Skip to content
Snippets Groups Projects
Commit 0894979a authored by Langella Olivier's avatar Langella Olivier
Browse files

new contaminant widget is available

parent 7b92caa6
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 284 additions and 144 deletions
src/gui/load_results_dialog/loadresultsdialog.cpp
+ 6
− 0
View file @ 0894979a
......@@ -104,3 +104,9 @@ void LoadResultsDialog::chooseFiles() {
// tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
}
}
void LoadResultsDialog::setProjectContaminants(Project * p_project) const {
ui->contaminant_widget->setProjectContaminants(p_project);
}
src/gui/load_results_dialog/loadresultsdialog.h
+ 2
− 0
View file @ 0894979a
......@@ -27,6 +27,7 @@
#include <QDialog>
#include <QStringListModel>
#include "../widgets/automatic_filter_widget/automaticfilterwidget.h"
#include "../../core/project.h"
namespace Ui {
......@@ -45,6 +46,7 @@ public:
AutomaticFilterParameters getAutomaticFilterParameters() const;
QStringList getFileList() const;
bool isIndividual() const;
void setProjectContaminants(Project * p_project) const;
public slots:
void chooseFiles();
void clearFileList();
......
src/gui/mainwindow.cpp
+ 9
− 0
View file @ 0894979a
......@@ -226,6 +226,15 @@ void MainWindow::doGroupingFinished() {
_project_window->setProjectSp(_project_sp);
}
void MainWindow::doLoadingResultsReady(ProjectSp project_sp) {
qDebug() << "MainWindow::doLoadingResultsReady begin";
if (_p_load_results_dialog != nullptr) {
_p_load_results_dialog->setProjectContaminants(project_sp.get());
}
doProjectReady(project_sp);
qDebug() << "MainWindow::doLoadingResultsReady end";
}
void MainWindow::doProjectReady(ProjectSp project_sp) {
qDebug() << "MainWindow::doProjectReady begin";
......
src/gui/mainwindow.h
+ 1
− 0
View file @ 0894979a
......@@ -82,6 +82,7 @@ public slots:
void doWorkerAppendText(char *);
void doWorkerSetText(QString);
void doProjectReady(ProjectSp project_sp);
void doLoadingResultsReady(ProjectSp project_sp);
void doProjectNotReady(QString error);
void doAcceptedLoadResultDialog();
void doAcceptedTandemRunDialog();
......
src/gui/project_view/project_view.ui
+ 34
− 91
View file @ 0894979a
......@@ -51,59 +51,29 @@
<item row="0" column="0">
<layout class="QVBoxLayout" name="filter_parameter_tab_layout">
<item>
<widget class="AutomaticFilterWidget" name="filter_parameter_widget" native="true"/>
<widget class="AutomaticFilterWidget" name="filter_parameter_widget" native="true">
<property name="minimumSize">
<size>
<width>0</width>
<height>10</height>
</size>
</property>
<property name="sizeIncrement">
<size>
<width>0</width>
<height>0</height>
</size>
</property>
</widget>
</item>
<item>
<widget class="QGroupBox" name="contaminant_groupbox">
<property name="title">
<string>Contaminants</string>
<widget class="ContaminantWidget" name="contaminant_widget" native="true">
<property name="minimumSize">
<size>
<width>0</width>
<height>10</height>
</size>
</property>
<layout class="QVBoxLayout" name="verticalLayout_6">
<item>
<layout class="QHBoxLayout" name="horizontalLayout_4">
<item>
<widget class="QRadioButton" name="contaminant_file_radiobutton">
<property name="toolTip">
<string>select contaminants from fasta files</string>
</property>
<property name="text">
<string>contaminant file</string>
</property>
<attribute name="buttonGroup">
<string notr="true">contaminant_source_buttongroup</string>
</attribute>
</widget>
</item>
<item>
<widget class="QRadioButton" name="contaminant_regexp_radiobutton">
<property name="toolTip">
<string>select contaminants using a regular expression</string>
</property>
<property name="text">
<string>contaminant &amp;regular expression</string>
</property>
<attribute name="buttonGroup">
<string notr="true">contaminant_source_buttongroup</string>
</attribute>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QListView" name="contaminant_database_listview"/>
</item>
<item>
<layout class="QVBoxLayout" name="verticalLayout_8">
<item>
<widget class="QLineEdit" name="contaminant_protein_regexp_line_edit">
<property name="placeholderText">
<string>^conta\\|</string>
</property>
</widget>
</item>
</layout>
</item>
