From c1317b80c7d2c0a2de32974d12341197524752ca Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 21 Jun 2018 22:00:03 +0200
Subject: [PATCH] xpip reader backward compatibility
---
src/input/xtpxpipsaxhandler.cpp | 1247 +++++++++++++++++++------------
1 file changed, 750 insertions(+), 497 deletions(-)
diff --git a/src/input/xtpxpipsaxhandler.cpp b/src/input/xtpxpipsaxhandler.cpp
index 596759c8..db923473 100644
--- a/src/input/xtpxpipsaxhandler.cpp
+++ b/src/input/xtpxpipsaxhandler.cpp
@@ -7,26 +7,27 @@
/*******************************************************************************
-* Copyright (c) 2017 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/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 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/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "xtpxpipsaxhandler.h"
@@ -36,626 +37,878 @@
#include "../utils/peptidestore.h"
#include "../utils/proteinstore.h"
-XtpXpipSaxHandler::XtpXpipSaxHandler(WorkMonitorInterface * p_monitor, Project * p_project):_p_project(p_project)
+XtpXpipSaxHandler::XtpXpipSaxHandler(WorkMonitorInterface *p_monitor,
+ Project *p_project)
+ : _p_project(p_project)
{
- qDebug() << "XtpXpipSaxHandler::XtpXpipSaxHandler begin" ;
- _p_monitor = p_monitor;
- qDebug() << "XtpXpipSaxHandler::XtpXpipSaxHandler end" ;
+ qDebug() << "XtpXpipSaxHandler::XtpXpipSaxHandler begin";
+ _p_monitor = p_monitor;
+ qDebug() << "XtpXpipSaxHandler::XtpXpipSaxHandler end";
}
XtpXpipSaxHandler::~XtpXpipSaxHandler()
{
-
}
-bool XtpXpipSaxHandler::isXtpXpip() const {
- return _is_xtpcpp_xpip;
+bool
+XtpXpipSaxHandler::isXtpXpip() const
+{
+ return _is_xtpcpp_xpip;
}
-bool XtpXpipSaxHandler::startElement(const QString & namespaceURI, const QString & localName,
- const QString & qName, const QXmlAttributes & attributes) {
- qDebug()<< "XtpXpipSaxHandler::startElement begin" << namespaceURI << " " << localName << " " << qName ;
- _tag_stack.push_back(qName);
- bool is_ok = true;
-
- try {
- //startElement_group
- if (_tag_stack.size() == 1) {
- _is_xtpcpp_xpip = true;
- if (qName != "xpip") {
- _is_xtpcpp_xpip = false;
- throw pappso::ExceptionNotFound(QObject::tr("ERROR this file is not an xpip file %1").arg(qName));
+bool
+XtpXpipSaxHandler::startElement(const QString &namespaceURI,
+ const QString &localName, const QString &qName,
+ const QXmlAttributes &attributes)
+{
+ qDebug() << "XtpXpipSaxHandler::startElement begin" << namespaceURI << " "
+ << localName << " " << qName;
+ _tag_stack.push_back(qName);
+ bool is_ok = true;
+
+ try
+ {
+ // startElement_group
+ if(_tag_stack.size() == 1)
+ {
+ _is_xtpcpp_xpip = true;
+ if(qName != "xpip")
+ {
+ _is_xtpcpp_xpip = false;
+ throw pappso::ExceptionNotFound(
+ QObject::tr("ERROR this file is not an xpip file %1")
+ .arg(qName));
}
- } else if (qName == "protein_match") {
- if ( _count_total % 100 == 0 )
+ }
+ else if(qName == "protein_match")
+ {
+ if(_count_total % 100 == 0)
{
- _p_monitor->message(QString("reading protein matches %1 on %2").arg(_count_protein_matches).arg(_total_protein_matches), _count_total);
+ _p_monitor->message(QString("reading protein matches %1 on %2")
+ .arg(_count_protein_matches)
+ .arg(_total_protein_matches),
+ _count_total);
}
- is_ok = startElement_protein_match(attributes);
- } else if (qName == "peptide_match") {
- is_ok = startElement_peptide_match(attributes);
- } else if (qName == "protein") {
- if ( _count_total % 100 == 0 )
+ is_ok = startElement_protein_match(attributes);
+ }
+ else if(qName == "peptide_match")
+ {
+ is_ok = startElement_peptide_match(attributes);
+ }
+ else if(qName == "protein")
+ {
+ if(_count_total % 100 == 0)
{
- _p_monitor->message(QString("reading proteins %1 on %2").arg(_count_proteins).arg(_total_proteins), _count_total);
+ _p_monitor->message(QString("reading proteins %1 on %2")
+ .arg(_count_proteins)
+ .arg(_total_proteins),
+ _count_total);
}
- is_ok = startElement_protein(attributes);
- } else if (qName == "identification_source") {
- is_ok = startElement_identification_source(attributes);
- } else if (qName == "param") {
- is_ok = startElement_param(attributes);
- } else if (qName == "stat") {
- is_ok = startElement_stat(attributes);
- } else if (qName == "identification_group") {
- is_ok = startElement_identification_group(attributes);
- }
- else if (qName == "peptide_evidence_list") {
- is_ok = startElement_peptide_evidence_list(attributes);
- }
- else if (qName == "counts") {
- is_ok = startElement_counts(attributes);
- }
- else if (qName == "label_method") {
- is_ok = startElement_label_method(attributes);
- }
- //<sample value="P6_08_10"/>
- else if (qName == "msrun") {
- is_ok = startElement_msrun(attributes);
- } else if (qName == "peptide") {
- if ( _count_total % 100 == 0 )
+ is_ok = startElement_protein(attributes);
+ }
+ else if(qName == "identification_source")
+ {
+ is_ok = startElement_identification_source(attributes);
+ }
+ else if(qName == "param")
+ {
+ is_ok = startElement_param(attributes);
+ }
+ else if(qName == "stat")
+ {
+ is_ok = startElement_stat(attributes);
+ }
+ else if(qName == "identification_group")
+ {
+ is_ok = startElement_identification_group(attributes);
+ }
+ else if(qName == "peptide_evidence_list")
+ {
+ is_ok = startElement_peptide_evidence_list(attributes);
+ }
+ else if(qName == "counts")
+ {
+ is_ok = startElement_counts(attributes);
+ }
+ else if(qName == "label_method")
+ {
+ is_ok = startElement_label_method(attributes);
+ }
+ //<sample value="P6_08_10"/>
+ else if(qName == "msrun")
+ {
+ is_ok = startElement_msrun(attributes);
+ }
+ else if(qName == "peptide")
+ {
+ if(_count_total % 100 == 0)
{
- _p_monitor->message(QObject::tr("reading peptide %1 on %2").arg(_count_peptides).arg(_total_peptides), _count_total);
+ _p_monitor->message(QObject::tr("reading peptide %1 on %2")
+ .arg(_count_peptides)
+ .arg(_total_peptides),
+ _count_total);
}
- is_ok = startElement_peptide(attributes);
- } else if (qName == "peptide_evidence") {
- if ( _count_total % 100 == 0 )
+ is_ok = startElement_peptide(attributes);
+ }
+ else if(qName == "peptide_evidence")
+ {
+ if(_count_total % 100 == 0)
{
