diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 462b946e2b353ed2d3e1d0df183a999ef29b36a7..ade8d7f8ff6358cefc73f955f75856bd65a4404a 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -74,18 +74,23 @@ INCLUDE_DIRECTORIES( ${CMAKE_CURRENT_SOURCE_DIR} )
SET(XTPCPP_SRCS
./gui/mainwindow.cpp
+ ./gui/peptide_list_view/peptidelistwindow.cpp
+ ./gui/peptide_list_view/peptidetablemodel.cpp
./gui/protein_list_view/proteinlistwindow.cpp
./gui/protein_list_view/proteintablemodel.cpp
)
SET (GUI_UIS
./gui/main.ui
+ ./gui/peptide_list_view/peptide_view.ui
./gui/protein_list_view/protein_view.ui
)
SET(XTPCPP_MOC_HDRS
./gui/mainwindow.h
+ ./gui/peptide_list_view/peptidelistwindow.h
+ ./gui/peptide_list_view/peptidetablemodel.h
./gui/protein_list_view/proteinlistwindow.h
./gui/protein_list_view/proteintablemodel.h
)
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index ba399e77e546c7fcf5867b615229b5bc71e6c398..d150c5ab5bd411a09f8b01c8e47814d8dec975e4 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -52,6 +52,27 @@ void PeptideMatch::setPeptideSp (pappso::PeptideSp peptide) {
void PeptideMatch::setChecked(bool arg1) {
_checked = arg1;
}
+
+bool PeptideMatch::isChecked() const {
+ return _checked;
+}
+
void PeptideMatch::setIdentificationDataSource(IdentificationDataSource* identification_source) {
_p_identification_source = identification_source;
}
+IdentificationDataSource* PeptideMatch::getIdentificationDataSource () const {
+ return _p_identification_source;
+}
+unsigned int PeptideMatch::getScan() const {
+ return _scan;
+}
+pappso::pappso_double PeptideMatch::getRetentionTime() const {
+ return _rt;
+}
+unsigned int PeptideMatch::getCharge() const {
+ return _charge;
+}
+
+pappso::PeptideSp PeptideMatch::getPeptideSp() const {
+ return _peptide_sp;
+}
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 1bcfe877dc95b90068bb47206f2db7a02254e7cf..6f2672febb49af0a69e03ee91121f38244b0f647 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -41,7 +41,13 @@ public :
void setPeptideSp (pappso::PeptideSp peptide);
void setIdentificationDataSource(IdentificationDataSource* identification_source);
void setChecked(bool arg1);
+ bool isChecked() const;
+ IdentificationDataSource* getIdentificationDataSource () const;
+ unsigned int getScan() const;
+ pappso::pappso_double getRetentionTime() const;
+ unsigned int getCharge() const;
+ pappso::PeptideSp getPeptideSp() const;
private :
pappso::MsRunIdSp _msrunid_sp;
@@ -53,11 +59,11 @@ private :
unsigned int _start;
unsigned int _charge;
IdentificationDataSource* _p_identification_source = nullptr;
-
+
/** @brief manually checked by user (true by default)
*/
bool _checked = true;
-
+
/** @brief automatic filter result (false by default)
*/
bool _proxy_valid = false;
diff --git a/src/core/project.cpp b/src/core/project.cpp
index bf7bf509456802e694340ab64d3c5406a48ff347..26c90667470ebe050adadd9ea7e1ba3c452f10ac 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -22,6 +22,7 @@
******************************************************************************/
#include "project.h"
#include "../input/xpipsaxhandler.h"
+#include "peptidematch.h"
Project::Project()
{
@@ -80,3 +81,7 @@ void Project::readXpipFile(QFileInfo xpip_fileinfo) {
IdentificationGroup* Project::getCurrentIdentificationGroupP() const {
return _p_current_identification_group;
}
+
+bool Project::isValid(PeptideMatch* p_peptide_match) const {
+ return true;
+}
diff --git a/src/core/project.h b/src/core/project.h
