[Biojava-l] More ssbind builders

[Keith James]

I've added SimilarityPairBuilder.java to the ssbind package. This will
annotate views of the query and subject sequences with
SimilarityPairFeatures.

This brings the current complement of builders to:

 BlastLikeSearchBuilder (builds SeqSimilaritySearchResult objects)
 BlastLikeHomologyBuilder (builds Homology objects)
 SimilarityPairBuilder (builds SimilarityPairFeatures)

Which one is best depends on the application; the first is a holder
for all the results plus alignments, the second creates Features and
has the potential to support similarity between many sequences, the
third also creates Features, but pairwise only and could be made
lighter by ditching the alignments.

The gui package has a rendering context and renderers capable of
filtering features and making overlays to display
SimilarityPairFeatures. Filtering by score seems to be working
okay. Things work in a way analagous to the SequenceRenderers as a
result of my copying much of Matthew's sequence renderer design -
cheers Matthew!

Keith

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK