From 9613d0152a9784a6e0612f3ff727832ea31a346d Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Thu, 18 May 2017 22:39:26 +0200
Subject: [PATCH] WIP: writing proticdbml
---
src/core/peptidematch.h | 38 +--
src/output/proticdbml.cpp | 497 +++++++++++++++++++-------------------
src/output/proticdbml.h | 5 +
src/utils/utils.cpp | 3 +
src/utils/utils.h | 1 +
5 files changed, 273 insertions(+), 271 deletions(-)
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 783c73cbf..ed9680c5a 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -46,19 +46,19 @@ public :
*/
pappso::pappso_double getExperimentalMass() const;
- /** @brief get experimental mz of this peptide
- * @return the real mass measured (precuror mass) by the spectrometer
- */
+ /** @brief get experimental mz of this peptide
+ * @return the real mass measured (precuror mass) by the spectrometer
+ */
pappso::pappso_double getExperimentalMz() const;
-
+
/** @brief set experimental mass of this peptide
* @arg exp_mass the computed mass given the precursor measured mass and the deduced peptide charge
*/
void setExperimentalMass(pappso::pappso_double exp_mass);
-
-
-
+
+
+
/** \brief set specific parameter value
*/
virtual void setParam(PeptideMatchParam param, const QVariant& value);
@@ -66,14 +66,14 @@ public :
*/
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)
- * */
+
+ /** @brief set start position of this peptide inside the protein sequence
+ * @param start position in the protein amino acid sequence (starts at 0)
+ * */
void setStart(unsigned int start);
-/** @brief get start position of this peptide inside the protein sequence
- * @return start position in the protein amino acid sequence (starts at 0)
- * */
+ /** @brief get start position of this peptide inside the protein sequence
+ * @return start position in the protein amino acid sequence (starts at 0)
+ * */
unsigned int getStart() const;
void setCharge(unsigned int charge);
void setPeptideXtpSp (PeptideXtpSp peptide);
@@ -91,19 +91,19 @@ public :
unsigned int getCharge() const;
const PeptideXtpSp & getPeptideXtpSp() const;
pappso::pappso_double getEvalue() const;
-
+
void setGrpPeptideSp(const pappso::GrpPeptideSp & sp_grp_peptide);
const pappso::GrpPeptideSp & getGrpPeptideSp() const;
- /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
- * */
+ /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
+ * */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
-
+
/** @brief get delta between theoretical mhplus mass and mhplus experimental mass
* theoretical mhplus mass - mhplus experimental mass
*/
pappso::mz getDeltaMass() const;
-
+
ValidationState getValidationState() const;
private :
diff --git a/src/output/proticdbml.cpp b/src/output/proticdbml.cpp
index 22ebf1fb7..a0b38052f 100644
--- a/src/output/proticdbml.cpp
+++ b/src/output/proticdbml.cpp
@@ -34,6 +34,7 @@
#include <pappsomspp/amino_acid/Aa.h>
#include "../core/msrun.h"
#include "../config.h"
+#include "../utils/utils.h"
ProticdbMl::ProticdbMl(const QString & out_filename)
{
@@ -453,280 +454,272 @@ void ProticdbMl::writepeptideHitsbyGroup(GroupingGroup * p_group) {
}
}
-private void writeMatchs(Identification identification)
-throws MSMSException {
- try {
- writer.writeStartElement("matchs");
- for (Group group : identification.getGrouping().getGroupList()) {
- for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
- writer.writeStartElement("match");
-
- // echantillons
- Hashtable<String, String> view = new Hashtable<String, String>();
- for (HashSampleScanSetProt hashProt : sg
- .getHashSampleScanSetProtList()) {
- Match match = (Match) hashProt.getGrpProtMatch();
- for (MsRun sample : match.get_sample_matchs()) {
- if (!view.containsKey(sample.getSampleName())) {
- writer.writeStartElement("matchSample");
- writer.writeAttribute(
- "sample_id",
- ""
- + sample_to_id.get(sample
- .getSampleName()));
- String name = sample.getSampleName();
- name = name.replaceAll(".xml", "");
- writer.writeAttribute("name", "" + name);
