peptide list work

src/CMakeLists.txt

@@ -85,6 +85,7 @@ SET(XTPCPP_SRCS
   ./gui/mainwindow.cpp
   ./gui/peptide_list_view/peptidelistwindow.cpp
   ./gui/peptide_list_view/peptidetablemodel.cpp
+  ./gui/peptide_list_view/peptidetableproxymodel.cpp
   ./gui/project_view/projectwindow.cpp
   ./gui/protein_view/proteinwindow.cpp
   ./gui/protein_list_view/proteinlistwindow.cpp
@@ -105,6 +106,7 @@ SET(XTPCPP_MOC_HDRS
   ./gui/mainwindow.h
   ./gui/peptide_list_view/peptidelistwindow.h
   ./gui/peptide_list_view/peptidetablemodel.h
+  ./gui/peptide_list_view/peptidetableproxymodel.h
   ./gui/project_view/projectwindow.h
   ./gui/protein_list_view/proteinlistwindow.h
   ./gui/protein_list_view/proteintablemodel.h

src/gui/peptide_list_view/peptidelistwindow.cpp

@@ -21,17 +21,32 @@
 *     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
 ******************************************************************************/
 
+#include <QSettings>
 #include "peptidelistwindow.h"
+#include "../project_view/projectwindow.h"
 
 #include "ui_peptide_view.h"
 
 
-PeptideListWindow::PeptideListWindow(QWidget *parent):
+PeptideListWindow::PeptideListWindow(ProjectWindow *parent):
     QMainWindow(parent),
     ui(new Ui::PeptideView)
 {
+    _project_window = parent;
     ui->setupUi(this);
 
+    _peptide_table_model_p = new PeptideTableModel(0);
+
+
+    _p_proxy_model = new PeptideTableProxyModel(this, _peptide_table_model_p);
+    _p_proxy_model->setSourceModel(_peptide_table_model_p);
+    _p_proxy_model->setDynamicSortFilter(true);
+    ui->tableView->setModel( _p_proxy_model );
+    ui->tableView->setSortingEnabled(true);
+
+    //connect(ui->tableView, SIGNAL(clicked(const QModelIndex &)), _p_proxy_model, SLOT(onTableClicked(const QModelIndex &)));
+    
+    
 #if QT_VERSION >= 0x050000
     // Qt5 code
     /*
@@ -41,6 +56,7 @@ PeptideListWindow::PeptideListWindow(QWidget *parent):
     */
 #else
 // Qt4 code
+connect (this, SIGNAL(peptideDataChanged()), _peptide_table_model_p, SLOT(onPeptideDataChanged())); 
     /*
         connect(&workerThread, SIGNAL(finished()), worker, SLOT(deleteLater()));
         connect(this, SIGNAL(operateMsDataFile(QString)), worker,SLOT(doMsDataFileLoad(QString)));
@@ -50,16 +66,6 @@ PeptideListWindow::PeptideListWindow(QWidget *parent):
     /*
     */
 
-    _peptide_table_model_p = new PeptideTableModel(0);
-
-
-    _p_proxy_model = new PeptideTableProxyModel(this, _peptide_table_model_p);
-    _p_proxy_model->setSourceModel(_peptide_table_model_p);
-    _p_proxy_model->setDynamicSortFilter(true);
-    ui->tableView->setModel( _p_proxy_model );
-    ui->tableView->setSortingEnabled(true);
-
-    //connect(ui->tableView, SIGNAL(clicked(const QModelIndex &)), _p_proxy_model, SLOT(onTableClicked(const QModelIndex &)));
 }
 
 PeptideListWindow::~PeptideListWindow()
@@ -83,3 +89,51 @@ void PeptideListWindow::setProteinMatch(Project * p_project, ProteinMatch * p_pr
 
 }
 
+
+void PeptideListWindow::edited() {
+    qDebug() << "PeptideListWindow::edited begin";
+    //emit dataChanged(index, index);
+    _project_window->doIdentificationGroupEdited(_p_identification_group);
+    //updateStatusBar();
+
+    qDebug() << "PeptideListWindow::edited end";
+}
+void PeptideListWindow::doNotValidHide(bool hide) {
+    qDebug() << "PeptideListWindow::doNotValidHide begin";
+    _p_proxy_model->hideNotValid(hide);
+    QSettings settings;
+    settings.setValue("peptidelistview/hidenotvalid", QString("%1").arg(hide));
+    emit peptideDataChanged();
+    qDebug() << "PeptideListWindow::doNotValidHide end";
+}
+
+void PeptideListWindow::doNotCheckedHide(bool hide) {
+    qDebug() << "PeptideListWindow::doNotCheckedHide begin";
+    _p_proxy_model->hideNotChecked(hide);
+    QSettings settings;
+    settings.setValue("peptidelistview/hidenotchecked", QString("%1").arg(hide));
+    emit peptideDataChanged();
+    qDebug() << "PeptideListWindow::doNotCheckedHide end";
+}
+void PeptideListWindow::doNotGroupedHide(bool hide) {
+    qDebug() << "PeptideListWindow::doNotGroupedHide begin";
+    _p_proxy_model->hideNotGrouped(hide);
+    QSettings settings;
+    settings.setValue("peptidelistview/hidenotgrouped", QString("%1").arg(hide));
+    emit peptideDataChanged();
+    qDebug() << "PeptideListWindow::doNotGroupedHide end";
+}
+
+
+void PeptideListWindow::onPeptideSearchEdit(QString protein_search_string) {
+    qDebug() << "PeptideListWindow::onProteinSearchEdit begin " << protein_search_string;
+    _p_proxy_model->setPeptideSearchString( protein_search_string);
+    emit peptideDataChanged();
+}
+
+void PeptideListWindow::askPeptideDetailView(PeptideMatch * p_peptide_match) {
+    qDebug() << "PeptideListWindow::askPeptideDetailView begin";
+    _project_window->doViewPeptideDetail(p_peptide_match);
+    qDebug() << "PeptideListWindow::askPeptideDetailView end";
+    //updateStatusBar();
+}

src/gui/peptide_list_view/peptidelistwindow.h

@@ -26,9 +26,11 @@
 
 #include <QMainWindow>
 #include "peptidetablemodel.h"
+#include "peptidetableproxymodel.h"
 #include "../../core/proteinmatch.h"
 #include "../../core/project.h"
 
+class ProjectWindow;
 //http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
 namespace Ui {
 class PeptideView;
@@ -37,11 +39,15 @@ class PeptideView;
 class PeptideListWindow: public QMainWindow {
     Q_OBJECT
 
+    friend class PeptideTableModel;
+    friend class PeptideTableProxyModel;
+
 public:
 
-    explicit PeptideListWindow(QWidget * parent = 0);
+    explicit PeptideListWindow(ProjectWindow * parent = 0);
     ~PeptideListWindow();
     void setProteinMatch(Project * p_project, ProteinMatch * p_protein_match);
+    void edited();
 
 public slots:
     //void peptideEdited(QString peptideStr);
@@ -50,13 +56,26 @@ public slots:
     void doIdentificationGroupGrouped(IdentificationGroup * p_identification_group);
 signals:
     void identificationGroupEdited(IdentificationGroup * p_identification_group);
+    void peptideDataChanged();
     //void peptideChanged(pappso::PeptideSp peptide);
 
+      
+protected :
+    void askPeptideDetailView(PeptideMatch * p_peptide_match);
+
+protected slots:
+    void doNotValidHide(bool hide);
+    void doNotCheckedHide(bool hide);
+    void doNotGroupedHide(bool hide);
+    void onPeptideSearchEdit(QString protein_search_string);
+    
 private:
     Ui::PeptideView *ui;
     PeptideTableModel * _peptide_table_model_p = nullptr;
     PeptideTableProxyModel * _p_proxy_model = nullptr;
     ProteinMatch* _p_protein_match;
+    ProjectWindow * _project_window;
+    IdentificationGroup * _p_identification_group=nullptr;
 
 };
 

src/gui/peptide_list_view/peptidetablemodel.cpp

@@ -28,45 +28,6 @@
 #include <pappsomspp/grouping/grppeptide.h>
 
 
-PeptideTableProxyModel::PeptideTableProxyModel(QObject *parent,PeptideTableModel* peptide_table_model_p): QSortFilterProxyModel(parent)
-{
-    _peptide_table_model_p = peptide_table_model_p;
-}
-
-bool PeptideTableProxyModel::filterAcceptsRow(int source_row,
-        const QModelIndex &source_parent) const {
-    return _peptide_table_model_p->acceptRow(source_row);
-    //return true;
-}
-
-void PeptideTableProxyModel::onTableClicked(const QModelIndex &index)
-{
-    qDebug() << "PeptideTableProxyModel::onTableClicked begin " << index.row();
-    qDebug() << "PeptideTableProxyModel::onTableClicked begin " << this->mapToSource(index).row();
-    _peptide_table_model_p->onTableClicked(this->mapToSource(index));
-}
-
-bool PeptideTableProxyModel::lessThan(const QModelIndex & left, const QModelIndex & right) const {
-    QVariant leftData = sourceModel()->data(left);
-    QVariant rightData = sourceModel()->data(right);
-    if (leftData.type() == QVariant::UInt) {
-        return leftData.toUInt() < rightData.toUInt();
-    }
-    if (leftData.type() == QVariant::UInt) {
-        return leftData.toUInt() < rightData.toUInt();
-    }
-    if (leftData.type() == QVariant::Double) {
-        return leftData.toDouble() < rightData.toDouble();
-    }
-    return leftData.toString() < rightData.toString();
-}
-
-QVariant PeptideTableProxyModel::headerData(int section, Qt::Orientation orientation,
-        int role) const {
-    return sourceModel()->headerData(section, orientation,
-                                     role);
-}
-
 PeptideTableModel::PeptideTableModel(QObject *parent)
     :QAbstractTableModel(parent)
 {
@@ -90,6 +51,9 @@ void PeptideTableModel::setProteinMatch(Project * p_project, ProteinMatch * p_pr
     qDebug() << "PeptideTableModel::setProteinMatch end " ;
 }
 
+ProteinMatch * PeptideTableModel::getProteinMatch() {
+    return _p_protein_match;
+}
 int PeptideTableModel::rowCount(const QModelIndex &parent ) const {
     if (_p_protein_match != nullptr) {
         //qDebug() << "PeptideTableModel::rowCount(const QModelIndex &parent ) " << _p_protein_match->getPeptideMatchList().size();
@@ -162,7 +126,7 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
             }
         }
         break;
-        case Qt::BackgroundRole:
+    case Qt::BackgroundRole:
         if (_p_protein_match->getPeptideMatchList().at(row)->isValid() == false)
         {
             return QVariant(QColor("grey"));
@@ -172,7 +136,7 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
         if (_p_protein_match == nullptr) {
         }
         else {
-            
+
             if (col == 0) {
                 return QVariant();
             }
@@ -210,23 +174,23 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
                 if (p_grp != nullptr) return QVariant((qreal)  p_grp->countSubgroupPresence(_p_protein_match->getPeptideMatchList().at(row)));
                 return QVariant();
             }
-        if (col ==11) {
+            if (col ==11) {
                 GroupingGroup * p_grp = _p_protein_match->getGroupingGroupSp().get();
                 if (p_grp != nullptr) return QVariant( p_grp->getSubgroupIdList(_p_protein_match->getPeptideMatchList().at(row)).join(" "));
                 return QVariant();
             }
-        if (col ==12) {
+            if (col ==12) {
                 return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row)->getEvalue());
             }
-        
-        if (col ==13) {
+
+            if (col ==13) {
                 return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getMz(1));
-            
-        }
-        if (col ==14) {
+
+            }
+            if (col ==14) {
                 return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row)->getDeltaMass());
-            
-        }
+
+            }
         }
         return QString("Row%1, Column%2")
                .arg(index.row() + 1)
@@ -254,9 +218,8 @@ void PeptideTableModel::onTableClicked(const QModelIndex &index)
     }
 }
 
-bool PeptideTableModel::acceptRow(int source_row) {
-    if (_p_protein_match->getPeptideMatchList().at(source_row)->isValid()) {
-        return true;
-    }
-    return true;
+void PeptideTableModel::onPeptideDataChanged() {
+    qDebug() << "PeptideTableModel::onPeptideDataChanged begin " << rowCount();
+    emit layoutAboutToBeChanged();
+    emit layoutChanged();
 }

src/gui/peptide_list_view/peptidetablemodel.h

@@ -24,26 +24,9 @@
 #define PEPTIDETABLEMODEL_H
 
 #include <QAbstractTableModel>
-#include <QSortFilterProxyModel>
 #include "../../core/project.h"
 
 class PeptideTableModel;
-class PeptideTableProxyModel : public QSortFilterProxyModel
-{
-    Q_OBJECT
-public:
-    PeptideTableProxyModel(QObject* parent,PeptideTableModel* peptide_table_model_p);
-    bool filterAcceptsRow(int source_row,
-                          const QModelIndex &source_parent) const override;
-    QVariant headerData(int section, Qt::Orientation orientation,
-                        int role) const override;
-    bool lessThan(const QModelIndex & left, const QModelIndex & right) const override;
-
-public slots:
-    void onTableClicked(const QModelIndex &index);
-private:
-    PeptideTableModel* _peptide_table_model_p;
-};
 
 class PeptideTableModel: public QAbstractTableModel
 {
@@ -57,10 +40,12 @@ public:
 
 
     void setProteinMatch(Project * p_project, ProteinMatch * p_protein_match);
-    bool acceptRow(int source_row);
+    ProteinMatch * getProteinMatch();
 signals:
     void peptideMatchClicked(PeptideMatch * p_peptide_match);
 
+public slots:
+    void onPeptideDataChanged();
 public slots:
     void onTableClicked(const QModelIndex &index);
 

src/gui/peptide_list_view/peptidetableproxymodel.cpp

+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+*     XTPcpp is free software: you can redistribute it and/or modify
+*     it under the terms of the GNU General Public License as published by
+*     the Free Software Foundation, either version 3 of the License, or
+*     (at your option) any later version.
+*
+*     XTPcpp is distributed in the hope that it will be useful,
+*     but WITHOUT ANY WARRANTY; without even the implied warranty of
+*     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+*     GNU General Public License for more details.
+*
+*     You should have received a copy of the GNU General Public License
+*     along with XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+*     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#include <QDebug>
+#include <pappsomspp/pappsoexception.h>
+#include "peptidetableproxymodel.h"
+#include "peptidetablemodel.h"
+#include "peptidelistwindow.h"
+
+PeptideTableProxyModel::PeptideTableProxyModel(PeptideListWindow * p_peptide_list_window, PeptideTableModel * peptide_table_model_p): QSortFilterProxyModel(peptide_table_model_p)
+{
+    _peptide_table_model_p = peptide_table_model_p;
+    _p_peptide_list_window = p_peptide_list_window;
+}
+bool PeptideTableProxyModel::filterAcceptsRow(int source_row,
+        const QModelIndex &source_parent) const {
+    try {
+        qDebug() << "PeptideTableProxyModel::filterAcceptsRow begin " << source_row;
+        PeptideMatch * peptide_match = _peptide_table_model_p->getProteinMatch()->getPeptideMatchList().at(source_row);
+        qDebug() << "PeptideTableProxyModel::filterAcceptsRow protein_match " << source_row;
+
+        if (!_peptide_search_string.isEmpty()) {
+            if (!peptide_match->getPeptideXtpSp().get()->getSequence().contains(_peptide_search_string)) {
+                return false;
+            }
+        }
+
+        qDebug() << "PeptideTableProxyModel::filterAcceptsRow valid ";
+        if (_hide_not_valid) {
+            if (! peptide_match->isValid()) {
+                return false;
+            }
+        }
+        qDebug() << "PeptideTableProxyModel::filterAcceptsRow checked ";
+        if (_hide_not_checked) {
+            if (! peptide_match->isChecked()) {
+                return false;
+            }
+        }
+
+        qDebug() << "PeptideTableProxyModel::filterAcceptsRow grouped ";
+        if (_hide_not_grouped) {
+            if (! peptide_match->isGrouped()) {
+                return false;
+            }
+
+        }
+    }
+
+    catch (pappso::PappsoException exception_pappso) {
+        //QMessageBox::warning(this,
+        //                     tr("Error in ProteinTableModel::acceptRow :"), exception_pappso.qwhat());
+        qDebug() << "Error in PeptideTableProxyModel::acceptRow :" << exception_pappso.qwhat();
+    }
+    catch (std::exception exception_std) {
+        //QMessageBox::warning(this,
+        //                    tr("Error in ProteinTableModel::acceptRow :"), exception_std.what());
+        qDebug() << "Error in PeptideTableProxyModel::acceptRow :" << exception_std.what();
+    }
+
+    return true;
+
+    //return true;
+}
+
+
+
+void PeptideTableProxyModel::onTableClicked(const QModelIndex &index)
+{
+    qDebug() << "PeptideTableProxyModel::onTableClicked begin " << index.row();
+    qDebug() << "PeptideTableProxyModel::onTableClicked begin " << this->mapToSource(index).row();
+
+    //_protein_table_model_p->onTableClicked(this->mapToSource(index));
+    QModelIndex source_index(this->mapToSource(index));
+    int row = source_index.row();
+    int col = source_index.column();
+    PeptideMatch * peptide_match = _peptide_table_model_p->getProteinMatch()->getPeptideMatchList().at(row);
+    if (col == 0) //add a checkbox to cell(1,0)
+    {
+
+        if ( peptide_match->isChecked()) {
+            peptide_match->setChecked(false);
+        }
+        else {
+            peptide_match->setChecked(true);
+        }
+        _p_peptide_list_window->edited();
+    }
+    else {
+            _p_peptide_list_window->askPeptideDetailView(peptide_match);
+    }
+    qDebug() << "PeptideTableProxyModel::onTableClicked end " << index.row();
+
+}
+
+bool PeptideTableProxyModel::lessThan(const QModelIndex & left, const QModelIndex & right) const {
+    QVariant leftData = sourceModel()->data(left);
+    QVariant rightData = sourceModel()->data(right);
+    if (leftData.type() == QVariant::UInt) {
+        return leftData.toUInt() < rightData.toUInt();
+    }
+    if (leftData.type() == QVariant::UInt) {
+        return leftData.toUInt() < rightData.toUInt();
+    }
+    if (leftData.type() == QVariant::Double) {
+        return leftData.toDouble() < rightData.toDouble();
+    }
+    return leftData.toString() < rightData.toString();
+}
+
+QVariant PeptideTableProxyModel::headerData(int section, Qt::Orientation orientation,
+        int role) const {
+    return sourceModel()->headerData(section, orientation,
+                                     role);
+}
+
+void PeptideTableProxyModel::hideNotValid(bool hide) {
+    _hide_not_valid = hide;
+}
+
+void PeptideTableProxyModel::hideNotChecked(bool hide) {
+    qDebug() << "PeptideTableProxyModel::hideNotChecked begin ";
+    _hide_not_checked = hide;
+    qDebug() << "PeptideTableProxyModel::hideNotChecked end ";
+}
+void PeptideTableProxyModel::hideNotGrouped(bool hide) {
+    _hide_not_grouped = hide;
+}
+
+void PeptideTableProxyModel::setPeptideSearchString(QString peptide_search_string) {
+    _peptide_search_string = peptide_search_string;
+}

