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

Methods in org.biojava.bio.program.ssbind with parameters of type SearchContentHandler
 void SeqSimilarityStAXAdapter.setSearchContentHandler(SearchContentHandler scHandler)
          setSearchContentHandler sets the handler which will recieve the method calls generated by the adapter.
 void SeqSimilarityAdapter.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 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.
 

Constructors in org.biojava.bio.search with parameters of type SearchContentHandler
SearchContentFilter(SearchContentHandler delegate)