Thanks for that information. That did the job!
Cheers,
Charles
Richard Holland wrote:
Your hits consist of numerous sub-hits, which means that the hits
themselves don't contain meaningful data. You can get the sub-hits by
doing this:
// existing code to list the hits
for (Iterator k = result.getHits().iterator(); k.hasNext(); ) {
SeqSimilaritySearchHit hit = (SeqSimilaritySearchHit)k.next();
System.out.print("\tmatch: "+hit.getSubjectID());
System.out.print("\tSubSeqStart: "+hit.getSubjectStart());
System.out.print("\tSubSeqStop: "+hit.getSubjectEnd());
System.out.println("\te score: "+hit.getEValue());
// new code to get the subhits
System.out.println("\t\t Subhits:");
for (Iterator j = hit.getSubHits().iterator(); j.hasNext(); ) {
SeqSimilaritySearchSubHit subhit =
(SeqSimilaritySearchSubHit)j.next();
System.out.print("\t\tSubSeqStart: "+subhit.getSubjectStart());
System.out.print("\t\tSubSeqStop: "+subhit.getSubjectEnd());
System.out.println("\t\te score: "+subhit.getEValue());
}
}
cheers,
Richard
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