[Biojava-l] blast parser alignment middle line

[Christian Gruber]

Hello!

Is there a way to get the middle line of an alignment that I parse out 
of the blast output? In the example below, it would be the "S++VGTR..." 
line. In the Alignment of the SeqSimilaritySearchSubHit, I only find a 
Sequence entry for Query and Sbjct.

Query: 2 SFEVGTRCWYPHKELGWIGAEVIKNEFNDGKYHLEL...
          S++VGTR W P    GW+ +EV+K   +  K  L  ...
Sbjct: 4 SYDVGTRAWQPDPTEGWVASEVVKKTVDGNKVTLIF...


Thanks,
Christian