Package org.biojava.bio.program.ssbind

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

See:
          Description

Interface Summary
StAXHandlerFactory StAXHandlerFactory is an interface for factories producing StAXContentHandlers which are used by the SeqSimilarityStAXAdapter.
 

Class Summary
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.
ViewSequenceFactory ViewSequenceFactory is a base class for creating search handlers which create and cache views on the query and subject sequences.
 

Package org.biojava.bio.program.ssbind Description

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