grab specific informations from MS-GF+ mzidentML files

src/gui/peptide_list_view/peptidetablemodel.cpp

@@ -651,7 +651,7 @@ PeptideTableModel::getTitle(std::int8_t column)
         return "MS-GF spectral E-value";
         break;
       case(std::int8_t)PeptideListColumn::msgfplus_isotope_error:
-        return "MS-GF istotope error";
+        return "MS-GF isotope error";
         break;
 
       case(std::int8_t)PeptideListColumn::comet_xcorr:
@@ -788,7 +788,7 @@ PeptideTableModel::getDescription(std::int8_t column)
         return "MS-GF spectral E-value";
         break;
       case(std::int8_t)PeptideListColumn::msgfplus_isotope_error:
-        return "MS-GF istotope error";
+        return "MS-GF isotope error";
         break;
       case(std::int8_t)PeptideListColumn::comet_xcorr:
         return "The Comet result 'XCorr'";

src/input/identificationpwizreader.cpp

@@ -200,6 +200,11 @@ IdentificationPwizReader::getIdentificationEngine(
     {
       identification_engine = IdentificationEngine::mascot;
     }
+  else if(analysis_software_p.get()->softwareName.hasCVParam(
+            pwiz::cv::MS_MS_GF_))
+    {
+      identification_engine = IdentificationEngine::MSGFplus;
+    }
   else
     {
       return IdentificationEngine::unknown;
@@ -521,6 +526,62 @@ IdentificationPwizReader::read(
                     }
 
 
+                  //<cvParam cvRef="PSI-MS" accession="MS:1002049"
+                  // name="MS-GF:RawScore" value="164"/>
+                  QVariant MSGFplus_rawscore = getQVariantDoubleParam(
+                    spid_item.get(), pwiz::cv::MS_MS_GF_RawScore);
+                  if(!MSGFplus_rawscore.isNull())
+                    {
+                      p_peptide_evidence->setParam(
+                        PeptideEvidenceParam::msgfplus_raw, MSGFplus_rawscore);
+                    }
+                  //<cvParam cvRef = "PSI-MS" accession = "MS:1002050" name
+                  //="MS-GF:DeNovoScore" value        = "170" />
+
+                  QVariant MSGFplus_denovoscore = getQVariantDoubleParam(
+                    spid_item.get(), pwiz::cv::MS_MS_GF_DeNovoScore);
+                  if(!MSGFplus_denovoscore.isNull())
+                    {
+                      p_peptide_evidence->setParam(
+                        PeptideEvidenceParam::msgfplus_denovo,
+                        MSGFplus_denovoscore);
+                    }
+
+                  //<cvParam cvRef = "PSI-MS" accession = "MS:1002052" name
+                  //="MS-GF:SpecEValue" value         = "5.4876387E-19"/>
+
+                  QVariant MSGFplus_specevalue = getQVariantDoubleParam(
+                    spid_item.get(), pwiz::cv::MS_MS_GF_SpecEValue);
+                  if(!MSGFplus_specevalue.isNull())
+                    {
+                      p_peptide_evidence->setParam(
+                        PeptideEvidenceParam::msgfplus_SpecEValue,
+                        MSGFplus_specevalue);
+                    }
+                  //<cvParam cvRef = "PSI-MS" accession = "MS:1002053" name =
+                  //"MS-GF:EValue" value             = "1.0822937E-11" />
+
+                  QVariant MSGFplus_evalue = getQVariantDoubleParam(
+                    spid_item.get(), pwiz::cv::MS_MS_GF_EValue);
+                  if(!MSGFplus_evalue.isNull())
+                    {
+                      p_peptide_evidence->setParam(
+                        PeptideEvidenceParam::msgfplus_EValue, MSGFplus_evalue);
+                      p_peptide_evidence->setEvalue(MSGFplus_evalue.toDouble());
+                    }
+
+                  //<userParam name="IsotopeError" value="0"/>
+                  QVariant isotope_error =
+                    QVariant(QString::fromStdString(
+                               spid_item.get()->userParam("IsotopeError").value)
+                               .toInt());
+                  if(!isotope_error.isNull())
+                    {
+                      p_peptide_evidence->setParam(
+                        PeptideEvidenceParam::msgfplus_isotope_error,
+                        isotope_error);
+                    }
+
                   for(pwiz::identdata::PeptideEvidencePtr peptide_evidence_sp :
                       spid_item.get()->peptideEvidencePtr)
                     {