get only amino acids one letter code to compute protein mass or count tryptic peptides

src/core/proteinxtp.cpp

@@ -109,16 +109,19 @@ bool ProteinXtp::isDecoy() const {
 
 QString ProteinXtp::getOnlyAminoAcidSequence() const {
     QString sequence(this->getSequence());
-    return sequence.replace(QRegExp("\\*"), "");
+    return sequence.replace(QRegExp("[^RNDBCEQZGHILKMFPSTWYVX]"),"");
 }
 
 pappso::pappso_double ProteinXtp::getMass() const {
     try {
-        pappso::Peptide peptide(getOnlyAminoAcidSequence().replace("X",""));
+        //qDebug() << "ProteinXtp::getMass() begin " << getOnlyAminoAcidSequence().replace("[BZX]","E");
+        // replace amino acid wildcard by E, just to give an random mass (assumed it is not perfect)
+        pappso::Peptide peptide(getOnlyAminoAcidSequence().replace(QRegExp("[BZX]"),"E"));
         return peptide.getMass();
 
     }
     catch (pappso::PappsoException error) {
+        qDebug() << "ProteinXtp::getMass() " << getOnlyAminoAcidSequence().replace(QRegExp("[BZX]"),"E");
         throw pappso::PappsoException(QObject::tr("Error computing mass for protein %1 :\n%2").arg(getAccession()).arg(error.qwhat()));
     }
 }