preparing new MassChroqR spectral count output

src/CMakeLists.txt

@@ -101,6 +101,8 @@ SET(CPP_FILES
   input/xtandemparamsaxhandler.cpp
   input/xtandemsaxhandler.cpp
   input/xtpxpipsaxhandler.cpp
+  output/mcqr/mcqrscprotein.cpp
+  output/mcqr/mcqrscpeptide.cpp
   output/ods/ptm/ptmislandsheet.cpp
   output/ods/ptm/ptmspectrasheet.cpp
   output/ods/comparbasesheet.cpp

src/gui/workerthread.cpp

@@ -357,8 +357,8 @@ void WorkerThread::doWritingMcqrSpectralCountFile(QString filename, ProjectSp pr
         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();
+        McqrSpectralCount spectra_sheet(project_sp.get());
+        spectra_sheet.write(p_writer, _p_work_monitor);
 
         p_writer->close();
         delete p_writer;

src/output/mcqr/mcqrscpeptide.cpp

+/**
+ * \file /output/mcqr/mcqrscpeptide.cpp
+ * \date 28/3/2018
+ * \author Olivier Langella
+ * \brief write peptide sheet in MassChroqR format
+ */
+
+/*******************************************************************************
+* 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>
+
+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"));
+    }
+
+    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::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()) {
+
+        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();
+        });
+
+        for (auto & protein_match:protein_match_list) {
+            writeOneProtein(group_pair.second.get(), protein_match);
+        }
+
+    }
+    _p_writer->writeLine();
+}
+
+
+void McqRscPeptide::writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match) {
+    try {
+
+        qDebug() << "McqRscPeptide::writeOneProtein begin" ;
+        ValidationState validation_state = ValidationState::grouped;
+
+        pappso::GrpProtein * p_grp_protein = p_protein_match->getGrpProteinSp().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 (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() << "McqRscPeptide::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()));
+    }
+}

src/output/mcqr/mcqrscpeptide.h

+/**
+ * \file /output/mcqr/mcqrscpeptide.h
+ * \date 28/3/2018
+ * \author Olivier Langella
+ * \brief write peptide sheet in MassChroqR format
+ */
+
+/*******************************************************************************
+* 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
+
+#include <odsstream/calcwriterinterface.h>
+#include "../../core/project.h"
+
+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 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 // MCQRSCPEPTIDE_H

src/output/mcqr/mcqrscprotein.cpp

+/**
+ * \file /output/mcqr/mcqrscprotein.cpp
+ * \date 28/3/2018
+ * \author Olivier Langella
+ * \brief write protein sheet in MassChroqR format
+ */
+
+/*******************************************************************************
+* 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;
+}
+
+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);
+    }
+}
+
+
+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) {
+
+    _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::sort(protein_match_list.begin(), protein_match_list.end(),
+                  [](const ProteinMatch * a, const ProteinMatch * b)
+        {
+            return a->getGrpProteinSp().get()->getSubGroupNumber() < b->getGrpProteinSp().get()->getSubGroupNumber();
+        });
+
+        for (auto & protein_match:protein_match_list) {
+            writeOneProtein(group_pair.second.get(), protein_match);
+        }
+
+    }
+    _p_writer->writeLine();
+}
+
+
+void McqRscProtein::writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match) {
+    try {
+
+        qDebug() << "McqRscProtein::writeOneProtein begin" ;
+        ValidationState validation_state = ValidationState::grouped;
+
+        pappso::GrpProtein * p_grp_protein = p_protein_match->getGrpProteinSp().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 (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" ;
+    }
+    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()));
+    }
+}
+

src/output/mcqr/mcqrscprotein.h

+/**
+ * \file /output/mcqr/mcqrscprotein.h
+ * \date 28/3/2018
+ * \author Olivier Langella
+ * \brief write protein sheet in MassChroqR format
+ */
+
+/*******************************************************************************
+* 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
+
+#include <odsstream/calcwriterinterface.h>
+#include "../../core/project.h"
+
+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;
+};
+
+#endif // MCQRSCPROTEIN_H

src/output/mcqrspectralcount.cpp

@@ -29,98 +29,21 @@
 
 #include "mcqrspectralcount.h"
 #include <pappsomspp/pappsoexception.h>
+#include <QSettings>
+#include "mcqr/mcqrscpeptide.h"
+#include "mcqr/mcqrscprotein.h"
 
 
-
-McqrSpectralCount::McqrSpectralCount (CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
-    _p_writer = p_writer;
+McqrSpectralCount::McqrSpectralCount (const Project * p_project): _p_project(p_project) {
 }
 
-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);
-    }
-}
-
-
-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) {
-
-    _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::sort(protein_match_list.begin(), protein_match_list.end(),
-                  [](const ProteinMatch * a, const ProteinMatch * b)
-        {
-            return a->getGrpProteinSp().get()->getSubGroupNumber() < b->getGrpProteinSp().get()->getSubGroupNumber();
-        });
-
-        for (auto & protein_match:protein_match_list) {
-            writeOneProtein(group_pair.second.get(), protein_match);
-        }
-
-    }
-    _p_writer->writeLine();
-}
-
-
-void McqrSpectralCount::writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match) {
-    try {
-
-        qDebug() << "McqrSpectralCount::writeOneProtein begin" ;
-        ValidationState validation_state = ValidationState::validAndChecked;
-
-        pappso::GrpProtein * p_grp_protein = p_protein_match->getGrpProteinSp().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());
+void McqrSpectralCount::write(CalcWriterInterface * p_writer, WorkMonitorInterface * p_monitor) {
+    QSettings settings;
 
-            //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" ;
-    }
-    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()));
-    }
+    p_monitor->message(QObject::tr("writing MassChroqR protein file"));
+    McqRscProtein( p_writer, _p_project).writeSheet();
+    p_monitor->message(QObject::tr("writing MassChroqR peptide file"));
+    McqRscPeptide( p_writer, _p_project).writeSheet();
 }
 

src/output/mcqrspectralcount.h

@@ -36,18 +36,12 @@
 class McqrSpectralCount
 {
 public :
-    McqrSpectralCount (CalcWriterInterface * p_writer, const Project * p_project);
+    McqrSpectralCount (const Project * 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);
+    void write(CalcWriterInterface * p_writer, WorkMonitorInterface * p_monitor);
 
 private :
     const Project * _p_project;
-    CalcWriterInterface * _p_writer;
-    std::vector<MsRunSp> _ms_run_sp_list;
 };
 
 #endif // MCQRSPECTRALCOUNT_H