From 494a5dab15be99f02a2ed94640a23588037dede0 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Tue, 23 Aug 2016 21:39:36 +0200
Subject: [PATCH] first protein table view
---
src/core/project.cpp | 7 ++++-
src/core/project.h | 7 +++--
src/files/xpipfile.cpp | 6 +++++
src/files/xpipfile.h | 2 ++
src/gui/main.ui | 24 +++++++++++++++--
src/gui/mainwindow.cpp | 26 +++++++++++++++++++
src/gui/mainwindow.h | 13 +++++++---
.../protein_list_view/proteinlistwindow.cpp | 12 ++++++---
src/gui/protein_list_view/proteinlistwindow.h | 3 +++
.../protein_list_view/proteintablemodel.cpp | 20 +++++++++++++-
src/gui/protein_list_view/proteintablemodel.h | 7 +++++
src/input/xpipsaxhandler.cpp | 11 +++++---
12 files changed, 120 insertions(+), 18 deletions(-)
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 2d848022..af17bcbd 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -78,5 +78,10 @@ void Project::readXpipFile(QFileInfo xpip_fileinfo) {
}
-void Project::addProteinSp(pappso::ProteinSp makeProteinSp) {
+void Project::addProteinSp(pappso::ProteinSp protein_sp) {
+ _protein_list.push_back(protein_sp);
}
+
+ std::vector<pappso::ProteinSp> & Project::getProteinList() {
+ return _protein_list;
+ }
\ No newline at end of file
diff --git a/src/core/project.h b/src/core/project.h
index 49338ace..07ea7a3a 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -39,9 +39,12 @@ public:
ProjectSp makeProjectSp() const;
void readXpipFile(QFileInfo xpip_source);
- void addProteinSp(pappso::ProteinSp makeProteinSp);
+ void addProteinSp(pappso::ProteinSp protein_sp);
+ std::vector<pappso::ProteinSp> & getProteinList();
- pappso::GrpExperiment * _p_grp_experiment= nullptr;
+ pappso::GrpExperiment * _p_grp_experiment= nullptr;
+private :
+ std::vector<pappso::ProteinSp> _protein_list;
};
#endif // PROJECT_H
diff --git a/src/files/xpipfile.cpp b/src/files/xpipfile.cpp
index e5e55f04..d3aa2cea 100644
--- a/src/files/xpipfile.cpp
+++ b/src/files/xpipfile.cpp
@@ -24,6 +24,12 @@
XpipFile::XpipFile(const QUrl & xpip_source) : _xpip_source(xpip_source)
{
+}
+
+
+ XpipFile::XpipFile(const QFileInfo & xpip_source): _xpip_source(xpip_source.absoluteFilePath())
+{
+
}
XpipFile::~XpipFile()
diff --git a/src/files/xpipfile.h b/src/files/xpipfile.h
index 86d162f2..666be151 100644
--- a/src/files/xpipfile.h
+++ b/src/files/xpipfile.h
@@ -23,12 +23,14 @@
#define XPIPFILE_H
#include <QUrl>
+#include <QFileInfo>
#include "../core/project.h"
class XpipFile
{
public:
XpipFile(const QUrl & xpip_source);
+ XpipFile(const QFileInfo & xpip_source);
~XpipFile();
ProjectSp getProjectSp() const;
diff --git a/src/gui/main.ui b/src/gui/main.ui
index c9ed6bdc..960706c9 100644
--- a/src/gui/main.ui
+++ b/src/gui/main.ui
@@ -20,7 +20,7 @@
<x>0</x>
<y>0</y>
<width>286</width>
- <height>22</height>
+ <height>19</height>
</rect>
</property>
<widget class="QMenu" name="menuFile">
@@ -39,5 +39,25 @@
</action>
</widget>
<resources/>
- <connections/>
+ <connections>
+ <connection>
+ <sender>actionLoad</sender>
+ <signal>triggered()</signal>
+ <receiver>Main</receiver>
+ <slot>selectXpipFile()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>-1</x>
+ <y>-1</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>142</x>
+ <y>185</y>
+ </hint>
+ </hints>
+ </connection>
+ </connections>
+ <slots>
+ <slot>selectXpipFile()</slot>
+ </slots>
</ui>
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index e368dee9..1bf9b7dd 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -22,9 +22,12 @@
******************************************************************************/
#include <QDockWidget>
+#include <QSettings>
+#include <QFileDialog>
#include "mainwindow.h"
#include "ui_main.h"
+#include "files/xpipfile.h"
MainWindow::MainWindow(QWidget *parent):
@@ -69,3 +72,26 @@ MainWindow::~MainWindow()
delete ui;
}
+
+
+void MainWindow::selectXpipFile() {
+
+ QSettings settings;
+ QString default_location = settings.value("path/xpipfile", "").toString();
+
+ QString filename = QFileDialog::getOpenFileName(this,
+ tr("Open XPIP File"), default_location,
+ tr("xpip files (*.xpip);;all files (*)"));
+
+ if (filename.isEmpty()) {
+ return;
+ }
+ QFileInfo new_xpip_file;
+ new_xpip_file.setFile(filename);
+
+ XpipFile xpip_file(new_xpip_file);
+
+ _project_sp = xpip_file.getProjectSp();
+ _protein_list_window->setProject(_project_sp.get());
+
+}
diff --git a/src/gui/mainwindow.h b/src/gui/mainwindow.h
index eeb5495c..4603e576 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -34,6 +34,7 @@
#include <pwiz/data/msdata/MSDataFile.hpp>
#include "../utils/readspectrum.h"
#include "protein_list_view/proteinlistwindow.h"
+#include "core/project.h"
@@ -45,7 +46,7 @@ class Main;
class PwizLoaderThread : public QObject
{
Q_OBJECT
- public:
+public:
public slots:
void doMsDataFileLoad(const QString & parameter) {
@@ -58,7 +59,7 @@ signals:
void msDataReady(pwiz::msdata::MSDataFile * p_ms_data_file);
};
-class MainWindow: public QMainWindow {
+class MainWindow: public QMainWindow {
Q_OBJECT
QThread workerThread;
@@ -68,6 +69,7 @@ public:
~MainWindow();
public slots:
+ void selectXpipFile();
//void peptideEdited(QString peptideStr);
// void setColor(const QColor &color);
// void setShape(Shape shape);
@@ -76,10 +78,13 @@ signals:
private:
Ui::Main *ui;
-
-
+
+
ProteinListWindow * _protein_list_window=nullptr;
+private :
+ ProjectSp _project_sp=nullptr;
+
};
#endif // MAINWINDOW_H
diff --git a/src/gui/protein_list_view/proteinlistwindow.cpp b/src/gui/protein_list_view/proteinlistwindow.cpp
index 7c646b25..55f272bc 100644
--- a/src/gui/protein_list_view/proteinlistwindow.cpp
+++ b/src/gui/protein_list_view/proteinlistwindow.cpp
@@ -24,7 +24,6 @@
#include "proteinlistwindow.h"
#include "ui_protein_view.h"
-#include "proteintablemodel.h"
ProteinListWindow::ProteinListWindow(QWidget *parent):
@@ -51,8 +50,8 @@ ProteinListWindow::ProteinListWindow(QWidget *parent):
/*
*/
- ProteinTableModel * p_myModel = new ProteinTableModel(0);
- ui->tableView->setModel( p_myModel );
+ _protein_table_model_p = new ProteinTableModel(0);
+ ui->tableView->setModel( _protein_table_model_p );
}
ProteinListWindow::~ProteinListWindow()
@@ -60,4 +59,9 @@ ProteinListWindow::~ProteinListWindow()
//if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
delete ui;
-}
\ No newline at end of file
+}
+
+
+ void ProteinListWindow::setProject(Project* project_p) {
+ _protein_table_model_p->setProject(project_p);
+ }
\ No newline at end of file
diff --git a/src/gui/protein_list_view/proteinlistwindow.h b/src/gui/protein_list_view/proteinlistwindow.h
index 19213454..826d7a2b 100644
--- a/src/gui/protein_list_view/proteinlistwindow.h
+++ b/src/gui/protein_list_view/proteinlistwindow.h
@@ -26,6 +26,7 @@
#include <QMainWindow>
+#include "proteintablemodel.h"
//http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
namespace Ui {
@@ -39,6 +40,7 @@ public:
explicit ProteinListWindow(QWidget * parent = 0);
~ProteinListWindow();
+ void setProject(Project* project_p);
public slots:
//void peptideEdited(QString peptideStr);
@@ -49,6 +51,7 @@ signals:
private:
Ui::ProteinView *ui;
+ ProteinTableModel * _protein_table_model_p = nullptr;
};
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index 7ef7e8e9..5ec0ff14 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -35,8 +35,21 @@ ProteinTableModel::ProteinTableModel(QObject *parent)
//emit dataChanged(topLeft, topLeft);
}
+
+void ProteinTableModel::setProject(Project * p_project) {
+ qDebug() << "ProteinTableModel::setProject begin " << p_project->getProteinList().size();
+ _p_project = p_project;
+
+ QModelIndex topLeft = createIndex(0,0);
+ emit headerDataChanged(Qt::Horizontal, 0,3);
+ emit dataChanged(topLeft, topLeft);
+}
+
int ProteinTableModel::rowCount(const QModelIndex &parent ) const {
- return 2;
+ if (_p_project != nullptr) {
+ return _p_project->getProteinList().size();
+ }
+ return 0;
}
int ProteinTableModel::columnCount(const QModelIndex &parent ) const {
return 3;
@@ -67,6 +80,11 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
.arg(row).arg(col).arg(role);
if (role == Qt::DisplayRole)
{
+ if (col == 2) {
+ if (_p_project != nullptr) {
+ return _p_project->getProteinList().at(row).get()->getDescription();
+ }
+ }
return QString("Row%1, Column%2")
.arg(index.row() + 1)
.arg(index.column() +1);
diff --git a/src/gui/protein_list_view/proteintablemodel.h b/src/gui/protein_list_view/proteintablemodel.h
index 473e630f..3d80ff26 100644
--- a/src/gui/protein_list_view/proteintablemodel.h
+++ b/src/gui/protein_list_view/proteintablemodel.h
@@ -25,6 +25,7 @@
#define PROTEINTABLEMODEL_H
#include <QAbstractTableModel>
+#include "../../core/project.h"
class ProteinTableModel: public QAbstractTableModel
{
@@ -35,6 +36,12 @@ public:
int columnCount(const QModelIndex &parent = QModelIndex()) const override;
QVariant headerData(int section, Qt::Orientation orientation, int role) const override;
QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override;
+
+
+ void setProject(Project * p_project);
+
+private :
+ Project * _p_project = nullptr;
};
#endif // PROTEINTABLEMODEL_H
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 38d82c6d..f05a2dd4 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -41,9 +41,9 @@ bool XpipSaxHandler::startElement(const QString & namespaceURI, const QString &
try {
//startElement_group
- if (qName == "group")
+ if (qName == "protein")
{
- //is_ok = startElement_group(attributes);
+ is_ok = startElement_protein(attributes);
}
_current_text.clear();
}
@@ -64,10 +64,13 @@ bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & lo
bool is_ok = true;
// endElement_peptide_list
try {
- if (qName == "group")
+ if (qName == "protein")
{
- //is_ok = endElement_group();
+ is_ok = endElement_protein();
}
+ else if (qName == "sequence") {
+ is_ok = endElement_sequence();
+ }
// end of detection_moulon
// else if ((_tag_stack.size() > 1) &&
--
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