Complete xtandem view and add no engine view

src/CMakeLists.txt

@@ -207,6 +207,7 @@ SET(XTPCPP_SRCS
   ./gui/waiting_message_dialog/waitingmessagedialog.cpp
   ./gui/widgets/automatic_filter_widget/automaticfilterwidget.cpp
   ./gui/widgets/engines_view/xtandemparamwidget.cpp
+  ./gui/widgets/engines_view/noengineparamwidget.cpp
   ./gui/widgets/contaminant_widget/contaminantwidget.cpp
   ./gui/widgets/decoy_widget/decoywidget.cpp
   ./gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.cpp
@@ -245,6 +246,7 @@ SET (GUI_UIS
   ./gui/waiting_message_dialog/waiting_message_dialog.ui
   ./gui/widgets/automatic_filter_widget/automatic_filter_widget.ui
   ./gui/widgets/engines_view/xtandem_view_widget.ui
+  ./gui/widgets/engines_view/no_engine_view_widget.ui
   ./gui/widgets/contaminant_widget/contaminant_widget.ui
   ./gui/widgets/decoy_widget/decoy_widget.ui
   ./gui/xic_view/xic_box/xic_box.ui

src/gui/lists/ms_identification_run_list_view/engine_detail_view/engine_detail_view.ui

@@ -20,63 +20,56 @@
    <property name="contextMenuPolicy">
     <enum>Qt::CustomContextMenu</enum>
    </property>
-   <layout class="QVBoxLayout" name="verticalLayout">
+   <layout class="QHBoxLayout" name="horizontalLayout_3">
     <item>
-     <layout class="QHBoxLayout" name="horizontalLayout_2">
+     <layout class="QVBoxLayout" name="verticalLayout">
       <item>
-       <widget class="QLabel" name="labelEngineName">
-        <property name="text">
-         <string>Engine name</string>
-        </property>
-       </widget>
+       <layout class="QHBoxLayout" name="horizontalLayout_2">
+        <item>
+         <widget class="QLabel" name="labelEngineName">
+          <property name="text">
+           <string>Engine name</string>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <widget class="QLabel" name="labelEngineVersion">
+          <property name="text">
+           <string>Engine Version</string>
+          </property>
+         </widget>
+        </item>
+       </layout>
       </item>
       <item>
-       <widget class="QLabel" name="labelEngineVersion">
-        <property name="text">
-         <string>Engine Version</string>
-        </property>
-       </widget>
-      </item>
-     </layout>
-    </item>
-    <item>
-     <widget class="XtandemParamWidget" name="xtandem_view_widget" native="true"/>
-    </item>
-    <item>
-     <layout class="QHBoxLayout" name="horizontalLayout">
-      <item>
-       <spacer name="horizontalSpacer">
-        <property name="orientation">
-         <enum>Qt::Horizontal</enum>
-        </property>
-        <property name="sizeHint" stdset="0">
-         <size>
-          <width>40</width>
-          <height>20</height>
-         </size>
-        </property>
-       </spacer>
-      </item>
-      <item>
-       <widget class="QPushButton" name="closeButton">
-        <property name="text">
-         <string>Close</string>
-        </property>
-       </widget>
+       <layout class="QHBoxLayout" name="horizontalLayout">
+        <item>
+         <spacer name="horizontalSpacer">
+          <property name="orientation">
+           <enum>Qt::Horizontal</enum>
+          </property>
+          <property name="sizeHint" stdset="0">
+           <size>
+            <width>40</width>
+            <height>20</height>
+           </size>
+          </property>
+         </spacer>
+        </item>
+        <item>
+         <widget class="QPushButton" name="closeButton">
+          <property name="text">
+           <string>Close</string>
+          </property>
+         </widget>
+        </item>
+       </layout>
       </item>
      </layout>
     </item>
    </layout>
   </widget>
  </widget>
- <customwidgets>
-  <customwidget>
-   <class>XtandemParamWidget</class>
-   <extends>QWidget</extends>
-   <header>gui/widgets/engines_view/xtandemparamwidget.h</header>
-   <container>1</container>
-  </customwidget>
- </customwidgets>
  <resources/>
  <connections>
   <connection>

src/gui/lists/ms_identification_run_list_view/engine_detail_view/enginedetailwindow.cpp

