Add ExportMassChroqDialog to ms identification window

src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui

@@ -35,7 +35,11 @@
          <item>
           <layout class="QVBoxLayout" name="verticalLayout_13">
            <item>
-            <widget class="QListView" name="group_listView"/>
+            <widget class="QListView" name="group_listView">
+             <property name="toolTip">
+              <string>Check which groups will be export in the masschroqml file</string>
+             </property>
+            </widget>
            </item>
            <item>
             <layout class="QHBoxLayout" name="horizontalLayout_12">
@@ -93,7 +97,7 @@
            <item>
             <widget class="QGroupBox" name="groupBox_5">
              <property name="title">
-              <string>Ms run in the selected group</string>
+              <string>Ms runs in the selected group</string>
              </property>
              <layout class="QHBoxLayout" name="horizontalLayout_9">
               <item>

src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp

@@ -47,6 +47,9 @@ ExportMasschroqDialog::ExportMasschroqDialog(MainWindow *parent,
   ui->setupUi(this);
   this->setModal(true);
 
+  ui->listWidget->clear();
+  ui->msrun_list_combo_box->clear();
+
   ui->label_msrun_not_found->setHidden(true);
   ui->toolButton_2->setHidden(true);
   ui->label_check->setHidden(true);
@@ -325,19 +328,22 @@ ExportMasschroqDialog::doShowMsRunsInAlignmentGroup(QModelIndex index)
 {
   ui->listWidget->clear();
   ui->msrun_list_combo_box->clear();
-  MsRunAlignmentGroupSp temp = msp_alignmentGroups.at(index.row());
-  for(MsRunSp ms_run : temp->getMsRunsInAlignmentGroup())
+  MsRunAlignmentGroupSp selected_group = msp_alignmentGroups.at(index.row());
+  ui->groupBox_5->setTitle("Ms runs in " +
+                           selected_group->getMsRunAlignmentGroupName());
+  for(MsRunSp ms_run : selected_group->getMsRunsInAlignmentGroup())
     {
       ui->listWidget->addItem(ms_run->getSampleName());
       ui->msrun_list_combo_box->addItem(ms_run->getSampleName());
     }
-  if(temp->getMsRunReference() != nullptr)
+  if(selected_group->getMsRunReference() != nullptr)
     {
       std::list<MsRunSp>::iterator it;
-      it      = std::find(temp->getMsRunsInAlignmentGroup().begin(),
-                     temp->getMsRunsInAlignmentGroup().end(),
-                     temp->getMsRunReference());
-      int idx = std::distance(temp->getMsRunsInAlignmentGroup().begin(), it);
+      it = std::find(selected_group->getMsRunsInAlignmentGroup().begin(),
+                     selected_group->getMsRunsInAlignmentGroup().end(),
+                     selected_group->getMsRunReference());
+      int idx =
+        std::distance(selected_group->getMsRunsInAlignmentGroup().begin(), it);
       ui->msrun_list_combo_box->setCurrentIndex(idx);
     }
   else

src/gui/lists/ms_identification_run_list_view/ms_identification_run_view.ui

@@ -69,7 +69,7 @@
      <x>0</x>
      <y>0</y>
      <width>1084</width>
-     <height>24</height>
+     <height>22</height>
     </rect>
    </property>
    <widget class="QMenu" name="menuExport">
@@ -88,12 +88,9 @@
      <bool>true</bool>
     </property>
     <property name="title">
-     <string>&amp;Alignment</string>
+     <string>M&amp;assChroQ</string>
     </property>
-    <addaction name="no_group_action"/>
-    <addaction name="separator"/>
-    <addaction name="actionAll_identifications"/>
-    <addaction name="separator"/>
+    <addaction name="actionExport"/>
    </widget>
    <addaction name="menuExport"/>
    <addaction name="menuColumns"/>
@@ -127,6 +124,11 @@
     <string>&amp;All identifications</string>
    </property>
   </action>
+  <action name="actionExport">
+   <property name="text">
+    <string>Export</string>
+   </property>
+  </action>
  </widget>
  <resources/>
  <connections>
@@ -178,6 +180,22 @@
     </hint>
    </hints>
   </connection>
+  <connection>
+   <sender>actionExport</sender>
+   <signal>triggered()</signal>
+   <receiver>MsIdentificationView</receiver>
+   <slot>doMassChroQParameters()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>250</x>
+     <y>45</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>541</x>
+     <y>201</y>
+    </hint>
+   </hints>
+  </connection>
  </connections>
  <slots>
   <slot>doNotValidHide(bool)</slot>
@@ -190,6 +208,6 @@
   <slot>doModificationSearch(QString)</slot>
   <slot>doExportAsOdsFile()</slot>
   <slot>onMsIdentificationSearchEdit(QString)</slot>
-  <slot>doAlignmentGroupParameters(QAction*)</slot>
+  <slot>doMassChroQParameters()</slot>
  </slots>
 </ui>

