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

[Mark Schreiber]

Hi -

This has come up before but a long time ago (and I can't remember the
solution). I think it is something like the parser does emit the
midline but nothing listens for it by default.  Try searching the mail
archives

You may need to extend one of the parsers or listeners for this.

- Mark

On Fri, Jun 6, 2008 at 12:20 AM, John David Osborne <ozborn at uab.edu> wrote:
> 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 >
>
>
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