@@ -24,7 +24,8 @@
 
 #include "ui_engine_detail_view.h"
 #include "enginedetailwindow.h"
-
+#include "gui/widgets/engines_view/xtandemparamwidget.h"
+#include "gui/widgets/engines_view/noengineparamwidget.h"
 #include "../../../mainwindow.h"
 #include <QSettings>
 
@@ -53,11 +54,33 @@ EngineDetailWindow::setIdentificationEngineParam(
 void
 EngineDetailWindow::updateDisplay()
 {
+  QString params_file = m_identificationEngine->get()->getResourceName();
+
   ui->labelEngineName->setText(
     m_identificationEngine->get()->getIdentificationEngineName());
   ui->labelEngineVersion->setText(
     m_identificationEngine->get()->getIdentificationEngineVersion());
-  m_params_file = m_identificationEngine->get()->getResourceName();
 
-  ui->xtandem_view_widget->setAutomaticXTandemParameters(m_params_file);
+  TandemParametersFile param_file(params_file);
+  if(param_file.exists())
+    {
+      TandemParameters xtandem_parameters = param_file.getTandemParameters();
+
+      if(m_identificationEngine->get()->getIdentificationEngineName() ==
+         "X!Tandem")
+        {
+          XtandemParamWidget *xtandem_view_widget;
+          xtandem_view_widget = new XtandemParamWidget(this);
+          ui->verticalLayout->insertWidget(1, xtandem_view_widget);
+
+          xtandem_view_widget->setAutomaticXTandemParameters(
+            xtandem_parameters);
+        }
+    }
+  else
+    {
+      NoEngineParamWidget *no_engine_view_widget;
+      no_engine_view_widget = new NoEngineParamWidget(this, params_file);
+      ui->verticalLayout->insertWidget(1, no_engine_view_widget);
+    }
 }

src/gui/lists/ms_identification_run_list_view/engine_detail_view/enginedetailwindow.h

@@ -55,6 +55,5 @@ class EngineDetailWindow : public QMainWindow
   private:
   Ui::EngineDetailView *ui;
   ProjectWindow *m_project_window;
-  QString m_params_file;
   IdentificationDataSourceSp *m_identificationEngine = nullptr;
 };

src/gui/widgets/engines_view/no_engine_view_widget.ui

+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>NoEngineParamWidget</class>
+ <widget class="QWidget" name="NoEngineParamWidget">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>605</width>
+    <height>740</height>
+   </rect>
+  </property>
+  <property name="font">
+   <font>
+    <pointsize>16</pointsize>
+   </font>
+  </property>
+  <property name="windowTitle">
+   <string>Form</string>
+  </property>
+  <layout class="QGridLayout" name="gridLayout_7">
+   <item row="0" column="0">
+    <layout class="QVBoxLayout" name="verticalLayout">
+     <item>
+      <spacer name="verticalSpacer_2">
+       <property name="orientation">
+        <enum>Qt::Vertical</enum>
+       </property>
+       <property name="sizeHint" stdset="0">
+        <size>
+         <width>20</width>
+         <height>40</height>
+        </size>
+       </property>
+      </spacer>
+     </item>
+     <item>
+      <widget class="QLabel" name="label">
+       <property name="text">
+        <string>label</string>
+       </property>
+       <property name="alignment">
+        <set>Qt::AlignCenter</set>
+       </property>
+      </widget>
+     </item>
+     <item>
+      <spacer name="verticalSpacer">
+       <property name="orientation">
+        <enum>Qt::Vertical</enum>
+       </property>
+       <property name="sizeHint" stdset="0">
+        <size>
+         <width>20</width>
+         <height>40</height>
+        </size>
+       </property>
+      </spacer>
+     </item>
+    </layout>
+   </item>
+  </layout>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>

