[Biojava-l] How to parse pairwise alignment result string

[David Zhao]

Hi there,

I've successfully aligned 2 peptide sequence using Needleman-Wunsch algorithm:
SequenceAlignment aligner.pairwiseAlignment( 
query, // first sequence
target // second one
);
Now, the only output I can get is this string returned by
aligner.getAlignmentString(); 

showing below:
 
Time (ms):	63
 Length:	25
  Score:	180
  Query:	query,	Length:	25
  Target:	target,	Length:	25


Query:	  1 KLFVGGIKEDTEEHHLRDYFEEYGK 25 
            | ||||||||||||||||||| ||| 
Target:	  1 KIFVGGIKEDTEEHHLRDYFEQYGK 25 

How can create an gapped alignment object in biojava from this, 
so I can retrieve 
score, gap information, etc. from the object?
Thanks in advance!

David