src/gui/peptide_list_view/peptidetableproxymodel.h

+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+*     XTPcpp is free software: you can redistribute it and/or modify
+*     it under the terms of the GNU General Public License as published by
+*     the Free Software Foundation, either version 3 of the License, or
+*     (at your option) any later version.
+*
+*     XTPcpp is distributed in the hope that it will be useful,
+*     but WITHOUT ANY WARRANTY; without even the implied warranty of
+*     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+*     GNU General Public License for more details.
+*
+*     You should have received a copy of the GNU General Public License
+*     along with XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+*     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#ifndef PEPTIDETABLEPROXYMODEL_H
+#define PEPTIDETABLEPROXYMODEL_H
+
+#include <QAbstractTableModel>
+#include <QSortFilterProxyModel>
+#include "../../core/project.h"
+
+class PeptideListWindow;
+
+class PeptideTableModel;
+class PeptideTableProxyModel : public QSortFilterProxyModel
+{
+    Q_OBJECT
+public:
+    PeptideTableProxyModel(PeptideListWindow * p_peptide_list_window, PeptideTableModel* peptide_table_model_p);
+    bool filterAcceptsRow(int source_row,
+                          const QModelIndex &source_parent) const override;
+                          
+    QVariant headerData(int section, Qt::Orientation orientation,
+                        int role) const override;
+    bool lessThan(const QModelIndex & left, const QModelIndex & right) const override;
+    
+    void hideNotValid(bool hide);
+    void hideNotChecked(bool hide);
+    void hideNotGrouped(bool hide);
+    void setPeptideSearchString(QString peptide_search_string);
+
+public slots:
+    void onTableClicked(const QModelIndex &index);
+
+private:
+    PeptideTableModel* _peptide_table_model_p;
+    PeptideListWindow * _p_peptide_list_window;
+    QString _peptide_search_string;
+    bool _hide_not_valid = true;
+    bool _hide_not_checked = true;
+    bool _hide_not_grouped = true;
+};
+
+#endif // PEPTIDETABLEPROXYMODEL_H

src/gui/project_view/projectwindow.cpp

@@ -177,6 +177,9 @@ void ProjectWindow::doViewPeptideList(ProteinMatch * protein_match) {
     qDebug() << "ProjectWindow::doViewPeptideList end";
 }
 
+void ProjectWindow::doViewPeptideDetail(PeptideMatch * peptide_match) {
+}
+
 void ProjectWindow::doViewProteinDetail(ProteinMatch * protein_match) {
 
 
@@ -198,7 +201,7 @@ void ProjectWindow::doViewProteinDetail(ProteinMatch * protein_match) {
 void ProjectWindow::doViewProteinList(IdentificationGroup* p_identification_group) {
     qDebug() << "ProjectWindow::doViewProteinList begin " << p_identification_group;
     //if (p_identification_group == nullptr) {
-        p_identification_group = _project_sp.get()->getCurrentIdentificationGroupP();
+    p_identification_group = _project_sp.get()->getCurrentIdentificationGroupP();
     //}
     if (_protein_list_window_collection.size() == 0) {
         connectNewProteinListWindow();
@@ -213,7 +216,7 @@ void ProjectWindow::doViewProteinList(IdentificationGroup* p_identification_grou
 
     qDebug() << "ProjectWindow::doViewProteinList end " << p_identification_group;
     _p_current_protein_list_window->setIdentificationGroup(p_identification_group);
-    
+
     emit identificationGroupGrouped(p_identification_group);
     qDebug() << "ProjectWindow::doViewProteinList end";
 }

src/gui/project_view/projectwindow.h

@@ -41,6 +41,7 @@ class ProjectWindow: public QMainWindow {
     Q_OBJECT
 
     friend class ProteinListWindow;
+    friend class PeptideListWindow;
 public:
 
     explicit ProjectWindow(MainWindow * parent = 0);
@@ -59,6 +60,7 @@ signals:
 protected :
     void doViewPeptideList(ProteinMatch * protein_match);
     void doViewProteinDetail(ProteinMatch * protein_match);
+    void doViewPeptideDetail(PeptideMatch * peptide_match);
     void doIdentificationGroupEdited(IdentificationGroup * p_identification_group);
 
 private :