From 750411176ba98d12c6457b37223304e15b44c752 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Wed, 24 Jan 2018 22:31:52 +0100
Subject: [PATCH] ptm island peptide evidence viewer bug fixed
---
src/core/peptidematch.cpp | 1 -
src/grouping/ptm/ptmsamplescan.cpp | 2 +-
src/grouping/ptm/ptmsamplescan.h | 2 +-
src/gui/peptide_detail_view/peptidewindow.cpp | 17 +++++++++++------
src/gui/project_view/projectwindow.cpp | 2 +-
.../ptmpeptidelistwindow.cpp | 8 +++++---
.../ptmpeptidelistwindow.h | 2 +-
.../ptmpeptidetablemodel.cpp | 2 +-
.../ptmpeptidetableproxymodel.cpp | 13 ++++++++-----
.../ptmpeptidetableproxymodel.h | 4 ++--
10 files changed, 31 insertions(+), 22 deletions(-)
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index 5498b269e..911e1b711 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -31,7 +31,6 @@ PeptideMatch::PeptideMatch() {
PeptideMatch::PeptideMatch(const PeptideMatch & other) {
_start=other._start;
_p_peptide_evidence = other._p_peptide_evidence;
-
}
bool PeptideMatch::operator==(const PeptideMatch & other) const {
if ((_p_peptide_evidence == other._p_peptide_evidence) && (_start == other._start)) {
diff --git a/src/grouping/ptm/ptmsamplescan.cpp b/src/grouping/ptm/ptmsamplescan.cpp
index 71a1abb57..328bbe4c5 100644
--- a/src/grouping/ptm/ptmsamplescan.cpp
+++ b/src/grouping/ptm/ptmsamplescan.cpp
@@ -136,6 +136,6 @@ const QString PtmSampleScan::getHtmlSequence(const PtmGroupingExperiment * p_ptm
return sequence_html;
}
-const std::vector<PeptideMatch> & PtmSampleScan::getPeptideMatchList() const {
+std::vector<PeptideMatch> & PtmSampleScan::getPeptideMatchList() {
return _peptide_match_list;
}
diff --git a/src/grouping/ptm/ptmsamplescan.h b/src/grouping/ptm/ptmsamplescan.h
index 3ff57ed59..78d07c167 100644
--- a/src/grouping/ptm/ptmsamplescan.h
+++ b/src/grouping/ptm/ptmsamplescan.h
@@ -53,7 +53,7 @@ public:
std::vector<unsigned int> getBestPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
std::vector<unsigned int> getObservedPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
const QString getHtmlSequence(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
- const std::vector<PeptideMatch> & getPeptideMatchList() const;
+ std::vector<PeptideMatch> & getPeptideMatchList();
private:
std::vector<PeptideMatch> _peptide_match_list;
diff --git a/src/gui/peptide_detail_view/peptidewindow.cpp b/src/gui/peptide_detail_view/peptidewindow.cpp
index 6a7aae175..54680bf48 100644
--- a/src/gui/peptide_detail_view/peptidewindow.cpp
+++ b/src/gui/peptide_detail_view/peptidewindow.cpp
@@ -84,7 +84,7 @@ PeptideWindow::PeptideWindow(ProjectWindow *parent):
ui->file_not_found->setVisible(false);
-
+
_mz_label = new QLabel("");
ui->statusbar->addWidget(_mz_label);
QWidget * p_spacer = new QWidget();
@@ -130,8 +130,8 @@ void PeptideWindow::setIon(pappso::PeakIonIsotopeMatch ion) {
QString plusstr = "+";
plusstr = plusstr.repeated(ion.getCharge());
_ion_label->setText(QString("%1%2%3 (+%4) - th. isotope ratio %5%").arg(ion.getPeptideFragmentIonSp().get()->getPeptideIonName()).arg(ion.getPeptideFragmentIonSp().get()->size()).arg(plusstr).arg(ion.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber()).arg((int)(ion.getPeptideNaturalIsotopeAverageSp().get()->getIntensityRatio()*100)));
-
-
+
+
}
void PeptideWindow::setPeak(const pappso::Peak * p_peak_match) {
@@ -206,7 +206,7 @@ void PeptideWindow::chooseDefaultMzDataDir() {
qDebug() << "PeptideWindow::chooseDefaultMzDataDir begin";
ui->file_not_found->setVisible(false);
- ui->xic_button->setEnabled(true);
+ ui->xic_button->setEnabled(true);
ui->spectrum_widget->setVisible(true);
emit loadSpectrumSp(_p_peptide_evidence);
ui->statusbar->showMessage(tr("loading spectrum"));
@@ -280,23 +280,28 @@ void PeptideWindow::doSpectrumSpReady(pappso::SpectrumSp spectrum_sp, QString er
}
void PeptideWindow::setPeptideEvidence(PeptideEvidence * p_peptide_evidence) {
- qDebug() << "PeptideWindow::setPeptideEvidence begin";
+ qDebug() << "PeptideWindow::setPeptideEvidence begin " << p_peptide_evidence;
_p_peptide_evidence = p_peptide_evidence;
_spectrum_is_ready = false;
- qDebug() << "PeptideWindow::setPeptideEvidence emit loadSpectrumSp(_p_peptide_match)";
+ qDebug() << "PeptideWindow::setPeptideEvidence 1";
ui->file_not_found->setVisible(false);
ui->spectrum_widget->setVisible(true);
ui->statusbar->showMessage(tr("loading spectrum"));
+ qDebug() << "PeptideWindow::setPeptideEvidence 2";
pappso::PeptideSp peptide = _p_peptide_evidence->getPeptideXtpSp();
+ qDebug() << "PeptideWindow::setPeptideEvidence 3";
ui->spectrum_widget->setMs2Precision(_p_precision);
ui->spectrum_widget->setPeptideCharge(_p_peptide_evidence->getCharge());
ui->spectrum_widget->setPeptideSp(peptide);
+
+ qDebug() << "PeptideWindow::setPeptideEvidence 4";
//ui->spectrum_widget->plot();
updateDisplay();
+ qDebug() << "PeptideWindow::setPeptideEvidence emit loadSpectrumSp(_p_peptide_match)";
emit loadSpectrumSp(_p_peptide_evidence);
qDebug() << "PeptideWindow::setPeptideEvidence end";
}
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index ae2680806..804241d0f 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -487,7 +487,7 @@ void ProjectWindow::doViewPeptideList(IdentificationGroup * p_ident_group, Prote
void ProjectWindow::doViewPeptideDetail(PeptideEvidence * peptide_evidence) {
- qDebug() << "ProjectWindow::doViewPeptideDetail begin";
+ qDebug() << "ProjectWindow::doViewPeptideDetail begin " << peptide_evidence;
if (_peptide_detail_window_collection.size() == 0) {
connectNewPeptideDetailWindow();
}
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
index bae3597fd..7babd9b4b 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
@@ -81,9 +81,11 @@ 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) {
- qDebug() << "PtmPeptideListWindow::askPeptideDetailView begin";
- emit requestPeptideDetailView(p_peptide_match.getPeptideEvidence());
+void PtmPeptideListWindow::askPeptideDetailView(PeptideEvidence * p_peptide_evidence) {
+ qDebug() << "PtmPeptideListWindow::askPeptideDetailView begin " << p_peptide_evidence;
+ //PeptideMatch peptide_match(* p_peptide_match);
+ //qDebug() << "PtmPeptideListWindow::askPeptideDetailView begin " << peptide_match.getPeptideEvidence();
+ emit requestPeptideDetailView(p_peptide_evidence);
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 de7c6288d..b467c3aea 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
@@ -49,7 +49,7 @@ public:
explicit PtmPeptideListWindow(PtmIslandListWindow * parent = 0);
~PtmPeptideListWindow();
void setPtmIsland(PtmIsland * p_ptm_island);
- void askPeptideDetailView(PeptideMatch p_peptide_match);
+ void askPeptideDetailView(PeptideEvidence * p_peptide_evidence);
signals:
void requestPeptideDetailView(PeptideEvidence * p_peptide_evidence);
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
index 94f7d00a9..20a4f59fa 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
@@ -143,7 +143,7 @@ const QString PtmPeptideTableModel::getDescription(std::int8_t column) {
return "peptide theoretical MH+";
break;
case (std::int8_t) PtmPeptideListColumn::delta_mhplus:
- return "peptide mass difference betwenn observed mass and theoretical mass";
+ return "peptide mass difference between observed mass and theoretical mass";
break;
case (std::int8_t) PtmPeptideListColumn::besthyperscore:
return "best X!Tandem hyperscore";
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
index f049f03c3..2110b9288 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
@@ -32,9 +32,8 @@
#include "../../grouping/ptm/ptmgroupingexperiment.h"
#include <QTextDocument>
-PtmPeptideMenuQicon::PtmPeptideMenuQicon(const PtmGroupingExperiment * p_ptm_grouping_experiment, const PtmSampleScan * p_ptm_sample, const PeptideMatch * p_peptide_match):QIcon() {
+PtmPeptideMenuQicon::PtmPeptideMenuQicon(const PtmGroupingExperiment * p_ptm_grouping_experiment, const PtmSampleScan * p_ptm_sample, const PeptideMatch * p_peptide_match):QIcon(), _peptide_match(*p_peptide_match) {
_p_ptm_sample_scan = p_ptm_sample;
- _p_peptide_match = p_peptide_match;
_p_ptm_grouping_experiment = p_ptm_grouping_experiment;
}
PtmPeptideMenuQicon::~PtmPeptideMenuQicon( ) {
@@ -60,7 +59,7 @@ void PtmPeptideMenuQicon::paint(QPainter *painter, const QRect &rect, Qt::Alignm
PtmPeptideMenuQaction::PtmPeptideMenuQaction(PtmPeptideTableProxyModel * parent, const PtmGroupingExperiment * p_ptm_grouping_experiment, const PtmSampleScan * p_ptm_sample, PeptideMatch * p_peptide_match):QAction(parent) {
_p_ptm_peptide_table_proxy_model = parent;
- _p_peptide_match = p_peptide_match;
+ _peptide_match = *p_peptide_match;
this->setIcon(PtmPeptideMenuQicon(p_ptm_grouping_experiment, p_ptm_sample, p_peptide_match));
//this->setText(p_peptide_match->getPeptideXtpSp().get()->getSequence());
@@ -81,7 +80,11 @@ PtmPeptideMenuQaction::PtmPeptideMenuQaction(PtmPeptideTableProxyModel * parent,
#endif
}
void PtmPeptideMenuQaction::doTriggered(bool triggered) {
- _p_ptm_peptide_table_proxy_model->getPtmPeptideListWindowP()->askPeptideDetailView(*_p_peptide_match);
+ PeptideEvidence * p_peptide_evidence = _peptide_match.getPeptideEvidence();
+ qDebug() << "PtmPeptideMenuQaction::doTriggered begin" << _peptide_match.getPeptideEvidence();
+ qDebug() << "PtmPeptideMenuQaction::doTriggered begin 2 " << p_peptide_evidence;
+ qDebug() << "PtmPeptideMenuQaction::doTriggered begin 3 " << p_peptide_evidence->getPeptideXtpSp().get()->toString();
+ _p_ptm_peptide_table_proxy_model->getPtmPeptideListWindowP()->askPeptideDetailView(p_peptide_evidence);
}
PtmPeptideMenuQaction::~PtmPeptideMenuQaction()
@@ -153,7 +156,7 @@ void PtmPeptideTableProxyModel::onTableClicked(const QModelIndex &index)
PtmSampleScanSp sp_ptm_sample_scan = _p_ptm_table_model->getPtmSampleScanSpList().at(row);
if (sp_ptm_sample_scan.get()->getPeptideMatchList().size() == 1) {
- _p_ptm_peptide_list_window->askPeptideDetailView(sp_ptm_sample_scan.get()->getPeptideMatchList().at(0));
+ _p_ptm_peptide_list_window->askPeptideDetailView(sp_ptm_sample_scan.get()->getPeptideMatchList().at(0).getPeptideEvidence());
}
else {
this->showContextMenu(index);
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
index a375082bb..373ca4d30 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
@@ -50,7 +50,7 @@ public:
private:
const PtmSampleScan * _p_ptm_sample_scan;
- const PeptideMatch * _p_peptide_match;
+ const PeptideMatch _peptide_match;
const PtmGroupingExperiment * _p_ptm_grouping_experiment;
};
@@ -65,7 +65,7 @@ public slots:
void doTriggered(bool triggered);
private:
- PeptideMatch * _p_peptide_match;
+ PeptideMatch _peptide_match;
PtmPeptideTableProxyModel * _p_ptm_peptide_table_proxy_model;
};
--
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