- _p_monitor->message(QObject::tr("reading peptide evidence %1 on %2").arg(_count_peptide_evidences).arg(_total_peptide_evidences), _count_total);
+ _p_monitor->message(
+ QObject::tr("reading peptide evidence %1 on %2")
+ .arg(_count_peptide_evidences)
+ .arg(_total_peptide_evidences),
+ _count_total);
}
- is_ok = startElement_peptide_evidence(attributes);
- } else if (qName == "modification") {
- is_ok = startElement_modification(attributes);
- } else if (qName == "mod") {
- is_ok = startElement_mod(attributes);
- } else if (qName == "filter_params") {
- is_ok = startElement_filter_params(attributes);
- } else if (qName == "description") {
- is_ok = startElement_description(attributes);
- } else if (qName == "fasta_file") {
- is_ok = startElement_fasta_file(attributes);
- } else if (qName == "contaminants") {
- is_ok = startElement_contaminants(attributes);
- } else if (qName == "decoys") {
- is_ok = startElement_decoys(attributes);
- }
-
- _current_text.clear();
+ is_ok = startElement_peptide_evidence(attributes);
+ }
+ else if(qName == "modification")
+ {
+ is_ok = startElement_modification(attributes);
+ }
+ else if(qName == "mod")
+ {
+ is_ok = startElement_mod(attributes);
+ }
+ else if(qName == "filter_params")
+ {
+ is_ok = startElement_filter_params(attributes);
+ }
+ else if(qName == "description")
+ {
+ is_ok = startElement_description(attributes);
+ }
+ else if(qName == "fasta_file")
+ {
+ is_ok = startElement_fasta_file(attributes);
+ }
+ else if(qName == "contaminants")
+ {
+ is_ok = startElement_contaminants(attributes);
+ }
+ else if(qName == "decoys")
+ {
+ is_ok = startElement_decoys(attributes);
+ }
+
+ _current_text.clear();
}
- catch (pappso::PappsoException exception_pappso) {
- _errorStr = QObject::tr("ERROR in XtpXpipSaxHandler::startElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
- return false;
+ catch(pappso::PappsoException exception_pappso)
+ {
+ _errorStr = QObject::tr("ERROR in XtpXpipSaxHandler::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 XtpXpipSaxHandler::startElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
- return false;
+ catch(std::exception exception_std)
+ {
+ _errorStr =
+ QObject::tr(
+ "ERROR in XtpXpipSaxHandler::startElement tag %1, std exception:\n%2")
+ .arg(qName)
+ .arg(exception_std.what());
+ return false;
}
- return is_ok;
+ return is_ok;
}
-bool XtpXpipSaxHandler::endElement(const QString & namespaceURI, const QString & localName,
- const QString & qName) {
+bool
+XtpXpipSaxHandler::endElement(const QString &namespaceURI,
+ const QString &localName, const QString &qName)
+{
- qDebug()<< "XtpXpipSaxHandler::endElement begin" << namespaceURI << " " << localName << " " << qName ;
- bool is_ok = true;
- // endElement_peptide_list
- try {
- if (qName == "protein")
+ qDebug() << "XtpXpipSaxHandler::endElement begin" << namespaceURI << " "
+ << localName << " " << qName;
+ bool is_ok = true;
+ // endElement_peptide_list
+ try
+ {
+ if(qName == "protein")
{
- is_ok = endElement_protein();
+ is_ok = endElement_protein();
}
- else if (qName == "peptide") {
- is_ok = endElement_peptide();
+ else if(qName == "peptide")
+ {
+ is_ok = endElement_peptide();
}
- else if (qName == "msrun") {
- is_ok = endElement_msrun();
+ else if(qName == "msrun")
+ {
+ is_ok = endElement_msrun();
}
- else if (qName == "sequence") {
- is_ok = endElement_sequence();
+ else if(qName == "sequence")
+ {
+ is_ok = endElement_sequence();
}
- else if (qName == "protein_match") {
- is_ok = endElement_protein_match();
+ else if(qName == "protein_match")
+ {
+ is_ok = endElement_protein_match();
}
- else if (qName == "peptide_evidence") {
- is_ok = endElement_peptide_evidence();
+ else if(qName == "peptide_evidence")
+ {
+ is_ok = endElement_peptide_evidence();
}
- else if (qName == "peptide_evidence_list") {
- is_ok = endElement_peptide_evidence_list();
+ else if(qName == "peptide_evidence_list")
+ {
+ is_ok = endElement_peptide_evidence_list();
}
- else if (qName == "identification_group") {
- is_ok = endElement_identification_group();
+ else if(qName == "identification_group")
+ {
+ is_ok = endElement_identification_group();
}
- else if (qName == "identification_source") {
- is_ok = endElement_identification_source();
+ else if(qName == "identification_source")
+ {
+ is_ok = endElement_identification_source();
}
- // end of detection_moulon
- // else if ((_tag_stack.size() > 1) &&
- // (_tag_stack[_tag_stack.size() - 2] == "detection_moulon"))
+ // end of detection_moulon
+ // else if ((_tag_stack.size() > 1) &&
+ // (_tag_stack[_tag_stack.size() - 2] == "detection_moulon"))
}
- catch (pappso::PappsoException exception_pappso) {
- _errorStr = QObject::tr("ERROR in XtpXpipSaxHandler::endElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
- return false;
+ catch(pappso::PappsoException exception_pappso)
+ {
+ _errorStr = QObject::tr("ERROR in XtpXpipSaxHandler::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 XtpXpipSaxHandler::endElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
- return false;
+ catch(std::exception exception_std)
+ {
+ _errorStr =
+ QObject::tr(
+ "ERROR in XtpXpipSaxHandler::endElement tag %1, std exception:\n%2")
+ .arg(qName)
+ .arg(exception_std.what());
+ return false;
}
- _current_text.clear();
- _tag_stack.pop_back();
+ _current_text.clear();
+ _tag_stack.pop_back();
- return is_ok;
+ return is_ok;
}
-bool XtpXpipSaxHandler::startElement_contaminants(QXmlAttributes attributes) {
-// <contaminants regexp="^contatruc\|" fasta_id=""/>
-
- qDebug() << "startElement_contaminants ";
- QString regexp(attributes.value("regexp"));
- QString fasta_id_list(attributes.value("fasta_id"));
- if (!regexp.isEmpty()) {
- _p_project->getProteinStore().setRegexpContaminantPattern(regexp);
+bool
+XtpXpipSaxHandler::startElement_contaminants(QXmlAttributes attributes)
+{
+ // <contaminants regexp="^contatruc\|" fasta_id=""/>
+
+ qDebug() << "startElement_contaminants ";
+ QString regexp(attributes.value("regexp"));
+ QString fasta_id_list(attributes.value("fasta_id"));
+ if(!regexp.isEmpty())
+ {
+ _p_project->getProteinStore().setRegexpContaminantPattern(regexp);
}
- if (!fasta_id_list.isEmpty()) {
