Add Ms Identification list window with run ID and file ID

src/CMakeLists.txt

@@ -181,6 +181,9 @@ SET(XTPCPP_SRCS
   ./gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
   ./gui/export/export_spreadsheet_dialog/exportspreadsheetdialog.cpp
   ./gui/load_results_dialog/loadresultsdialog.cpp
+  ./gui/lists/ms_identification_run_list_view/msidentificationlistwindow.cpp
+  ./gui/lists/ms_identification_run_list_view/msidentificationtablemodel.cpp
+  ./gui/lists/ms_identification_run_list_view/msidentificationtableproxymodel.cpp
   ./gui/mainwindow.cpp
   ./gui/peptide_detail_view/peptidewindow.cpp
   ./gui/peptide_list_view/peptidelistwindow.cpp
@@ -224,6 +227,7 @@ SET (GUI_UIS
   ./gui/edit/edit_tandem_preset_dialog/edit_tandem_preset_dialog.ui
   ./gui/export/export_masschroq_dialog/export_masschroq_dialog.ui
   ./gui/export/export_spreadsheet_dialog/export_spreadsheet_dialog.ui
+  ./gui/lists/ms_identification_run_list_view/ms_identification_run_view.ui
   ./gui/load_results_dialog/load_results_dialog.ui
   ./gui/main.ui
   ./gui/peptide_detail_view/peptide_detail_view.ui

src/core/project.h

@@ -111,6 +111,7 @@ class Project
   LabelingMethodSp _labeling_method_sp;
   ProjectMode _project_mode = ProjectMode::combined;
   std::vector<IdentificationGroup *> _identification_goup_list;
+  std::vector<IdentificationDataSourceSp> m_identificationDataSourceSpList;
   IdentificationGroup *_p_current_identification_group = nullptr;
 
   AutomaticFilterParameters _automatic_filter_parameters;

src/gui/lists/ms_identification_run_list_view/ms_identification_run_view.ui

+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>MsIdentificationView</class>
+ <widget class="QMainWindow" name="MsIdentificationView">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>826</width>
+    <height>404</height>
+   </rect>
+  </property>
+  <property name="contextMenuPolicy">
+   <enum>Qt::CustomContextMenu</enum>
+  </property>
+  <property name="windowTitle">
+   <string>Protein list</string>
+  </property>
+  <widget class="QWidget" name="centralwidget">
+   <property name="contextMenuPolicy">
+    <enum>Qt::CustomContextMenu</enum>
+   </property>
+   <layout class="QVBoxLayout" name="verticalLayout">
+    <item>
+     <widget class="QTableView" name="tableView">
+      <property name="contextMenuPolicy">
+       <enum>Qt::DefaultContextMenu</enum>
+      </property>
+     </widget>
+    </item>
+   </layout>
+  </widget>
+  <widget class="QMenuBar" name="menubar">
+   <property name="geometry">
+    <rect>
+     <x>0</x>
+     <y>0</y>
+     <width>826</width>
+     <height>24</height>
+    </rect>
+   </property>
+   <widget class="QMenu" name="menuExport">
+    <property name="title">
+     <string>e&amp;xport</string>
+    </property>
+    <addaction name="actionAs_ODS_file"/>
+   </widget>
+   <addaction name="menuExport"/>
+  </widget>
+  <widget class="QStatusBar" name="statusbar"/>
+  <action name="actionAs_ODS_file">
+   <property name="text">
+    <string>&amp;as ODS file</string>
+   </property>
+  </action>
+  <action name="actionValid_proteins">
+   <property name="checkable">
+    <bool>true</bool>
+   </property>
+   <property name="text">
+    <string>&amp;valid proteins</string>
+   </property>
+  </action>
+  <action name="actionChecked_proteins">
+   <property name="checkable">
+    <bool>true</bool>
+   </property>
+   <property name="text">
+    <string>&amp;checked proteins</string>
+   </property>
+  </action>
+  <action name="actionGrouped_proteins">
+   <property name="checkable">
+    <bool>true</bool>
+   </property>
+   <property name="text">
+    <string>&amp;grouped proteins</string>
+   </property>
+  </action>
+ </widget>
+ <resources/>
+ <connections>
+  <connection>
+   <sender>actionAs_ODS_file</sender>
+   <signal>triggered()</signal>
+   <receiver>MsIdentificationView</receiver>
+   <slot>doExportAsOdsFile()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>-1</x>
+     <y>-1</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>412</x>
+     <y>201</y>
+    </hint>
+   </hints>
+  </connection>
+ </connections>
+ <slots>
+  <slot>doNotValidHide(bool)</slot>
+  <slot>doNotCheckedHide(bool)</slot>
+  <slot>doNotGroupedHide(bool)</slot>
+  <slot>onProteinSearchEdit(QString)</slot>
+  <slot>doSearchOn(QString)</slot>
+  <slot>doMsrunFileSearch(QString)</slot>
+  <slot>doScanNumberSearch(int)</slot>
+  <slot>doModificationSearch(QString)</slot>
+  <slot>doExportAsOdsFile()</slot>
+ </slots>
+</ui>

src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.cpp

+
+/*******************************************************************************
+ * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.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@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
+
+#include "ui_ms_identification_run_view.h"
+#include "msidentificationlistwindow.h"
+
+#include "../../mainwindow.h"
+#include <QSettings>
+#include <odsstream/odsdocwriter.h>
+#include <odsstream/qtablewriter.h>
+
+MsIdentificationListQactionColumn::MsIdentificationListQactionColumn(MsIdentificationListWindow *parent,
+                                                   msIdentificationListColumn column)
+  : QAction(parent)
+{
+
+  this->setText(MsIdentificationTableModel::getTitle(column));
+  this->setCheckable(true);
+
+
+  // evalue_action.setChecked(_display_evalue);
+  // connect(p_action, SIGNAL(toggled(bool)), this,
+  // SLOT(showEvalueColumn(bool)));
+  m_column            = column;
+  m_msid_list_window = parent;
+
+#if QT_VERSION >= 0x050000
+  // Qt5 code
+  connect(this,
+          &MsIdentificationListQactionColumn::toggled,
+          this,
+          &MsIdentificationListQactionColumn::doToggled);
+
+#else
+  // Qt4 code
+  connect(this, SIGNAL(toggled(bool)), this, SLOT(doToggled(bool)));
+#endif
+}
+
+MsIdentificationListQactionColumn::~MsIdentificationListQactionColumn()
+{
+  // if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
+  qDebug() << "MsIdentificationListQactionColumn::~MsIdentificationListQactionColumn begin ";
+}
+void
+MsIdentificationListQactionColumn::doToggled(bool toggled)
+{
+  qDebug() << "MsIdentificationListQactionColumn::doToggled begin " << toggled;
+  setChecked(toggled);
+  m_msid_list_window->setMsIdentificationListColumnDisplay(m_column, toggled);
+
+  qDebug() << "MsIdentificationListQactionColumn::doToggled end";
+}
+
+
+MsIdentificationListWindow::MsIdentificationListWindow(ProjectWindow *parent)
+  : QMainWindow(parent), ui(new Ui::MsIdentificationView)
+{
+  m_project_window = parent;
+  ui->setupUi(this);
+  setWindowIcon(QIcon(":/xtpcpp_icon/resources/xtandempipeline_icon.svg"));
+
+  m_msid_table_model_p = new MsIdentificationTableModel(this);
+
+
+  m_proxy_model = new MsIdentificationTableProxyModel(this, m_msid_table_model_p);
+  m_proxy_model->setSourceModel(m_msid_table_model_p);
+  m_proxy_model->setDynamicSortFilter(true);
+
+  ui->tableView->setModel(m_proxy_model);
+  ui->tableView->setSortingEnabled(true);
+  ui->tableView->setAlternatingRowColors(true);
+  
+     connect(ui->centralwidget,
+          &QWidget::customContextMenuRequested,
+          this,
+          &MsIdentificationListWindow::showContextMenu);
+}
+
+void
+MsIdentificationListWindow::showContextMenu(const QPoint &pos)
+{
+  if(_p_context_menu == nullptr)
+    {
+      _p_context_menu = new QMenu(tr("Context menu"), this);
+
+
+      MsIdentificationListQactionColumn *p_action;
+      for(unsigned int i = 0; i < m_msid_table_model_p->columnCount(); i++)
+        {
+          p_action = new MsIdentificationListQactionColumn(
+            this, MsIdentificationTableModel::getMsIdentificationListColumn(i));
+          _p_context_menu->addAction(p_action);
+        }
+
+      _p_context_menu->exec(mapToGlobal(pos));
+    }
+  _p_context_menu->move(mapToGlobal(pos));
+  _p_context_menu->show();
+}
+
+void
+MsIdentificationListWindow::resizeColumnsToContents()
+{
+  ui->tableView->resizeColumnsToContents();
+}
+
+MsIdentificationListWindow::~MsIdentificationListWindow()
+{
+  // if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
+  //   delete ui;
+  //   if(_p_context_menu != nullptr)
+  //     {
+  //       delete _p_context_menu;
+  //     }
+}
+
+void
+MsIdentificationListWindow::setIdentificationDataSourceSpList(std::vector<IdentificationDataSourceSp>& identificationDataSourceSpList)
+{
+  qDebug() << "MsIdentificationListWindow::setIdentificationGroup begin ";
+
+  m_msid_table_model_p->setIdentificationDataSourceSpList(identificationDataSourceSpList);
+
+  qDebug() << "MsIdentificationListWindow::setIdentificationGroup end";
+}
+
+
+void
+MsIdentificationListWindow::setMsIdentificationListColumnDisplay(msIdentificationListColumn column,
+                                             bool toggled)
+{
+  m_proxy_model->setMsIdentificationListColumnDisplay(column, toggled);
+}

src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.h

+
+/*******************************************************************************
+ * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.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@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
+
+#pragma once
+
+#include <QMainWindow>
+#include <QAction>
+#include <QMenu>
+#include "msidentificationtablemodel.h"
+#include "msidentificationtableproxymodel.h"
+#include "ui_ms_identification_run_view.h"
+
+class ProjectWindow;
+
+// http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
+namespace Ui
+{
+class MsIdentificationView;
+}
+
+class MsIdentificationListWindow;
+class MsIdentificationListQactionColumn : public QAction
+{
+  Q_OBJECT
+  public:
+  explicit MsIdentificationListQactionColumn(MsIdentificationListWindow *parent,
+                                    msIdentificationListColumn column);
+  ~MsIdentificationListQactionColumn();
+
+  public slots:
+  void doToggled(bool toggled);
+
+  private:
+  MsIdentificationListWindow *m_msid_list_window;
+  msIdentificationListColumn m_column;
+};
+
+class MsIdentificationListWindow : public QMainWindow
+{
+  friend class MsIdentificationTableModel;
+  friend class MsIdentificationTableProxyModel;
+
+  Q_OBJECT
+
+  public:
+  explicit MsIdentificationListWindow(ProjectWindow *parent = 0);
+  ~MsIdentificationListWindow();
+  void setIdentificationDataSourceSpList(std::vector<IdentificationDataSourceSp>& identificationDataSourceSpList);
+  void setMsIdentificationListColumnDisplay(msIdentificationListColumn column, bool toggled);
+  void resizeColumnsToContents();
+
+  protected slots:
+  void showContextMenu(const QPoint &);
+  
+  private:
+  Ui::MsIdentificationView *ui;
+  MsIdentificationTableModel *m_msid_table_model_p = nullptr;
+  MsIdentificationTableProxyModel *m_proxy_model    = nullptr;
+  ProjectWindow *m_project_window;
+  QMenu *_p_context_menu  = nullptr;
+  bool _display_evalue    = true;
+  bool _display_accession = true;
+};

src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.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 "msidentificationtablemodel.h"
+
+#include <QDebug>
+#include <pappsomspp/pappsoexception.h>
+#include "msidentificationlistwindow.h"
+#include "../../../utils/identificationdatasourcestore.h"
+
+MsIdentificationTableModel::MsIdentificationTableModel(MsIdentificationListWindow *ms_id_list_window)
+  : QAbstractTableModel(ms_id_list_window)
+{
+  m_ms_id_list_window = ms_id_list_window;
+}
+
+void
+MsIdentificationTableModel::setIdentificationDataSourceSpList(
+ std::vector<IdentificationDataSourceSp>& identificationDataSourceSpList)
+{
+  qDebug() << " identificationDataSourceSpList.size()=" << identificationDataSourceSpList.size();
+           
+  beginResetModel();
+  m_identificationDataSourceSpList = identificationDataSourceSpList;
+
+  // emit headerDataChanged(Qt::Horizontal, 0,11);
+  // refresh();
+  qDebug() ;
+  endResetModel();
+
+  m_ms_id_list_window->resizeColumnsToContents();
+}
+
+
+int
+MsIdentificationTableModel::rowCount(const QModelIndex &parent) const
+{
+  // qDebug() << "MsIdentificationTableModel::rowCount begin ";
+  if(m_identificationDataSourceSpList.size() != 0)
+    {
+      // qDebug() << "MsIdentificationTableModel::rowCount(const QModelIndex &parent ) "
+      // << _p_identification_group->getProteinMatchList().size();
+      return (int)m_identificationDataSourceSpList.size();
+    }
+  return 0;
+}
+int
+MsIdentificationTableModel::columnCount(const QModelIndex &parent) const
+{
+  return (std::int8_t)msIdentificationListColumn::last;
+}
+const QString
+MsIdentificationTableModel::getTitle(msIdentificationListColumn column)
+{
+  qDebug() << "MsIdentificationTableModel::getTitle begin ";
+  return MsIdentificationTableModel::getTitle((std::int8_t)column);
+  // qDebug() << "MsIdentificationTableModel::getTitle end ";
+}
+const QString
+MsIdentificationTableModel::getDescription(msIdentificationListColumn column)
+{
+  qDebug() << "MsIdentificationTableModel::columnCount begin ";
+  return MsIdentificationTableModel::getDescription((std::int8_t)column);
+  // qDebug() << "MsIdentificationTableModel::columnCount end ";
+}
+
+const QString
+MsIdentificationTableModel::getTitle(std::int8_t column)
+{
+
+  qDebug() << "MsIdentificationTableModel::getTitle begin " << column;
+  switch(column)
+    {
+
+      case(std::int8_t)msIdentificationListColumn::run_id:
+        return "Run ID";
+        break;
+
+      case(std::int8_t)msIdentificationListColumn::id_file:
+        return "File ID";
+        break;
+      case(std::int8_t)msIdentificationListColumn::mzML:
+        return "mzML";
+        break;
+//       case(std::int8_t)msIdentificationListColumn::test:
+//         return "Test";
+//         break;
+    }
+  return "";
+}
+
+const QString
+MsIdentificationTableModel::getDescription(std::int8_t column)
+{
+
+  qDebug() << "MsIdentificationTableModel::getDescription begin " << column;
+  switch(column)
+    {
+
+      case(std::int8_t)msIdentificationListColumn::run_id:
+        return "Run ID";
+        break;
+
+      case(std::int8_t)msIdentificationListColumn::id_file:
+        return "File ID pathway";
+        break;
+      case(std::int8_t)msIdentificationListColumn::mzML:
+        return "mzML file pathway";
+        break;
+    }
+  return "";
+}
+
+QVariant
+MsIdentificationTableModel::headerData(int section,
+                              Qt::Orientation orientation,
+                              int role) const
+{
+  if(orientation == Qt::Horizontal)
+    {
+      switch(role)
+        {
+          case Qt::DisplayRole:
+            qDebug() << section;
+            return QVariant(getTitle(section));
+            break;
+          case Qt::ToolTipRole:
+            return QVariant(getDescription(section));
+            break;
+          case Qt::SizeHintRole:
+            qDebug() << section;
+            return QSize(getColumnWidth(section),40);
+            break;
+        }
+    }
+  return QVariant();
+}
+
+int
+MsIdentificationTableModel::getColumnWidth(int column)
+{
+  qDebug() << "Test " << column;
+  switch(column)
+    {
+      case(int)msIdentificationListColumn::run_id:
+        return 300;
+        break;
+      case(int)msIdentificationListColumn::id_file:
+        return 300;
+        break;
+      case(int)msIdentificationListColumn::mzML:
+        return 300;
+        break;
+    }
+  return 300;
+}
+
+msIdentificationListColumn
+MsIdentificationTableModel::getMsIdentificationListColumn(std::int8_t column)
+{
+  return static_cast<msIdentificationListColumn>(column);
+}
+
+QVariant
+MsIdentificationTableModel::data(const QModelIndex &index, int role) const
+{
+  int row = index.row();
+  int col = index.column();
+
+  switch(role)
+    {
+      case Qt::SizeHintRole:
+        qDebug() << MsIdentificationTableModel::getColumnWidth(col);
+        
+        return QSize(MsIdentificationTableModel::getColumnWidth(col), 30);
+        break;
+      case Qt::DisplayRole:
+        switch(col)
+          {
+            case(std::int8_t)msIdentificationListColumn::run_id:
+            return QVariant(m_identificationDataSourceSpList
+              .at(row)
+              ->getSampleName());
+          }
+        if(col == (std::int8_t)msIdentificationListColumn::id_file)
+          {
+            return QVariant(m_identificationDataSourceSpList