add xtandem parameters to engine detail

src/CMakeLists.txt

@@ -206,6 +206,7 @@ SET(XTPCPP_SRCS
   ./gui/tandem_run_dialog/tandemrundialog.cpp
   ./gui/waiting_message_dialog/waitingmessagedialog.cpp
   ./gui/widgets/automatic_filter_widget/automaticfilterwidget.cpp
+  ./gui/widgets/engines_view/xtandemparamwidget.cpp
   ./gui/widgets/contaminant_widget/contaminantwidget.cpp
   ./gui/widgets/decoy_widget/decoywidget.cpp
   ./gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.cpp
@@ -243,6 +244,7 @@ SET (GUI_UIS
   ./gui/tandem_run_dialog/tandem_run_dialog.ui
   ./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/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/enginedetailwindow.cpp

@@ -27,8 +27,7 @@
 
 #include "../../../mainwindow.h"
 #include <QSettings>
-#include <odsstream/odsdocwriter.h>
-#include <odsstream/qtablewriter.h>
+
 
 EngineDetailWindow::EngineDetailWindow(ProjectWindow *parent)
   : QMainWindow(parent), ui(new Ui::EngineDetailView)
@@ -36,7 +35,6 @@ EngineDetailWindow::EngineDetailWindow(ProjectWindow *parent)
   m_project_window = parent;
   ui->setupUi(this);
   setWindowIcon(QIcon(":/xtpcpp_icon/resources/xtandempipeline_icon.svg"));
-
 }
 
 
@@ -45,15 +43,21 @@ EngineDetailWindow::~EngineDetailWindow()
 }
 
 void
-EngineDetailWindow::setIdentificationEngineParam(IdentificationDataSourceSp *identificationEngine)
+EngineDetailWindow::setIdentificationEngineParam(
+  IdentificationDataSourceSp *identificationEngine)
 {
   m_identificationEngine = identificationEngine;
   updateDisplay();
 }
 
-void EngineDetailWindow::updateDisplay()
+void
+EngineDetailWindow::updateDisplay()
 {
-  ui->labelEngineName->setText(m_identificationEngine->get()->getIdentificationEngineName());
-  ui->labelEngineVersion->setText(m_identificationEngine->get()->getIdentificationEngineVersion());
-  //ui->alterFixedModifications1Label->setText(m_identificationEngine->get()->getIdentificationEngine));
+  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);
 }

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

@@ -46,13 +46,15 @@ class EngineDetailWindow : public QMainWindow
   public:
   explicit EngineDetailWindow(ProjectWindow *parent = 0);
   ~EngineDetailWindow();
-  void setIdentificationEngineParam(IdentificationDataSourceSp *identificationEngine);
+  void setIdentificationEngineParam(
+    IdentificationDataSourceSp *identificationEngine);
 
   protected:
   void updateDisplay();
-  
+
   private:
   Ui::EngineDetailView *ui;
   ProjectWindow *m_project_window;
+  QString m_params_file;
   IdentificationDataSourceSp *m_identificationEngine = nullptr;
 };

src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.cpp

@@ -146,7 +146,8 @@ MsIdentificationListWindow::doExportAsOdsFile()
 }
 
 void
-MsIdentificationListWindow::askEngineDetailView(IdentificationDataSourceSp *identificationEngine)
+MsIdentificationListWindow::askEngineDetailView(
+  IdentificationDataSourceSp *identificationEngine)
 {
   qDebug() << "begin";
   m_project_window->doViewEngineDetail(identificationEngine);

src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.h

@@ -67,7 +67,7 @@ class MsIdentificationListWindow : public QMainWindow
 
   protected:
   void askEngineDetailView(IdentificationDataSourceSp *identificationEngine);
-  
+
   private:
   Ui::MsIdentificationView *ui;
   MsIdentificationTableModel *m_msid_table_model_p = nullptr;

src/gui/lists/ms_identification_run_list_view/msidentificationtableproxymodel.cpp

@@ -192,9 +192,10 @@ MsIdentificationTableProxyModel::onTableClicked(const QModelIndex &index)
 
   QModelIndex source_index(this->mapToSource(index));
   int row = source_index.row();
-  
-  m_identificationEngine = m_msid_table_model_p->getIdentificationDataSourceSpList().at(row);
-  
+
+  m_identificationEngine =
+    m_msid_table_model_p->getIdentificationDataSourceSpList().at(row);
+
   msIdentificationListColumn col =
     (msIdentificationListColumn)source_index.column();
   if(col == msIdentificationListColumn::engine_name)