- for (QString fasta_id:fasta_id_list.split(" ")) {
- _p_project->getProteinStore().addContaminantFastaFile(_map_fasta_files.at(fasta_id).get());
+ if(!fasta_id_list.isEmpty())
+ {
+ for(QString fasta_id : fasta_id_list.split(" "))
+ {
+ _p_project->getProteinStore().addContaminantFastaFile(
+ _map_fasta_files.at(fasta_id).get());
}
}
- qDebug() << "startElement_contaminants end" ;
- return true;
+ qDebug() << "startElement_contaminants end";
+ return true;
}
-bool XtpXpipSaxHandler::startElement_decoys(QXmlAttributes attributes) {
-// <decoys regexp=".*reversedi" fasta_id=""/>
- qDebug() << "startElement_decoys ";
- QString regexp(attributes.value("regexp"));
- QString fasta_id_list(attributes.value("fasta_id"));
- if (!regexp.isEmpty()) {
- _p_project->getProteinStore().setRegexpDecoyPattern(regexp);
+bool
+XtpXpipSaxHandler::startElement_decoys(QXmlAttributes attributes)
+{
+ // <decoys regexp=".*reversedi" fasta_id=""/>
+ qDebug() << "startElement_decoys ";
+ QString regexp(attributes.value("regexp"));
+ QString fasta_id_list(attributes.value("fasta_id"));
+ if(!regexp.isEmpty())
+ {
+ _p_project->getProteinStore().setRegexpDecoyPattern(regexp);
}
- if (!fasta_id_list.isEmpty()) {
- for (QString fasta_id:fasta_id_list.split(" ")) {
- _p_project->getProteinStore().addDecoyFastaFile(_map_fasta_files.at(fasta_id).get());
+ if(!fasta_id_list.isEmpty())
+ {
+ for(QString fasta_id : fasta_id_list.split(" "))
+ {
+ _p_project->getProteinStore().addDecoyFastaFile(
+ _map_fasta_files.at(fasta_id).get());
}
}
- qDebug() << "startElement_decoys end" ;
- return true;
-}
-
-bool XtpXpipSaxHandler::startElement_label_method(QXmlAttributes attributes) {
-// <label_method id="dimethyl">
- qDebug() << "startElement_label_method ";
- LabelingMethod method(attributes.value("id").simplified());
- _sp_labeling_method = method.makeLabelingMethodSp();
- _p_project->setLabelingMethodSp(_sp_labeling_method);
- qDebug() << "startElement_label_method end" ;
- return true;
-}
-
-bool XtpXpipSaxHandler::startElement_counts(QXmlAttributes attributes) {
-// <counts proteins="6019" peptides="6194" peptide_evidences="7123" protein_matches="6019"/>
- qDebug() << "startElement_counts ";
- _total_proteins = (std::size_t) attributes.value("proteins").toLong();
- _total_peptides = (std::size_t) attributes.value("peptides").toLong();
- _total_peptide_evidences = (std::size_t) attributes.value("peptide_evidences").toLong();
- _total_protein_matches = (std::size_t) attributes.value("protein_matches").toLong();
- _count_proteins=0;
- _count_peptides=0;
- _count_peptide_evidences=0;
- _count_protein_matches=0;
-
- _total = _total_proteins+ _total_peptides + _total_peptide_evidences+_total_protein_matches;
-
- _p_monitor->setProgressMaximumValue((std::size_t)_total);
- qDebug() << "startElement_counts end" ;
- return true;
-}
-
-bool XtpXpipSaxHandler::startElement_filter_params(QXmlAttributes attributes) {
-
-// <filter_params pep_evalue="0.01" prot_evalue="0.01" pep_number="1" cross_sample="false"/>
- qDebug() << "startElement_filter_params ";
- _automatic_filter_parameters.setFilterPeptideEvalue( attributes.value("pep_evalue").simplified().toDouble());
- _automatic_filter_parameters.setFilterProteinEvalue(attributes.value("prot_evalue").simplified().toDouble());
- _automatic_filter_parameters.setFilterMinimumPeptidePerMatch( attributes.value("pep_number").simplified().toUInt());
- _automatic_filter_parameters.setFilterCrossSamplePeptideNumber(false);
- if (attributes.value("cross_sample").simplified() == "true") {
- _automatic_filter_parameters.setFilterCrossSamplePeptideNumber(true);
+ qDebug() << "startElement_decoys end";
+ return true;
+}
+
+bool
+XtpXpipSaxHandler::startElement_label_method(QXmlAttributes attributes)
+{
+ // <label_method id="dimethyl">
+ qDebug() << "startElement_label_method ";
+ LabelingMethod method(attributes.value("id").simplified());
+ _sp_labeling_method = method.makeLabelingMethodSp();
+ _p_project->setLabelingMethodSp(_sp_labeling_method);
+ qDebug() << "startElement_label_method end";
+ return true;
+}
+
+bool
+XtpXpipSaxHandler::startElement_counts(QXmlAttributes attributes)
+{
+ // <counts proteins="6019" peptides="6194" peptide_evidences="7123"
+ // protein_matches="6019"/>
+ qDebug() << "startElement_counts ";
+ _total_proteins = (std::size_t)attributes.value("proteins").toLong();
+ _total_peptides = (std::size_t)attributes.value("peptides").toLong();
+ _total_peptide_evidences =
+ (std::size_t)attributes.value("peptide_evidences").toLong();
+ _total_protein_matches =
+ (std::size_t)attributes.value("protein_matches").toLong();
+ _count_proteins = 0;
+ _count_peptides = 0;
+ _count_peptide_evidences = 0;
+ _count_protein_matches = 0;
+
+ _total = _total_proteins + _total_peptides + _total_peptide_evidences +
+ _total_protein_matches;
+
+ _p_monitor->setProgressMaximumValue((std::size_t)_total);
+ qDebug() << "startElement_counts end";
+ return true;
+}
+
+bool
+XtpXpipSaxHandler::startElement_filter_params(QXmlAttributes attributes)
+{
+
+ // <filter_params pep_evalue="0.01" prot_evalue="0.01" pep_number="1"
+ // cross_sample="false"/>
+ qDebug() << "startElement_filter_params ";
+ _automatic_filter_parameters.setFilterPeptideEvalue(
+ attributes.value("pep_evalue").simplified().toDouble());
+ _automatic_filter_parameters.setFilterProteinEvalue(
+ attributes.value("prot_evalue").simplified().toDouble());
+ _automatic_filter_parameters.setFilterMinimumPeptidePerMatch(
+ attributes.value("pep_number").simplified().toUInt());
+ _automatic_filter_parameters.setFilterCrossSamplePeptideNumber(false);
+ if(attributes.value("cross_sample").simplified() == "true")
+ {
+ _automatic_filter_parameters.setFilterCrossSamplePeptideNumber(true);
}
- //_p_project->getFastaFileStore().getInstance(FastaFile(attributes.value("database_filter")));
- qDebug() << "startElement_filter_params end" ;
- return true;
+ //_p_project->getFastaFileStore().getInstance(FastaFile(attributes.value("database_filter")));
+ qDebug() << "startElement_filter_params end";
+ return true;
}
-bool XtpXpipSaxHandler::startElement_description(QXmlAttributes attributes) {
