compar specific spectra OK

src/CMakeLists.txt

@@ -70,6 +70,7 @@ SET(CPP_FILES
   input/xpipsaxhandler.cpp
   input/xtandemsaxhandler.cpp
   output/masschroqml.cpp
+  output/ods/comparspecificspectrasheet.cpp
   output/ods/comparspectrasheet.cpp
   output/ods/infosheet.cpp
   output/ods/odsexport.cpp

src/grouping/groupinggroup.cpp

@@ -91,14 +91,21 @@ unsigned int GroupingGroup::countSubgroupPresence(const PeptideMatch * p_peptide
     return subgroup_list.size();
 }
 
-std::size_t GroupingGroup::countSpecificSampleScan(const ProteinMatch * p_protein_match, ValidationState state) const {
+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);
+        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->getValidationState() >= state) {
-            spectrum_list_in.insert(p_peptide_match->getHashSampleScan());
+            if(p_msrun_id == nullptr) {
+                spectrum_list_in.insert(p_peptide_match->getHashSampleScan());
+            }
+            else {
+                if (p_peptide_match->getMsRunP() == p_msrun_id) {
+                    spectrum_list_in.insert(p_peptide_match->getHashSampleScan());
+                }
+            }
         }
     }
     std::set<size_t> spectrum_list_out;
@@ -119,14 +126,21 @@ std::size_t GroupingGroup::countSpecificSampleScan(const ProteinMatch * p_protei
     return count;
 }
 
-std::size_t GroupingGroup::countSpecificSequenceLi(const ProteinMatch * p_protein_match, ValidationState state) const {
+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->countUniqueSequenceLi(state);
     }
     std::set<QString> sequence_list_in;
     for (auto && p_peptide_match :p_protein_match->getPeptideMatchList()) {
         if (p_peptide_match->getValidationState() >= state) {
-            sequence_list_in.insert(p_peptide_match->getPeptideXtpSp().get()->getSequenceLi());
+            if(p_msrun_id == nullptr) {
+                sequence_list_in.insert(p_peptide_match->getPeptideXtpSp().get()->getSequenceLi());
+            }
+            else {
+                if (p_peptide_match->getMsRunP() == p_msrun_id) {
+                    sequence_list_in.insert(p_peptide_match->getPeptideXtpSp().get()->getSequenceLi());
+                }
+            }
         }
     }
     std::set<QString> sequence_list_out;

src/grouping/groupinggroup.h

@@ -28,6 +28,7 @@
 #include <vector>
 #include <QStringList>
 #include "../utils/types.h"
+#include "../core/msrun.h"
 
 class ProteinMatch;
 class PeptideMatch;
@@ -45,8 +46,8 @@ public:
     unsigned int getGroupNumber() const ;
 
     void add(const ProteinMatch * p_protein_match);
-    std::size_t countSpecificSampleScan(const ProteinMatch * p_protein_match, ValidationState state) const;
-    std::size_t countSpecificSequenceLi(const ProteinMatch * p_protein_match, ValidationState state) const;
+    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;
     

src/output/ods/comparspecificspectrasheet.cpp

+/**
+ * \file output/ods/comparspecificspectrasheet.cpp
+ * \date 1/5/2017
+ * \author Olivier Langella
+ * \brief ODS compar specific spectra sheet
+ */
+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+*     XTPcpp is free software: you can redistribute it and/or modify
+*     it under the terms of the GNU General Public License as published by
+*     the Free Software Foundation, either version 3 of the License, or
+*     (at your option) any later version.
+*
+*     XTPcpp is distributed in the hope that it will be useful,
+*     but WITHOUT ANY WARRANTY; without even the implied warranty of
+*     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+*     GNU General Public License for more details.
+*
+*     You should have received a copy of the GNU General Public 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"
+
+#include <tuple>
+#include <pappsomspp/utils.h>
+#include <QDebug>
+
+
+ComparSpecificSpectraSheet::ComparSpecificSpectraSheet (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("compar specific spectra");
+
+    std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
+    for (IdentificationGroup * p_ident:identification_list) {
+        //writeHeaders(p_ident);
+        writeIdentificationGroup(p_ident);
+    }
+}
+
+
+void ComparSpecificSpectraSheet::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
+    _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();
+    }
+
+    std::sort(_msrun_list.begin(), _msrun_list.end(),
+              [](MsRunSp & a, MsRunSp & b)
+    {
+        return  a.get()->getXmlId() < b.get()->getXmlId();
+    });
+
+
+    _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("Number of proteins");
+
+    for (MsRunSp & msrun_sp: _msrun_list) {
+        _p_writer->writeCell(msrun_sp.get()->getSampleName());
+    }
+
+
+}
+
+void ComparSpecificSpectraSheet::writeProteinMatch(const ProteinMatch * p_protein_match) {
+    qDebug() << "ComparSpecificSpectraSheet::writeProteinMatch begin";
+    _p_writer->writeLine();
+
+
+    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_protein_match->getGroupingGroupSp().get()->countProteinInSubgroup(subgroup_number));
+
+    for (MsRunSp & msrun_sp: _msrun_list) {
+        _p_writer->writeCell((unsigned int) p_protein_match->getGroupingGroupSp().get()->countSpecificSampleScan(p_protein_match, ValidationState::validAndChecked, msrun_sp.get()));
+    }
+
+
+    qDebug() << "ComparSpecificSpectraSheet::writeProteinMatch end";
+
+
+}
+
+void ComparSpecificSpectraSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
+    qDebug() << "ComparSpecificSpectraSheet::writeIdentificationGroup begin";
+    writeHeaders(p_ident);
+
+
+    std::vector<ProteinMatch *> protein_match_list;
+
+    for (ProteinMatch * p_protein_match: p_ident->getProteinMatchList()) {
+        if (p_protein_match->getValidationState() < ValidationState::grouped) continue;
+        if (p_protein_match->getGrpProteinSp().get()->getRank() == 1) {
+            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);
+    });
+
+    for (ProteinMatch * p_protein_match : protein_match_list) {
+        writeProteinMatch(p_protein_match);
+    }
+    _p_writer->writeLine();
+    _p_writer->writeLine();
+    qDebug() << "ComparSpecificSpectraSheet::writeIdentificationGroup end";
+}

src/output/ods/comparspecificspectrasheet.h

+/**
+ * \file output/ods/comparspecificspectrasheet.h
+ * \date 1/5/2017
+ * \author Olivier Langella
+ * \brief ODS compar specific spectra sheet
+ */
+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+*     XTPcpp is free software: you can redistribute it and/or modify
+*     it under the terms of the GNU General Public License as published by
+*     the Free Software Foundation, either version 3 of the License, or
+*     (at your option) any later version.
+*
+*     XTPcpp is distributed in the hope that it will be useful,
+*     but WITHOUT ANY WARRANTY; without even the implied warranty of
+*     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+*     GNU General Public License for more details.
+*
+*     You should have received a copy of the GNU General Public 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 "../../core/project.h"
+#include <odsstream/calcwriterinterface.h>
+#include "../../core/proteinmatch.h"
+#include "odsexport.h"
+
+class ComparSpecificSpectraSheet
+{
+public :
+    ComparSpecificSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
+private :
+    void writeIdentificationGroup(IdentificationGroup * p_ident);
+    void writeHeaders(IdentificationGroup * p_ident);
+    void writeProteinMatch(const ProteinMatch * p_protein_match);
+
+private :
+    OdsExport * _p_ods_export;
+    const Project * _p_project;
+    CalcWriterInterface * _p_writer;
+    std::vector<MsRunSp> _msrun_list;
+};
+
+#endif // COMPARSPECIFICSPECTRASHEET_H

src/output/ods/odsexport.cpp

@@ -34,6 +34,7 @@
 #include "spectrasheet.h"
 #include "peptidepossheet.h"
 #include "comparspectrasheet.h"
+#include "comparspecificspectrasheet.h"
 #include "infosheet.h"
 #include <QSettings>
 
@@ -78,4 +79,7 @@ void OdsExport::write(CalcWriterInterface * p_writer) {
     if (settings.value("export_ods/comparspectra", "true").toBool()) {
         ComparSpectraSheet(this, p_writer, _p_project);
     }
+    if (settings.value("export_ods/comparspecificspectra", "true").toBool()) {
+        ComparSpecificSpectraSheet(this, p_writer, _p_project);
+    }
 }