From f02ed81ff1f8eb6ee9d7c11e1ddbbb20c55c3392 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 23 Nov 2017 09:24:53 +0100
Subject: [PATCH] PeptideMatchParam renamed to PeptideEvidenceParam
---
src/core/peptideevidence.cpp | 8 +++----
src/core/peptideevidence.h | 8 +++----
src/gui/peptide_detail_view/peptidewindow.cpp | 2 +-
.../peptide_list_view/peptidetablemodel.cpp | 2 +-
.../ptmpeptidetablemodel.cpp | 2 +-
src/input/identificationpwizreader.cpp | 2 +-
src/input/xpipsaxhandler.cpp | 2 +-
src/input/xtandemsaxhandler.cpp | 2 +-
src/input/xtpxpipsaxhandler.cpp | 23 +++++++++++++++++--
src/input/xtpxpipsaxhandler.h | 2 ++
src/output/ods/spectrasheet.cpp | 2 +-
src/output/proticdbml.cpp | 2 +-
src/output/xpip.cpp | 4 ++--
src/utils/types.h | 8 +++----
14 files changed, 45 insertions(+), 24 deletions(-)
diff --git a/src/core/peptideevidence.cpp b/src/core/peptideevidence.cpp
index bd9d6a306..2ca7d6b3e 100644
--- a/src/core/peptideevidence.cpp
+++ b/src/core/peptideevidence.cpp
@@ -75,10 +75,10 @@ void PeptideEvidence::setEvalue(pappso::pappso_double evalue) {
/** \brief set specific parameter value
*/
-void PeptideEvidence::setParam(PeptideMatchParam param, const QVariant& value) {
- _params.insert(std::pair<PeptideMatchParam, QVariant>(param, value));
+void PeptideEvidence::setParam(PeptideEvidenceParam param, const QVariant& value) {
+ _params.insert(std::pair<PeptideEvidenceParam, QVariant>(param, value));
}
-const QVariant PeptideEvidence::getParam(PeptideMatchParam param) const {
+const QVariant PeptideEvidence::getParam(PeptideEvidenceParam param) const {
try {
return _params.at(param);
}
@@ -86,7 +86,7 @@ const QVariant PeptideEvidence::getParam(PeptideMatchParam param) const {
return QVariant();
}
}
-const std::map<PeptideMatchParam, QVariant> & PeptideEvidence::getParamList() const {
+const std::map<PeptideEvidenceParam, QVariant> & PeptideEvidence::getParamList() const {
return _params;
}
diff --git a/src/core/peptideevidence.h b/src/core/peptideevidence.h
index b294cd57f..89f1771b6 100644
--- a/src/core/peptideevidence.h
+++ b/src/core/peptideevidence.h
@@ -77,12 +77,12 @@ public :
/** \brief set specific parameter value
*/
- virtual void setParam(PeptideMatchParam param, const QVariant& value);
+ virtual void setParam(PeptideEvidenceParam param, const QVariant& value);
/** \brief get specific parameter value
*/
- virtual const QVariant getParam(PeptideMatchParam param) const;
+ virtual const QVariant getParam(PeptideEvidenceParam param) const;
- const std::map<PeptideMatchParam, QVariant> & getParamList() const;
+ const std::map<PeptideEvidenceParam, QVariant> & getParamList() const;
void setCharge(unsigned int charge);
@@ -133,7 +133,7 @@ private :
pappso::pappso_double _exp_mass;
unsigned int _charge;
IdentificationDataSource* _p_identification_source = nullptr;
- std::map<PeptideMatchParam, QVariant> _params;
+ std::map<PeptideEvidenceParam, QVariant> _params;
/** @brief manually checked by user (true by default)
*/
diff --git a/src/gui/peptide_detail_view/peptidewindow.cpp b/src/gui/peptide_detail_view/peptidewindow.cpp
index 4f8011af8..c500a83d4 100644
--- a/src/gui/peptide_detail_view/peptidewindow.cpp
+++ b/src/gui/peptide_detail_view/peptidewindow.cpp
@@ -138,7 +138,7 @@ void PeptideWindow::updateDisplay() {
ui->scan_label->setText(QString("%1").arg(_p_peptide_evidence->getScan()));
ui->sample_label->setText(_p_peptide_evidence->getMsRunP()->getSampleName());
ui->modification_label->setText(_p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
- ui->hyperscore_label->setText(_p_peptide_evidence->getParam(PeptideMatchParam::tandem_hyperscore).toString());
+ ui->hyperscore_label->setText(_p_peptide_evidence->getParam(PeptideEvidenceParam::tandem_hyperscore).toString());
ui->evalue_label->setText(QString::number(_p_peptide_evidence->getEvalue(), 'g', 4));
ui->mh_label->setText(QString::number(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(1), 'f', 4));
ui->mz_label->setText(QString::number(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(_p_peptide_evidence->getCharge()), 'f', 4));
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index 8dcdeb6d8..840099458 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -186,7 +186,7 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getDeltaMass());
