Uses of Package
org.biojava.bio.search

Packages that use org.biojava.bio.search

Package	Description
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

Class	Description
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

Class	Description
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

Class	Description
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.