From 8341bea56a2a5bc263bcd5f98de0c850eed84783 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Wed, 5 Apr 2017 22:26:52 +0200
Subject: [PATCH] WIP : xtandem sax parser
---
src/CMakeLists.txt | 4 +-
.../identificationxtandemfile.cpp | 32 ++-
src/core/identificationgroup.cpp | 28 +++
src/core/identificationgroup.h | 3 +
src/core/project.cpp | 5 +-
src/core/project.h | 3 +-
src/core/proteinmatch.cpp | 3 -
src/core/proteinmatch.h | 10 +-
src/core/proteinxtp.cpp | 8 +-
src/core/proteinxtp.h | 2 +
src/gui/mainwindow.cpp | 2 +-
src/gui/peptide_list_view/peptide_view.ui | 13 +-
.../peptide_list_view/peptidelistwindow.cpp | 3 +-
.../automatic_filter_widget.ui | 4 +-
src/gui/protein_view/protein_detail_view.ui | 12 +-
src/gui/protein_view/proteinwindow.cpp | 4 +-
src/input/xpipsaxhandler.cpp | 4 +-
src/input/xtandemsaxhandler.cpp | 195 ++++++------------
src/input/xtandemsaxhandler.h | 33 ++-
19 files changed, 182 insertions(+), 186 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 42d4fb8ff..9d83c2838 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -29,8 +29,8 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
#sudo apt-get install libpappsomspp-dev
#FIND_PACKAGE( Pappsomspp REQUIRED )
-# SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
- SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
+ SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
+# SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
diff --git a/src/core/identification_sources/identificationxtandemfile.cpp b/src/core/identification_sources/identificationxtandemfile.cpp
index e5fd50852..1f21279ea 100644
--- a/src/core/identification_sources/identificationxtandemfile.cpp
+++ b/src/core/identification_sources/identificationxtandemfile.cpp
@@ -50,16 +50,40 @@ pappso::SpectrumSp IdentificationXtandemFile::getSpectrumSp(unsigned int scan_nu
void IdentificationXtandemFile::parseTo(Project* p_project) {
- qDebug() << "Project::readXpipFile begin";
+ qDebug() << "Project::readXpipFile begin";
- XtandemSaxHandler * parser = new XtandemSaxHandler(p_project);
+ qDebug() << "Read X!Tandem XML result file '" << _xtandem_file.absoluteFilePath() << "'";
+
+ MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(QFileInfo(_xtandem_file).baseName());
+ setMsRunSp(msrun_sp);
+ std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
+ IdentificationGroup * identification_group_p = nullptr;
+ if (p_project->isCombineMode()) {
+ if (identification_list.size() == 0) {
+ identification_group_p = p_project->newIdentificationGroup();
+ }
+ else {
+ identification_group_p = identification_list[0];
+ }
+ }
+ else {
+ for (IdentificationGroup * identification_p_flist : identification_list) {
+ if (identification_p_flist->contains(msrun_sp.get())) {
+ identification_group_p = identification_p_flist;
+ break;
+ }
+ }
+ if (identification_group_p == nullptr) {
+ identification_group_p = p_project->newIdentificationGroup();
+ }
+ }
+
+ XtandemSaxHandler * parser = new XtandemSaxHandler(p_project, identification_group_p);
QXmlSimpleReader simplereader;
simplereader.setContentHandler(parser);
simplereader.setErrorHandler(parser);
- qDebug() << "Read X!Tandem XML result file '" << _xtandem_file.absoluteFilePath() << "'";
-
QFile qfile(_xtandem_file.absoluteFilePath());
QXmlInputSource xmlInputSource(&qfile);
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 75e8d1c63..f85a149bc 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -24,6 +24,7 @@
#include "identificationgroup.h"
#include "project.h"
#include "../utils/groupstore.h"
+#include <pappsomspp/pappsoexception.h>
