From 53540ba192e787365351f8b2741ceafe4e66b813 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Mon, 10 Apr 2017 14:53:26 +0200
Subject: [PATCH] contaminant regexp
---
src/gui/project_view/project_view.ui | 98 +++++++++++++++-----------
src/gui/project_view/projectwindow.cpp | 2 +
src/input/xtandemsaxhandler.cpp | 72 +++++++++++++++++++
src/utils/proteinstore.cpp | 17 ++++-
src/utils/proteinstore.h | 4 ++
5 files changed, 150 insertions(+), 43 deletions(-)
diff --git a/src/gui/project_view/project_view.ui b/src/gui/project_view/project_view.ui
index 4e92c6dc..70b513cf 100644
--- a/src/gui/project_view/project_view.ui
+++ b/src/gui/project_view/project_view.ui
@@ -21,7 +21,7 @@
<bool>true</bool>
</property>
<property name="currentIndex">
- <number>3</number>
+ <number>1</number>
</property>
<widget class="QWidget" name="identifications">
<attribute name="title">
@@ -39,10 +39,26 @@
</attribute>
<layout class="QGridLayout" name="gridLayout_3">
<item row="0" column="0">
- <layout class="QFormLayout" name="filter_parameter_layout">
- <property name="fieldGrowthPolicy">
- <enum>QFormLayout::AllNonFixedFieldsGrow</enum>
- </property>
+ <layout class="QVBoxLayout" name="filter_parameter_tab_layout">
+ <item>
+ <layout class="QVBoxLayout" name="filter_parameter_layout"/>
+ </item>
+ <item>
+ <widget class="QGroupBox" name="groupBox_4">
+ <property name="title">
+ <string>Contaminants</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout_6">
+ <item>
+ <widget class="QLineEdit" name="contaminant_protein_regexp_line_edit">
+ <property name="placeholderText">
+ <string>^conta\\|</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
</layout>
</item>
</layout>
@@ -127,45 +143,45 @@
</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$</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item row="3" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_2">
<item>
- <spacer name="horizontalSpacer_2">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
+ <widget class="QGroupBox" name="groupBox_2">
+ <property name="title">
+ <string>Decoy protein regular expression</string>
</property>
- </spacer>
+ <layout class="QVBoxLayout" name="verticalLayout_4">
+ <item>
+ <widget class="QLineEdit" name="decoy_protein_regexp_line_edit">
+ <property name="placeholderText">
+ <string>.*\\|reversed$</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
</item>
<item>
- <widget class="QPushButton" name="pushButton_2">
- <property name="text">
- <string>OK</string>
- </property>
- </widget>
+ <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="fdr_button">
+ <property name="text">
+ <string>OK</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
</item>
</layout>
</item>
@@ -264,7 +280,7 @@
<resources/>
<connections>
<connection>
- <sender>pushButton_2</sender>
+ <sender>fdr_button</sender>
<signal>clicked()</signal>
<receiver>ProjectView</receiver>
<slot>doFdrChanged()</slot>
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index cffc67cd..ec66c9ca 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -201,6 +201,7 @@ void ProjectWindow::doFdrChanged() {
}
void ProjectWindow::doAutomaticFilterParametersChanged(AutomaticFilterParameters parameters) {
qDebug() << "ProjectWindow::doAutomaticFilterParametersChanged begin ";
+ _project_sp.get()->getProteinStore().setRegexpDecoyPattern(ui->contaminant_protein_regexp_line_edit->text());
_project_sp.get()->updateAutomaticFilters(parameters);
//re group
@@ -381,6 +382,7 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
//_protein_list_window->show();
ui->decoy_protein_regexp_line_edit->setText(_project_sp.get()->getProteinStore().getRegexpDecoy().pattern());
+ ui->contaminant_protein_regexp_line_edit->setText(_project_sp.get()->getProteinStore().getRegexpContaminant().pattern());
computeFdr(ValidationState::grouped);
computeMassPrecision(ValidationState::validAndChecked);
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index 001cb943..5647756b 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -197,6 +197,78 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
// delta="0.998" hyperscore="32.9" nextscore="12.2" y_score="10.7"
// y_ions="9" b_score="0.0" b_ions="0"
// pre="VLGR" post="VEFM" seq="TGSQGQCTQVR" missed_cleavages="10">
+ /*
+ * id
+ – the identifier for t
+his particular identified dom
+ain (s
+pectrum
+ #).(i
+d
+#).(dom
+ain#)
+start
+ – the first residue
+ of t
+he dom
+ain
+end
+ – the last residue
+ of t
+he dom
+ain
+expect
+ – the expe
+ctation va
+lue for t
+he peptide identification
+mh
+ – the calculated pe
+ptide mass + a prot
+on
+delta
+ – the spectrum
+ mh m
+inus
+ the calculated m
+h
+hyperscore
+ – T
+ande
+m’s score for t
+he identification
+peak_count
+ – the num
+ber of pe
+aks that matched be
+tween the theoretical
+and t
+he test mass spectrum
+pre
+ – the four re
+sidue
+s pre
+ceding t
+he dom
+ain
+post
+ – the four re
+sidue
+s fol
+lowing t
+he dom
+ain
+seq
+ – the seque
+nce of t
+he dom
+ain
+missed_cleavages
+ – the num
+ber of pot
+ential cleavage sites in this
+peptide seque
+nce*/
// valeur généric du scan
_current_peptide_sp = PeptideXtp(attributes.value("seq").simplified()).makePeptideXtpSp();
diff --git a/src/utils/proteinstore.cpp b/src/utils/proteinstore.cpp
index d2d95dc2..e8619a13 100644
--- a/src/utils/proteinstore.cpp
+++ b/src/utils/proteinstore.cpp
@@ -41,6 +41,16 @@ ProteinStore::ProteinStore()
ProteinStore::~ProteinStore()
{
+}
+QRegExp ProteinStore::getRegexpContaminant() const {
+ return (_regexp_contaminant);
+}
+void ProteinStore::setRegexpContaminantPattern(const QString & pattern) {
+ _regexp_contaminant.setPattern(pattern);
+
+ for (std::pair<const QString, ProteinXtpSp> & acc_protein :_map_accession_protein_list) {
+ setProteinInformations(acc_protein.second);
+ }
}
QRegExp ProteinStore::getRegexpDecoy() const {
return (_regexp_decoy);
@@ -66,12 +76,15 @@ ProteinXtpSp & ProteinStore::getInstance(ProteinXtpSp & peptide_in) {
void ProteinStore::setProteinInformations(ProteinXtpSp & peptide_in) {
//qDebug() << "ProteinStore::setProteinInformations begin" << peptide_in.get()->getSequence();
+ peptide_in.get()->setIsContaminant(false);
+ peptide_in.get()->setIsDecoy(false);
QString accession = peptide_in.get()->getAccession();
- if (_regexp_contaminant.indexIn(accession, 0)>-1) {
+
+ if ((!_regexp_contaminant.isEmpty()) && (_regexp_contaminant.indexIn(accession, 0)>-1)) {
//qDebug() << "ProteinStore::setProteinInformations is contaminant " << accession;
peptide_in.get()->setIsContaminant(true);
}
- if (_regexp_decoy.indexIn(accession, 0)>-1) {
+ if ((!_regexp_decoy.isEmpty()) && (_regexp_decoy.indexIn(accession, 0)>-1) ) {
peptide_in.get()->setIsDecoy(true);
}
//qDebug() << "ProteinStore::setProteinInformations end";
diff --git a/src/utils/proteinstore.h b/src/utils/proteinstore.h
index 93c755ce..2208156c 100644
--- a/src/utils/proteinstore.h
+++ b/src/utils/proteinstore.h
@@ -49,6 +49,10 @@ public:
void setRegexpDecoyPattern(const QString & pattern);
QRegExp getRegexpDecoy() const;
+
+ void setRegexpContaminantPattern(const QString & pattern);
+
+ QRegExp getRegexpContaminant() const;
private :
void setProteinInformations(ProteinXtpSp & protein_in);
--
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