diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index aa21e177a7dfc1715228ae9061e6985a2c931eff..d1c701709fddb9d1dcf82dce52436972c51def85 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -195,7 +195,8 @@ pappso::MassSpectrumCstSPtr
IdentificationDataSource::getMassSpectrumCstSPtr(unsigned int scan_number) const
{
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << scan_number;
if(_ms_run_sp.get()->getMzFormat() == pappso::MzFormat::MGF)
{
scan_number = scan_number - 1;
@@ -222,8 +223,14 @@ IdentificationDataSource::getMassSpectrumCstSPtr(unsigned int scan_number) const
// qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ <<
// _ms_run_sp.get()->getMsRunReaderSp().get()->getSpectrumListSize();
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ ;
+ std::size_t spectrum_index =
+ msrun_reader_sp.get()->scanNumber2SpectrumIndex(scan_number);
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << spectrum_index;
pappso::MassSpectrumCstSPtr spectrum_sp =
- msrun_reader_sp.get()->massSpectrumCstSPtr(scan_number);
+ msrun_reader_sp.get()->massSpectrumCstSPtr(spectrum_index);
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
return spectrum_sp;
}
diff --git a/src/core/peptideevidence.cpp b/src/core/peptideevidence.cpp
index 8361313666a156d25304832040c3e199aeee26b9..21a52fcd45a32ad9a3e99267d72ca8ef51c868ed 100644
--- a/src/core/peptideevidence.cpp
+++ b/src/core/peptideevidence.cpp
@@ -38,17 +38,17 @@ std::hash<std::string> PeptideEvidence::_hash_fn;
PeptideEvidence::PeptideEvidence(MsRun *msrunid_sp, std::size_t scan_index)
{
_msrunid_sp = msrunid_sp;
- m_scan_index = scan_index;
+ m_scan_number = scan_index;
_hash_sample_scan = PeptideEvidence::_hash_fn(QString("%1 %2")
.arg(msrunid_sp->getXmlId())
- .arg(m_scan_index)
+ .arg(m_scan_number)
.toStdString());
_identification_engine = IdentificationEngine::unknown;
}
PeptideEvidence::PeptideEvidence(const PeptideEvidence &other)
- : PeptideEvidence(other._msrunid_sp, other.m_scan_index)
+ : PeptideEvidence(other._msrunid_sp, other.m_scan_number)
{
_hash_sample_scan = other._hash_sample_scan;
_sp_grp_peptide = other._sp_grp_peptide;
@@ -62,9 +62,7 @@ PeptideEvidence::PeptideEvidence(const PeptideEvidence &other)
_checked = other._checked;
_proxy_valid = other._proxy_valid;
_identification_engine = other._identification_engine;
- m_scan_index = other.m_scan_index;
m_scan_number = other.m_scan_number;
- m_mzml_id = other.m_mzml_id;
}
pappso::pappso_double
diff --git a/src/core/peptideevidence.h b/src/core/peptideevidence.h
index ddbd0368261d8ab1c9987bf1d5e5b24555bf5f10..414fbcf601cd703fe7eb48b35d4a3383e18f73a2 100644
--- a/src/core/peptideevidence.h
+++ b/src/core/peptideevidence.h
@@ -29,8 +29,7 @@
* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
*implementation
******************************************************************************/
-#ifndef PEPTIDEEVIDENCE_H
-#define PEPTIDEEVIDENCE_H
+#pragma once
#include <pappsomspp/types.h>
#include "peptidextp.h"
@@ -118,8 +117,6 @@ class PeptideEvidence
const MsRun *getMsRunP() const;
IdentificationDataSource *getIdentificationDataSource() const;
unsigned int getScanNumber() const;