IdentificationGroup::IdentificationGroup(Project * project)
@@ -49,9 +50,36 @@ void IdentificationGroup::updateAutomaticFilters(const AutomaticFilterParameters
}
}
+ProteinMatch * IdentificationGroup::getProteinMatch(const QString accession) {
+ if (accession.isEmpty()) {
+ throw pappso::PappsoException(QObject::tr("Error protein match not found : accession is empty"));
+ }
+ for (ProteinMatch * p_protein_match : _protein_match_list) {
+ if (p_protein_match->getProteinXtpSp().get()->getAccession() == accession) {
+ return p_protein_match;
+ }
+ }
+ return nullptr;
+}
void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
+ QString accession = protein_match->getProteinXtpSp().get()->getAccession();
+ if (accession.isEmpty()) {
+ throw pappso::PappsoException(QObject::tr("Error adding protein match : accession is empty"));
+ }
+ for (ProteinMatch * p_protein_match : _protein_match_list) {
+ if (p_protein_match->getProteinXtpSp().get()->getAccession() == accession) {
+ throw pappso::PappsoException(QObject::tr("Error adding protein match : accession %1 already registered").arg(accession));
+ }
+ }
_protein_match_list.push_back(protein_match);
}
+
+bool IdentificationGroup::contains (const MsRun * p_msrun) const {
+ for (const MsRunSp & msrun: _ms_run_list) {
+ if (msrun.get() == p_msrun) return true;
+ }
+ return false;
+}
void IdentificationGroup::addMsRunSp(MsRunSp ms_run_sp) {
_ms_run_list.push_back(ms_run_sp);
}
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 587bde926..e71793757 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -43,6 +43,7 @@ public:
IdentificationGroup(Project * project);
~IdentificationGroup();
+ ProteinMatch * getProteinMatch(const QString accession);
void addProteinMatch(ProteinMatch * protein_match);
std::vector<ProteinMatch *> & getProteinMatchList();
void addMsRunSp(MsRunSp ms_run_sp);
@@ -79,6 +80,8 @@ public:
/** @brief get tab name for qtabwidget
* */
const QString getTabName() const;
+
+ bool contains (const MsRun * p_msrun) const;
private :
GroupingExperiment * _p_grp_experiment= nullptr;
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 1ae87c29a..210b0e11c 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -46,7 +46,10 @@ void Project::readResultFile(QString filename) {
ident_source.get()->parseTo(this);
}
-void Project::setCombine(bool is_combine_mode) {
+ bool Project::isCombineMode() const {
+ return _is_combine_mode;
+ }
+void Project::setCombineMode(bool is_combine_mode) {
_is_combine_mode = is_combine_mode;
}
std::vector<IdentificationGroup *> Project::getIdentificationGroupList() {
diff --git a/src/core/project.h b/src/core/project.h
index 1f9e7190a..3d04785b8 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -62,7 +62,8 @@ public:
const GroupingType getGroupingType() const;
std::vector<IdentificationGroup *> getIdentificationGroupList();
- void setCombine(bool is_combine_mode);
+ void setCombineMode(bool is_combine_mode);
+ bool isCombineMode() const;
void readResultFile(QString filename);
private :
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 1b49536a9..0df923cc2 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -99,9 +99,6 @@ void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
const ProteinXtpSp & ProteinMatch::getProteinXtpSp() const {
return _protein_sp;
}
-void ProteinMatch::setEvalue(pappso::pappso_double evalue) {
- _evalue = evalue;
-}
void ProteinMatch::setProteinXtpSp(ProteinXtpSp protein_sp) {
_protein_sp = protein_sp;
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index dfce9d760..3044d8d70 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -44,7 +44,6 @@ public:
~ProteinMatch();
const ProteinXtpSp & getProteinXtpSp() const;
- void setEvalue(pappso::pappso_double evalue);
/** @brief compute protein Evalue within samples
* */
@@ -109,16 +108,15 @@ private :
unsigned int countValidAndCheckedPeptideMassCharge(const MsRun * sp_msrun_id) const;
private:
- static QColor _color_peptide_background;
- static QColor _color_highlighted_peptide_background;
-
-
+ static QColor _color_peptide_background;
+ static QColor _color_highlighted_peptide_background;
+
+
pappso::GrpProteinSp _sp_grp_protein;
GroupingGroupSp _sp_group;
std::vector<PeptideMatch *> _peptide_match_list;
ProteinXtpSp _protein_sp = nullptr;
- pappso::pappso_double _evalue=0;
/** @brief manually checked by user (true by default)
*/
bool _checked = true;
diff --git a/src/core/proteinxtp.cpp b/src/core/proteinxtp.cpp
index f08e97e20..6a3bcf802 100644
--- a/src/core/proteinxtp.cpp
+++ b/src/core/proteinxtp.cpp
@@ -50,7 +50,13 @@ ProteinXtpSp ProteinXtp::makeProteinXtpSp() const {
return std::make_shared<ProteinXtp>(*this);
}
-
+void ProteinXtp::setCompleteDescription(const QString & full_description) {
+ setAccession (full_description.simplified().section(" ", 0,0));
+ setDescription (full_description.simplified().section(" ", 1));
+
+
+
+}
void ProteinXtp::setIsContaminant(bool conta) {
_is_contaminant = conta;
}
diff --git a/src/core/proteinxtp.h b/src/core/proteinxtp.h
index 0dfa8ff7a..b98318142 100644
--- a/src/core/proteinxtp.h
+++ b/src/core/proteinxtp.h
@@ -44,6 +44,8 @@ public:
ProteinXtpSp makeProteinXtpSp() const;
+ void setCompleteDescription(const QString & full_description);
+
void setIsContaminant(bool conta);
void setIsDecoy(bool conta);
bool isContaminant() const;
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index bf5b9901e..609e69950 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -58,7 +58,7 @@ void XtpLoaderThread::doLoadingResults(bool is_individual, AutomaticFilterParame
qDebug() << "XtpLoaderThread::doLoadingResults begin ";
try {
ProjectSp project_sp = Project().makeProjectSp();
- project_sp.get()->setCombine(!is_individual);
+ project_sp.get()->setCombineMode(!is_individual);
for (QString filename : file_list) {
project_sp.get()->readResultFile(filename);
diff --git a/src/gui/peptide_list_view/peptide_view.ui b/src/gui/peptide_list_view/peptide_view.ui
index 726daae14..139cdcd40 100644
--- a/src/gui/peptide_list_view/peptide_view.ui
+++ b/src/gui/peptide_list_view/peptide_view.ui
@@ -16,7 +16,14 @@
<widget class="QWidget" name="centralwidget">
<layout class="QVBoxLayout" name="verticalLayout">
<item>
- <widget class="QLabel" name="proteinLabel">
+ <widget class="QLabel" name="accession_label">
+ <property name="text">
+ <string>TextLabel</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="description_label">
<property name="text">
<string>TextLabel</string>
</property>
@@ -25,7 +32,6 @@
</property>
</widget>
</item>
-
<item>
<layout class="QHBoxLayout" name="horizontalLayoutcb">
<item>
@@ -69,14 +75,13 @@
<x>0</x>
<y>0</y>
<width>826</width>
- <height>31</height>
+ <height>25</height>
</rect>
</property>
</widget>
<widget class="QStatusBar" name="statusbar"/>
</widget>
<resources/>
-
<connections>
<connection>
<sender>hideNotValidCheckBox</sender>
diff --git a/src/gui/peptide_list_view/peptidelistwindow.cpp b/src/gui/peptide_list_view/peptidelistwindow.cpp
index 9cda7c0fd..ceff83e95 100644
--- a/src/gui/peptide_list_view/peptidelistwindow.cpp
+++ b/src/gui/peptide_list_view/peptidelistwindow.cpp
@@ -108,7 +108,8 @@ void PeptideListWindow::setProteinMatch(IdentificationGroup * p_identification_g
_p_protein_match = p_protein_match;
