From f4f1fdad687e6e859733d5633a9c96bdc89f3595 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Wed, 7 Feb 2018 22:27:55 +0100
Subject: [PATCH] new ui to select decoy proteins
---
src/gui/project_view/project_view.ui | 91 ++++++++++++++++++++++++--
src/gui/project_view/projectwindow.cpp | 46 +++++++++----
src/gui/project_view/projectwindow.h | 1 +
3 files changed, 118 insertions(+), 20 deletions(-)
diff --git a/src/gui/project_view/project_view.ui b/src/gui/project_view/project_view.ui
index b6425a66a..358663a03 100644
--- a/src/gui/project_view/project_view.ui
+++ b/src/gui/project_view/project_view.ui
@@ -7,7 +7,7 @@
<x>0</x>
<y>0</y>
<width>465</width>
- <height>493</height>
+ <height>533</height>
</rect>
</property>
<property name="windowTitle">
@@ -24,7 +24,7 @@
<string/>
</property>
<property name="currentIndex">
- <number>0</number>
+ <number>2</number>
</property>
<widget class="QWidget" name="identifications">
<attribute name="title">
@@ -133,9 +133,39 @@
</widget>
</item>
<item>
- <widget class="QGroupBox" name="groupBox">
+ <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>database 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>Decoy database files</string>
+ <string>Choose decoy database files</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout_3">
<item>
@@ -169,9 +199,9 @@
</widget>
</item>
<item>
- <widget class="QGroupBox" name="groupBox_2">
+ <widget class="QGroupBox" name="decoy_regexp_groupbox">
<property name="title">
- <string>Decoy protein regular expression</string>
+ <string>Set regular expression to select decoy proteins</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout_4">
<item>
@@ -181,6 +211,19 @@
</property>
</widget>
</item>
+ <item>
+ <spacer name="verticalSpacer">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
</layout>
</widget>
</item>
@@ -388,10 +431,46 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>decoy_database_files_radiobutton</sender>
+ <signal>clicked()</signal>
+ <receiver>ProjectView</receiver>
+ <slot>doSelectDecoySource()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>110</x>
+ <y>184</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>682</x>
+ <y>256</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>decoy_regexp_radiobutton</sender>
+ <signal>clicked()</signal>
+ <receiver>ProjectView</receiver>
+ <slot>doSelectDecoySource()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>326</x>
+ <y>192</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>693</x>
+ <y>239</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>doFdrChanged()</slot>
<slot>doMassPrecisionUnitChanged(QString)</slot>
<slot>doIdentificationsComboboxChanged(int)</slot>
+ <slot>doSelectDecoySource()</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 804241d0f..06ddc310a 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -155,7 +155,7 @@ void ProjectWindow::connectNewPtmIslandListWindow() {
void ProjectWindow::connectNewProteinListWindow() {
qDebug() << "ProjectWindow::connectNewProteinListWindow begin";
_p_current_protein_list_window = new ProteinListWindow(this);
-
+
_protein_list_window_collection.push_back(_p_current_protein_list_window);
qDebug() << "ProjectWindow::connectNewProteinListWindow end";
@@ -341,23 +341,25 @@ void ProjectWindow::doFdrChanged() {
try {
showWaitingMessage(tr("FDR modifications"));
doDisplayLoadingMessage(tr("tagging decoy proteins"));
- QModelIndexList index_list = ui->decoy_database_listview->selectionModel()->selectedIndexes();
- if (index_list.size() > 0) {
- qDebug() << "ProjectWindow::doFdrChanged index_list.size()=" << index_list.size();
+ if (ui->decoy_regexp_radiobutton->isChecked()) {
+ _project_sp.get()->getProteinStore().setRegexpDecoyPattern(ui->decoy_protein_regexp_line_edit->text());
+ }
+ else {
_project_sp.get()->getProteinStore().clearDecoys();
- 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->setDecoys(_project_sp.get()->getProteinStore());
- }
- else {
- throw pappso::PappsoException(QObject::tr("can not convert to FastaFile index.data().canConvert<FastaFile *>()"));
+ QModelIndexList index_list = ui->decoy_database_listview->selectionModel()->selectedIndexes();
+ if (index_list.size() > 0) {
+ qDebug() << "ProjectWindow::doFdrChanged index_list.size()=" << index_list.size();
+ 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->setDecoys(_project_sp.get()->getProteinStore());
+ }
+ else {
+ throw pappso::PappsoException(QObject::tr("can not convert to FastaFile index.data().canConvert<FastaFile *>()"));
+ }
}
}
}
- else {
- _project_sp.get()->getProteinStore().setRegexpDecoyPattern(ui->decoy_protein_regexp_line_edit->text());
- }
doDisplayLoadingMessage(tr("updating filters"));
_project_sp.get()->updateAutomaticFilters(_project_sp.get()->getAutomaticFilterParameters());
@@ -587,6 +589,8 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
qDebug() << "ProjectWindow::setProjectSp begin" ;
_project_sp = project_sp;
+ ui->decoy_regexp_radiobutton->setChecked(true);
+ ui->decoy_database_groupbox->setVisible(false);
qDebug() << "ProjectWindow::setProjectSp begin " << _project_sp.get()->getFastaFileStore().getFastaFileList().size() ;
_fastafile_list = _project_sp.get()->getFastaFileStore().getFastaFileList();
@@ -782,3 +786,17 @@ void ProjectWindow::openInXicViewer(const PeptideEvidence * p_peptide_evidence)
_p_xic_window->addXic(p_peptide_evidence);
qDebug() << "ProjectWindow::openInXicViewer end";
}
+
+
+void ProjectWindow::doSelectDecoySource() {
+ qDebug() << "ProjectWindow::doSelectDecoySource begin";
+ ui->decoy_database_groupbox->setVisible(false);
+ ui->decoy_regexp_groupbox->setVisible(false);
+ if (ui->decoy_database_files_radiobutton->isChecked()) {
+ ui->decoy_database_groupbox->setVisible(true);
+ }
+ else {
+ ui->decoy_regexp_groupbox->setVisible(true);
+ }
+ qDebug() << "ProjectWindow::doSelectDecoySource end";
+}
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index a9439ef4f..a0701fd86 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -69,6 +69,7 @@ public slots:
void setDefaultProteinListWindow(ProteinListWindow* p_protein_list_window);
void doAutomaticFilterParametersChanged(AutomaticFilterParameters parameters);
void doFdrChanged();
+ void doSelectDecoySource();
void doMassPrecisionUnitChanged(QString combo_value);
void doOperationFailed(QString);
void doOperationFinished();
--
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