break;
case (std::int8_t)PeptideListColumn::hyperscore:
- return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getParam(PeptideMatchParam::tandem_hyperscore);
+ return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getParam(PeptideEvidenceParam::tandem_hyperscore);
break;
}
}
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
index a68a0ad09..94f7d00a9 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
@@ -228,7 +228,7 @@ QVariant PtmPeptideTableModel::data(const QModelIndex &index, int role ) const {
return QVariant((qreal) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getDeltaMass());
break;
case (std::int8_t)PtmPeptideListColumn::besthyperscore:
- return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getParam(PeptideMatchParam::tandem_hyperscore);
+ return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getParam(PeptideEvidenceParam::tandem_hyperscore);
break;
case (std::int8_t)PtmPeptideListColumn::bestposition:
for (unsigned int position :_ptm_sample_scan_list.at(row).get()->getBestPtmPositionList(_p_ptm_grouping_experiment)) {
diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index 11680a241..ea35b9797 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -255,7 +255,7 @@ void IdentificationPwizReader::read(
QVariant hyperscore = getQVariantDoubleParam(spid_item.get(), pwiz::cv::MS_X_Tandem_hyperscore);
if (!hyperscore.isNull())
{
- p_peptide_evidence->setParam(PeptideMatchParam::tandem_hyperscore, hyperscore);
+ p_peptide_evidence->setParam(PeptideEvidenceParam::tandem_hyperscore, hyperscore);
}
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index c1ce0f21a..31f249be1 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -263,7 +263,7 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
_p_peptide_evidence->setExperimentalMass(exp_mass);
_current_peptide_match.setStart(attributes.value("start").simplified().toUInt()-1);
_p_peptide_evidence->setCharge(attributes.value("charge").simplified().toUInt());
- _p_peptide_evidence->setParam(PeptideMatchParam::tandem_hyperscore, QVariant( attributes.value("hypercorr").toDouble()));
+ _p_peptide_evidence->setParam(PeptideEvidenceParam::tandem_hyperscore, QVariant( attributes.value("hypercorr").toDouble()));
IdentificationDataSource* p_identification_data_source = _p_project->getIdentificationDataSourceStore().getInstance(attributes.value("sample_file").simplified()).get();
_p_peptide_evidence->setIdentificationDataSource( p_identification_data_source);
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index e24b944d2..2a15bc44b 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -299,7 +299,7 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
_current_peptide_match.setStart(attributes.value("start").simplified().toUInt()-1);
_p_peptide_evidence->setCharge(_charge);
- _p_peptide_evidence->setParam(PeptideMatchParam::tandem_hyperscore, QVariant( attributes.value("hyperscore").toDouble()));
+ _p_peptide_evidence->setParam(PeptideEvidenceParam::tandem_hyperscore, QVariant( attributes.value("hyperscore").toDouble()));
_p_peptide_evidence->setIdentificationDataSource( _p_identification_data_source);
_p_peptide_evidence->setChecked(true);
diff --git a/src/input/xtpxpipsaxhandler.cpp b/src/input/xtpxpipsaxhandler.cpp
index 90520333e..abf30e56d 100644
--- a/src/input/xtpxpipsaxhandler.cpp
+++ b/src/input/xtpxpipsaxhandler.cpp
@@ -74,6 +74,8 @@ bool XtpXpipSaxHandler::startElement(const QString & namespaceURI, const QString
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);
}
//<sample value="P6_08_10"/>
else if (qName == "sample") {
@@ -180,6 +182,23 @@ bool XtpXpipSaxHandler::startElement_description(QXmlAttributes attributes) {
return true;
}
+
+bool XtpXpipSaxHandler::startElement_param(QXmlAttributes attributes) {
+
+ /*
+ <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").toDouble()));
+ }
+
+ qDebug() << "startElement_param end" ;
+ return true;
+}
+
bool XtpXpipSaxHandler::startElement_modification(QXmlAttributes attributes) {
/*
@@ -249,8 +268,8 @@ bool XtpXpipSaxHandler::startElement_peptide_evidence(QXmlAttributes attributes)
_p_peptide_evidence->setExperimentalMass(attributes.value("exp_mass").toDouble());
_p_peptide_evidence->setPeptideXtpSp(_map_peptides.at( attributes.value("peptide_id").simplified()));
