diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index be34dc01a7c27b5a25b6ada00e8aca796c32d4d1..1399e04c9e9aa639b6b97970a5cfbee4403bd78c 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -31,14 +31,23 @@
#include <pappsomspp/pappsoexception.h>
#include <pappsomspp/utils.h>
#include <pappsomspp/grouping/grpprotein.h>
+#include <pappsomspp/amino_acid/Aa.h>
struct McqPeptide {
QString id;
- pappso::pappso_double mh;
QStringList mods;
QStringList prot_ids;
QString seq;
+ const pappso::Peptide * native_peptide;
+ std::vector<QString> data;
+ std::vector<unsigned int> scan;
+ std::vector<unsigned int> charge;
+};
+
+struct McqPsimod {
+ unsigned int at;
+ QString accession;
};
MassChroQml::MassChroQml(const QString & out_filename)
@@ -121,7 +130,26 @@ void MassChroQml::write(ProjectSp sp_project) {
writeGroups();
writeProteinList();
writePeptideList();
+ writeIsotopeLabelList();
+}
+
+
+void MassChroQml::writeIsotopeLabelList() {
+ //<isotope_label_list>
+ _output_stream->writeStartElement("isotope_label_list");
+ /*
+ <isotope_label id="iso1">
+ <mod at="Nter" value="28.0" acc="MOD:00429"/>
+ <mod at="K" value="28.0" acc="MOD:00429"/>
+ </isotope_label>
+ <isotope_label id="iso2">
+ <mod at="Nter" value="32.0" />
+ <mod at="K" value="32.0" />
+ </isotope_label>*/
+ //</isotope_label_list>
+ _output_stream->writeEndElement();
}
+
void MassChroQml::writePeptideList() {
//<peptide_list>
_output_stream->writeStartElement("peptide_list");
@@ -136,7 +164,10 @@ void MassChroQml::writePeptideList() {
mcq_peptide.mods << peptide_match->getPeptideXtpSp().get()->getModifString();
mcq_peptide.prot_ids << p_protein_match->getGrpProteinSp().get()->getGroupingId();
mcq_peptide.seq = peptide_match->getPeptideXtpSp().get()->getSequence();
- mcq_peptide.mh = peptide_match->getPeptideXtpSp().get()->getNativePeptideP()->getMz(1);
+ mcq_peptide.native_peptide = peptide_match->getPeptideXtpSp().get()->getNativePeptideP();
+ mcq_peptide.data.push_back(peptide_match->getMsRunP()->getXmlId());
+ mcq_peptide.scan.push_back(peptide_match->getScan());
+ mcq_peptide.charge.push_back(peptide_match->getCharge());
mcq_peptide_list.push_back(mcq_peptide);
}
@@ -152,6 +183,23 @@ void MassChroQml::writePeptideList() {
McqPeptide cumul = mcq_peptide_list[0];
for (McqPeptide & mcq_peptide : mcq_peptide_list) {
if (cumul.id == mcq_peptide.id) {
+ unsigned int charge = mcq_peptide.charge[0];
+ QString data = mcq_peptide.data[0];
+ unsigned int scan = mcq_peptide.scan[0];
+
+ bool not_found= true;
+ for (unsigned int i=0; i < cumul.scan.size(); i++) {
+ if ((cumul.charge[i] == charge)&&(cumul.data[i] == data)&&(cumul.scan[i] == scan)) {
+ not_found= false;
+ break;
+ }
+ }
+
+ if (not_found) {
+ cumul.charge.push_back(mcq_peptide.charge[0]);
+ cumul.data.push_back(mcq_peptide.data[0]);
+ cumul.scan.push_back(mcq_peptide.scan[0]);
+ }
if (!cumul.prot_ids.contains(mcq_peptide.prot_ids[0])) {
cumul.prot_ids << mcq_peptide.prot_ids[0];
}
@@ -175,15 +223,47 @@ void MassChroQml::writePeptideList() {
_output_stream->writeAttribute("id",mcq_peptide.id);
_output_stream->writeAttribute("mods",mcq_peptide.mods.join("|"));
_output_stream->writeAttribute("prot_ids",mcq_peptide.prot_ids.join(" "));
- _output_stream->writeAttribute("mh",QString::number(mcq_peptide.mh, 'f', 10));
+ _output_stream->writeAttribute("mh",QString::number(mcq_peptide.native_peptide->getMz(1), 'f', 10));
_output_stream->writeAttribute("seq",mcq_peptide.seq);
- /*
- <modifications><!-- this tag is optional but gives an exact mass computation -->
- <psimod at="2" acc="MOD:00397"></psimod>
- <psimod at="11" acc="MOD:00397"></psimod>
- </modifications>
- <observed_in data="samp0" scan="655" z="2" />
- <observed_in data="samp1" scan="798" z="2" />*/
+
+ //<modifications><!-- this tag is optional but gives an exact mass computation -->
+ std::vector<McqPsimod> mod_list;
+ unsigned int pos=1;
+ for (const pappso::Aa & aa: *(mcq_peptide.native_peptide)) {
+ const std::list<pappso::AaModificationP> aa_mod_list = aa.getModificationList();
+ for (pappso::AaModificationP mod : aa_mod_list) {
+ if (!mod->isInternal()) {
+ McqPsimod psimod;
+ psimod.accession = mod->getAccession();
+ psimod.at = pos;
+ mod_list.push_back(psimod);
+ }
+ }
+ pos++;
+ }
+ if (mod_list.size() > 0) {
+ _output_stream->writeStartElement("modifications");
+ for (McqPsimod & psimod :mod_list) {
+ //<psimod at="2" acc="MOD:00397"></psimod>
+ _output_stream->writeStartElement("psimod");
+ _output_stream->writeAttribute("at",QString("%1").arg(psimod.at));
+ _output_stream->writeAttribute("acc",psimod.accession);
+ //<psimod at="11" acc="MOD:00397"></psimod>
+ _output_stream->writeEndElement();
+ }
+ //</modifications>
+ _output_stream->writeEndElement();
+ }
+
+ //<observed_in data="samp0" scan="655" z="2" />
+ for (unsigned int i=0; i < mcq_peptide.scan.size(); i++) {
+ _output_stream->writeStartElement("observed_in");
+ _output_stream->writeAttribute("data",mcq_peptide.data[i]);
+ _output_stream->writeAttribute("scan",QString("%1").arg(mcq_peptide.scan[i]));
+ _output_stream->writeAttribute("z",QString("%1").arg(mcq_peptide.charge[i]));
+ _output_stream->writeEndElement();
+ }
+ //<observed_in data="samp1" scan="798" z="2" />*/
//</peptide>
_output_stream->writeEndElement();
}
diff --git a/src/output/masschroqml.h b/src/output/masschroqml.h
index c9cb8583476292eaf4ff9bef7c46e1f6ed2053da..d52c87363645491d163e627539327af71332eb4a 100644
--- a/src/output/masschroqml.h
+++ b/src/output/masschroqml.h
@@ -48,6 +48,7 @@ private:
void writeGroups();
void writeProteinList();
void writePeptideList();
+ void writeIsotopeLabelList();
private :
QFile * _output_file;
QXmlStreamWriter * _output_stream;