Uses of Interface
org.biojava.bio.search.SearchContentHandler

Packages that use SearchContentHandler

org.biojava.bio.program.sax	Parsers which offer XML representations of the output from common bioinformatics tools.
org.biojava.bio.program.ssbind	Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.

Uses of SearchContentHandler in org.biojava.bio.program.sax

Classes in org.biojava.bio.program.sax that implement SearchContentHandler

class

FastaSearchSAXParser 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 SearchContentHandler

class	BlastLikeHomologyBuilder BlastLikeHomologyBuilder populates a List with Homology instances created from SAX events supplied via a SeqSimilarityAdapter.
class	BlastLikeSearchBuilder BlastLikeSearchBuilder will create SeqSimilaritySearchResults from SAX events via a SeqSimilarityAdapter.
class	SimilarityPairBuilder SimilarityPairBuilder annotates query and subject Sequence with SimilarityPairFeatures created from SAX events supplied via a SeqSimilarityAdapter.

Methods in org.biojava.bio.program.ssbind that return SearchContentHandler

SearchContentHandler	SeqSimilarityAdapter.getSearchContentHandler() getSearchContentHandler gets the handler which will recieve the method calls generated by the adapter.
SearchContentHandler	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 SearchContentHandler

void	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.search

interface

SearchBuilder The SearchBuilder interface is to be used by objects which accumulate state via a SearchContentHandler and then construct a SeqSimilaritySearchResult object.

Classes in org.biojava.bio.search that implement SearchContentHandler

class	FilteringContentHandler
class	SearchContentAdapter An adapter for SearchContentHandler.
class	SearchContentFilter Filtering implementation of SearchContentHandler that by default passes all messages on to the next delegate in the chain.
class	SearchContentHandlerDebugger 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 SearchContentHandler

void	FilteringContentHandler.setSearchContentHandler(SearchContentHandler delegate)

Constructors in org.biojava.bio.search with parameters of type SearchContentHandler

FilteringContentHandler(BlastLikeSearchFilter filter, SearchContentHandler delegate)

SearchContentFilter(SearchContentHandler delegate)