Hello - They are immutable because the Annotation object (and others) throw ChangeVetoExceptions when altered. This is probably a good thing.
The decision to not include the query ID is pretty contraversial and ran along the lines of ... you knew what it was when you did the search you should know it now. Probably not the best reason. I'm pretty sure the query is emmitted by the BLASTLikeSAXParser it's just not listened for by the subsequent SeqSimilarityAdapter or BlastLikeSearchBuilder (see http://www.biojava.org/docs/bj_in_anger/BlastParser.htm for a description of the Blast parsing pipeline). To check if the Query is emitted, and what type of event it generates, you could use the example here (http://www.biojava.org/docs/bj_in_anger/blastecho.htm). If the event is emitted then a simple modification to SeqSimilarityAdapter of BlastLikeSearchBuilder should allow it to be included in the Annotation object of the SeqSimilaritySearchHit. - Mark Douglas Hoen <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 04/13/2005 01:34 AM To: biojava-l@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Can I modify a SeqSimilaritySearchSubHit? Hi, I want to modify the annotation of a SeqSimilaritySearchSubHit. (Specifically, I want to add the query ID, since I can't find a way to get at it from a SeqSimilaritySearchSubHit.) However, SeqSimilaritySearchSubHit appears to be immutable. Is there any way I can make this class mutable, or do I have to write my own class (e.g. a wrapper)? Thanks, Doug _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
