Package org.biojava.bio.program.ssbind

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

Interface Summary

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

Class Summary

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