- std::size_t getSpectrumIndex() const;
- const QString getSpectrumNativeId() const;
pappso::pappso_double getRetentionTime() const;
unsigned int getCharge() const;
const PeptideXtpSp &getPeptideXtpSp() const;
@@ -156,9 +153,7 @@ class PeptideEvidence
private:
static std::hash<std::string> _hash_fn;
MsRun *_msrunid_sp;
- std::size_t m_scan_index = 0;
unsigned int m_scan_number = 0;
- QString m_mzml_id;
size_t _hash_sample_scan;
pappso::GrpPeptideSp _sp_grp_peptide;
PeptideXtpSp _peptide_sp;
@@ -181,4 +176,3 @@ class PeptideEvidence
*/
IdentificationEngine _identification_engine;
};
-#endif // PEPTIDEEVIDENCE_H
diff --git a/src/gui/peptide_detail_view/peptidewindow.cpp b/src/gui/peptide_detail_view/peptidewindow.cpp
index 00a1cbb38c8ea45a976dd899e678fd9ca1b49374..33d21dad54bf3ac853b22a80251891304424c2b2 100644
--- a/src/gui/peptide_detail_view/peptidewindow.cpp
+++ b/src/gui/peptide_detail_view/peptidewindow.cpp
@@ -46,7 +46,7 @@ SpectrumSpLoaderThread::doLoadSpectrumSp(PeptideEvidence *p_peptide_evidence)
try
{
spectrum = p_peptide_evidence->getIdentificationDataSource()
- ->getMassSpectrumCstSPtr(p_peptide_evidence->getScan());
+ ->getMassSpectrumCstSPtr(p_peptide_evidence->getScanNumber());
emit spectrumSpReady(spectrum, QString(""), QString(""));
}
@@ -231,7 +231,7 @@ PeptideWindow::updateDisplay()
_p_peptide_evidence->getCharge())));
ui->z_label->setText(QString("%1").arg(_p_peptide_evidence->getCharge()));
ui->scan_label->setText(
- QString("%1").arg(_p_peptide_evidence->getScan()));
+ QString("%1").arg(_p_peptide_evidence->getScanNumber()));
ui->sample_label->setText(
_p_peptide_evidence->getMsRunP()->getSampleName());
ui->modification_label->setText(
@@ -307,7 +307,7 @@ PeptideWindow::openInPeptideViewer()
arguments << _p_peptide_evidence->getPeptideXtpSp().get()->toString()
<< QString("%1").arg(_p_peptide_evidence->getCharge())
<< _p_peptide_evidence->getMsRunP()->getFilename()
- << QString("%1").arg(_p_peptide_evidence->getScan());
+ << QString("%1").arg(_p_peptide_evidence->getScanNumber());
qDebug() << "PeptideWindow::openInPeptideViewer " << program << " "
<< arguments.join(" ");
@@ -439,7 +439,7 @@ PeptideWindow::doSaveSvg()
QString("%1/%2_%3.svg")
.arg(default_location)
.arg(_p_peptide_evidence->getMsRunP()->getSampleName())
- .arg(_p_peptide_evidence->getScan());
+ .arg(_p_peptide_evidence->getScanNumber());
if(_p_peptide_evidence->getValidationState() == ValidationState::grouped)
{
@@ -449,7 +449,7 @@ PeptideWindow::doSaveSvg()
.arg(
_p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId())
.arg(_p_peptide_evidence->getMsRunP()->getSampleName())
- .arg(_p_peptide_evidence->getScan());
+ .arg(_p_peptide_evidence->getScanNumber());
}
QString filename = QFileDialog::getSaveFileName(
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index b867cf00da3e73ad822be3bca5fd580029ff80b0..ab608f74c3ec036bd3d061fce409b8ddf59a9074 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -259,7 +259,7 @@ PeptideTableModel::data(const QModelIndex &index, int role) const
(quint32)_p_protein_match->getPeptideMatchList()
.at(row)
.getPeptideEvidence()
- ->getScan());
+ ->getScanNumber());
break;
case(std::int8_t)PeptideListColumn::rtmin:
return QVariant(
diff --git a/src/gui/peptide_list_view/peptidetableproxymodel.cpp b/src/gui/peptide_list_view/peptidetableproxymodel.cpp
index 3993cd41216919b5d97d242828271b8d9e6a68f6..9eb0a037a6756e92a786d8b9c882aefcb72884a9 100644
--- a/src/gui/peptide_list_view/peptidetableproxymodel.cpp
+++ b/src/gui/peptide_list_view/peptidetableproxymodel.cpp
@@ -136,7 +136,7 @@ PeptideTableProxyModel::filterAcceptsRow(int source_row,
if(scan_num > 0)
{
scan_ok = false;
- if(peptide_evidence->getScan() == scan_num)
+ if(peptide_evidence->getScanNumber() == scan_num)
{
scan_ok = true;
}
@@ -317,7 +317,8 @@ PeptideTableProxyModel::lessThan(const QModelIndex &left,
QVariant
-PeptideTableProxyModel::headerData(int section, Qt::Orientation orientation,
+PeptideTableProxyModel::headerData(int section,
+ Qt::Orientation orientation,
int role) const
{
int col = mapToSource(index(0, section)).column();
diff --git a/src/gui/protein_list_view/proteintableproxymodel.cpp b/src/gui/protein_list_view/proteintableproxymodel.cpp
index 2db9e8aefd9c6201009b2deed12f2e57c81e2fe2..7ebb39c35d7ecbfcc7ba173c75f88cfc7942d744 100644
--- a/src/gui/protein_list_view/proteintableproxymodel.cpp
+++ b/src/gui/protein_list_view/proteintableproxymodel.cpp
@@ -131,7 +131,7 @@ ProteinTableProxyModel::filterAcceptsRow(int source_row,
if(scan_num > 0)
{
scan_ok = false;
- if(p_peptide_match.getPeptideEvidence()->getScan() ==
+ if(p_peptide_match.getPeptideEvidence()->getScanNumber() ==
scan_num)
{
scan_ok = true;
@@ -378,7 +378,8 @@ ProteinTableProxyModel::data(const QModelIndex &index, int role) const
}
QVariant
-ProteinTableProxyModel::headerData(int section, Qt::Orientation orientation,
+ProteinTableProxyModel::headerData(int section,
+ Qt::Orientation orientation,
int role) const
{
int col = mapToSource(index(0, section)).column();
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
index ca333c6a2eb8909b7351cb914800d21ba344f689..ba001ecf8089b26cf8ec4a01315071967b31f549 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
@@ -243,7 +243,7 @@ PtmPeptideTableModel::data(const QModelIndex &index, int role) const
.get()
->getRepresentativePeptideMatch()
.getPeptideEvidence()
- ->getScan());
+ ->getScanNumber());
break;
case(std::int8_t)PtmPeptideListColumn::rt:
return QVariant((qreal)_ptm_sample_scan_list.at(row)
diff --git a/src/output/ods/spectrasheet.cpp b/src/output/ods/spectrasheet.cpp
index 7508d588acda3f8946b3b188549727e575e4b9aa..eb966e9e7a9fa53da99d4597df6d9858a4eb9e1f 100644
--- a/src/output/ods/spectrasheet.cpp
+++ b/src/output/ods/spectrasheet.cpp
@@ -184,7 +184,7 @@ SpectraSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
unsigned int arank = a->getGrpPeptideSp().get()->getRank();
unsigned int ascan = a->getScanNumber();
unsigned int brank = b->getGrpPeptideSp().get()->getRank();
- unsigned int bscan = b->getScan();
+ unsigned int bscan = b->getScanNumber();
return std::tie(arank, a->getMsRunP()->getSampleName(), ascan) <
std::tie(brank, b->getMsRunP()->getSampleName(), bscan);
});
@@ -200,10 +200,10 @@ SpectraSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
// change spectra :
unsigned int arank =
p_best_peptide_evidence->getGrpPeptideSp().get()->getRank();
