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See:
Description
Interface Summary | |
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StAXHandlerFactory | StAXHandlerFactory is an interface for factories
producing StAXContentHandler s which are used by the
SeqSimilarityStAXAdapter . |
Class Summary | |
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AlignmentStAXHandler | AlignmentStAXHandler handles the BlastLikeAlignment
element of BioJava BlastLike XML. |
AlphabetResolver | AlphabetResolver s are helpers which determine which
type of sequence Alphabet to expect from a search
result. |
AnnotationFactory | AnnotationFactory is a utility class for making
Annotation s from Map s. |
BlastLikeHomologyBuilder | BlastLikeHomologyBuilder populates a
List with Homology instances created from
SAX events supplied via a SeqSimilarityAdapter . |
BlastLikeSearchBuilder | BlastLikeSearchBuilder will create
SeqSimilaritySearchResult s 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 SimilarityPairFeature s
created from SAX events supplied via a
SeqSimilarityAdapter . |
StAXHandlerBinding | StAXHandlerBinding s associates an
ElementRecognizer with a factory which creates
StAXContentHandler s 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. |
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
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