ods export system

src/CMakeLists.txt

@@ -72,6 +72,8 @@ SET(CPP_FILES
   input/xpipsaxhandler.cpp
   input/xtandemsaxhandler.cpp
   output/masschroqml.cpp
+  output/ods/odsexport.cpp
+  output/ods/simplesheet.cpp
   utils/identificationdatasourcestore.cpp
   utils/groupstore.cpp
   utils/msrunstore.cpp
@@ -86,6 +88,7 @@ set(QTLIBS ${Qt5Xml_LIBRARIES} ${Qt5Gui_LIBRARIES}  ${Qt5Svg_LIBRARIES})
 # (CMAKE_BINARY_DIR holds a path to the build directory, while INCLUDE_DIRECTORIES() works just like INCLUDEPATH from qmake)
 
 SET(XTPCPP_SRCS
+  ./gui/export_spreadsheet_dialog/exportspreadsheetdialog.cpp
   ./gui/load_results_dialog/loadresultsdialog.cpp
   ./gui/mainwindow.cpp
   ./gui/peptide_detail_view/peptidewindow.cpp
@@ -103,6 +106,7 @@ SET(XTPCPP_SRCS
 )
 
 SET (GUI_UIS
+  ./gui/export_spreadsheet_dialog/export_spreadsheet_dialog.ui
   ./gui/load_results_dialog/load_results_dialog.ui
   ./gui/main.ui
   ./gui/peptide_detail_view/peptide_detail_view.ui
@@ -116,6 +120,7 @@ SET (GUI_UIS
 
 SET(XTPCPP_MOC_HDRS
 
+  ./gui/export_spreadsheet_dialog/exportspreadsheetdialog.h
   ./gui/load_results_dialog/loadresultsdialog.h
   ./gui/mainwindow.h
   ./gui/peptide_detail_view/peptidewindow.h

src/core/msrun.cpp

@@ -49,6 +49,10 @@ MsRun::~MsRun() {
 }
 
 
+    const QString & MsRun::getSampleName() const {
+        return _name;
+    }
+
 void MsRun::setFilename(const QString filename) {
     _location = filename;
 }

src/core/msrun.h

@@ -50,6 +50,7 @@ public:
     void setXmlId(const QString xmlid);
     
     const QString & getFilename() const;
+    const QString & getSampleName() const;
     const QString & getXmlId() const;
     
     MzFormat getMzFormat() const;

src/core/project.cpp

@@ -55,6 +55,10 @@ void Project::setCombineMode(bool is_combine_mode) {
 std::vector<IdentificationGroup *> Project::getIdentificationGroupList() {
     return _identification_goup_list;
 }
+
+    const std::vector<IdentificationGroup *> Project::getIdentificationGroupList() const {
+        return _identification_goup_list;
+    }
 const GroupingType Project::getGroupingType() const {
     return _grouping_type;
 }

src/core/project.h

@@ -61,6 +61,7 @@ public:
     const GroupingType getGroupingType() const;
 
     std::vector<IdentificationGroup *> getIdentificationGroupList();
+    const std::vector<IdentificationGroup *> getIdentificationGroupList() const;
     void setCombineMode(bool is_combine_mode);
     bool isCombineMode() const;
     void readResultFile(QString filename);

src/gui/export_spreadsheet_dialog/export_spreadsheet_dialog.ui

+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>ExportSpreadsheetDialog</class>
+ <widget class="QWidget" name="ExportSpreadsheetDialog">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>573</width>
+    <height>559</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Form</string>
+  </property>
+  <layout class="QVBoxLayout" name="verticalLayout_2">
+   <item>
+    <widget class="QGroupBox" name="groupBox">
+     <property name="title">
+      <string>Available spreadsheets</string>
+     </property>
+     <layout class="QVBoxLayout" name="verticalLayout_3">
+      <item>
+       <widget class="QCheckBox" name="simple_checkbox">
+        <property name="text">
+         <string>simple protein and peptide list</string>
+        </property>
+       </widget>
+      </item>
+      <item>
+       <widget class="QCheckBox" name="checkBox_2">
+        <property name="text">
+         <string>CheckBox</string>
+        </property>
+       </widget>
+      </item>
+     </layout>
+    </widget>
+   </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="pushButton_2">
+       <property name="text">
+        <string>Cancel</string>
+       </property>
+      </widget>
+     </item>
+     <item>
+      <widget class="QPushButton" name="pushButton">
+       <property name="text">
+        <string>OK</string>
+       </property>
+      </widget>
+     </item>
+    </layout>
+   </item>
+  </layout>
+ </widget>
+ <resources/>
+ <connections>
+  <connection>
+   <sender>pushButton</sender>
+   <signal>clicked()</signal>
+   <receiver>ExportSpreadsheetDialog</receiver>
+   <slot>accept()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>522</x>
+     <y>415</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>286</x>
+     <y>279</y>
+    </hint>
+   </hints>
+  </connection>
+  <connection>
+   <sender>pushButton_2</sender>
+   <signal>clicked()</signal>
+   <receiver>ExportSpreadsheetDialog</receiver>
+   <slot>reject()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>436</x>
+     <y>415</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>286</x>
+     <y>279</y>
+    </hint>
+   </hints>
+  </connection>
+  <connection>
+   <sender>simple_checkbox</sender>
+   <signal>toggled(bool)</signal>
+   <receiver>ExportSpreadsheetDialog</receiver>
+   <slot>doSimpleProteinPeptideList(bool)</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>115</x>
+     <y>110</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>633</x>
+     <y>369</y>
+    </hint>
+   </hints>
+  </connection>
+ </connections>
+ <slots>
+  <slot>reject()</slot>
+  <slot>accept()</slot>
+  <slot>doSimpleProteinPeptideList(bool)</slot>
+ </slots>
+</ui>

src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.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 "ui_export_spreadsheet_dialog.h"
+#include "exportspreadsheetdialog.h"
+#include <QDebug>
+#include <QSettings>
+
+ExportSpreadsheetDialog::ExportSpreadsheetDialog(QWidget * parent):
+    QDialog(parent),
+    ui(new Ui::ExportSpreadsheetDialog)
+{
+    qDebug() << "ExportSpreadsheetDialog::ExportSpreadsheetDialog begin";
+    ui->setupUi(this);
+    this->setModal(true);
+
+
+    
+    QSettings settings;
+    ui->simple_checkbox->setCheckState(Qt::Unchecked);
+    if (settings.value("export_ods/simple", "true").toBool()) {
+        ui->simple_checkbox->setCheckState(Qt::Checked);
+    }
+    //param.setFilterCrossSamplePeptideNumber(settings.value("automatic_filter/cross_sample", "true").toBool());
+    
+#if QT_VERSION >= 0x050000
+    // Qt5 code
+    /*
+    connect(&workerThread, &QThread::finished, worker, &QObject::deleteLater);
+    connect(this, &PtSpectrumViewer::operateMsDataFile, worker, &PwizLoaderThread::doMsDataFileLoad);
+    connect(worker, &PwizLoaderThread::msDataReady, this, &PtSpectrumViewer::handleMsDataFile);
+    */
+#else
+// Qt4 code
+
+#endif
+
+    qDebug() << "ExportSpreadsheetDialog::ExportSpreadsheetDialog end";
+}
+
+ExportSpreadsheetDialog::~ExportSpreadsheetDialog()
+{
+    delete ui;
+}
+
+void ExportSpreadsheetDialog::doSimpleProteinPeptideList(bool simple) {
+    
+    QSettings settings;
+    settings.setValue("export_ods/simple", QString("%1").arg(simple));
+}

src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.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
+******************************************************************************/
+
+#ifndef EXPORTSPREADSHEETDIALOG_H
+#define EXPORTSPREADSHEETDIALOG_H
+
+#include <QDialog>
+#include <QStringListModel>
+#include "../project_view/automatic_filter_widget/automaticfilterwidget.h"
+
+
+namespace Ui {
+class ExportSpreadsheetDialog;
+}
+
+class ProjectWindow;
+
+class ExportSpreadsheetDialog : public QDialog
+{
+    Q_OBJECT
+
+public:
+    explicit ExportSpreadsheetDialog(QWidget * parent);
+    ~ExportSpreadsheetDialog();
+
+
+public slots:
+    void doSimpleProteinPeptideList(bool simple);
+signals:
+
+private:
+    Ui::ExportSpreadsheetDialog *ui;
+
+};
+
+#endif // EXPORTSPREADSHEETDIALOG_H

src/gui/load_results_dialog/loadresultsdialog.h

@@ -33,7 +33,6 @@ namespace Ui {
 class LoadResultsDialog;
 }
 
-class ProjectWindow;
 
 class LoadResultsDialog : public QDialog
 {

src/gui/mainwindow.cpp

@@ -30,7 +30,9 @@
 
 #include "ui_main.h"
 #include <pappsomspp/pappsoexception.h>
+#include <odsstream/odsdocwriter.h>
 #include "../output/masschroqml.h"
+#include "../output/ods/odsexport.h"
 
 
 void XtpLoaderThread::doXpipFileLoad(QString filename) {
@@ -90,6 +92,7 @@ MainWindow::MainWindow(QWidget *parent):
     workerThread.start();
 
