From 14a62e114a5edfc61f6c602884639c86945dd956 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 8 Feb 2018 22:28:34 +0100
Subject: [PATCH] new ui to select contaminants
---
src/CMakeLists.txt | 4 +-
src/gui/project_view/project_view.ui | 153 +++++++++++++++++--------
src/gui/project_view/projectwindow.cpp | 47 ++++++--
src/gui/project_view/projectwindow.h | 1 +
4 files changed, 146 insertions(+), 59 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 159b03b3f..71bd578d3 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -28,8 +28,8 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
#sudo apt-get install libpappsomspp-dev
#FIND_PACKAGE( Pappsomspp REQUIRED )
-# SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
- SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
+ SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
+# SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
SET (PAPPSOMSPP_QT5_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt5.so")
SET (PAPPSOMSPP_WIDGET_QT5_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/pappsomspp/widget/libpappsomspp-widget-qt5.so")
diff --git a/src/gui/project_view/project_view.ui b/src/gui/project_view/project_view.ui
index 358663a03..674a4dd86 100644
--- a/src/gui/project_view/project_view.ui
+++ b/src/gui/project_view/project_view.ui
@@ -6,7 +6,7 @@
<rect>
<x>0</x>
<y>0</y>
- <width>465</width>
+ <width>471</width>
<height>533</height>
</rect>
</property>
@@ -24,7 +24,7 @@
<string/>
</property>
<property name="currentIndex">
- <number>2</number>
+ <number>0</number>
</property>
<widget class="QWidget" name="identifications">
<attribute name="title">
@@ -59,21 +59,68 @@
<string>Contaminants</string>
</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 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>
- <widget class="QLineEdit" name="contaminant_protein_regexp_line_edit">
- <property name="placeholderText">
- <string>^conta\\|</string>
- </property>
- </widget>
+ <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>
</item>
+ <item row="1" column="0">
+ <spacer name="verticalSpacer_2">
+ <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>
<widget class="QWidget" name="fdr">
@@ -140,7 +187,7 @@
<string>select decoy sequences from fasta files</string>
</property>
<property name="text">
- <string>database files</string>
+ <string>data&base files</string>
</property>
<attribute name="buttonGroup">
<string notr="true">decoy_source_buttongroup</string>
@@ -153,7 +200,7 @@
<string>select decoy sequences based on a regular expression</string>
</property>
<property name="text">
- <string>regular expression</string>
+ <string>&regular expression</string>
</property>
<attribute name="buttonGroup">
<string notr="true">decoy_source_buttongroup</string>
@@ -171,30 +218,6 @@
<item>
<widget class="QListView" name="decoy_database_listview"/>
</item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <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>add</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
</layout>
</widget>
</item>
@@ -211,19 +234,6 @@
</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>
@@ -253,6 +263,19 @@
</item>
</layout>
</item>
+ <item row="1" column="0">
+ <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>
<widget class="QWidget" name="mass_precision">
@@ -366,7 +389,7 @@
<rect>
<x>0</x>
<y>0</y>
- <width>465</width>
+ <width>471</width>
<height>25</height>
</rect>
</property>
@@ -391,7 +414,7 @@
<hints>
<hint type="sourcelabel">
<x>442</x>
- <y>430</y>
+ <y>485</y>
</hint>
<hint type="destinationlabel">
<x>484</x>
@@ -463,14 +486,48 @@
</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>
<slot>doMassPrecisionUnitChanged(QString)</slot>
<slot>doIdentificationsComboboxChanged(int)</slot>
<slot>doSelectDecoySource()</slot>
+ <slot>doSelectContaminantSource()</slot>
</slots>
<buttongroups>
<buttongroup name="decoy_source_buttongroup"/>
+ <buttongroup name="contaminant_source_buttongroup"/>
</buttongroups>
</ui>
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 06ddc310a..870001f64 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -392,16 +392,18 @@ void ProjectWindow::doAutomaticFilterParametersChanged(AutomaticFilterParameters
showWaitingMessage(tr("Updating filters"));
doDisplayLoadingMessage(tr("tagging contaminant proteins"));
- QModelIndexList index_list = ui->contaminant_database_listview->selectionModel()->selectedIndexes();
- if (index_list.size() > 0) {
+ if (ui->contaminant_file_radiobutton->isChecked()) {
+ QModelIndexList index_list = ui->contaminant_database_listview->selectionModel()->selectedIndexes();
_project_sp.get()->getProteinStore().clearContaminants();
- 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 *>()"));
+ 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 *>()"));
+ }
}
}
}
@@ -591,6 +593,20 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
_project_sp = project_sp;
ui->decoy_regexp_radiobutton->setChecked(true);
ui->decoy_database_groupbox->setVisible(false);
+ if (_project_sp.get()->getProteinStore().getDecoyFastaFileList().size() > 0) {
+ ui->decoy_database_files_radiobutton->setChecked(true);
+ ui->decoy_regexp_groupbox->setVisible(false);
+ 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);
+ }
+
qDebug() << "ProjectWindow::setProjectSp begin " << _project_sp.get()->getFastaFileStore().getFastaFileList().size() ;
_fastafile_list = _project_sp.get()->getFastaFileStore().getFastaFileList();
@@ -800,3 +816,16 @@ 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";
+}
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index a0701fd86..ff2a4111e 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -70,6 +70,7 @@ public slots:
void doAutomaticFilterParametersChanged(AutomaticFilterParameters parameters);
void doFdrChanged();
void doSelectDecoySource();
+ void doSelectContaminantSource();
void doMassPrecisionUnitChanged(QString combo_value);
void doOperationFailed(QString);
void doOperationFinished();
--
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