diff --git a/src/output/proticdbml.cpp b/src/output/proticdbml.cpp
index 92052431759edcdf03d0562e57637af27132d8b9..eb1a5923bbdcf98ebb80e0c6b2c16b5b44d75237 100644
--- a/src/output/proticdbml.cpp
+++ b/src/output/proticdbml.cpp
@@ -68,7 +68,7 @@ ProticdbMl::~ProticdbMl()
void ProticdbMl::close() {
_output_stream->writeEndDocument();
_output_file->close();
-
+
qDebug() << "ProticdbMl::close end duration = " << _duracel.elapsed() << "ms";
}
@@ -563,91 +563,121 @@ void ProticdbMl::writeMatchs(IdentificationGroup * p_identification) {
_output_stream->writeEndElement();// "matchs");
}
-
-void ProticdbMl::writeMatch(std::vector<const ProteinMatch *> & protein_match_sg_list) {
-
- if (protein_match_sg_list.size() == 0) return;
- //for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
- _output_stream->writeStartElement("match");
-
- // samples
- QStringList sample_name_list;
- for (const PeptideMatch * p_peptide_match: protein_match_sg_list[0]->getPeptideMatchList(ValidationState::grouped)) {
- sample_name_list << p_peptide_match->getMsRunP()->getSampleName();
- }
- sample_name_list = sample_name_list.toSet().toList();
- for (QString sample_name :sample_name_list) {
- _output_stream->writeStartElement("matchSample");
- _output_stream->writeAttribute(
- "sample_id",_sample_to_id[sample_name]);
- _output_stream->writeAttribute("name", sample_name);
- _output_stream->writeEndElement();// "matchSample");
+const QString & ProticdbMl::getPeptideXmlId(const PeptideMatch* p_peptide_match) const {
+ QString peptide_key = getProticPeptideHitKey(p_peptide_match);
+ auto it = _peptidekey_to_id.find(peptide_key);
+ if (it == _peptidekey_to_id.end()) {
+ throw pappso::PappsoException(QObject::tr("Error peptide key %1 not found for peptide match %2 sample=%3 scan=%4 start=%5").arg(peptide_key)
+ .arg(p_peptide_match->getPeptideXtpSp().get()->toString())
+ .arg(p_peptide_match->getMsRunP()->getXmlId())
+ .arg(p_peptide_match->getScan())
+ .arg(p_peptide_match->getStart())
+ );
}
+ return it->second;
- // proteins
- for (const ProteinMatch * p_protein_match: protein_match_sg_list) {
- _output_stream->writeStartElement("proteinHit");
- _output_stream->writeAttribute("sequence_id",QString("%1 %2").arg(p_protein_match->getProteinXtpSp().get()->getAccession()).arg(p_protein_match->getProteinXtpSp().get()->getDescription()));
- // proteinHit.setAttribute("score", "");
- _output_stream->writeAttribute("rank", QString("%1").arg(p_protein_match->getGrpProteinSp().get()->getRank()));
-
- // //cvparam
- writeCvParam("PROTICdbO:0000284",QString("%1").arg(p_protein_match->getProteinXtpSp().get()->getMass()),
- "MW computation");
- // evalue
- writeCvParam("PROTICdbO:0000291", Utils::getXmlDouble(p_protein_match->getLogEvalue())
- , "Xtandem log evalue");
-
- // coverage
- writeCvParam(
- "PROTICdbO:0000285", Utils::getXmlDouble(p_protein_match->getCoverage()),
- "protein coverage");
-
- // [Term]
- // id: PROTICdbO:0000335
- // name: X!TandemPipeline PAI
- writeCvParam("PROTICdbO:0000335",Utils::getXmlDouble(p_protein_match->getPAI()), "PAI");
-
- // [Term]
- // id: PROTICdbO:0000337
- // name: protein group number
- writeCvParam("PROTICdbO:0000337",p_protein_match->getGrpProteinSp().get()->getGroupingId(), "grouping number");
-
- _output_stream->writeEndElement();// "proteinHit");
+}
+const QString & ProticdbMl::getProteinXmlId(const ProteinMatch* p_protein_match) const {
+ auto it = _map_accession2xmlid.find(p_protein_match->getProteinXtpSp().get()->getAccession());