_peptide_table_model_p->setProteinMatch( p_protein_match);
_p_proxy_model->setSourceModel(_peptide_table_model_p);
- ui->proteinLabel->setText(p_protein_match->getProteinXtpSp().get()->getDescription());
+ ui->description_label->setText(p_protein_match->getProteinXtpSp().get()->getDescription());
+ ui->accession_label->setText(p_protein_match->getProteinXtpSp().get()->getAccession());
}
}
diff --git a/src/gui/project_view/automatic_filter_widget/automatic_filter_widget.ui b/src/gui/project_view/automatic_filter_widget/automatic_filter_widget.ui
index 7c929c0d7..e297d67e2 100644
--- a/src/gui/project_view/automatic_filter_widget/automatic_filter_widget.ui
+++ b/src/gui/project_view/automatic_filter_widget/automatic_filter_widget.ui
@@ -50,13 +50,13 @@
<item row="0" column="1">
<widget class="QDoubleSpinBox" name="peptide_evalue_spinbox">
<property name="decimals">
- <number>3</number>
+ <number>6</number>
</property>
<property name="maximum">
<double>1.000000000000000</double>
</property>
<property name="singleStep">
- <double>0.010000000000000</double>
+ <double>0.001000000000000</double>
</property>
<property name="value">
<double>0.050000000000000</double>
diff --git a/src/gui/protein_view/protein_detail_view.ui b/src/gui/protein_view/protein_detail_view.ui
index 1695aee60..9529e1d91 100644
--- a/src/gui/protein_view/protein_detail_view.ui
+++ b/src/gui/protein_view/protein_detail_view.ui
@@ -20,7 +20,7 @@
<item>
<layout class="QHBoxLayout" name="horizontalLayout">
<item>
- <widget class="QLabel" name="descriptionLabel">
+ <widget class="QLabel" name="accession_label">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
<horstretch>0</horstretch>
@@ -72,6 +72,16 @@
</item>
</layout>
</item>
+ <item>
+ <widget class="QLabel" name="description_label">
+ <property name="text">
+ <string>TextLabel</string>
+ </property>
+ <property name="wordWrap">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
<item>
<widget class="QTextEdit" name="sequenceTextEdit">
<property name="lineWrapMode">
diff --git a/src/gui/protein_view/proteinwindow.cpp b/src/gui/protein_view/proteinwindow.cpp
index b683f1680..7f04c882c 100644
--- a/src/gui/protein_view/proteinwindow.cpp
+++ b/src/gui/protein_view/proteinwindow.cpp
@@ -73,8 +73,8 @@ void ProteinWindow::updateDisplay() {
try {
ui->validCheckBox->setCheckState(Qt::Unchecked);
if (_p_protein_match->isValid()) ui->validCheckBox->setCheckState(Qt::Checked);
- ui->descriptionLabel->setText(_p_protein_match->getProteinXtpSp().get()->getAccession());
- //ui->sequenceLabel->setText(_p_protein_match->getProteinXtpSp().get()->getSequence());
+ ui->accession_label->setText(_p_protein_match->getProteinXtpSp().get()->getAccession());
+ ui->description_label->setText(_p_protein_match->getProteinXtpSp().get()->getDescription());
ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence());
ui->coverage_label->setText(QString("%1 %").arg(_p_protein_match->getCoverage()*100));
pappso::Peptide peptide(_p_protein_match->getProteinXtpSp().get()->getSequence());
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index fc4057431..f494d5fd6 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -215,9 +215,7 @@ bool XpipSaxHandler::startElement_protein(QXmlAttributes attributes) {
<sequence>MASTKAPGPGEKHHSIDAQLRQLVPGKVSEDDKLIEYDALLVDRFLNILQDLHGPSLREFVQECYEVSADYEGKGDTTKLGELGAKLTGLAPADAILVASSILHMLNLANLAEEVQIAHRRRNSKLKKGGFADEGSATTESDIEETLKRLVSEVGKSPEEVFEALKNQTVDLVFTAHPTQSARRSLLQKNARIRNCLTQLNAKDITDDDKQELDEALQREIQAAFRTDEIRRAQPTPQDEMRYGMSYIHETVWKGVPKFLRRVDTALKNIGINERLPYNVSLIRFSSWMGGDRDGNPRVTPEVTRDVCLLARMMAANLYIDQIEELMFELSMWRCNDELRVRAEELHSSSGSKVTKYYIEFWKQIPPNEPYRVILGHVRDKLYNTRERARHLLASGVSEISAESSFTSIEEFLEPLELCYKSLCDCGDKAIADGSLLDLLRQVFTFGLSLVKLDIRQESERHTDVIDAITTHLGIGSYREWPEDKRQEWLLSELRGKRPLLPPDLPQTDEIADVIGAFHVLAELPPDSFGPYIISMATAPSDVLAVELLQRECGVRQPLPVVPLFERLADLQSAPASVERLFSVDWYMDRIKGKQQVMVGYSDSGKDAGRLSAAWQLYRAQEEMAQVAKRYGVKLTLFHGRGGTVGRGGGPTHLAILSQPPDTINGSIRVTVQGEVIEFCFGEEHLCFQTLQRFTAATLEHGMHPPVSPKPEWRKLMDEMAVVATEEYRSVVVKEARFVEYFRSATPETEYGRMNIGSRPAKRRPGGGITTLRAIPWIFSWTQTRFHLPVWLGVGAAFKFAIDKDVRNFQVLKEMYNEWPFFRVTLDLLEMVFAKGDPGIAGLYDELLVAEELKPFGKQLRDKYVETQQLLLQIAGHKDILEGDPFLKQGLVLRNPYITTLNVFQAYTLKRIRDPNFKVTPQPPLSKEFADENKPAGLVKLNPASEYPPGLEDTLILTMKGIAAGMQNTG</sequence>
</protein>
*/
- _p_protein_match->setEvalue(std::pow ((double) 10.0, attributes.value("evalue").toDouble()));
- _current_protein.setDescription(attributes.value("description").simplified());
- _current_protein.setAccession(_current_protein.getDescription().split(" ").at(0));
+ _current_protein.setCompleteDescription(attributes.value("description"));
qDebug() << "startElement_protein end" ;
return true;
}
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index e5dd55ac4..a720f5839 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -35,9 +35,9 @@
#include "../utils/peptidestore.h"
#include "../utils/proteinstore.h"
-XtandemSaxHandler::XtandemSaxHandler(Project * p_project):_p_project(p_project)
+XtandemSaxHandler::XtandemSaxHandler(Project * p_project, IdentificationGroup * p_identification_group):_p_project(p_project)
{
-
+ _p_identification_group = p_identification_group;
}
XtandemSaxHandler::~XtandemSaxHandler()
@@ -54,36 +54,31 @@ bool XtandemSaxHandler::startElement(const QString & namespaceURI, const QString
try {
//startElement_group
- if (qName == "match") {
- is_ok = startElement_match(attributes);
+ if (qName == "group") {
+ is_ok = startElement_group(attributes);
} else if (qName == "protein") {
is_ok = startElement_protein(attributes);
- } else if (qName == "identification") {
- is_ok = startElement_identification(attributes);
+ } else if (qName == "note") {
+ is_ok = startElement_note(attributes);
}
- //<sample value="P6_08_10"/>
- else if (qName == "sample") {
- is_ok = startElement_sample(attributes);
+ else if (qName == "file") {
+ is_ok = startElement_file(attributes);
} else if (qName == "peptide") {
is_ok = startElement_peptide(attributes);
- } else if (qName == "modifs_mass") {
- is_ok = startElement_modifs_mass(attributes);
- } else if (qName == "modif") {
- is_ok = startElement_modif(attributes);
- } else if (qName == "filter_params") {
- is_ok = startElement_filter_params(attributes);
- } else if (qName == "information") {
- is_ok = startElement_information(attributes);
+ } else if (qName == "aa") {
+ is_ok = startElement_aa(attributes);
+ } else if (qName == "domain") {
+ is_ok = startElement_domain(attributes);
}
_current_text.clear();
}
catch (pappso::PappsoException exception_pappso) {
- _errorStr = QObject::tr("ERROR in XpipSaxHandler::startElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
+ _errorStr = QObject::tr("ERROR in XtandemSaxHandler::startElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
return false;
}
catch (std::exception exception_std) {
- _errorStr = QObject::tr("ERROR in XpipSaxHandler::startElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
+ _errorStr = QObject::tr("ERROR in XtandemSaxHandler::startElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
return false;
}
return is_ok;
@@ -95,21 +90,9 @@ bool XtandemSaxHandler::endElement(const QString & namespaceURI, const QString &
bool is_ok = true;
// endElement_peptide_list
try {
- if (qName == "protein")
+ if (qName == "note")
{
- is_ok = endElement_protein();
- }
- else if (qName == "identification") {
- is_ok = endElement_identification();
- }
- else if (qName == "peptide") {
- is_ok = endElement_peptide();
- }
- else if (qName == "sequence") {
- is_ok = endElement_sequence();
- }
- else if (qName == "match") {
- is_ok = endElement_match();
+ is_ok = endElement_note();
}
// end of detection_moulon
@@ -117,11 +100,11 @@ bool XtandemSaxHandler::endElement(const QString & namespaceURI, const QString &
// (_tag_stack[_tag_stack.size() - 2] == "detection_moulon"))
}
catch (pappso::PappsoException exception_pappso) {
- _errorStr = QObject::tr("ERROR in XpipSaxHandler::endElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
+ _errorStr = QObject::tr("ERROR in XtandemSaxHandler::endElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
return false;
}
catch (std::exception exception_std) {
- _errorStr = QObject::tr("ERROR in XpipSaxHandler::endElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
+ _errorStr = QObject::tr("ERROR in XtandemSaxHandler::endElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
return false;
}
@@ -143,91 +126,61 @@ bool XtandemSaxHandler::startElement_group(QXmlAttributes attrs) {
_scan = attrs.value("id").toUInt();
_mhplus_obser = attrs.value("mh").toDouble();
_charge = attrs.value("z").toUInt();
- _RT = attrs.value("rt");
+ //_retention_time = attrs.value("rt");
}
}
-bool XtandemSaxHandler::startElement_match(QXmlAttributes attributes) {
-
- qDebug() << "startElement_match ";
- /*
- * <match_list><match validate="true">
- */
- _p_protein_match = new ProteinMatch();
- _p_protein_match->setChecked(false);
- if (attributes.value("validate").simplified().toLower() == "true") {
- _p_protein_match->setChecked(true);
+bool XtandemSaxHandler::startElement_note(QXmlAttributes attributes) {
+//<note label="description">GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC //4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01;
+ ////parent_gene=GRMZM2G083841</note>
+ _is_protein_description = false;
+ if (attributes.value("label") == "description") {
+ if (_tag_stack[_tag_stack.size() - 2] == "protein") {
+ _is_protein_description = true;
+ }
}
- qDebug() << "startElement_match end" ;
- return true;
}
bool XtandemSaxHandler::startElement_protein(QXmlAttributes attributes) {
//<protein expect="-704.6" id="1976.1" uid="195701" label="GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC..." sumI="9.36" >
qDebug() << "startElement_protein ";
- _p_protein_match->setEvalue(std::pow ((double) 10.0, attributes.value("expect").toDouble()));
- _current_protein.setDescription(attributes.value("label").simplified());
- _current_protein.setAccession(_current_protein.getDescription().split(" ").at(0));
- qDebug() << "startElement_protein end" ;
- return true;
-}
+ QString accession = attributes.value("label").simplified().split(" ", QString::SkipEmptyParts).at(0);
+ ProteinMatch * p_protein_match = _p_identification_group->getProteinMatch(accession);
-bool XtandemSaxHandler::startElement_file(QXmlAttributes attributes) {
- if (attrs.getValue("type").equals("peptide"))
- prot_.setDatabase(identification_.getDatabaseSet().getInstance(
- attrs.getValue("URL")));
-}
+ _current_protein.setAccession(accession);
+ if (p_protein_match == nullptr) {
+ _p_protein_match = new ProteinMatch();
+ _p_protein_match->setChecked(false);
-bool XtandemSaxHandler::startElement_identification(QXmlAttributes attributes) {
-
- qDebug() << "startElement_identification ";
- _map_massstr_aamod.clear();
- _current_identification_group_p = _p_project->newIdentificationGroup();
- qDebug() << "startElement_identification end" ;
+ }
+ ProteinXtpSp sp_xtp_protein = _current_protein.makeProteinXtpSp();
+ p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
+ qDebug() << "startElement_protein end" ;
return true;
}
-bool XtandemSaxHandler::startElement_information(QXmlAttributes attributes) {
-
-//<information Data_Type="indiv" match_number="223"/>
- qDebug() << "startElement_information ";
- qDebug() << "startElement_information end" ;
- return true;
-}
-bool XtandemSaxHandler::startElement_modifs_mass(QXmlAttributes attributes) {
-
- /*
- <modifs_list_mass><modifs_mass modvalue="-18.01056"/>
- <modifs_mass modvalue="-17.02655"/>
- <modifs_mass modvalue="15.99491"/>
- <modifs_mass modvalue="42.01057"/>
- <modifs_mass modvalue="42.01056"/>
- <modifs_mass modvalue="57.02146"/>
- </modifs_list_mass>
- */
- qDebug() << "startElement_modifs_mass ";
- QString mass_str(attributes.value("modvalue").simplified());
- pappso::mz mass = mass_str.toDouble();
-
- pappso::AaModificationP mod = getAaModificationP(mass);
-
- _map_massstr_aamod[mass_str] = mod;
- qDebug() << "startElement_modifs_mass end" ;
- return true;
+bool XtandemSaxHandler::startElement_file(QXmlAttributes attributes) {
+ //<file type="peptide" URL="/gorgone/pappso/formation/TD/Database/Genome_Z_mays_5a.fasta"/>
+ if (attributes.value("type") == "peptide") {
+ //prot_.setDatabase(identification_.getDatabaseSet().getInstance(
+ // attrs.getValue("URL")));
+ }
}
-//<sample value="P6_21_23"/>
-bool XtandemSaxHandler::startElement_sample(QXmlAttributes attributes) {
+bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
+//<domain id="1976.1.1" start="620" end="629" expect="9.7e-04" mh="1120.5307" delta="-0.0012" hyperscore="29.9"
+ //nextscore="10.2" y_score="10.4" y_ions="7" b_score="11.2" b_ions="3" pre="QLYR" post="RYGV"
+ //seq="AQEEMAQVAK" missed_cleavages="0">
- qDebug() << "startElement_sample ";
+ qDebug() << "startElement_domain ";
MsRunSp ms_run = _p_project->getMsRunStore().getInstance(attributes.value("value").simplified());
ms_run.get()->setXmlId(attributes.value("value").simplified());
ms_run.get()->setFilename(attributes.value("value").simplified());
- _current_identification_group_p->addMsRunSp(ms_run);
- qDebug() << "startElement_sample end" ;
+ _p_identification_group->addMsRunSp(ms_run);
+ qDebug() << "startElement_domain end" ;
return true;
}
bool XtandemSaxHandler::startElement_peptide(QXmlAttributes attributes) {
@@ -270,52 +223,25 @@ bool XtandemSaxHandler::startElement_peptide(QXmlAttributes attributes) {
return true;
}
-bool XtandemSaxHandler::startElement_modif(QXmlAttributes attributes) {
-
- //<modifs><modif aa="M" modvalue="15.99491" posi="17" posi_in_prot="49"/>
- qDebug() << "startElement_modif ";
+bool XtandemSaxHandler::startElement_aa(QXmlAttributes attributes) {
+//<aa type="M" at="624" modified="15.99491" />
+ qDebug() << "startElement_aa ";
pappso::AaModificationP modif = _map_massstr_aamod[attributes.value("modvalue").simplified()];
unsigned int position = attributes.value("posi").simplified().toUInt();
_current_peptide_sp.get()->addAaModification(modif, position-1);
- qDebug() << "startElement_modif end" ;
- return true;
-}
-bool XtandemSaxHandler::endElement_peptide() {
- qDebug() << "endElement_peptide ";
-
- PeptideXtpSp peptide_const = PeptideXtp(*(_current_peptide_sp.get())).makePeptideXtpSp();
- peptide_const = _p_project->getPeptideStore().getInstance(peptide_const);
- _p_peptide_match->setPeptideXtpSp(peptide_const);
- return true;
-}
-
-bool XtandemSaxHandler::endElement_sequence() {
- //if ((_tag_stack.size() > 1) && (_tag_stack[_tag_stack.size() - 1] == "protein")) {
- _current_protein.setSequence(_current_text);
- //}
- //else {
- // XtandemHyperscore hyperscore(_curent_spectrum, _current_peptide_sp, _precision, _ion_list, _max_charge,_refine_spectrum_synthesis);
- //}
- return true;
-}
-bool XtandemSaxHandler::endElement_protein() {
- ProteinXtpSp sp_xtp_protein = _current_protein.makeProteinXtpSp();
-
- _p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
-
+ qDebug() << "startElement_aa end" ;
return true;
}
-bool XtandemSaxHandler::endElement_identification() {
-
+bool XtandemSaxHandler::endElement_note() {
+//<note label="description">GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC //4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01;
+ ////parent_gene=GRMZM2G083841</note>
+ if (_is_protein_description) {
+ _p_protein_match->getProteinXtpSp().get()->setDescription(_current_text.section(" ",1));
+ }
return true;
}
-bool XtandemSaxHandler::endElement_match() {
- _current_identification_group_p->addProteinMatch(_p_protein_match);
- _p_protein_match = nullptr;
- return true;
-}
bool XtandemSaxHandler::error(const QXmlParseException &exception) {
@@ -340,7 +266,6 @@ QString XtandemSaxHandler::errorString() const {
bool XtandemSaxHandler::endDocument() {
- _p_project->updateAutomaticFilters(_automatic_filter_parameters);
return true;
}
diff --git a/src/input/xtandemsaxhandler.h b/src/input/xtandemsaxhandler.h
index f794a3499..c1864f9d8 100644
--- a/src/input/xtandemsaxhandler.h
+++ b/src/input/xtandemsaxhandler.h
@@ -43,7 +43,7 @@
class XtandemSaxHandler: public QXmlDefaultHandler
{
public:
- XtandemSaxHandler(Project * p_project);
+ XtandemSaxHandler(Project * p_project, IdentificationGroup * p_identification_group);
~XtandemSaxHandler();
bool startElement(const QString & namespaceURI, const QString & localName,
@@ -66,21 +66,13 @@ public:
private:
bool startElement_group(QXmlAttributes attrs);
-
- bool startElement_filter_params(QXmlAttributes attributes);
- bool startElement_information(QXmlAttributes attributes);
- bool startElement_identification(QXmlAttributes attributes);
- bool startElement_match(QXmlAttributes attributes);
bool startElement_peptide(QXmlAttributes attributes);
bool startElement_protein(QXmlAttributes attributes);
- bool startElement_sample(QXmlAttributes attributes);
- bool startElement_modifs_mass(QXmlAttributes attributes);
- bool startElement_modif(QXmlAttributes attributes);
- bool endElement_identification();
- bool endElement_sequence();
- bool endElement_protein();
- bool endElement_peptide();
- bool endElement_match();
+ bool startElement_note(QXmlAttributes attributes);
+ bool startElement_file(QXmlAttributes attributes);
+ bool startElement_aa(QXmlAttributes attributes);
+ bool startElement_domain(QXmlAttributes attributes);
+ bool endElement_note();
pappso::AaModificationP getAaModificationP(pappso::mz mass) const;
@@ -90,19 +82,22 @@ private:
QString _current_text;
Project * _p_project;
+ IdentificationGroup * _p_identification_group;
+
ProteinMatch * _p_protein_match;
PeptideMatch * _p_peptide_match;
ProteinXtp _current_protein;
PeptideXtpSp _current_peptide_sp;
- IdentificationGroup * _current_identification_group_p;
QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
+
QString _current_group_label;
QString _current_group_type;
- uint _scan;
- double _mhplus_obser;
- uint _charge;
- getValue _RT;
+ unsigned int _scan;
+ pappso::pappso_double _mhplus_obser;
+ unsigned int _charge;
+ pappso::pappso_double _retention_time;
+ bool _is_protein_description = false;
};
#endif // XTANDEMSAXHANDLER_H
--
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