- view.put(sample.getSampleName(), "ok");
- writer.writeEndElement();// "matchSample");
- }
- }
- }
- // proteins
- int k = 1;
- for (HashSampleScanSetProt hashProt : sg
- .getHashSampleScanSetProtList()) {
- writer.writeStartElement("proteinHit");
- Protein prot = (Protein) hashProt.getGrpProtMatch()
- .getGrpProtein();
- writer.writeAttribute("sequence_id",
- "" + prot_to_id.get(prot.get_description()));
- // proteinHit.setAttribute("score", "");
- writer.writeAttribute("rank", "" + k);
-
- // //cvparam
- this.writeCvParam("PROTICdbO:0000284",
- "" + prot.get_mw(),
- "MW determination by Benuch");
- /*
- * writer.writeStartElement("cvParam");
- * writer.writeAttribute("value", "" + prot.get_mw());
- * writer.writeAttribute("name",
- * "MW determination by Benuch");
- * writer.writeAttribute("cvLabel", "PROTICdbO");
- * writer.writeAttribute("accession",
- * "PROTICdbO:0000284"); writer.writeEndElement();//
- * cvParam
- */
- // evalue
- MsRunSet samples = ((Match) hashProt.getGrpProtMatch())
- .get_sample_matchs();
- this.writeCvParam("PROTICdbO:0000291",
- "" + prot.get_evalue(), "Xtandem log evalue");
- /*
- * writer.writeStartElement("cvParam");
- * writer.writeAttribute("value", "" +
- * prot.get_evalue());
- *
- * writer.writeAttribute("name", "Xtandem log evalue");
- * writer.writeAttribute("cvLabel", "PROTICdbO");
- * writer.writeAttribute("accession",
- * "PROTICdbO:0000291"); writer.writeEndElement();//
- * cvParam
- */
-
- // coverage
- if (samples.size() == 1) {
- this.writeCvParam(
- "PROTICdbO:0000285",
- ""
- + ((Match) hashProt
- .getGrpProtMatch())
- .get_coverage(),
- "protein coverage");
- }
- // [Term]
- // id: PROTICdbO:0000335
- // name: X!TandemPipeline PAI
- this.writeCvParam("PROTICdbO:0000335",
- "" + hashProt.getPAI(), "PAI");
-
- // [Term]
- // id: PROTICdbO:0000337
- // name: protein group number
- String pappsoGroupingNumber = Utils
- .getPappsoGroupingNumber(group, sg, k);
- if (pappsoGroupingNumber != null) {
- this.writeCvParam("PROTICdbO:0000337",
- pappsoGroupingNumber, "grouping number");
- }
+void ProticdbMl::writePeptideHit(QString xml_id, ProticPeptideHit & protic_peptide_hit) {
- writer.writeEndElement();// "proteinHit");
- k++;
- }
- for (HashSampleScanSetProt hashProt : sg
- .getHashSampleScanSetProtList()) {
- Protein prot2 = (Protein) hashProt.getGrpProtMatch()
- .getGrpProtein();
- // peptidesHitRef
-
- ArrayList<Peptide> peptideList = null;
- if (this.xtpExperimentType.equals("phospho")) {
- peptideList = ((Match) hashProt.getGrpProtMatch())
- .getValidPeptideInPhosphoIsland((HashSampleScanSetPhospho) hashProt);
- } else {
- peptideList = ((Match) hashProt.getGrpProtMatch())
- .get_valid_peptides();
- }
+ // param par default
+ _output_stream->writeStartElement("peptideHit");
+ _output_stream->writeAttribute("calc_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match->setPeptideXtpSp().get()->getMass()));
+ _output_stream->writeAttribute("exp_mz", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getExperimentalMz()));
+ _output_stream->writeAttribute("delta", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getDeltaMass()));
+ _output_stream->writeAttribute("exp_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getExperimentalMz()- pappso::MHPLUS));
+ _output_stream->writeAttribute("acq_number", QString ("%1").arg(protic_peptide_hit.peptide_match->getScan()));
+ _output_stream->writeAttribute("ms_run_id", protic_peptide_hit.peptide_match->getMsRunP()->getXmlId());
+ _output_stream->writeAttribute("id", xml_id);
+ _output_stream->writeAttribute("exp_z", QString ("%1").arg(protic_peptide_hit.peptide_match->getCharge()));
+
+ writeCvParam("PROTICdbO:0000339",protic_peptide_hit.peptide_match->setGrpPeptideSp().get()->getGroupingId(),
+ "peptide mass id");
+ /*
+ if (xtpExperimentType.equals("phospho")) {
+ this.writeCvParam("PROTICdbO:0000349",
+ Utils.getPappsoPhosphoPeptideMassId(group, peptideMass),
+ "phosphopeptide mass id");
+ }
+ */
+ // pep.getMsRun().
+ IdentificationEngine identification_engine = protic_peptide_hit.peptide_match->getIdentificationDataSource()->getIdentificationEngine();
+ if (identification_engine == IdentificationEngine::XTandem) {
+ // cvparam specifique xtandem
- for (Peptide pep : peptideList) {
- // for (Peptide pep : ((Match)
- // hashProt.getGrpProtMatch())
- // .get_peptide_order_inclus_redon()) {
- String xmlId = pepSampleScanCle2xmlId.get(pep
- .get_sample_scan_sequencepeptide_cle());
- if (xmlId == null) {
- String message = "the xml of peptide "
- + pep.get_sample_scan_sequencepeptide_cle()
- + " is not known in pepSampleScanCle2xmlId";
- logger.debug(message);
- throw new Exception(message);
- }
- writer.writeStartElement("peptideHitRef");
- writer.writeAttribute("peptide_hit_id", "" + xmlId);
-
- writer.writeStartElement("fromSeq");
- writer.writeAttribute(
- "seq_id",
- ""
- + prot_to_id.get(prot2
- .get_description()));
- writer.writeAttribute("start", "" + pep.get_start());
- writer.writeAttribute("stop", "" + pep.get_stop());
- String res1 = pep.get_pre();
- res1 = res1.replaceAll("]", "-");
- writer.writeAttribute("residue_before_nter", ""
- + res1.charAt((res1.length() - 1)));
- String res2 = pep.get_post();
- res2 = res2.replaceAll("]", "-");
- writer.writeAttribute("residue_after_cter", ""
- + res2.charAt(0));
-
- writer.writeEndElement();// fromSeq
- writer.writeEndElement();// peptideHitRef
- }
+ writeCvParam("PROTICdbO:0000287", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getEvalue()),
+ "xtandem peptide evalue");
- }
- writer.writeEndElement();// "match");
+ writeCvParam("PROTICdbO:0000288", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getParam(PeptideMatchParam::tandem_hyperscore)),
+ "xtandem peptide hyperscore");
+ }
+
+ writeCvParam("PROTICdbO:0000289",QString ("%1").arg(protic_peptide_hit.peptide_match->getRetentionTime()),
+ "xtandem peptide retention time");
+
+ // sequences avec les modifs
+ _output_stream->writeStartElement("pepSeq");
+ _output_stream->writeStartElement("peptide");
+ _output_stream->writeCharacters(protic_peptide_hit.peptide_match->getPeptideXtpSp().get()->getSequence());
+ _output_stream->writeEndElement();// peptide
+
+ if (!protic_peptide_hit.peptide_match->getPeptideXtpSp().get()->getModifString().isEmpty()) {
+ writePtms(protic_peptide_hit.peptide_match->getPeptideXtpSp().get());
+ }
+ _output_stream->writeEndElement();// pepSeq
+ _output_stream->writeEndElement();// peptideHit
+}
+
+
+void ProticdbMl::writePtms(PeptideXtp * p_peptide) {
+ _output_stream->writeStartElement("ptms");
+ QStringList modif_list;
+ unsigned int i=1;
+ for (const pappso::Aa & amino_acid: *p_peptide) {
+ std::list<pappso::AaModificationP> aa_modif_list = amino_acid.getModificationList();
+ QStringList aamodif;
+ for (auto && aa_modif : aa_modif_list) {
+ if (!aa_modif->isInternal()) {
+ aamodif << QString::number(aa_modif->getMass(), 'f', 2);
+ _output_stream->writeStartElement("ptm");
+ _output_stream->writeAttribute("diff_mono", Utils::getXmlDouble(aa_modif->getMass()));