+bool
+XtpXpipSaxHandler::startElement_description(QXmlAttributes attributes)
+{
-// <description version="0.1.23" grouping="peptidemass" combine="true" date="2017-11-17T16:02:47"/>
+ // <description version="0.1.23" grouping="peptidemass" combine="true"
+ // date="2017-11-17T16:02:47"/>
- qDebug() << "startElement_description ";
- _p_project->setProjectMode(ProjectMode::individual);
- if (attributes.value("combine") == "true") {
- _p_project->setProjectMode(ProjectMode::combined);
+ qDebug() << "startElement_description ";
+ _p_project->setProjectMode(ProjectMode::individual);
+ if(attributes.value("combine") == "true")
+ {
+ _p_project->setProjectMode(ProjectMode::combined);
}
- //_total_protein_match = attributes.value("match_number").toUInt();
+ //_total_protein_match = attributes.value("match_number").toUInt();
- //_p_monitor->setProgressMaximumValue(_total_protein_match);
- qDebug() << "startElement_description end" ;
- return true;
+ //_p_monitor->setProgressMaximumValue(_total_protein_match);
+ qDebug() << "startElement_description end";
+ return true;
}
-bool XtpXpipSaxHandler::startElement_stat(QXmlAttributes attributes) {
+bool
+XtpXpipSaxHandler::startElement_stat(QXmlAttributes attributes)
+{
- /*
- <stat key="0" value="48.5"/>
- */
- qDebug() << "startElement_stat ";
+ /*
+ <stat key="0" value="48.5"/>
+ */
+ qDebug() << "startElement_stat ";
- if (_sp_msrun.get() != nullptr) {
- MsRunStatistics type = static_cast<MsRunStatistics>(attributes.value("key").toUInt());
- _sp_msrun.get()->setMsRunStatistics(type, attributes.value("value"));
+ if(_sp_msrun.get() != nullptr)
+ {
+ MsRunStatistics type =
+ static_cast<MsRunStatistics>(attributes.value("key").toUInt());
+ _sp_msrun.get()->setMsRunStatistics(type, attributes.value("value"));
}
- else if (_sp_current_identification_source.get() != nullptr) {
- IdentificationEngineStatistics type = static_cast<IdentificationEngineStatistics>(attributes.value("key").toUInt());
- _sp_current_identification_source.get()->setIdentificationEngineStatistics(type, attributes.value("value"));
+ else if(_sp_current_identification_source.get() != nullptr)
+ {
+ IdentificationEngineStatistics type =
+ static_cast<IdentificationEngineStatistics>(
+ attributes.value("key").toUInt());
+ _sp_current_identification_source.get()
+ ->setIdentificationEngineStatistics(type, attributes.value("value"));
}
- qDebug() << "startElement_stat end" ;
- return true;
+ qDebug() << "startElement_stat end";
+ return true;
}
-bool XtpXpipSaxHandler::startElement_param(QXmlAttributes attributes) {
-
- /*
- <param key="0" value="48.5"/>
- */
- qDebug() << "startElement_param ";
+bool
+XtpXpipSaxHandler::startElement_param(QXmlAttributes attributes)
+{
- if (_sp_current_peptide_evidence.get() != nullptr) {
- PeptideEvidenceParam type = static_cast<PeptideEvidenceParam>(attributes.value("key").toUInt());
- _sp_current_peptide_evidence.get()->setParam(type, QVariant( attributes.value("value")));
+ /*
+ <param key="0" value="48.5"/>
+ */
+ qDebug() << "startElement_param ";
+
+ if(_sp_current_peptide_evidence.get() != nullptr)
+ {
+ PeptideEvidenceParam type =
+ static_cast<PeptideEvidenceParam>(attributes.value("key").toUInt());
+ _sp_current_peptide_evidence.get()->setParam(
+ type, QVariant(attributes.value("value")));
}
- else if (_sp_current_identification_source.get() != nullptr) {
- IdentificationEngineParam type = static_cast<IdentificationEngineParam>(attributes.value("key").toUInt());
- _sp_current_identification_source.get()->setIdentificationEngineParam(type, attributes.value("value"));
+ else if(_sp_current_identification_source.get() != nullptr)
+ {
+ IdentificationEngineParam type = static_cast<IdentificationEngineParam>(
+ attributes.value("key").toUInt());
+ _sp_current_identification_source.get()->setIdentificationEngineParam(
+ type, attributes.value("value"));
}
- qDebug() << "startElement_param end" ;
- return true;
+ qDebug() << "startElement_param end";
+ return true;
}
-bool XtpXpipSaxHandler::startElement_modification(QXmlAttributes attributes) {
+bool
+XtpXpipSaxHandler::startElement_modification(QXmlAttributes attributes)
+{
- /*
- <modification id="moda1" mod="MOD:00719"/>
- */
- qDebug() << "startElement_modifs_mass ";
+ /*
+ <modification id="moda1" mod="MOD:00719"/>
+ */
+ qDebug() << "startElement_modifs_mass ";
- pappso::AaModificationP mod = pappso::AaModification::getInstance(attributes.value("mod").simplified());
- _map_modifs.insert(std::pair<QString, pappso::AaModificationP>(attributes.value("id").simplified(), mod));
+ pappso::AaModificationP mod =
+ pappso::AaModification::getInstance(attributes.value("mod").simplified());
+ _map_modifs.insert(std::pair<QString, pappso::AaModificationP>(
+ attributes.value("id").simplified(), mod));
- qDebug() << "startElement_modifs_mass end" ;
- return true;
+ qDebug() << "startElement_modifs_mass end";
+ return true;
}
-bool XtpXpipSaxHandler::startElement_identification_group(QXmlAttributes attributes) {
+bool
+XtpXpipSaxHandler::startElement_identification_group(QXmlAttributes attributes)
+{
- qDebug() << "startElement_identification_group ";
- _current_identification_group_p = _p_project->newIdentificationGroup();
+ qDebug() << "startElement_identification_group ";
+ _current_identification_group_p = _p_project->newIdentificationGroup();
- qDebug() << "startElement_identification_group end" ;
- return true;
+ qDebug() << "startElement_identification_group end";
+ return true;
}
-bool XtpXpipSaxHandler::startElement_identification_source(QXmlAttributes attributes) {
- //<identification_source id="identa0" msrun_id="sampa0" path="/espace/bio/tandem/20120906_balliau_extract_1_A01_urnb-1.xml" engine="1" version="2017.2.1.4" fasta_ids="fastaa0">
-
- qDebug() << "startElement_identification_source ";
-
- IdentificationEngine engine = static_cast<IdentificationEngine>(attributes.value("engine").toUInt());
- _sp_current_identification_source = _p_project->getIdentificationDataSourceStore().getInstance(attributes.value("path").simplified(), engine);
- _sp_current_identification_source.get()->setXmlId(attributes.value("id").simplified());
