first PTM island table !

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;
 }

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
     * */

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;
 }
 

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;

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);
-    
-    
+
+
 }
 
 

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;

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";
 }

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;

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

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

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 ";

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);
 };