Correct best msRun issues (clicked didn't work, reference didn't used in mcqml file)

src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui

@@ -120,7 +120,7 @@
                   <item>
                    <widget class="QPushButton" name="pushButton">
                     <property name="text">
-                     <string>Best</string>
+                     <string>Find Best</string>
                     </property>
                    </widget>
                   </item>
@@ -464,8 +464,8 @@
    <slot>doBrowseMsrunDirectory()</slot>
    <hints>
     <hint type="sourcelabel">
-     <x>195</x>
-     <y>381</y>
+     <x>214</x>
+     <y>421</y>
     </hint>
     <hint type="destinationlabel">
      <x>736</x>
@@ -473,6 +473,22 @@
     </hint>
    </hints>
   </connection>
+  <connection>
+   <sender>msrun_list_combo_box</sender>
+   <signal>activated(int)</signal>
+   <receiver>ExportMasschroqDialog</receiver>
+   <slot>doUpdateReferenceInSelectedGroup(int)</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>417</x>
+     <y>432</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>817</x>
+     <y>444</y>
+    </hint>
+   </hints>
+  </connection>
  </connections>
  <slots>
   <slot>reject()</slot>
@@ -481,5 +497,6 @@
   <slot>doBrowseMsrunDirectory()</slot>
   <slot>doFindBestMsrunForAlignment()</slot>
   <slot>doShowMsRunsInAlignmentGroup(QModelIndex)</slot>
+  <slot>doUpdateReferenceInSelectedGroup(int)</slot>
  </slots>
 </ui>

src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp

@@ -157,16 +157,6 @@ ExportMasschroqDialog::getMasschroqFileParameters() const
   params.xic_extraction_method =
     ui->xic_extraction_method_widget->getXicExtractionMethod();
 
-
-  int index = ui->msrun_list_combo_box->currentIndex();
-  if(index != -1)
-    {
-      MsRunSp msrun_sp =
-        qvariant_cast<MsRunSp>(ui->msrun_list_combo_box->itemData(index));
-      params.msrun_alignment_reference = msrun_sp;
-    }
-
-
   qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
            << (int)params.xic_extraction_method;
   return params;
@@ -278,17 +268,17 @@ ExportMasschroqDialog::setBestMsrunForAlignment(MsRunSp best_msrun_sp)
   mp_main->hideWaitingMessage();
   if(best_msrun_sp != nullptr)
     {
-      qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
-               << best_msrun_sp.get()->getXmlId();
+      qDebug() << best_msrun_sp.get();
 
-      for(int index = 0; index < ui->msrun_list_combo_box->count(); index++)
+      int index = 0;
+      for(MsRunSp ms_run : msp_selected_group->getMsRunsInAlignmentGroup())
         {
-          MsRunSp msrun_sp =
-            qvariant_cast<MsRunSp>(ui->msrun_list_combo_box->itemData(index));
-          if(msrun_sp.get() == best_msrun_sp.get())
+          if(ms_run == best_msrun_sp)
             {
               ui->msrun_list_combo_box->setCurrentIndex(index);
+              msp_selected_group->setMsRunReference(best_msrun_sp);
             }
+          index++;
         }
     }
 }
@@ -346,16 +336,33 @@ ExportMasschroqDialog::doShowMsRunsInAlignmentGroup(QModelIndex index)
     }
   if(msp_selected_group->getMsRunReference() != nullptr)
     {
-      std::list<MsRunSp>::iterator it;
-      it = std::find(msp_selected_group->getMsRunsInAlignmentGroup().begin(),
-                     msp_selected_group->getMsRunsInAlignmentGroup().end(),
-                     msp_selected_group->getMsRunReference());
-      int idx = std::distance(
-        msp_selected_group->getMsRunsInAlignmentGroup().begin(), it);
-      ui->msrun_list_combo_box->setCurrentIndex(idx);
+      int index = 0;
+      for(MsRunSp ms_run : msp_selected_group->getMsRunsInAlignmentGroup())
+        {
+          if(ms_run == msp_selected_group->getMsRunReference())
+            {
+              ui->msrun_list_combo_box->setCurrentIndex(index);
+            }
+          index++;
+        }
     }
   else
     {
       ui->msrun_list_combo_box->setCurrentIndex(-1);
     }
 }
+
+void
+ExportMasschroqDialog::doUpdateReferenceInSelectedGroup(int index)
+{
+  int temp_index = 0;
+  for(MsRunSp ms_run : msp_selected_group->getMsRunsInAlignmentGroup())
+    {
+      if(temp_index == index)
+        {
+          msp_selected_group->setMsRunReference(ms_run);
+        }
+      temp_index++;
+    }
+  qDebug() << index;
+}

src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h

@@ -76,6 +76,7 @@ class ExportMasschroqDialog : public QDialog
   void doBrowseMsrunDirectory();
   void doFindBestMsrunForAlignment();
   void doShowMsRunsInAlignmentGroup(QModelIndex index);
+  void doUpdateReferenceInSelectedGroup(int index);
 
   private:
   Ui::ExportMasschroqDialog *ui;

src/gui/export/export_masschroq_dialog/masschroqfileparameters.h

@@ -61,6 +61,5 @@ struct MasschroqFileParameters
 
   pappso::XicExtractMethod xic_extraction_method; // sum or max
 
-  MsRunSp msrun_alignment_reference;
   std::vector<MsRunAlignmentGroupSp> alignment_groups;
 };