From 22d2e76e14bc21ba6b5068ddcbe20232392e8a99 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 16 Nov 2017 21:54:50 +0100
Subject: [PATCH] xpip output almost done
---
src/core/peptidematch.cpp | 3 +++
src/core/peptidematch.h | 2 ++
src/output/xpip.cpp | 56 +++++++++++++++++++++++++++++++++++++--
src/output/xpip.h | 1 +
src/utils/types.h | 4 +--
5 files changed, 62 insertions(+), 4 deletions(-)
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index ab3a9377b..4e51d36a7 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -76,6 +76,9 @@ const QVariant PeptideMatch::getParam(PeptideMatchParam param) const {
return QVariant();
}
}
+const std::map<PeptideMatchParam, QVariant> & PeptideMatch::getParamList() const {
+ return _params;
+}
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 0c5ccf6a0..1da789cd2 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -66,6 +66,8 @@ public :
/** \brief get specific parameter value
*/
virtual const QVariant getParam(PeptideMatchParam param) const;
+
+ const std::map<PeptideMatchParam, QVariant> & getParamList() const;
/** @brief set start position of this peptide inside the protein sequence
diff --git a/src/output/xpip.cpp b/src/output/xpip.cpp
index 20f9077c2..0e7df072d 100644
--- a/src/output/xpip.cpp
+++ b/src/output/xpip.cpp
@@ -233,14 +233,20 @@ void Xpip::writeProteinList() {
_output_stream->writeStartElement("protein");
_output_stream->writeAttribute("acc",p_protein->getAccession());
_output_stream->writeAttribute("description",p_protein->getDescription());
- _output_stream->writeAttribute("is_decoy","false");
+
if (p_protein->isDecoy()) {
_output_stream->writeAttribute("is_decoy","true");
}
- _output_stream->writeAttribute("is_contaminant","false");
+ else {
+ _output_stream->writeAttribute("is_decoy","false");
+ }
+
if (p_protein->isContaminant()) {
_output_stream->writeAttribute("is_contaminant","true");
}
+ else {
+ _output_stream->writeAttribute("is_contaminant","false");
+ }
_output_stream->writeStartElement("sequence");
_output_stream->writeCharacters(p_protein->getSequence());
@@ -362,8 +368,54 @@ void Xpip::writeIdentificationGroup(const IdentificationGroup * p_identification
//std::vector<ProteinMatch *> & getProteinMatchList()
_output_stream->writeStartElement("protein_match");
_output_stream->writeAttribute("acc", p_protein_match->getProteinXtpSp().get()->getAccession());
+ if (p_protein_match->isChecked()) {
+ _output_stream->writeAttribute("checked","true");
+ }
+ else {
+ _output_stream->writeAttribute("checked","false");
+ }
+ for (const PeptideMatch * p_peptide_match : p_protein_match->getPeptideMatchList()) {
+ writePeptideMatch(p_peptide_match);
+ }
_output_stream->writeEndElement();// protein_match
}
_output_stream->writeEndElement(); //protein_match_list
qDebug() << "Xpip::writeIdentificationGroup end";
}
+
+void Xpip::writePeptideMatch(const PeptideMatch * p_peptide_match) {
+ qDebug() << "Xpip::writePeptideMatch begin";
+ _output_stream->writeStartElement("peptide_match");
+ _output_stream->writeAttribute("source_id",p_peptide_match->getIdentificationDataSource()->getXmlId());
+ //_output_stream->writeAttribute("ms_id",p_peptide_match->getMsRunP()->getXmlId());
+ _output_stream->writeAttribute("peptide_id",_map_peptides.at( p_peptide_match->getPeptideXtpSp().get()));
+ _output_stream->writeAttribute("scan",QString("%1").arg(p_peptide_match->getScan()));
+ writeDoubleAttribute("rt",p_peptide_match->getRetentionTime());
+ writeDoubleAttribute("evalue",p_peptide_match->getEvalue());
+ writeDoubleAttribute("exp_mass",p_peptide_match->getExperimentalMass());
+ _output_stream->writeAttribute("start",QString("%1").arg(p_peptide_match->getStart()));
+ _output_stream->writeAttribute("charge",QString("%1").arg(p_peptide_match->getCharge()));
+
+ if (p_peptide_match->isChecked()) {
+ _output_stream->writeAttribute("checked","true");
+ }
+ else {
+ _output_stream->writeAttribute("checked","false");
+ }
+
+ const std::map<PeptideMatchParam, QVariant> & params = p_peptide_match->getParamList();
+
+ //if (params.size() > 0) {
+ // _output_stream->writeStartElement("stats");
+ for (const std::pair<PeptideMatchParam, 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());
+ _output_stream->writeEndElement();
+ }
+ // _output_stream->writeEndElement();
+ //}
+
+ _output_stream->writeEndElement(); //protein_match_list
+ qDebug() << "Xpip::writePeptideMatch end";
+}
diff --git a/src/output/xpip.h b/src/output/xpip.h
index 2775fb89b..ec52fb03f 100644
--- a/src/output/xpip.h
+++ b/src/output/xpip.h
@@ -59,6 +59,7 @@ private :
void writeLabelingMethod();
void writeIdentificationGroupList();
void writeIdentificationGroup(const IdentificationGroup * p_identification_group);
+ void writePeptideMatch(const PeptideMatch * p_peptide_match);
QString getPeptideId(std::size_t crc_peptide) const;
diff --git a/src/utils/types.h b/src/utils/types.h
index 68c5507b7..116c3b0f2 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -53,8 +53,8 @@ enum class IdentificationEngine: std::int8_t {
/** \def PeptideMatchParam peptide match specific parameters
*
*/
-enum class PeptideMatchParam {
- tandem_hyperscore ///< X!Tandem hyperscore
+enum class PeptideMatchParam: std::int8_t {
+ tandem_hyperscore=0 ///< X!Tandem hyperscore
};
/** \def IdentificationEngineParam identification engine parameters
--
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