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 TypeClassDescriptionclass
FastaSearchSAXParser
is 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 TypeClassDescriptionclass
BlastLikeHomologyBuilder
populates aList
withHomology
instances created from SAX events supplied via aSeqSimilarityAdapter
.class
BlastLikeSearchBuilder
will createSeqSimilaritySearchResult
s from SAX events via aSeqSimilarityAdapter
.class
SimilarityPairBuilder
annotates query and subjectSequence
withSimilarityPairFeature
s created from SAX events supplied via aSeqSimilarityAdapter
.Methods in org.biojava.bio.program.ssbind that return SearchContentHandlerModifier and TypeMethodDescriptionSeqSimilarityAdapter.getSearchContentHandler()
getSearchContentHandler
gets the handler which will recieve the method calls generated by the adapter.SeqSimilarityStAXAdapter.getSearchContentHandler()
getSearchContentHandler
gets 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 TypeMethodDescriptionvoid
SeqSimilarityAdapter.setSearchContentHandler
(SearchContentHandler scHandler) setSearchContentHandler
sets the handler which will recieve the method calls generated by the adapter.void
SeqSimilarityStAXAdapter.setSearchContentHandler
(SearchContentHandler scHandler) setSearchContentHandler
sets 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 TypeInterfaceDescriptioninterface
TheSearchBuilder
interface is to be used by objects which accumulate state via aSearchContentHandler
and then construct aSeqSimilaritySearchResult
object.Classes in org.biojava.bio.search that implement SearchContentHandlerModifier and TypeClassDescriptionclass
class
An adapter for SearchContentHandler.class
Filtering implementation of SearchContentHandler that by default passes all messages on to the next delegate in the chain.class
This 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 TypeMethodDescriptionvoid
FilteringContentHandler.setSearchContentHandler
(SearchContentHandler delegate) Constructors in org.biojava.bio.search with parameters of type SearchContentHandlerModifierConstructorDescriptionFilteringContentHandler
(BlastLikeSearchFilter filter, SearchContentHandler delegate) SearchContentFilter
(SearchContentHandler delegate)