+ _output_stream->writeAttribute("position", QString ("%1").arg(i));
+ _output_stream->writeAttribute("aa", amino_acid.getLetter());
+ _output_stream->writeEndElement();// ptm
}
}
- writer.writeEndElement();// "matchs");
- } catch (Exception e) {
- String message = "error writing Matchs in ProticDbMl \n"
- + e.getMessage();
- logger.error(message);
- throw new MSMSException(message);
+ i++;
}
+
+ _output_stream->writeEndElement();// ptms
}
-void ProticdbMl::writePeptideHit(Peptide pep, Group group,
- PeptideMass peptideMass) throws XMLStreamException, MSMSException {
+void ProticdbMl::writeMatchs(IdentificationGroup * p_identification) {
- if (peptideMass == null) {
- String message = "peptideMass == null";
- logger.error(message);
- throw new MSMSException(message);
+ _output_stream->writeStartElement("matchs");
+ for (std::pair <unsigned int, GroupingGroupSp > group_pair : p_identification->getGroupStore().getGroupMap()) {
+ //for (Group group : identification.getGrouping().getGroupList()) {
+ std::vector<const ProteinMatch *> protein_match_list = group_pair.second.get()->getProteinMatchList();
+ //sort protein match by subgroup
+ std::sort(protein_match_list.begin(), protein_match_list.end(),
+ [](const ProteinMatch * a, const ProteinMatch * b)
+ {
+ return a->getGrpProteinSp().get()->getSubGroupNumber() < b->getGrpProteinSp().get()->getSubGroupNumber();
+ });
+
+ std::vector<const ProteinMatch *> protein_match_subgroup_list;
+ for (const ProteinMatch * p_protein_match: protein_match_list) {
+ if (protein_match_subgroup_list.size() == 0) {
+ protein_match_subgroup_list.push_back(p_protein_match);
+ }
+ else {
+ if (protein_match_subgroup_list[0]->getGrpProteinSp().get()->getSubGroupNumber() != p_protein_match->getGrpProteinSp().get()->getSubGroupNumber()) {
+ writeMatch(protein_match_subgroup_list);
+ protein_match_subgroup_list.clear();
+ protein_match_subgroup_list.push_back(p_protein_match);
+ }
+ else {
+ protein_match_subgroup_list.push_back(p_protein_match);
+ }
+ }
+ }
+ writeMatch(protein_match_subgroup_list);
}
+ _output_stream->writeEndElement();// "matchs");
+}
- 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
+void ProticdbMl::writeMatch(std::vector<const ProteinMatch *> protein_match_sg_list) {
- this.writeCvParam("PROTICdbO:0000287", "" + pep.get_evalue(),
- "xtandem peptide evalue");
+ //for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
+ _output_stream->writeStartElement("match");
- this.writeCvParam("PROTICdbO:0000288", "" + pep.get_hypercorr(),
- "xtandem peptide hyperscore");
- }
+ // echantillons
+ Hashtable<String, String> view = new Hashtable<String, String>();
+ for (HashSampleScanSetProt hashProt : sg
+ .getHashSampleScanSetProtList()) {
+ Match match = (Match) hashProt.getGrpProtMatch();
+ for (MsRun sample : match.get_sample_matchs()) {
+ if (!view.containsKey(sample.getSampleName())) {
+ writer.writeStartElement("matchSample");
+ writer.writeAttribute(
+ "sample_id",
+ ""
+ + sample_to_id.get(sample
+ .getSampleName()));
