SequenceI prot = mapping.findAlignedSequence(dnaSeq, protein);
if (prot != null)
{
- Mapping seqMap = mapping.getMappingForSequence(dnaSeq);
+ Mapping seqMap = mapping.getMappingForSequence(dnaSeq, false);
addCodonPositions(dnaSeq, prot, protein.getGapCharacter(), seqMap,
alignedCodons);
unmappedProtein.remove(prot);
static int computePeptideVariants(SequenceI peptide, int peptidePos,
List<DnaVariant>[] codonVariants)
{
- String residue = String.valueOf(peptide.getCharAt(peptidePos - 1));
+ String residue = String
+ .valueOf(peptide.getCharAt(peptidePos - peptide.getStart()));
int count = 0;
String base1 = codonVariants[0].get(0).base;
String base2 = codonVariants[1].get(0).base;