Package org.biojava.bio.program.ssbind


package org.biojava.bio.program.ssbind

Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.

  • Class
    Description
    AlignmentStAXHandler handles the BlastLikeAlignment element of BioJava BlastLike XML.
    AlphabetResolvers are helpers which determine which type of sequence Alphabet to expect from a search result.
    AnnotationFactory is a utility class for making Annotations from Maps.
    BlastLikeHomologyBuilder populates a List with Homology instances created from SAX events supplied via a SeqSimilarityAdapter.
    BlastLikeSearchBuilder will create SeqSimilaritySearchResults from SAX events via a SeqSimilarityAdapter.
    HeaderStAXHandler handles the Header element of BioJava BlastLike XML.
    AlignmentStAXHandler handles the Hit element of BioJava BlastLike XML.
    HSPStAXHandler handles the HSP element of BioJava BlastLike XML.
    HSPSummaryStAXHandler handles the HSPSummary element of BioJava BlastLike XML.
    A SeqSimilarityAdapter converts SAX events into method calls on a SearchContentHandler implementation.
    SeqSimilarityStAXAdapter is a handler for XML conforming to the BioJava BlastLike DTD.
    SeqSimilarityStAXHandler is a base class for creating modular StAX handlers which send callbacks to a SeqSimilarityStAXAdapter.
    SimilarityPairBuilder annotates query and subject Sequence with SimilarityPairFeatures created from SAX events supplied via a SeqSimilarityAdapter.
    StAXHandlerBindings associates an ElementRecognizer with a factory which creates StAXContentHandlers for elements which it the ElementRecognizer accepts.
    StAXHandlerFactory is an interface for factories producing StAXContentHandlers which are used by the SeqSimilarityStAXAdapter.
    ViewSequenceFactory is a base class for creating search handlers which create and cache views on the query and subject sequences.