</layout>
</widget>
</item>
</layout>
......@@ -409,6 +379,12 @@
<header>gui/widgets/automatic_filter_widget/automaticfilterwidget.h</header>
<container>1</container>
</customwidget>
<customwidget>
<class>ContaminantWidget</class>
<extends>QWidget</extends>
<header>gui/widgets/contaminant_widget/contaminantwidget.h</header>
<container>1</container>
</customwidget>
</customwidgets>
<resources/>
<connections>
......@@ -419,8 +395,8 @@
<slot>doFdrChanged()</slot>
<hints>
<hint type="sourcelabel">
<x>442</x>
<y>485</y>
<x>119</x>
<y>104</y>
</hint>
<hint type="destinationlabel">
<x>484</x>
......@@ -435,8 +411,8 @@
<slot>doMassPrecisionUnitChanged(QString)</slot>
<hints>
<hint type="sourcelabel">
<x>253</x>
<y>113</y>
<x>119</x>
<y>104</y>
</hint>
<hint type="destinationlabel">
<x>489</x>
......@@ -467,8 +443,8 @@
<slot>doSelectDecoySource()</slot>
<hints>
<hint type="sourcelabel">
<x>110</x>
<y>184</y>
<x>119</x>
<y>104</y>
</hint>
<hint type="destinationlabel">
<x>682</x>
......@@ -483,8 +459,8 @@
<slot>doSelectDecoySource()</slot>
<hints>
<hint type="sourcelabel">
<x>326</x>
<y>192</y>
<x>119</x>
<y>104</y>
</hint>
<hint type="destinationlabel">
<x>693</x>
......@@ -492,38 +468,6 @@
</hint>
</hints>
</connection>
<connection>
<sender>contaminant_file_radiobutton</sender>
<signal>clicked()</signal>
<receiver>ProjectView</receiver>
<slot>doSelectContaminantSource()</slot>
<hints>
<hint type="sourcelabel">
<x>159</x>
<y>127</y>
</hint>
<hint type="destinationlabel">
<x>581</x>
<y>113</y>
</hint>
</hints>
</connection>
<connection>
<sender>contaminant_regexp_radiobutton</sender>
<signal>clicked()</signal>
<receiver>ProjectView</receiver>
<slot>doSelectContaminantSource()</slot>
<hints>
<hint type="sourcelabel">
<x>408</x>
<y>129</y>
</hint>
<hint type="destinationlabel">
<x>578</x>
<y>62</y>
</hint>
</hints>
</connection>
</connections>
<slots>
<slot>doFdrChanged()</slot>
......@@ -533,7 +477,6 @@
<slot>doSelectContaminantSource()</slot>
</slots>
<buttongroups>
<buttongroup name="contaminant_source_buttongroup"/>
<buttongroup name="decoy_source_buttongroup"/>
</buttongroups>
</ui>
src/gui/project_view/projectwindow.cpp
+ 3
− 42
View file @ 0894979a
......@@ -53,9 +53,6 @@ ProjectWindow::ProjectWindow(MainWindow *parent):
_p_fasta_str_li = new QStandardItemModel();
ui->decoy_database_listview->setModel(_p_fasta_str_li);
ui->contaminant_database_listview->setModel(_p_fasta_str_li);
QItemSelectionModel * selection_model = ui->contaminant_database_listview->selectionModel();
ui->contaminant_database_listview->setSelectionMode(QAbstractItemView::MultiSelection);
ui->decoy_database_listview->setSelectionMode(QAbstractItemView::MultiSelection);
......@@ -387,24 +384,8 @@ void ProjectWindow::doAutomaticFilterParametersChanged(AutomaticFilterParameters
showWaitingMessage(tr("Updating filters"));
doDisplayLoadingMessage(tr("tagging contaminant proteins"));
if (ui->contaminant_file_radiobutton->isChecked()) {
QModelIndexList index_list = ui->contaminant_database_listview->selectionModel()->selectedIndexes();
_project_sp.get()->getProteinStore().clearContaminants();
if (index_list.size() > 0) {
for (QModelIndex index :index_list) {
if (index.data(Qt::UserRole).canConvert<FastaFile *>()) {
FastaFile * p_fasta_file = index.data(Qt::UserRole).value<FastaFile *>();
p_fasta_file->setContaminants(_project_sp.get()->getProteinStore());
}
else {
throw pappso::PappsoException(QObject::tr("can not convert to FastaFile index.data().canConvert<FastaFile *>()"));
}
}
}
}
else {
_project_sp.get()->getProteinStore().setRegexpContaminantPattern(ui->contaminant_protein_regexp_line_edit->text());
}
ui->contaminant_widget->setProjectContaminants(_project_sp.get());
doDisplayLoadingMessage(tr("updating filters"));
_project_sp.get()->updateAutomaticFilters(parameters);
......@@ -594,13 +575,7 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
ui->decoy_database_groupbox->setVisible(true);
}
ui->contaminant_regexp_radiobutton->setChecked(true);
ui->contaminant_database_listview->setVisible(false);
if (_project_sp.get()->getProteinStore().getContaminantFastaFileList().size() > 0) {
ui->contaminant_file_radiobutton->setChecked(true);
ui->contaminant_protein_regexp_line_edit->setVisible(false);
ui->contaminant_database_listview->setVisible(true);
}
ui->contaminant_widget->getProjectContaminants(_project_sp.get());
qDebug() << "ProjectWindow::setProjectSp begin " << _project_sp.get()->getFastaFileStore().getFastaFileList().size() ;
......@@ -710,7 +685,6 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
//_protein_list_window->show();
ui->decoy_protein_regexp_line_edit->setText(_project_sp.get()->getProteinStore().getRegexpDecoy().pattern());
ui->contaminant_protein_regexp_line_edit->setText(_project_sp.get()->getProteinStore().getRegexpContaminant().pattern());
refresh();
this->setEnabled(true);
......@@ -811,16 +785,3 @@ void ProjectWindow::doSelectDecoySource() {
}
qDebug() << "ProjectWindow::doSelectDecoySource end";
}
void ProjectWindow::doSelectContaminantSource() {
qDebug() << "ProjectWindow::doSelectContaminantSource begin";
ui->contaminant_database_listview->setVisible(false);
ui->contaminant_protein_regexp_line_edit->setVisible(false);
if (ui->contaminant_file_radiobutton->isChecked()) {
ui->contaminant_database_listview->setVisible(true);
}
else {
ui->contaminant_protein_regexp_line_edit->setVisible(true);
}
qDebug() << "ProjectWindow::doSelectContaminantSource end";
}
src/gui/project_view/projectwindow.h
+ 0
− 1
View file @ 0894979a
......@@ -70,7 +70,6 @@ public slots:
void doAutomaticFilterParametersChanged(AutomaticFilterParameters parameters);
void doFdrChanged();
void doSelectDecoySource();
void doSelectContaminantSource();
void doMassPrecisionUnitChanged(QString combo_value);
void doOperationFailed(QString);
void doOperationFinished();
......
src/gui/widgets/contaminant_widget/contaminant_widget.ui
+ 119
− 1
View file @ 0894979a
......@@ -30,6 +30,9 @@
<property name="text">
<string>contaminant file</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
<attribute name="buttonGroup">
<string notr="true">contaminant_source_buttongroup</string>
</attribute>
......@@ -53,6 +56,51 @@
<item>
<widget class="QListView" name="contaminant_database_listview"/>
</item>
<item>
<widget class="QWidget" name="control_list_widget" native="true">
<layout class="QHBoxLayout" name="horizontalLayout">
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>0</number>
</property>
<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">
<property name="text">
<string>clear list</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="pushButton_2">
<property name="text">
<string>add files</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<layout class="QVBoxLayout" name="verticalLayout_8">
<item>
......@@ -70,7 +118,77 @@
</layout>
</widget>
<resources/>
<connections/>
<connections>
<connection>
<sender>contaminant_file_radiobutton</sender>
<signal>clicked()</signal>
<receiver>ContaminantWidget</receiver>
<slot>doSelectContaminantSource()</slot>
<hints>
<hint type="sourcelabel">
<x>113</x>
<y>58</y>
</hint>
<hint type="destinationlabel">
<x>735</x>
<y>64</y>
</hint>
</hints>
</connection>
<connection>
<sender>contaminant_regexp_radiobutton</sender>
<signal>clicked()</signal>
<receiver>ContaminantWidget</receiver>
<slot>doSelectContaminantSource()</slot>
<hints>
<hint type="sourcelabel">
<x>226</x>
<y>52</y>
</hint>
<hint type="destinationlabel">
<x>670</x>
<y>79</y>
</hint>
</hints>
</connection>
<connection>
<sender>pushButton_2</sender>
<signal>clicked()</signal>
<receiver>ContaminantWidget</receiver>
<slot>doSelectFastaFile()</slot>
<hints>
<hint type="sourcelabel">
<x>333</x>
<y>229</y>
</hint>
<hint type="destinationlabel">
<x>690</x>
<y>146</y>
</hint>
</hints>
</connection>
<connection>
<sender>pushButton</sender>
<signal>clicked()</signal>
<receiver>ContaminantWidget</receiver>
<slot>doClearList()</slot>
<hints>
<hint type="sourcelabel">
<x>269</x>
<y>220</y>
</hint>
<hint type="destinationlabel">
<x>508</x>
<y>201</y>
</hint>
</hints>
</connection>
</connections>
<slots>
<slot>doSelectContaminantSource()</slot>
<slot>doSelectFastaFile()</slot>
<slot>doClearList()</slot>
</slots>
<buttongroups>
<buttongroup name="contaminant_source_buttongroup"/>
</buttongroups>
......
src/gui/widgets/contaminant_widget/contaminantwidget.cpp
+ 95
− 5
View file @ 0894979a
......@@ -32,7 +32,9 @@
#include "ui_contaminant_widget.h"
#include <QDebug>
#include <pappsomspp/pappsoexception.h>
#include <QSettings>
#include <QFileDialog>
ContaminantWidget::ContaminantWidget(QWidget * parent):
QWidget(parent),
......@@ -45,6 +47,8 @@ ContaminantWidget::ContaminantWidget(QWidget * parent):
ui->contaminant_database_listview->setModel(_p_fasta_str_li);
QItemSelectionModel * selection_model = ui->contaminant_database_listview->selectionModel();
ui->contaminant_database_listview->setSelectionMode(QAbstractItemView::MultiSelection);
doSelectContaminantSource();
qDebug() << "ContaminantWidget::ContaminantWidget end";
}
......@@ -61,13 +65,10 @@ void ContaminantWidget::setRegexpContaminantPattern(const QString & pattern) {
ui->contaminant_protein_regexp_line_edit->setText(pattern);
}
const QString ContaminantWidget::getRegexpContaminant() const {
return ui->contaminant_protein_regexp_line_edit->text();
}
void ContaminantWidget::setFastaFileList(std::vector<FastaFileSp> fasta_file_list) {
_fasta_file_list = fasta_file_list;
_p_fasta_str_li->removeRows(0, _p_fasta_str_li->rowCount());
for (FastaFileSp fasta_file : fasta_file_list ) {
......@@ -80,3 +81,92 @@ void ContaminantWidget::setFastaFileList(std::vector<FastaFileSp> fasta_file_lis
}
}
void ContaminantWidget::getProjectContaminants(const Project * p_project) {
ui->contaminant_regexp_radiobutton->setChecked(true);
ui->contaminant_database_listview->setVisible(false);
if (p_project->getProteinStore().getContaminantFastaFileList().size() > 0) {
ui->contaminant_file_radiobutton->setChecked(true);
ui->contaminant_protein_regexp_line_edit->setVisible(false);
ui->contaminant_database_listview->setVisible(true);
}
ui->contaminant_protein_regexp_line_edit->setText(p_project->getProteinStore().getRegexpContaminant().pattern());
this->setFastaFileList( p_project->getFastaFileStore().getFastaFileList());
ui->control_list_widget->setVisible(false);
_no_project = false;
}
void ContaminantWidget::setProjectContaminants(Project * p_project) {
qDebug() << "ContaminantWidget::setProjectContaminants begin";
if (ui->contaminant_file_radiobutton->isChecked()) {
QModelIndexList index_list = ui->contaminant_database_listview->selectionModel()->selectedIndexes();
p_project->getProteinStore().clearContaminants();
if (index_list.size() > 0) {
for (QModelIndex index :index_list) {
if (index.data(Qt::UserRole).canConvert<FastaFile *>()) {
FastaFile * p_fasta_file = index.data(Qt::UserRole).value<FastaFile *>();
p_fasta_file->setContaminants(p_project->getProteinStore());
}
else {
throw pappso::PappsoException(QObject::tr("can not convert to FastaFile index.data().canConvert<FastaFile *>()"));
}
}
}
if (_no_project) {
ui->control_list_widget->setVisible(true);
}
}
else {
p_project->getProteinStore().setRegexpContaminantPattern(ui->contaminant_protein_regexp_line_edit->text());
ui->control_list_widget->setVisible(false);
}
qDebug() << "ContaminantWidget::setProjectContaminants end";
}
void ContaminantWidget::doSelectContaminantSource() {
qDebug() << "ContaminantWidget::doSelectContaminantSource begin";
ui->contaminant_database_listview->setVisible(false);
ui->contaminant_protein_regexp_line_edit->setVisible(false);
if (ui->contaminant_file_radiobutton->isChecked()) {
ui->contaminant_database_listview->setVisible(true);
}
else {
ui->contaminant_protein_regexp_line_edit->setVisible(true);
}
qDebug() << "ContaminantWidget::doSelectContaminantSource end";
}
void ContaminantWidget::doSelectFastaFile() {
try {
QSettings settings;
QString default_fasta_location = settings.value("path/fastafiles_directory", "").toString();
QStringList filenames = QFileDialog::getOpenFileNames(this,tr("FASTA files"),default_fasta_location,
tr("FASTA files (*.fasta);;all files (*)") );
if (filenames.size() > 0) {
settings.setValue("path/fastafiles_directory", QFileInfo(filenames[0]).absolutePath());
}
std::vector<FastaFileSp> fasta_file_list;
for (QString filename :filenames) {
fasta_file_list.push_back(std::make_shared<FastaFile>(filename));
}
this->setFastaFileList(fasta_file_list);
}
catch (pappso::PappsoException & error) {
//QMessageBox::warning(this,
// tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
}
}
void ContaminantWidget::doClearList() {
_p_fasta_str_li->removeRows( 0, _p_fasta_str_li->rowCount() );
}
src/gui/widgets/contaminant_widget/contaminantwidget.h
+ 11
− 2
View file @ 0894979a
......@@ -34,6 +34,7 @@
#include <QWidget>
#include <QStandardItemModel>
#include "../../../files/fastafile.h"
#include "../../../core/project.h"
namespace Ui {
......@@ -50,19 +51,27 @@ public:
void setRegexpContaminantPattern(const QString & pattern);
const QString getRegexpContaminant() const;
void setFastaFileList(std::vector<FastaFileSp> fasta_file_list);
void setProjectContaminants(Project * p_project);
void getProjectContaminants(const Project * p_project);
public slots:
void doSelectContaminantSource();
void doSelectFastaFile();
void doClearList();
signals:
private:
Ui::ContaminantWidget *ui;
bool _no_project = true;
QStandardItemModel * _p_fasta_str_li;
std::vector<FastaFileSp> _fasta_file_list;
};
......
src/gui/workerthread.cpp
+ 3
− 2
View file @ 0894979a
......@@ -62,6 +62,7 @@ WorkerThread::WorkerThread(MainWindow * p_main_window)
connect(p_main_window, &MainWindow::operateXpipFile, this,&WorkerThread::doXpipFileLoad);
connect(p_main_window, &MainWindow::operateWritingXpipFile, this,&WorkerThread::doWritingXpipFile);
connect(this, &WorkerThread::projectReady, p_main_window,&MainWindow::doProjectReady);
connect(this, &WorkerThread::loadingResultsFinished, p_main_window,&MainWindow::doLoadingResultsReady);
connect(p_main_window, &MainWindow::operateLoadingResults, this,&WorkerThread::doLoadingResults);
......@@ -361,8 +362,8 @@ void WorkerThread::doLoadingResults(bool is_individual, AutomaticFilterParameter
emit loadingMessage(tr("filtering proteins"));
project_sp.get()->updateAutomaticFilters(param);
qDebug() << "WorkerThread::doLoadingResults emit projectReady(project_sp) ";
emit projectReady(project_sp);
qDebug() << "WorkerThread::doLoadingResults emit loadingResultsFinished(project_sp) ";
emit loadingResultsFinished(project_sp);
}
catch (pappso::PappsoException & error) {
......
src/gui/workerthread.h
+ 1
− 0
View file @ 0894979a
......@@ -72,6 +72,7 @@ public slots:
signals:
void loadingMessage(QString message);
void projectReady(ProjectSp project_sp);
void loadingResultsFinished(ProjectSp project_sp);
void projectNotReady(QString error);
void groupingFinished();
void groupingOnIdentificationFinished(IdentificationGroup * p_identification_group);
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment