From 4a50ada7bc9e03f65424ede1320179bfbb758c91 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 7 Apr 2017 17:38:41 +0200
Subject: [PATCH] FDR computation OK
---
src/core/identificationgroup.cpp | 52 +++++++++
src/core/identificationgroup.h | 7 ++
src/gui/project_view/project_view.ui | 146 ++++++++++++++++++++++++-
src/gui/project_view/projectwindow.cpp | 29 ++++-
src/gui/project_view/projectwindow.h | 2 +
src/utils/proteinstore.cpp | 10 ++
src/utils/proteinstore.h | 5 +
src/utils/types.h | 11 ++
8 files changed, 254 insertions(+), 8 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index a56976d9a..a2c3f253a 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -41,6 +41,58 @@ IdentificationGroup::~IdentificationGroup()
}
}
+
+unsigned int IdentificationGroup::countDecoyProtein(ValidationState state) const {
+ unsigned int i=0;
+ for (auto & p_protein_match : _protein_match_list) {
+ if (!p_protein_match->getProteinXtpSp().get()->isDecoy()) continue;
+ if (state == ValidationState::grouped) {
+ if (p_protein_match->isGrouped()) {
+ i++;
+ }
+ }
+ else if(state == ValidationState::valid) {
+ if (p_protein_match->isValid()) {
+ i++;
+ }
+
+ }
+ else if (state == ValidationState::validAndChecked) {
+ if (p_protein_match->isValidAndChecked()) {
+ i++;
+ }
+
+ }
+ }
+ return i;
+}
+
+unsigned int IdentificationGroup::countProtein(ValidationState state) const {
+ unsigned int i=0;
+ if (state == ValidationState::grouped) {
+ for (auto & p_protein_match : _protein_match_list) {
+ if (p_protein_match->isGrouped()) {
+ i++;
+ }
+ }
+ }
+ else if(state == ValidationState::valid) {
+ for (auto & p_protein_match : _protein_match_list) {
+ if (p_protein_match->isValid()) {
+ i++;
+ }
+ }
+ }
+ else if (state == ValidationState::validAndChecked) {
+ for (auto & p_protein_match : _protein_match_list) {
+ if (p_protein_match->isValidAndChecked()) {
+ i++;
+ }
+ }
+ }
+ return i;
+}
+
void IdentificationGroup::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
for (auto & p_protein_match : _protein_match_list) {
p_protein_match->updateAutomaticFilters(automatic_filter_parameters);
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 27986627f..767f8cc25 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -68,6 +68,13 @@ public:
/** @brief count subgroups
* */
std::size_t countSubGroup()const;
+
+ /** @brief count proteins
+ * */
+ unsigned int countProtein(ValidationState state) const;
+ /** @brief count decoy proteins
+ * */
+ unsigned int countDecoyProtein(ValidationState state) const;
/** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
diff --git a/src/gui/project_view/project_view.ui b/src/gui/project_view/project_view.ui
index c2a73be55..eaad0707a 100644
--- a/src/gui/project_view/project_view.ui
+++ b/src/gui/project_view/project_view.ui
@@ -6,8 +6,8 @@
<rect>
<x>0</x>
<y>0</y>
- <width>445</width>
- <height>392</height>
+ <width>465</width>
+ <height>493</height>
</rect>
</property>
<property name="windowTitle">
@@ -53,7 +53,121 @@
</attribute>
<layout class="QGridLayout" name="gridLayout2">
<item row="0" column="0">
- <layout class="QFormLayout" name="formLayout_2"/>
+ <layout class="QVBoxLayout" name="verticalLayout_2">
+ <item>
+ <widget class="QGroupBox" name="groupBox_3">
+ <property name="title">
+ <string>FDR</string>
+ </property>
+ <layout class="QFormLayout" name="formLayout">
+ <item row="0" column="0">
+ <widget class="QLabel" name="label">
+ <property name="text">
+ <string>FDR on peptides</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLabel" name="peptide_fdr_label">
+ <property name="text">
