[Biojava-l] dp pairwisealignment demo

[Stephen Montgomery]

hi -
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