From ca5e27e10b74efd83f90e62564a2d444bf16ba9c Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 21 Apr 2017 14:48:01 +0200
Subject: [PATCH] new dialog to choose psimod
---
src/CMakeLists.txt | 4 +
.../choose_modification_dialog.ui | 102 ++++++++++++++++++
.../choosemodificationdialog.cpp | 80 ++++++++++++++
.../choosemodificationdialog.h | 57 ++++++++++
.../edit_modifications/edit_modifications.ui | 24 ++++-
.../edit_modifications/editmodifications.cpp | 20 +++-
.../edit_modifications/editmodifications.h | 3 +
src/gui/mainwindow.cpp | 2 +
src/utils/utils.cpp | 8 ++
src/utils/utils.h | 34 ++++++
10 files changed, 328 insertions(+), 6 deletions(-)
create mode 100644 src/gui/choose_modification_dialog/choose_modification_dialog.ui
create mode 100644 src/gui/choose_modification_dialog/choosemodificationdialog.cpp
create mode 100644 src/gui/choose_modification_dialog/choosemodificationdialog.h
create mode 100644 src/utils/utils.cpp
create mode 100644 src/utils/utils.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 6b845843c..7aca9cc91 100644
--- a/src/CMakeLists.txt
+++ b/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
diff --git a/src/gui/choose_modification_dialog/choose_modification_dialog.ui b/src/gui/choose_modification_dialog/choose_modification_dialog.ui
new file mode 100644
index 000000000..8a590026c
--- /dev/null
+++ b/src/gui/choose_modification_dialog/choose_modification_dialog.ui
@@ -0,0 +1,102 @@
+<?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>
diff --git a/src/gui/choose_modification_dialog/choosemodificationdialog.cpp b/src/gui/choose_modification_dialog/choosemodificationdialog.cpp
new file mode 100644
index 000000000..fa39dd74a
--- /dev/null
+++ b/src/gui/choose_modification_dialog/choosemodificationdialog.cpp
@@ -0,0 +1,80 @@
+
+/*******************************************************************************
+* 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;
+}
diff --git a/src/gui/choose_modification_dialog/choosemodificationdialog.h b/src/gui/choose_modification_dialog/choosemodificationdialog.h
new file mode 100644
index 000000000..64ebf170c
--- /dev/null
+++ b/src/gui/choose_modification_dialog/choosemodificationdialog.h
@@ -0,0 +1,57 @@
+
+/*******************************************************************************
+* 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
diff --git a/src/gui/edit_modifications/edit_modifications.ui b/src/gui/edit_modifications/edit_modifications.ui
index 651c0bb6c..822547d3b 100644
--- a/src/gui/edit_modifications/edit_modifications.ui
+++ b/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>
diff --git a/src/gui/edit_modifications/editmodifications.cpp b/src/gui/edit_modifications/editmodifications.cpp
index 055d17647..1c851fa1a 100644
--- a/src/gui/edit_modifications/editmodifications.cpp
+++ b/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";
+}
diff --git a/src/gui/edit_modifications/editmodifications.h b/src/gui/edit_modifications/editmodifications.h
index f0e15006c..be7e36234 100644
--- a/src/gui/edit_modifications/editmodifications.h
+++ b/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;
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index fdfd2c261..cd5fec6bc 100644
--- a/src/gui/mainwindow.cpp
+++ b/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);
diff --git a/src/utils/utils.cpp b/src/utils/utils.cpp
new file mode 100644
index 000000000..b70d4398f
--- /dev/null
+++ b/src/utils/utils.cpp
@@ -0,0 +1,8 @@
+#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;
+}
diff --git a/src/utils/utils.h b/src/utils/utils.h
new file mode 100644
index 000000000..3480d89df
--- /dev/null
+++ b/src/utils/utils.h
@@ -0,0 +1,34 @@
+
+/*******************************************************************************
+* 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
--
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