[Biojava-l] Per-sequence information from PairwiseAlignment

[Rahul Karnik]

Hello,

[I am a new user of BioJava, so please forgive any obvious errors I may 
make.]

I was trying to modify the PairwiseAlignment demo to show the 
traditional output of alignment programs, i.e. the aligned sequences 
alongside one another. It seems this information is available from:

StatePath result = aligner.viterbi(seqs, ScoreType.PROBABILITY);

I was able to get result.symbolListForLabel(StatePath.SEQUENCE) and 
display the symbols, but these seem to have both sequences in each 
symbol (of class SimpleAtomicSymbol). I could parse out each sequence 
from the combined SymbolList, but I was wondering if there is a better 
way to achieve this.

Thanks,
Rahul