Package org.biojava.bio.program.ssbind

Class SimilarityPairBuilder

java.lang.Object
org.biojava.bio.program.ssbind.ViewSequenceFactory
org.biojava.bio.program.ssbind.SimilarityPairBuilder
All Implemented Interfaces:
SearchContentHandler
public class SimilarityPairBuilder extends ViewSequenceFactory implements SearchContentHandler

SimilarityPairBuilder annotates query and subject Sequence with SimilarityPairFeatures created from SAX events supplied via a SeqSimilarityAdapter. The objective is to describe a simple pairwise relationship between the two sequences. This differs slightly from using HomologyFeatures which are slightly heavier, have to contain a full alignment and don't have an explicit distinction between query and subject sequences in the alignment. The SAX events should describe elements conforming to the BioJava BlastLikeDataSetCollection DTD. Suitable sources are BlastLikeSAXParser or FastaSAXParser.

Annotated ViewSequences wrapping both query and subject sequences are created.

The current implementation should be used with care on streams containing more than one search output. This is because the builder will not stop after each report has been processed and as a result all the subject sequences get instantiated and a large object network could be created during processing.

Since:
1.2
Author:
Keith James, Greg Cox