From a2f9fbf06ac8b93107f2ddffe0fd931e4a216a4c Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Mon, 15 Oct 2018 08:42:45 +0200
Subject: [PATCH] WIP: replacing decoy selection with new widget
---
src/gui/project_view/project_view.ui | 122 +++++++------------------
src/gui/project_view/projectwindow.cpp | 112 ++++++++++++++++-------
src/gui/project_view/projectwindow.h | 11 +--
3 files changed, 113 insertions(+), 132 deletions(-)
diff --git a/src/gui/project_view/project_view.ui b/src/gui/project_view/project_view.ui
index 773a39e2f..b89a7c5dd 100644
--- a/src/gui/project_view/project_view.ui
+++ b/src/gui/project_view/project_view.ui
@@ -174,61 +174,13 @@
</widget>
</item>
<item>
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <item>
- <widget class="QRadioButton" name="decoy_database_files_radiobutton">
- <property name="toolTip">
- <string>select decoy sequences from fasta files</string>
- </property>
- <property name="text">
- <string>data&base files</string>
- </property>
- <attribute name="buttonGroup">
- <string notr="true">decoy_source_buttongroup</string>
- </attribute>
- </widget>
- </item>
- <item>
- <widget class="QRadioButton" name="decoy_regexp_radiobutton">
- <property name="toolTip">
- <string>select decoy sequences based on a regular expression</string>
- </property>
- <property name="text">
- <string>&regular expression</string>
- </property>
- <attribute name="buttonGroup">
- <string notr="true">decoy_source_buttongroup</string>
- </attribute>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QGroupBox" name="decoy_database_groupbox">
- <property name="title">
- <string>Choose decoy database files</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_3">
- <item>
- <widget class="QListView" name="decoy_database_listview"/>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <widget class="QGroupBox" name="decoy_regexp_groupbox">
- <property name="title">
- <string>Set regular expression to select decoy proteins</string>
+ <widget class="DecoyWidget" name="decoy_widget" native="true">
+ <property name="minimumSize">
+ <size>
+ <width>10</width>
+ <height>10</height>
+ </size>
</property>
- <layout class="QVBoxLayout" name="verticalLayout_4">
- <item>
- <widget class="QLineEdit" name="decoy_protein_regexp_line_edit">
- <property name="placeholderText">
- <string>.*\\|reversed$</string>
- </property>
- </widget>
- </item>
- </layout>
</widget>
</item>
<item>
@@ -412,6 +364,15 @@
<signal>changed()</signal>
</slots>
</customwidget>
+ <customwidget>
+ <class>DecoyWidget</class>
+ <extends>QWidget</extends>
+ <header>gui/widgets/decoy_widget/decoywidget.h</header>
+ <container>1</container>
+ <slots>
+ <signal>changed()</signal>
+ </slots>
+ </customwidget>
</customwidgets>
<resources/>
<connections>
@@ -422,8 +383,8 @@
<slot>doFdrChanged()</slot>
<hints>
<hint type="sourcelabel">
- <x>119</x>
- <y>104</y>
+ <x>448</x>
+ <y>219</y>
</hint>
<hint type="destinationlabel">
<x>484</x>
@@ -464,66 +425,50 @@
</hints>
</connection>
<connection>
- <sender>decoy_database_files_radiobutton</sender>
- <signal>clicked()</signal>
+ <sender>contaminant_widget</sender>
+ <signal>changed()</signal>
<receiver>ProjectView</receiver>
- <slot>doSelectDecoySource()</slot>
+ <slot>doFilterChanged()</slot>
<hints>
<hint type="sourcelabel">
- <x>68</x>
+ <x>119</x>
<y>104</y>
</hint>
<hint type="destinationlabel">
- <x>682</x>
- <y>256</y>
+ <x>815</x>
+ <y>196</y>
</hint>
</hints>
</connection>
<connection>
- <sender>decoy_regexp_radiobutton</sender>
+ <sender>apply_filter_button</sender>
<signal>clicked()</signal>
<receiver>ProjectView</receiver>
- <slot>doSelectDecoySource()</slot>
+ <slot>doApplyFilter()</slot>
<hints>
<hint type="sourcelabel">
<x>119</x>
<y>104</y>
</hint>
<hint type="destinationlabel">
- <x>693</x>
- <y>239</y>
+ <x>689</x>
+ <y>147</y>
</hint>
</hints>
</connection>
<connection>
- <sender>contaminant_widget</sender>
+ <sender>decoy_widget</sender>
<signal>changed()</signal>
<receiver>ProjectView</receiver>
<slot>doFilterChanged()</slot>
<hints>
<hint type="sourcelabel">
- <x>368</x>
- <y>99</y>
+ <x>180</x>
+ <y>182</y>
</hint>
<hint type="destinationlabel">
- <x>815</x>
- <y>196</y>
- </hint>
- </hints>
- </connection>
- <connection>
- <sender>apply_filter_button</sender>
- <signal>clicked()</signal>
- <receiver>ProjectView</receiver>
- <slot>doApplyFilter()</slot>
- <hints>
- <hint type="sourcelabel">
- <x>412</x>
- <y>120</y>
- </hint>
- <hint type="destinationlabel">
- <x>689</x>
- <y>147</y>
+ <x>763</x>
+ <y>179</y>
</hint>
</hints>
</connection>
@@ -537,7 +482,4 @@
<slot>doFilterChanged()</slot>
<slot>doApplyFilter()</slot>
</slots>
- <buttongroups>
- <buttongroup name="decoy_source_buttongroup"/>
- </buttongroups>
</ui>
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index b270acd28..8ee7b7e54 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -50,11 +50,6 @@ ProjectWindow::ProjectWindow(MainWindow *parent)
p_worker->moveToThread(&_worker_thread);
_worker_thread.start();
- _p_fasta_str_li = new QStandardItemModel();
- ui->decoy_database_listview->setModel(_p_fasta_str_li);
- ui->decoy_database_listview->setSelectionMode(
- QAbstractItemView::MultiSelection);
-
_p_edit_modifications = new EditModifications(this);
_p_edit_label_methods = new EditLabelMethods(this);
@@ -89,12 +84,21 @@ ProjectWindow::ProjectWindow(MainWindow *parent)
#if QT_VERSION >= 0x050000
// Qt5 code
connect(ui->filter_parameter_widget,
- &AutomaticFilterWidget::automaticFilterParametersChanged, this,
+ &AutomaticFilterWidget::automaticFilterParametersChanged,
+ this,
&ProjectWindow::doAutomaticFilterParametersChanged);
- connect(ui->contaminant_widget, &ContaminantWidget::changed, this,
+ connect(ui->contaminant_widget,
+ &ContaminantWidget::changed,
+ this,
&ProjectWindow::doContaminantSelectionChanged);
+ connect(ui->decoy_widget,
+ &DecoyWidget::changed,
+ this,
+ &ProjectWindow::doDecoySelectionChanged);
- connect(_p_edit_label_methods, &EditLabelMethods::accepted, this,
+ connect(_p_edit_label_methods,
+ &EditLabelMethods::accepted,
+ this,
&ProjectWindow::doAcceptedLabelingMethod);
#else
@@ -106,7 +110,9 @@ ProjectWindow::ProjectWindow(MainWindow *parent)
this,
SLOT(doAutomaticFilterParametersChanged(AutomaticFilterParameters)));
- connect(_p_edit_label_methods, SIGNAL(accepted()), this,
+ connect(_p_edit_label_methods,
+ SIGNAL(accepted()),
+ this,
SLOT(doAcceptedLabelingMethod()));
// connect(this, SIGNAL(operateGrouping(ProjectSp)),
@@ -217,13 +223,13 @@ ProjectWindow::refreshPtmGroup(IdentificationGroup *p_ident_group)
}
catch(pappso::PappsoException exception_pappso)
{
- QMessageBox::warning(this, tr("Unable to display project :"),
- exception_pappso.qwhat());
+ QMessageBox::warning(
+ this, tr("Unable to display project :"), exception_pappso.qwhat());
}
catch(std::exception exception_std)
{
- QMessageBox::warning(this, tr("Unable to display project :"),
- exception_std.what());
+ QMessageBox::warning(
+ this, tr("Unable to display project :"), exception_std.what());
}
}
qDebug() << "ProjectWindow::refreshPtmGroup end";
@@ -245,13 +251,13 @@ ProjectWindow::refreshGroup(IdentificationGroup *p_ident_group)
}
catch(pappso::PappsoException exception_pappso)
{
- QMessageBox::warning(this, tr("Unable to display project :"),
- exception_pappso.qwhat());
+ QMessageBox::warning(
+ this, tr("Unable to display project :"), exception_pappso.qwhat());
}
catch(std::exception exception_std)
{
- QMessageBox::warning(this, tr("Unable to display project :"),
- exception_std.what());
+ QMessageBox::warning(
+ this, tr("Unable to display project :"), exception_std.what());
}
}
qDebug() << "ProjectWindow::refreshGroup end";
@@ -284,13 +290,13 @@ ProjectWindow::computeFdr()
}
catch(pappso::PappsoException exception_pappso)
{
- QMessageBox::warning(this, tr("Unable to compute FDR :"),
- exception_pappso.qwhat());
+ QMessageBox::warning(
+ this, tr("Unable to compute FDR :"), exception_pappso.qwhat());
}
catch(std::exception exception_std)
{
- QMessageBox::warning(this, tr("Unable to compute FDR :"),
- exception_std.what());
+ QMessageBox::warning(
+ this, tr("Unable to compute FDR :"), exception_std.what());
}
qDebug() << "ProjectWindow::computeFdr end";
}
@@ -375,7 +381,8 @@ ProjectWindow::computeMassPrecision()
ui->mass_precision_mean_label->setText("0");
ui->mass_precision_median_label->setText("0");
ui->mass_precision_sd_label->setText("0");
- QMessageBox::warning(this, tr("Unable to compute mass precision :"),
+ QMessageBox::warning(this,
+ tr("Unable to compute mass precision :"),
exception_pappso.qwhat());
}
catch(std::exception exception_std)
@@ -383,8 +390,8 @@ ProjectWindow::computeMassPrecision()
ui->mass_precision_mean_label->setText("0");
ui->mass_precision_median_label->setText("0");
ui->mass_precision_sd_label->setText("0");
- QMessageBox::warning(this, tr("Unable to compute mass precision :"),
- exception_std.what());
+ QMessageBox::warning(
+ this, tr("Unable to compute mass precision :"), exception_std.what());
}
qDebug() << "ProjectWindow::computeMassPrecision end";
}
@@ -439,14 +446,14 @@ ProjectWindow::doFdrChanged()
catch(pappso::PappsoException exception_pappso)
{
hideWaitingMessage();
- QMessageBox::warning(this, tr("Unable to compute FDR :"),
- exception_pappso.qwhat());
+ QMessageBox::warning(
+ this, tr("Unable to compute FDR :"), exception_pappso.qwhat());
}
catch(std::exception exception_std)
{
hideWaitingMessage();
- QMessageBox::warning(this, tr("Unable to compute FDR :"),
- exception_std.what());
+ QMessageBox::warning(
+ this, tr("Unable to compute FDR :"), exception_std.what());
}
qDebug() << "ProjectWindow::doFdrChanged end ";
@@ -964,6 +971,44 @@ void
ProjectWindow::doFilterChanged()
{
ui->apply_filter_button->setEnabled(true);
+ ui->fdr_button->setEnabled(true);
+}
+
+void
+ProjectWindow::doApplyDecoy()
+{
+ ui->fdr_button->setEnabled(false);
+ // doAutomaticFilterParametersChanged(automatic_filter);
+ try
+ {
+ showWaitingMessage(tr("Updating decoy sequences"));
+
+ doDisplayLoadingMessage(tr("tagging decoy proteins"));
+
+ ui->decoy_widget->setProjectDecoys(_project_sp.get());
+ // doDisplayLoadingMessage(tr("updating FDR"));
+ //_project_sp.get()->updateAutomaticFilters(automatic_filter);
+ doDisplayLoadingMessage(tr("updating filters"));
+ _project_sp.get()->updateAutomaticFilters(
+ _project_sp.get()->getAutomaticFilterParameters());
+
+
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ emit operateGrouping(_project_sp);
+ }
+ catch(pappso::PappsoException exception_pappso)
+ {
+ hideWaitingMessage();
+ QMessageBox::warning(
+ this, tr("Error filtering results :"), exception_pappso.qwhat());
+ }
+ catch(std::exception exception_std)
+ {
+ hideWaitingMessage();
+ QMessageBox::warning(
+ this, tr("Error filtering results :"), exception_std.what());
+ }
}
void
@@ -983,20 +1028,19 @@ ProjectWindow::doApplyFilter()
doDisplayLoadingMessage(tr("updating filters"));
_project_sp.get()->updateAutomaticFilters(automatic_filter);
- qDebug() << "ProjectWindow::doAutomaticFilterParametersChanged emit "
- "operateGrouping(_project_sp) ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
emit operateGrouping(_project_sp);
}
catch(pappso::PappsoException exception_pappso)
{
hideWaitingMessage();
- QMessageBox::warning(this, tr("Error filtering results :"),
- exception_pappso.qwhat());
+ QMessageBox::warning(
+ this, tr("Error filtering results :"), exception_pappso.qwhat());
}
catch(std::exception exception_std)
{
hideWaitingMessage();
- QMessageBox::warning(this, tr("Error filtering results :"),
- exception_std.what());
+ QMessageBox::warning(
+ this, tr("Error filtering results :"), exception_std.what());
}
}
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index 7855d705d..6ff7aa6cb 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -17,13 +17,9 @@
* 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 PROJECTWINDOW_H
-#define PROJECTWINDOW_H
+#pragma once
#include <QMainWindow>
#include <QThread>
@@ -46,7 +42,7 @@ class MainWindow;
// http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
namespace Ui
{
- class ProjectView;
+class ProjectView;
}
class ProjectWindow : public QMainWindow
@@ -107,6 +103,7 @@ class ProjectWindow : public QMainWindow
void doViewProteinDetail(ProteinMatch *protein_match);
void doIdentificationGroupEdited(IdentificationGroup *p_identification_group);
void doContaminantSelectionChanged();
+ void doDecoySelectionChanged();
void computeFdr();
void computeMassPrecision();
@@ -150,5 +147,3 @@ class ProjectWindow : public QMainWindow
// QCPBars *_p_bars;
};
-
-#endif // PROJECTWINDOW_H
--
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