WIP: reading identification using pwiz library

src/input/identificationpwizreader.cpp

@@ -38,6 +38,7 @@
 
 #include <pwiz/data/identdata/IdentData.hpp>
 #include <pwiz/data/identdata/IdentDataFile.hpp>
+#include "../core/peptidematch.h"
 #include <locale>
 #include "../core/proteinxtp.h"
 #include "../core/peptidextp.h"
@@ -120,13 +121,63 @@ void IdentificationPwizReader::read(
         }
         for (pwiz::identdata::PeptideEvidencePtr seq_ptr :_pwiz_ident_data_file->sequenceCollection.peptideEvidence) {
         }
+        //std::vector<SpectrumIdentificationListPtr> spectrumIdentificationList
+        //std::vector<SpectrumIdentificationResultPtr> spectrumIdentificationResult
+        for (pwiz::identdata::SpectrumIdentificationListPtr spectrum_ident_list_ptr :_pwiz_ident_data_file->dataCollection.analysisData.spectrumIdentificationList) {
+            for (pwiz::identdata::SpectrumIdentificationResultPtr spectrum_ptr :spectrum_ident_list_ptr.get()->spectrumIdentificationResult) {
+                unsigned int scan=0;
+
+                if (spectrum_ptr.get()->hasCVParam(pwiz::cv::MS_scan_number_s__OBSOLETE))
+                {
+                    scan =
+                        std::stoi(spectrum_ptr.get()->cvParam(pwiz::cv::MS_scan_number_s__OBSOLETE).value);
+                }
+                else {
+                    throw pappso::PappsoException(QObject::tr("Scan number not found"));
+                }
+                //<cvParam accession="MS:1001115" cvRef="PSI-MS" value="4925" name="scan number(s)"/>
+               PeptideMatch * p_peptide_match = new PeptideMatch(_sp_msrun.get(), scan);
+
+                double  rt=0;
+
+                if (spectrum_ptr.get()->hasCVParam(pwiz::cv::MS_retention_time))
+                {
+                    rt =
+                        std::stod(spectrum_ptr.get()->cvParam(pwiz::cv::MS_retention_time).value);
+                        p_peptide_match->setRetentionTime(rt);
+                }
+                else {
+                    //throw pappso::PappsoException(QObject::tr("Scan number not found"));
+                }
+                /*
+                p_peptide_match->setEvalue(attributes.value("expect").simplified().toDouble());
+                //qDebug() << "XtandemSaxHandler::startElement_domain evalue "  << _p_peptide_match->getEvalue() << " scan " << _p_peptide_match->getScan();
+
+                pappso::pappso_double xtandem_mhtheo = attributes.value("mh").simplified().toDouble();
+                pappso::pappso_double xtandem_delta = attributes.value("delta").simplified().toDouble();
+
+                pappso::pappso_double exp_mass = xtandem_mhtheo + xtandem_delta - pappso::MHPLUS;
+
+                p_peptide_match->setExperimentalMass(exp_mass);
+                p_peptide_match->setStart(attributes.value("start").simplified().toUInt()-1);
+                p_peptide_match->setCharge(_charge);
+
+                p_peptide_match->setParam(PeptideMatchParam::tandem_hyperscore,  QVariant( attributes.value("hyperscore").toDouble()));
+
+                p_peptide_match->setIdentificationDataSource( _p_identification_data_source);
+                p_peptide_match->setChecked(true);
+                _p_protein_match->addPeptideMatch(p_peptide_match);
+                */
+            }
+        }
+
 
     }
     catch (pappso::PappsoException & error) {
         qDebug() << "IdentificationPwizReader::read error ";
         throw pappso::PappsoException(QObject::tr("Error reading file (%1) using proteowizard library : %2").arg(_identfile.absoluteFilePath()).arg(error.qwhat()));
     }
-    
+
     catch (std::exception& error)
     {
         qDebug() << "IdentificationPwizReader::read std error ";