store msgf isotope error

src/gui/peptide_list_view/peptidetablemodel.cpp

@@ -104,6 +104,8 @@ PeptideTableModel::setProteinMatch(ProteinMatch *p_protein_match)
           _engine_columns_to_display.insert(
             PeptideListColumn::msgfplus_SpecEValue);
           _engine_columns_to_display.insert(PeptideListColumn::msgfplus_EValue);
+          _engine_columns_to_display.insert(
+            PeptideListColumn::msgfplus_isotope_error);
         }
       else if(engine == IdentificationEngine::Comet)
         {
@@ -147,7 +149,7 @@ PeptideTableModel::rowCount(const QModelIndex &parent) const
 int
 PeptideTableModel::columnCount(const QModelIndex &parent) const
 {
-  return 39;
+  return 40;
 }
 QVariant
 PeptideTableModel::headerData(int section, Qt::Orientation orientation,
@@ -456,6 +458,12 @@ PeptideTableModel::data(const QModelIndex &index, int role) const
                     ->getParam(PeptideEvidenceParam::msgfplus_SpecEValue);
                   break;
 
+                case(std::int8_t)PeptideListColumn::msgfplus_isotope_error:
+                  return _p_protein_match->getPeptideMatchList()
+                    .at(row)
+                    .getPeptideEvidence()
+                    ->getParam(PeptideEvidenceParam::msgfplus_isotope_error);
+                  break;
                 case(std::int8_t)PeptideListColumn::comet_xcorr:
                   return _p_protein_match->getPeptideMatchList()
                     .at(row)
@@ -635,6 +643,9 @@ PeptideTableModel::getTitle(std::int8_t column)
       case(std::int8_t)PeptideListColumn::msgfplus_SpecEValue:
         return "MS-GF spectral E-value";
         break;
+      case(std::int8_t)PeptideListColumn::msgfplus_isotope_error:
+        return "MS-GF istotope error";
+        break;
 
       case(std::int8_t)PeptideListColumn::comet_xcorr:
         return "Comet XCorr";
@@ -769,6 +780,9 @@ PeptideTableModel::getDescription(std::int8_t column)
       case(std::int8_t)PeptideListColumn::msgfplus_SpecEValue:
         return "MS-GF spectral E-value";
         break;
+      case(std::int8_t)PeptideListColumn::msgfplus_isotope_error:
+        return "MS-GF istotope error";
+        break;
       case(std::int8_t)PeptideListColumn::comet_xcorr:
         return "The Comet result 'XCorr'";
         break;

src/gui/peptide_list_view/peptidetablemodel.h

@@ -68,14 +68,15 @@ enum class PeptideListColumn : std::int8_t
   msgfplus_energy     = 30, ///< MS:1002051  "MS-GF energy score." [PSI:PI]
   msgfplus_SpecEValue = 31, ///< MS:1002052  "MS-GF spectral E-value." [PSI:PI]
   msgfplus_EValue     = 32, ///< MS:1002053  "MS-GF E-value." [PSI:PI]
-  comet_xcorr   = 33, ///< MS:1002252  "The Comet result 'XCorr'." [PSI:PI]
-  comet_deltacn = 34, ///< MS:1002253  "The Comet result 'DeltaCn'." [PSI:PI]
+  msgfplus_isotope_error     = 33, ///< MS:1002053  "MS-GF E-value." [PSI:PI]
+  comet_xcorr   = 34, ///< MS:1002252  "The Comet result 'XCorr'." [PSI:PI]
+  comet_deltacn = 35, ///< MS:1002253  "The Comet result 'DeltaCn'." [PSI:PI]
   comet_deltacnstar =
-    35, ///< MS:1002254  "The Comet result 'DeltaCnStar'." [PSI:PI]
-  comet_spscore = 36, ///< MS:1002255  "The Comet result 'SpScore'." [PSI:PI]
-  comet_sprank  = 37, ///< MS:1002256  "The Comet result 'SpRank'." [PSI:PI]
+    36, ///< MS:1002254  "The Comet result 'DeltaCnStar'." [PSI:PI]
+  comet_spscore = 37, ///< MS:1002255  "The Comet result 'SpScore'." [PSI:PI]
+  comet_sprank  = 38, ///< MS:1002256  "The Comet result 'SpRank'." [PSI:PI]
   comet_expectation_value =
-    38, ///< MS:1002257  "The Comet result 'Expectation value'." [PSI:PI]
+    39, ///< MS:1002257  "The Comet result 'Expectation value'." [PSI:PI]
 };
 
 class PeptideListWindow;

src/input/pepxmlsaxhandler.cpp

@@ -326,7 +326,7 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
 
 //<alternative_protein protein="sp|P46784|RS10B_YEAST" protein_descr="40S
 //       ribosomal protein S10-B OS=Saccharomyces cerevisiae (strain ATCC 204508
-//                                          \
+//                                           \
 //S288c) GN=RPS10B PE=1 SV=1" num_tol_term="2" peptide_prev_aa="K"
 // peptide_next_aa="N"/>
 bool
@@ -603,6 +603,19 @@ PepXmlSaxHandler::startElement_search_score(QXmlAttributes attributes)
                 QVariant(valueStr.simplified().toDouble()));
               _p_peptide_evidence->setEvalue(valueStr.simplified().toDouble());
             }
+
+          else if(name == "denovo")
+            {
+              _p_peptide_evidence->setParam(
+                PeptideEvidenceParam::msgfplus_denovo,
+                QVariant(valueStr.simplified().toDouble()));
+            }
+          else if(name == "IsotopeError")
+            {
+              _p_peptide_evidence->setParam(
+                PeptideEvidenceParam::msgfplus_isotope_error,
+                QVariant(valueStr.simplified().toInt()));
+            }
         }
     }
   return is_ok;

src/utils/types.h

@@ -80,12 +80,13 @@ enum class PeptideEvidenceParam : std::int8_t
   msgfplus_energy = 10, ///< MS:1002051  "MS-GF energy score." [PSI:PI]
   msgfplus_SpecEValue = 11, ///< MS:1002052  "MS-GF spectral E-value." [PSI:PI]
   msgfplus_EValue = 12, ///< MS:1002053  "MS-GF E-value." [PSI:PI]
-  comet_xcorr = 13, ///< MS:1002252  "The Comet result 'XCorr'." [PSI:PI]
-  comet_deltacn = 14, ///< MS:1002253  "The Comet result 'DeltaCn'." [PSI:PI]
-  comet_deltacnstar = 15, ///< MS:1002254  "The Comet result 'DeltaCnStar'." [PSI:PI]
-  comet_spscore = 16, ///< MS:1002255  "The Comet result 'SpScore'." [PSI:PI]
-  comet_sprank = 17, ///< MS:1002256  "The Comet result 'SpRank'." [PSI:PI]
-  comet_expectation_value = 18, ///< MS:1002257  "The Comet result 'Expectation value'." [PSI:PI]
+  msgfplus_isotope_error = 13, ///< MS-GF isotope error
+  comet_xcorr = 14, ///< MS:1002252  "The Comet result 'XCorr'." [PSI:PI]
+  comet_deltacn = 15, ///< MS:1002253  "The Comet result 'DeltaCn'." [PSI:PI]
+  comet_deltacnstar = 16, ///< MS:1002254  "The Comet result 'DeltaCnStar'." [PSI:PI]
+  comet_spscore = 17, ///< MS:1002255  "The Comet result 'SpScore'." [PSI:PI]
+  comet_sprank = 18, ///< MS:1002256  "The Comet result 'SpRank'." [PSI:PI]
+  comet_expectation_value = 19, ///< MS:1002257  "The Comet result 'Expectation value'." [PSI:PI]
 
 };