first sc output : it works, but needs refinement to take into account labelled experiments

src/core/proteinmatch.cpp

@@ -182,13 +182,21 @@ void ProteinMatch::countPeptideMassSample(std::vector<size_t> & count_peptide_ma
         }
     }
 }
-std::vector<PeptideMatch> ProteinMatch::getPeptideMatchList(ValidationState state) const  {
+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) {
-            peptide_match_list.push_back(peptide_match);
+            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);
+                }
+            }
         }
     }
+    //it should automatically use the move semantic :
     return peptide_match_list;
 }
 

src/core/proteinmatch.h

@@ -80,8 +80,11 @@ public:
     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;
+    std::vector<PeptideMatch> getPeptideMatchList(ValidationState state, const MsRun * sp_msrun_id = nullptr) const;
+
     void setChecked(bool arg1);
 
     bool isChecked() const;

src/output/mcqr/mcqrscpeptide.cpp

@@ -57,7 +57,7 @@ void McqRscPeptide::writeHeaders(IdentificationGroup * p_ident)  {
     _p_writer->writeCell("label");
     _p_writer->writeCell("msrun");
     _p_writer->writeCell("msrunfile");
-    _p_writer->writeCell("sequence");
+    //_p_writer->writeCell("sequence");
     _p_writer->writeCell("sc");
     //_p_writer->writeCell(p_protein_match->countSampleScan(state, p_msrun));
 
@@ -66,8 +66,9 @@ void McqRscPeptide::writeHeaders(IdentificationGroup * p_ident)  {
 
 
 void McqRscPeptide::writeIdentificationGroup(IdentificationGroup * p_ident) {
+    ValidationState validation_state = ValidationState::grouped;
 
-    _ms_run_sp_list =  p_ident->getMsRunSpList();
+    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()) {
 
@@ -80,7 +81,17 @@ void McqRscPeptide::writeIdentificationGroup(IdentificationGroup * p_ident) {
         });
 
         for (auto & protein_match:protein_match_list) {
-            writeOneProtein(group_pair.second.get(), protein_match);
+
+            //count number of scan fore each GrpPeptide
+            std::map<const pappso::GrpPeptide *, std::size_t> count_scan_zero;
+            for (const PeptideMatch & peptide_match:protein_match->getPeptideMatchList(validation_state) ) {
+                count_scan_zero.insert ( std::pair<const pappso::GrpPeptide *, std::size_t>(peptide_match.getPeptideEvidence()->getGrpPeptideSp().get(),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);
+            }
         }
 
     }
@@ -88,33 +99,40 @@ void McqRscPeptide::writeIdentificationGroup(IdentificationGroup * p_ident) {
 }
 
 
-void McqRscPeptide::writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match) {
+void McqRscPeptide::writePeptidesInMsrun(const MsRun * p_msrun,const std::vector<PeptideMatch> & peptide_match_in_msrun, const std::map<const pappso::GrpPeptide *, std::size_t> & count_scan_zero) {
     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());
+        qDebug() << "McqRscPeptide::writePeptidesInMsrun begin" ;
+        //count number of scan fore each GrpPeptide
+        std::map<const pappso::GrpPeptide *, std::size_t> count_scan(count_scan_zero);
+
+
+        for (const PeptideMatch & peptide_match:peptide_match_in_msrun) {
+            std::pair<std::map<const pappso::GrpPeptide *, std::size_t>::iterator,bool> ret;
+            ret = count_scan.insert ( std::pair<const pappso::GrpPeptide *, std::size_t>(peptide_match.getPeptideEvidence()->getGrpPeptideSp().get(),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__));
+            }
         }
-        
-        for (const QString & peptide_str :peptide_list) {
+
+        for (const  std::pair<const pappso::GrpPeptide *, std::size_t> & pair_count :count_scan) {
             _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());
+            _p_writer->writeCell(pair_count.first->getGroupingId());
+            _p_writer->writeCell("");
+            _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::writeOneProtein end" ;
+        qDebug() << "McqRscPeptide::writePeptidesInMsrun 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()));
+        throw pappso::PappsoException(QObject::tr("Error writing scan count in msrun %1 :\n%2").arg(p_msrun->getXmlId()).arg(error.qwhat()));
     }
 }

src/output/mcqr/mcqrscpeptide.h

@@ -32,22 +32,22 @@
 
 #include <odsstream/calcwriterinterface.h>
 #include "../../core/project.h"
+#include <pappsomspp/grouping/grppeptide.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);
+    void writePeptidesInMsrun(const MsRun * p_msrun,const std::vector<PeptideMatch> & peptide_match_in_msrun, const std::map<const pappso::GrpPeptide *, std::size_t> & count_scan_zero);
 
 private :
     const Project * _p_project;
     CalcWriterInterface * _p_writer;
-    std::vector<MsRunSp> _ms_run_sp_list;
 };
 
 #endif // MCQRSCPEPTIDE_H