From 5052807750346ef0476407100f4b61745bf96045 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Tue, 21 Nov 2017 22:30:15 +0100
Subject: [PATCH] WIP: refactoring using PeptideEvidence
---
src/gui/peptide_detail_view/peptidewindow.cpp | 48 +++++++--------
src/gui/peptide_detail_view/peptidewindow.h | 8 +--
.../peptide_list_view/peptidelistwindow.cpp | 4 +-
src/gui/peptide_list_view/peptidelistwindow.h | 2 +-
.../peptide_list_view/peptidetablemodel.cpp | 44 +++++++-------
src/gui/peptide_list_view/peptidetablemodel.h | 2 +-
.../peptidetableproxymodel.cpp | 24 ++++----
src/gui/project_view/projectwindow.cpp | 6 +-
src/gui/project_view/projectwindow.h | 4 +-
.../proteintableproxymodel.cpp | 4 +-
src/gui/protein_view/proteinwindow.cpp | 8 +--
src/gui/protein_view/proteinwindow.h | 2 +-
.../ptmpeptidelistwindow.cpp | 4 +-
.../ptmpeptidelistwindow.h | 4 +-
.../ptmpeptidetablemodel.cpp | 24 ++++----
.../ptmpeptidetableproxymodel.cpp | 10 ++--
src/input/identificationpwizreader.cpp | 4 +-
src/output/proticdbml.cpp | 58 +++++++++----------
src/output/xpip.cpp | 28 ++++-----
src/output/xpip.h | 2 +-
20 files changed, 145 insertions(+), 145 deletions(-)
diff --git a/src/gui/peptide_detail_view/peptidewindow.cpp b/src/gui/peptide_detail_view/peptidewindow.cpp
index edf50ac39..4f8011af8 100644
--- a/src/gui/peptide_detail_view/peptidewindow.cpp
+++ b/src/gui/peptide_detail_view/peptidewindow.cpp
@@ -36,11 +36,11 @@
#include <QMessageBox>
-void SpectrumSpLoaderThread::doLoadSpectrumSp (PeptideMatch * p_peptide_match) {
+void SpectrumSpLoaderThread::doLoadSpectrumSp (PeptideEvidence * p_peptide_evidence) {
qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp begin";
pappso::SpectrumSp spectrum;
try {
- spectrum = p_peptide_match->getIdentificationDataSource()->getSpectrumSp(p_peptide_match->getScan());
+ spectrum = p_peptide_evidence->getIdentificationDataSource()->getSpectrumSp(p_peptide_evidence->getScan());
emit spectrumSpReady(spectrum, QString(""), QString(""));
}
@@ -132,18 +132,18 @@ void PeptideWindow::doIdentificationGroupGrouped(IdentificationGroup * p_identif
void PeptideWindow::updateDisplay() {
try {
- ui->sequence_label->setText(_p_peptide_match->getPeptideXtpSp().get()->toString());
- ui->mz_label->setText(QString("%1").arg(_p_peptide_match->getPeptideXtpSp().get()->getMz(_p_peptide_match->getCharge())));
- ui->z_label->setText(QString("%1").arg(_p_peptide_match->getCharge()));
- ui->scan_label->setText(QString("%1").arg(_p_peptide_match->getScan()));
- ui->sample_label->setText(_p_peptide_match->getMsRunP()->getSampleName());
- ui->modification_label->setText(_p_peptide_match->getPeptideXtpSp().get()->getModifString());
- ui->hyperscore_label->setText(_p_peptide_match->getParam(PeptideMatchParam::tandem_hyperscore).toString());
- ui->evalue_label->setText(QString::number(_p_peptide_match->getEvalue(), 'g', 4));
- ui->mh_label->setText(QString::number(_p_peptide_match->getPeptideXtpSp().get()->getMz(1), 'f', 4));
- ui->mz_label->setText(QString::number(_p_peptide_match->getPeptideXtpSp().get()->getMz(_p_peptide_match->getCharge()), 'f', 4));
- ui->expmz_label->setText(QString::number(_p_peptide_match->getExperimentalMz(), 'f', 4));
- ui->delta_label->setText(QString::number(_p_peptide_match->getDeltaMass(), 'g', 4));
+ ui->sequence_label->setText(_p_peptide_evidence->getPeptideXtpSp().get()->toString());
+ ui->mz_label->setText(QString("%1").arg(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(_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()));
+ ui->sample_label->setText(_p_peptide_evidence->getMsRunP()->getSampleName());
+ ui->modification_label->setText(_p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
+ ui->hyperscore_label->setText(_p_peptide_evidence->getParam(PeptideMatchParam::tandem_hyperscore).toString());
+ ui->evalue_label->setText(QString::number(_p_peptide_evidence->getEvalue(), 'g', 4));
+ ui->mh_label->setText(QString::number(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(1), 'f', 4));
+ ui->mz_label->setText(QString::number(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(_p_peptide_evidence->getCharge()), 'f', 4));
+ ui->expmz_label->setText(QString::number(_p_peptide_evidence->getExperimentalMz(), 'f', 4));
+ ui->delta_label->setText(QString::number(_p_peptide_evidence->getDeltaMass(), 'g', 4));
}
@@ -179,7 +179,7 @@ void PeptideWindow::chooseDefaultMzDataDir() {
_p_spectrum_overlay->displayLoadingMessage();
ui->file_not_found->setVisible(false);
ui->spectrumWidget->setVisible(true);
- emit loadSpectrumSp(_p_peptide_match);
+ emit loadSpectrumSp(_p_peptide_evidence);
ui->statusbar->showMessage(tr("loading spectrum"));
}
@@ -188,7 +188,7 @@ void PeptideWindow::openInPeptideViewer() {
QSettings settings;
QString program = settings.value("application/peptideviewer", "/usr/bin/pt-peptideviewer").toString();
QStringList arguments;
- arguments << _p_peptide_match->getPeptideXtpSp().get()->toString() << QString("%1").arg(_p_peptide_match->getCharge()) << _p_peptide_match->getMsRunP()->getFilename() << QString("%1").arg(_p_peptide_match->getScan());
+ 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());
qDebug() << "PeptideWindow::openInPeptideViewer " << program << " " << arguments.join(" ");
QProcess *myProcess = new QProcess(this);
@@ -201,7 +201,7 @@ void PeptideWindow::doSpectrumSpReady(SpectrumSp spectrum_sp, QString error, QSt
if ((error.isEmpty()) && (fatal_error.isEmpty())) {
ui->statusbar->showMessage(tr(""));
pappso::QualifiedSpectrum spectrum_copy;
- spectrum_copy.setPrecursorCharge(_p_peptide_match->getCharge());
+ spectrum_copy.setPrecursorCharge(_p_peptide_evidence->getCharge());
spectrum_copy.setOriginalSpectrumSp(spectrum_sp);
ui->spectrumWidget->setQualifiedSpectrum(spectrum_copy);
@@ -241,20 +241,20 @@ void PeptideWindow::doSpectrumSpReady(SpectrumSp spectrum_sp, QString error, QSt
}
-void PeptideWindow::setPeptideMatch(PeptideMatch * p_peptide_match) {
+void PeptideWindow::setPeptideEvidence(PeptideEvidence * p_peptide_evidence) {
