_match : _protein_match_list) {
- p_protein_match->updateAutomaticFilters(automatic_filter_parameters);
+unsigned int
+IdentificationGroup::countProteinMatch(ValidationState state) const
+{
+ return std::count_if(_protein_match_list.begin(),
+ _protein_match_list.end(),
+ [state](const ProteinMatch *p_protein_match) {
+ if(p_protein_match->getValidationState() >= state)
+ {
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ });
+}
+
+void
+IdentificationGroup::updateAutomaticFilters(
+ const AutomaticFilterParameters &automatic_filter_parameters)
+{
+ qDebug() << "IdentificationGroup::updateAutomaticFilters begin";
+ for(IdentificationDataSource *p_identification_source_list : _id_source_list)
+ {
+ p_identification_source_list->getPeptideEvidenceStore()
+ .updateAutomaticFilters(automatic_filter_parameters);
}
- if (_p_grp_experiment != nullptr) {
+ qDebug()
+ << "IdentificationGroup::updateAutomaticFilters begin p_protein_match";
+ for(auto &p_protein_match : _protein_match_list)
+ {
+ p_protein_match->updateAutomaticFilters(automatic_filter_parameters);
}
- qDebug() << "IdentificationGroup::updateAutomaticFilters end" ;
+ if(_p_grp_experiment != nullptr)
+ {
+ }
+ qDebug() << "IdentificationGroup::updateAutomaticFilters end";
}
-ProteinMatch * IdentificationGroup::getProteinMatchInstance(const QString accession) {
- if (accession.isEmpty()) {
- throw pappso::PappsoException(QObject::tr("Error protein match not found : accession is empty"));
+ProteinMatch *
+IdentificationGroup::getProteinMatchInstance(const QString accession)
+{
+ if(accession.isEmpty())
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Error protein match not found : accession is empty"));
}
- auto it_cache = _cache_accession_protein_match.find(accession);
- if (it_cache == _cache_accession_protein_match.end()) {
- //accession not found in cache
- ProteinMatch * p_protein_match = new ProteinMatch();
- _cache_accession_protein_match.insert(std::pair<QString, ProteinMatch *>(accession, p_protein_match));
- _protein_match_list.push_back(p_protein_match);
- return p_protein_match;
+ auto it_cache = _cache_accession_protein_match.find(accession);
+ if(it_cache == _cache_accession_protein_match.end())
+ {
+ // accession not found in cache
+ ProteinMatch *p_protein_match = new ProteinMatch();
+ _cache_accession_protein_match.insert(
+ std::pair<QString, ProteinMatch *>(accession, p_protein_match));
+ _protein_match_list.push_back(p_protein_match);
+ return p_protein_match;
}
- else {
- return it_cache->second;
+ else
+ {
+ return it_cache->second;
}
- return nullptr;
+ return nullptr;
}
-void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
- _protein_match_list.push_back(protein_match);
+void
+IdentificationGroup::addProteinMatch(ProteinMatch *protein_match)
+{
+ _protein_match_list.push_back(protein_match);
}
-bool IdentificationGroup::contains (const MsRun * p_msrun) const {
- for (const MsRunSp & msrun: _ms_run_list) {
- if (msrun.get() == p_msrun) return true;
+bool
+IdentificationGroup::contains(const MsRun *p_msrun) const
+{
+ for(const MsRunSp &msrun : _ms_run_list)
+ {
+ if(msrun.get() == p_msrun)
+ return true;
}
- return false;
+ return false;
}
-bool IdentificationGroup::containSample (const QString & sample) const {
- for (const MsRunSp & msrun: _ms_run_list) {
- if (msrun.get()->getSampleName() == sample) return true;
