From 57061e97f603663fa92056d293f2454111e57a4a Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Mon, 15 Oct 2018 08:05:12 +0200
Subject: [PATCH] new decoy selection widget
---
src/CMakeLists.txt | 2 +
src/gui/widgets/decoy_widget/decoy_widget.ui | 228 +++++++++++++++++
src/gui/widgets/decoy_widget/decoywidget.cpp | 243 +++++++++++++++++++
src/gui/widgets/decoy_widget/decoywidget.h | 78 ++++++
4 files changed, 551 insertions(+)
create mode 100644 src/gui/widgets/decoy_widget/decoy_widget.ui
create mode 100644 src/gui/widgets/decoy_widget/decoywidget.cpp
create mode 100644 src/gui/widgets/decoy_widget/decoywidget.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 97ef748f..26fec38f 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -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
diff --git a/src/gui/widgets/decoy_widget/decoy_widget.ui b/src/gui/widgets/decoy_widget/decoy_widget.ui
new file mode 100644
index 00000000..2530fec8
--- /dev/null
+++ b/src/gui/widgets/decoy_widget/decoy_widget.ui
@@ -0,0 +1,228 @@
+<?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 &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>
diff --git a/src/gui/widgets/decoy_widget/decoywidget.cpp b/src/gui/widgets/decoy_widget/decoywidget.cpp
new file mode 100644
index 00000000..9c8101f8
--- /dev/null
+++ b/src/gui/widgets/decoy_widget/decoywidget.cpp
@@ -0,0 +1,243 @@
+/**
+ * \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());
+}
diff --git a/src/gui/widgets/decoy_widget/decoywidget.h b/src/gui/widgets/decoy_widget/decoywidget.h
new file mode 100644
index 00000000..9cd64c78
--- /dev/null
+++ b/src/gui/widgets/decoy_widget/decoywidget.h
@@ -0,0 +1,78 @@
+/**
+ * \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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