WIP: Mascot parser

src/core/peptideevidence.h

@@ -134,7 +134,7 @@ public :
 private :
     static std::hash<std::string> _hash_fn;
     MsRun * _msrunid_sp;
-    unsigned int _scan;
+    unsigned int _scan=0;
     size_t _hash_sample_scan;
     pappso::GrpPeptideSp _sp_grp_peptide;
     PeptideXtpSp _peptide_sp;

src/core/proteinmatch.cpp

@@ -53,7 +53,7 @@ ValidationState ProteinMatch::getValidationState() const {
 }
 
 void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
-    //qDebug() <<"ProteinMatch::updateAutomaticFilters begin " ;
+    //qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
     _proxy_valid = false;
     unsigned int number_of_valid_peptides =0;
     bool cross_sample = automatic_filter_parameters.getFilterCrossSamplePeptideNumber();
@@ -75,7 +75,7 @@ void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
             }
         }
     }
-
+    //qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
     // qDebug() <<"ProteinMatch::updateAutomaticFilters begin 2" ;
     if (number_of_valid_peptides == 0) {
 
@@ -90,7 +90,8 @@ void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
             }
         }
     }
-    // qDebug() <<"ProteinMatch::updateAutomaticFilters end " << number_of_valid_peptides ;
+
+    //qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
 }
 
 const ProteinXtpSp & ProteinMatch::getProteinXtpSp() const {
@@ -223,6 +224,7 @@ unsigned int ProteinMatch::countPeptideMatch(ValidationState state) const {
 }
 
 size_t ProteinMatch::countSequenceLi(ValidationState state, const MsRun * p_msrun_id) const {
+    //qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
     std::set<QString> sequence_list;
     for (auto & peptide_match : _peptide_match_list) {
         if (peptide_match.getPeptideEvidence()->getValidationState() >= state) {
@@ -239,6 +241,7 @@ size_t ProteinMatch::countSequenceLi(ValidationState state, const MsRun * p_msru
         }
     }
     //qDebug() <<"ProteinMatch::countValidAndCheckedPeptide end " << sequence_list.size();
+    //qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
     return sequence_list.size();
 }
 

src/input/mascot/mascotdatparser.cpp

@@ -281,7 +281,7 @@ void MascotDatParser::parseQueryLine(const QString & query_line) {
             }
             //charge=2+
             else if (index == "charge") {
-                _current_query.charge = value.toUInt();
+                _current_query.charge = value.mid(0,value.size()-1).toUInt();
             }
         }
         /*
@@ -360,7 +360,7 @@ void MascotDatParser::saveAndClearPeptide() {
 
 
 void MascotDatParser::saveQuery() {
-    qDebug() << "MascotDatParser::saveQuery begin";
+    qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
     if (_current_query.query_index > 0) {
         std::vector< PeptideLine> peptide_list = _query_peptide_results[_current_query.query_index-1];
 
@@ -392,11 +392,11 @@ void MascotDatParser::saveQuery() {
             }
             PeptideXtpSp peptide_sp;
             peptide_sp = PeptideXtp(peptide_str).makePeptideXtpSp();
-            peptide_sp = _p_project->getPeptideStore().getInstance(peptide_sp);
 
+            peptide_evidence.setPeptideXtpSp(_p_project->getPeptideStore().getInstance(peptide_sp));
 
 
-            qDebug() << "MascotDatParser::saveQuery peptide=" << peptide_str << " evalue="  << peptide_evidence.getEvalue() << " ionscore=" << ion_score;
+            qDebug() << __FILE__ << " " << __FUNCTION__<< " peptide=" << peptide_str << " evalue="  << peptide_evidence.getEvalue() << " ionscore=" << ion_score;
 
             if (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) {
                 throw pappso::PappsoException(QObject::tr("ERROR (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) %1").arg(peptide_line.protein_string_list.join(",\"")));
@@ -413,7 +413,7 @@ void MascotDatParser::saveQuery() {
                 }
                 unsigned int start = position_list.at(1).toUInt();
                 unsigned int stop = position_list.at(2).toUInt();
-
+                qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
                 ProteinXtp protein;
                 protein.setAccession(accession);
 
@@ -421,7 +421,7 @@ void MascotDatParser::saveQuery() {
                 if (p_protein_match == nullptr) {
                     throw pappso::PappsoException(QObject::tr("ERROR (p_protein_match == nullptr) %1").arg(str));
                 }
-
+                qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
                 ProteinXtpSp sp_xtp_protein = protein.makeProteinXtpSp();
                 p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
                 p_protein_match->setChecked(true);
@@ -434,8 +434,7 @@ void MascotDatParser::saveQuery() {
             }
         }
     }
-
-    qDebug() << "MascotDatParser::saveQuery end";
+    qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
 }
 
 pappso::pappso_double MascotDatParser::getEvalue(pappso::pappso_double ion_score, unsigned int query_index,  pappso::pappso_double confidence_interval) const {

src/utils/peptideevidencestore.cpp

@@ -42,13 +42,13 @@ std::shared_ptr<PeptideEvidence> & PeptideEvidenceStore::recordInstance(const Pe
 }
 
 std::shared_ptr<PeptideEvidence> & PeptideEvidenceStore::getInstance(const PeptideEvidence * p_peptide_evidence) {
-
+    //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ << " scan=" << p_peptide_evidence->getScan();
     //qDebug() << "PeptideEvidenceStore::getInstance begin" ;
     std::multimap<unsigned int ,PeptideEvidenceSp>::iterator it = _multimap_scan_evidence.find(p_peptide_evidence->getScan());
     std::multimap<unsigned int ,PeptideEvidenceSp>::iterator find_it = _multimap_scan_evidence.end();
 
 
-    while ((find_it == _multimap_scan_evidence.end()) && (it->first == p_peptide_evidence->getScan())) {
+    while ((find_it == _multimap_scan_evidence.end()) && (it->first == p_peptide_evidence->getScan()) && (it != find_it)) {
         if (it->second.get()->getPeptideXtpSp().get() == p_peptide_evidence->getPeptideXtpSp().get()) {
             //it is the same peptide
             find_it = it;
@@ -65,6 +65,7 @@ std::shared_ptr<PeptideEvidence> & PeptideEvidenceStore::getInstance(const Pepti
         _peptide_evidence_list.push_back(find_it->second);
     }
     //qDebug() << "PeptideEvidenceStore::getInstance end " << find_it->second.get()->getScan() << " size=" << _multimap_scan_evidence.size();
+    //qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
     return find_it->second;
 
 }