qDebug() << "PeptideWindow::setPeptideMatch begin";
- _p_peptide_match = p_peptide_match;
+ _p_peptide_evidence = p_peptide_evidence;
_spectrum_is_ready = false;
qDebug() << "PeptideWindow::setPeptideMatch emit loadSpectrumSp(_p_peptide_match)";
- emit loadSpectrumSp(_p_peptide_match);
+ emit loadSpectrumSp(_p_peptide_evidence);
_p_spectrum_overlay->displayLoadingMessage();
ui->file_not_found->setVisible(false);
ui->spectrumWidget->setVisible(true);
ui->statusbar->showMessage(tr("loading spectrum"));
- pappso::PeptideSp peptide = _p_peptide_match->getPeptideXtpSp();
+ pappso::PeptideSp peptide = _p_peptide_evidence->getPeptideXtpSp();
ui->spectrumWidget->setPrecision(_p_precision);
ui->spectrumWidget->setPeptideSp(peptide);
@@ -305,10 +305,10 @@ void PeptideWindow::doSaveSvg() {
QSettings settings;
QString default_location = settings.value("path/export_svg", "").toString();
- QString proposed_filename = QString("%1/%2_%3.svg").arg(default_location).arg(_p_peptide_match->getMsRunP()->getSampleName()).arg(_p_peptide_match->getScan());
+ QString proposed_filename = QString("%1/%2_%3.svg").arg(default_location).arg(_p_peptide_evidence->getMsRunP()->getSampleName()).arg(_p_peptide_evidence->getScan());
- if (_p_peptide_match->getValidationState() == ValidationState::grouped) {
- proposed_filename = QString("%1/%2_%3_%4.svg").arg(default_location).arg(_p_peptide_match->getGrpPeptideSp().get()->getGroupingId()).arg(_p_peptide_match->getMsRunP()->getSampleName()).arg(_p_peptide_match->getScan());
+ if (_p_peptide_evidence->getValidationState() == ValidationState::grouped) {
+ proposed_filename = QString("%1/%2_%3_%4.svg").arg(default_location).arg(_p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId()).arg(_p_peptide_evidence->getMsRunP()->getSampleName()).arg(_p_peptide_evidence->getScan());
}
QString filename = QFileDialog::getSaveFileName(this, tr("Save SVG file"),
diff --git a/src/gui/peptide_detail_view/peptidewindow.h b/src/gui/peptide_detail_view/peptidewindow.h
index ec52c982c..419cd3b39 100644
--- a/src/gui/peptide_detail_view/peptidewindow.h
+++ b/src/gui/peptide_detail_view/peptidewindow.h
@@ -46,7 +46,7 @@ public:
public slots:
- void doLoadSpectrumSp(PeptideMatch * p_peptide_match);
+ void doLoadSpectrumSp(PeptideEvidence * p_peptide_evidence);
signals:
void spectrumSpReady(pappso::SpectrumSp spectrum_sp, QString error, QString fatal_error);
@@ -65,14 +65,14 @@ public:
explicit PeptideWindow(ProjectWindow * parent = 0);
~PeptideWindow();
- void setPeptideMatch(PeptideMatch * p_peptide_match);
+ void setPeptideEvidence(PeptideEvidence * p_peptide_evidence);
public slots:
void doIdentificationGroupGrouped(IdentificationGroup * p_identification_group);
void setMz(double);
signals:
- void loadSpectrumSp(PeptideMatch * p_peptide_match);
+ void loadSpectrumSp(PeptideEvidence * p_peptide_evidence);
protected slots:
void doSpectrumSpReady(pappso::SpectrumSp spectrum_sp, QString error, QString fatal_error);
@@ -90,7 +90,7 @@ private:
Ui::PeptideDetailView *ui;
ProjectWindow * _p_project_window;
- PeptideMatch * _p_peptide_match = nullptr;
+ PeptideEvidence * _p_peptide_evidence = nullptr;
pappso::PrecisionP _p_precision;
LoadingOverlay * _p_spectrum_overlay;
diff --git a/src/gui/peptide_list_view/peptidelistwindow.cpp b/src/gui/peptide_list_view/peptidelistwindow.cpp
index 8d3630e52..b57498227 100644
--- a/src/gui/peptide_list_view/peptidelistwindow.cpp
+++ b/src/gui/peptide_list_view/peptidelistwindow.cpp
@@ -158,9 +158,9 @@ void PeptideListWindow::doNotGroupedHide(bool hide) {
}
-void PeptideListWindow::askPeptideDetailView(PeptideMatch * p_peptide_match) {
+void PeptideListWindow::askPeptideDetailView(PeptideEvidence * p_peptide_evidence) {
qDebug() << "PeptideListWindow::askPeptideDetailView begin";
- _project_window->doViewPeptideDetail(p_peptide_match);
+ _project_window->doViewPeptideDetail(p_peptide_evidence);
qDebug() << "PeptideListWindow::askPeptideDetailView end";
//updateStatusBar();
}
diff --git a/src/gui/peptide_list_view/peptidelistwindow.h b/src/gui/peptide_list_view/peptidelistwindow.h
index d6d291e8b..b90f64ad5 100644
--- a/src/gui/peptide_list_view/peptidelistwindow.h
+++ b/src/gui/peptide_list_view/peptidelistwindow.h
@@ -63,7 +63,7 @@ signals:
protected :
- void askPeptideDetailView(PeptideMatch * p_peptide_match);
+ void askPeptideDetailView(PeptideEvidence * p_peptide_evidence);
protected slots:
void doNotValidHide(bool hide);
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index 6c091efc1..8dcdeb6d8 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -98,7 +98,7 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
if (col == 0) //add a checkbox to cell(1,0)
{
- if ( _p_protein_match->getPeptideMatchList().at(row)->isChecked()) {
+ if ( _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->isChecked()) {
return Qt::Checked;
}
else {
@@ -107,7 +107,7 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
}
break;
case Qt::BackgroundRole:
- if (_p_protein_match->getPeptideMatchList().at(row)->isValid() == false)
+ if (_p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->isValid() == false)
{
return QVariant(QColor("grey"));
}
@@ -129,30 +129,30 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
break;
case (std::int8_t)PeptideListColumn::peptide_grouping_id:
- p_grp_peptide = _p_protein_match->getPeptideMatchList().at(row)->getGrpPeptideSp().get();
+ p_grp_peptide = _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getGrpPeptideSp().get();
if (p_grp_peptide != nullptr) return p_grp_peptide->getGroupingId();
return QVariant();
break;
case (std::int8_t)PeptideListColumn::sample:
- return _p_protein_match->getPeptideMatchList().at(row)->getIdentificationDataSource()->getSampleName();
+ return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getIdentificationDataSource()->getSampleName();
break;
case (std::int8_t)PeptideListColumn::scan:
- return QVariant ((quint32) _p_protein_match->getPeptideMatchList().at(row)->getScan());
+ return QVariant ((quint32) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getScan());
break;
case (std::int8_t)PeptideListColumn::rt:
- return QVariant ((qreal) _p_protein_match->getPeptideMatchList().at(row)->getRetentionTime());
+ return QVariant ((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getRetentionTime());
break;
case (std::int8_t)PeptideListColumn::charge:
- return QVariant ((quint32) _p_protein_match->getPeptideMatchList().at(row)->getCharge());
+ return QVariant ((quint32) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getCharge());
break;
case (std::int8_t)PeptideListColumn::sequence:
- return _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getSequence();
+ return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getPeptideXtpSp().get()->getSequence();
break;
case (std::int8_t)PeptideListColumn::modifs:
- return _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getModifString();
+ return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getPeptideXtpSp().get()->getModifString();
break;
case (std::int8_t)PeptideListColumn::label:
- p_label = _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getLabel();
+ p_label = _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getPeptideXtpSp().get()->getLabel();
if (p_label != nullptr) {
return QVariant(p_label->getXmlId());
}
@@ -161,32 +161,32 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
}
break;
case (std::int8_t)PeptideListColumn::start:
- return QVariant((quint32) _p_protein_match->getPeptideMatchList().at(row)->getStart()+1);
+ return QVariant((quint32) _p_protein_match->getPeptideMatchList().at(row).getStart()+1);
break;
case (std::int8_t)PeptideListColumn::length:
- return QVariant((quint32) _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->size());
+ return QVariant((quint32) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getPeptideXtpSp().get()->size());
break;
case (std::int8_t)PeptideListColumn::used:
p_grp = _p_protein_match->getGroupingGroupSp().get();
- if (p_grp != nullptr) return QVariant((qreal) p_grp->countSubgroupPresence(_p_protein_match->getPeptideMatchList().at(row)));
+ if (p_grp != nullptr) return QVariant((qreal) p_grp->countSubgroupPresence(_p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()));
return QVariant();
break;
case (std::int8_t)PeptideListColumn::subgroups:
p_grp = _p_protein_match->getGroupingGroupSp().get();
- if (p_grp != nullptr) return QVariant( p_grp->getSubgroupIdList(_p_protein_match->getPeptideMatchList().at(row)).join(" "));
+ if (p_grp != nullptr) return QVariant( p_grp->getSubgroupIdList(_p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()).join(" "));
return QVariant();
break;
case (std::int8_t)PeptideListColumn::Evalue:
- return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row)->getEvalue());
+ return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getEvalue());
break;
case (std::int8_t)PeptideListColumn::theoretical_mhplus:
- return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getMz(1));
+ return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getPeptideXtpSp().get()->getMz(1));
break;
case (std::int8_t)PeptideListColumn::delta_mhplus:
- return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row)->getDeltaMass());
+ return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getDeltaMass());
break;
case (std::int8_t)PeptideListColumn::hyperscore:
- return _p_protein_match->getPeptideMatchList().at(row)->getParam(PeptideMatchParam::tandem_hyperscore);
+ return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getParam(PeptideMatchParam::tandem_hyperscore);
break;
}
}
@@ -203,16 +203,16 @@ void PeptideTableModel::onTableClicked(const QModelIndex &index)
int col = index.column();
if (col == 0) //add a checkbox to cell(1,0)
{
- if ( _p_protein_match->getPeptideMatchList().at(row)->isChecked()) {
- _p_protein_match->getPeptideMatchList().at(row)->setChecked(false);
+ if ( _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->isChecked()) {
+ _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->setChecked(false);
}
else {
- _p_protein_match->getPeptideMatchList().at(row)->setChecked(true);
+ _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->setChecked(true);
}
//emit dataChanged(index, index);
}
else {
- emit peptideMatchClicked(_p_protein_match->getPeptideMatchList().at(row));
+ emit peptideEvidenceClicked(_p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence());
}
}
diff --git a/src/gui/peptide_list_view/peptidetablemodel.h b/src/gui/peptide_list_view/peptidetablemodel.h
index 7efe6a53c..9d9b90cf2 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.h
+++ b/src/gui/peptide_list_view/peptidetablemodel.h
@@ -70,7 +70,7 @@ public:
void setProteinMatch(ProteinMatch * p_protein_match);
ProteinMatch * getProteinMatch();
signals:
- void peptideMatchClicked(PeptideMatch * p_peptide_match);
+ void peptideEvidenceClicked(PeptideEvidence * p_peptide_evidence);
public slots:
void onPeptideDataChanged();
diff --git a/src/gui/peptide_list_view/peptidetableproxymodel.cpp b/src/gui/peptide_list_view/peptidetableproxymodel.cpp
index 981ae5e58..a62ccb55b 100644
--- a/src/gui/peptide_list_view/peptidetableproxymodel.cpp
+++ b/src/gui/peptide_list_view/peptidetableproxymodel.cpp
@@ -50,21 +50,21 @@ bool PeptideTableProxyModel::filterAcceptsRow(int source_row,
const QModelIndex &source_parent) const {
try {
qDebug() << "PeptideTableProxyModel::filterAcceptsRow begin " << source_row;
- PeptideMatch * peptide_match = _peptide_table_model_p->getProteinMatch()->getPeptideMatchList().at(source_row);
+ PeptideEvidence * peptide_evidence = _peptide_table_model_p->getProteinMatch()->getPeptideMatchList().at(source_row).getPeptideEvidence();
qDebug() << "PeptideTableProxyModel::filterAcceptsRow protein_match " << source_row;
if (!_peptide_search_string.isEmpty()) {
if (_search_on == "peptide") {
- if (!peptide_match->getPeptideXtpSp().get()->getSequence().contains(_peptide_search_string)) {
+ if (!peptide_evidence->getPeptideXtpSp().get()->getSequence().contains(_peptide_search_string)) {
return false;
}
}
