WIP: refactoring using PeptideEvidence

src/input/xtandemsaxhandler.cpp

@@ -329,12 +329,12 @@ bool XtandemSaxHandler::endElement_domain() {
     bool is_ok = true;
     _current_peptide_sp = _p_project->getPeptideStore().getInstance(_current_peptide_sp);
 
-    _p_peptide_match->setPeptideXtpSp(_current_peptide_sp);
+    _p_peptide_evidence->setPeptideXtpSp(_current_peptide_sp);
     
+    _current_peptide_match.setPeptideEvidenceSp(_p_peptide_evidence->getIdentificationDataSource()->getPeptideEvidenceStore().getInstance(_p_peptide_evidence));
+    _p_protein_match->addPeptideMatch(_current_peptide_match);
     
-    _p_protein_match->addPeptideMatchSp(_p_peptide_match->getIdentificationDataSource()->getPeptideMatchStore().getInstance(_p_peptide_match));
-    
-    delete _p_peptide_match;
+    delete _p_peptide_evidence;
     return is_ok;
 }
 bool XtandemSaxHandler::endElement_note() {

src/output/masschroqml.cpp

@@ -360,20 +360,20 @@ void MassChroQml::writePeptideList() {
 
 void MassChroQml::writePeptideListInGroup(const GroupingGroup * p_group) {
 
-    const std::vector<std::pair<unsigned int, const PeptideMatch *>> & sg_peptide_match_list =  p_group->getPairSgNumberPeptideMatchList();
+    const std::vector<std::pair<unsigned int, const PeptideEvidence *>> & sg_peptide_evidence_list =  p_group->getPairSgNumberPeptideEvidenceList();
     std::vector<McqPeptide> mcq_peptide_list;
 
-    for (auto & sg_peptide_pair :sg_peptide_match_list) {
+    for (auto & sg_peptide_pair :sg_peptide_evidence_list) {
         unsigned int sg_number = sg_peptide_pair.first;
-        const PeptideMatch * peptide_match = sg_peptide_pair.second;
+        const PeptideEvidence * peptide_evidence = sg_peptide_pair.second;
 
         McqPeptide mcq_peptide;
-        mcq_peptide.id = peptide_match->getGrpPeptideSp().get()->getGroupingId();
-        mcq_peptide.mods << peptide_match->getPeptideXtpSp().get()->getModifString();
+        mcq_peptide.id = peptide_evidence->getGrpPeptideSp().get()->getGroupingId();
+        mcq_peptide.mods << peptide_evidence->getPeptideXtpSp().get()->getModifString();
         mcq_peptide.prot_ids << p_group->getProteinGroupingIdOfSubgroup(sg_number);
-        mcq_peptide.seq = peptide_match->getPeptideXtpSp().get()->getSequence();
-        mcq_peptide.native_peptide = peptide_match->getPeptideXtpSp().get()->getNativePeptideP();
-        McqObserved observed = {peptide_match->getMsRunP(),peptide_match->getScan(),peptide_match->getCharge() };
+        mcq_peptide.seq = peptide_evidence->getPeptideXtpSp().get()->getSequence();
+        mcq_peptide.native_peptide = peptide_evidence->getPeptideXtpSp().get()->getNativePeptideP();
+        McqObserved observed = {peptide_evidence->getMsRunP(),peptide_evidence->getScan(),peptide_evidence->getCharge() };
         mcq_peptide.observed_in.push_back(observed);
         mcq_peptide_list.push_back(mcq_peptide);
 

src/output/ods/peptidepossheet.cpp

@@ -77,9 +77,10 @@ void PeptidePosSheet::writeHeaders(IdentificationGroup * p_ident)  {
 
 }
 
-void PeptidePosSheet::writeBestPeptideMatch(const ProteinMatch * p_protein_match,const PeptideMatch * p_peptide_match) {
+void PeptidePosSheet::writeBestPeptideMatch(const ProteinMatch * p_protein_match,const PeptideMatch & peptide_match) {
 
     _p_writer->writeLine();
+    const PeptideEvidence * p_peptide_evidence = peptide_match.getPeptideEvidence();
 
 
     unsigned int group_number = p_protein_match->getGrpProteinSp().get()->getGroupNumber();
@@ -95,12 +96,12 @@ void PeptidePosSheet::writeBestPeptideMatch(const ProteinMatch * p_protein_match
     _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_peptide_match->getGrpPeptideSp().get()->getGroupingId());
-    _p_writer->writeCell(p_peptide_match->getPeptideXtpSp().get()->getSequence());
-    _p_writer->writeCell(p_peptide_match->getPeptideXtpSp().get()->getModifString());
-    _p_writer->writeCell(p_peptide_match->getStart()+1);
-    _p_writer->writeCell(p_peptide_match->getStart()+p_peptide_match->getPeptideXtpSp().get()->getSequence().size());
-    _p_writer->writeCell(p_peptide_match->getPeptideXtpSp().get()->getMz(1));
+    _p_writer->writeCell(p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
+    _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getSequence());
+    _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
+    _p_writer->writeCell(peptide_match.getStart()+1);
+    _p_writer->writeCell(peptide_match.getStart()+p_peptide_evidence->getPeptideXtpSp().get()->getSequence().size());
+    _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getMz(1));
 
 
 }

src/output/ods/peptidepossheet.h

@@ -44,7 +44,7 @@ public :
 private :
     void writeIdentificationGroup(IdentificationGroup * p_ident);
     void writeHeaders(IdentificationGroup * p_ident);
-    void writeBestPeptideMatch(const ProteinMatch * p_protein_match, const PeptideMatch * p_peptide_match);
+    void writeBestPeptideMatch(const ProteinMatch * p_protein_match, const PeptideMatch & peptide_match);
 
 private :
     OdsExport * _p_ods_export;

src/output/ods/peptidesheet.cpp

@@ -79,10 +79,10 @@ void PeptideSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
     writeHeaders(p_ident);
     for (const std::pair<unsigned int, GroupingGroupSp> & group_pair : p_ident->getGroupStore().getGroupMap()) {
 
-        std::vector<const PeptideMatch *> peptide_match_list = group_pair.second.get()->getPeptideMatchList();
+        std::vector<const PeptideEvidence *> peptide_evidence_list = group_pair.second.get()->getPeptideEvidenceList();
 
-        std::sort(peptide_match_list.begin(), peptide_match_list.end(),
-                  [](const PeptideMatch * a, const PeptideMatch * b)
+        std::sort(peptide_evidence_list.begin(), peptide_evidence_list.end(),
+                  [](const PeptideEvidence * a, const PeptideEvidence * b)
         {
             return a->getGrpPeptideSp().get()->getRank() < b->getGrpPeptideSp().get()->getRank();
         });
@@ -90,13 +90,13 @@ void PeptideSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
         const PeptideMatch * p_best_peptide_match = nullptr;
         _sample_scan_list.clear();
 
-        for (auto & peptide_match:peptide_match_list) {
+        for (auto & peptide_match: peptide_match_list) {
             if (p_best_peptide_match == nullptr) {
-                p_best_peptide_match = peptide_match;
+                p_best_peptide_match = &peptide_match;
             }
             if (p_best_peptide_match->getGrpPeptideSp().get() != peptide_match->getGrpPeptideSp().get()) {
                 //write p_best_peptide_match
-                writeBestPeptideMatch(group_pair.second.get(), p_best_peptide_match);
+                writeBestPeptideMatch(group_pair.second.get(), *p_best_peptide_match);
                 p_best_peptide_match = peptide_match;
             }
             else {

src/utils/peptideevidencestore.h

@@ -32,6 +32,7 @@
 #define PEPTIDEEVIDENCESTORE_H
 
 #include <memory>
+#include <vector>
 #include "../core/automaticfilterparameters.h"
 
 class PeptideEvidence;