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 - [EMAIL PROTECTED] - http://www.sanger.ac.uk/Users/kdj =- Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