+ <string>0 %</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_3">
+ <property name="text">
+ <string>FDR on proteins</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QLabel" name="protein_fdr_label">
+ <property name="text">
+ <string>0 %</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item>
+ <widget class="QGroupBox" name="groupBox">
+ <property name="title">
+ <string>Decoy database files</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout_3">
+ <item>
+ <widget class="QListWidget" name="decoy_database_list_widget"/>
+ </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>
+ </layout>
+ </item>
+ <item row="1" column="0">
+ <widget class="QGroupBox" name="groupBox_2">
+ <property name="title">
+ <string>Decoy protein regular expression</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout_4">
+ <item>
+ <widget class="QLineEdit" name="decoy_protein_regexp_line_edit">
+ <property name="placeholderText">
+ <string>.*\\|reversed$</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item row="3" column="0">
+ <layout class="QHBoxLayout" name="horizontalLayout_2">
+ <item>
+ <spacer name="horizontalSpacer_2">
+ <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_2">
+ <property name="text">
+ <string>OK</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
</item>
</layout>
</widget>
@@ -76,13 +190,33 @@
<rect>
<x>0</x>
<y>0</y>
- <width>445</width>
- <height>23</height>
+ <width>465</width>
+ <height>25</height>
</rect>
</property>
</widget>
<widget class="QStatusBar" name="statusbar"/>
</widget>
<resources/>
- <connections/>
+ <connections>
+ <connection>
+ <sender>pushButton_2</sender>
+ <signal>clicked()</signal>
+ <receiver>ProjectView</receiver>
+ <slot>doFdrChanged()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>403</x>
+ <y>329</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>484</x>
+ <y>334</y>
+ </hint>
+ </hints>
+ </connection>
+ </connections>
+ <slots>
+ <slot>doFdrChanged()</slot>
+ </slots>
</ui>
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 551022b34..125b57b45 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -45,7 +45,7 @@ ProjectWindow::ProjectWindow(MainWindow *parent):
_p_automatic_filter_widget = new AutomaticFilterWidget(this);
ui->filter_parameter_layout->addWidget(_p_automatic_filter_widget);
-
+
#if QT_VERSION >= 0x050000
// Qt5 code
@@ -58,7 +58,7 @@ ProjectWindow::ProjectWindow(MainWindow *parent):
// Qt4 code
//connect (_protein_list_window, SIGNAL(proteinMatchClicked(ProteinMatch *)), this //,SLOT(doProteinMatchClicked(ProteinMatch *)));
connect (_p_automatic_filter_widget, SIGNAL(automaticFilterParametersChanged(AutomaticFilterParameters)), this,SLOT(doAutomaticFilterParametersChanged(AutomaticFilterParameters)));
-
+
#endif
/*
*/
@@ -138,7 +138,29 @@ void ProjectWindow::refreshGroup(IdentificationGroup * p_ident_group) {
qDebug() << "ProjectWindow::refreshGroup end";
}
+void ProjectWindow::computeFdr() {
+ pappso::pappso_double total_prot=0;
+ pappso::pappso_double false_prot=0;
+ for (IdentificationGroup * identification_group : _project_sp.get()->getIdentificationGroupList()) {
+ total_prot += identification_group->countProtein(ValidationState::grouped);
+ false_prot += identification_group->countDecoyProtein(ValidationState::grouped);
+ }
+ ui->protein_fdr_label->setText(QString("%1 %").arg(false_prot/total_prot));
+}
+
+void ProjectWindow::doFdrChanged() {
+ qDebug() << "ProjectWindow::doFdrChanged begin ";
+ _project_sp.get()->getProteinStore().setRegexpDecoyPattern(ui->decoy_protein_regexp_line_edit->text());
+ _project_sp.get()->updateAutomaticFilters(_project_sp.get()->getAutomaticFilterParameters());
+ //re group
+ for (IdentificationGroup * identification_group : _project_sp.get()->getIdentificationGroupList()) {
+ doIdentificationGroupEdited(identification_group);
+ }
+
+ computeFdr();
+ qDebug() << "ProjectWindow::doFdrChanged end ";
+}
void ProjectWindow::doAutomaticFilterParametersChanged(AutomaticFilterParameters parameters) {
qDebug() << "ProjectWindow::doAutomaticFilterParametersChanged begin ";
_project_sp.get()->updateAutomaticFilters(parameters);
@@ -312,5 +334,8 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
_p_automatic_filter_widget->setAutomaticFilterParameters(params);
//_protein_list_window->setIdentificationGroup(_project_sp.get()->getCurrentIdentificationGroupP());
//_protein_list_window->show();
+
+ ui->decoy_protein_regexp_line_edit->setText(_project_sp.get()->getProteinStore().getRegexpDecoy().pattern());
+ computeFdr();
this->setEnabled(true);
}
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index 6a47e2cb6..c9b140fdb 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -55,6 +55,7 @@ public slots:
void doViewProteinList(IdentificationGroup* p_identification_group =nullptr);
void setDefaultProteinListWindow(ProteinListWindow* p_protein_list_window);
void doAutomaticFilterParametersChanged(AutomaticFilterParameters parameters);
+ void doFdrChanged();
// void setColor(const QColor &color);
// void setShape(Shape shape);
signals:
@@ -67,6 +68,7 @@ protected :
void doViewPeptideDetail(PeptideMatch * peptide_match);
void doViewProteinDetail(ProteinMatch * protein_match);
void doIdentificationGroupEdited(IdentificationGroup * p_identification_group);
+ void computeFdr();
private :
void connectNewProteinListWindow();
diff --git a/src/utils/proteinstore.cpp b/src/utils/proteinstore.cpp
index 7eab25a11..d2d95dc24 100644
--- a/src/utils/proteinstore.cpp
+++ b/src/utils/proteinstore.cpp
@@ -42,6 +42,16 @@ ProteinStore::~ProteinStore()
{
}
+QRegExp ProteinStore::getRegexpDecoy() const {
+ return (_regexp_decoy);
+}
+void ProteinStore::setRegexpDecoyPattern(const QString & pattern) {
+ _regexp_decoy.setPattern(pattern);
+
+ for (std::pair<const QString, ProteinXtpSp> & acc_protein :_map_accession_protein_list) {
+ setProteinInformations(acc_protein.second);
+ }
+}
ProteinXtpSp & ProteinStore::getInstance(ProteinXtpSp & peptide_in) {
diff --git a/src/utils/proteinstore.h b/src/utils/proteinstore.h
index 14d7f1945..93c755cea 100644
--- a/src/utils/proteinstore.h
+++ b/src/utils/proteinstore.h
@@ -33,6 +33,7 @@
#define PROTEINSTORE_H
#include "../core/proteinxtp.h"
+#include "types.h"
#include <QString>
#include <QRegExp>
#include <map>
@@ -44,6 +45,10 @@ public:
~ProteinStore();
ProteinXtpSp & getInstance(ProteinXtpSp & protein_in);
+
+ void setRegexpDecoyPattern(const QString & pattern);
+
+ QRegExp getRegexpDecoy() const;
private :
void setProteinInformations(ProteinXtpSp & protein_in);
diff --git a/src/utils/types.h b/src/utils/types.h
index 7a5be71be..e3cbf9b1c 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -46,6 +46,17 @@ enum class MzFormat {
mzXML, ///< mzXML
};
+/** \def ValidationState
+ *
+ */
+
+enum class ValidationState {
+ valid, ///< valid : automatic filter validation passed
+ validAndChecked, ///< validAndChecked : automatic filter validation passed + manual checking
+ grouped, ///< grouped : automatic filter validation passed + manual checking + grouped
+};
+
+
/** \def ProteinListColumn list of available fields to display in protein list
*
*/
--
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