Class BlastLikeHomologyBuilder

  • All Implemented Interfaces:

    public class BlastLikeHomologyBuilder
    extends ViewSequenceFactory
    implements SearchContentHandler

    BlastLikeHomologyBuilder populates a List with Homology instances created from SAX events supplied via a SeqSimilarityAdapter. 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 and populated with HomologyFeatures. See the documentation of Homology and HomologyFeature.

    As SimpleHomologyFeatures are created on views of the query and subject sequences, both query and subject should be nucleotide sequences (SimpleHomologyFeature extends StrandedFeature.). This limits the searches currently handled to BLASTN, TBLASTX and Fasta DNA.

    Keith James, Greg Cox