add remove old MsRun from alignment group

src/core/alignmentgroup.cpp

@@ -46,8 +46,19 @@ MsRunAlignmentGroup::setMsRunAlignmentGroupName(QString group_name)
   m_groupName = group_name;
 }
 
-std::vector<MsRunSp>
+std::list<MsRunSp>
 MsRunAlignmentGroup::getMsRunsInAlignmentGroup()
 {
   return m_msrunAlignmentGroupList;
 }
+
+void
+MsRunAlignmentGroup::addMsRunToMsRunAlignmentGroupList(MsRunSp new_msrun)
+{
+  m_msrunAlignmentGroupList.push_back(new_msrun);
+}
+
+void MsRunAlignmentGroup::removeMsRunFromMsRunAlignmentGroupList(MsRunSp removed_msrun)
+{
+  m_msrunAlignmentGroupList.remove(removed_msrun);
+}

src/core/alignmentgroup.h

@@ -34,15 +34,17 @@ class MsRunAlignmentGroup
   public:
   MsRunAlignmentGroup(QString group_name);
   ~MsRunAlignmentGroup();
-  
+
   void setMsRunAlignmentGroupName(QString group_name);
   QString getMsRunAlignmentGroupName();
-  
-  std::vector<MsRunSp> getMsRunsInAlignmentGroup();
-  
+
+  std::list<MsRunSp> getMsRunsInAlignmentGroup();
+
+  void addMsRunToMsRunAlignmentGroupList(MsRunSp new_msrun);
+  void removeMsRunFromMsRunAlignmentGroupList(MsRunSp removed_msrun);
 
   private:
   QString m_groupName;
-  std::vector<MsRunSp> m_msrunAlignmentGroupList;
-  //MsRunSp msp_reference_ms_run = nullptr;
+  std::list<MsRunSp> m_msrunAlignmentGroupList;
+  // MsRunSp msp_reference_ms_run = nullptr;
 };

src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.cpp

@@ -317,13 +317,35 @@ MsIdentificationListWindow::doProjectNameChanged(QString name)
 }
 
 void
-MsIdentificationListWindow::setAlignmentGroup(QString group_name)
+MsIdentificationListWindow::setAlignmentGroup(
+  MsRunAlignmentGroupSp msrun_alignment_group)
 {
-  qDebug()
-    << m_project_window->getProjectP()->getMsRunAlignmentGroupList().size();
   foreach(QModelIndex index, getSelectedIndexes())
     {
-      m_proxy_model->setData(index, group_name, Qt::EditRole);
+      int position = m_proxy_model->mapToSource(index).row();
+
+      MsRunSp ms_run = m_msid_table_model_p->getIdentificationDataSourceSpList()
+                         .at(position)
+                         ->getMsRunSp();
+
+      if(msrun_alignment_group != nullptr)
+        {
+          msrun_alignment_group.get()->addMsRunToMsRunAlignmentGroupList(
+            ms_run);
+
+          m_proxy_model->setData(
+            index,
+            msrun_alignment_group->getMsRunAlignmentGroupName(),
+            Qt::EditRole);
+        }
+      else
+        {
+          ms_run.get()
+            ->getAlignmentGroup()
+            ->removeMsRunFromMsRunAlignmentGroupList(ms_run);
+
+          m_proxy_model->setData(index, QVariant(), Qt::EditRole);
+        }
     }
 }
 

src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.h

@@ -74,7 +74,7 @@ class MsIdentificationListWindow : public QMainWindow
                                             bool toggled);
   bool
   getMsIdentificationListColumnDisplay(msIdentificationListColumn column) const;
-  void setAlignmentGroup(QString group_name);
+  void setAlignmentGroup(MsRunAlignmentGroupSp msrun_alignment_group);
   void resizeColumnsToContents();
   QModelIndexList getSelectedIndexes();
   void virtual closeEvent(QCloseEvent *event) override;

