[Biojava-dev] BlastEcho, midline and other blast data

[John David Osborne]

Hello,

Can anybody offer me any pointers on getting additional information such
as
the midline from the blast parser? I¹m using the BlastEcho example code
from
biojava in anger which works nicely, but I would also like to get the
midline or the match consensus sequence for hits from the parser.

Digging into the code, I¹m not sure what I need to do to get this info.
Do I
just need to modify BlastLikeDataSetCollection.dtd. It already has
MatchConsensus defined though (see below) but I don¹t know how to pull
it
out.

 -John
<!-- A MatchConsensus element represents the consensus information
     present in a pairwise alignment produced by Blast-like programs
     (i.e. the middle line of the alignment).
-->

<!ELEMENT biojava:MatchConsensus (#PCDATA)>
<!ATTLIST biojava:MatchConsensus
                     xml:space       (default|preserve) #IMPLIED >