Add Xic export settings

src/gui/edit/edit_settings/edit_settings.ui

@@ -9,8 +9,8 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>366</width>
-    <height>348</height>
+    <width>422</width>
+    <height>395</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -61,6 +61,36 @@
      </item>
     </layout>
    </item>
+   <item>
+    <widget class="QGroupBox" name="groupBox">
+     <property name="title">
+      <string>XIC export</string>
+     </property>
+     <layout class="QHBoxLayout" name="horizontalLayout_4">
+      <item>
+       <widget class="QRadioButton" name="radioButton_3">
+        <property name="text">
+         <string>Area onl&amp;y</string>
+        </property>
+       </widget>
+      </item>
+      <item>
+       <widget class="QRadioButton" name="all_point_radioButton">
+        <property name="text">
+         <string>All points only</string>
+        </property>
+       </widget>
+      </item>
+      <item>
+       <widget class="QRadioButton" name="area_radioButton">
+        <property name="text">
+         <string>Area + All points</string>
+        </property>
+       </widget>
+      </item>
+     </layout>
+    </widget>
+   </item>
    <item>
     <widget class="QGroupBox" name="timstof_setting_group">
      <property name="title">

src/gui/edit/edit_settings/editsettings.cpp

@@ -53,6 +53,17 @@ EditSettings::EditSettings(MainWindow *parent)
     {
       ui->xic_reader_buffered_button->setChecked(false);
     }
+  QString xic_export_type =
+    settings.value("export/xic_files", "area").toString();
+  ui->area_radioButton->setChecked(true);
+  if(xic_export_type == "all")
+    {
+      ui->all_point_radioButton->setChecked(true);
+    }
+  else if(xic_export_type == "both")
+    {
+      ui->radioButton_3->setChecked(true);
+    }
 
   QString tandemwrapper_path =
     settings.value("timstof/tandemwrapper_path", "").toString();
@@ -96,6 +107,17 @@ EditSettings::done(int r)
         }
       settings.setValue("global/xic_extractor", xic_extraction_method);
 
+      QString xic_export_type = "area";
+      if(ui->all_point_radioButton->isChecked())
+        {
+          xic_export_type = "all";
+        }
+      else if(ui->radioButton_3->isChecked())
+        {
+          xic_export_type = "both";
+        }
+      settings.setValue("export/xic_files", xic_export_type);
+
       QString tandemwrapper_path   = ui->tandemwrapper_path_line->text();
       QFileInfo tandemwrapper_file = QFileInfo(tandemwrapper_path);
       if(tandemwrapper_file.exists() && tandemwrapper_file.isExecutable())

src/gui/workerthread.cpp

@@ -879,10 +879,25 @@ WorkerThread::doWriteXicAreaInCsv(QString filename,
   CalcWriterInterface *p_writer = nullptr;
 
   emit loadingMessage(tr("writing TSV files, please wait"));
+  QSettings settings;
+  QString xic_export_file =
+    settings.value("export/xic_files", "area").toString();
   p_writer = new TsvDirectoryWriter(filename);
-  XicAreaSheet(p_writer, xic_boxs);
-  bool all_data = true;
-  XicAreaSheet(p_writer, xic_boxs, all_data);
+  if(xic_export_file == "both")
+    {
+      XicAreaSheet(p_writer, xic_boxs);
+      bool all_data = true;
+      XicAreaSheet(p_writer, xic_boxs, all_data);
+    }
+  else if(xic_export_file == "all")
+    {
+      bool all_data = true;
+      XicAreaSheet(p_writer, xic_boxs, all_data);
+    }
+  else // xic_export_file == "area"
+    {
+      XicAreaSheet(p_writer, xic_boxs);
+    }
   p_writer->close();
   emit exportXicToCsvFinished();
 }

src/output/ods/xicareasheet.cpp

@@ -103,7 +103,8 @@ XicAreaSheet::writeAreaPeackdata(XicBox *xic_box)
       for(pappso::TracePeakCstSPtr trace : isotope.detected_peak_list)
         {
           mp_writer->writeLine();
-          mp_writer->writeCell(xic_box->getMsRunSp()->getFileName());
+          mp_writer->writeCell(
+            QFileInfo(xic_box->getMsRunSp()->getFileName()).fileName());
           mp_writer->writeCell(trace->getArea());
           mp_writer->writeCell(trace->getLeftBoundary().x);
           mp_writer->writeCell(trace->getMaxXicElement().x);
@@ -122,7 +123,8 @@ XicAreaSheet::writeXicAllData(XicBox *xic_box)
       for(std::size_t i = 0; i < isotope.xic_sp->xValues().size(); i++)
         {
           mp_writer->writeLine();
-          mp_writer->writeCell(xic_box->getMsRunSp()->getFileName());
+          mp_writer->writeCell(
+            QFileInfo(xic_box->getMsRunSp()->getFileName()).fileName());
           mp_writer->writeCell(
             int(isotope.peptide_natural_isotope_sp->getIsotopeNumber()));
           mp_writer->writeCell(isotope.xic_sp->xValues().at(i));