new dialog to choose psimod

src/CMakeLists.txt

@@ -78,6 +78,7 @@ SET(CPP_FILES
   utils/peptidestore.cpp
   utils/proteinstore.cpp
   utils/readspectrum.cpp
+  utils/utils.cpp
 )
 
 set(QTLIBS ${Qt5Xml_LIBRARIES} ${Qt5Gui_LIBRARIES}  ${Qt5Svg_LIBRARIES})
@@ -86,6 +87,7 @@ 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/choose_modification_dialog/choosemodificationdialog.cpp
   ./gui/edit_modifications/editmodifications.cpp
   ./gui/export_spreadsheet_dialog/exportspreadsheetdialog.cpp
   ./gui/load_results_dialog/loadresultsdialog.cpp
@@ -106,6 +108,7 @@ SET(XTPCPP_SRCS
 )
 
 SET (GUI_UIS
+  ./gui/choose_modification_dialog/choose_modification_dialog.ui
   ./gui/edit_modifications/edit_modifications.ui
   ./gui/export_spreadsheet_dialog/export_spreadsheet_dialog.ui
   ./gui/load_results_dialog/load_results_dialog.ui
@@ -120,6 +123,7 @@ SET (GUI_UIS
 )
 
 SET(XTPCPP_MOC_HDRS
+  ./gui/choose_modification_dialog/choosemodificationdialog.h
   ./gui/edit_modifications/editmodifications.h
   ./gui/export_spreadsheet_dialog/exportspreadsheetdialog.h
   ./gui/load_results_dialog/loadresultsdialog.h

src/gui/choose_modification_dialog/choose_modification_dialog.ui

+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>ChooseModificationDialog</class>
+ <widget class="QWidget" name="ChooseModificationDialog">
+  <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 modifications</string>
+     </property>
+     <layout class="QVBoxLayout" name="verticalLayout_3">
+      <item>
+       <widget class="QListView" name="modification_listview"/>
+      </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>ChooseModificationDialog</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>ChooseModificationDialog</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>
+ </connections>
+ <slots>
+  <slot>reject()</slot>
+  <slot>accept()</slot>
+  <slot>doSimpleProteinPeptideList(bool)</slot>
+ </slots>
+</ui>

src/gui/choose_modification_dialog/choosemodificationdialog.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 "choosemodificationdialog.h"
+
+#include "ui_choose_modification_dialog.h"
+#include <QDebug>
+#include <QDesktopServices>
+#include "../../utils/utils.h"
+
+ChooseModificationDialog::ChooseModificationDialog(QWidget * parent):
+    QDialog(parent),
+    ui(new Ui::ChooseModificationDialog)
+{
+    qDebug() << "ChooseModificationDialog::ChooseModificationDialog begin";
+    ui->setupUi(this);
+    this->setModal(true);
+
+    _p_modification_str_li = new QStandardItemModel();
+    ui->modification_listview->setModel(_p_modification_str_li);
+    //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
+
+}
+
+ChooseModificationDialog::~ChooseModificationDialog()
+{
+    delete ui;
+}
+
+void ChooseModificationDialog::setMassRange(const pappso::MassRange & massrange) {
+}
+
+
+void ChooseModificationDialog::ItemDoubleClicked (QModelIndex index )
+{
+    qDebug() << "ChooseModificationDialog::ItemClicked data=" << index.data().toString();
+    qDebug() << "ChooseModificationDialog::ItemClicked acc=" << _p_modification_str_li->data(index,Qt::UserRole).toString();
+    QDesktopServices::openUrl (Utils::getOlsUrl(_p_modification_str_li->data(index,Qt::UserRole).toString())) ;
+}
+
+void ChooseModificationDialog::ItemClicked (QModelIndex index )
+{
+    qDebug() << "ChooseModificationDialog::ItemClicked data=" << index.data().toString();
+    qDebug() << "ChooseModificationDialog::ItemClicked acc=" << _p_modification_str_li->data(index,Qt::UserRole).toString();
+    qDebug() << "ChooseModificationDialog::ItemClicked str=" << _p_modification_str_li->data(index,Qt::DisplayRole).toString();
+    pappso::AaModificationP modification = pappso::AaModification::getInstance(index.data(Qt::UserRole).toString());
+    _selected_modification = modification;
+}

src/gui/choose_modification_dialog/choosemodificationdialog.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 CHOOSEMODIFICATIONDIALOG_H
+#define CHOOSEMODIFICATIONDIALOG_H
+
+#include <QDialog>
+#include <QStandardItemModel>
+#include <pappsomspp/mass_range.h>
+#include <pappsomspp/amino_acid/aamodification.h>
+
+
+namespace Ui {
+class ChooseModificationDialog;
+}
+
+class ChooseModificationDialog : public QDialog
+{
+    Q_OBJECT
+
+public:
+    explicit ChooseModificationDialog(QWidget * parent);
+    ~ChooseModificationDialog();
+
+    void setMassRange(const pappso::MassRange & massrange);
+        public slots:
+    void ItemClicked (QModelIndex index );
+    void ItemDoubleClicked (QModelIndex index );
+
+private:
+    Ui::ChooseModificationDialog *ui;
+    QStandardItemModel * _p_modification_str_li=nullptr;
+    pappso::AaModificationP _selected_modification;
+
+};
+
+#endif // CHOOSEMODIFICATIONDIALOG_H

src/gui/edit_modifications/edit_modifications.ui

@@ -7,7 +7,7 @@
     <x>0</x>
     <y>0</y>
     <width>826</width>
-    <height>559</height>
+    <height>574</height>
    </rect>
   </property>
   <property name="contextMenuPolicy">
@@ -175,17 +175,35 @@
      <x>0</x>
      <y>0</y>
      <width>826</width>
-     <height>25</height>
+     <height>46</height>
     </rect>
    </property>
   </widget>
   <widget class="QStatusBar" name="statusbar"/>
  </widget>
  <resources/>
- <connections/>
+ <connections>
+  <connection>
+   <sender>pushButton</sender>
+   <signal>clicked()</signal>
+   <receiver>EditModificationView</receiver>
+   <slot>doActionBrowse()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>763</x>
+     <y>388</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>875</x>
+     <y>448</y>
+    </hint>
+   </hints>
+  </connection>
+ </connections>
  <slots>
   <slot>doNotValidHide(bool)</slot>
   <slot>doNotCheckedHide(bool)</slot>
   <slot>doNotGroupedHide(bool)</slot>
+  <slot>doActionBrowse()</slot>
  </slots>
 </ui>

src/gui/edit_modifications/editmodifications.cpp

@@ -23,6 +23,7 @@
 
 #include "editmodifications.h"
 #include "../project_view/projectwindow.h"
+#include "../../utils/utils.h"
 #include <QDesktopServices>
 
 #include "ui_edit_modifications.h"
@@ -35,6 +36,8 @@ EditModifications::EditModifications(ProjectWindow *parent):
     _project_window = parent;
     _p_modification_str_li = new QStandardItemModel();
     ui->modification_list_view->setModel(_p_modification_str_li);
+    
+    _p_browse_modification_dialog = new ChooseModificationDialog(this);
 
 
     connect(ui->modification_list_view,SIGNAL(clicked(const QModelIndex)),this,SLOT(ItemClicked(QModelIndex)));
@@ -72,9 +75,7 @@ void EditModifications::ItemDoubleClicked (QModelIndex index )
 {
     qDebug() << "EditModifications::ItemClicked data=" << index.data().toString();
     qDebug() << "EditModifications::ItemClicked acc=" << _p_modification_str_li->data(index,Qt::UserRole).toString();
-    QString iri(QString("http://purl.obolibrary.org/obo/%1").arg(_p_modification_str_li->data(index,Qt::UserRole).toString().replace(":","_")));
-    QUrl url(QString("http://www.ebi.ac.uk/ols/ontologies/mod/terms?iri=%1").arg(iri));
-    QDesktopServices::openUrl (url) ;
+    QDesktopServices::openUrl (Utils::getOlsUrl(_p_modification_str_li->data(index,Qt::UserRole).toString())) ;
 }
 
 void EditModifications::ItemClicked (QModelIndex index )
@@ -111,3 +112,16 @@ void EditModifications::setSelectedModification (pappso::AaModificationP modific
     ui->delta_label->setText(QString::number(modification->getMass(), 'f', 10));
 
 }
+
+
+void EditModifications::doActionBrowse() {
+    qDebug() << "EditModifications::doActionBrowse begin";
+    if (_selected_modification != nullptr) {
+        pappso::MassRange massrange(_selected_modification->getMass(), pappso::Precision::getDaltonInstance(0.1));
+    _p_browse_modification_dialog->setMassRange(massrange);
+        _p_browse_modification_dialog->show();
+        _p_browse_modification_dialog->raise();
+        _p_browse_modification_dialog->activateWindow();
+    }
+    qDebug() << "EditModifications::doActionBrowse end";
+}

src/gui/edit_modifications/editmodifications.h

@@ -27,6 +27,7 @@
 
 #include <QMainWindow>
 #include <QStandardItemModel>
+#include "../choose_modification_dialog/choosemodificationdialog.h"
 #include "../../core/project.h"
 
 class ProjectWindow;
@@ -48,6 +49,7 @@ public:
     public slots:
     void ItemClicked (QModelIndex index );
     void ItemDoubleClicked (QModelIndex index );
+    void doActionBrowse();
 private :
     void setSelectedModification (pappso::AaModificationP modification);
     void setReplaceModification (pappso::AaModificationP modification);
@@ -55,6 +57,7 @@ private :
 private:
     Ui::EditModificationView *ui;
     ProjectWindow * _project_window;
+    ChooseModificationDialog * _p_browse_modification_dialog;
     QStandardItemModel * _p_modification_str_li=nullptr;
     pappso::AaModificationP _selected_modification;
     pappso::AaModificationP _replace_modification;

src/gui/mainwindow.cpp

@@ -26,6 +26,7 @@
 #include <QFileDialog>
 #include <QMessageBox>
 #include <QDebug>
+#include "../config.h"
 #include "mainwindow.h"
 
 #include "ui_main.h"
@@ -87,6 +88,7 @@ MainWindow::MainWindow(QWidget *parent):
     ui(new Ui::Main)
 {
     ui->setupUi(this);
+    setWindowTitle(QString("%1 %2").arg(SOFTWARE_NAME).arg(XTPCPP_VERSION));
 
     XtpLoaderThread *worker = new XtpLoaderThread;
     worker->moveToThread(&workerThread);

src/utils/utils.cpp

+#include "utils.h"
+
+const QUrl Utils::getOlsUrl(QString psimod_accession) {
+    
+    QString iri(QString("http://purl.obolibrary.org/obo/%1").arg(psimod_accession.replace(":","_")));
+    QUrl url(QString("http://www.ebi.ac.uk/ols/ontologies/mod/terms?iri=%1").arg(iri));
+    return url;
+}

src/utils/utils.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
+******************************************************************************/
+#include<QUrl>
+#include <QString>
+
+#ifndef UTILS_H
+#define UTILS_H
+class Utils
+{
+public:
+    static const QUrl getOlsUrl(QString modification);
+};
+
+#endif // UTILS_H