Add columns and export menu in ms id list

src/gui/lists/ms_identification_run_list_view/ms_identification_run_view.ui

@@ -72,16 +72,31 @@
      <height>24</height>
     </rect>
    </property>
+   <widget class="QMenu" name="menuCompare">
+    <property name="enabled">
+     <bool>false</bool>
+    </property>
+    <property name="title">
+     <string>&amp;Compare</string>
+    </property>
+    <addaction name="actionAlignement"/>
+   </widget>
    <widget class="QMenu" name="menuExport">
     <property name="title">
      <string>e&amp;xport</string>
     </property>
-    <addaction name="actionAs_ODS_file"/>
+    <addaction name="action_as_ODS_file"/>
    </widget>
    <addaction name="menuExport"/>
+   <addaction name="menuCompare"/>
   </widget>
   <widget class="QStatusBar" name="statusbar"/>
-  <action name="actionAs_ODS_file">
+  <action name="actionAlignement">
+   <property name="text">
+    <string>&amp;Alignement</string>
+   </property>
+  </action>
+  <action name="action_as_ODS_file">
    <property name="text">
     <string>&amp;as ODS file</string>
    </property>
@@ -90,7 +105,7 @@
  <resources/>
  <connections>
   <connection>
-   <sender>actionAs_ODS_file</sender>
+   <sender>action_as_ODS_file</sender>
    <signal>triggered()</signal>
    <receiver>MsIdentificationView</receiver>
    <slot>doExportAsOdsFile()</slot>

src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.cpp

@@ -30,46 +30,6 @@
 #include <odsstream/odsdocwriter.h>
 #include <odsstream/qtablewriter.h>
 
-MsIdentificationListQactionColumn::MsIdentificationListQactionColumn(
-  MsIdentificationListWindow *parent, msIdentificationListColumn column)
-  : QAction(parent)
-{
-
-  this->setText(MsIdentificationTableModel::getTitle(column));
-  // this->setCheckable(true);
-
-  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()
-{
-  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)
 {
@@ -89,6 +49,8 @@ MsIdentificationListWindow::MsIdentificationListWindow(ProjectWindow *parent)
   ui->tableView->setSortingEnabled(true);
   ui->tableView->setAlternatingRowColors(true);
 
+  m_proxy_model->resteItemDelegates();
+
   connect(this,
           &MsIdentificationListWindow::MsIdentificationDataChanged,
           m_msid_table_model_p,
@@ -97,6 +59,10 @@ MsIdentificationListWindow::MsIdentificationListWindow(ProjectWindow *parent)
           &MsIdentificationTableModel::layoutChanged,
           this,
           &MsIdentificationListWindow::updateStatusBar);
+  connect(ui->tableView,
+          &QTableView::clicked,
+          m_proxy_model,
+          &MsIdentificationTableProxyModel::onTableClicked);
 }
 
 void
@@ -149,10 +115,32 @@ MsIdentificationListWindow::setIdentificationDataSourceSpList(
   qDebug() << "MsIdentificationListWindow::setIdentificationGroup end";
 }
 
-
 void
-MsIdentificationListWindow::setMsIdentificationListColumnDisplay(
-  msIdentificationListColumn column, bool toggled)
+MsIdentificationListWindow::doExportAsOdsFile()
 {
-  m_proxy_model->setMsIdentificationListColumnDisplay(column, toggled);
+  QSettings settings;
+  QString default_location = settings.value("path/export_ods", "").toString();
+
+  QString filename;
+  filename = QFileDialog::getSaveFileName(
+    this,
+    tr("Save ODS file"),
+    QString("%1/untitled.ods").arg(default_location),
+    tr("Open Document Spreadsheet (*.ods)"));
+
+  if(!filename.isEmpty())
+    {
+      CalcWriterInterface *p_writer            = new OdsDocWriter(filename);
+      const QAbstractProxyModel *p_table_model = m_proxy_model;
+
+      QtableWriter table_writer(p_writer, p_table_model);
+
+      table_writer.setFormatPercentForColumn(m_msid_table_model_p->index(
+        0, (int)msIdentificationListColumn::percent_assign));
+
+      table_writer.writeSheet("Ms Identification list");
+
+      p_writer->close();
+      delete p_writer;
+    }
 }

src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.h

@@ -39,23 +39,6 @@ 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;
@@ -68,10 +51,12 @@ class MsIdentificationListWindow : public QMainWindow
   ~MsIdentificationListWindow();
   void setIdentificationDataSourceSpList(
     std::vector<IdentificationDataSourceSp> &identificationDataSourceSpList);
-  void setMsIdentificationListColumnDisplay(msIdentificationListColumn column,
-                                            bool toggled);
+
   void resizeColumnsToContents();
 
+  public slots:
+  void doExportAsOdsFile();
+
   signals:
   void MsIdentificationDataChanged();
 

src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.cpp

@@ -97,13 +97,30 @@ MsIdentificationTableModel::getTitle(std::int8_t column)
       case(std::int8_t)msIdentificationListColumn::run_id:
         return "Identification RunID";
         break;
-
       case(std::int8_t)msIdentificationListColumn::id_file:
         return "Identification File";
         break;
       case(std::int8_t)msIdentificationListColumn::mzML:
         return "Peak-list file";
         break;
+      case(std::int8_t)msIdentificationListColumn::engine_name:
+        return "Engine Name";
+        break;
+      case(std::int8_t)msIdentificationListColumn::nbr_spectrum:
+        return "Number of Spectrum";
+        break;
+      case(std::int8_t)msIdentificationListColumn::nbr_peptide:
+        return "Number of peptide";
+        break;
+      case(std::int8_t)msIdentificationListColumn::nbr_unique:
+        return "Number of unique";
+        break;
+      case(std::int8_t)msIdentificationListColumn::percent_assign:
+        return "% Assignation";
+        break;
+      case(std::int8_t)msIdentificationListColumn::id_msrun_id:
+        return "MsRunID";
+        break;
     }
   return "";
 }
@@ -119,13 +136,30 @@ MsIdentificationTableModel::getDescription(std::int8_t column)
       case(std::int8_t)msIdentificationListColumn::run_id:
         return "Identification of RunID";
         break;
-
       case(std::int8_t)msIdentificationListColumn::id_file:
         return "Identification File pathway";
         break;
       case(std::int8_t)msIdentificationListColumn::mzML:
         return "peak-list data file pathway";
         break;
+      case(std::int8_t)msIdentificationListColumn::engine_name:
+        return "Engine Name";
+        break;
+      case(std::int8_t)msIdentificationListColumn::nbr_spectrum:
+        return "Number of Spectrum";
+        break;
+      case(std::int8_t)msIdentificationListColumn::nbr_peptide:
+        return "Number of peptide identified";
+        break;
+      case(std::int8_t)msIdentificationListColumn::nbr_unique:
+        return "Number of unique peptide";
+        break;
+      case(std::int8_t)msIdentificationListColumn::percent_assign:
+        return "Percentage of Assignation";
+        break;
+      case(std::int8_t)msIdentificationListColumn::id_msrun_id:
+        return "Identification of MsRunID";
+        break;
     }
   return "";
 }
@@ -158,20 +192,28 @@ MsIdentificationTableModel::headerData(int section,
 int
 MsIdentificationTableModel::getColumnWidth(int column)
 {
-  qDebug() << "Test " << column;
   switch(column)
     {
       case(int)msIdentificationListColumn::run_id:
         return 200;
         break;
       case(int)msIdentificationListColumn::id_file:
-        return 500;
+        return 400;
         break;
       case(int)msIdentificationListColumn::mzML:
-        return 500;
+        return 400;
+        break;
+      case(int)msIdentificationListColumn::nbr_spectrum:
+        return 160;
+        break;
+      case(int)msIdentificationListColumn::nbr_peptide:
+        return 160;
+        break;
+      case(int)msIdentificationListColumn::nbr_unique:
+        return 160;
         break;
     }
-  return 300;
+  return 120;
 }
 
 msIdentificationListColumn
@@ -200,6 +242,66 @@ MsIdentificationTableModel::data(const QModelIndex &index, int role) const
               return QVariant(
                 m_identificationDataSourceSpList.at(row)->getXmlId());
           }
+        if(col == (std::int8_t)msIdentificationListColumn::id_file)
+          {
+            QFileInfo fi(
+              m_identificationDataSourceSpList.at(row)->getResourceName());
+            return QVariant(fi.fileName());
+          }
+
+        if(col == (std::int8_t)msIdentificationListColumn::mzML)
+          {
+            QFileInfo fi(m_identificationDataSourceSpList.at(row)
+                           ->getMsRunSp()
+                           .get()
+                           ->getFileName());
+            return QVariant(fi.fileName());
+          }
+        if(col == (std::int8_t)msIdentificationListColumn::engine_name)
+          {
+            return QVariant(m_identificationDataSourceSpList.at(row)
+                              ->getIdentificationEngineName());
+          }
+        if(col == (std::int8_t)msIdentificationListColumn::id_msrun_id)
+          {
+            return QVariant(m_identificationDataSourceSpList.at(row)
+                              ->getMsRunSp()
+                              ->getXmlId());
+          }
+        if(col == (std::int8_t)msIdentificationListColumn::nbr_peptide)
+          {
+            return QVariant(
+              m_identificationDataSourceSpList.at(row)
+                ->getIdentificationEngineStatistics(
+                  IdentificationEngineStatistics::total_spectra_assigned));
+          }
+        if(col == (std::int8_t)msIdentificationListColumn::nbr_unique)
+          {
+            return QVariant(
+              m_identificationDataSourceSpList.at(row)
+                ->getIdentificationEngineStatistics(
+                  IdentificationEngineStatistics::total_unique_assigned));
+          }
+        if(col == (std::int8_t)msIdentificationListColumn::nbr_spectrum)
+          {
+            return QVariant(
+              m_identificationDataSourceSpList.at(row)
+                ->getIdentificationEngineStatistics(
+                  IdentificationEngineStatistics::total_spectra_used));
+          }
+        if(col == (std::int8_t)msIdentificationListColumn::percent_assign)
+          {
+            return QVariant(
+              m_identificationDataSourceSpList.at(row)
+                ->getIdentificationEngineStatistics(
+                  IdentificationEngineStatistics::total_spectra_assigned)
+                .toDouble() /
+              m_identificationDataSourceSpList.at(row)
+                ->getIdentificationEngineStatistics(
+                  IdentificationEngineStatistics::total_spectra_used)
+                .toDouble());
+          }
+      case Qt::ToolTipRole:
         if(col == (std::int8_t)msIdentificationListColumn::id_file)
           {
             return QVariant(

src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.h

@@ -35,10 +35,16 @@
 
 enum class msIdentificationListColumn : std::int8_t
 {
-  run_id  = 0, ///< msRun ID
-  id_file = 1, ///< file ID
-  mzML    = 2, ///< accession
-  last    = 3, ///< get list size
+  run_id         = 0, ///< msRun ID
+  id_file        = 1, ///< file ID
+  mzML           = 2, ///< accession
+  engine_name    = 3, ///< engine name
+  nbr_spectrum   = 4, ///< number of spectrum
+  nbr_peptide    = 5, ///< number of peptide identified
+  nbr_unique     = 6, ///< number of unique spectra
+  percent_assign = 7, ///< percent of assignation
+  id_msrun_id    = 8, ///< identification of MsRunId
+  last           = 9, ///< get list size
 };
 
 class MsIdentificationListWindow;

src/gui/lists/ms_identification_run_list_view/msidentificationtableproxymodel.cpp

@@ -184,18 +184,42 @@ MsIdentificationTableProxyModel::headerData(int section,
   return sourceModel()->headerData(col, orientation, role);
 }
 
+void
+MsIdentificationTableProxyModel::onTableClicked(const QModelIndex &index)
+{
+  qDebug() << "MsIdentificationTableProxyModel::onTableClicked begin "
+           << index.row();
+  qDebug() << "MsIdentificationTableProxyModel::onTableClicked begin "
+           << this->mapToSource(index).row();
+
+  QModelIndex source_index(this->mapToSource(index));
+  int row = source_index.row();
+  msIdentificationListColumn col =
+    (msIdentificationListColumn)source_index.column();
+  if(col == msIdentificationListColumn::engine_name)
+    {
+      // m_msid_list_window->askProteinDetailView();
+    }
+  qDebug() << "MsIdentificationTableProxyModel::onTableClicked end "
+           << index.row();
+}
 
 void
-MsIdentificationTableProxyModel::setMsIdentificationListColumnDisplay(
-  msIdentificationListColumn column, bool toggled)
+MsIdentificationTableProxyModel::resteItemDelegates() const
 {
-  qDebug() << toggled;
-  beginResetModel();
-  QSettings settings;
-  settings.setValue(QString("protein_list_columns/%1")
-                      .arg(m_msid_table_model_p->getTitle(column)),
-                    toggled);
 
-  m_column_display[(std::int8_t)column] = toggled;
-  endResetModel();
+  for(int i = 0; i < columnCount(); ++i)
+    {
+      qDebug() << i;
+      qDebug() << (std::int8_t)msIdentificationListColumn::percent_assign;
+      qDebug() << mapToSource(index(0, i)).column();
+      //       m_msid_list_window->ui->tableView->setItemDelegateForColumn(
+      //         i, m_msid_list_window->ui->tableView->itemDelegate());
+      if(i == (std::int8_t)msIdentificationListColumn::percent_assign)
+        {
+          qDebug() << "AAAAAAAAAAAAAAAAAAAAA";
+          m_msid_list_window->ui->tableView->setItemDelegateForColumn(
+            i, m_percent_delegate);
+        }
+    }
 }

src/gui/lists/ms_identification_run_list_view/msidentificationtableproxymodel.h

@@ -54,9 +54,11 @@ class MsIdentificationTableProxyModel : public QSortFilterProxyModel
                 const QModelIndex &right) const override;
   void setSearchOn(QString search_on);
   void setMsIdentificationSearchString(QString ms_id_search_string);
-  void setMsIdentificationListColumnDisplay(msIdentificationListColumn column,
-                                            bool toggled);
 
+  void resteItemDelegates() const;
+
+  public slots:
+  void onTableClicked(const QModelIndex &index);
 
   private:
   std::vector<IdentificationDataSourceSp> m_identificationDataSourceSpList;