Uses of Package
org.biojava.bio.search

Packages that use org.biojava.bio.search
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. 
 

Classes in org.biojava.bio.search used by org.biojava.bio.program.sax
SearchContentHandler
          SearchContentHandler is a notification interface for objects which listen to search stream parsers.
 

Classes in org.biojava.bio.search used by org.biojava.bio.program.ssbind
SearchBuilder
          The SearchBuilder interface is to be used by objects which accumulate state via a SearchContentHandler and then construct a SeqSimilaritySearchResult object.
SearchContentHandler
          SearchContentHandler is a notification interface for objects which listen to search stream parsers.
SeqSimilaritySearchResult
          Objects of this type represent one particular result of a sequence similarity search.
 

Classes in org.biojava.bio.search used by org.biojava.bio.search
BioMatcher
          Interface for things that perform matches.
BioPattern
           
BlastLikeSearchFilter
          A SearchContentHandler class that implements filtering in chains of SearchContentHandler instances.
BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
           
BlastLikeSearchFilter.ByHitProperty
          Applies test to the value specified by the key in hit properties.
BlastLikeSearchFilter.BySearchProperty
          Applies test to the value specified by the key in search properties.
BlastLikeSearchFilter.BySubHitProperty
          Applies test to the value specified by the key in subhit properties.
BlastLikeSearchFilter.Node
           
FilterTest
          Class for implementing tests with BlastLikeSearchFilter objects.
SearchContentAdapter
           An adapter for SearchContentHandler.
SearchContentHandler
          SearchContentHandler is a notification interface for objects which listen to search stream parsers.
SeqSimilaritySearchHit
          Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.
SeqSimilaritySearchHit.ByScoreComparator
          ByScoreComparator compares SeqSimilaritySearchHits by their score.
SeqSimilaritySearchHit.BySubHitCountComparator
          BySubHitCountComparator compares SeqSimilaritySearchHits by their number of sub-hits.
SeqSimilaritySearchResult
          Objects of this type represent one particular result of a sequence similarity search.
SeqSimilaritySearchSubHit
          Objects of this type represent one particular sub-hit (one concrete sequence stretch within a sequence and associated information) from a sequence similarity search hit.
SeqSimilaritySearchSubHit.ByScoreComparator
          ByScoreComparator compares SeqSimilaritySearchSubHits by their score.
SeqSimilaritySearchSubHit.BySubjectStartComparator
          BySubjectStartComparator compares SeqSimilaritySearchSubHits by their start position on the subject sequence.