Package org.biojava.bio.program.ssbind
package org.biojava.bio.program.ssbind
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
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ClassDescription
AlignmentStAXHandler
handles the BlastLikeAlignment element of BioJava BlastLike XML.AlphabetResolver
s are helpers which determine which type of sequenceAlphabet
to expect from a search result.AnnotationFactory
is a utility class for makingAnnotation
s fromMap
s.BlastLikeHomologyBuilder
populates aList
withHomology
instances created from SAX events supplied via aSeqSimilarityAdapter
.BlastLikeSearchBuilder
will createSeqSimilaritySearchResult
s from SAX events via aSeqSimilarityAdapter
.HeaderStAXHandler
handles the Header element of BioJava BlastLike XML.AlignmentStAXHandler
handles the Hit element of BioJava BlastLike XML.HSPStAXHandler
handles the HSP element of BioJava BlastLike XML.HSPSummaryStAXHandler
handles the HSPSummary element of BioJava BlastLike XML.ASeqSimilarityAdapter
converts SAX events into method calls on aSearchContentHandler
implementation.SeqSimilarityStAXAdapter
is a handler for XML conforming to the BioJava BlastLike DTD.SeqSimilarityStAXHandler
is a base class for creating modular StAX handlers which send callbacks to aSeqSimilarityStAXAdapter
.SimilarityPairBuilder
annotates query and subjectSequence
withSimilarityPairFeature
s created from SAX events supplied via aSeqSimilarityAdapter
.StAXHandlerBinding
s associates anElementRecognizer
with a factory which createsStAXContentHandler
s for elements which it theElementRecognizer
accepts.StAXHandlerFactory
is an interface for factories producingStAXContentHandler
s which are used by theSeqSimilarityStAXAdapter
.ViewSequenceFactory
is a base class for creating search handlers which create and cache views on the query and subject sequences.