src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.cpp

@@ -134,10 +134,10 @@ MsIdentificationListWindow::MsIdentificationListWindow(ProjectWindow *parent)
           &MsIdentificationTableModel::projectStatusChanged,
           mp_projectWindow,
           &ProjectWindow::doProjectStatusChanged);
-  connect(ui->menuAlignment,
-          &QMenu::triggered,
-          this,
-          &MsIdentificationListWindow::doAlignmentGroupParameters);
+  connect(ui->actionExport,
+          &QAction::triggered,
+          mp_projectWindow,
+          &ProjectWindow::doOpenMassChroQDialog);
 }
 
 
@@ -327,8 +327,6 @@ MsIdentificationListWindow::setAlignmentGroup(
           mp_proxyModel->setData(index, QVariant(), Qt::EditRole);
         }
     }
-
-  checkMsRunAlignmentGroupContent();
 }
 
 QModelIndexList
@@ -338,50 +336,9 @@ MsIdentificationListWindow::getSelectedIndexes()
 }
 
 void
-MsIdentificationListWindow::doAlignmentGroupParameters(
-  QAction *action_triggered)
+MsIdentificationListWindow::doMassChroQParameters()
 {
-  qDebug() << action_triggered->text();
-  MsRunAlignmentGroupSp alignment_group;
-  if(action_triggered == ui->actionAll_identifications)
-    {
-      
-    }
-  else
-    {
-      alignment_group =
-        mp_projectWindow->getProjectP()->getMsRunAlignmentGroupFromList(
-          action_triggered->text());
-    }
-
-  if(alignment_group != nullptr)
-    {
-      openMassChroQParametersView(alignment_group);
-    }
-}
-
-void
-MsIdentificationListWindow::checkMsRunAlignmentGroupContent()
-{
-  foreach(QAction *action, ui->menuAlignment->actions())
-    {
-      if(action != ui->no_group_action &&
-         action != ui->actionAll_identifications && !action->isSeparator())
-        {
-          qDebug() << "test";
-          MsRunAlignmentGroupSp alignment_group =
-            mp_projectWindow->getProjectP()->getMsRunAlignmentGroupFromList(
-              action->text());
-          if(alignment_group->getMsRunsInAlignmentGroup().size() >= 2)
-            {
-              action->setEnabled(true);
-            }
-          else
-            {
-              action->setEnabled(false);
-            }
-        }
-    }
+  emit operateMassChroqExportDialog();
 }
 
 MsIdentificationTableProxyModel *
@@ -395,23 +352,3 @@ MsIdentificationListWindow::getMsIdentificationModel()
 {
   return mp_msidTableModel;
 }
-
-void
-MsIdentificationListWindow::addValueToAlignmentMenu(QString action_name)
-{
-  if(ui->menuAlignment->actions()[0] == ui->no_group_action)
-    {
-      ui->menuAlignment->removeAction(ui->no_group_action);
-    }
-
-  QAction *new_group = new QAction(action_name);
-  new_group->setEnabled(false);
-  ui->menuAlignment->addAction(new_group);
-}
-
-void
-MsIdentificationListWindow::openMassChroQParametersView(
-  MsRunAlignmentGroupSp alignment_group)
-{
-  qDebug();
-}

src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.h

@@ -31,6 +31,7 @@
 #include "msidentificationtableproxymodel.h"
 #include "ui_ms_identification_run_view.h"
 #include "../../widgets/Alignment_group_menu/alignmentgroupmenu.h"
+#include "../../export/export_masschroq_dialog/exportmasschroqdialog.h"
 
 class ProjectWindow;
 