- unsigned int ascan = p_best_peptide_evidence->getScan();
+ unsigned int ascan = p_best_peptide_evidence->getScanNumber();
unsigned int brank =
peptide_evidence->getGrpPeptideSp().get()->getRank();
- unsigned int bscan = peptide_evidence->getScan();
+ unsigned int bscan = peptide_evidence->getScanNumber();
if(std::tie(arank,
p_best_peptide_evidence->getMsRunP()->getSampleName(),
diff --git a/src/output/xpip.cpp b/src/output/xpip.cpp
index 8df777c902ed42ff6b8f9d4512ba1f94863ec9ce..51a542c8af1fdea4e8f46993b030cc2460b59d0b 100644
--- a/src/output/xpip.cpp
+++ b/src/output/xpip.cpp
@@ -592,18 +592,8 @@ Xpip::writePeptideEvidence(const PeptideEvidence *p_peptide_evidence)
.arg(exception_std.what()));
}
qDebug() << "Xpip::writePeptideEvidence scan";
- if(p_peptide_evidence->getSpectrumNativeId().isEmpty())
- {
- _output_stream->writeAttribute(
- "scan", QString("%1").arg(p_peptide_evidence->getScanNumber()));
- }
- else
- {
- _output_stream->writeAttribute(
- "idx", QString("%1").arg(p_peptide_evidence->getSpectrumIndex()));
- _output_stream->writeAttribute("mzmlid",
- p_peptide_evidence->getSpectrumNativeId());
- }
+ _output_stream->writeAttribute(
+ "scan", QString("%1").arg(p_peptide_evidence->getScanNumber()));
writeDoubleAttribute("rt", p_peptide_evidence->getRetentionTime());
_output_stream->writeAttribute(
"eng",
diff --git a/src/utils/peptideevidencestore.cpp b/src/utils/peptideevidencestore.cpp
index d87c0be3a3c31a29efa0abe3da08ccc0b3d443c8..8970a7d2e4cf1a4e3d6eb883a71d8cf7aee96ac5 100644
--- a/src/utils/peptideevidencestore.cpp
+++ b/src/utils/peptideevidencestore.cpp
@@ -52,17 +52,13 @@ PeptideEvidenceStore::getInstance(const PeptideEvidence *p_peptide_evidence)
// << p_peptide_evidence->getScan(); qDebug() <<
// "PeptideEvidenceStore::getInstance begin" ;
std::multimap<unsigned int, PeptideEvidenceSp>::iterator it =
- _multimap_scan_evidence.find(p_peptide_evidence->getSpectrumIndex());
- if(p_peptide_evidence->getSpectrumNativeId().isEmpty())
- {
- it = _multimap_scan_evidence.find(p_peptide_evidence->getScanNumber());
- }
+ _multimap_scan_evidence.find(p_peptide_evidence->getScanNumber());
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()) && (it != find_it))
+ (it->first == p_peptide_evidence->getScanNumber()) && (it != find_it))
{
if(it->second.get()->getPeptideXtpSp().get() ==
p_peptide_evidence->getPeptideXtpSp().get())
@@ -84,7 +80,7 @@ PeptideEvidenceStore::getInstance(const PeptideEvidence *p_peptide_evidence)
// insert it
find_it = _multimap_scan_evidence.insert(
std::pair<unsigned int, PeptideEvidenceSp>(
- p_peptide_evidence->getScan(),
+ p_peptide_evidence->getScanNumber(),
p_peptide_evidence->makePeptideEvidenceSp()));
_peptide_evidence_list.push_back(find_it->second);
}
@@ -133,9 +129,7 @@ PeptideEvidenceStore::getPeptideEvidenceList() const
void
PeptideEvidenceStore::getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list,
- const MsRun *p_msrun,
- const PeptideXtp *p_peptide,
- unsigned int charge) const
+ const MsRun *p_msrun, const PeptideXtp *p_peptide, unsigned int charge) const
{
for(const PeptideEvidenceSp &peptide_evidence_sp : _peptide_evidence_list)
{