GUI updated to choose msrun for alignment either automatic or manual

src/core/msrun.h

@@ -98,3 +98,6 @@ class MsRun : public pappso::MsRunId
   pappso::MsRunRetentionTime<const pappso::Peptide *> *mpa_msrunRetentionTime =
     nullptr;
 };
+
+
+Q_DECLARE_METATYPE(MsRunSp)

src/core/project.cpp

@@ -299,6 +299,13 @@ void
 Project::prepareMsrunRetentionTimesForAlignment() const
 {
   qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+
+  for(auto &msrun_sp : this->getMsRunStore().getMsRunList())
+    {
+      msrun_sp.get()->clearMsRunRetentionTime();
+    }
+
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
   bool is_ok = true;
   PeptideEvidenceStore empty_store;
   for(IdentificationDataSourceSp p_ident_data_source :

src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui

@@ -6,8 +6,8 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>613</width>
-    <height>371</height>
+    <width>635</width>
+    <height>515</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -176,10 +176,22 @@
         </widget>
        </item>
        <item>
-        <widget class="QPushButton" name="pushButton">
-         <property name="text">
-          <string>Find best MS run reference for alignment</string>
+        <widget class="QGroupBox" name="groupBox_4">
+         <property name="title">
+          <string>MSrun reference for alignment</string>
          </property>
+         <layout class="QVBoxLayout" name="verticalLayout_11">
+          <item>
+           <widget class="QPushButton" name="pushButton">
+            <property name="text">
+             <string>Find best MS run reference for alignment</string>
+            </property>
+           </widget>
+          </item>
+          <item>
+           <widget class="QComboBox" name="msrun_list_combo_box"/>
+          </item>
+         </layout>
         </widget>
        </item>
        <item>

src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp

@@ -71,6 +71,7 @@ void
 ExportMasschroqDialog::setProject(const Project *p_project)
 {
   mp_project = p_project;
+  fillMsrunListComboBox();
 }
 
 void
@@ -144,6 +145,15 @@ ExportMasschroqDialog::getMasschroqFileParameters() const
     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;
@@ -327,7 +337,18 @@ ExportMasschroqDialog::doFindBestMsrunForAlignment()
       if(ms_run_best_reference != nullptr)
         {
           qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
-                   << ms_run_best_reference.get()->getXmlId()<< " best_number=" << best_number;
+                   << ms_run_best_reference.get()->getXmlId()
+                   << " best_number=" << best_number;
+
+          for(int index = 0; index < ui->msrun_list_combo_box->count(); index++)
+            {
+              MsRunSp msrun_sp = qvariant_cast<MsRunSp>(
+                ui->msrun_list_combo_box->itemData(index));
+              if(msrun_sp.get() == ms_run_best_reference.get())
+                {
+                  ui->msrun_list_combo_box->setCurrentIndex(index);
+                }
+            }
         }
     }
   catch(pappso::PappsoException &error)
@@ -340,3 +361,23 @@ ExportMasschroqDialog::doFindBestMsrunForAlignment()
       msgBox.exec();
     }
 }
+
+
+void
+ExportMasschroqDialog::fillMsrunListComboBox()
+{
+  ui->msrun_list_combo_box->clear();
+
+  int index = -1;
+  for(auto &msrun_sp : mp_project->getMsRunStore().getMsRunList())
+    {
+      index = 0;
+      ui->msrun_list_combo_box->addItem(
+        QString("%1").arg(msrun_sp.get()->getSampleName()),
+        QVariant::fromValue(msrun_sp));
+    }
+  if(index != -1)
+    { // -1 for not found
+      ui->msrun_list_combo_box->setCurrentIndex(index);
+    }
+}

src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h

@@ -36,21 +36,13 @@
 
 namespace Ui
 {
-  class ExportMasschroqDialog;
+class ExportMasschroqDialog;
 }
 
 class ExportMasschroqDialog : public QDialog
 {
   Q_OBJECT
 
-  private:
-  Ui::ExportMasschroqDialog *ui;
-  const Project *mp_project;
-
-  protected slots:
-  void doCheckMsrunFilepath();
-  void doBrowseMsrunDirectory();
-  void doFindBestMsrunForAlignment();
 
   public:
   explicit ExportMasschroqDialog(QWidget *parent);
@@ -63,5 +55,18 @@ class ExportMasschroqDialog : public QDialog
   void setProject(const Project *p_project);
 
 
+  private:
+  Ui::ExportMasschroqDialog *ui;
+  const Project *mp_project;
+
+  protected slots:
+  void doCheckMsrunFilepath();
+  void doBrowseMsrunDirectory();
+  void doFindBestMsrunForAlignment();
+
+  private:
+  void fillMsrunListComboBox();
+
+
   signals:
 };

src/gui/export/export_masschroq_dialog/masschroqfileparameters.h

@@ -33,6 +33,7 @@
 #include "../../../utils/types.h"
 #include <QString>
 #include <pappsomspp/mzrange.h>
+#include "../../../core/msrun.h"
 
 struct MasschroqFileParameters
 {
@@ -59,4 +60,6 @@ struct MasschroqFileParameters
   pappso::PrecisionPtr xic_extraction_range;
 
   pappso::XicExtractMethod xic_extraction_method; // sum or max
+
+  MsRunSp msrun_alignment_reference;
 };

src/gui/mainwindow.h

@@ -23,8 +23,7 @@
  ******************************************************************************/
 
 
-#ifndef MAINWINDOW_H
-#define MAINWINDOW_H
+#pragma once
 
 #include <QMainWindow>
 #include <QFileInfo>
@@ -150,5 +149,3 @@ class MainWindow : public QMainWindow
 
   HttpVersion m_onlineVersion;
 };
-
-#endif // MAINWINDOW_H

src/gui/project_view/identification_group_widget/identificationgroupwidget.h

@@ -22,8 +22,7 @@
  *implementation
  ******************************************************************************/
 
-#ifndef IDENTIFICATIONGROUPWIDGET_H
-#define IDENTIFICATIONGROUPWIDGET_H
+#pragma once
 
 #include "../projectwindow.h"
 
@@ -59,4 +58,3 @@ class IdentificationGroupWidget : public QWidget
 };
 
 Q_DECLARE_METATYPE(IdentificationGroupWidget *)
-#endif // IDENTIFICATIONGROUPWIDGET_H

src/output/masschroqml.cpp

@@ -452,8 +452,17 @@ MassChroQml::writeAlignments()
   _output_stream->writeAttribute("method_id", "my_ms2");
   std::vector<MsRunSp> msrun_list =
     _sp_project.get()->getMsRunStore().getMsRunList();
-  _output_stream->writeAttribute("reference_data_id",
-                                 msrun_list.front().get()->getXmlId());
+  if(m_params.msrun_alignment_reference == nullptr)
+    {
+      _output_stream->writeAttribute("reference_data_id",
+                                     msrun_list.front().get()->getXmlId());
+    }
+  else
+    {
+      _output_stream->writeAttribute(
+        "reference_data_id",
+        m_params.msrun_alignment_reference.get()->getXmlId());
+    }
   _output_stream->writeEndElement();
   //</alignments>
   _output_stream->writeEndElement();