+ String name = sample.getSampleName();
+ name = name.replaceAll(".xml", "");
+ writer.writeAttribute("name", "" + name);
+ view.put(sample.getSampleName(), "ok");
+ writer.writeEndElement();// "matchSample");
+ }
+ }
+ }
- 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);
+ // proteins
+ int k = 1;
+ for (HashSampleScanSetProt hashProt : sg
+ .getHashSampleScanSetProtList()) {
+ writer.writeStartElement("proteinHit");
+ Protein prot = (Protein) hashProt.getGrpProtMatch()
+ .getGrpProtein();
+ writer.writeAttribute("sequence_id",
+ "" + prot_to_id.get(prot.get_description()));
+ // proteinHit.setAttribute("score", "");
+ writer.writeAttribute("rank", "" + k);
+
+ // //cvparam
+ this.writeCvParam("PROTICdbO:0000284",
+ "" + prot.get_mw(),
+ "MW determination by Benuch");
+ /*
+ * writer.writeStartElement("cvParam");
+ * writer.writeAttribute("value", "" + prot.get_mw());
+ * writer.writeAttribute("name",
+ * "MW determination by Benuch");
+ * writer.writeAttribute("cvLabel", "PROTICdbO");
+ * writer.writeAttribute("accession",
+ * "PROTICdbO:0000284"); writer.writeEndElement();//
+ * cvParam
+ */
+ // evalue
+ MsRunSet samples = ((Match) hashProt.getGrpProtMatch())
+ .get_sample_matchs();
+ this.writeCvParam("PROTICdbO:0000291",
+ "" + prot.get_evalue(), "Xtandem log evalue");
+ /*
+ * writer.writeStartElement("cvParam");
+ * writer.writeAttribute("value", "" +
+ * prot.get_evalue());
+ *
+ * writer.writeAttribute("name", "Xtandem log evalue");
+ * writer.writeAttribute("cvLabel", "PROTICdbO");
+ * writer.writeAttribute("accession",
+ * "PROTICdbO:0000291"); writer.writeEndElement();//
+ * cvParam
+ */
+
+ // coverage
+ if (samples.size() == 1) {
+ this.writeCvParam(
+ "PROTICdbO:0000285",
+ ""
+ + ((Match) hashProt
+ .getGrpProtMatch())
+ .get_coverage(),
+ "protein coverage");
+ }
- // 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
+ // [Term]
+ // id: PROTICdbO:0000335
+ // name: X!TandemPipeline PAI
+ this.writeCvParam("PROTICdbO:0000335",
+ "" + hashProt.getPAI(), "PAI");
+
+ // [Term]
+ // id: PROTICdbO:0000337
+ // name: protein group number
+ String pappsoGroupingNumber = Utils
+ .getPappsoGroupingNumber(group, sg, k);
+ if (pappsoGroupingNumber != null) {
+ this.writeCvParam("PROTICdbO:0000337",
+ pappsoGroupingNumber, "grouping number");
+ }
- pepSampleScanCle2xmlId.put(pep.get_sample_scan_sequencepeptide_cle(),
- pep_hit_id);
- writer.writeEndElement();// peptideHit
-}
+ writer.writeEndElement();// "proteinHit");
+ k++;
+ }
+ for (HashSampleScanSetProt hashProt : sg
+ .getHashSampleScanSetProtList()) {
+ Protein prot2 = (Protein) hashProt.getGrpProtMatch()
+ .getGrpProtein();
+ // peptidesHitRef
+
+ ArrayList<Peptide> peptideList = null;
+ if (this.xtpExperimentType.equals("phospho")) {
+ peptideList = ((Match) hashProt.getGrpProtMatch())
+ .getValidPeptideInPhosphoIsland((HashSampleScanSetPhospho) hashProt);
+ } else {
+ peptideList = ((Match) hashProt.getGrpProtMatch())
+ .get_valid_peptides();
+ }
-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
+ for (Peptide pep : peptideList) {
+ // for (Peptide pep : ((Match)
+ // hashProt.getGrpProtMatch())
+ // .get_peptide_order_inclus_redon()) {
+ String xmlId = pepSampleScanCle2xmlId.get(pep
+ .get_sample_scan_sequencepeptide_cle());
+ if (xmlId == null) {
+ String message = "the xml of peptide "
+ + pep.get_sample_scan_sequencepeptide_cle()
+ + " is not known in pepSampleScanCle2xmlId";
+ logger.debug(message);
+ throw new Exception(message);
+ }
+ writer.writeStartElement("peptideHitRef");
+ writer.writeAttribute("peptide_hit_id", "" + xmlId);
+
+ writer.writeStartElement("fromSeq");
+ writer.writeAttribute(
+ "seq_id",
+ ""
+ + prot_to_id.get(prot2
+ .get_description()));
+ writer.writeAttribute("start", "" + pep.get_start());
+ writer.writeAttribute("stop", "" + pep.get_stop());
+ String res1 = pep.get_pre();
+ res1 = res1.replaceAll("]", "-");
+ writer.writeAttribute("residue_before_nter", ""
+ + res1.charAt((res1.length() - 1)));
+ String res2 = pep.get_post();
+ res2 = res2.replaceAll("]", "-");
+ writer.writeAttribute("residue_after_cter", ""
+ + res2.charAt(0));
+
+ writer.writeEndElement();// fromSeq
+ writer.writeEndElement();// peptideHitRef
+ }
- }
- writer.writeEndElement();// ptms
+ }
+ writer.writeEndElement();// "match");
}
-
void ProticdbMl::writeOboModif(pappso::AaModificationP mod) {
_output_stream->writeStartElement("cvParam");
_output_stream->writeAttribute("name", mod->getName());
diff --git a/src/output/proticdbml.h b/src/output/proticdbml.h
index 98f9ae9ce..64d82d046 100644
--- a/src/output/proticdbml.h
+++ b/src/output/proticdbml.h
@@ -38,6 +38,8 @@
#include "../core/project.h"
#include "../grouping/groupinggroup.h"
+struct ProticPeptideHit;
+
class ProticdbMl
{
public:
@@ -59,6 +61,9 @@ private :
void writeIdentificationDataSource(IdentificationDataSource * p_identification_data_source);
void writepeptideHits(IdentificationGroup * p_identification);
void writepeptideHitsbyGroup(GroupingGroup * p_group);
+ void writePeptideHit(QString xml_id, ProticPeptideHit & protic_peptide_hit);
+ void writePtms(PeptideXtp * p_peptide);
+ void writeMatchs(IdentificationGroup * p_identification);
private :
QFile * _output_file;
diff --git a/src/utils/utils.cpp b/src/utils/utils.cpp
index 9f4abcb4d..d3c583be7 100644
--- a/src/utils/utils.cpp
+++ b/src/utils/utils.cpp
@@ -7,6 +7,9 @@ const QUrl Utils::getOlsUrl(QString psimod_accession) {
return url;
}
+const QString Utils::getXmlDouble(pappso::pappso_double number){
+ return QString::number(number,'g',6);
+}
const QString Utils::getDatabaseName(ExternalDatabase database) {
QString database_name;
diff --git a/src/utils/utils.h b/src/utils/utils.h
index 47e451c01..6dc65bd07 100644
--- a/src/utils/utils.h
+++ b/src/utils/utils.h
@@ -31,6 +31,7 @@ class Utils
public:
static const QUrl getOlsUrl(QString modification);
static const QString getDatabaseName(ExternalDatabase database);
+ static const QString getXmlDouble(pappso::pappso_double number);
};
#endif // UTILS_H
--
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