reading mzIdentML

src/input/identificationpwizreader.cpp

@@ -162,6 +162,30 @@ void IdentificationPwizReader::read(
         for (pwiz::identdata::PeptidePtr seq_ptr :_pwiz_ident_data_file->sequenceCollection.peptides) {
             pwiz::identdata::Peptide * peptide_pwiz = seq_ptr.get();
             PeptideXtp peptide(QString::fromStdString( peptide_pwiz->peptideSequence));
+            
+            
+            //<Modification monoisotopicMassDelta="42.01056468" location="1">
+            //    <cvParam accession="MOD:00394" cvRef="PSI-MOD" name="acetylated residue"/>
+            //</Modification>
+            for (pwiz::identdata::ModificationPtr mod_ptr :peptide_pwiz->modification) {
+                unsigned int location = mod_ptr.get()->location;
+                //std::vector<CVParam> cvParams;
+                for (const pwiz::data::CVParam & param: mod_ptr.get()->cvParams) {
+                    qDebug() << "IdentificationPwizReader::read param "  << QString::fromStdString(param.name());
+                    /*
+                    if (pwiz::cv::cvTermInfo(param.cvid).prefix() == "PSI-MOD") {
+                    }
+                    else {
+                        throw pappso::PappsoException(QObject::tr("Error reading file (%1) using proteowizard library : cvParam %2 not handled").arg(_identfile.absoluteFilePath()).arg(QString::fromStdString( pwiz::cv::cvTermInfo(param.cvid).id)));
+                    }
+                    */
+                }
+                
+                for (const pwiz::data::UserParam & param: mod_ptr.get()->userParams) {
+                     qDebug() << "IdentificationPwizReader::read UserParams "  << QString::fromStdString(param.name);
+                }
+            }
+            
             PeptideXtpSp peptide_sp(peptide.makePeptideXtpSp());
             peptide_sp = peptide_store.getInstance(peptide_sp);
             map_id2peptide.insert(std::pair<QString, PeptideXtpSp>(QString::fromStdString( peptide_pwiz->id), peptide_sp));