org.biojava.bio.program.ssbind (BioJava-1.5-beta API)
Keywords: org.biojava.bio.program.ssbind package

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## 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 `StAXContentHandler`s which are used by the `SeqSimilarityStAXAdapter`.

Class Summary
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.

## Package org.biojava.bio.program.ssbind Description

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

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