@@ -78,12 +79,9 @@ class MsIdentificationListWindow : public QMainWindow
   void setAlignmentGroup(MsRunAlignmentGroupSp msrun_alignment_group);
   void resizeColumnsToContents();
   QModelIndexList getSelectedIndexes();
-  void checkMsRunAlignmentGroupContent();
   MsIdentificationTableProxyModel *getMsIdentificationProxyModel();
   MsIdentificationTableModel *getMsIdentificationModel();
-  void addValueToAlignmentMenu(QString action_name);
   void virtual closeEvent(QCloseEvent *event) override;
-  void openMassChroQParametersView(MsRunAlignmentGroupSp alignment_group);
 
   public slots:
   void doExportAsOdsFile();
@@ -92,9 +90,10 @@ class MsIdentificationListWindow : public QMainWindow
 
   signals:
   void MsIdentificationDataChanged();
+  void operateMassChroqExportDialog();
 
   protected slots:
-  void doAlignmentGroupParameters(QAction *action_triggered);
+  void doMassChroQParameters();
   void doSearchOn(QString search_on);
   void updateStatusBar();
   void onMsIdentificationSearchEdit(QString protein_search_string);
@@ -105,8 +104,9 @@ class MsIdentificationListWindow : public QMainWindow
 
   private:
   Ui::MsIdentificationView *ui;
-  MsIdentificationTableModel *mp_msidTableModel  = nullptr;
-  MsIdentificationTableProxyModel *mp_proxyModel = nullptr;
+  MsIdentificationTableModel *mp_msidTableModel     = nullptr;
+  MsIdentificationTableProxyModel *mp_proxyModel    = nullptr;
+  ExportMasschroqDialog *mp_export_masschroq_dialog = nullptr;
   ProjectWindow *mp_projectWindow;
-  AlignmentGroupsQMenu *mp_groups_context_menu  = nullptr;
+  AlignmentGroupsQMenu *mp_groups_context_menu = nullptr;
 };

src/gui/project_view/projectwindow.cpp

@@ -107,7 +107,11 @@ ProjectWindow::ProjectWindow(MainWindow *parent)
           &WorkerThread::bestMsrunForAlignmentGroupFinished,
           this,
           &ProjectWindow::doBestMsRunForAlignmentFinished);
-
+  connect(this,
+          &ProjectWindow::operateMassChroqExportDialog,
+          main_window,
+          &MainWindow::doActionMassChroQ);
+  //
   // grouping
   /*
   connect(this,
@@ -143,6 +147,13 @@ ProjectWindow::getProjectP()
 {
   return _project_sp.get();
 }
+
+ProjectSp
+ProjectWindow::getProjectSP()
+{
+  return _project_sp;
+}
+
 void
 ProjectWindow::setDefaultProteinListWindow(
   ProteinListWindow *p_protein_list_window)
@@ -1125,3 +1136,10 @@ ProjectWindow::doCleanMsRunReaders()
         }
     }
 }
+
+void
+ProjectWindow::doOpenMassChroQDialog()
+{
+  qDebug() << "AAAAAAAA";
+  emit operateMassChroqExportDialog();
+}

src/gui/project_view/projectwindow.h

@@ -59,6 +59,7 @@ class ProjectWindow : public QMainWindow
   explicit ProjectWindow(MainWindow *parent = 0);
   Project *getProjectP();
   void setProjectSp(ProjectSp project_sp);
+  ProjectSp getProjectSP();
   void editModifications();
   void editLabelingMethods();
   void openInXicViewer(const PeptideEvidence *p_peptide_evidence);
@@ -92,6 +93,7 @@ class ProjectWindow : public QMainWindow
   void doProjectStatusChanged();
   void doBestMsRunForAlignmentFinished(MsRunSp msrun_sp);
   void doCleanMsRunReaders();
+  void doOpenMassChroQDialog();
   // void setColor(const QColor &color);
   // void setShape(Shape shape);
 
@@ -112,6 +114,7 @@ class ProjectWindow : public QMainWindow
   void projectNameChanged(QString name);
   void projectStatusChanged();
   void bestMsRunFound(MsRunSp msrun_sp);
+  void operateMassChroqExportDialog();
 
   protected:
   void doViewPeptideList(IdentificationGroup *p_ident_group,

src/gui/widgets/Alignment_group_menu/alignmentgroupmenu.cpp

@@ -254,7 +254,6 @@ AlignmentGroupsQMenu::createNewAlignmentGroup()
       if(msrun_alignment_group_position == -1)
         {
           mp_subMenuGroup->addAction(value);
-          mp_msIdListWindow->addValueToAlignmentMenu(value);
           MsRunAlignmentGroupSp new_alignment_group =
             std::make_shared<MsRunAlignmentGroup>(mp_project, value);
           mp_project->addMsRunAlignmentGroupToList(new_alignment_group);