src/gui/widgets/engines_view/xtandemparamwidget.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 "xtandemparamwidget.h"
+
+#include "../../project_view/projectwindow.h"
+#include "ui_xtandem_view_widget.h"
+#include <QDebug>
+#include <files/tandemparametersfile.h>
+
+
+XtandemParamWidget::XtandemParamWidget(QWidget *parent)
+  : QWidget(parent), ui(new Ui::XtandemParamWidget)
+{
+  qDebug() << "begin";
+  ui->setupUi(this);
+
+  qDebug() << "end";
+}
+
+XtandemParamWidget::~XtandemParamWidget()
+{
+  qDebug() << "XtandemParamWidget::~XtandemParamWidget";
+  delete ui;
+  qDebug() << "end";
+}
+
+void
+XtandemParamWidget::setAutomaticXTandemParameters(QString params_file)
+{
+  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);
+  setScoringParameters(xtandem_parameters);
+  setRefineParameters(xtandem_parameters);
+  setOutputParameters(xtandem_parameters);
+
+  qDebug() << "end ";
+}
+
+void
+XtandemParamWidget::setSpectrumParameters(TandemParameters xtandem_parameters)
+{
+}
+
+void
+XtandemParamWidget::setProteinParameters(TandemParameters xtandem_parameters)
+{
+}
+
+void
+XtandemParamWidget::setResidueParameters(TandemParameters xtandem_parameters)
+{
+  ui->fixedModificationsLineEdit->setText(
+    xtandem_parameters.getValue("residue, modification mass"));
+  ui->fixedModifications1LineEdit->setText(
+    xtandem_parameters.getValue("residue, modification mass 1"));
+  ui->fixedModifications2LineEdit->setText(
+    xtandem_parameters.getValue("residue, modification mass 2"));
+
+  ui->potentialModificationsLineEdit->setText(
+    xtandem_parameters.getValue("residue, potential modification mass"));
+  ui->potentialModificationsMotifLineEdit->setText(
+    xtandem_parameters.getValue("residue, potential modification motif"));
+}
+
+void
+XtandemParamWidget::setScoringParameters(TandemParameters xtandem_parameters)
+{
+}
+
+void
+XtandemParamWidget::setRefineParameters(TandemParameters xtandem_parameters)
+{
+  ui->useOfTheRefinementModuleLineEdit->setText(
+    xtandem_parameters.getValue("refine"));
+  ui->maximumEValueToAcceptPeptideLineEdit->setText(
+    xtandem_parameters.getValue("refine, maximum valid expectation value"));
+
+  ui->peptideNTerPotentialModificationsLineEdit->setText(
+    xtandem_parameters.getValue("refine, potential N-terminus modifications"));
+  ui->peptideCTerPotentialModificationsLineEdit->setText(
+    xtandem_parameters.getValue("refine, potential C-terminus modifications"));
+
+  ui->alterFixedModificationsLineEdit->setText(
+    xtandem_parameters.getValue("refine, modification mass"));
+  ui->alterFixedModifications1LineEdit->setText(
+    xtandem_parameters.getValue("refine, modification mass 1"));
+  ui->alterFixedModifications2LineEdit->setText(
+    xtandem_parameters.getValue("refine, modification mass 2"));
+
+  ui->alterFixedModificationsLineEdit->setText(
+    xtandem_parameters.getValue("refine, potential modification mass"));
+  ui->alterFixedModifications1LineEdit->setText(
+    xtandem_parameters.getValue("refine, potential modification mass 1"));
+  ui->alterFixedModifications2LineEdit->setText(
+    xtandem_parameters.getValue("refine, potential modification mass 2"));
+
+  ui->potentialModificationsMotifLineEdit_2->setText(
+    xtandem_parameters.getValue("refine, potential modification motif"));
+  ui->potentialModificationsMotif1LineEdit->setText(
+    xtandem_parameters.getValue("refine, potential modification motif 1"));
+  ui->potentialModificationsMotif2LineEdit->setText(
+    xtandem_parameters.getValue("refine, potential modification motif 2"));
+
+  ui->usePotentialModificationsInRefinementModuleLineEdit->setText(
+    xtandem_parameters.getValue(
+      "refine, use potential modifications for full refinement"));
+  ui->useSemiEnzymaticCleavageRulesLineEdit_2->setText(
+    xtandem_parameters.getValue("refine, cleavage semi"));
+  ui->cleavageAtEachResiduesLineEdit->setText(
+    xtandem_parameters.getValue("refine, unanticipated cleavage"));
+  ui->spectrumIntensityModelSynthesisLineEdit->setText(
+    xtandem_parameters.getValue("refine, spectrum synthesis"));
+  ui->pointMutationsLineEdit->setText(
+    xtandem_parameters.getValue("refine, point mutations"));
+}
+
+void
+XtandemParamWidget::setOutputParameters(TandemParameters xtandem_parameters)
+{
+}

src/gui/widgets/engines_view/xtandemparamwidget.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>
+#include <core/tandem_run/tandemparameters.h>
+
+
+namespace Ui
+{
+class XtandemParamWidget;
+}
+
+class XtandemParamWidget : public QWidget
+{
+  Q_OBJECT
+
+  public:
+  explicit XtandemParamWidget(QWidget *parent);
+  ~XtandemParamWidget();
+
+  void setAutomaticXTandemParameters(QString params_file);
+
+  private slots:
+
+
+  private:
+  void setSpectrumParameters(TandemParameters xtandem_parameters);
+  void setProteinParameters(TandemParameters xtandem_parameters);
+  void setResidueParameters(TandemParameters xtandem_parameters);
+  void setScoringParameters(TandemParameters xtandem_parameters);
+  void setRefineParameters(TandemParameters xtandem_parameters);
+  void setOutputParameters(TandemParameters xtandem_parameters);
+
+  Ui::XtandemParamWidget *ui;
+};