From 86b2c9df5d737166481213b39fab2c6e9d238741 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Tue, 19 Jun 2018 15:26:55 +0200
Subject: [PATCH] new: store identification engine in peptide evidence
---
src/core/peptideevidence.cpp | 6 ++++++
src/core/peptideevidence.h | 6 ++++++
src/input/pepxmlsaxhandler.cpp | 21 ++++++++++++++++++---
src/input/xtpxpipsaxhandler.cpp | 1 +
src/output/xpip.cpp | 1 +
src/utils/types.h | 4 ++++
6 files changed, 36 insertions(+), 3 deletions(-)
diff --git a/src/core/peptideevidence.cpp b/src/core/peptideevidence.cpp
index 5cfd69cf4..be909da73 100644
--- a/src/core/peptideevidence.cpp
+++ b/src/core/peptideevidence.cpp
@@ -102,6 +102,12 @@ PeptideEvidence::setIdentificationEngine(
_identification_engine = identification_engine;
}
+IdentificationEngine
+PeptideEvidence::getIdentificationEngine() const
+{
+ return _identification_engine;
+}
+
/** \brief set specific parameter value
*/
void
diff --git a/src/core/peptideevidence.h b/src/core/peptideevidence.h
index 628aaf09e..acda0872c 100644
--- a/src/core/peptideevidence.h
+++ b/src/core/peptideevidence.h
@@ -99,6 +99,12 @@ public :
* by default, this is the identification engine of the datasource
*/
void setIdentificationEngine(IdentificationEngine identification_engine);
+
+ /** @brief get the identification engine
+ * by default, this is the identification engine of the datasource
+ */
+ IdentificationEngine getIdentificationEngine() const;
+
void setChecked(bool arg1);
bool isChecked() const;
bool isValid() const;
diff --git a/src/input/pepxmlsaxhandler.cpp b/src/input/pepxmlsaxhandler.cpp
index a031df10c..05090d158 100644
--- a/src/input/pepxmlsaxhandler.cpp
+++ b/src/input/pepxmlsaxhandler.cpp
@@ -297,7 +297,7 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
//<alternative_protein protein="sp|P46784|RS10B_YEAST" protein_descr="40S
// ribosomal protein S10-B OS=Saccharomyces cerevisiae (strain ATCC 204508
-// \
+// \
//S288c) GN=RPS10B PE=1 SV=1" num_tol_term="2" peptide_prev_aa="K"
// peptide_next_aa="N"/>
bool
@@ -482,18 +482,33 @@ PepXmlSaxHandler::startElement_search_score(QXmlAttributes attributes)
if(name == "expect")
{
_p_peptide_evidence->setEvalue(valueStr.simplified().toDouble());
+ if(_p_peptide_evidence->getIdentificationEngine() ==
+ IdentificationEngine::OMSSA)
+ {
+ _p_peptide_evidence->setParam(PeptideEvidenceParam::omssa_evalue,
+ valueStr.simplified().toDouble());
+ }
}
- if(name == "EValue")
+ else if(name == "EValue")
{
_p_peptide_evidence->setEvalue(valueStr.simplified().toDouble());
}
// <search_score name="hyperscore" value="232"/>
- if(name == "hyperscore")
+ else if(name == "hyperscore")
{
_p_peptide_evidence->setParam(
PeptideEvidenceParam::tandem_hyperscore,
QVariant(attributes.value("hyperscore").toDouble()));
}
+ else if(name == "pvalue")
+ {
+ if(_p_peptide_evidence->getIdentificationEngine() ==
+ IdentificationEngine::OMSSA)
+ {
+ _p_peptide_evidence->setParam(PeptideEvidenceParam::omssa_pvalue,
+ valueStr.simplified().toDouble());
+ }
+ }
}
return is_ok;
}
diff --git a/src/input/xtpxpipsaxhandler.cpp b/src/input/xtpxpipsaxhandler.cpp
index 3d9fa5c31..596759c86 100644
--- a/src/input/xtpxpipsaxhandler.cpp
+++ b/src/input/xtpxpipsaxhandler.cpp
@@ -423,6 +423,7 @@ bool XtpXpipSaxHandler::startElement_peptide_evidence(QXmlAttributes attributes)
_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());
diff --git a/src/output/xpip.cpp b/src/output/xpip.cpp
index ce0ecf20b..5a7761cd3 100644
--- a/src/output/xpip.cpp
+++ b/src/output/xpip.cpp
@@ -438,6 +438,7 @@ void Xpip::writePeptideEvidence(const PeptideEvidence * p_peptide_evidence) {
qDebug() << "Xpip::writePeptideEvidence scan";
_output_stream->writeAttribute("scan",QString("%1").arg(p_peptide_evidence->getScan()));
writeDoubleAttribute("rt",p_peptide_evidence->getRetentionTime());
+ _output_stream->writeAttribute("eng",QString("%1").arg((unsigned int) p_peptide_evidence->getIdentificationEngine()));
writeDoubleAttribute("evalue",p_peptide_evidence->getEvalue());
writeDoubleAttribute("exp_mass",p_peptide_evidence->getExperimentalMass());
_output_stream->writeAttribute("charge",QString("%1").arg(p_peptide_evidence->getCharge()));
diff --git a/src/utils/types.h b/src/utils/types.h
index 1a193327c..9c7ed47c5 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -73,6 +73,10 @@ enum class PeptideEvidenceParam : std::int8_t
3, ///< PSI-MS MS:1001172 mascot:expectation value 2.42102904673618e-006
peptide_prophet_probability = 4, ///< no PSI MS description
peptide_inter_prophet_probability = 5, ///< no PSI MS description
+ omssa_evalue = 6, ///< MS:1001328 "OMSSA E-value." [PSI:PI]
+ omssa_pvalue = 7, ///< MS:1001329 "OMSSA p-value." [PSI:PI]
+
+
};
/** \def IdentificationEngineParam identification engine parameters
--
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