From 37ea0a23a6c04141215549f7ce9e85315bb1961f Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Sun, 17 Dec 2017 08:10:09 +0100
Subject: [PATCH] compute FDR also on grouped proteins
---
src/gui/project_view/project_view.ui | 78 ++++++++++++++++++++++----
src/gui/project_view/projectwindow.cpp | 21 ++++++-
2 files changed, 85 insertions(+), 14 deletions(-)
diff --git a/src/gui/project_view/project_view.ui b/src/gui/project_view/project_view.ui
index e559751f5..72e0934a4 100644
--- a/src/gui/project_view/project_view.ui
+++ b/src/gui/project_view/project_view.ui
@@ -24,7 +24,7 @@
<string/>
</property>
<property name="currentIndex">
- <number>1</number>
+ <number>2</number>
</property>
<widget class="QWidget" name="identifications">
<attribute name="title">
@@ -82,23 +82,16 @@
<item>
<widget class="QGroupBox" name="groupBox_3">
<property name="toolTip">
- <string/>
+ <string><html><head/><body><p>FDR is computed using proteins tagged as &quot;decoy&quot; on all valid peptides in valid proteins (check filter parameters)</p></body></html></string>
</property>
<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>
+ <layout class="QGridLayout" name="gridLayout_4">
<item row="0" column="1">
<widget class="QLabel" name="peptide_fdr_label">
<property name="toolTip">
- <string><html><head/><body><p>FDR is computed using peptides tagged as &quot;decoy&quot; on all valid peptides in valid proteins (check filter parameters)</p></body></html></string>
+ <string/>
</property>
<property name="text">
<string>0 %</string>
@@ -112,11 +105,72 @@
</property>
</widget>
</item>
+ <item row="0" column="2">
+ <spacer name="horizontalSpacer_3">
+ <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 row="0" column="3">
+ <widget class="QLabel" name="label_6">
+ <property name="text">
+ <string>grouped peptides</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label">
+ <property name="text">
+ <string>FDR on peptides</string>
+ </property>
+ </widget>
+ </item>
<item row="1" column="1">
<widget class="QLabel" name="protein_fdr_label">
<property name="toolTip">
- <string>FDR is computed using proteins tagged as "decoy" on all valid proteins (check filter parameters)</string>
+ <string/>
+ </property>
+ <property name="text">
+ <string>0 %</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="4">
+ <widget class="QLabel" name="grouped_peptide_fdr_label">
+ <property name="text">
+ <string>0 %</string>
</property>
+ </widget>
+ </item>
+ <item row="1" column="2">
+ <spacer name="horizontalSpacer_4">
+ <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 row="1" column="3">
+ <widget class="QLabel" name="label_7">
+ <property name="text">
+ <string>grouped proteins</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="4">
+ <widget class="QLabel" name="grouped_protein_fdr_label">
<property name="text">
<string>0 %</string>
</property>
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 2ed43bf75..4a1896ef9 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -221,8 +221,25 @@ void ProjectWindow::computeFdr() {
total_peptide += identification_group->countPeptideMassSample(state);
false_peptide += identification_group->countDecoyPeptideMassSample(state);
}
- ui->protein_fdr_label->setText(QString("%1 %").arg(QString::number((false_prot/total_prot)*100.0,'f',10)));
- ui->peptide_fdr_label->setText(QString("%1 %").arg(QString::number((false_peptide/total_peptide)*100.0,'f',10)));
+ ui->protein_fdr_label->setText(QString("%1 %").arg(QString::number((false_prot/total_prot)*100.0,'f',2)));
+ ui->peptide_fdr_label->setText(QString("%1 %").arg(QString::number((false_peptide/total_peptide)*100.0,'f',2)));
+
+
+ state = ValidationState::grouped;
+ total_prot=0;
+ false_prot=0;
+ total_peptide=0;
+ false_peptide=0;
+ for (IdentificationGroup * identification_group : _project_sp.get()->getIdentificationGroupList()) {
+ total_prot += identification_group->countProteinMatch(state);
+ false_prot += identification_group->countDecoyProteinMatch(state);
+ //total_peptide += identification_group->countPeptideMatch(state);
+ //false_peptide += identification_group->countDecoyPeptideMatch(state);
+ total_peptide += identification_group->countPeptideMassSample(state);
+ false_peptide += identification_group->countDecoyPeptideMassSample(state);
+ }
+ ui->grouped_protein_fdr_label->setText(QString("%1 %").arg(QString::number((false_prot/total_prot)*100.0,'f',2)));
+ ui->grouped_peptide_fdr_label->setText(QString("%1 %").arg(QString::number((false_peptide/total_peptide)*100.0,'f',2)));
}
catch (pappso::PappsoException exception_pappso) {
QMessageBox::warning(this,
--
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