[Biojava-dev] How to use SimilarityPairBuilder?

[Tim Troup]

Hi,

I was wondering if someone could give me a few pointers as to how to use 
the class: 

org.biojava.bio.program.ssbind.SimilarityPairBuilder

I tied to use this class in place of:

org.biojava.bio.program.ssbind.BlastLikeSearchBuilder 

in the BioJava in anger Blast Parser:

http://www.biojava.org/docs/bj_in_anger/BlastParser.htm

in the hope of being able to re-generate the alignments as they are 
displayed in the orginal output file.

However, i can't quite understand how i get the results back as you 
do not pass the constructor a java.util.List in which to store the 
results (as you do with both BlastLikeSerachBuilder and BlastLikeHomology 
Builder)

Also it would appear that you cannot

1) call the method setQuerySeqHolder with DummySequenceDB as a parameter

2) call the method setSubjectDBInstallation with 
DummySequenceDBInstallation as a parameter.

It is really handy to be able to do this. Is there a way round it?

Thanks, Tim
-- 


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Tim Troup
Room F151
17 Lilybank Gardens
Department of Computing Science
University of Glasgow
Glasgow
G12 8RZ

Tel: +44 (0)141 339 8855 ext 0989
E-mail: troup at dcs.gla.ac.uk
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