src/gui/widgets/engines_view/noengineparamwidget.cpp

+
+/*******************************************************************************
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ *     XTPcpp is free software: you can redistribute it and/or modify
+ *     it under the terms of the GNU General Public License as published by
+ *     the Free Software Foundation, either version 3 of the License, or
+ *     (at your option) any later version.
+ *
+ *     XTPcpp is distributed in the hope that it will be useful,
+ *     but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *     GNU General Public License for more details.
+ *
+ *     You should have received a copy of the GNU General Public License
+ *     along with XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ *     Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
+
+#include "noengineparamwidget.h"
+
+#include "../../project_view/projectwindow.h"
+#include "ui_no_engine_view_widget.h"
+#include <QDebug>
+
+NoEngineParamWidget::NoEngineParamWidget(QWidget *parent, QString file_name)
+  : QWidget(parent), ui(new Ui::NoEngineParamWidget)
+{
+  qDebug() << "begin";
+  ui->setupUi(this);
+
+  QString message =
+    file_name + "\nwasn't found !!\n Please check if the file exist";
+  ui->label->setText(message);
+  qDebug() << "end";
+}
+
+NoEngineParamWidget::~NoEngineParamWidget()
+{
+  qDebug() << "NoEngineParamWidget::~NoEngineParamWidget";
+  delete ui;
+  qDebug() << "end";
+}

src/gui/widgets/engines_view/noengineparamwidget.h

+
+/*******************************************************************************
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ *     XTPcpp is free software: you can redistribute it and/or modify
+ *     it under the terms of the GNU General Public License as published by
+ *     the Free Software Foundation, either version 3 of the License, or
+ *     (at your option) any later version.
+ *
+ *     XTPcpp is distributed in the hope that it will be useful,
+ *     but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *     GNU General Public License for more details.
+ *
+ *     You should have received a copy of the GNU General Public License
+ *     along with XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ *     Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
+
+#pragma once
+
+#include <QWidget>
+
+
+namespace Ui
+{
+class NoEngineParamWidget;
+}
+
+class NoEngineParamWidget : public QWidget
+{
+  Q_OBJECT
+
+  public:
+  explicit NoEngineParamWidget(QWidget *parent, QString file_name);
+  ~NoEngineParamWidget();
+
+  Ui::NoEngineParamWidget *ui;
+};