     _p_load_results_dialog = new LoadResultsDialog(this);
+    _p_export_spreadsheet_dialog = new ExportSpreadsheetDialog(this);
 
 
     _project_window = new ProjectWindow(this);
@@ -118,6 +121,7 @@ MainWindow::MainWindow(QWidget *parent):
     connect(worker, SIGNAL(projectReady(ProjectSp)), this,SLOT(doProjectReady(ProjectSp)));
     connect(this, SIGNAL(operateLoadingResults(bool,AutomaticFilterParameters,QStringList)), worker,SLOT(doLoadingResults(bool,AutomaticFilterParameters,QStringList)));
     connect(_p_load_results_dialog, SIGNAL(accepted()), this,SLOT(doAcceptedLoadResultDialog()));
+    connect(_p_export_spreadsheet_dialog, SIGNAL(accepted()), this,SLOT(doAcceptedExportSpreadsheetDialog()));
     connect(worker, SIGNAL(loadingMessage(QString)), this,SLOT(doDisplayLoadingMessage(QString)));
     connect(worker, SIGNAL(projectNotReady(QString)), this,SLOT(doProjectNotReady(QString)));
     /*
@@ -157,6 +161,35 @@ void MainWindow::doDisplayLoadingMessage(QString message) {
     ui->statusbar->showMessage(message);
 }
 
+void MainWindow::doAcceptedExportSpreadsheetDialog() {
+    qDebug() << "MainWindow::doAcceptedExportSpreadsheetDialog begin";
+    try {
+        QSettings settings;
+        QString default_location = settings.value("path/export_ods", "").toString();
+
+        QString filename = QFileDialog::getSaveFileName(this, tr("Save ODS file"),
+                           QString("%1/untitled.ods").arg(default_location),
+                           tr("Open Document Spreadsheet (*.ods)"));
+
+        if (filename.isEmpty()) {
+            return;
+        }
+
+        settings.setValue("path/export_ods", QFileInfo(filename).absolutePath());
+        
+        OdsDocWriter writer(filename);
+        OdsExport export_ods(_project_sp.get());
+        export_ods.write(&writer);
+        
+        writer.close();
+        //emit operateXpipFile(filename);
+    }
+    catch (pappso::PappsoException & error) {
+        viewError(tr("Error while writing ODS file :\n%1").arg(error.qwhat()));
+    }
+    qDebug() << "MainWindow::doAcceptedExportSpreadsheetDialog end";
+}
+
 void MainWindow::doAcceptedLoadResultDialog() {
     qDebug() << "MainWindow::doAcceptedLoadResultDialog begin";
     AutomaticFilterParameters param = _p_load_results_dialog->getAutomaticFilterParameters();
@@ -227,12 +260,12 @@ void MainWindow::selectXpipFile() {
     qDebug() << "MainWindow::doActionSpreadsheet begin";
     try {
         
-    _p_load_results_dialog->show();
-    _p_load_results_dialog->raise();
-    _p_load_results_dialog->activateWindow();
+    _p_export_spreadsheet_dialog->show();
+    _p_export_spreadsheet_dialog->raise();
+    _p_export_spreadsheet_dialog->activateWindow();
     }
     catch (pappso::PappsoException & error) {
-        viewError(tr("Error while writing MassChroqML file :\n%1").arg(error.qwhat()));
+        viewError(tr("Error doActionSpreadsheet :\n%1").arg(error.qwhat()));
     }
     qDebug() << "MainWindow::doActionSpreadsheet end";
     }

src/gui/mainwindow.h

@@ -38,6 +38,7 @@
 #include "files/xpipfile.h"
 #include "project_view/projectwindow.h"
 #include "load_results_dialog/loadresultsdialog.h"
+#include "export_spreadsheet_dialog/exportspreadsheetdialog.h"
 
 
 