index 997d750309e3736d6449cb9a852740779d7a5703..2bc65e7e0108677242f198d1eb95cd6083f89f7a 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -29,6 +29,8 @@
class Project;
typedef std::shared_ptr<Project> ProjectSp;
+class PeptideMatch;
+
class Project
{
public:
@@ -39,6 +41,10 @@ public:
void readXpipFile(QFileInfo xpip_source);
IdentificationGroup* newIdentificationGroup();
IdentificationGroup* getCurrentIdentificationGroupP() const;
+ /** @brief is it valid regarding threshold and project rules
+ */
+ bool isValid(PeptideMatch* p_peptide_match) const;
+
private :
std::vector<IdentificationGroup *> _identification_goup_list;
IdentificationGroup* _p_current_identification_group = nullptr;
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 487df39db2e6bb21d2a0066aed66cfaa8de621b3..491c0958a466d415a85fc71736abb0cb8f744616 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -28,8 +28,14 @@
#include "ui_main.h"
#include "files/xpipfile.h"
+#include "gui/peptide_list_view/peptidelistwindow.h"
+void PwizLoaderThread::doMsDataFileLoad(const QString & parameter) {
+ pwiz::msdata::MSDataFile* p_ms_data_file = getPwizMSDataFile(parameter);
+ /* ... here is the expensive or blocking operation ... */
+ emit msDataReady(p_ms_data_file);
+}
MainWindow::MainWindow(QWidget *parent):
QMainWindow(parent),
ui(new Ui::Main)
@@ -38,6 +44,17 @@ MainWindow::MainWindow(QWidget *parent):
PwizLoaderThread *worker = new PwizLoaderThread;
worker->moveToThread(&workerThread);
+ /*
+ */
+ workerThread.start();
+
+ QDockWidget *dock = new QDockWidget(tr("Protein List"), this);
+ _protein_list_window = new ProteinListWindow(this);
+ //_protein_list_window->show();
+ dock->setWidget(_protein_list_window);
+ addDockWidget(Qt::RightDockWidgetArea, dock);
+
+
#if QT_VERSION >= 0x050000
// Qt5 code
/*
@@ -47,21 +64,13 @@ MainWindow::MainWindow(QWidget *parent):
*/
#else
// Qt4 code
+ connect (_protein_list_window, SIGNAL(proteinMatchClicked(ProteinMatch *)), this ,SLOT(doProteinMatchClicked(ProteinMatch *)));
/*
connect(&workerThread, SIGNAL(finished()), worker, SLOT(deleteLater()));
connect(this, SIGNAL(operateMsDataFile(QString)), worker,SLOT(doMsDataFileLoad(QString)));
connect(worker, SIGNAL(msDataReady(pwiz::msdata::MSDataFile *)), this, SLOT(handleMsDataFile(pwiz::msdata::MSDataFile *)));
*/
#endif
- /*
- */
- workerThread.start();
-
- QDockWidget *dock = new QDockWidget(tr("Protein List"), this);
- _protein_list_window = new ProteinListWindow(this);
- //_protein_list_window->show();
- dock->setWidget(_protein_list_window);
- addDockWidget(Qt::RightDockWidgetArea, dock);
}
MainWindow::~MainWindow()
@@ -74,6 +83,12 @@ MainWindow::~MainWindow()
}
+void MainWindow::doProteinMatchClicked(ProteinMatch * protein_match) {
+ PeptideListWindow * peptide_window = new PeptideListWindow(this);
+ peptide_window->setProteinMatch(_project_sp.get(), protein_match);
+ peptide_window->show();
+}
+
void MainWindow::selectXpipFile() {
QSettings settings;
@@ -88,10 +103,10 @@ void MainWindow::selectXpipFile() {
}
QFileInfo new_xpip_file;
new_xpip_file.setFile(filename);
-
+
XpipFile xpip_file(new_xpip_file);
-
+
_project_sp = xpip_file.getProjectSp();
_protein_list_window->setIdentificationGroup(_project_sp.get()->getCurrentIdentificationGroupP());
-
+
}
diff --git a/src/gui/mainwindow.h b/src/gui/mainwindow.h
index 4603e576f3f8fa82b66e040d361e81df6a204e9b..536da3dc36eaf261bc59699f70405f45a4cc140b 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -49,11 +49,7 @@ class PwizLoaderThread : public QObject
public:
public slots:
- void doMsDataFileLoad(const QString & parameter) {
- pwiz::msdata::MSDataFile* p_ms_data_file = getPwizMSDataFile(parameter);
- /* ... here is the expensive or blocking operation ... */
- emit msDataReady(p_ms_data_file);
- }
+ void doMsDataFileLoad(const QString & parameter);
signals:
void msDataReady(pwiz::msdata::MSDataFile * p_ms_data_file);
@@ -70,6 +66,7 @@ public:
public slots:
void selectXpipFile();
+ void doProteinMatchClicked(ProteinMatch * protein_match);
//void peptideEdited(QString peptideStr);
// void setColor(const QColor &color);
// void setShape(Shape shape);
diff --git a/src/gui/peptide_list_view/peptide_view.ui b/src/gui/peptide_list_view/peptide_view.ui
new file mode 100644
index 0000000000000000000000000000000000000000..fda502b32f6ea791bd7d756a810099a22edfdf46
--- /dev/null
+++ b/src/gui/peptide_list_view/peptide_view.ui
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>PeptideView</class>
+ <widget class="QMainWindow" name="PeptideView">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>826</width>
+ <height>404</height>
+ </rect>
+ </property>
+ <property name="windowTitle">
+ <string>Protein list</string>
+ </property>
+ <widget class="QWidget" name="centralwidget">
+ <layout class="QVBoxLayout" name="verticalLayout">
+ <item>
+ <widget class="QTableView" name="tableView"/>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QMenuBar" name="menubar">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>826</width>
+ <height>19</height>
+ </rect>
+ </property>
+ </widget>
+ <widget class="QStatusBar" name="statusbar"/>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>
diff --git a/src/gui/peptide_list_view/peptidelistwindow.cpp b/src/gui/peptide_list_view/peptidelistwindow.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..ff0fd533c624b66d9b3780e2419ef0f671f040d1
--- /dev/null
+++ b/src/gui/peptide_list_view/peptidelistwindow.cpp
@@ -0,0 +1,78 @@
+
+/*******************************************************************************
+* 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 "peptidelistwindow.h"
+
+#include "ui_peptide_view.h"
+
+
+PeptideListWindow::PeptideListWindow(QWidget *parent):
+ QMainWindow(parent),
+ ui(new Ui::PeptideView)
+{
+ ui->setupUi(this);
+
+#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
+ /*
+ connect(&workerThread, SIGNAL(finished()), worker, SLOT(deleteLater()));
+ connect(this, SIGNAL(operateMsDataFile(QString)), worker,SLOT(doMsDataFileLoad(QString)));
+ connect(worker, SIGNAL(msDataReady(pwiz::msdata::MSDataFile *)), this, SLOT(handleMsDataFile(pwiz::msdata::MSDataFile *)));
+ */
+#endif
+ /*
+ */
+
+ _peptide_table_model_p = new PeptideTableModel(0);
+
+
+ _p_proxy_model = new PeptideTableProxyModel(this, _peptide_table_model_p);
+ _p_proxy_model->setSourceModel(_peptide_table_model_p);
+ _p_proxy_model->setDynamicSortFilter(true);
+ ui->tableView->setModel( _p_proxy_model );
+ ui->tableView->setSortingEnabled(true);
+
+ connect(ui->tableView, SIGNAL(clicked(const QModelIndex &)), _p_proxy_model, SLOT(onTableClicked(const QModelIndex &)));
+}
+
+PeptideListWindow::~PeptideListWindow()
+{
+ //if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
+ delete ui;
+
+}
+
+
+void PeptideListWindow::setProteinMatch(Project * p_project, ProteinMatch * p_protein_match) {
+ _peptide_table_model_p->setProteinMatch(p_project, p_protein_match);
+ _p_proxy_model->setSourceModel(_peptide_table_model_p);
+
+}
+
diff --git a/src/gui/peptide_list_view/peptidelistwindow.h b/src/gui/peptide_list_view/peptidelistwindow.h
new file mode 100644
index 0000000000000000000000000000000000000000..9917d62c84f6cb98db08eb66e9ecfe142623f783
--- /dev/null
+++ b/src/gui/peptide_list_view/peptidelistwindow.h
@@ -0,0 +1,60 @@
+
+/*******************************************************************************
+* 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 PEPTIDELISTWINDOW_H
+#define PEPTIDELISTWINDOW_H
+
+#include <QMainWindow>
+#include "peptidetablemodel.h"
+#include "../../core/proteinmatch.h"
+#include "../../core/project.h"
+
+//http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
+namespace Ui {
+class PeptideView;
+}
+
+class PeptideListWindow: public QMainWindow {
+ Q_OBJECT
+
+public:
+
+ explicit PeptideListWindow(QWidget * parent = 0);
+ ~PeptideListWindow();
+ void setProteinMatch(Project * p_project, ProteinMatch * p_protein_match);
+
+public slots:
+ //void peptideEdited(QString peptideStr);
+ // void setColor(const QColor &color);
+ // void setShape(Shape shape);
+signals:
+ //void peptideChanged(pappso::PeptideSp peptide);
+
+private:
+ Ui::PeptideView *ui;
+ PeptideTableModel * _peptide_table_model_p = nullptr;
+ PeptideTableProxyModel * _p_proxy_model = nullptr;
+
+};
+
+#endif // PEPTIDELISTWINDOW_H
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..3096830a85debce124ce42832fa23b923e511294
--- /dev/null
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -0,0 +1,198 @@
+
+/*******************************************************************************
+* 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 "peptidetablemodel.h"
+
+#include <QDebug>
+
+
+PeptideTableProxyModel::PeptideTableProxyModel(QObject *parent,PeptideTableModel* peptide_table_model_p): QSortFilterProxyModel(parent)
+{
+ _peptide_table_model_p = peptide_table_model_p;
+}
+
+bool PeptideTableProxyModel::filterAcceptsRow(int source_row,
+ const QModelIndex &source_parent) const {
+ return _peptide_table_model_p->acceptRow(source_row);
+ //return true;
+}
+
+void PeptideTableProxyModel::onTableClicked(const QModelIndex &index)
+{
+ qDebug() << "PeptideTableProxyModel::onTableClicked begin " << index.row();
+ qDebug() << "PeptideTableProxyModel::onTableClicked begin " << this->mapToSource(index).row();
+ _peptide_table_model_p->onTableClicked(this->mapToSource(index));
+}
+
+bool PeptideTableProxyModel::lessThan(const QModelIndex & left, const QModelIndex & right) const {
+ QVariant leftData = sourceModel()->data(left);
+ QVariant rightData = sourceModel()->data(right);
+ if (leftData.type() == QVariant::UInt) {
+ return leftData.toUInt() < rightData.toUInt();
+ }
+ if (leftData.type() == QVariant::UInt) {
+ return leftData.toUInt() < rightData.toUInt();
+ }
+ if (leftData.type() == QVariant::Double) {
+ return leftData.toDouble() < rightData.toDouble();
+ }
+ return leftData.toString() < rightData.toString();
+}
+
+QVariant PeptideTableProxyModel::headerData(int section, Qt::Orientation orientation,
+ int role) const {
+ return sourceModel()->headerData(section, orientation,
+ role);
+}
+
+PeptideTableModel::PeptideTableModel(QObject *parent)
+ :QAbstractTableModel(parent)
+{
+
+ //ui->tableView->show();
+ // QModelIndex topLeft = createIndex(0,0);
+ //emit a signal to make the view reread identified data
+ //emit dataChanged(topLeft, topLeft);
+}
+
+
+void PeptideTableModel::setProteinMatch(Project * p_project, ProteinMatch * p_protein_match) {
+ qDebug() << "PeptideTableModel::setProteinMatch begin " ;
+ _p_project = p_project;
+ _p_protein_match = p_protein_match;
+
+ QModelIndex topLeft = createIndex(0,0);
+ QModelIndex bottomRight = createIndex(rowCount(),columnCount());
+ emit dataChanged(topLeft, bottomRight);
+ emit headerDataChanged(Qt::Horizontal, 0,3);
+}
+
+int PeptideTableModel::rowCount(const QModelIndex &parent ) const {
+ if (_p_protein_match != nullptr) {
+ qDebug() << "PeptideTableModel::rowCount(const QModelIndex &parent ) " << _p_protein_match->getPeptideMatchList().size();
+ return _p_protein_match->getPeptideMatchList().size();
+ }
+ return 0;
+}
+int PeptideTableModel::columnCount(const QModelIndex &parent ) const {
+ return 6;
+}
+QVariant PeptideTableModel::headerData(int section, Qt::Orientation orientation, int role) const
+{
+ if (role == Qt::DisplayRole)
+ {
+ if (orientation == Qt::Horizontal) {
+ switch (section)
+ {
+ case 0:
+ return QString("checked");
+ case 1:
+ return QString("sample");
+ case 2:
+ return QString("scan");
+ case 3:
+ return QString("RT");
+ case 4:
+ return QString("charge");
+ case 5:
+ return QString("sequence");
+ }
+ }
+ }
+ return QVariant();
+}
+QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
+ // generate a log message when this method gets called
+ int row = index.row();
+ int col = index.column();
+ qDebug() << QString("row %1, col%2, role %3")
+ .arg(row).arg(col).arg(role);
+
+ switch(role) {
+ case Qt::CheckStateRole:
+
+ if (col == 0) //add a checkbox to cell(1,0)
+ {
+ if ( _p_protein_match->getPeptideMatchList().at(row)->isChecked()) {
+ return Qt::Checked;
+ }
+ else {
+ return Qt::Unchecked;
+ }
+ }
+ break;
+ case Qt::DisplayRole:
+ if (_p_protein_match == nullptr) {
+ }
+ else {
+ if (col == 0) {
+ return QVariant();
+ }
+ if (col == 1) {
+ return _p_protein_match->getPeptideMatchList().at(row)->getIdentificationDataSource()->getResourceName();
+ }
+ if (col == 2) {
+ return QVariant ((quint16) _p_protein_match->getPeptideMatchList().at(row)->getScan());
+ }
+ if (col == 3) {
+ return QVariant ((qreal) _p_protein_match->getPeptideMatchList().at(row)->getRetentionTime());
+ }
+ if (col == 4) {
+ return QVariant ((quint8) _p_protein_match->getPeptideMatchList().at(row)->getCharge());
+ }
+ if (col == 5) {
+ return _p_protein_match->getPeptideMatchList().at(row)->getPeptideSp().get()->getSequence();
+ }
+ }
+ return QString("Row%1, Column%2")
+ .arg(index.row() + 1)
+ .arg(index.column() +1);
+ }
+ return QVariant();
+}
+
+void PeptideTableModel::onTableClicked(const QModelIndex &index)
+{
+ int row = index.row();
+ int col = index.column();
+ if (col == 0) //add a checkbox to cell(1,0)
+ {
+ if ( _p_protein_match->getPeptideMatchList().at(row)->isChecked()) {
+ _p_protein_match->getPeptideMatchList().at(row)->setChecked(false);
+ }
+ else {
+ _p_protein_match->getPeptideMatchList().at(row)->setChecked(true);
+ }
+ //emit dataChanged(index, index);
+ }
+ else {
+ emit peptideMatchClicked(_p_protein_match->getPeptideMatchList().at(row));
+ }
+}
+
+bool PeptideTableModel::acceptRow(int source_row) {
+ if (_p_project->isValid(_p_protein_match->getPeptideMatchList().at(source_row))) {
+ return true;
+ }
+ return false;
+}
diff --git a/src/gui/peptide_list_view/peptidetablemodel.h b/src/gui/peptide_list_view/peptidetablemodel.h
new file mode 100644
index 0000000000000000000000000000000000000000..b1f935532b374eb891fd755debcf21884bc0ae7f
--- /dev/null
+++ b/src/gui/peptide_list_view/peptidetablemodel.h
@@ -0,0 +1,72 @@
+
+/*******************************************************************************
+* 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 PEPTIDETABLEMODEL_H
+#define PEPTIDETABLEMODEL_H
+
+#include <QAbstractTableModel>
+#include <QSortFilterProxyModel>
+#include "../../core/project.h"
+
+class PeptideTableModel;
+class PeptideTableProxyModel : public QSortFilterProxyModel
+{
+ Q_OBJECT
+public:
+ PeptideTableProxyModel(QObject* parent,PeptideTableModel* peptide_table_model_p);
+ bool filterAcceptsRow(int source_row,
+ const QModelIndex &source_parent) const override;
+ QVariant headerData(int section, Qt::Orientation orientation,
+ int role) const override;
+ bool lessThan(const QModelIndex & left, const QModelIndex & right) const override;
+
+public slots:
+ void onTableClicked(const QModelIndex &index);
+private:
+ PeptideTableModel* _peptide_table_model_p;
+};
+
+class PeptideTableModel: public QAbstractTableModel
+{
+ Q_OBJECT
+public:
+ PeptideTableModel(QObject *parent=0);
+ int rowCount(const QModelIndex &parent = QModelIndex()) const override;
+ 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 setProteinMatch(Project * p_project, ProteinMatch * p_protein_match);
+ bool acceptRow(int source_row);
+signals:
+ void peptideMatchClicked(PeptideMatch * p_peptide_match);
+
+public slots:
+ void onTableClicked(const QModelIndex &index);
+
+private :
+ Project * _p_project;
+ ProteinMatch * _p_protein_match= nullptr;
+};
+
+#endif // PEPTIDETABLEMODEL_H
diff --git a/src/gui/protein_list_view/proteinlistwindow.cpp b/src/gui/protein_list_view/proteinlistwindow.cpp
index c071a0c4eb547c9c08e980095b4fda8b478d5f9a..c56c6365c33d8a40c7af54a097f0da2fb570b04b 100644
--- a/src/gui/protein_list_view/proteinlistwindow.cpp
+++ b/src/gui/protein_list_view/proteinlistwindow.cpp
@@ -50,7 +50,7 @@ ProteinListWindow::ProteinListWindow(QWidget *parent):
/*
*/
- _protein_table_model_p = new ProteinTableModel(0);
+ _protein_table_model_p = new ProteinTableModel(this, this);
_p_proxy_model = new ProteinTableProxyModel(this, _protein_table_model_p);
@@ -58,10 +58,14 @@ ProteinListWindow::ProteinListWindow(QWidget *parent):
_p_proxy_model->setDynamicSortFilter(true);
ui->tableView->setModel( _p_proxy_model );
ui->tableView->setSortingEnabled(true);
-
+
connect(ui->tableView, SIGNAL(clicked(const QModelIndex &)), _p_proxy_model, SLOT(onTableClicked(const QModelIndex &)));
}
+void ProteinListWindow::clickOnproteinMatch(ProteinMatch * p_protein_match) {
+ emit proteinMatchClicked(p_protein_match);
+}
+
ProteinListWindow::~ProteinListWindow()
{
//if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
diff --git a/src/gui/protein_list_view/proteinlistwindow.h b/src/gui/protein_list_view/proteinlistwindow.h
index e30f7aabefe2eef7e45207c01b46b28f602aed27..b982156d486fcfa7f658c873c35ffd6c9b0b0c02 100644
--- a/src/gui/protein_list_view/proteinlistwindow.h
+++ b/src/gui/protein_list_view/proteinlistwindow.h
@@ -41,14 +41,14 @@ public:
explicit ProteinListWindow(QWidget * parent = 0);
~ProteinListWindow();
void setIdentificationGroup(IdentificationGroup * p_identification_group);
+ void clickOnproteinMatch(ProteinMatch * p_protein_match);
public slots:
//void peptideEdited(QString peptideStr);
// void setColor(const QColor &color);
// void setShape(Shape shape);
signals:
- //void peptideChanged(pappso::PeptideSp peptide);
-
+ void proteinMatchClicked(ProteinMatch * p_protein_match);
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 71a639df8528b48758746d4aafe8657252ef5ef1..eef60b8ee8eeeb4f00b82ea5fd4bdbb847b5a0f5 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -22,6 +22,7 @@
******************************************************************************/
#include "proteintablemodel.h"
+#include "proteinlistwindow.h"
#include <QDebug>
@@ -40,8 +41,8 @@ bool ProteinTableProxyModel::filterAcceptsRow(int source_row,
void ProteinTableProxyModel::onTableClicked(const QModelIndex &index)
{
- qDebug() << "ProteinTableProxyModel::onTableClicked begin " << index.row();
- qDebug() << "ProteinTableProxyModel::onTableClicked begin " << this->mapToSource(index).row();
+ qDebug() << "ProteinTableProxyModel::onTableClicked begin " << index.row();
+ qDebug() << "ProteinTableProxyModel::onTableClicked begin " << this->mapToSource(index).row();
_protein_table_model_p->onTableClicked(this->mapToSource(index));
}
@@ -82,10 +83,10 @@ QVariant ProteinTableProxyModel::headerData(int section, Qt::Orientation orienta
role);
}
-ProteinTableModel::ProteinTableModel(QObject *parent)
+ProteinTableModel::ProteinTableModel(QObject *parent, ProteinListWindow * p_protein_list_window)
:QAbstractTableModel(parent)
{
-
+ _p_protein_list_window = p_protein_list_window;
//ui->tableView->show();
// QModelIndex topLeft = createIndex(0,0);
//emit a signal to make the view reread identified data
@@ -170,7 +171,7 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
if (col == 3) {
if (_p_identification_group != nullptr) {
- return _p_identification_group->getProteinMatchList().at(row)->getEvalue();
+ return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getEvalue());
}
}
@@ -190,18 +191,22 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
void ProteinTableModel::onTableClicked(const QModelIndex &index)
{
- int row = index.row();
+ int row = index.row();
int col = index.column();
if (col == 0) //add a checkbox to cell(1,0)
- {
- if ( _p_identification_group->getProteinMatchList().at(row)->isChecked()) {
- _p_identification_group->getProteinMatchList().at(row)->setChecked(false);
- }
- else {
- _p_identification_group->getProteinMatchList().at(row)->setChecked(true);
- }
- //emit dataChanged(index, index);
+ {
+ if ( _p_identification_group->getProteinMatchList().at(row)->isChecked()) {
+ _p_identification_group->getProteinMatchList().at(row)->setChecked(false);
+ }
+ else {
+ _p_identification_group->getProteinMatchList().at(row)->setChecked(true);
}
+ //emit dataChanged(index, index);
+ }
+
+ else {
+ _p_protein_list_window->clickOnproteinMatch(_p_identification_group->getProteinMatchList().at(row));
+ }
}
bool ProteinTableModel::acceptRow(int source_row) {
diff --git a/src/gui/protein_list_view/proteintablemodel.h b/src/gui/protein_list_view/proteintablemodel.h
index f548695e74e3b9da499bb6bb6be149931a66c0bc..307a55426436dc27bb2f82986a951ff795c7457e 100644
--- a/src/gui/protein_list_view/proteintablemodel.h
+++ b/src/gui/protein_list_view/proteintablemodel.h
@@ -28,6 +28,8 @@
#include <QSortFilterProxyModel>
#include "../../core/project.h"
+class ProteinListWindow;
+
class ProteinTableModel;
class ProteinTableProxyModel : public QSortFilterProxyModel
{
@@ -52,7 +54,7 @@ class ProteinTableModel: public QAbstractTableModel
{
Q_OBJECT
public:
- ProteinTableModel(QObject *parent=0);
+ ProteinTableModel(QObject *parent, ProteinListWindow * p_protein_list_window);
int rowCount(const QModelIndex &parent = QModelIndex()) const override;
int columnCount(const QModelIndex &parent = QModelIndex()) const override;
QVariant headerData(int section, Qt::Orientation orientation, int role) const override;
@@ -61,10 +63,12 @@ public:
void setIdentificationGroup(IdentificationGroup * p_identification_group);
bool acceptRow(int source_row);
+
public slots:
void onTableClicked(const QModelIndex &index);
private :
IdentificationGroup * _p_identification_group = nullptr;
+ ProteinListWindow * _p_protein_list_window;
};
#endif // PROTEINTABLEMODEL_H