redefined parameters as userParam

percolator · Mar 28, 2014 · e2f6e62 · e2f6e62
1 parent 397d514
commit e2f6e62
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Showing 2 changed files with 8 additions and 5 deletions.
diff --git a/xmlio.cpp b/xmlio.cpp
@@ -245,6 +245,7 @@ bool PercolatorOutI::getPoutValues(boost::unordered_map<PercolatorOutFeatures, s
       if (psmidfile.length()==0)
         THROW_ERROR_VALUE(PRINT_TEXT::NO_UNIQUE_MZID_FILE,psmid);
       pout_values[PercolatorOutFeatures(psmidfile,psmid,PERCOLATOR_PARAM::SVM_SCORE)]=global::to_string(psmit->svm_score());
+      pout_values[PercolatorOutFeatures(psmidfile,psmid,PERCOLATOR_PARAM::P_VALUE)]=global::to_string(psmit->p_value());
       pout_values[PercolatorOutFeatures(psmidfile,psmid,PERCOLATOR_PARAM::Q_VALUE)]=global::to_string(psmit->q_value());
       pout_values[PercolatorOutFeatures(psmidfile,psmid,PERCOLATOR_PARAM::PEP)]=global::to_string(psmit->pep());
       }

diff --git a/xmlio.h b/xmlio.h
@@ -37,6 +37,8 @@ using namespace std;
 //------------------------------------------------------------------------------
 // Namespaces containing parameters for mzID and percolator out files
 // in case future version of MZID, and percolator out parameters change
+// Accession and cvRef are kept for future migration of obtained values
+// into mzIdentML Controlled Vocabulary
 //------------------------------------------------------------------------------
 namespace MZID_PARAM {
   const char SCHEMA_NAME[]="http://psidev.info/psi/pi/mzIdentML/1.1";
@@ -46,24 +48,24 @@ namespace MZID_PARAM {
 
   namespace ELEMENT_DATA {
     const int ELEMENTS[]={
-      USERPARAM,CVPARAM,CVPARAM,CVPARAM,USERPARAM
+      USERPARAM,USERPARAM,USERPARAM,USERPARAM,USERPARAM,USERPARAM
       };
     const string ACCESSIONS[]={
-      "","MS:1002054","MS:1002056","MS:1002055",""
+      "","MS:1002054","MS:1002056","MS:1002055","",""
       };
     const string CVREFS[]={
-      "","PSI-PI","PSI-PI","PSI-PI",""
+      "","PSI-PI","PSI-PI","PSI-PI","",""
       };
     const string NAMES[]={
-      "svm-score","MS-GF:QValue","MS-GF:PEP","MS-GF:PepQValue","peptide-level-PEP"
+      "percolator:score","percolator:psm_p_value","percolator:psm_q_value","percolator:psm_pep","percolator:peptide_q_value","percolator:peptide_pep"
       };
     }
   }
 //------------------------------------------------------------------------------
 namespace PERCOLATOR_PARAM {
   const int N_DELIMINATOR_PSM_ID=3;
   const char PSMID_START[]="_SII";
-  enum VALUES { SVM_SCORE,Q_VALUE,PEP,PEPTIDE_Q_VALUE,PEPTIDE_PEP };
+  enum VALUES { SVM_SCORE,P_VALUE,Q_VALUE,PEP,PEPTIDE_Q_VALUE,PEPTIDE_PEP };
   }
 //------------------------------------------------------------------------------
 class PercolatorOutFeatures {