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## 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 `SeqSimilaritySearchHit`s by their score.
SeqSimilaritySearchHit.BySubHitCountComparator `BySubHitCountComparator` compares `SeqSimilaritySearchHit`s 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 `SeqSimilaritySearchSubHit`s by their score.
SeqSimilaritySearchSubHit.BySubjectStartComparator `BySubjectStartComparator` compares `SeqSimilaritySearchSubHit`s by their start position on the subject sequence.

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