- _map_ident_sources.insert(std::pair<QString, IdentificationDataSourceSp>(_sp_current_identification_source.get()->getXmlId(), _sp_current_identification_source));
-
- qDebug() << "startElement_identification_source setMsRunSp";
- _sp_current_identification_source->setMsRunSp(_map_msruns.at(attributes.value("msrun_id").simplified()));
- qDebug() << "startElement_identification_source setIdentificationEngineVersion";
- _sp_current_identification_source->setIdentificationEngineVersion(attributes.value("version"));
-
- for (const QString & fasta_id : attributes.value("fasta_ids").split(" ")) {
- _sp_current_identification_source.get()->addFastaFile(_map_fasta_files.at(fasta_id));
+bool
+XtpXpipSaxHandler::startElement_identification_source(QXmlAttributes attributes)
+{
+ //<identification_source id="identa0" msrun_id="sampa0"
+ //path="/espace/bio/tandem/20120906_balliau_extract_1_A01_urnb-1.xml"
+ //engine="1" version="2017.2.1.4" fasta_ids="fastaa0">
+
+ qDebug() << "startElement_identification_source ";
+
+ IdentificationEngine engine =
+ static_cast<IdentificationEngine>(attributes.value("engine").toUInt());
+ _sp_current_identification_source =
+ _p_project->getIdentificationDataSourceStore().getInstance(
+ attributes.value("path").simplified(), engine);
+ _sp_current_identification_source.get()->setXmlId(
+ attributes.value("id").simplified());
+ _map_ident_sources.insert(std::pair<QString, IdentificationDataSourceSp>(
+ _sp_current_identification_source.get()->getXmlId(),
+ _sp_current_identification_source));
+
+ qDebug() << "startElement_identification_source setMsRunSp";
+ _sp_current_identification_source->setMsRunSp(
+ _map_msruns.at(attributes.value("msrun_id").simplified()));
+ qDebug()
+ << "startElement_identification_source setIdentificationEngineVersion";
+ _sp_current_identification_source->setIdentificationEngineVersion(
+ attributes.value("version"));
+
+ for(const QString &fasta_id : attributes.value("fasta_ids").split(" "))
+ {
+ _sp_current_identification_source.get()->addFastaFile(
+ _map_fasta_files.at(fasta_id));
}
- //_current_identification_group_p->addMsRunSp(ms_run);
- qDebug() << "startElement_identification_source end" ;
- return true;
+ //_current_identification_group_p->addMsRunSp(ms_run);
+ qDebug() << "startElement_identification_source end";
+ return true;
}
-bool XtpXpipSaxHandler::startElement_msrun(QXmlAttributes attributes) {
-//<msrun id="sampa0" name="20120906_balliau_extract_1_A01_urnb-1" format="0" path="20120906_balliau_extract_1_A01_urnb-1"/>
+bool
+XtpXpipSaxHandler::startElement_msrun(QXmlAttributes attributes)
+{
+ //<msrun id="sampa0" name="20120906_balliau_extract_1_A01_urnb-1" format="0"
+ //path="20120906_balliau_extract_1_A01_urnb-1"/>
- qDebug() << "startElement_msrun ";
+ qDebug() << "startElement_msrun ";
- _sp_msrun = _p_project->getMsRunStore().getInstance(attributes.value("path").simplified());
- _sp_msrun.get()->setFilename(attributes.value("path").simplified());
- _sp_msrun.get()->setSampleName(attributes.value("name").simplified());
- _sp_msrun.get()->setXmlId(attributes.value("id").simplified());
- _map_msruns.insert(std::pair<QString, MsRunSp>(_sp_msrun.get()->getXmlId(), _sp_msrun));
- //_current_identification_group_p->addMsRunSp(ms_run);
- qDebug() << "startElement_msrun end" ;
- return true;
+ _sp_msrun = _p_project->getMsRunStore().getInstance(
+ attributes.value("path").simplified());
+ _sp_msrun.get()->setFilename(attributes.value("path").simplified());
+ _sp_msrun.get()->setSampleName(attributes.value("name").simplified());
+ _sp_msrun.get()->setXmlId(attributes.value("id").simplified());
+ _map_msruns.insert(
+ std::pair<QString, MsRunSp>(_sp_msrun.get()->getXmlId(), _sp_msrun));
+ //_current_identification_group_p->addMsRunSp(ms_run);
+ qDebug() << "startElement_msrun end";
+ return true;
}
-bool XtpXpipSaxHandler::startElement_peptide_evidence_list(QXmlAttributes attributes) {
- //<peptide_evidence_list ident_source_id="identa0">
+bool
+XtpXpipSaxHandler::startElement_peptide_evidence_list(QXmlAttributes attributes)
+{
+ //<peptide_evidence_list ident_source_id="identa0">
- qDebug() << "startElement_peptide_evidence_list ";
- _sp_current_identification_source = _map_ident_sources.at(attributes.value("ident_source_id").simplified());
- _current_identification_group_p->addIdentificationDataSourceP(_sp_current_identification_source.get());
+ qDebug() << "startElement_peptide_evidence_list ";
+ _sp_current_identification_source =
+ _map_ident_sources.at(attributes.value("ident_source_id").simplified());
+ _current_identification_group_p->addIdentificationDataSourceP(
+ _sp_current_identification_source.get());
- //_current_identification_group_p->addMsRunSp(ms_run);
- qDebug() << "startElement_peptide_evidence_list end" ;
- return true;
+ //_current_identification_group_p->addMsRunSp(ms_run);
+ qDebug() << "startElement_peptide_evidence_list end";
+ return true;
}
-bool XtpXpipSaxHandler::startElement_peptide_evidence(QXmlAttributes attributes) {
+bool
+XtpXpipSaxHandler::startElement_peptide_evidence(QXmlAttributes attributes)
+{
- qDebug() << "startElement_peptide_evidence ";
- /*
- * <peptide_evidence id="peb76" source_id="identa0" peptide_id="pd7688" scan="11743" rt="2170" evalue="8.1e-10" exp_mass="1655.755648" charge="2" checked="true">
- <param key="0" value="48.5"/>
- </peptide_evidence>
+ qDebug() << "startElement_peptide_evidence ";
+ /*
+ * <peptide_evidence id="peb76" source_id="identa0" peptide_id="pd7688"
+ scan="11743" rt="2170" evalue="8.1e-10" exp_mass="1655.755648" charge="2"
+ checked="true"> <param key="0" value="48.5"/>
+ </peptide_evidence>
+
+ */
+
+ unsigned int scan = attributes.value("scan").toUInt();
+ _p_peptide_evidence = new PeptideEvidence(
+ _sp_current_identification_source.get()->getMsRunSp().get(), scan);
+ _p_peptide_evidence->setIdentificationDataSource(
+ _sp_current_identification_source.get());
+
+ _p_peptide_evidence->setChecked(false);
+ if(attributes.value("checked").simplified().toLower() == "true")
+ {
+ _p_peptide_evidence->setChecked(true);
+ }
+ _p_peptide_evidence->setCharge(attributes.value("charge").toUInt());
