From d0769d1cab01fbe3805086cc5380238fa2fd1643 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Tue, 6 Mar 2018 22:52:40 +0100
Subject: [PATCH] WIP: Mascot parser
---
src/core/peptideevidence.h | 2 +-
src/core/proteinmatch.cpp | 9 ++++++---
src/input/mascot/mascotdatparser.cpp | 15 +++++++--------
src/utils/peptideevidencestore.cpp | 5 +++--
4 files changed, 17 insertions(+), 14 deletions(-)
diff --git a/src/core/peptideevidence.h b/src/core/peptideevidence.h
index 296efc9b..4e727774 100644
--- a/src/core/peptideevidence.h
+++ b/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;
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 43438cbc..1bf326c9 100644
--- a/src/core/proteinmatch.cpp
+++ b/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();
}
diff --git a/src/input/mascot/mascotdatparser.cpp b/src/input/mascot/mascotdatparser.cpp
index d90a480f..cc2be6ef 100644
--- a/src/input/mascot/mascotdatparser.cpp
+++ b/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 {
diff --git a/src/utils/peptideevidencestore.cpp b/src/utils/peptideevidencestore.cpp
index c6ab7295..e2ebd231 100644
--- a/src/utils/peptideevidencestore.cpp
+++ b/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;
}
--
GitLab