From 6354d8b10388e8f1837ee692251d93d22611ad98 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Tue, 30 May 2017 17:02:53 +0200
Subject: [PATCH] first PTM island table !
---
src/core/identificationgroup.cpp | 4 +-
src/core/identificationgroup.h | 2 +
src/grouping/ptm/ptmgroupingexperiment.cpp | 2 +-
src/grouping/ptm/ptmgroupingexperiment.h | 2 +-
src/gui/project_view/projectwindow.cpp | 61 +++++++++++++++----
src/gui/project_view/projectwindow.h | 7 +++
.../ptmislandlistwindow.cpp | 31 ++++++++++
.../ptmislandlistwindow.h | 5 ++
.../ptmislandtablemodel.cpp | 45 +++++++++++---
.../ptmislandtablemodel.h | 9 ++-
src/gui/workerthread.cpp | 27 ++++++++
src/gui/workerthread.h | 2 +
12 files changed, 171 insertions(+), 26 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 287f58151..da181d529 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -41,7 +41,9 @@ IdentificationGroup::~IdentificationGroup()
}
}
-
+const PtmGroupingExperiment * IdentificationGroup::getPtmGroupingExperiment() const {
+ return _p_grp_ptm_experiment;
+}
const GroupStore & IdentificationGroup::getGroupStore() const {
return _group_store;
}
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 56ea6baa9..f6d112bfd 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -50,6 +50,8 @@ public:
void addProteinMatch(ProteinMatch * protein_match);
std::vector<ProteinMatch *> & getProteinMatchList();
void addIdentificationDataSourceP(IdentificationDataSource * p_identification_source);
+
+ const PtmGroupingExperiment * getPtmGroupingExperiment() const;
/** @brief count groups
* */
diff --git a/src/grouping/ptm/ptmgroupingexperiment.cpp b/src/grouping/ptm/ptmgroupingexperiment.cpp
index b43e6ff5c..cf62c0ed6 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.cpp
+++ b/src/grouping/ptm/ptmgroupingexperiment.cpp
@@ -72,7 +72,7 @@ PtmGroupingExperiment::~PtmGroupingExperiment()
}
-const std::vector<PtmIslandSp> & PtmGroupingExperiment::getPtmIslandList() {
+const std::vector<PtmIslandSp> & PtmGroupingExperiment::getPtmIslandList() const {
return _ptm_island_list;
}
diff --git a/src/grouping/ptm/ptmgroupingexperiment.h b/src/grouping/ptm/ptmgroupingexperiment.h
index b2f85f491..e51e27cba 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.h
+++ b/src/grouping/ptm/ptmgroupingexperiment.h
@@ -46,7 +46,7 @@ public:
void addProteinMatch(const ProteinMatch* p_protein_match);
void startGrouping();
- const std::vector<PtmIslandSp> & getPtmIslandList();
+ const std::vector<PtmIslandSp> & getPtmIslandList() const;
private:
std::vector<unsigned int> getPtmPositions(const ProteinMatch * protein_match) const;
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 7d4810a58..383d64802 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -107,6 +107,12 @@ void ProjectWindow::setDefaultProteinListWindow(ProteinListWindow* p_protein_lis
qDebug() << "ProjectWindow::setDefaultProteinListWindow end";
}
+void ProjectWindow::connectNewPtmIslandListWindow() {
+ qDebug() << "ProjectWindow::connectNewPtmIslandListWindow begin";
+ _p_current_ptm_island_list_window = new PtmIslandListWindow(this);
+ _ptm_island_list_window_collection.push_back(_p_current_ptm_island_list_window);
+ qDebug() << "ProjectWindow::connectNewPtmIslandListWindow end";
+}
void ProjectWindow::connectNewProteinListWindow() {
qDebug() << "ProjectWindow::connectNewProteinListWindow begin";
_p_current_protein_list_window = new ProteinListWindow(this);
@@ -141,6 +147,27 @@ void ProjectWindow::connectNewPeptideListWindow() {
qDebug() << "ProjectWindow::connectNewPeptideListWindow end";
}
+void ProjectWindow::refreshPtmGroup(IdentificationGroup * p_ident_group) {
+ qDebug() << "ProjectWindow::refreshPtmGroup begin";
+ hideWaitingMessage();
+ if (p_ident_group == nullptr) {
+ qDebug() << "ProjectWindow::refreshPtmGroup p_ident_group == nullptr";
+ }
+ else {
+ try {
+ emit identificationPtmGroupGrouped(p_ident_group);
+ }
+ catch (pappso::PappsoException exception_pappso) {
+ QMessageBox::warning(this,
+ tr("Unable to display project :"), exception_pappso.qwhat());
+ }
+ catch (std::exception exception_std) {
+ QMessageBox::warning(this,
+ tr("Unable to display project :"), exception_std.what());
+ }
+ }
+ qDebug() << "ProjectWindow::refreshPtmGroup end";
+}
void ProjectWindow::refreshGroup(IdentificationGroup * p_ident_group) {
qDebug() << "ProjectWindow::refreshGroup begin";
hideWaitingMessage();
@@ -281,7 +308,7 @@ void ProjectWindow::doGroupingFinished() {
}
refresh();
-
+
qDebug() << "ProjectWindow::doGroupingFinished end";
}
@@ -358,23 +385,29 @@ void ProjectWindow::doViewPtmIslandList(IdentificationGroup* p_identification_gr
qDebug() << "ProjectWindow::doViewPtmIslandList begin " << p_identification_group;
//if (p_identification_group == nullptr) {
//}
- if (_protein_list_window_collection.size() == 0) {
- connectNewProteinListWindow();
+ if (_ptm_island_list_window_collection.size() == 0) {
+ connectNewPtmIslandListWindow();
}
Qt::KeyboardModifiers modifier = QApplication::keyboardModifiers();
if (modifier == Qt::ControlModifier) {
- connectNewProteinListWindow();
+ connectNewPtmIslandListWindow();
}
- _p_current_protein_list_window->show();
+ _p_current_ptm_island_list_window->show();
//_p_current_protein_list_window->raise();
//_p_current_protein_list_window->activateWindow();
qDebug() << "ProjectWindow::doViewPtmIslandList end " << p_identification_group;
- _p_current_protein_list_window->setIdentificationGroup(p_identification_group);
+ _p_current_ptm_island_list_window->setIdentificationGroup(p_identification_group);
- emit identificationGroupGrouped(p_identification_group);
+
+ if (p_identification_group->getPtmGroupingExperiment() == nullptr) {
+ showWaitingMessage(tr("Computing PTM islands"));
+ emit operatePtmGroupingOnIdentification(p_identification_group);
+ }
+
+ //emit identificationGroupGrouped(p_identification_group);
qDebug() << "ProjectWindow::doViewPtmIslandList end";
}
@@ -420,6 +453,12 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
item->setData(QVariant(QString("%1").arg(fasta_file.get()->getAbsoluteFilePath())),Qt::UserRole);
}
+ for (auto && p_window :_ptm_island_list_window_collection) {
+ delete p_window;
+ }
+ _ptm_island_list_window_collection.clear();
+ _p_current_ptm_island_list_window = nullptr;
+
for (auto && p_window :_peptide_list_window_collection) {
delete p_window;
@@ -450,8 +489,8 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
}
std::vector<IdentificationGroup *> identification_list = _project_sp.get()->getIdentificationGroupList();
-
-
+
+
doViewProteinList(identification_list[0]);
qDebug() << " ProjectWindow::setProjectSp size=" << identification_list.size();
if (identification_list.size() == 1) {
@@ -485,8 +524,8 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
refresh();
this->setEnabled(true);
-
-
+
+
}
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index 857760998..eebbaea80 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -32,6 +32,7 @@
#include "../edit_modifications/editmodifications.h"
#include "../protein_list_view/proteinlistwindow.h"
#include "../peptide_list_view/peptidelistwindow.h"
+#include "../ptm_island_list_view/ptmislandlistwindow.h"
#include "../protein_view/proteinwindow.h"
#include "../peptide_detail_view/peptidewindow.h"
#include "gui/project_view/automatic_filter_widget/automaticfilterwidget.h"
@@ -70,13 +71,16 @@ public slots:
void doGroupingFinished();
void doDisplayLoadingMessage(QString message);
void refreshGroup(IdentificationGroup * p_ident_group);
+ void refreshPtmGroup(IdentificationGroup * p_ident_group);
void doAcceptedLabelingMethod();
// 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 operateGrouping(ProjectSp project_sp);
+ void operatePtmGroupingOnIdentification(IdentificationGroup * p_identification_group);
void operateGroupingOnIdentification(IdentificationGroup * p_identification_group, GroupingType grouping_type);
//void peptideChanged(pappso::PeptideSp peptide);
@@ -89,6 +93,7 @@ protected :
void computeMassPrecision();
private :
+ void connectNewPtmIslandListWindow();
void connectNewProteinListWindow();
void connectNewPeptideListWindow();
void connectNewProteinDetailWindow();
@@ -113,6 +118,8 @@ private:
ProteinWindow * _p_current_protein_detail_window = nullptr;
std::list <PeptideWindow *> _peptide_detail_window_collection;
PeptideWindow * _p_current_peptide_detail_window = nullptr;
+ std::list <PtmIslandListWindow *> _ptm_island_list_window_collection;
+ PtmIslandListWindow * _p_current_ptm_island_list_window = nullptr;
EditModifications * _p_edit_modifications = nullptr;
EditLabelMethods * _p_edit_label_methods = nullptr;
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index 66fceaba7..b5135ac6c 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
@@ -63,6 +63,10 @@ PtmIslandListWindow::PtmIslandListWindow(ProjectWindow *parent):
*/
#else
// Qt4 code
+connect (this, SIGNAL(ptmIslandDataChanged()), _ptm_table_model_p, SLOT(onPtmIslandDataChanged()));
+
+ connect (_project_window, SIGNAL(identificationPtmGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationPtmGroupGrouped(IdentificationGroup *)));
+
#endif
}
@@ -72,4 +76,31 @@ PtmIslandListWindow::~PtmIslandListWindow()
}
void PtmIslandListWindow::setIdentificationGroup(IdentificationGroup * p_identification_group) {
+
+ qDebug() << "PtmIslandListWindow::setIdentificationGroup begin " ;
+ if (p_identification_group != nullptr) {
+ qDebug() << "PtmIslandListWindow::setIdentificationGroup not null";
+ _p_identification_group = p_identification_group;
+ _ptm_table_model_p->setIdentificationGroup(p_identification_group);
+ //_p_proxy_model->setSourceModel(_protein_table_model_p);
+
+
+ }
+ else {
+ qDebug() << "PtmIslandListWindow::setIdentificationGroup null";
+ }
+
+ qDebug() << "PtmIslandListWindow::setIdentificationGroup end";
+}
+
+
+void PtmIslandListWindow::doIdentificationPtmGroupGrouped(IdentificationGroup * p_identification_group) {
+ qDebug() << "PtmIslandListWindow::doIdentificationPtmGroupGrouped begin";
+ if (_p_identification_group == p_identification_group) {
+ //_protein_table_model_p->setIdentificationGroup(p_identification_group);
+ //_p_proxy_model->setSourceModel(_protein_table_model_p);
+ emit ptmIslandDataChanged();
+ }
+
+ qDebug() << "PtmIslandListWindow::doIdentificationPtmGroupGrouped end";
}
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.h b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
index 6e30764bc..cba6b04e6 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.h
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
@@ -50,6 +50,11 @@ public:
void setIdentificationGroup(IdentificationGroup * p_identification_group);
+public slots:
+ void doIdentificationPtmGroupGrouped(IdentificationGroup * p_identification_group);
+
+signals:
+ void ptmIslandDataChanged();
private:
IdentificationGroup * _p_identification_group=nullptr;
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
index d6026e5f7..bfd6082bf 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
@@ -39,35 +39,39 @@ PtmIslandTableModel::~PtmIslandTableModel()
{
}
-void PtmIslandTableModel::setPtmGroupingExperiment(PtmGroupingExperiment * p_grp_ptm_experiment) {
- qDebug() << "PtmIslandTableModel::setPtmGroupingExperiment begin ";
+void PtmIslandTableModel::setIdentificationGroup(IdentificationGroup * p_identification_group) {
+ qDebug() << "PtmIslandTableModel::setIdentificationGroup begin ";
beginResetModel();
- _p_grp_ptm_experiment = p_grp_ptm_experiment;
+ _p_identification_group = p_identification_group;
//emit headerDataChanged(Qt::Horizontal, 0,11);
//refresh();
- qDebug() << "PtmIslandTableModel::setPtmGroupingExperiment end ";
+ qDebug() << "PtmIslandTableModel::setIdentificationGroup end ";
endResetModel();
}
-
+const PtmGroupingExperiment * PtmIslandTableModel::getPtmGroupingExperiment() const {
+ if (_p_identification_group == nullptr) {return nullptr;
+ }
+ return _p_identification_group->getPtmGroupingExperiment();
+}
int PtmIslandTableModel::rowCount(const QModelIndex &parent ) const {
//qDebug() << "ProteinTableModel::rowCount begin ";
- if (_p_grp_ptm_experiment != nullptr) {
+ if (getPtmGroupingExperiment() != nullptr) {
//qDebug() << "ProteinTableModel::rowCount(const QModelIndex &parent ) " << _p_identification_group->getProteinMatchList().size();
- return (int) _p_grp_ptm_experiment->getPtmIslandList().size();
+ return (int) getPtmGroupingExperiment()->getPtmIslandList().size();
}
return 0;
}
int PtmIslandTableModel::columnCount(const QModelIndex &parent ) const {
//qDebug() << "ProteinTableModel::columnCount begin ";
- if (_p_grp_ptm_experiment != nullptr) {
+ if (getPtmGroupingExperiment() != nullptr) {
return 3;
}
return 0;
}
QVariant PtmIslandTableModel::headerData(int section, Qt::Orientation orientation, int role) const
{
- if (_p_grp_ptm_experiment == nullptr) return QVariant();
+ if (getPtmGroupingExperiment() == nullptr) return QVariant();
if (orientation == Qt::Horizontal)
{
}
@@ -75,8 +79,29 @@ QVariant PtmIslandTableModel::headerData(int section, Qt::Orientation orientatio
}
QVariant PtmIslandTableModel::data(const QModelIndex &index, int role ) const {
// generate a log message when this method gets called
- if (_p_grp_ptm_experiment == nullptr) return QVariant();
+ if (getPtmGroupingExperiment() == nullptr) return QVariant();
int row = index.row();
int col = index.column();
+ switch(role) {
+ case Qt::DisplayRole:
+ if (_p_identification_group == nullptr) {
+ return QVariant();
+ }
+ switch (col) {
+ case 0:
+ return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getGroupingId());
+ break;
+ case 1:
+ return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getProteinMatch()->getProteinXtpSp().get()->getAccession());
+ break;
+ }
+ }
return QVariant();
}
+
+
+void PtmIslandTableModel::onPtmIslandDataChanged() {
+ qDebug() << "PtmIslandTableModel::onPtmIslandDataChanged begin " << rowCount();
+ emit layoutAboutToBeChanged();
+ emit layoutChanged();
+}
\ No newline at end of file
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.h b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
index 523770d6e..11ee41c3e 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
@@ -31,6 +31,7 @@
#define PTMISLANDTABLEMODEL_H
#include <QAbstractTableModel>
+#include "../../core/identificationgroup.h"
#include "../../grouping/ptm/ptmgroupingexperiment.h"
class PtmIslandListWindow;
@@ -42,14 +43,18 @@ public:
~PtmIslandTableModel();
- void setPtmGroupingExperiment(PtmGroupingExperiment * p_grp_ptm_experiment);
+ void setIdentificationGroup(IdentificationGroup * p_identification_group);
virtual int rowCount(const QModelIndex &parent = QModelIndex()) const override;
virtual int columnCount(const QModelIndex &parent = QModelIndex()) const override;
virtual QVariant headerData(int section, Qt::Orientation orientation, int role) const override;
virtual QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override;
+public slots:
+ void onPtmIslandDataChanged();
private :
- PtmGroupingExperiment * _p_grp_ptm_experiment=nullptr;
+ const PtmGroupingExperiment * getPtmGroupingExperiment() const;
+private :
+ IdentificationGroup * _p_identification_group=nullptr;
};
#endif // PTMISLANDTABLEMODEL_H
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index 083e52e0d..2ca0effa8 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -91,7 +91,12 @@ WorkerThread::WorkerThread(ProjectWindow * p_project_window)
//grouping
connect(p_project_window, SIGNAL(operateGrouping(ProjectSp)), this,SLOT(doGrouping(ProjectSp)));
connect(this, SIGNAL(groupingFinished()), p_project_window,SLOT(doGroupingFinished()));
+
+ //PTM grouping on IdentificationGroup
+ connect(p_project_window, SIGNAL(operatePtmGroupingOnIdentification(IdentificationGroup *)), this,SLOT(doPtmGroupingOnIdentification(IdentificationGroup *)));
+ connect(this, SIGNAL(ptmGroupingOnIdentificationFinished(IdentificationGroup *)), p_project_window,SLOT(refreshPtmGroup(IdentificationGroup *)));
+
//grouping on IdentificationGroup
connect(p_project_window, SIGNAL(operateGroupingOnIdentification(IdentificationGroup *, GroupingType)), this,SLOT(doGroupingOnIdentification(IdentificationGroup *, GroupingType)));
connect(this, SIGNAL(groupingOnIdentificationFinished(IdentificationGroup *)), p_project_window,SLOT(refreshGroup(IdentificationGroup *)));
@@ -128,6 +133,28 @@ void WorkerThread::doXpipFileLoad(QString filename) {
qDebug() << "WorkerThread::doXpipFileLoad end";
}
+void WorkerThread::doPtmGroupingOnIdentification(IdentificationGroup * p_identification_group) {
+ qDebug() << "WorkerThread::doPtmGroupingOnIdentification begin ";
+ try {
+ emit loadingMessage(tr("computing PTM islands"));
+ try {
+ p_identification_group->startPtmGrouping();
+
+ }
+ catch (pappso::PappsoException exception_pappso) {
+ emit operationFailed(tr("Error computing PTM islands : %1").arg(exception_pappso.qwhat()));
+ }
+ catch (std::exception exception_std) {
+ emit operationFailed(tr("Error computing PTM islands : %1").arg(exception_std.what()));
+ }
+ emit loadingMessage(tr("computing PTM islands finished"));
+ emit ptmGroupingOnIdentificationFinished(p_identification_group);
+ }
+ catch (pappso::PappsoException & error) {
+ emit operationFailed(tr("Error while computing PTM islands :\n%1").arg(error.qwhat()));
+ }
+ qDebug() << "WorkerThread::doPtmGroupingOnIdentification end ";
+}
void WorkerThread::doGroupingOnIdentification(IdentificationGroup * p_identification_group, GroupingType grouping_type) {
qDebug() << "WorkerThread::doGroupingOnIdentification begin ";
diff --git a/src/gui/workerthread.h b/src/gui/workerthread.h
index 6cf0c3c9e..7ebca7552 100644
--- a/src/gui/workerthread.h
+++ b/src/gui/workerthread.h
@@ -61,6 +61,7 @@ public slots:
void doWritingProticFile(QString filename, ProjectSp project_sp);
void doGrouping(ProjectSp project_sp);
void doGroupingOnIdentification(IdentificationGroup * p_identification_group, GroupingType grouping_type);
+ void doPtmGroupingOnIdentification(IdentificationGroup * p_identification_group);
signals:
@@ -69,6 +70,7 @@ signals:
void projectNotReady(QString error);
void groupingFinished();
void groupingOnIdentificationFinished(IdentificationGroup * p_identification_group);
+ void ptmGroupingOnIdentificationFinished(IdentificationGroup * p_identification_group);
void operationFinished();
void operationFailed(QString error);
};
--
GitLab