From cc48fd86b31e7fa4c7424dd0967fe2fd7c0ffca3 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Sun, 13 Aug 2017 15:58:05 +0200
Subject: [PATCH] WIP: show several peptide match if needed in ptm islands
---
src/grouping/ptm/ptmsamplescan.cpp | 62 ++++++++-------
src/grouping/ptm/ptmsamplescan.h | 1 +
.../ptmpeptidelistwindow.cpp | 3 +
.../ptmpeptidelistwindow.h | 3 +
.../ptmpeptidetableproxymodel.cpp | 76 +++++++++++++++----
.../ptmpeptidetableproxymodel.h | 16 ++++
6 files changed, 116 insertions(+), 45 deletions(-)
diff --git a/src/grouping/ptm/ptmsamplescan.cpp b/src/grouping/ptm/ptmsamplescan.cpp
index 2d9de0a7d..bf8cdce78 100644
--- a/src/grouping/ptm/ptmsamplescan.cpp
+++ b/src/grouping/ptm/ptmsamplescan.cpp
@@ -40,7 +40,7 @@ PtmSampleScan::PtmSampleScan(const PeptideMatch * p_peptide_match) {
_peptide_match_list.push_back(p_peptide_match);
}
-PtmSampleScan::PtmSampleScan(const PtmSampleScan& other){
+PtmSampleScan::PtmSampleScan(const PtmSampleScan& other) {
}
PtmSampleScan::~PtmSampleScan() {
@@ -59,8 +59,8 @@ bool PtmSampleScan::add(const PeptideMatch * p_peptide_match) {
return false;
}
_peptide_match_list.push_back(p_peptide_match);
-
- //sort list
+
+ //sort list
std::sort(_peptide_match_list.begin(),_peptide_match_list.end(),[](const PeptideMatch * first, const PeptideMatch * second) {
return (first->getEvalue() < second->getEvalue()) ;
});
@@ -68,24 +68,24 @@ bool PtmSampleScan::add(const PeptideMatch * p_peptide_match) {
return true;
}
- std::vector<unsigned int> PtmSampleScan::getBestPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const {
- return p_ptm_grouping_experiment->getPtmPositions(getRepresentativePeptideMatch());
- }
+std::vector<unsigned int> PtmSampleScan::getBestPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const {
+ return p_ptm_grouping_experiment->getPtmPositions(getRepresentativePeptideMatch());
+}
- std::vector<unsigned int> PtmSampleScan::getObservedPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const {
- std::vector<unsigned int> position_list;
+std::vector<unsigned int> PtmSampleScan::getObservedPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const {
+ std::vector<unsigned int> position_list;
- for (const PeptideMatch * p_peptide_match: _peptide_match_list) {
- std::vector<unsigned int> positionb_list = p_ptm_grouping_experiment->getPtmPositions(p_peptide_match);
- for (unsigned int position: positionb_list) {
- position_list.push_back(position);
- }
+ for (const PeptideMatch * p_peptide_match: _peptide_match_list) {
+ std::vector<unsigned int> positionb_list = p_ptm_grouping_experiment->getPtmPositions(p_peptide_match);
+ for (unsigned int position: positionb_list) {
+ position_list.push_back(position);
}
- std::sort(position_list.begin(), position_list.end());
- auto last = std::unique(position_list.begin(), position_list.end());
- position_list.erase(last, position_list.end());
- return position_list;
}
+ std::sort(position_list.begin(), position_list.end());
+ auto last = std::unique(position_list.begin(), position_list.end());
+ position_list.erase(last, position_list.end());
+ return position_list;
+}
const QString PtmSampleScan::getHtmlSequence(const PtmGroupingExperiment * p_ptm_grouping_experiment) const
{
@@ -98,7 +98,7 @@ const QString PtmSampleScan::getHtmlSequence(const PtmGroupingExperiment * p_ptm
bool nobest_bool[pep_size] = {false};
double best_evalue = p_representative_peptide->getEvalue();
-
+
for (auto & p_peptide_match : _peptide_match_list) {
bool is_best= false;
if (p_peptide_match->getEvalue() == best_evalue) {
@@ -121,17 +121,21 @@ const QString PtmSampleScan::getHtmlSequence(const PtmGroupingExperiment * p_ptm
QString sequence_html;
for (unsigned int i=0; i < pep_size; i++) {
if (best_bool[i]) {
- sequence_html.append(QString("<span style=\"color:%2;\">%1</span>").arg(sequence[i]).arg(_color_best.name()));
- }
- else if (other_best_bool[i]) {
- sequence_html.append(QString("<span style=\"color:%2;\">%1</span>").arg(sequence[i]).arg(_color_other_best.name()));
- }
- else if (nobest_bool[i]){
- sequence_html.append(QString("<span style=\"color:%2;\">%1</span>").arg(sequence[i]).arg(_color_no_best.name()));
- }
- else {
- sequence_html.append(sequence[i]);
- }
+ sequence_html.append(QString("<span style=\"color:%2;\">%1</span>").arg(sequence[i]).arg(_color_best.name()));
+ }
+ else if (other_best_bool[i]) {
+ sequence_html.append(QString("<span style=\"color:%2;\">%1</span>").arg(sequence[i]).arg(_color_other_best.name()));
+ }
+ else if (nobest_bool[i]) {
+ sequence_html.append(QString("<span style=\"color:%2;\">%1</span>").arg(sequence[i]).arg(_color_no_best.name()));
+ }
+ else {
+ sequence_html.append(sequence[i]);
+ }
}
return sequence_html;
}
+
+const std::vector<const PeptideMatch *> & PtmSampleScan::getPeptideMatchList() const {
+ return _peptide_match_list;
+}
diff --git a/src/grouping/ptm/ptmsamplescan.h b/src/grouping/ptm/ptmsamplescan.h
index a6fa35f5e..5ae26bc05 100644
--- a/src/grouping/ptm/ptmsamplescan.h
+++ b/src/grouping/ptm/ptmsamplescan.h
@@ -53,6 +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<const PeptideMatch *> & getPeptideMatchList() const;
private:
std::vector<const PeptideMatch *> _peptide_match_list;
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
index 9724b410d..32cd36467 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
@@ -34,6 +34,9 @@
#include "ui_ptm_peptide_list_view.h"
+
+
+
PtmPeptideListWindow::PtmPeptideListWindow(PtmIslandListWindow * parent):QMainWindow(parent),
ui(new Ui::PtmPeptideListWindow) {
_p_ptm_island_list_window = parent;
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
index 5a6af5cf6..26bbcc747 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
@@ -41,6 +41,7 @@ namespace Ui {
class PtmPeptideListWindow;
}
+
class PtmPeptideListWindow: public QMainWindow {
Q_OBJECT
public:
@@ -49,12 +50,14 @@ public:
~PtmPeptideListWindow();
void setPtmIsland(PtmIsland * p_ptm_island);
+
private:
PtmIsland * _p_ptm_island=nullptr;
Ui::PtmPeptideListWindow *ui;
PtmPeptideTableModel * _ptm_table_model_p = nullptr;
PtmPeptideTableProxyModel * _ptm_proxy_model_p = nullptr;
PtmIslandListWindow * _p_ptm_island_list_window;
+ QMenu * _p_context_menu = nullptr;
};
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
index fb0a15811..608b4e8b8 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
@@ -30,10 +30,35 @@
#include "ptmpeptidetablemodel.h"
#include "ptmpeptidelistwindow.h"
+PtmPeptideMenuQaction::PtmPeptideMenuQaction(PtmPeptideTableProxyModel * parent, const PtmSampleScan * p_ptm_sample, const PeptideMatch * p_peptide_match):QAction(parent) {
+
+ this->setText(p_peptide_match->getPeptideXtpSp().get()->getSequence());
+ //evalue_action.setChecked(_display_evalue);
+ //connect(p_action, SIGNAL(toggled(bool)), this, SLOT(showEvalueColumn(bool)));
+
+#if QT_VERSION >= 0x050000
+ // Qt5 code
+ /*
+ connect(&workerThread, &QThread::finished, worker, &QObject::deleteLater);
