From ee378003d766fbf779c2ccf2a48cfa58fe291f50 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Sat, 29 Apr 2017 14:24:53 +0200
Subject: [PATCH] parameters added to peptide match, hyperscore column in ODS
spectra
---
src/core/peptidematch.cpp | 15 ++++++++++++++-
src/core/peptidematch.h | 10 ++++++++++
src/input/xpipsaxhandler.cpp | 1 +
src/input/xtandemsaxhandler.cpp | 2 ++
src/utils/types.h | 7 +++++++
5 files changed, 34 insertions(+), 1 deletion(-)
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index 2bcde69a5..2c92fc785 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -45,7 +45,20 @@ void PeptideMatch::setRetentionTime(pappso::pappso_double rt) {
void PeptideMatch::setEvalue(pappso::pappso_double evalue) {
_evalue = evalue;
}
-
+
+ /** \brief set specific parameter value
+ */
+void PeptideMatch::setParam(PeptideMatchParam param, const QVariant& value) {
+ _params.insert(std::pair<PeptideMatchParam, QVariant>(param, value));
+}
+const QVariant PeptideMatch::getParam(PeptideMatchParam param) const {
+ try {
+ return _params.at(param);
+ }
+ catch (std::out_of_range) {
+ return QVariant();
+ }
+}
std::size_t PeptideMatch::getHashPeptideMassSample() const {
return PeptideMatch::_hash_fn (QString("%1 %2").arg(_peptide_sp.get()->toAbsoluteString()).arg(_msrunid_sp->getXmlId()).toStdString());
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 42bcbabfe..573442a6a 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -42,6 +42,15 @@ public :
void setEvalue(pappso::pappso_double evalue);
void setExperimentalMass(pappso::pappso_double exp_mass);
+
+ /** \brief set specific parameter value
+ */
+ virtual void setParam(PeptideMatchParam param, const QVariant& value);
+ /** \brief get specific parameter value
+ */
+ virtual const QVariant getParam(PeptideMatchParam param) const;
+
+
/** @brief set start position of this peptide inside the protein sequence
* @param start position in the protein amino acid sequence (starts at 0)
* */
@@ -94,6 +103,7 @@ private :
unsigned int _start=0;
unsigned int _charge;
IdentificationDataSource* _p_identification_source = nullptr;
+ std::map<PeptideMatchParam, QVariant> _params;
/** @brief manually checked by user (true by default)
*/
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index a8f9b20c5..c9288cd27 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -239,6 +239,7 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
_p_peptide_match->setExperimentalMass(exp_mass);
_p_peptide_match->setStart(attributes.value("start").simplified().toUInt()-1);
_p_peptide_match->setCharge(attributes.value("charge").simplified().toUInt());
+ _p_peptide_match->setParam(PeptideMatchParam::tandem_hyperscore, QVariant( attributes.value("hypercorr").toDouble()));
IdentificationDataSource* p_identification_data_source = _p_project->getIdentificationDataSourceStore().getInstance(attributes.value("sample_file").simplified()).get();
_p_peptide_match->setIdentificationDataSource( p_identification_data_source);
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index 58c59468c..acef364d2 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -293,6 +293,8 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
_p_peptide_match->setExperimentalMass(exp_mass);
_p_peptide_match->setStart(attributes.value("start").simplified().toUInt()-1);
_p_peptide_match->setCharge(_charge);
+
+ _p_peptide_match->setParam(PeptideMatchParam::tandem_hyperscore, QVariant( attributes.value("hyperscore").toDouble()));
_p_peptide_match->setIdentificationDataSource( _p_identification_data_source);
_p_peptide_match->setChecked(true);
diff --git a/src/utils/types.h b/src/utils/types.h
index aa354e8cd..7244df994 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -37,6 +37,13 @@ enum class IdentificationEngine {
peptider ///< peptider
};
+/** \def PeptideMatchParam peptide match specific parameters
+ *
+ */
+enum class PeptideMatchParam {
+ tandem_hyperscore ///< X!Tandem hyperscore
+};
+
/** \def IdentificationEngineParam identification engine parameters
*
*/
--
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