+bool
+IdentificationGroup::containSample(const QString &sample) const
+{
+ for(const MsRunSp &msrun : _ms_run_list)
+ {
+ if(msrun.get()->getSampleName() == sample)
+ return true;
}
- return false;
+ return false;
}
-void 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);
- if (it == _id_source_list.end()) {
- _id_source_list.push_back(p_identification_source);
+void
+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);
+ if(it == _id_source_list.end())
+ {
+ _id_source_list.push_back(p_identification_source);
}
}
-void IdentificationGroup::addMsRunSp(MsRunSp ms_run_sp) {
- auto it = std::find (_ms_run_list.begin() ,_ms_run_list.end(),ms_run_sp);
- if (it == _ms_run_list.end()) {
- _ms_run_list.push_back(ms_run_sp);
+void
+IdentificationGroup::addMsRunSp(MsRunSp ms_run_sp)
+{
+ auto it = std::find(_ms_run_list.begin(), _ms_run_list.end(), ms_run_sp);
+ if(it == _ms_run_list.end())
+ {
+ _ms_run_list.push_back(ms_run_sp);
}
}
-const std::vector<MsRunSp> & IdentificationGroup::getMsRunSpList() const {
- return _ms_run_list;
+const std::vector<MsRunSp> &
+IdentificationGroup::getMsRunSpList() const
+{
+ return _ms_run_list;
}
-const std::vector<IdentificationDataSource *> & IdentificationGroup::getIdentificationDataSourceList() const {
- return _id_source_list;
+const std::vector<IdentificationDataSource *> &
+IdentificationGroup::getIdentificationDataSourceList() const
+{
+ return _id_source_list;
}
-const std::vector<ProteinMatch *> & IdentificationGroup::getProteinMatchList() const {
- return _protein_match_list;
+const std::vector<ProteinMatch *> &
+IdentificationGroup::getProteinMatchList() const
+{
+ return _protein_match_list;
}
-std::vector<ProteinMatch *> & IdentificationGroup::getProteinMatchList() {
- return _protein_match_list;
+std::vector<ProteinMatch *> &
+IdentificationGroup::getProteinMatchList()
+{
+ return _protein_match_list;
}
-std::size_t IdentificationGroup::countGroup()const {
- return _group_store.countGroup();
+std::size_t
+IdentificationGroup::countGroup() const
+{
+ return _group_store.countGroup();
}
-std::size_t IdentificationGroup::countSubGroup()const {
- return _group_store.countSubGroup();
+std::size_t
+IdentificationGroup::countSubGroup() const
+{
+ return _group_store.countSubGroup();
}
-void IdentificationGroup::collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const {
- std::set<const PeptideEvidence *> peptide_evidence_list;
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->getValidationState() >= state) {
- if (!p_protein_match->getProteinXtpSp().get()->isDecoy()) {
- //p_protein_match->collectMhDelta(already_counted, delta_list, unit, state);
- p_protein_match->collectPeptideEvidences(peptide_evidence_list, state);
+void
+IdentificationGroup::collectMhDelta(
+ std::vector<pappso::pappso_double> &delta_list,
+ pappso::PrecisionUnit unit,
+ ValidationState state) const
+{
+ std::set<const PeptideEvidence *> peptide_evidence_list;
+ for(auto &p_protein_match : _protein_match_list)
+ {
+ if(p_protein_match->getValidationState() >= state)
+ {
+ if(!p_protein_match->getProteinXtpSp().get()->isDecoy())
+ {
+ // p_protein_match->collectMhDelta(already_counted, delta_list,
+ // unit, state);
+ p_protein_match->collectPeptideEvidences(peptide_evidence_list,
+ state);
}
}
}