else if (_search_on == "sample") {
- if (!peptide_match->getMsRunP()->getSampleName().contains(_peptide_search_string)) {
+ if (!peptide_evidence->getMsRunP()->getSampleName().contains(_peptide_search_string)) {
return false;
}
} else if (_search_on == "subgroup") {
- if (peptide_match->getValidationState() != ValidationState::grouped) {
+ if (peptide_evidence->getValidationState() != ValidationState::grouped) {
return false;
}
unsigned int subgroup = _peptide_search_string.toUInt();
@@ -76,20 +76,20 @@ bool PeptideTableProxyModel::filterAcceptsRow(int source_row,
qDebug() << "PeptideTableProxyModel::filterAcceptsRow valid ";
if (_hide_not_valid) {
- if (! peptide_match->isValid()) {
+ if (! peptide_evidence->isValid()) {
return false;
}
}
qDebug() << "PeptideTableProxyModel::filterAcceptsRow checked ";
if (_hide_not_checked) {
- if (! peptide_match->isChecked()) {
+ if (! peptide_evidence->isChecked()) {
return false;
}
}
qDebug() << "PeptideTableProxyModel::filterAcceptsRow grouped ";
if (_hide_not_grouped) {
- if (! peptide_match->isGrouped()) {
+ if (! peptide_evidence->isGrouped()) {
return false;
}
@@ -124,20 +124,20 @@ void PeptideTableProxyModel::onTableClicked(const QModelIndex &index)
QModelIndex source_index(this->mapToSource(index));
int row = source_index.row();
int col = source_index.column();
- PeptideMatch * peptide_match = _peptide_table_model_p->getProteinMatch()->getPeptideMatchList().at(row);
+ PeptideMatch * peptide_match = &_peptide_table_model_p->getProteinMatch()->getPeptideMatchList().at(row);
if (col == 0) //add a checkbox to cell(1,0)
{
- if ( peptide_match->isChecked()) {
- peptide_match->setChecked(false);
+ if ( peptide_match->getPeptideEvidence()->isChecked()) {
+ peptide_match->getPeptideEvidence()->setChecked(false);
}
else {
- peptide_match->setChecked(true);
+ peptide_match->getPeptideEvidence()->setChecked(true);
}
_p_peptide_list_window->edited();
}
else {
- _p_peptide_list_window->askPeptideDetailView(peptide_match);
+ _p_peptide_list_window->askPeptideDetailView(peptide_match->getPeptideEvidence());
}
qDebug() << "PeptideTableProxyModel::onTableClicked end " << index.row();
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 755cfdfc0..ba6779254 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -445,7 +445,7 @@ void ProjectWindow::doViewPeptideList(IdentificationGroup * p_ident_group, Prote
qDebug() << "ProjectWindow::doViewPeptideList end";
}
-void ProjectWindow::doViewPeptideDetail(PeptideMatch * peptide_match) {
+void ProjectWindow::doViewPeptideDetail(PeptideEvidence * peptide_evidence) {
qDebug() << "ProjectWindow::doViewPeptideDetail begin";
if (_peptide_detail_window_collection.size() == 0) {
@@ -457,12 +457,12 @@ void ProjectWindow::doViewPeptideDetail(PeptideMatch * peptide_match) {
}
- _p_current_peptide_detail_window->setPeptideMatch(peptide_match);
+ _p_current_peptide_detail_window->setPeptideEvidence(peptide_evidence);
_p_current_peptide_detail_window->show();
//_p_current_peptide_detail_window->raise();
//_p_current_peptide_detail_window->activateWindow();
- emit peptideMatchSelected(peptide_match);
+ emit peptideEvidenceSelected(peptide_evidence);
qDebug() << "ProjectWindow::doViewPeptideDetail end";
}
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index 773d4a756..713be30e4 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -75,13 +75,13 @@ public slots:
void refreshGroup(IdentificationGroup * p_ident_group);
void refreshPtmGroup(IdentificationGroup * p_ident_group);
void doAcceptedLabelingMethod();
- void doViewPeptideDetail(PeptideMatch * peptide_match);
+ void doViewPeptideDetail(PeptideEvidence * peptide_evidence);
// void setColor(const QColor &color);
// void setShape(Shape shape);
signals:
void identificationGroupGrouped(IdentificationGroup * p_identification_group);
void identificationPtmGroupGrouped(IdentificationGroup * p_identification_group);
- void peptideMatchSelected(PeptideMatch * peptide_match);
+ void peptideEvidenceSelected(PeptideEvidence * peptide_evidence);
void operateGrouping(ProjectSp project_sp);
void operatePtmGroupingOnIdentification(IdentificationGroup * p_identification_group);
void operateGroupingOnIdentification(IdentificationGroup * p_identification_group, GroupingType grouping_type);
diff --git a/src/gui/protein_list_view/proteintableproxymodel.cpp b/src/gui/protein_list_view/proteintableproxymodel.cpp
index d1169018a..e133174cd 100644
--- a/src/gui/protein_list_view/proteintableproxymodel.cpp
+++ b/src/gui/protein_list_view/proteintableproxymodel.cpp
@@ -73,8 +73,8 @@ bool ProteinTableProxyModel::filterAcceptsRow(int source_row,
}
else if (_search_on == "peptide") {
QString peptide_search_string = QString(_protein_search_string).replace("L","I");
- for (PeptideMatch * p_peptide_match: protein_match->getPeptideMatchList()) {
- if (p_peptide_match->getPeptideXtpSp().get()->getSequenceLi().contains(peptide_search_string)) {
+ for (const PeptideMatch & p_peptide_match: protein_match->getPeptideMatchList()) {
+ if (p_peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequenceLi().contains(peptide_search_string)) {
return true;
}
}
diff --git a/src/gui/protein_view/proteinwindow.cpp b/src/gui/protein_view/proteinwindow.cpp
index 21c066466..ef29d4712 100644
--- a/src/gui/protein_view/proteinwindow.cpp
+++ b/src/gui/protein_view/proteinwindow.cpp
@@ -60,7 +60,7 @@ ProteinWindow::ProteinWindow(ProjectWindow *parent):
#if QT_VERSION >= 0x050000
// Qt5 code
connect (_p_project_window, &ProjectWindow::identificationGroupGrouped, this,&ProteinWindow::doIdentificationGroupGrouped);
- connect (_p_project_window, &ProjectWindow::peptideMatchSelected, this,&ProteinWindow::doPeptideMatchSelected);
+ connect (_p_project_window, &ProjectWindow::peptideEvidenceSelected, this,&ProteinWindow::doPeptideEvidenceSelected);
#else
// Qt4 code
connect (_p_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
@@ -79,9 +79,9 @@ void ProteinWindow::doIdentificationGroupGrouped(IdentificationGroup * p_identif
updateDisplay();
}