@@ -85,6 +86,7 @@ public slots:
     void doProjectReady(ProjectSp project_sp);
     void doProjectNotReady(QString error);
     void doAcceptedLoadResultDialog();
+    void doAcceptedExportSpreadsheetDialog();
     //void peptideEdited(QString peptideStr);
     // void setColor(const QColor &color);
     // void setShape(Shape shape);
@@ -109,6 +111,7 @@ private :
 
     ProjectWindow * _project_window=nullptr;
     LoadResultsDialog * _p_load_results_dialog=nullptr;
+    ExportSpreadsheetDialog * _p_export_spreadsheet_dialog;
 
 };
 

src/gui/project_view/project_view.ui

@@ -21,7 +21,7 @@
        <bool>true</bool>
       </property>
       <property name="currentIndex">
-       <number>1</number>
+       <number>0</number>
       </property>
       <widget class="QWidget" name="identifications">
        <attribute name="title">

src/output/ods/odsexport.cpp

+/**
+ * \file output/ods/odsexport.cpp
+ * \date 11/4/2017
+ * \author Olivier Langella
+ * \brief ODS export
+ */
+
+/*******************************************************************************
+* 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 "odsexport.h"
+#include "simplesheet.h"
+#include <QSettings>
+
+OdsExport::OdsExport(const Project * project):_p_project(project) {
+}
+
+void OdsExport::write(CalcWriterInterface * p_writer) {
+    QSettings settings;
+    if (settings.value("export_ods/simple", "false").toBool()) {
+        SimpleSheet(p_writer, _p_project);
+    }
+}

src/output/ods/odsexport.h

+/**
+ * \file output/ods/odsexport.h
+ * \date 11/4/2017
+ * \author Olivier Langella
+ * \brief ODS export
+ */
+
+/*******************************************************************************
+* 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
+******************************************************************************/
+
+#ifndef ODSEXPORT_H
+#define ODSEXPORT_H
+
+#include "../../core/project.h"
+#include <odsstream/calcwriterinterface.h>
+
+class OdsExport
+{
+public:
+    OdsExport(const Project * project);
+    
+    void write(CalcWriterInterface * p_writer);
+    
+private:
+    const Project * _p_project;
+};
+
+#endif // ODSEXPORT_H

src/output/ods/simplesheet.cpp

+/**
+ * \file output/ods/simplesheet.h
+ * \date 11/4/2017
+ * \author Olivier Langella
+ * \brief ODS simple sheet
+ */
+
+/*******************************************************************************
+* 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 "simplesheet.h"
+#include "../../core/identificationgroup.h"
+
+SimpleSheet::SimpleSheet (CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
+    _p_writer = p_writer;
+    p_writer->writeSheet("simple");
+    
+    std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
+    
+    for (IdentificationGroup * p_ident:identification_list) {
+        writeIdentificationGroup(p_ident);
+    }
+}
+
+void SimpleSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
+    
+    //_p_writer->writeSheet("simple");
+    const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
+    _p_writer->writeCell("protein");
+    _p_writer->writeLine();
+    _p_writer->writeEmptyCell();
+    _p_writer->writeCell("peptide");
+    _p_writer->writeLine();
+    if (msrun_list.size() == 1) {
+    _p_writer->writeCell("sample");
+    _p_writer->writeLine();
+    _p_writer->writeCell(msrun_list[0].get()->getSampleName());
+    _p_writer->writeLine();
+    }
+    
+    for (ProteinMatch * p_protein_match :p_ident->getProteinMatchList()) {
+        _p_writer->writeCell(p_protein_match->getProteinXtpSp().get()->getAccession());
+    _p_writer->writeLine();
+    }
+    
+}

src/output/ods/simplesheet.h

+/**
+ * \file output/ods/simplesheet.h
+ * \date 11/4/2017
+ * \author Olivier Langella
+ * \brief ODS simple sheet
+ */
+
+/*******************************************************************************
+* 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
+******************************************************************************/
+
+#ifndef SIMPLESHEET_H
+#define SIMPLESHEET_H
+
+#include "../../core/project.h"
+#include <odsstream/calcwriterinterface.h>
+#include "../../core/proteinmatch.h"
+
+class SimpleSheet
+{
+    public :
+        SimpleSheet (CalcWriterInterface * p_writer, const Project * p_project);
+private :
+    void writeIdentificationGroup(IdentificationGroup * p_ident);
+private :
+    const Project * _p_project;
+    CalcWriterInterface * _p_writer;
+};
+
+#endif // SIMPLESHEET_H