diff --git a/src/core/identification_sources/identificationpepxmlfile.cpp b/src/core/identification_sources/identificationpepxmlfile.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..cbf39e195208f973dfc5963211f97451b0ae2272
--- /dev/null
+++ b/src/core/identification_sources/identificationpepxmlfile.cpp
@@ -0,0 +1,97 @@
+/**
+ * \file /core/identification_sources/identificationpepxmlfile.cpp
+ * \date 16/6/2018
+ * \author Olivier Langella
+ * \brief pep xml identification file handler
+ */
+
+/*******************************************************************************
+* 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/>.
+*
+******************************************************************************/
+
+#include "identificationpepxmlfile.h"
+
+#include <pappsomspp/pappsoexception.h>
+#include "../project.h"
+#include "../../input/mascot/mascotdatparser.h"
+
+IdentificationPepXmlFile::IdentificationPepXmlFile(const QFileInfo & mascot_dat_file) : IdentificationDataSource(mascot_dat_file.absoluteFilePath()), _pep_xml_file(mascot_dat_file)
+{
+ _engine = IdentificationEngine::unknown;
+}
+
+IdentificationPepXmlFile::IdentificationPepXmlFile(const IdentificationPepXmlFile& other) : IdentificationDataSource(other),_pep_xml_file (other._pep_xml_file)
+{
+ _engine = IdentificationEngine::unknown;
+}
+
+IdentificationPepXmlFile::~IdentificationPepXmlFile()
+{
+
+}
+
+bool IdentificationPepXmlFile::operator==(const IdentificationPepXmlFile& other) const
+{
+
+}
+
+pappso::SpectrumSp IdentificationPepXmlFile::getSpectrumSp(unsigned int scan_number) const {
+ pappso::SpectrumSp spectrum_sp = IdentificationDataSource::getSpectrumSp(scan_number);
+ return spectrum_sp;
+}
+
+
+void IdentificationPepXmlFile::parseTo(Project* p_project) {
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+
+
+ MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(QFileInfo(_pep_xml_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 {
+ 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();
+ }
+ }
+
+ identification_group_p->addIdentificationDataSourceP(this);
+ MascotDatParser mascot_parser(p_project, identification_group_p, this);
+
+ QFile qfile(_pep_xml_file.absoluteFilePath());
+ mascot_parser.parse(&qfile);
+
+ qfile.close();
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+}
diff --git a/src/core/identification_sources/identificationpepxmlfile.h b/src/core/identification_sources/identificationpepxmlfile.h
new file mode 100644
index 0000000000000000000000000000000000000000..168c6dc043e6d174edf824eb34db1f94316096ad
--- /dev/null
+++ b/src/core/identification_sources/identificationpepxmlfile.h
@@ -0,0 +1,51 @@
+/**
+ * \file /core/identification_sources/identificationpepxmlfile.h
+ * \date 16/6/2018
+ * \author Olivier Langella
+ * \brief pep xml identification file handler
+ */
+
+/*******************************************************************************
+* 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
+
+#include "identificationdatasource.h"
+#include <QFileInfo>
+
+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;
+};
+
+#endif // IDENTIFICATIONPEPXMLFILE_H
diff --git a/src/core/identification_sources/identificationpwizfile.cpp b/src/core/identification_sources/identificationpwizfile.cpp
index c2f5cc4535c17f51175f4a20f2306a36539e9bbb..6a7d0b83f9df21262e7db6c8a93272b7f3ad45fb 100644
--- a/src/core/identification_sources/identificationpwizfile.cpp
+++ b/src/core/identification_sources/identificationpwizfile.cpp
@@ -5,7 +5,6 @@
* \brief read identification files with proteowizard library
*/
-
/*******************************************************************************
* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
*
@@ -25,77 +24,75 @@
* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+*implementation
******************************************************************************/
+#include "../../input/identificationpwizreader.h"
+#include "../project.h"
#include "identificationpwizfile.h"
#include <pappsomspp/pappsoexception.h>
-#include "../project.h"
-#include "../../input/identificationpwizreader.h"
-
-IdentificationPwizFile::IdentificationPwizFile(const QFileInfo & ident_file) : IdentificationDataSource(ident_file.absoluteFilePath()), _ident_file(ident_file)
-{
- //_engine = IdentificationEngine::XTandem;
- _engine = IdentificationEngine::peptider;
-}
-IdentificationPwizFile::IdentificationPwizFile(const IdentificationPwizFile& other) : IdentificationDataSource(other),_ident_file (other._ident_file)
-{
- _engine = other._engine;
+IdentificationPwizFile::IdentificationPwizFile(const QFileInfo &ident_file)
+ : IdentificationDataSource(ident_file.absoluteFilePath()),
+ _ident_file(ident_file) {
+ //_engine = IdentificationEngine::XTandem;
+ _engine = IdentificationEngine::peptider;
}
-IdentificationPwizFile::~IdentificationPwizFile()
-{
-
+IdentificationPwizFile::IdentificationPwizFile(
+ const IdentificationPwizFile &other)
+ : IdentificationDataSource(other), _ident_file(other._ident_file) {
+ _engine = other._engine;
}
-bool IdentificationPwizFile::operator==(const IdentificationPwizFile& other) const
-{
+IdentificationPwizFile::~IdentificationPwizFile() {}
-}
+bool IdentificationPwizFile::
+operator==(const IdentificationPwizFile &other) const {}
-pappso::SpectrumSp IdentificationPwizFile::getSpectrumSp(unsigned int scan_number) const {
- pappso::SpectrumSp spectrum_sp = IdentificationDataSource::getSpectrumSp(scan_number);
- return spectrum_sp;
+pappso::SpectrumSp
+IdentificationPwizFile::getSpectrumSp(unsigned int scan_number) const {
+ pappso::SpectrumSp spectrum_sp =
+ IdentificationDataSource::getSpectrumSp(scan_number);
+ return spectrum_sp;
}
+void IdentificationPwizFile::parseTo(Project *p_project) {
+ qDebug() << "IdentificationPwizFile::parseTo begin";
-void IdentificationPwizFile::parseTo(Project* p_project) {
- qDebug() << "IdentificationPwizFile::parseTo begin";
+ IdentificationPwizReader pwiz_reader(_ident_file);
- IdentificationPwizReader pwiz_reader(_ident_file);
+ MsRunSp msrun_sp =
+ p_project->getMsRunStore().getInstance(pwiz_reader.getMsrunName());
- MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(pwiz_reader.getMsrunName());
-
- _engine = pwiz_reader.getIdentificationEngine();
- 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];
- }
+ _engine = pwiz_reader.getIdentificationEngine();
+ 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 {
- 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();
- }
+ } else {
+ for (IdentificationGroup *identification_p_flist : identification_list) {
+ if (identification_p_flist->containSample(
+ msrun_sp.get()->getSampleName())) {
+ identification_group_p = identification_p_flist;
+ break;
+ }
}
- identification_group_p->addIdentificationDataSourceP(this);
- pwiz_reader.read(this, p_project, identification_group_p);
-
-
- qDebug() << "IdentificationPwizFile::parseTo end";
- // throw pappso::PappsoException(QObject::tr("Error reading %1 XPIP file :\n %2").arg(_xtandem_file.absoluteFilePath()).arg(parser->errorString()));
-
+ if (identification_group_p == nullptr) {
+ identification_group_p = p_project->newIdentificationGroup();
+ }
+ }
+ identification_group_p->addIdentificationDataSourceP(this);
+ pwiz_reader.read(this, p_project, identification_group_p);
+ qDebug() << "IdentificationPwizFile::parseTo end";
+ // throw pappso::PappsoException(QObject::tr("Error reading %1 XPIP file :\n
+ // %2").arg(_xtandem_file.absoluteFilePath()).arg(parser->errorString()));
}
diff --git a/src/gui/xic_view/xicworkerthread.cpp b/src/gui/xic_view/xicworkerthread.cpp
index ee895b4984260d64d84c8dee2ab8515f91823136..f82119f59266ccd5df1cc7911e6c835bde3ee98f 100644
--- a/src/gui/xic_view/xicworkerthread.cpp
+++ b/src/gui/xic_view/xicworkerthread.cpp
@@ -45,23 +45,19 @@ void XicWorkerThread::doXicLoad(MsRunSp p_msrun, std::vector<pappso::mz> mz_list
if (p_msrun.get()->findMsRunFile()) {
pappso::MsRunId msrun_id = * (p_msrun.get());
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " << msrun_id.getFilename() << " " << msrun_id.getXmlId();
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " << msrun_id.getFilename();
auto it = std::find_if(_extractor_list.begin(), _extractor_list.end(), [msrun_id](const pappso::MsRunXicExtractorSp & extractor_sp) {
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " << extractor_sp.get()->getMsRunId().getXmlId();
return extractor_sp.get()->getMsRunId().getXmlId() == msrun_id.getXmlId();
});
pappso::MsRunXicExtractorSp extractor;
if (it == _extractor_list.end()) {
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " NOT FOUND " << msrun_id.getXmlId() << " " << _extractor_list.size();
pappso::MsRunXicExtractorFactory::getInstance().setTmpDir("/tmp");
extractor = pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorDiskBufferSp(msrun_id);
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " NOT FOUND " << extractor.get()->getMsRunId().getXmlId(); _extractor_list.push_back(extractor);
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " NOT FOUND " << _extractor_list.size();
+ _extractor_list.push_back(extractor);
}
else {
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " FOUND " << msrun_id.getXmlId();
extractor = *it;
}
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ ;