From c4bb6ded8f6fd8a1d4621812ad5a7f125b5aa345 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Mon, 14 Aug 2017 22:37:16 +0200
Subject: [PATCH] peptide match pointer not const in ptmpeptidescan
---
src/grouping/ptm/ptmisland.cpp | 6 +++---
src/grouping/ptm/ptmisland.h | 4 ++--
src/grouping/ptm/ptmsamplescan.cpp | 6 +++---
src/grouping/ptm/ptmsamplescan.h | 8 ++++----
src/gui/project_view/projectwindow.h | 2 +-
src/gui/ptm_island_list_view/ptmislandlistwindow.cpp | 11 +++++++----
src/gui/ptm_island_list_view/ptmislandlistwindow.h | 1 +
.../ptm_peptide_list_view/ptmpeptidelistwindow.cpp | 4 +++-
src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h | 4 ++--
9 files changed, 26 insertions(+), 20 deletions(-)
diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index ff6e52a9..767c52a4 100644
--- a/src/grouping/ptm/ptmisland.cpp
+++ b/src/grouping/ptm/ptmisland.cpp
@@ -112,7 +112,7 @@ bool PtmIsland::containsPeptideMatch(const PeptideMatch* peptide_match) const {
});
}
-void PtmIsland::addPeptideMatch(const PeptideMatch* p_peptide_match) {
+void PtmIsland::addPeptideMatch(PeptideMatch* p_peptide_match) {
if (_position_list.size()==1) {
unsigned int position = _position_list[0];
if (p_peptide_match->containsPosition(position)) {
@@ -155,7 +155,7 @@ bool PtmIsland::merge(PtmIslandSp ptm_island_sp) {
_position_list.erase(std::unique(_position_list.begin(), _position_list.end()), _position_list.end());
- std::vector<const PeptideMatch *>::const_iterator it_result = std::max_element(_peptide_match_list.begin(), _peptide_match_list.end(), [](const PeptideMatch * a, const PeptideMatch * b)
+ std::vector<PeptideMatch *>::const_iterator it_result = std::max_element(_peptide_match_list.begin(), _peptide_match_list.end(), [](const PeptideMatch * a, const PeptideMatch * b)
{
return (a->getStop() < b->getStop());
});
@@ -173,7 +173,7 @@ bool PtmIsland::merge(PtmIslandSp ptm_island_sp) {
std::vector<PtmSampleScanSp> PtmIsland::getPtmSampleScanSpList() const {
qDebug() << "PtmIsland::getPtmSampleScanSpList begin" ;
std::vector<PtmSampleScanSp> sample_scan_list;
- for (const PeptideMatch * p_peptide_match:_peptide_match_list) {
+ for (PeptideMatch * p_peptide_match:_peptide_match_list) {
std::vector<PtmSampleScanSp>::iterator it_ptm = sample_scan_list.begin();
std::vector<PtmSampleScanSp>::iterator it_ptm_end = sample_scan_list.end();
diff --git a/src/grouping/ptm/ptmisland.h b/src/grouping/ptm/ptmisland.h
index 5e5f80e2..845ae342 100644
--- a/src/grouping/ptm/ptmisland.h
+++ b/src/grouping/ptm/ptmisland.h
@@ -50,7 +50,7 @@ public:
PtmIsland(const ProteinMatch* p_protein_match, unsigned int position);
PtmIsland(const PtmIsland & other);
~PtmIsland();
- void addPeptideMatch(const PeptideMatch* p_peptide_match);
+ void addPeptideMatch(PeptideMatch* p_peptide_match);
/** @brief merge with the given ptm island if there is at least one common peptide match
* */
@@ -77,7 +77,7 @@ public:
private:
const ProteinMatch * _protein_match_p;
- std::vector<const PeptideMatch *> _peptide_match_list;
+ std::vector<PeptideMatch *> _peptide_match_list;
//std::vector<std::size_t> _sample_scan_set;
std::vector<unsigned int> _position_list;
unsigned int _protein_stop=0;
diff --git a/src/grouping/ptm/ptmsamplescan.cpp b/src/grouping/ptm/ptmsamplescan.cpp
index bf8cdce7..36110810 100644
--- a/src/grouping/ptm/ptmsamplescan.cpp
+++ b/src/grouping/ptm/ptmsamplescan.cpp
@@ -36,7 +36,7 @@ QColor PtmSampleScan::_color_other_best = QColor("#ff7878");
QColor PtmSampleScan::_color_no_best = QColor("yellow");
-PtmSampleScan::PtmSampleScan(const PeptideMatch * p_peptide_match) {
+PtmSampleScan::PtmSampleScan(PeptideMatch * p_peptide_match) {
_peptide_match_list.push_back(p_peptide_match);
}
@@ -48,7 +48,7 @@ PtmSampleScan::~PtmSampleScan() {
const PeptideMatch * PtmSampleScan::getRepresentativePeptideMatch() const {
return _peptide_match_list[0];
}
-bool PtmSampleScan::add(const PeptideMatch * p_peptide_match) {
+bool PtmSampleScan::add(PeptideMatch * p_peptide_match) {
if(getRepresentativePeptideMatch()->getHashSampleScan() != p_peptide_match->getHashSampleScan()) {
return false;
}
@@ -136,6 +136,6 @@ const QString PtmSampleScan::getHtmlSequence(const PtmGroupingExperiment * p_ptm
return sequence_html;
}
-const std::vector<const PeptideMatch *> & PtmSampleScan::getPeptideMatchList() const {
+const std::vector<PeptideMatch *> & PtmSampleScan::getPeptideMatchList() const {
return _peptide_match_list;
}
diff --git a/src/grouping/ptm/ptmsamplescan.h b/src/grouping/ptm/ptmsamplescan.h
index 5ae26bc0..3533ff92 100644
--- a/src/grouping/ptm/ptmsamplescan.h
+++ b/src/grouping/ptm/ptmsamplescan.h
@@ -44,19 +44,19 @@ typedef std::shared_ptr<PtmSampleScan> PtmSampleScanSp;
class PtmSampleScan
{
public:
- PtmSampleScan(const PeptideMatch * p_peptide_match);
+ PtmSampleScan(PeptideMatch * p_peptide_match);
PtmSampleScan(const PtmSampleScan& other);
~PtmSampleScan();
const PeptideMatch * getRepresentativePeptideMatch() const;
- bool add(const PeptideMatch * p_peptide_match);
+ bool add(PeptideMatch * p_peptide_match);
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<const PeptideMatch *> & getPeptideMatchList() const;
+ const std::vector<PeptideMatch *> & getPeptideMatchList() const;
private:
- std::vector<const PeptideMatch *> _peptide_match_list;
+ std::vector<PeptideMatch *> _peptide_match_list;
static QColor _color_best;
static QColor _color_other_best;
static QColor _color_no_best;
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index 9caca2bd..7c517980 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -74,6 +74,7 @@ public slots:
void refreshGroup(IdentificationGroup * p_ident_group);
void refreshPtmGroup(IdentificationGroup * p_ident_group);
void doAcceptedLabelingMethod();
+ void doViewPeptideDetail(PeptideMatch * peptide_match);
// void setColor(const QColor &color);
// void setShape(Shape shape);
signals:
@@ -87,7 +88,6 @@ signals:
protected :
void doViewPeptideList(IdentificationGroup * p_ident_group, ProteinMatch * protein_match);
- void doViewPeptideDetail(PeptideMatch * peptide_match);
void doViewProteinDetail(ProteinMatch * protein_match);
void doIdentificationGroupEdited(IdentificationGroup* p_identification_group);
void computeFdr();
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index 23c23804..8d8bd778 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
@@ -80,6 +80,9 @@ PtmIslandListWindow::~PtmIslandListWindow()
delete _ptm_proxy_model_p;
}
+ProjectWindow * PtmIslandListWindow::getProjectWindowP() {
+ return _project_window;
+}
void PtmIslandListWindow::setIdentificationGroup(IdentificationGroup * p_identification_group) {
qDebug() << "PtmIslandListWindow::setIdentificationGroup begin " ;
@@ -117,7 +120,7 @@ void PtmIslandListWindow::doIdentificationPtmGroupGrouped(IdentificationGroup *
//_p_proxy_model->setSourceModel(_protein_table_model_p);
_ptm_table_model_p->setIdentificationGroup(p_identification_group);
emit ptmIslandDataChanged();
-
+
//ui->ptm_island_tableview->resizeRowToContents(_ptm_table_model_p->rowCount());
}
@@ -151,6 +154,6 @@ void PtmIslandListWindow::askViewPtmPeptideList(PtmIsland * ptm_island) {
}
- const IdentificationGroup * PtmIslandListWindow::getIdentificationGroup() const {
- return _p_identification_group;
- }
+const IdentificationGroup * PtmIslandListWindow::getIdentificationGroup() const {
+ return _p_identification_group;
+}
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.h b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
index e454e983..8b965291 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.h
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
@@ -51,6 +51,7 @@ public:
void setIdentificationGroup(IdentificationGroup * p_identification_group);
void resizeColumnsToContents();
const IdentificationGroup * getIdentificationGroup() const;
+ ProjectWindow * getProjectWindowP();
public slots:
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
index b9b99626..d461b5f2 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
@@ -31,6 +31,7 @@
#include "../ptm_island_list_view/ptmislandlistwindow.h"
#include "ptmpeptidetablemodel.h"
#include "ptmsequencedelegate.h"
+#include "../project_view/projectwindow.h"
#include "ui_ptm_peptide_list_view.h"
@@ -72,6 +73,7 @@ PtmPeptideListWindow::PtmPeptideListWindow(PtmIslandListWindow * parent):QMainWi
//connect (_project_window, SIGNAL(identificationPtmGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationPtmGroupGrouped(IdentificationGroup *)));
//connect (_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
connect(ui->ptm_peptide_tableview, SIGNAL(clicked(const QModelIndex &)), _ptm_proxy_model_p, SLOT(onTableClicked(const QModelIndex &)));
+ connect (this, SIGNAL(requestPeptideDetailView(PeptideMatch *)), _p_ptm_island_list_window->getProjectWindowP(),SLOT(doViewPeptideDetail(PeptideMatch *)));
#endif
}
@@ -82,7 +84,7 @@ 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(const PeptideMatch * p_peptide_match) {
+void PtmPeptideListWindow::askPeptideDetailView(PeptideMatch * p_peptide_match) {
qDebug() << "PtmPeptideListWindow::askPeptideDetailView begin";
emit requestPeptideDetailView(p_peptide_match);
qDebug() << "PtmPeptideListWindow::askPeptideDetailView end";
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
index b9fe1bfd..7ef95d5a 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(const PeptideMatch * p_peptide_match);
+ void askPeptideDetailView(PeptideMatch * p_peptide_match);
signals:
- void requestPeptideDetailView(const PeptideMatch * p_peptide_match);
+ void requestPeptideDetailView(PeptideMatch * p_peptide_match);
private:
--
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