-void ProteinWindow::doPeptideMatchSelected(PeptideMatch * peptide_match) {
- if (_p_protein_match != nullptr) {
- ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence(peptide_match));
+void ProteinWindow::doPeptideEvidenceSelected(PeptideEvidence * peptide_evidence) {
+ if (peptide_evidence != nullptr) {
+ ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence(peptide_evidence));
}
}
diff --git a/src/gui/protein_view/proteinwindow.h b/src/gui/protein_view/proteinwindow.h
index f5bbe42dd..68e61560a 100644
--- a/src/gui/protein_view/proteinwindow.h
+++ b/src/gui/protein_view/proteinwindow.h
@@ -56,7 +56,7 @@ public:
public slots:
void doIdentificationGroupGrouped(IdentificationGroup * p_identification_group);
- void doPeptideMatchSelected(PeptideMatch * peptide_match);
+ void doPeptideEvidenceSelected(PeptideEvidence * peptide_evidence);
protected slots:
void browseUrl(int i);
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
index 3a459722d..bae3597fd 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
@@ -81,9 +81,9 @@ void PtmPeptideListWindow::setPtmIsland(PtmIsland * p_ptm_island) {
_ptm_table_model_p->setPtmIsland(_p_ptm_island_list_window->getIdentificationGroup()->getPtmGroupingExperiment(), _p_ptm_island);
}
-void PtmPeptideListWindow::askPeptideDetailView(PeptideMatch * p_peptide_match) {
+void PtmPeptideListWindow::askPeptideDetailView(PeptideMatch p_peptide_match) {
qDebug() << "PtmPeptideListWindow::askPeptideDetailView begin";
- emit requestPeptideDetailView(p_peptide_match);
+ emit requestPeptideDetailView(p_peptide_match.getPeptideEvidence());
qDebug() << "PtmPeptideListWindow::askPeptideDetailView end";
//updateStatusBar();
}
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
index 7ef95d5a9..de7c6288d 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
@@ -49,10 +49,10 @@ public:
explicit PtmPeptideListWindow(PtmIslandListWindow * parent = 0);
~PtmPeptideListWindow();
void setPtmIsland(PtmIsland * p_ptm_island);
- void askPeptideDetailView(PeptideMatch * p_peptide_match);
+ void askPeptideDetailView(PeptideMatch p_peptide_match);
signals:
- void requestPeptideDetailView(PeptideMatch * p_peptide_match);
+ void requestPeptideDetailView(PeptideEvidence * p_peptide_evidence);
private:
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
index 8b455b208..a68a0ad09 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
@@ -192,43 +192,43 @@ QVariant PtmPeptideTableModel::data(const QModelIndex &index, int role ) const {
switch (col) {
case (std::int8_t)PtmPeptideListColumn::peptide_ptm_grouping_id:
- return QVariant (_ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch()->getGrpPeptideSp().get()->getGroupingId());
+ return QVariant (_ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getGrpPeptideSp().get()->getGroupingId());
break;
case (std::int8_t)PtmPeptideListColumn::sample:
- return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch()->getIdentificationDataSource()->getSampleName();
+ return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getIdentificationDataSource()->getSampleName();
break;
case (std::int8_t)PtmPeptideListColumn::scan:
- return QVariant ((quint32) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch()->getScan());
+ return QVariant ((quint32) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getScan());
break;
case (std::int8_t)PtmPeptideListColumn::rt:
- return QVariant ((qreal) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch()->getRetentionTime());
+ return QVariant ((qreal) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getRetentionTime());
break;
case (std::int8_t)PtmPeptideListColumn::charge:
- return QVariant ((quint32) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch()->getCharge());
+ return QVariant ((quint32) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getCharge());
break;
case (std::int8_t)PtmPeptideListColumn::sequence:
return QVariant::fromValue( _ptm_sample_scan_list.at(row).get());
break;
case (std::int8_t)PtmPeptideListColumn::modifs:
- return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch()->getPeptideXtpSp().get()->getModifString();
+ return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getPeptideXtpSp().get()->getModifString();
break;
case (std::int8_t)PtmPeptideListColumn::start:
- return QVariant((quint32) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch()->getStart()+1);
+ return QVariant((quint32) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getStart()+1);
break;
case (std::int8_t)PtmPeptideListColumn::length:
- return QVariant((quint32) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch()->getPeptideXtpSp().get()->size());
+ return QVariant((quint32) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getPeptideXtpSp().get()->size());
break;
case (std::int8_t)PtmPeptideListColumn::bestEvalue:
- return QVariant((qreal) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch()->getEvalue());
+ return QVariant((qreal) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getEvalue());
break;
case (std::int8_t)PtmPeptideListColumn::theoretical_mhplus:
- return QVariant((qreal) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch()->getPeptideXtpSp().get()->getMz(1));
+ return QVariant((qreal) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getPeptideXtpSp().get()->getMz(1));
break;
case (std::int8_t)PtmPeptideListColumn::delta_mhplus:
- return QVariant((qreal) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch()->getDeltaMass());
+ return QVariant((qreal) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getDeltaMass());
break;
case (std::int8_t)PtmPeptideListColumn::besthyperscore:
- return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch()->getParam(PeptideMatchParam::tandem_hyperscore);
+ return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getParam(PeptideMatchParam::tandem_hyperscore);
break;
case (std::int8_t)PtmPeptideListColumn::bestposition:
for (unsigned int position :_ptm_sample_scan_list.at(row).get()->getBestPtmPositionList(_p_ptm_grouping_experiment)) {