+ if(!attributes.value("eng").isEmpty())
+ {
+ _p_peptide_evidence->setIdentificationEngine(
+ static_cast<IdentificationEngine>(attributes.value("eng").toUInt()));
+ }
+ _p_peptide_evidence->setRetentionTime(attributes.value("rt").toDouble());
+ _p_peptide_evidence->setEvalue(attributes.value("evalue").toDouble());
+ _p_peptide_evidence->setExperimentalMass(
+ attributes.value("exp_mass").toDouble());
+ _p_peptide_evidence->setPeptideXtpSp(
+ _map_peptides.at(attributes.value("peptide_id").simplified()));
+
+ _sp_current_peptide_evidence = _sp_current_identification_source.get()
+ ->getPeptideEvidenceStore()
+ .recordInstance(_p_peptide_evidence);
+ _map_peptide_evidences.insert(std::pair<QString, PeptideEvidenceSp>(
+ attributes.value("id").simplified(), _sp_current_peptide_evidence));
+ qDebug() << "startElement_peptide_evidence end";
+ return true;
+}
+
+bool
+XtpXpipSaxHandler::startElement_peptide_match(QXmlAttributes attributes)
+{
- */
+ qDebug() << "startElement_peptide_match ";
+ /*
+ *<peptide_match peptide_evidence_id="pea1" start="619"/>
+ */
+ PeptideMatch peptide_match;
+ peptide_match.setPeptideEvidenceSp(_map_peptide_evidences.at(
+ attributes.value("peptide_evidence_id").simplified()));
+ peptide_match.setStart(attributes.value("start").toUInt());
+ qDebug() << "startElement_peptide_match end";
+ _p_protein_match->addPeptideMatch(peptide_match);
+ qDebug() << "startElement_peptide_match "
+ << _p_protein_match->getPeptideMatchList().size();
+ return true;
+}
+
+bool
+XtpXpipSaxHandler::startElement_protein_match(QXmlAttributes attributes)
+{
- unsigned int scan = attributes.value("scan").toUInt();
- _p_peptide_evidence = new PeptideEvidence(_sp_current_identification_source.get()->getMsRunSp().get(), scan);
- _p_peptide_evidence->setIdentificationDataSource(_sp_current_identification_source.get());
+ qDebug() << "startElement_protein_match ";
+ /*
+ * <protein_match acc="GRMZM2G083841_P01" checked="true">
+ <peptide_match peptide_evidence_id="pea1" start="619"/>
+ <peptide_match peptide_evidence_id="pea2" start="12"/>
- _p_peptide_evidence->setChecked(false);
- if (attributes.value("checked").simplified().toLower() == "true") {
- _p_peptide_evidence->setChecked(true);
- }
- _p_peptide_evidence->setCharge(attributes.value("charge").toUInt());
- _p_peptide_evidence->setIdentificationEngine(static_cast<IdentificationEngine>(attributes.value("eng").toUInt()));
- _p_peptide_evidence->setRetentionTime(attributes.value("rt").toDouble());
- _p_peptide_evidence->setEvalue(attributes.value("evalue").toDouble());
- _p_peptide_evidence->setExperimentalMass(attributes.value("exp_mass").toDouble());
- _p_peptide_evidence->setPeptideXtpSp(_map_peptides.at( attributes.value("peptide_id").simplified()));
-
- _sp_current_peptide_evidence = _sp_current_identification_source.get()->getPeptideEvidenceStore().recordInstance(_p_peptide_evidence);
- _map_peptide_evidences.insert(std::pair<QString, PeptideEvidenceSp>(attributes.value("id").simplified(), _sp_current_peptide_evidence));
- qDebug() << "startElement_peptide_evidence end" ;
- return true;
-}
-
-bool XtpXpipSaxHandler::startElement_peptide_match(QXmlAttributes attributes) {
-
- qDebug() << "startElement_peptide_match ";
- /*
- *<peptide_match peptide_evidence_id="pea1" start="619"/>
- */
- PeptideMatch peptide_match;
- peptide_match.setPeptideEvidenceSp(_map_peptide_evidences.at(attributes.value("peptide_evidence_id").simplified()));
- peptide_match.setStart(attributes.value("start").toUInt());
- qDebug() << "startElement_peptide_match end" ;
- _p_protein_match->addPeptideMatch(peptide_match);
- qDebug() << "startElement_peptide_match " << _p_protein_match->getPeptideMatchList().size();
- return true;
-}
-
-bool XtpXpipSaxHandler::startElement_protein_match(QXmlAttributes attributes) {
-
- qDebug() << "startElement_protein_match ";
- /*
- * <protein_match acc="GRMZM2G083841_P01" checked="true">
- <peptide_match peptide_evidence_id="pea1" start="619"/>
- <peptide_match peptide_evidence_id="pea2" start="12"/>
-
- */
- _p_protein_match = new ProteinMatch();
-
-
- _p_protein_match->setProteinXtpSp(_map_proteins.at(attributes.value("acc").simplified()));
- _p_protein_match->setChecked(false);
- if (attributes.value("checked").simplified().toLower() == "true") {
- _p_protein_match->setChecked(true);
+ */
+ _p_protein_match = new ProteinMatch();
+
+
+ _p_protein_match->setProteinXtpSp(
+ _map_proteins.at(attributes.value("acc").simplified()));
+ _p_protein_match->setChecked(false);
+ if(attributes.value("checked").simplified().toLower() == "true")
+ {
+ _p_protein_match->setChecked(true);
}
- qDebug() << "startElement_protein_match end" ;
- return true;
+ qDebug() << "startElement_protein_match end";
+ return true;
}
-bool XtpXpipSaxHandler::startElement_fasta_file(QXmlAttributes attributes) {
- //<fasta_file id="fastaa0" path="/espace/Genome_Z_mays_5a.fasta"/>
- qDebug() << "startElement_fasta_file ";
+bool
+XtpXpipSaxHandler::startElement_fasta_file(QXmlAttributes attributes)
+{
+ //<fasta_file id="fastaa0" path="/espace/Genome_Z_mays_5a.fasta"/>
+ qDebug() << "startElement_fasta_file ";
- FastaFileSp fasta_file_sp = _p_project->getFastaFileStore().getInstance(FastaFile(attributes.value("path")));
- fasta_file_sp.get()->setXmlId(attributes.value("id"));
+ FastaFileSp fasta_file_sp = _p_project->getFastaFileStore().getInstance(
+ FastaFile(attributes.value("path")));
+ fasta_file_sp.get()->setXmlId(attributes.value("id"));
- _map_fasta_files.insert(std::pair<QString, FastaFileSp>(attributes.value("id"), fasta_file_sp));
- qDebug() << "startElement_fasta_file end" ;
- return true;
+ _map_fasta_files.insert(
+ std::pair<QString, FastaFileSp>(attributes.value("id"), fasta_file_sp));
+ qDebug() << "startElement_fasta_file end";
+ return true;
}
-bool XtpXpipSaxHandler::startElement_protein(QXmlAttributes attributes) {
+bool
+XtpXpipSaxHandler::startElement_protein(QXmlAttributes attributes)
+{
- qDebug() << "startElement_protein ";
- _count_proteins++;
- _count_total++;
- /*
- * <protein fasta_id="fastaa0" acc="AC149475.2_FGP003" description="seq=translation; coord=9:152490486..152495067:-1; parent_transcript=AC149475.2_FGT003; parent_gene=AC149475.2_FG003" is_decoy="false" is_contaminant="false">
- <sequence>MFLTRTEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGLKTKDGVVLAVEKRVTSPLLEPSSVEKIMEIDEHIGCAMSGLIADARTLVEHARVETQNHRFSYGEPMTVESSTQAICDLALRFGEGDEESMSRPFGVSLLIAGHDENGPSLYYTDPSGTFWQCNAKAIGSGSEGADSSLQEQYNKELALEEAETIALSILKQVMEEKVTPNNVDIAKVAPKYHLYTPAEVEAVIARL</sequence>
- </protein>
- */
- _sp_current_protein = ProteinXtp().makeProteinXtpSp();
-
- auto fasta_it = _map_fasta_files.find(attributes.value("fasta_id"));
- if (fasta_it == _map_fasta_files.end()) {
- throw pappso::ExceptionNotFound(QObject::tr("ERROR fasta_id %1 not found").arg(attributes.value("fasta_id")));
+ qDebug() << "startElement_protein ";
+ _count_proteins++;
+ _count_total++;
+ /*
+ * <protein fasta_id="fastaa0" acc="AC149475.2_FGP003"
+ description="seq=translation; coord=9:152490486..152495067:-1;
+ parent_transcript=AC149475.2_FGT003; parent_gene=AC149475.2_FG003"
+ is_decoy="false" is_contaminant="false">
+ <sequence>MFLTRTEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGLKTKDGVVLAVEKRVTSPLLEPSSVEKIMEIDEHIGCAMSGLIADARTLVEHARVETQNHRFSYGEPMTVESSTQAICDLALRFGEGDEESMSRPFGVSLLIAGHDENGPSLYYTDPSGTFWQCNAKAIGSGSEGADSSLQEQYNKELALEEAETIALSILKQVMEEKVTPNNVDIAKVAPKYHLYTPAEVEAVIARL</sequence>
+ </protein>
+ */
+ _sp_current_protein = ProteinXtp().makeProteinXtpSp();
+
+ auto fasta_it = _map_fasta_files.find(attributes.value("fasta_id"));
+ if(fasta_it == _map_fasta_files.end())
+ {
+ throw pappso::ExceptionNotFound(QObject::tr("ERROR fasta_id %1 not found")
+ .arg(attributes.value("fasta_id")));
}
- //qDebug() << "startElement_protein fastaid=" << attributes.value("fasta_id");
- _sp_current_protein.get()->setFastaFileP(fasta_it->second.get());
- _sp_current_protein.get()->setAccession(attributes.value("acc"));
-
- //qDebug() << "startElement_protein acc=" << attributes.value("acc");
- //qDebug() << "startElement_protein description=" << attributes.value("description");
- _sp_current_protein.get()->setDescription(attributes.value("description"));
- _sp_current_protein.get()->setIsContaminant(false);
- if (attributes.value("is_contaminant").simplified().toLower() == "true") {
- _sp_current_protein.get()->setIsContaminant(true);
+ // qDebug() << "startElement_protein fastaid=" <<
+ // attributes.value("fasta_id");
+ _sp_current_protein.get()->setFastaFileP(fasta_it->second.get());
+ _sp_current_protein.get()->setAccession(attributes.value("acc"));
+
+ // qDebug() << "startElement_protein acc=" << attributes.value("acc");
+ // qDebug() << "startElement_protein description=" <<
+ // attributes.value("description");
+ _sp_current_protein.get()->setDescription(attributes.value("description"));
+ _sp_current_protein.get()->setIsContaminant(false);
+ if(attributes.value("is_contaminant").simplified().toLower() == "true")
+ {
+ _sp_current_protein.get()->setIsContaminant(true);
}
- //qDebug() << "startElement_protein iscontaminant";
- _sp_current_protein.get()->setIsDecoy(false);
- if (attributes.value("is_decoy").simplified().toLower() == "true") {
- _sp_current_protein.get()->setIsDecoy(true);
+ // qDebug() << "startElement_protein iscontaminant";
+ _sp_current_protein.get()->setIsDecoy(false);
+ if(attributes.value("is_decoy").simplified().toLower() == "true")
+ {
+ _sp_current_protein.get()->setIsDecoy(true);
}
- //qDebug() << "startElement_protein isdecoy";
+ // qDebug() << "startElement_protein isdecoy";
- qDebug() << "startElement_protein end" ;
- return true;
+ qDebug() << "startElement_protein end";
+ return true;
}
-bool XtpXpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
+bool
+XtpXpipSaxHandler::startElement_peptide(QXmlAttributes attributes)
+{
-// <peptide id="pd1493" seq="FEGVPMAPPDPILGVSEAFK">
-// <mod ref="moda1" position="6" aa="M"/>
-// </peptide>
- qDebug() << "startElement_peptide ";
- _current_peptide_sp = PeptideXtp(attributes.value("seq").simplified()).makePeptideXtpSp();
- _current_id = attributes.value("id").simplified();
- qDebug() << "startElement_peptide end" ;
- return true;
+ // <peptide id="pd1493" seq="FEGVPMAPPDPILGVSEAFK">
+ // <mod ref="moda1" position="6" aa="M"/>
+ // </peptide>
+ qDebug() << "startElement_peptide ";
+ _current_peptide_sp =
+ PeptideXtp(attributes.value("seq").simplified()).makePeptideXtpSp();
+ _current_id = attributes.value("id").simplified();
+ qDebug() << "startElement_peptide end";
+ return true;
}
-bool XtpXpipSaxHandler::startElement_mod(QXmlAttributes attributes) {
+bool
+XtpXpipSaxHandler::startElement_mod(QXmlAttributes attributes)
+{
- //<mod ref="moda1" position="6" aa="M"/>
- qDebug() << "startElement_mod ";
- pappso::AaModificationP modif = _map_modifs[attributes.value("ref").simplified()];
- unsigned int position = attributes.value("position").simplified().toUInt();
- _current_peptide_sp.get()->addAaModification(modif, position);
- qDebug() << "startElement_mod end" ;
- return true;
-}
-bool XtpXpipSaxHandler::endElement_identification_group() {
- qDebug() << "endElement_identification_group ";
- _current_identification_group_p = nullptr;
- return true;
+ //<mod ref="moda1" position="6" aa="M"/>
+ qDebug() << "startElement_mod ";
+ pappso::AaModificationP modif =
+ _map_modifs[attributes.value("ref").simplified()];
+ unsigned int position = attributes.value("position").simplified().toUInt();
+ _current_peptide_sp.get()->addAaModification(modif, position);
+ qDebug() << "startElement_mod end";
+ return true;
+}
+bool
+XtpXpipSaxHandler::endElement_identification_group()
+{
+ qDebug() << "endElement_identification_group ";
+ _current_identification_group_p = nullptr;
+ return true;
}
-bool XtpXpipSaxHandler::endElement_identification_source() {
- qDebug() << "endElement_identification_source ";
- _sp_current_identification_source = nullptr;
- return true;
+bool
+XtpXpipSaxHandler::endElement_identification_source()
+{
+ qDebug() << "endElement_identification_source ";
+ _sp_current_identification_source = nullptr;
+ return true;
}
-bool XtpXpipSaxHandler::endElement_peptide_evidence_list() {
- qDebug() << "endElement_peptide_evidence_list ";
- _sp_current_identification_source.get()->getPeptideEvidenceStore().clearMap();
- _sp_current_identification_source = nullptr;
- return true;
+bool
+XtpXpipSaxHandler::endElement_peptide_evidence_list()
+{
+ qDebug() << "endElement_peptide_evidence_list ";
+ _sp_current_identification_source.get()->getPeptideEvidenceStore().clearMap();
+ _sp_current_identification_source = nullptr;
+ return true;
}
-bool XtpXpipSaxHandler::endElement_peptide() {
- qDebug() << "endElement_peptide ";
- _current_peptide_sp = _p_project->getPeptideStore().getInstance(_current_peptide_sp);
- _map_peptides.insert(std::pair<QString, PeptideXtpSp>(_current_id, _current_peptide_sp));
-
- if (_sp_labeling_method.get() != nullptr) {
- _current_peptide_sp.get()->applyLabelingMethod(_sp_labeling_method);
+bool
+XtpXpipSaxHandler::endElement_peptide()
+{
+ qDebug() << "endElement_peptide ";
+ _current_peptide_sp =
+ _p_project->getPeptideStore().getInstance(_current_peptide_sp);
+ _map_peptides.insert(
+ std::pair<QString, PeptideXtpSp>(_current_id, _current_peptide_sp));
+
+ if(_sp_labeling_method.get() != nullptr)
+ {
+ _current_peptide_sp.get()->applyLabelingMethod(_sp_labeling_method);
}
- _current_peptide_sp = nullptr;
+ _current_peptide_sp = nullptr;
- _count_peptides++;
- _count_total++;
- return true;
+ _count_peptides++;
+ _count_total++;
+ return true;
}
-bool XtpXpipSaxHandler::endElement_peptide_evidence() {
- qDebug() << "endElement_peptide_evidence begin ";
- _sp_current_peptide_evidence = nullptr;
- _count_peptide_evidences++;
- _count_total++;
+bool
+XtpXpipSaxHandler::endElement_peptide_evidence()
+{
+ qDebug() << "endElement_peptide_evidence begin ";
+ _sp_current_peptide_evidence = nullptr;
+ _count_peptide_evidences++;
+ _count_total++;
- qDebug() << "endElement_peptide_evidence end ";
- return true;
+ qDebug() << "endElement_peptide_evidence end ";
+ return true;
}
-bool XtpXpipSaxHandler::endElement_msrun() {
- qDebug() << "endElement_msrun begin ";
- _sp_msrun = nullptr;
- qDebug() << "endElement_msrun end ";
- return true;
+bool
+XtpXpipSaxHandler::endElement_msrun()
+{
+ qDebug() << "endElement_msrun begin ";
+ _sp_msrun = nullptr;
+ qDebug() << "endElement_msrun end ";
+ return true;
}
-bool XtpXpipSaxHandler::endElement_sequence() {
- qDebug() << "endElement_sequence begin ";
- //if ((_tag_stack.size() > 1) && (_tag_stack[_tag_stack.size() - 1] == "protein")) {
-
- //._sequence.replace(QRegExp("\\*"), "")).removeTranslationStop()
- _sp_current_protein.get()->setSequence(_current_text);
- //}
- //else {
- // XtandemHyperscore hyperscore(_curent_spectrum, _current_peptide_sp, _precision, _ion_list, _max_charge,_refine_spectrum_synthesis);
- //}
- qDebug() << "endElement_sequence end ";
- return true;
-}
-bool XtpXpipSaxHandler::endElement_protein() {
+bool
+XtpXpipSaxHandler::endElement_sequence()
+{
+ qDebug() << "endElement_sequence begin ";
+ // if ((_tag_stack.size() > 1) && (_tag_stack[_tag_stack.size() - 1] ==
+ // "protein")) {
+
+ //._sequence.replace(QRegExp("\\*"), "")).removeTranslationStop()
+ _sp_current_protein.get()->setSequence(_current_text);
+ //}
+ // else {
+ // XtandemHyperscore hyperscore(_curent_spectrum, _current_peptide_sp,
+ // _precision, _ion_list, _max_charge,_refine_spectrum_synthesis);
+ //}
+ qDebug() << "endElement_sequence end ";
+ return true;
+}
+bool
+XtpXpipSaxHandler::endElement_protein()
+{
- _sp_current_protein = _p_project->getProteinStore().getInstance(_sp_current_protein);
- _map_proteins.insert(std::pair<QString, ProteinXtpSp>(_sp_current_protein.get()->getAccession(), _sp_current_protein));
- _sp_current_protein = nullptr;
- return true;
+ _sp_current_protein =
+ _p_project->getProteinStore().getInstance(_sp_current_protein);
+ _map_proteins.insert(std::pair<QString, ProteinXtpSp>(
+ _sp_current_protein.get()->getAccession(), _sp_current_protein));
+ _sp_current_protein = nullptr;
+ return true;
}
-bool XtpXpipSaxHandler::endElement_protein_match() {
- _count_protein_matches++;
- _count_total++;
- _current_identification_group_p->addProteinMatch(_p_protein_match);
- _p_protein_match = nullptr;
- return true;
+bool
+XtpXpipSaxHandler::endElement_protein_match()
+{
+ _count_protein_matches++;
+ _count_total++;
+ _current_identification_group_p->addProteinMatch(_p_protein_match);
+ _p_protein_match = nullptr;
+ return true;
}
-bool XtpXpipSaxHandler::error(const QXmlParseException &exception) {
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
- exception.message());
+bool
+XtpXpipSaxHandler::error(const QXmlParseException &exception)
+{
+ _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+ "%3")
+ .arg(exception.lineNumber())
+ .arg(exception.columnNumber())
+ .arg(exception.message());
- return false;
+ return false;
}
-bool XtpXpipSaxHandler::fatalError(const QXmlParseException &exception) {
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
- exception.message());
- return false;
+bool
+XtpXpipSaxHandler::fatalError(const QXmlParseException &exception)
+{
+ _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+ "%3")
+ .arg(exception.lineNumber())
+ .arg(exception.columnNumber())
+ .arg(exception.message());
+ return false;
}
-QString XtpXpipSaxHandler::errorString() const {
- return _errorStr;
+QString
+XtpXpipSaxHandler::errorString() const
+{
+ return _errorStr;
}
-bool XtpXpipSaxHandler::endDocument() {
- //_p_project->getProteinStore().setRegexpDecoyPattern(_p_project->getProteinStore().getRegexpDecoy().pattern());
- _p_project->updateAutomaticFilters(_automatic_filter_parameters);
- return true;
+bool
+XtpXpipSaxHandler::endDocument()
+{
+ //_p_project->getProteinStore().setRegexpDecoyPattern(_p_project->getProteinStore().getRegexpDecoy().pattern());
+ _p_project->updateAutomaticFilters(_automatic_filter_parameters);
+ return true;
}
-bool XtpXpipSaxHandler::startDocument() {
- return true;
+bool
+XtpXpipSaxHandler::startDocument()
+{
+ return true;
}
-bool XtpXpipSaxHandler::characters(const QString &str) {
- _current_text += str;
- return true;
+bool
+XtpXpipSaxHandler::characters(const QString &str)
+{
+ _current_text += str;
+ return true;
}
-
--
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