Uses of Interface
org.biojava.bio.search.SearchContentHandler
Packages that use SearchContentHandler
Package
Description
Parsers which offer XML representations of the output from common
bioinformatics tools.
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
Interfaces and classes for representing sequence similarity search results.
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Uses of SearchContentHandler in org.biojava.bio.program.sax
Classes in org.biojava.bio.program.sax that implement SearchContentHandlerModifier and TypeClassDescriptionclassFastaSearchSAXParseris a SAX2 compliant parser for '-m 10' format output from the the Fasta search program (see the Fasta documentation for details of this format). -
Uses of SearchContentHandler in org.biojava.bio.program.ssbind
Classes in org.biojava.bio.program.ssbind that implement SearchContentHandlerModifier and TypeClassDescriptionclassBlastLikeHomologyBuilderpopulates aListwithHomologyinstances created from SAX events supplied via aSeqSimilarityAdapter.classBlastLikeSearchBuilderwill createSeqSimilaritySearchResults from SAX events via aSeqSimilarityAdapter.classSimilarityPairBuilderannotates query and subjectSequencewithSimilarityPairFeatures created from SAX events supplied via aSeqSimilarityAdapter.Methods in org.biojava.bio.program.ssbind that return SearchContentHandlerModifier and TypeMethodDescriptionSeqSimilarityAdapter.getSearchContentHandler()getSearchContentHandlergets the handler which will recieve the method calls generated by the adapter.SeqSimilarityStAXAdapter.getSearchContentHandler()getSearchContentHandlergets the handler which will receive the method calls generated by the adapter.Methods in org.biojava.bio.program.ssbind with parameters of type SearchContentHandlerModifier and TypeMethodDescriptionvoidSeqSimilarityAdapter.setSearchContentHandler(SearchContentHandler scHandler) setSearchContentHandlersets the handler which will recieve the method calls generated by the adapter.voidSeqSimilarityStAXAdapter.setSearchContentHandler(SearchContentHandler scHandler) setSearchContentHandlersets the handler which will recieve the method calls generated by the adapter. -
Uses of SearchContentHandler in org.biojava.bio.search
Subinterfaces of SearchContentHandler in org.biojava.bio.searchModifier and TypeInterfaceDescriptioninterfaceTheSearchBuilderinterface is to be used by objects which accumulate state via aSearchContentHandlerand then construct aSeqSimilaritySearchResultobject.Classes in org.biojava.bio.search that implement SearchContentHandlerModifier and TypeClassDescriptionclassclassAn adapter for SearchContentHandler.classFiltering implementation of SearchContentHandler that by default passes all messages on to the next delegate in the chain.classThis class prints to a PrintStream calls to the SearchContentHandler interface in human readable form.Methods in org.biojava.bio.search with parameters of type SearchContentHandlerModifier and TypeMethodDescriptionvoidFilteringContentHandler.setSearchContentHandler(SearchContentHandler delegate) Constructors in org.biojava.bio.search with parameters of type SearchContentHandlerModifierConstructorDescriptionFilteringContentHandler(BlastLikeSearchFilter filter, SearchContentHandler delegate) SearchContentFilter(SearchContentHandler delegate)