diff --git a/src/output/proticdbml.cpp b/src/output/proticdbml.cpp
index 371b400b55cc3f60d262b2bfa6449928e01ee553..22ebf1fb7ea356b0edfa51c7e1d64c9f7cd37391 100644
--- a/src/output/proticdbml.cpp
+++ b/src/output/proticdbml.cpp
@@ -392,10 +392,10 @@ void ProticdbMl::writeIdentificationRun(IdentificationGroup * p_identification)
//}
writeCvParam("PROTICdbO:0000325", QString("%1").arg(_sp_project.get()->getAutomaticFilterParameters().getFilterMinimumPeptidePerMatch()),
- "X!TandemPipeline filter on minimal number of peptide per protein");
+ "X!TandemPipeline filter on minimal number of peptide per protein");
writeCvParam("PROTICdbO:0000324", QString("%1").arg(_sp_project.get()->getAutomaticFilterParameters().getFilterPeptideEvalue()),
- "X!TandemPipeline filter on peptide evalue");
+ "X!TandemPipeline filter on peptide evalue");
// TODO write database filter
// this.writeCvParam("PROTICdbO:0000324", ""
@@ -410,173 +410,46 @@ void ProticdbMl::writeIdentificationRun(IdentificationGroup * p_identification)
_output_stream->writeEndElement();// description
}
-private void writePeptideHit(Peptide pep, Group group,
- PeptideMass peptideMass) throws XMLStreamException, MSMSException {
- if (peptideMass == null) {
- String message = "peptideMass == null";
- logger.error(message);
- throw new MSMSException(message);
- }
-
- String pep_hit_id = "pep" + pepSampleScanCle2xmlId.size();
- // param par default
- writer.writeStartElement("peptideHit");
- writer.writeAttribute("calc_mr", "" + (pep.get_mhplus_theo() - 1.00794));
- double exp_mz = (pep.get_mhplus_obser() + (1.00794 * (pep.getCharge() - 1)))
- / pep.getCharge();
- writer.writeAttribute("exp_mz", "" + exp_mz);
- writer.writeAttribute("delta", "" + pep.get_deltamass());
- writer.writeAttribute("exp_mr", "" + (pep.get_mhplus_obser() - 1.00794));
- writer.writeAttribute("acq_number", "" + pep.get_scan());
- writer.writeAttribute("ms_run_id",
- "" + msrun_to_id.get(pep.get_sample()));
- writer.writeAttribute("id", pep_hit_id);
- writer.writeAttribute("exp_z", "" + pep.getCharge());
-
- this.writeCvParam("PROTICdbO:0000339",
- Utils.getPappsoPeptideMassId(group, peptideMass),
- "peptide mass id");
-
- if (xtpExperimentType.equals("phospho")) {
- this.writeCvParam("PROTICdbO:0000349",
- Utils.getPappsoPhosphoPeptideMassId(group, peptideMass),
- "phosphopeptide mass id");
+void ProticdbMl::writepeptideHits(IdentificationGroup * p_identification) {
+ _output_stream->writeStartElement("peptideHits");
+ for (std::pair <unsigned int, GroupingGroupSp > group_pair : p_identification->getGroupStore().getGroupMap()) {
+ writepeptideHitsbyGroup(group_pair.second);
}
-
- // pep.getMsRun().
