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Commit 57061e97 authored by Langella Olivier's avatar Langella Olivier
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new decoy selection widget

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src/CMakeLists.txt
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View file @ 57061e97
......@@ -194,6 +194,7 @@ SET(XTPCPP_SRCS
./gui/waiting_message_dialog/waitingmessagedialog.cpp
./gui/widgets/automatic_filter_widget/automaticfilterwidget.cpp
./gui/widgets/contaminant_widget/contaminantwidget.cpp
./gui/widgets/decoy_widget/decoywidget.cpp
./gui/widgets/massitemdelegate.cpp
./gui/xic_view/xic_box/xicbox.cpp
./gui/xic_view/xic_widgets/zivydialog.cpp
......@@ -225,6 +226,7 @@ SET (GUI_UIS
./gui/waiting_message_dialog/waiting_message_dialog.ui
./gui/widgets/automatic_filter_widget/automatic_filter_widget.ui
./gui/widgets/contaminant_widget/contaminant_widget.ui
./gui/widgets/decoy_widget/decoy_widget.ui
./gui/xic_view/xic_box/xic_box.ui
./gui/xic_view/xic_widgets/zivy_widget.ui
./gui/xic_view/xic_window.ui
......
src/gui/widgets/decoy_widget/decoy_widget.ui 0 → 100644
+ 228
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View file @ 57061e97
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>DecoyWidget</class>
<widget class="QWidget" name="DecoyWidget">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>405</width>
<height>300</height>
</rect>
</property>
<property name="windowTitle">
<string>Form</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout">
<item>
<widget class="QGroupBox" name="decoy_groupbox">
<property name="title">
<string>Contaminants</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout_6">
<item>
<layout class="QHBoxLayout" name="horizontalLayout_4">
<item>
<widget class="QRadioButton" name="decoy_file_radiobutton">
<property name="toolTip">
<string>select decoys from fasta files</string>
</property>
<property name="text">
<string>decoy file</string>
</property>
<property name="checked">
<bool>true</bool>
</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 decoys using a regular expression</string>
</property>
<property name="text">
<string>decoy &amp;regular expression</string>
</property>
<attribute name="buttonGroup">
<string notr="true">decoy_source_buttongroup</string>
</attribute>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QListView" name="decoy_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>
<widget class="QLineEdit" name="decoy_protein_regexp_line_edit">
<property name="placeholderText">
<string>reversed$</string>
</property>
</widget>
</item>
</layout>
</item>
</layout>
</widget>
</item>
</layout>
</widget>
<resources/>
<connections>
<connection>
<sender>decoy_file_radiobutton</sender>
<signal>clicked()</signal>
<receiver>DecoyWidget</receiver>
<slot>doSelectDecoySource()</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>
<connection>
<sender>contaminant_database_listview</sender>
<signal>clicked(QModelIndex)</signal>
<receiver>ContaminantWidget</receiver>
<slot>doChanged()</slot>
<hints>
<hint type="sourcelabel">
<x>317</x>
<y>102</y>
</hint>
<hint type="destinationlabel">
<x>714</x>
<y>107</y>
</hint>
</hints>
</connection>
<connection>
<sender>decoy_protein_regexp_line_edit</sender>
<signal>textChanged(QString)</signal>
<receiver>DecoyWidget</receiver>
<slot>doChanged()</slot>
<hints>
<hint type="sourcelabel">
<x>167</x>
<y>267</y>
</hint>
<hint type="destinationlabel">
<x>657</x>
<y>303</y>
</hint>
</hints>
</connection>
</connections>
<slots>
<slot>doSelectDecoySource()</slot>
<slot>doSelectFastaFile()</slot>
<slot>doClearList()</slot>
<slot>doChanged()</slot>
</slots>
<buttongroups>
<buttongroup name="decoy_source_buttongroup"/>
</buttongroups>
</ui>
src/gui/widgets/decoy_widget/decoywidget.cpp 0 → 100644
+ 243
− 0
View file @ 57061e97
/**
* \file gui/widgets/decoy_widget/decoywidget.cpp
* \date 20/2/2018
* \author Olivier Langella
* \brief graphic widget to choose decoy files or regular expression
*/
/*******************************************************************************
* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
*
* This file is part of XTPcpp.
*
* XTPcpp is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* XTPcpp is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#include "decoywidget.h"
#include "ui_decoy_widget.h"
#include <QDebug>
#include <pappsomspp/pappsoexception.h>
#include <QSettings>
#include <QFileDialog>
DecoyWidget::DecoyWidget(QWidget *parent)
: QWidget(parent), ui(new Ui::DecoyWidget)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
ui->setupUi(this);
_emit_changed = false;
_p_fasta_str_li = new QStandardItemModel();
ui->decoy_database_listview->setModel(_p_fasta_str_li);
QItemSelectionModel *selection_model =
ui->decoy_database_listview->selectionModel();
ui->decoy_database_listview->setSelectionMode(
QAbstractItemView::MultiSelection);
doSelectDecoySource();
_emit_changed = true;
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
DecoyWidget::~DecoyWidget()
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
delete ui;
delete _p_fasta_str_li;
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
DecoyWidget::setRegexpDecoyPattern(const QString &pattern)
{
_emit_changed = false;
ui->decoy_protein_regexp_line_edit->setText(pattern);
_emit_changed = true;
}
void
DecoyWidget::setFastaFileList(std::vector<FastaFileSp> fasta_file_list)
{
_p_fasta_str_li->removeRows(0, _p_fasta_str_li->rowCount());
for(FastaFileSp fasta_file : fasta_file_list)
{
QStandardItem *item;
item =
new QStandardItem(QString("%1").arg(fasta_file.get()->getFilename()));
item->setEditable(false);
item->setData(QVariant::fromValue(fasta_file), Qt::UserRole);
_p_fasta_str_li->appendRow(item);
// item->setData(QVariant(QString("%1").arg(fasta_file.get()->getAbsoluteFilePath())),Qt::UserRole);
}
}
void
DecoyWidget::getProjectDecoys(const Project *p_project)
{
_emit_changed = false;
ui->decoy_regexp_radiobutton->setChecked(true);
ui->decoy_protein_regexp_line_edit->setVisible(true);
ui->decoy_database_listview->setVisible(false);
if(p_project->getProteinStore().getContaminantFastaFileList().size() > 0)
{
ui->decoy_file_radiobutton->setChecked(true);
ui->decoy_protein_regexp_line_edit->setVisible(false);
ui->decoy_database_listview->setVisible(true);
}
ui->decoy_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;
_emit_changed = true;
}
void
DecoyWidget::setProjectDecoys(Project *p_project)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_emit_changed = false;
if(ui->decoy_file_radiobutton->isChecked())
{
QModelIndexList index_list =
ui->decoy_database_listview->selectionModel()->selectedIndexes();
p_project->getProteinStore().clearContaminants();
if(index_list.size() > 0)
{
for(QModelIndex index : index_list)
{
if(index.data(Qt::UserRole).canConvert<FastaFileSp>())
{
FastaFileSp p_fasta_file =
index.data(Qt::UserRole).value<FastaFileSp>();
p_fasta_file.get()->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->decoy_protein_regexp_line_edit->text());
ui->control_list_widget->setVisible(false);
}
_emit_changed = true;
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
DecoyWidget::doChanged()
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
if(_emit_changed)
emit changed();
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
DecoyWidget::doSelectDecoySource()
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
ui->decoy_database_listview->setVisible(false);
ui->decoy_protein_regexp_line_edit->setVisible(false);
if(ui->decoy_file_radiobutton->isChecked())
{
ui->decoy_database_listview->setVisible(true);
}
else
{
ui->decoy_protein_regexp_line_edit->setVisible(true);
}
if(_emit_changed)
emit changed();
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
DecoyWidget::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));
}
for(FastaFileSp fasta_file : fasta_file_list)
{
QStandardItem *item;
item = new QStandardItem(
QString("%1").arg(fasta_file.get()->getFilename()));
item->setEditable(false);
item->setData(QVariant::fromValue(fasta_file), Qt::UserRole);
_p_fasta_str_li->appendRow(item);
// item->setData(QVariant(QString("%1").arg(fasta_file.get()->getAbsoluteFilePath())),Qt::UserRole);
}
}
catch(pappso::PappsoException &error)
{
// QMessageBox::warning(this,
// tr("Error choosing identification result files :
// %1").arg(error.qwhat()), error);
}
}
void
DecoyWidget::doClearList()
{
_p_fasta_str_li->removeRows(0, _p_fasta_str_li->rowCount());
}
src/gui/widgets/decoy_widget/decoywidget.h 0 → 100644
+ 78
− 0
View file @ 57061e97
/**
* \file gui/widgets/decoy_widget/decoywidget.h
* \date 20/2/2018
* \author Olivier Langella
* \brief graphic widget to choose decoy files or regular expression
*/
/*******************************************************************************
* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
*
* This file is part of XTPcpp.
*
* XTPcpp is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* XTPcpp is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#pragma once
#include <QWidget>
#include <QStandardItemModel>
#include "../../../files/fastafile.h"
#include "../../../core/project.h"
namespace Ui
{
class DecoyWidget;
}
class DecoyWidget : public QWidget
{
Q_OBJECT
public:
explicit DecoyWidget(QWidget *parent);
~DecoyWidget();
void setRegexpDecoyPattern(const QString &pattern);
void setFastaFileList(std::vector<FastaFileSp> fasta_file_list);
void setProjectDecoys(Project *p_project);
void getProjectDecoys(const Project *p_project);
public slots:
signals:
void changed();
private slots:
void doSelectDecoySource();
void doSelectFastaFile();
void doClearList();
void doChanged();
private:
Ui::DecoyWidget *ui;
bool _no_project = true;
QStandardItemModel *_p_fasta_str_li;
bool _emit_changed = true;
};
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