- PeptideEvidenceSp sp_peptide_evidence = sp_ident_source.get()->getPeptideEvidenceStore().getInstance(_p_peptide_evidence);
- _map_peptide_evidences.insert(std::pair<QString, PeptideEvidenceSp>(attributes.value("id").simplified(), sp_peptide_evidence));
+ _sp_current_peptide_evidence = sp_ident_source.get()->getPeptideEvidenceStore().getInstance(_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;
}
diff --git a/src/input/xtpxpipsaxhandler.h b/src/input/xtpxpipsaxhandler.h
index 7aff217af..830feef13 100644
--- a/src/input/xtpxpipsaxhandler.h
+++ b/src/input/xtpxpipsaxhandler.h
@@ -78,6 +78,7 @@ private:
bool startElement_identification_source(QXmlAttributes attributes);
bool startElement_modification(QXmlAttributes attributes);
bool startElement_mod(QXmlAttributes attributes);
+ bool startElement_param(QXmlAttributes attributes);
//bool endElement_identification();
bool endElement_sequence();
bool endElement_protein();
@@ -103,6 +104,7 @@ private:
std::map<QString, MsRunSp> _map_msruns;
std::map<QString, IdentificationDataSourceSp> _map_ident_sources;
std::map<QString, PeptideEvidenceSp> _map_peptide_evidences;
+ PeptideEvidenceSp _sp_current_peptide_evidence;
ProteinXtp _current_protein;
PeptideXtpSp _current_peptide_sp;
std::map<QString, PeptideXtpSp> _map_peptides;
diff --git a/src/output/ods/spectrasheet.cpp b/src/output/ods/spectrasheet.cpp
index e4eed6da6..3a815e4c9 100644
--- a/src/output/ods/spectrasheet.cpp
+++ b/src/output/ods/spectrasheet.cpp
@@ -107,7 +107,7 @@ void SpectraSheet::writeBestPeptideEvidence(const GroupingGroup * p_group,const
}
}
_p_writer->writeCell(p_peptide_evidence->getEvalue());
- _p_writer->writeCell(p_peptide_evidence->getParam(PeptideMatchParam::tandem_hyperscore).toDouble());
+ _p_writer->writeCell(p_peptide_evidence->getParam(PeptideEvidenceParam::tandem_hyperscore).toDouble());
}
diff --git a/src/output/proticdbml.cpp b/src/output/proticdbml.cpp
index c70fb5af5..656eb8505 100644
--- a/src/output/proticdbml.cpp
+++ b/src/output/proticdbml.cpp
@@ -487,7 +487,7 @@ void ProticdbMl::writePeptideHit(QString xml_id, ProticPeptideHit & protic_pepti
writeCvParam("PROTICdbO:0000287", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getEvalue()),
"xtandem peptide evalue");
- writeCvParam("PROTICdbO:0000288", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getParam(PeptideMatchParam::tandem_hyperscore).toDouble()),
+ writeCvParam("PROTICdbO:0000288", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getParam(PeptideEvidenceParam::tandem_hyperscore).toDouble()),
"xtandem peptide hyperscore");
}
diff --git a/src/output/xpip.cpp b/src/output/xpip.cpp
index 43d56b1ff..68be493a2 100644
--- a/src/output/xpip.cpp
+++ b/src/output/xpip.cpp
@@ -389,11 +389,11 @@ void Xpip::writePeptideEvidence(const PeptideEvidence * p_peptide_evidence) {
_output_stream->writeAttribute("checked","false");
}
- const std::map<PeptideMatchParam, QVariant> & params = p_peptide_evidence->getParamList();
+ const std::map<PeptideEvidenceParam, QVariant> & params = p_peptide_evidence->getParamList();
//if (params.size() > 0) {
// _output_stream->writeStartElement("stats");
- for (const std::pair<PeptideMatchParam, QVariant> param_pair: params) {
+ for (const std::pair<PeptideEvidenceParam, QVariant> param_pair: params) {
_output_stream->writeStartElement("param");
_output_stream->writeAttribute("key",QString("%1").arg(static_cast<std::int8_t>(param_pair.first)));
_output_stream->writeAttribute("value",param_pair.second.toString());
diff --git a/src/utils/types.h b/src/utils/types.h
index 116c3b0f2..32925ba16 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -50,18 +50,18 @@ enum class IdentificationEngine: std::int8_t {
peptider=3 ///< peptider
};
-/** \def PeptideMatchParam peptide match specific parameters
+/** \def PeptideEvidenceParam peptide evidence specific parameters
*
*/
-enum class PeptideMatchParam: std::int8_t {
+enum class PeptideEvidenceParam: std::int8_t {
tandem_hyperscore=0 ///< X!Tandem hyperscore
};
/** \def IdentificationEngineParam identification engine parameters
*
*/
-enum class IdentificationEngineParam {
- tandem_param ///< X!Tandem xml parameters file
+enum class IdentificationEngineParam: std::int8_t {
+ tandem_param=0 ///< X!Tandem xml parameters file
};
--
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