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 and 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 and 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 and 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.