i've been trying out the PairwiseAlignment demo to align to piece of genomic dna (after changing the alphabet from protein to dna).
i would like to view the optimum path generated by the viterbi algorithm but i seem to be a bit stumped as to how to extract this from the statepath. it is extracted in the viterbialign demo but under a different hmm scenario (not a pairwise alignment).
i tried this (among other things, to no avail)
SymbolList sl = result.symbolListForLabel(StatePath.SEQUENCE);
Iterator i = sl.iterator();
while (i.hasNext()) {
Symbol sym = (Symbol) i.next();
System.out.println(sym.getName());}
//iterate through symbol list and printing symbol names give this output
gap (thymine cytosine) ([] []) (adenine cytosine) ([] []) (guanine adenine) ([] []) (guanine guanine) ([] []) (guanine cytosine) ([] []) (guanine adenine)
this seems to correlate with the input sequence files.
thanks for the help. cheers, stephen
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