src/gui/widgets/engines_view/xtandemparamwidget.cpp

@@ -47,13 +47,10 @@ XtandemParamWidget::~XtandemParamWidget()
 }
 
 void
-XtandemParamWidget::setAutomaticXTandemParameters(QString params_file)
+XtandemParamWidget::setAutomaticXTandemParameters(
+  TandemParameters xtandem_parameters)
 {
   qDebug() << "begin ";
-  // TandemParametersFile param_file(params_file);
-  TandemParametersFile param_file("/home/trenne/test_tandem.xml");
-  TandemParameters xtandem_parameters = param_file.getTandemParameters();
-
   setSpectrumParameters(xtandem_parameters);
   setProteinParameters(xtandem_parameters);
   setResidueParameters(xtandem_parameters);
@@ -67,11 +64,77 @@ XtandemParamWidget::setAutomaticXTandemParameters(QString params_file)
 void
 XtandemParamWidget::setSpectrumParameters(TandemParameters xtandem_parameters)
 {
+  ui->parenttIonMHMassToleranceWindowUnitLineEdit->setText(
+    xtandem_parameters.getValue(
+      "spectrum, parent monoisotopic mass error units"));
+  ui->parentIonMHMassToleranceLowerWindowLineEdit->setText(
+    xtandem_parameters.getValue(
+      "spectrum, parent monoisotopic mass error minus"));
+  ui->parentIonMHMassToleranceUpperWindowLineEdit->setText(
+    xtandem_parameters.getValue(
+      "spectrum, parent monoisotopic mass error plus"));
+  ui->anticipateCarbonIsotopeParentIonAssignmentsErrorsLineEdit->setText(
+    xtandem_parameters.getValue(
+      "spectrum, parent monoisotopic mass isotope error"));
+  ui->setTheMaximumPrecursorChargeToBeScoredLineEdit->setText(
+    xtandem_parameters.getValue("spectrum, maximum parent charge"));
+  ui->useChemicalAverageOrMonoisotopicMassForFragmentIonsLineEdit->setText(
+    xtandem_parameters.getValue("spectrum, fragment mass type"));
+  ui->unitsForFragmentIonMassToleranceMonoisotopicLineEdit->setText(
+    xtandem_parameters.getValue(
+      "spectrum, fragment monoisotopic mass error units"));
+  ui->fragmentIonMassToleranceMonoisotopicLineEdit->setText(
+    xtandem_parameters.getValue(
+      "spectrum, parent monoisotopic mass error minus"));
+  ui->controlTheUseOfTheNeutralLossWindowLineEdit->setText(
+    xtandem_parameters.getValue("spectrum, use neutral loss window"));
+  ui->neutralLossMassLineEdit->setText(
+    xtandem_parameters.getValue("spectrum, neutral loss mass"));
+  ui->neutralLossWindowDaltonsLineEdit->setText(
+    xtandem_parameters.getValue("spectrum, neutral loss window"));
+  ui->setTheDynamicRangeToScoreSpectraLineEdit->setText(
+    xtandem_parameters.getValue("spectrum, dynamic range"));
+  ui->maximumNumberOfPeaksToUseInASpectrumLineEdit->setText(
+    xtandem_parameters.getValue("spectrum, total peaks"));
+  ui->minimumNumberOfPeaksForASpectrumToBeConsideredLineEdit->setText(
+    xtandem_parameters.getValue("spectrum, minimum peaks"));
+  ui->minimumMZFragmentToBeConsideredLineEdit->setText(
+    xtandem_parameters.getValue("spectrum, minimum fragment mz"));
+  ui->minimumParentMHToBeConsideredLineEdit->setText(
+    xtandem_parameters.getValue("spectrum, minimum parent m+h"));
+  ui->alterHowProteinSequencesAreRetrievedFromFASTAFilesLineEdit->setText(
+    xtandem_parameters.getValue("spectrum, sequence batch size"));
+  ui->useContrastAngleLineEdit->setText(
+    xtandem_parameters.getValue("spectrum, use contrast angle"));
+  ui->setNumberOfThreadsLineEdit->setText(
+    xtandem_parameters.getValue("spectrum, threads"));
 }
 
 void
 XtandemParamWidget::setProteinParameters(TandemParameters xtandem_parameters)
 {
+  ui->defineProteinCleavageSiteLineEdit->setText(
+    xtandem_parameters.getValue("protein, cleavage site"));
+  ui->useSemiEnzymaticCleavageRulesLineEdit->setText(
+    xtandem_parameters.getValue("protein, cleavage semi"));
+  ui->moietyAddedToPeptideCTerminusByCleavageLineEdit->setText(
+    xtandem_parameters.getValue("protein, cleavage C-terminal mass change"));
+  ui->moietyAddedToPeptideNTerminusByCleavageLineEdit->setText(
+    xtandem_parameters.getValue("protein, cleavage N-terminal mass change"));
+  ui->moietyAddedToProteinCTerminusLineEdit->setText(
+    xtandem_parameters.getValue(
+      "protein, C-terminal residue modification mass"));
+  ui->moietyAddedToProteinNTerminusLineEdit->setText(
+    xtandem_parameters.getValue(
+      "protein, N-terminal residue modification mass"));
+  ui->proteinNTerminusCommonModificationsLineEdit->setText(
+    xtandem_parameters.getValue("protein, quick acetyl"));
+  ui->proteinNTerminusCyclisationLineEdit->setText(
+    xtandem_parameters.getValue("protein, quick pyrolidone"));
+  ui->interpretationOfPeptidePhosphorylationModelLineEdit->setText(
+    xtandem_parameters.getValue("protein, stP bias"));
+  ui->modifyTheResidueMassesOfOneAllAminoAcidsLineEdit->setText(
+    xtandem_parameters.getValue("protein, modified residue mass file"));
 }
 