src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.cpp

@@ -470,19 +470,30 @@ MsIdentificationTableModel::setData(const QModelIndex &index,
       if(index.column() ==
          (std::int8_t)msIdentificationListColumn::align_groups)
         {
-          foreach(MsRunAlignmentGroupSp temp,
-                  mp_project->getMsRunAlignmentGroupList())
+          if(!new_data.isNull())
             {
-              if(temp->getMsRunAlignmentGroupName() == new_data)
+              foreach(MsRunAlignmentGroupSp msrun_alignment_group,
+                      mp_project->getMsRunAlignmentGroupList())
                 {
-                  m_identificationDataSourceSpList.at(index.row())
-                    ->getMsRunSp()
-                    ->setAlignmentGroup(temp);
+                  if(msrun_alignment_group->getMsRunAlignmentGroupName() ==
+                     new_data)
+                    {
+                      m_identificationDataSourceSpList.at(index.row())
+                        ->getMsRunSp()
+                        ->setAlignmentGroup(msrun_alignment_group);
+                      return true;
+                    }
                 }
             }
-
-          return true;
+          else
+            {
+              m_identificationDataSourceSpList.at(index.row())
+                ->getMsRunSp()
+                ->setAlignmentGroup(nullptr);
+              return true;
+            }
         }
+      return false;
     }
   return false;
 }

src/gui/widgets/Alignment_group_menu/alignmentgroupmenu.cpp

@@ -72,7 +72,7 @@ AlignmentGroupsQMenu::actionTriggered(QAction *action_triggered)
   if(action_triggered->text() == "&Ungroup")
     {
       qDebug() << "ungroup";
-      mp_msIdListWindow->setAlignmentGroup(NULL);
+      mp_msIdListWindow->setAlignmentGroup(nullptr);
     }
   else if(action_triggered->text() == "&New Group")
     {
@@ -87,35 +87,53 @@ AlignmentGroupsQMenu::actionTriggered(QAction *action_triggered)
       if(ok_clicked)
         {
           qDebug() << value;
-          if(alignmentGroupNameIsNew(value))
+          int msrun_alignment_group_position =
+            getMsRunAlignmentGroupPosition(value);
+            
+          if(msrun_alignment_group_position == -1)
             {
               mp_subMenuGroup->addAction(value);
 
-              msp_alignmentGroup = std::make_shared<MsRunAlignmentGroup>(value);
+              MsRunAlignmentGroupSp new_alignment_group =
+                std::make_shared<MsRunAlignmentGroup>(value);
 
-              mp_project->addMsRunAlignmentGroupToList(msp_alignmentGroup);
+              mp_project->addMsRunAlignmentGroupToList(new_alignment_group);
+              mp_msIdListWindow->setAlignmentGroup(new_alignment_group);
+            }
+          else
+            {
+              mp_msIdListWindow->setAlignmentGroup(
+                m_msrunAlignmentGroupList.at(msrun_alignment_group_position));
             }
-          mp_msIdListWindow->setAlignmentGroup(value);
         }
     }
   else
     {
       qDebug() << "Existing Group ";
-      mp_msIdListWindow->setAlignmentGroup(action_triggered->text());
+
+      foreach(MsRunAlignmentGroupSp existing_group,
+              mp_project->getMsRunAlignmentGroupList())
+        {
+          mp_msIdListWindow->setAlignmentGroup(existing_group);
+        }
     }
 }
 
-bool
-AlignmentGroupsQMenu::alignmentGroupNameIsNew(QString new_name)
+int
+AlignmentGroupsQMenu::getMsRunAlignmentGroupPosition(QString new_name)
 {
-  bool group_name_is_new = true;
+  int group_name_position = -1;
+  auto it                 = std::find_if(m_msrunAlignmentGroupList.begin(),
+                         m_msrunAlignmentGroupList.end(),
+                         [&new_name](const MsRunAlignmentGroupSp &obj) {
+                           return obj->getMsRunAlignmentGroupName() == new_name;
+                         });
 
-  foreach(MsRunAlignmentGroupSp alignment_group, m_msrunAlignmentGroupList)
+  if(it != m_msrunAlignmentGroupList.end())
     {
-      if(alignment_group->getMsRunAlignmentGroupName() == new_name)
-        {
-          return group_name_is_new = false;
-        }
+      group_name_position =
+        std::distance(m_msrunAlignmentGroupList.begin(), it);
     }
-  return group_name_is_new;
+
+  return group_name_position;
 }

src/gui/widgets/Alignment_group_menu/alignmentgroupmenu.h

@@ -45,14 +45,13 @@ class AlignmentGroupsQMenu : public QMenu
   void createGroupsSubMenu();
 
   private:
-  bool alignmentGroupNameIsNew(QString new_name);
+  int getMsRunAlignmentGroupPosition(QString new_name);
 
   public slots:
   void actionTriggered(QAction *action);
 
   private:
   MsIdentificationListWindow *mp_msIdListWindow;
-  MsRunAlignmentGroupSp msp_alignmentGroup;
   std::vector<MsRunAlignmentGroupSp> m_msrunAlignmentGroupList;
   QMenu *mp_subMenuGroup;
   Project *mp_project;