+ if (it == _map_accession2xmlid.end()) {
+ throw pappso::PappsoException(QObject::tr("Error protein accession %1 not found for protein %2")
+ .arg(p_protein_match->getProteinXtpSp().get()->getAccession())
+ .arg(p_protein_match->getProteinXtpSp().get()->getAccession()));
}
+ return it->second;
+}
+void ProticdbMl::writeMatch(std::vector<const ProteinMatch *> & protein_match_sg_list) {
+ try {
+ if (protein_match_sg_list.size() == 0) return;
+ //for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
+ _output_stream->writeStartElement("match");
+
+ // samples
+ QStringList sample_name_list;
+ for (const PeptideMatch * p_peptide_match: protein_match_sg_list[0]->getPeptideMatchList(ValidationState::grouped)) {
+ sample_name_list << p_peptide_match->getMsRunP()->getSampleName();
+ }
+ sample_name_list = sample_name_list.toSet().toList();
+ for (QString sample_name :sample_name_list) {
+ _output_stream->writeStartElement("matchSample");
+ _output_stream->writeAttribute(
+ "sample_id",_sample_to_id[sample_name]);
+ _output_stream->writeAttribute("name", sample_name);
+ _output_stream->writeEndElement();// "matchSample");
+ }
- for (const ProteinMatch * p_protein_match: protein_match_sg_list) {
- //peptides
- for (const PeptideMatch * p_peptide_match: p_protein_match->getPeptideMatchList(ValidationState::grouped)) {
- // peptidesHitRef
- QString peptide_key = getProticPeptideHitKey(p_peptide_match);
- QString peptide_xml_id = _peptidekey_to_id.at(peptide_key);
+ // proteins
+ for (const ProteinMatch * p_protein_match: protein_match_sg_list) {
+ _output_stream->writeStartElement("proteinHit");
+ _output_stream->writeAttribute("sequence_id",QString("%1 %2").arg(p_protein_match->getProteinXtpSp().get()->getAccession()).arg(p_protein_match->getProteinXtpSp().get()->getDescription()));
+ // proteinHit.setAttribute("score", "");
+ _output_stream->writeAttribute("rank", QString("%1").arg(p_protein_match->getGrpProteinSp().get()->getRank()));
+
+ // //cvparam
+ writeCvParam("PROTICdbO:0000284",QString("%1").arg(p_protein_match->getProteinXtpSp().get()->getMass()),
+ "MW computation");
+ // evalue
+ writeCvParam("PROTICdbO:0000291", Utils::getXmlDouble(p_protein_match->getLogEvalue())
+ , "Xtandem log evalue");
+
+ // coverage
+ writeCvParam(
+ "PROTICdbO:0000285", Utils::getXmlDouble(p_protein_match->getCoverage()),
+ "protein coverage");
+
+ // [Term]
+ // id: PROTICdbO:0000335
+ // name: X!TandemPipeline PAI
+ writeCvParam("PROTICdbO:0000335",Utils::getXmlDouble(p_protein_match->getPAI()), "PAI");
+
+ // [Term]
+ // id: PROTICdbO:0000337
+ // name: protein group number
+ writeCvParam("PROTICdbO:0000337",p_protein_match->getGrpProteinSp().get()->getGroupingId(), "grouping number");
+
+ _output_stream->writeEndElement();// "proteinHit");
+ }
- _output_stream->writeStartElement("peptideHitRef");
- _output_stream->writeAttribute("peptide_hit_id", peptide_xml_id);
+ for (const ProteinMatch * p_protein_match: protein_match_sg_list) {
+ //peptides
+ for (const PeptideMatch * p_peptide_match: p_protein_match->getPeptideMatchList(ValidationState::grouped)) {
+ // peptidesHitRef
+ QString peptide_xml_id = getPeptideXmlId(p_peptide_match);
+
+ _output_stream->writeStartElement("peptideHitRef");
+ _output_stream->writeAttribute("peptide_hit_id", peptide_xml_id);
+
+ _output_stream->writeStartElement("fromSeq");
+ _output_stream->writeAttribute(
+ "seq_id", getProteinXmlId(p_protein_match));
