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