- for (const PeptideEvidence * p_peptide_evidence: peptide_evidence_list) {
- if (unit == pappso::PrecisionUnit::ppm) {
- delta_list.push_back(p_peptide_evidence->getPpmDeltaMass());
+ for(const PeptideEvidence *p_peptide_evidence : peptide_evidence_list)
+ {
+ if(unit == pappso::PrecisionUnit::ppm)
+ {
+ delta_list.push_back(p_peptide_evidence->getPpmDeltaMass());
}
- else {
- delta_list.push_back(p_peptide_evidence->getDeltaMass());
+ else
+ {
+ delta_list.push_back(p_peptide_evidence->getDeltaMass());
}
}
-
}
-void IdentificationGroup::startGrouping (const GroupingType & grouping_type, WorkMonitorInterface * p_work_monitor) {
- qDebug() << "IdentificationGroup::startGrouping begin ";
- if (_p_grp_experiment != nullptr) {
- delete _p_grp_experiment;
+void
+IdentificationGroup::startGrouping(const GroupingType &grouping_type,
+ WorkMonitorInterface *p_work_monitor)
+{
+ qDebug() << "IdentificationGroup::startGrouping begin ";
+ if(_p_grp_experiment != nullptr)
+ {
+ delete _p_grp_experiment;
}
- _p_grp_experiment = GroupingExperiment::newInstance(grouping_type, p_work_monitor);
- for (ProteinMatch * p_protein_match : _protein_match_list) {
- p_protein_match->setGroupingExperiment(_p_grp_experiment);
+ _p_grp_experiment =
+ GroupingExperiment::newInstance(grouping_type, p_work_monitor);
+ for(ProteinMatch *p_protein_match : _protein_match_list)
+ {
+ p_protein_match->setGroupingExperiment(_p_grp_experiment);
}
- _p_grp_experiment->startGrouping();
- _group_store.clear();
- for (ProteinMatch * p_protein_match : _protein_match_list) {
- p_protein_match->setGroupInstance(_group_store);
+ _p_grp_experiment->startGrouping();
+ _group_store.clear();
+ for(ProteinMatch *p_protein_match : _protein_match_list)
+ {
+ p_protein_match->setGroupInstance(_group_store);
}
- if (_p_grp_ptm_experiment != nullptr) {
- delete _p_grp_ptm_experiment;
- _p_grp_ptm_experiment = nullptr;
+ if(_p_grp_ptm_experiment != nullptr)
+ {
+ delete _p_grp_ptm_experiment;
+ _p_grp_ptm_experiment = nullptr;
}
- qDebug() << "IdentificationGroup::startGrouping end ";
+ qDebug() << "IdentificationGroup::startGrouping end ";
}
-void IdentificationGroup::startPtmGrouping () {
- qDebug() << "IdentificationGroup::startPtmGrouping begin ";
- if (_p_grp_ptm_experiment != nullptr) {
- delete _p_grp_ptm_experiment;
- _p_grp_ptm_experiment = nullptr;
+void
+IdentificationGroup::startPtmGrouping()
+{
+ qDebug() << "IdentificationGroup::startPtmGrouping begin ";
+ if(_p_grp_ptm_experiment != nullptr)
+ {
+ delete _p_grp_ptm_experiment;
+ _p_grp_ptm_experiment = nullptr;
}
- _p_grp_ptm_experiment = new PtmGroupingExperiment();
- _p_grp_ptm_experiment->setValidationState(ValidationState::grouped);
- for (ProteinMatch * p_protein_match : _protein_match_list) {
- _p_grp_ptm_experiment->addProteinMatch(p_protein_match);
+ _p_grp_ptm_experiment = new PtmGroupingExperiment();
+ _p_grp_ptm_experiment->setValidationState(ValidationState::grouped);
+ for(ProteinMatch *p_protein_match : _protein_match_list)
+ {
+ _p_grp_ptm_experiment->addProteinMatch(p_protein_match);
}
- _p_grp_ptm_experiment->startGrouping();
+ _p_grp_ptm_experiment->startGrouping();
- qDebug() << "IdentificationGroup::startPtmGrouping end ";
+ qDebug() << "IdentificationGroup::startPtmGrouping end ";
}
-const QString IdentificationGroup::getTabName() const {
- return _ms_run_list[0]->getSampleName();
+const QString
+IdentificationGroup::getTabName() const
+{
+ return _ms_run_list[0]->getSampleName();
}
+pappso::pappso_double
+IdentificationGroup::getPeptideMassFdr(ValidationState state) const
+{
+ // ValidationState state = ValidationState::valid;
+ pappso::pappso_double total_peptide = countPeptideMassSample(state);
+ pappso::pappso_double false_peptide = countDecoyPeptideMassSample(state);
-pappso::pappso_double IdentificationGroup::getPeptideMassFdr(ValidationState state) const {
- //ValidationState state = ValidationState::valid;
- pappso::pappso_double total_peptide=countPeptideMassSample(state);
- pappso::pappso_double false_peptide=countDecoyPeptideMassSample(state);
-
- return (false_peptide/total_peptide);
+ return (false_peptide / total_peptide);
}
-pappso::pappso_double IdentificationGroup::getProteinFdr(ValidationState state) const {
- //ValidationState state = ValidationState::valid;
- pappso::pappso_double total_prot=countProteinMatch(state);
- pappso::pappso_double false_prot=countDecoyProteinMatch(state);
+pappso::pappso_double
+IdentificationGroup::getProteinFdr(ValidationState state) const
+{
+ // ValidationState state = ValidationState::valid;
+ pappso::pappso_double total_prot = countProteinMatch(state);
+ pappso::pappso_double false_prot = countDecoyProteinMatch(state);
- return (false_prot/total_prot);
+ return (false_prot / total_prot);
}
-void IdentificationGroup::getSameXicPeptideEvidenceList(std::vector<const PeptideEvidence *> & peptide_evidence_list, const MsRun * p_msrun, const PeptideXtp * p_peptide, unsigned int charge) const {
- if (!contains(p_msrun)) return;
- for (const IdentificationDataSource * p_identification_source:_id_source_list) {
- if (p_msrun == p_identification_source->getMsRunSp().get()) {
- p_identification_source->getPeptideEvidenceStore().getSameXicPeptideEvidenceList(peptide_evidence_list, p_msrun, p_peptide, charge);
+void
+IdentificationGroup::getSameXicPeptideEvidenceList(
+ std::vector<const PeptideEvidence *> &peptide_evidence_list,
+ const MsRun *p_msrun,
+ const PeptideXtp *p_peptide,
+ unsigned int charge) const
+{
+ if(!contains(p_msrun))
+ return;
+ for(const IdentificationDataSource *p_identification_source : _id_source_list)
+ {
+ if(p_msrun == p_identification_source->getMsRunSp().get())
+ {
+ p_identification_source->getPeptideEvidenceStore()
+ .getSameXicPeptideEvidenceList(
+ peptide_evidence_list, p_msrun, p_peptide, charge);
}
}
}
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index 0ec6f36e7f4cf2818e34e0883b65b45588f2f932..d817296e5192eec87a1d8aa7403969b1a6e30e91 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -56,6 +56,21 @@ MsRun::~MsRun()
pappso::MsRunReaderSp &
MsRun::getMsRunReaderSp()
{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
+ << " filename=" << getFilename();
+ if(_msrun_reader_sp == nullptr)
+ {
+ try
+ {
+ _msrun_reader_sp =
+ pappso::MsRunReaderFactory::getInstance().buildPwizMsRunReaderSp(
+ *this);
+ }
+ catch(pappso::PappsoException &error)
+ {
+ _msrun_reader_sp = nullptr;
+ }
+ }
return _msrun_reader_sp;
}
@@ -87,6 +102,8 @@ MsRun::getMsRunStatistics(MsRunStatistics param) const
bool
MsRun::findMsRunFile()
{
+ // first look at the file path :)
+ _msrun_reader_sp = getMsRunReaderSp();
if(_msrun_reader_sp != nullptr)
return true;
QFileInfo file_original(this->getFilename());