diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 1bf326c9ee30a942169854df148eb4b21649e6c0..2ffadd6fd2072ec3f92668196895ca845595b18b 100644
--- a/src/core/proteinmatch.cpp
+++ b/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;
}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index 37ccefb7e4ac1e039c046f18c4a30e8368da2d89..2104a7120e82bc6dfa9864f67c0ab9e672edbbfb 100644
--- a/src/core/proteinmatch.h
+++ b/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;
diff --git a/src/output/mcqr/mcqrscpeptide.cpp b/src/output/mcqr/mcqrscpeptide.cpp
index e3331a745eb4f3e74260df2b9ef692fed05e95db..aac947d7aee3d7d801f8438f6e860b9a691555f3 100644
--- a/src/output/mcqr/mcqrscpeptide.cpp
+++ b/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()));
}
}
diff --git a/src/output/mcqr/mcqrscpeptide.h b/src/output/mcqr/mcqrscpeptide.h
index 68641e21a1c7984c417db5fcce1852c3bade28d6..a2f2a80e91530ed0fa44ee70eb9e67fbc1f2139b 100644
--- a/src/output/mcqr/mcqrscpeptide.h
+++ b/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