+ _output_stream->writeAttribute("start", QString("%1").arg(p_peptide_match->getStart()+1));
+ _output_stream->writeAttribute("stop", QString("%1").arg(p_peptide_match->getStop()+1));
+ QString residue_before_nter = "-";
+ if (p_peptide_match->getStart() > 0) {
+ residue_before_nter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(p_peptide_match->getStart()-1,1);
+ }
+ _output_stream->writeAttribute("residue_before_nter", residue_before_nter);
+ QString residue_after_cter = "-";
+ if (p_peptide_match->getStop() < (p_protein_match->getProteinXtpSp().get()->getSequence().size()-1)) {
+ residue_after_cter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(p_peptide_match->getStop(),1);
+ }
+ _output_stream->writeAttribute("residue_after_cter", residue_after_cter);
- _output_stream->writeStartElement("fromSeq");
- _output_stream->writeAttribute(
- "seq_id",_map_accession2xmlid.at(p_protein_match->getProteinXtpSp().get()->getAccession()));
- _output_stream->writeAttribute("start", QString("%1").arg(p_peptide_match->getStart()+1));
- _output_stream->writeAttribute("stop", QString("%1").arg(p_peptide_match->getStop()+1));
- QString residue_before_nter = "-";
- if (p_peptide_match->getStart() > 0) {
- residue_before_nter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(p_peptide_match->getStart()-1,1);
- }
- _output_stream->writeAttribute("residue_before_nter", residue_before_nter);
- QString residue_after_cter = "-";
- if (p_peptide_match->getStop() < (p_protein_match->getProteinXtpSp().get()->getSequence().size()-1)) {
- residue_after_cter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(p_peptide_match->getStop(),1);
+ _output_stream->writeEndElement();// fromSeq
+ _output_stream->writeEndElement();// peptideHitRef
}
- _output_stream->writeAttribute("residue_after_cter", residue_after_cter);
- _output_stream->writeEndElement();// fromSeq
- _output_stream->writeEndElement();// peptideHitRef
}
-
+ _output_stream->writeEndElement();// "match");
+ }
+ catch (pappso::PappsoException &error)
+ {
+ throw pappso::PappsoException(QObject::tr("Error in ProticdbMl::writeMatch :\n%1").arg(error.qwhat()));
+ }
+ catch (std::exception &error)
+ {
+ throw pappso::PappsoException(QObject::tr("Error in ProticdbMl::writeMatch stdex :\n%1").arg(error.what()));
}
- _output_stream->writeEndElement();// "match");
}
void ProticdbMl::writeOboModif(pappso::AaModificationP mod) {
_output_stream->writeStartElement("cvParam");
diff --git a/src/output/proticdbml.h b/src/output/proticdbml.h
index 65f6bbb06159dab8bdb8747ba58549d3de6a389c..df91fcb066716e9b917ae34249b4e16e98585b00 100644
--- a/src/output/proticdbml.h
+++ b/src/output/proticdbml.h
@@ -66,6 +66,9 @@ private :
void writeMatchs(IdentificationGroup * p_identification);
void writeMatch(std::vector<const ProteinMatch *> & protein_match_sg_list);
+ const QString & getPeptideXmlId(const PeptideMatch* p_peptide_match) const;
+ const QString & getProteinXmlId(const ProteinMatch* p_protein_match) const;
+
private :
QFile * _output_file;
QXmlStreamWriter * _output_stream;
diff --git a/src/resources/catalog_label.xml b/src/resources/catalog_label.xml
index 0da0a47b47dcc5088974790c38226fa2e18b6295..c3cdb178ce9ce0021a27e98a497aabeaed74a521 100644
--- a/src/resources/catalog_label.xml
+++ b/src/resources/catalog_label.xml
@@ -12,5 +12,4 @@
<mod at="Nter" value="36.0" acc="MOD:00638"/>
<mod at="K" value="36.0" acc="MOD:00638"/>
</isotope_label>
- </isotope_label_list>
</catalog>