WIP: Mascot parser

src/input/mascot/mascotdatparser.cpp

@@ -152,7 +152,16 @@ void MascotDatParser::saveAndClearPeptide() {
     if (_current_peptide.query_index > 0) {
         //parse and save
 
-        pappso::Peptide peptide(_current_peptide.peptide_string_list.at(4));
+        QString peptide_str =_current_peptide.peptide_string_list.at(4);
+        if (!_current_peptide.subst.isEmpty()) {
+            //q856_p9_subst=1,X,W
+            //q24379_p2_subst=1,B,D,8,B,D
+            QStringList subst_list = _current_peptide.subst.split(",");
+            for (unsigned int i=0; i < subst_list.size(); i+=3) {
+                peptide_str = peptide_str.replace(subst_list.at(0+i).toInt()-1,1,subst_list.at(2+i));
+            }
+        }
+        pappso::Peptide peptide(peptide_str);
 
         if (_current_peptide.protein_string_list.size() != _current_peptide.fasta_file_list.size()) {
             throw pappso::PappsoException(QObject::tr("ERROR (_current_peptide.protein_string_list.size() != _current_peptide.fasta_file_list.size()) %1").arg(_current_peptide.protein_string_list.join(",\"")));