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
index 2f03ac690..f049f03c3 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
@@ -65,10 +65,10 @@ PtmPeptideMenuQaction::PtmPeptideMenuQaction(PtmPeptideTableProxyModel * parent,
//this->setText(p_peptide_match->getPeptideXtpSp().get()->getSequence());
QStringList position_list;
- for (unsigned int position : p_ptm_grouping_experiment->getPtmPositions(p_peptide_match)) {
+ for (unsigned int position : p_ptm_grouping_experiment->getPtmPositions(*p_peptide_match)) {
position_list << QString("%1").arg(position+1);
}
- this->setText(QString("%1 (%2)").arg(p_peptide_match->getPeptideXtpSp().get()->toString()).arg(position_list.join(" ")));
+ this->setText(QString("%1 (%2)").arg(p_peptide_match->getPeptideEvidence()->getPeptideXtpSp().get()->toString()).arg(position_list.join(" ")));
//evalue_action.setChecked(_display_evalue);
//connect(p_action, SIGNAL(toggled(bool)), this, SLOT(showEvalueColumn(bool)));
@@ -81,7 +81,7 @@ PtmPeptideMenuQaction::PtmPeptideMenuQaction(PtmPeptideTableProxyModel * parent,
#endif
}
void PtmPeptideMenuQaction::doTriggered(bool triggered) {
- _p_ptm_peptide_table_proxy_model->getPtmPeptideListWindowP()->askPeptideDetailView(_p_peptide_match);
+ _p_ptm_peptide_table_proxy_model->getPtmPeptideListWindowP()->askPeptideDetailView(*_p_peptide_match);
}
PtmPeptideMenuQaction::~PtmPeptideMenuQaction()
@@ -113,7 +113,7 @@ bool PtmPeptideTableProxyModel::lessThan(const QModelIndex &left,
if (leftData.canConvert<PtmSampleScan *>()) {
PtmSampleScan * p_ptm_sample_scan_left = qvariant_cast<PtmSampleScan *>(leftData);
PtmSampleScan * p_ptm_sample_scan_right = qvariant_cast<PtmSampleScan *>(rightData);
- return p_ptm_sample_scan_left->getRepresentativePeptideMatch()->getPeptideXtpSp().get()->toAbsoluteString() < p_ptm_sample_scan_right->getRepresentativePeptideMatch()->getPeptideXtpSp().get()->toAbsoluteString();
+ return p_ptm_sample_scan_left->getRepresentativePeptideMatch().getPeptideEvidence()->getPeptideXtpSp().get()->toAbsoluteString() < p_ptm_sample_scan_right->getRepresentativePeptideMatch().getPeptideEvidence()->getPeptideXtpSp().get()->toAbsoluteString();
} else {
return QSortFilterProxyModel::lessThan(left, right);
}
@@ -130,7 +130,7 @@ void PtmPeptideTableProxyModel::showContextMenu(const QModelIndex &index) {
PtmPeptideMenuQaction * p_action;
for (auto p_peptide_match : sp_ptm_sample_scan.get()->getPeptideMatchList()) {
- p_action = new PtmPeptideMenuQaction(this, _p_ptm_table_model->getPtmGroupingExperiment(), sp_ptm_sample_scan.get(), p_peptide_match);
+ p_action = new PtmPeptideMenuQaction(this, _p_ptm_table_model->getPtmGroupingExperiment(), sp_ptm_sample_scan.get(), &p_peptide_match);
_p_context_menu->addAction(p_action);
}
diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index 78d69dacf..11680a241 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -274,9 +274,9 @@ void IdentificationPwizReader::read(
p_peptide_evidence->setPeptideXtpSp(it_pep->second);
- PeptideEvidenceSp peptide_evidence_sp = p_identification_data_source->getPeptideEvidenceStore().getInstance(p_peptide_evidence);
+ PeptideEvidenceSp peptide_evidence_sp_pappso = p_identification_data_source->getPeptideEvidenceStore().getInstance(p_peptide_evidence);
- peptide_match.setPeptideEvidenceSp(peptide_evidence_sp);
+ peptide_match.setPeptideEvidenceSp(peptide_evidence_sp_pappso);
auto it = map_id2protein.find(QString::fromStdString(peptide_evidence_sp.get()->dbSequencePtr.get()->id));
if (it == map_id2protein.end()) {
diff --git a/src/output/proticdbml.cpp b/src/output/proticdbml.cpp
index 7fe9ae170..c70fb5af5 100644
--- a/src/output/proticdbml.cpp
+++ b/src/output/proticdbml.cpp
@@ -461,16 +461,16 @@ void ProticdbMl::writePeptideHit(QString xml_id, ProticPeptideHit & protic_pepti
// param par default
_output_stream->writeStartElement("peptideHit");
- _output_stream->writeAttribute("calc_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideXtpSp().get()->getMass()));
- _output_stream->writeAttribute("exp_mz", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getExperimentalMz()));
- _output_stream->writeAttribute("delta", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getDeltaMass()));
- _output_stream->writeAttribute("exp_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getExperimentalMz()- pappso::MHPLUS));
- _output_stream->writeAttribute("acq_number", QString ("%1").arg(protic_peptide_hit.peptide_match->getScan()));
- _output_stream->writeAttribute("ms_run_id", protic_peptide_hit.peptide_match->getMsRunP()->getXmlId());
+ _output_stream->writeAttribute("calc_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getPeptideXtpSp().get()->getMass()));
+ _output_stream->writeAttribute("exp_mz", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getExperimentalMz()));
+ _output_stream->writeAttribute("delta", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getDeltaMass()));
+ _output_stream->writeAttribute("exp_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getExperimentalMz()- pappso::MHPLUS));
+ _output_stream->writeAttribute("acq_number", QString ("%1").arg(protic_peptide_hit.peptide_match->getPeptideEvidence()->getScan()));
+ _output_stream->writeAttribute("ms_run_id", protic_peptide_hit.peptide_match->getPeptideEvidence()->getMsRunP()->getXmlId());
_output_stream->writeAttribute("id", xml_id);
- _output_stream->writeAttribute("exp_z", QString ("%1").arg(protic_peptide_hit.peptide_match->getCharge()));
+ _output_stream->writeAttribute("exp_z", QString ("%1").arg(protic_peptide_hit.peptide_match->getPeptideEvidence()->getCharge()));
- writeCvParam("PROTICdbO:0000339",protic_peptide_hit.peptide_match->getGrpPeptideSp().get()->getGroupingId(),
+ writeCvParam("PROTICdbO:0000339",protic_peptide_hit.peptide_match->getPeptideEvidence()->getGrpPeptideSp().get()->getGroupingId(),
"peptide mass id");
/*
if (xtpExperimentType.equals("phospho")) {
@@ -480,28 +480,28 @@ void ProticdbMl::writePeptideHit(QString xml_id, ProticPeptideHit & protic_pepti
}
*/
// pep.getMsRun().
- IdentificationEngine identification_engine = protic_peptide_hit.peptide_match->getIdentificationDataSource()->getIdentificationEngine();
+ IdentificationEngine identification_engine = protic_peptide_hit.peptide_match->getPeptideEvidence()->getIdentificationDataSource()->getIdentificationEngine();
if (identification_engine == IdentificationEngine::XTandem) {
// cvparam specifique xtandem
- writeCvParam("PROTICdbO:0000287", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getEvalue()),
+ writeCvParam("PROTICdbO:0000287", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getEvalue()),
"xtandem peptide evalue");
- writeCvParam("PROTICdbO:0000288", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getParam(PeptideMatchParam::tandem_hyperscore).toDouble()),
+ writeCvParam("PROTICdbO:0000288", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getParam(PeptideMatchParam::tandem_hyperscore).toDouble()),
"xtandem peptide hyperscore");
}
- writeCvParam("PROTICdbO:0000289",QString ("%1").arg(protic_peptide_hit.peptide_match->getRetentionTime()),
+ writeCvParam("PROTICdbO:0000289",QString ("%1").arg(protic_peptide_hit.peptide_match->getPeptideEvidence()->getRetentionTime()),
"xtandem peptide retention time");
// sequences avec les modifs
_output_stream->writeStartElement("pepSeq");
_output_stream->writeStartElement("peptide");
- _output_stream->writeCharacters(protic_peptide_hit.peptide_match->getPeptideXtpSp().get()->getSequence());
+ _output_stream->writeCharacters(protic_peptide_hit.peptide_match->getPeptideEvidence()->getPeptideXtpSp().get()->getSequence());
_output_stream->writeEndElement();// peptide
- if (!protic_peptide_hit.peptide_match->getPeptideXtpSp().get()->getModifString().isEmpty()) {
- writePtms(protic_peptide_hit.peptide_match->getPeptideXtpSp().get());
+ if (!protic_peptide_hit.peptide_match->getPeptideEvidence()->getPeptideXtpSp().get()->getModifString().isEmpty()) {
+ writePtms(protic_peptide_hit.peptide_match->getPeptideEvidence()->getPeptideXtpSp().get());
}
_output_stream->writeEndElement();// pepSeq
_output_stream->writeEndElement();// peptideHit
@@ -566,13 +566,13 @@ void ProticdbMl::writeMatchs(IdentificationGroup * p_identification) {
}
const QString & ProticdbMl::getPeptideXmlId(const PeptideMatch* p_peptide_match) const {
- QString peptide_key = getProticPeptideHitKey(p_peptide_match);
+ QString peptide_key = getProticPeptideHitKey(p_peptide_match->getPeptideEvidence());
auto it = _peptidekey_to_id.find(peptide_key);
if (it == _peptidekey_to_id.end()) {
throw pappso::PappsoException(QObject::tr("Error peptide key %1 not found for peptide match %2 sample=%3 scan=%4 start=%5").arg(peptide_key)
- .arg(p_peptide_match->getPeptideXtpSp().get()->toString())
- .arg(p_peptide_match->getMsRunP()->getXmlId())
- .arg(p_peptide_match->getScan())
+ .arg(p_peptide_match->getPeptideEvidence()->getPeptideXtpSp().get()->toString())
+ .arg(p_peptide_match->getPeptideEvidence()->getMsRunP()->getXmlId())
+ .arg(p_peptide_match->getPeptideEvidence()->getScan())
.arg(p_peptide_match->getStart())
);
}
@@ -596,8 +596,8 @@ void ProticdbMl::writeMatch(std::vector<const ProteinMatch *> & protein_match_sg
// samples
QStringList sample_name_list;
- for (const PeptideMatch * p_peptide_match: protein_match_sg_list[0]->getPeptideMatchList(ValidationState::grouped)) {
- sample_name_list << p_peptide_match->getMsRunP()->getSampleName();
+ for (const PeptideMatch & peptide_match: protein_match_sg_list[0]->getPeptideMatchList(ValidationState::grouped)) {
+ sample_name_list << peptide_match.getPeptideEvidence()->getMsRunP()->getSampleName();
}
sample_name_list = sample_name_list.toSet().toList();
for (QString sample_name :sample_name_list) {
@@ -642,9 +642,9 @@ void ProticdbMl::writeMatch(std::vector<const ProteinMatch *> & protein_match_sg
for (const ProteinMatch * p_protein_match: protein_match_sg_list) {
//peptides
- for (const PeptideMatch * p_peptide_match: p_protein_match->getPeptideMatchList(ValidationState::grouped)) {
+ for (const PeptideMatch & peptide_match: p_protein_match->getPeptideMatchList(ValidationState::grouped)) {
// peptidesHitRef
- QString peptide_xml_id = getPeptideXmlId(p_peptide_match);
+ QString peptide_xml_id = getPeptideXmlId(&peptide_match);
_output_stream->writeStartElement("peptideHitRef");
_output_stream->writeAttribute("peptide_hit_id", peptide_xml_id);
@@ -652,16 +652,16 @@ void ProticdbMl::writeMatch(std::vector<const ProteinMatch *> & protein_match_sg
_output_stream->writeStartElement("fromSeq");
_output_stream->writeAttribute(
"seq_id", getProteinXmlId(p_protein_match));
- _output_stream->writeAttribute("start", QString("%1").arg(p_peptide_match->getStart()+1));
- _output_stream->writeAttribute("stop", QString("%1").arg(p_peptide_match->getStop()+1));