+ connect(this, &PtSpectrumViewer::operateMsDataFile, worker, &PwizLoaderThread::doMsDataFileLoad);
+ connect(worker, &PwizLoaderThread::msDataReady, this, &PtSpectrumViewer::handleMsDataFile);
+ */
+#else
+// Qt4 code
+ connect (this, SIGNAL(toggled(bool)), this,SLOT(doToggled(bool)));
+#endif
+}
+
+PtmPeptideMenuQaction::~PtmPeptideMenuQaction()
+{
+ //if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
+ qDebug() << "PtmPeptideMenuQaction::~PtmPeptideMenuQaction begin ";
+
+}
PtmPeptideTableProxyModel::PtmPeptideTableProxyModel(PtmPeptideListWindow * p_ptm_peptide_list_window, PtmPeptideTableModel* ptm_table_model_p)
{
- _p_ptm_peptide_list_window = p_ptm_peptide_list_window;
- _p_ptm_table_model = ptm_table_model_p;
+ _p_ptm_peptide_list_window = p_ptm_peptide_list_window;
+ _p_ptm_table_model = ptm_table_model_p;
}
PtmPeptideTableProxyModel::~PtmPeptideTableProxyModel()
@@ -41,17 +66,36 @@ PtmPeptideTableProxyModel::~PtmPeptideTableProxyModel()
}
- bool PtmPeptideTableProxyModel::lessThan(const QModelIndex &left,
- const QModelIndex &right) const
- {
- QVariant leftData = sourceModel()->data(left);
- QVariant rightData = sourceModel()->data(right);
-
- 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();
- } else {
- return QSortFilterProxyModel::lessThan(left, right);
- }
- }
+bool PtmPeptideTableProxyModel::lessThan(const QModelIndex &left,
+ const QModelIndex &right) const
+{
+ QVariant leftData = sourceModel()->data(left);
+ QVariant rightData = sourceModel()->data(right);
+
+ 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();
+ } else {
+ return QSortFilterProxyModel::lessThan(left, right);
+ }
+}
+
+void PtmPeptideTableProxyModel::showContextMenu(const QModelIndex &index) {
+ if (_p_context_menu == nullptr) {
+ _p_context_menu = new QMenu(tr("Context menu"));
+
+ QVariant index_data = sourceModel()->data(index);
+
+ if (index_data.canConvert<PtmSampleScan *>()) {
+ PtmSampleScan * p_ptm_sample = qvariant_cast<PtmSampleScan *>(index_data);
+ PtmPeptideMenuQaction * p_action;
+ for (auto p_peptide_match : p_ptm_sample->getPeptideMatchList()) {
+ p_action = new PtmPeptideMenuQaction(this, p_ptm_sample, p_peptide_match);
+ _p_context_menu->addAction(p_action);
+ }
+ }
+ //_p_context_menu->exec(mapToGlobal(pos));
+ }
+ _p_context_menu->show();
+}
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
index 95efc6f00..f20a6d2f7 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
@@ -31,11 +31,25 @@
#include <QAbstractTableModel>
#include <QSortFilterProxyModel>
+#include <QMenu>
+#include "../../grouping/ptm/ptmsamplescan.h"
class PtmPeptideListWindow;
class PtmPeptideTableModel;
+class PtmPeptideTableProxyModel;
+class PtmPeptideMenuQaction: public QAction {
+ Q_OBJECT
+public:
+
+ explicit PtmPeptideMenuQaction(PtmPeptideTableProxyModel * parent, const PtmSampleScan * p_ptm_sample, const PeptideMatch * p_peptide_match);
+ ~PtmPeptideMenuQaction();
+
+private:
+};
+
+
class PtmPeptideTableProxyModel: public QSortFilterProxyModel
{
Q_OBJECT
@@ -45,9 +59,11 @@ public:
protected:
bool lessThan(const QModelIndex &left, const QModelIndex &right) const override;
+ void showContextMenu(const QModelIndex &index);
private:
PtmPeptideListWindow * _p_ptm_peptide_list_window;
PtmPeptideTableModel* _p_ptm_table_model;
+ QMenu * _p_context_menu = nullptr;
};
#endif // PTMPEPTIDETABLEPROXYMODEL_H
--
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