WIP : writing MassChroqML

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();
     }

src/output/masschroqml.h

@@ -48,6 +48,7 @@ private:
     void writeGroups();
     void writeProteinList();
     void writePeptideList();
+    void writeIsotopeLabelList();
 private :
     QFile * _output_file;
     QXmlStreamWriter * _output_stream;