+ _output_stream->writeAttribute("start", QString("%1").arg(peptide_match.getStart()+1));
+ _output_stream->writeAttribute("stop", QString("%1").arg(peptide_match.getStop()+1));
QString residue_before_nter = "-";
- if (p_peptide_match->getStart() > 0) {
- residue_before_nter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(p_peptide_match->getStart()-1,1);
+ if (peptide_match.getStart() > 0) {
+ residue_before_nter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(peptide_match.getStart()-1,1);
}
_output_stream->writeAttribute("residue_before_nter", residue_before_nter);
QString residue_after_cter = "-";
- if (p_peptide_match->getStop() < (p_protein_match->getProteinXtpSp().get()->getSequence().size()-1)) {
- residue_after_cter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(p_peptide_match->getStop(),1);
+ if (peptide_match.getStop() < (p_protein_match->getProteinXtpSp().get()->getSequence().size()-1)) {
+ residue_after_cter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(peptide_match.getStop(),1);
}
_output_stream->writeAttribute("residue_after_cter", residue_after_cter);
diff --git a/src/output/xpip.cpp b/src/output/xpip.cpp
index ab80b93f8..1d1edf391 100644
--- a/src/output/xpip.cpp
+++ b/src/output/xpip.cpp
@@ -396,8 +396,8 @@ void Xpip::writeIdentificationGroup(const IdentificationGroup * p_identification
else {
_output_stream->writeAttribute("checked","false");
}
- for (const PeptideMatch * p_peptide_match : p_protein_match->getPeptideMatchList()) {
- writePeptideMatch(p_peptide_match);
+ for (const PeptideMatch & peptide_match : p_protein_match->getPeptideMatchList()) {
+ writePeptideMatch(peptide_match);
}
_output_stream->writeEndElement();// protein_match
}
@@ -406,27 +406,27 @@ void Xpip::writeIdentificationGroup(const IdentificationGroup * p_identification
qDebug() << "Xpip::writeIdentificationGroup end";
}
-void Xpip::writePeptideMatch(const PeptideMatch * p_peptide_match) {
+void Xpip::writePeptideMatch(const PeptideMatch & peptide_match) {
qDebug() << "Xpip::writePeptideMatch begin";
_output_stream->writeStartElement("peptide_match");
- _output_stream->writeAttribute("source_id",p_peptide_match->getIdentificationDataSource()->getXmlId());
+ _output_stream->writeAttribute("source_id",peptide_match.getPeptideEvidence()->getIdentificationDataSource()->getXmlId());
//_output_stream->writeAttribute("ms_id",p_peptide_match->getMsRunP()->getXmlId());
- _output_stream->writeAttribute("peptide_id",_map_peptides.at( p_peptide_match->getPeptideXtpSp().get()));
- _output_stream->writeAttribute("scan",QString("%1").arg(p_peptide_match->getScan()));
- writeDoubleAttribute("rt",p_peptide_match->getRetentionTime());
- writeDoubleAttribute("evalue",p_peptide_match->getEvalue());
- writeDoubleAttribute("exp_mass",p_peptide_match->getExperimentalMass());
- _output_stream->writeAttribute("start",QString("%1").arg(p_peptide_match->getStart()));
- _output_stream->writeAttribute("charge",QString("%1").arg(p_peptide_match->getCharge()));
-
- if (p_peptide_match->isChecked()) {
+ _output_stream->writeAttribute("peptide_id",_map_peptides.at( peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()));
+ _output_stream->writeAttribute("scan",QString("%1").arg(peptide_match.getPeptideEvidence()->getScan()));
+ writeDoubleAttribute("rt",peptide_match.getPeptideEvidence()->getRetentionTime());
+ writeDoubleAttribute("evalue",peptide_match.getPeptideEvidence()->getEvalue());
+ writeDoubleAttribute("exp_mass",peptide_match.getPeptideEvidence()->getExperimentalMass());
+ _output_stream->writeAttribute("start",QString("%1").arg(peptide_match.getStart()));
+ _output_stream->writeAttribute("charge",QString("%1").arg(peptide_match.getPeptideEvidence()->getCharge()));
+
+ if (peptide_match.getPeptideEvidence()->isChecked()) {
_output_stream->writeAttribute("checked","true");
}
else {
_output_stream->writeAttribute("checked","false");
}
- const std::map<PeptideMatchParam, QVariant> & params = p_peptide_match->getParamList();
+ const std::map<PeptideMatchParam, QVariant> & params = peptide_match.getPeptideEvidence()->getParamList();
//if (params.size() > 0) {
// _output_stream->writeStartElement("stats");
diff --git a/src/output/xpip.h b/src/output/xpip.h
index 6e0a37287..169719c9b 100644
--- a/src/output/xpip.h
+++ b/src/output/xpip.h
@@ -61,7 +61,7 @@ private :
void writeIdentificationGroup(const IdentificationGroup * p_identification_group);
void dedupPeptideMatch(const IdentificationGroup * p_identification_group);
void writeUniquePeptideMatch(const IdentificationGroup * p_identification_group);
- void writePeptideMatch(const PeptideMatch * p_peptide_match);
+ void writePeptideMatch(const PeptideMatch & peptide_match);
QString getPeptideId(std::size_t crc_peptide) const;
--
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