- IdentificationDataSource idDataSource = pep
- .getIdentificationDataSource();
- if (idDataSource.getClass().equals(IdentificationXtandemFile.class)) {
- // cvparam specifique xtandem
-
- this.writeCvParam("PROTICdbO:0000287", "" + pep.get_evalue(),
- "xtandem peptide evalue");
-
- this.writeCvParam("PROTICdbO:0000288", "" + pep.get_hypercorr(),
- "xtandem peptide hyperscore");
- }
-
- this.writeCvParam("PROTICdbO:0000289",
- "" + pep.getRetentionTimeInMinutes(),
- "xtandem peptide retention time");
- /*
- * writer.writeStartElement("cvParam"); writer.writeAttribute("value",
- * "" + pep.get_RT()); writer.writeAttribute("name",
- * "xtandem peptide retention time"); writer.writeAttribute("cvLabel",
- * "PROTICdbO"); writer.writeAttribute("accession",
- * "PROTICdbO:0000289"); writer.writeEndElement();// cvParam
- */
-
- // Element cvParam4 = doc.createElement("cvParam");
- // cvParam4.setAttribute("value", "" + pep.get_post());
- // cvParam4.setAttribute("name", "xtandem peptide post");
- // cvParam4.setAttribute("cvLabel", "PROTICdbO");
- // cvParam4.setAttribute("accession", "PROTICdbO:00000XX");
- // peptideHit.appendChild(cvParam4);
- //
- // Element cvParam5 = doc.createElement("cvParam");
- // cvParam5.setAttribute("value", "" + pep.get_pre());
- // cvParam5.setAttribute("name", "xtandem peptide pre");
- // cvParam5.setAttribute("cvLabel", "PROTICdbO");
- // cvParam5.setAttribute("accession", "PROTICdbO:00000XX");
- // peptideHit.appendChild(cvParam5);
-
- // sequences avec les modifs
- writer.writeStartElement("pepSeq");
- writer.writeStartElement("peptide");
- writer.writeCharacters("" + pep.getSequence());
- writer.writeEndElement();// peptide
- if (pep.get_Modifs().size() != 0) {
- this.writePtms(pep.get_Modifs());
- }
- writer.writeEndElement();// pepSeq
-
- pepSampleScanCle2xmlId.put(pep.get_sample_scan_sequencepeptide_cle(),
- pep_hit_id);
- writer.writeEndElement();// peptideHit
-}
-
-private void writePtms(ArrayList<Modifs> mods) throws XMLStreamException {
- writer.writeStartElement("ptms");
- for (Modifs mod : mods) {
- writer.writeStartElement("ptm");
- writer.writeAttribute("diff_mono", "" + mod.get_modvalue());
- writer.writeAttribute("position", "" + mod.get_posi());
- writer.writeAttribute("aa", "" + mod.get_AA());
- try {
- this.writeOboModif(mod.getPsiMod());
- } catch (MSMSException e) {
- String message = "error writing OBO modif : " + e.getMessage();
- logger.warn(message);
- }
- writer.writeEndElement();// ptm
-
- }
- writer.writeEndElement();// ptms
+ _output_stream->writeEndElement();// "peptideHits");
}
-void ProticdbMl::writeOboModif(pappso::AaModificationP mod) {
- _output_stream->writeStartElement("cvParam");
- _output_stream->writeAttribute("name", mod->getName());
- _output_stream->writeAttribute("cvLabel", "MOD");
- _output_stream->writeAttribute("accession", mod->getAccession());
- _output_stream->writeEndElement();// cvParam
+QString getProticPeptideHitKey(PeptideMatch * p_peptide_match) {
+ return (QString ("%1 %2 %3").arg(p_peptide_match->getHashSampleScan()).arg(p_peptide_match->getPeptideXtpSp().get()->toAbsoluteString()).arg(p_peptide_match->getIdentificationDataSource()->getResourceName()));
}
-private void writepeptideHits(Identification identification)
-throws MSMSException {
- try {
- writer.writeStartElement("peptideHits");
- for (Group group : identification.getGrouping().getGroupList()) {
- // generating peptide numbers
- PeptideMassSet pepMassSet = new PeptideMassSet();
+struct ProticPeptideHit {
+ bool operator ==(const ProticPeptideHit &other) const {
+ return (key == other.key);
+ };
+ /** key = getProticPeptideHitKey
+ * */
+ QString key;
+ PeptideMatch * peptide_match;
+};
- Hashtable<String, PeptideMass> pepSampleScanCle2peptideMass;
- if (this.xtpExperimentType.equals("phospho")) {
- pepSampleScanCle2peptideMass = pepMassSet
- .numberingPhosphoGetSampleScanCle2peptideMass(group);
+void ProticdbMl::writepeptideHitsbyGroup(GroupingGroup * p_group) {
- } else {
- pepSampleScanCle2peptideMass = pepMassSet
- .numberingGetSampleScanCle2peptideMass(group);
- }
-
- for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
- for (HashSampleScanSetProt hashProt : sg
- .getHashSampleScanSetProtList()) {
-
- ArrayList<Peptide> peptideList = null;
- if (this.xtpExperimentType.equals("phospho")) {
- peptideList = ((Match) hashProt.getGrpProtMatch())
- .getValidPeptideInPhosphoIsland((HashSampleScanSetPhospho) hashProt);
- } else {
- peptideList = ((Match) hashProt.getGrpProtMatch())
- .get_valid_peptides();
- }
-
- for (Peptide pep : peptideList) {
+ std::vector <ProticPeptideHit> protic_peptide_hit_list;
- if (pepSampleScanCle2xmlId.containsKey(pep
- .get_sample_scan_sequencepeptide_cle()) == false) {
-
- writePeptideHit(
- pep,
- group,
- pepSampleScanCle2peptideMass.get(pep
- .get_sample_scan_sequencepeptide_cle()));
-
- }
- }
- }
- }
- }
- writer.writeEndElement();// "peptideHits");
- } catch (Exception e) {
- String message = "error writing peptideHits in ProticDbMl \n"
- + e.getMessage();
- logger.error(message);
- throw new MSMSException(message);
+ for (PeptideMatch* p_peptide_match : p_group->getPeptideMatchList()) {
+ protic_peptide_hit_list.push_back(ProticPeptideHit(getProticPeptideHitKey(p_peptide_match), p_peptide_match));
+ }
+ std::sort(protic_peptide_hit_list.begin(),protic_peptide_hit_list.end(),[](const ProticPeptideHit & first, const ProticPeptideHit & second) {
+ return (first.key < second.key) ;
+ });
+ auto last = std::unique(protic_peptide_hit_list.begin(), protic_peptide_hit_list.end());
+ protic_peptide_hit_list.erase(last, protic_peptide_hit_list.end());
+
+ for (ProticPeptideHit & protic_peptide_hit :protic_peptide_hit_list) {
+ QString xml_id = QString("pep%1").arg(_peptidekey_to_id.size()+1);
+ writePeptideHit(xml_id, protic_peptide_hit);
+ _peptidekey_to_id.insert(std::pair<QString, QString>(protic_peptide_hit.key, xml_id));
}
}
@@ -748,6 +621,120 @@ throws MSMSException {
}
}
+void ProticdbMl::writePeptideHit(Peptide pep, Group group,
+ PeptideMass peptideMass) throws XMLStreamException, MSMSException {
+
+ if (peptideMass == null) {
+ String message = "peptideMass == null";
+ logger.error(message);
+ throw new MSMSException(message);
+ }
+
+ String pep_hit_id = "pep" + pepSampleScanCle2xmlId.size();
+ // param par default
+ writer.writeStartElement("peptideHit");
+ writer.writeAttribute("calc_mr", "" + (pep.get_mhplus_theo() - 1.00794));
+ double exp_mz = (pep.get_mhplus_obser() + (1.00794 * (pep.getCharge() - 1)))
+ / pep.getCharge();
+ writer.writeAttribute("exp_mz", "" + exp_mz);
+ writer.writeAttribute("delta", "" + pep.get_deltamass());
+ writer.writeAttribute("exp_mr", "" + (pep.get_mhplus_obser() - 1.00794));
+ writer.writeAttribute("acq_number", "" + pep.get_scan());
+ writer.writeAttribute("ms_run_id",
+ "" + msrun_to_id.get(pep.get_sample()));
+ writer.writeAttribute("id", pep_hit_id);
+ writer.writeAttribute("exp_z", "" + pep.getCharge());
+
+ this.writeCvParam("PROTICdbO:0000339",
+ Utils.getPappsoPeptideMassId(group, peptideMass),
+ "peptide mass id");
+
+ if (xtpExperimentType.equals("phospho")) {
+ this.writeCvParam("PROTICdbO:0000349",
+ Utils.getPappsoPhosphoPeptideMassId(group, peptideMass),
+ "phosphopeptide mass id");
+ }
+
+ // pep.getMsRun().
+ IdentificationDataSource idDataSource = pep
+ .getIdentificationDataSource();
+ if (idDataSource.getClass().equals(IdentificationXtandemFile.class)) {
+ // cvparam specifique xtandem
+
+ this.writeCvParam("PROTICdbO:0000287", "" + pep.get_evalue(),
+ "xtandem peptide evalue");
+
+ this.writeCvParam("PROTICdbO:0000288", "" + pep.get_hypercorr(),
+ "xtandem peptide hyperscore");
+ }
+
+ this.writeCvParam("PROTICdbO:0000289",
+ "" + pep.getRetentionTimeInMinutes(),
+ "xtandem peptide retention time");
+ /*
+ * writer.writeStartElement("cvParam"); writer.writeAttribute("value",
+ * "" + pep.get_RT()); writer.writeAttribute("name",
+ * "xtandem peptide retention time"); writer.writeAttribute("cvLabel",
+ * "PROTICdbO"); writer.writeAttribute("accession",
+ * "PROTICdbO:0000289"); writer.writeEndElement();// cvParam
+ */
+
+ // Element cvParam4 = doc.createElement("cvParam");
+ // cvParam4.setAttribute("value", "" + pep.get_post());
+ // cvParam4.setAttribute("name", "xtandem peptide post");
+ // cvParam4.setAttribute("cvLabel", "PROTICdbO");
+ // cvParam4.setAttribute("accession", "PROTICdbO:00000XX");
+ // peptideHit.appendChild(cvParam4);
+ //
+ // Element cvParam5 = doc.createElement("cvParam");
+ // cvParam5.setAttribute("value", "" + pep.get_pre());
+ // cvParam5.setAttribute("name", "xtandem peptide pre");
+ // cvParam5.setAttribute("cvLabel", "PROTICdbO");
+ // cvParam5.setAttribute("accession", "PROTICdbO:00000XX");
+ // peptideHit.appendChild(cvParam5);
+
+ // sequences avec les modifs
+ writer.writeStartElement("pepSeq");
+ writer.writeStartElement("peptide");
+ writer.writeCharacters("" + pep.getSequence());
+ writer.writeEndElement();// peptide
+ if (pep.get_Modifs().size() != 0) {
+ this.writePtms(pep.get_Modifs());
+ }
+ writer.writeEndElement();// pepSeq
+
+ pepSampleScanCle2xmlId.put(pep.get_sample_scan_sequencepeptide_cle(),
+ pep_hit_id);
+ writer.writeEndElement();// peptideHit
+}
+
+private void writePtms(ArrayList<Modifs> mods) throws XMLStreamException {
+ writer.writeStartElement("ptms");
+ for (Modifs mod : mods) {
+ writer.writeStartElement("ptm");
+ writer.writeAttribute("diff_mono", "" + mod.get_modvalue());
+ writer.writeAttribute("position", "" + mod.get_posi());
+ writer.writeAttribute("aa", "" + mod.get_AA());
+ try {
+ this.writeOboModif(mod.getPsiMod());
+ } catch (MSMSException e) {
+ String message = "error writing OBO modif : " + e.getMessage();
+ logger.warn(message);
+ }
+ writer.writeEndElement();// ptm
+
+ }
+ writer.writeEndElement();// ptms
+}
+
+void ProticdbMl::writeOboModif(pappso::AaModificationP mod) {
+ _output_stream->writeStartElement("cvParam");
+ _output_stream->writeAttribute("name", mod->getName());
+ _output_stream->writeAttribute("cvLabel", "MOD");
+ _output_stream->writeAttribute("accession", mod->getAccession());
+ _output_stream->writeEndElement();// cvParam
+}
+
void ProticdbMl::writeCvParam(QString acc, QString value, QString description) {
_output_stream->writeStartElement("cvParam");
diff --git a/src/output/proticdbml.h b/src/output/proticdbml.h
index d1c58b4293f9dc16fd6b817bc439eb89da8f6917..98f9ae9cefbdeb61feb787e14a0c6c006f3daf74 100644
--- a/src/output/proticdbml.h
+++ b/src/output/proticdbml.h
@@ -57,6 +57,8 @@ private :
void writeMsRuns();
void writeIdentificationRun(IdentificationGroup * p_identification);
void writeIdentificationDataSource(IdentificationDataSource * p_identification_data_source);
+ void writepeptideHits(IdentificationGroup * p_identification);
+ void writepeptideHitsbyGroup(GroupingGroup * p_group);
private :
QFile * _output_file;
@@ -66,6 +68,7 @@ private :
QTime _duracel;
std::map<QString, QString> _map_accession2xmlid;
std::map<QString, QString> _sample_to_id;
+ std::map<QString, QString> _peptidekey_to_id;
};
#endif // PROTICDBML_H