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Commit 14a62e11 authored by Langella Olivier's avatar Langella Olivier
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new ui to select contaminants

parent 869c9466
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src/CMakeLists.txt
+ 2
− 2
View file @ 14a62e11
......@@ -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")
......
src/gui/project_view/project_view.ui
+ 105
− 48
View file @ 14a62e11
......@@ -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&amp;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>&amp;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>
src/gui/project_view/projectwindow.cpp
+ 38
− 9
View file @ 14a62e11
......@@ -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";
}
src/gui/project_view/projectwindow.h
+ 1
− 0
View file @ 14a62e11
......@@ -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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