same evalue as computed by MASCOT java dat parser

src/input/mascot/mascotdatparser.cpp

@@ -320,6 +320,7 @@ void MascotDatParser::parseSummaryLine(const QString & summary_line) {
         //qmass1=598.300206
         if (index.startsWith("qmass")) {
             unsigned int query_index = index.mid(5).toUInt();
+            qDebug() << __FILE__ << " " << __FUNCTION__<< " "  << __LINE__ <<  " " << query_index << " " << index;
             //_current_query.title = value;
             _summary_list[query_index-1].exp_mass=value.toDouble();
         }
@@ -380,7 +381,6 @@ void MascotDatParser::saveQuery() {
 
             peptide_evidence.setParam(PeptideEvidenceParam::mascot_expectation_value,  QVariant(peptide_evidence.getEvalue()));
 
-
             QString peptide_str =peptide_line.peptide_string_list.at(4);
             if (!peptide_line.subst.isEmpty()) {
                 //q856_p9_subst=1,X,W
@@ -394,6 +394,10 @@ void MascotDatParser::saveQuery() {
             peptide_sp = PeptideXtp(peptide_str).makePeptideXtpSp();
             peptide_sp = _p_project->getPeptideStore().getInstance(peptide_sp);
 
+
+
+            qDebug() << "MascotDatParser::saveQuery peptide=" << peptide_str << " evalue="  << peptide_evidence.getEvalue() << " ionscore=" << ion_score;
+
             if (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) {
                 throw pappso::PappsoException(QObject::tr("ERROR (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) %1").arg(peptide_line.protein_string_list.join(",\"")));
             }
@@ -435,6 +439,12 @@ void MascotDatParser::saveQuery() {
 }
 
 pappso::pappso_double MascotDatParser::getEvalue(pappso::pappso_double ion_score, unsigned int query_index,  pappso::pappso_double confidence_interval) const {
-    double identity_threshold = 10.0 * std::log(_summary_list.at(query_index-1).match / (confidence_interval * 20.0)) / log(10);;
-    return (confidence_interval * pow(10, ((identity_threshold - ion_score) / 10)));
+    pappso::pappso_double identity_threshold = (pappso::pappso_double)10.0 * std::log(_summary_list.at(query_index-1).match / (confidence_interval * (pappso::pappso_double)20.0)) / log((pappso::pappso_double)10);;
+    return (confidence_interval * pow((pappso::pappso_double)10, ((identity_threshold - ion_score) / (pappso::pappso_double)10)));
+}
+
+pappso::pappso_double MascotDatParser::getEvalueExperimental(pappso::pappso_double ion_score, unsigned int query_index,  pappso::pappso_double confidence_interval) const {
+    // Evalue experimental  Homology threshold (QPlughole value from .dat file).
+    pappso::pappso_double eval = (ion_score - _summary_list.at(query_index-1).plug_hole) / (pappso::pappso_double)10;
+    eval = confidence_interval / pow((pappso::pappso_double)10, eval);
 }

src/input/mascot/mascotdatparser.h

@@ -47,11 +47,14 @@ private:
     void parseSummaryLine(const QString & summary_line);
     void saveQuery();
     void saveAndClearPeptide();
-    
-    
+
+
     pappso::pappso_double getEvalue(pappso::pappso_double ion_score, unsigned int query_index, pappso::pappso_double confidence_interval = 0.05) const;
+    pappso::pappso_double getEvalueExperimental(pappso::pappso_double ion_score, unsigned int query_index, pappso::pappso_double confidence_interval = 0.05) const;
+
+
+
 
-    
     struct PeptideLine {
         unsigned int query_index=0;
         unsigned int peptide_index=0;
@@ -80,21 +83,21 @@ private:
     ProteinXtp _current_protein;
     std::vector<FastaFileSp> _fasta_file_list;
 
-    
+
 
     QRegExp   _regexp_header_line;
     unsigned int _number_of_queries=0;
     unsigned int _number_of_residues=0;
     unsigned int _current_query_index=0;
     QString _error_str;
-    
+
     PeptideLine _current_peptide;
     QueryLine _current_query;
-    
+
     std::vector<std::vector<PeptideLine>> _query_peptide_results;
     std::vector<SummaryLine> _summary_list;
-    
-    
+
+
 };
 
 #endif // MASCOTDATPARSER_H