 void
@@ -93,6 +156,20 @@ XtandemParamWidget::setResidueParameters(TandemParameters xtandem_parameters)
 void
 XtandemParamWidget::setScoringParameters(TandemParameters xtandem_parameters)
 {
+  ui->minimumNumberOfIonsToScoreAPeptideLineEdit->setText(
+    xtandem_parameters.getValue("scoring, minimum ion count"));
+  ui->maximumMissedCleavageSitesLineEdit->setText(
+    xtandem_parameters.getValue("scoring, maximum missed cleavage sites"));
+  ui->compensateForVerySmallSequenceListFileLineEdit->setText(
+    xtandem_parameters.getValue("scoring, cyclic permutation"));
+  ui->automaticallyPerformReverseDatabaseSearchLineEdit->setText(
+    xtandem_parameters.getValue("scoring, include reverse"));
+  ui->useYIonsLineEdit->setText(xtandem_parameters.getValue("scoring, y ions"));
+  ui->useBIonsLineEdit->setText(xtandem_parameters.getValue("scoring, b ions"));
+  ui->useCIonsLineEdit->setText(xtandem_parameters.getValue("scoring, c ions"));
+  ui->useZIonsLineEdit->setText(xtandem_parameters.getValue("scoring, z ions"));
+  ui->useAIonsLineEdit->setText(xtandem_parameters.getValue("scoring, a ions"));
+  ui->useXIonsLineEdit->setText(xtandem_parameters.getValue("scoring, x ions"));
 }
 
 void
@@ -145,4 +222,31 @@ XtandemParamWidget::setRefineParameters(TandemParameters xtandem_parameters)
 void
 XtandemParamWidget::setOutputParameters(TandemParameters xtandem_parameters)
 {
+  ui->highestEValueToRecordPeptidesLineEdit->setText(
+    xtandem_parameters.getValue("output, maximum valid expectation value"));
+  ui->highestEValueToRecordProteinsLineEdit->setText(
+    xtandem_parameters.getValue(
+      "output, maximum valid protein expectation value"));
+  ui->resultsTypeLineEdit->setText(
+    xtandem_parameters.getValue("output, results"));
+  ui->sortResultsByLineEdit->setText(
+    xtandem_parameters.getValue("output, sort results by"));
+  ui->writeProteinsLineEdit->setText(
+    xtandem_parameters.getValue("output, proteins"));
+  ui->writeProteinSequencesLineEdit->setText(
+    xtandem_parameters.getValue("output, sequences"));
+  ui->writeOnlyFirstProteinSequenceLineEdit->setText(
+    xtandem_parameters.getValue("output, one sequence copy"));
+  ui->writeSpectrumInformationsLineEdit->setText(
+    xtandem_parameters.getValue("output, spectra"));
+  ui->writeParametersLineEdit->setText(
+    xtandem_parameters.getValue("output, parameters"));
+  ui->writeHistogramsLineEdit->setText(
+    xtandem_parameters.getValue("output, histograms"));
+  ui->histogramColumnWidthLineEdit->setText(
+    xtandem_parameters.getValue("output, histogram column width"));
+  ui->hashFilenameWithDateAndTimeStampLineEdit->setText(
+    xtandem_parameters.getValue("output, path hashing"));
+  ui->xSLTStyleSheetPathToViewXMLResultsLineEdit->setText(
+    xtandem_parameters.getValue("output, xsl path"));
 }

src/gui/widgets/engines_view/xtandemparamwidget.h

@@ -41,7 +41,7 @@ class XtandemParamWidget : public QWidget
   explicit XtandemParamWidget(QWidget *parent);
   ~XtandemParamWidget();
 
-  void setAutomaticXTandemParameters(QString params_file);
+  void setAutomaticXTandemParameters(TandemParameters xtandem_parameters);
 
   private slots: