Package org.biojava.bio.search

Interfaces and classes for representing sequence similarity search results.

See:
Description

Interface Summary

BioMatcher	Interface for things that perform matches.
BioPattern
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.
SeqSimilaritySearcher	Objects of this type represent one particular installation (not just implementation) of a sequence similarity searcher such as BLASTP.
SeqSimilaritySearchHit	Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.
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.

Class Summary

KnuthMorrisPrattSearch	An object to find exact subsequences within a sequence.
MaxMissmatchPattern
SearchContentAdapter	An adapter for SearchContentHandler.
SearchContentFilter	Filtering implementation of SearchContentHandler that by default passes all messages on to the next delegate in the chain.
SeqContentPattern	A pattern that can be used to find regions with given sequence content.
SeqSimilaritySearchHit.ByScoreComparator	ByScoreComparator compares SeqSimilaritySearchHits by their score.
SeqSimilaritySearchHit.BySubHitCountComparator	BySubHitCountComparator compares SeqSimilaritySearchHits by their number of sub-hits.
SeqSimilaritySearchSubHit.ByScoreComparator	ByScoreComparator compares SeqSimilaritySearchSubHits by their score.
SeqSimilaritySearchSubHit.BySubjectStartComparator	BySubjectStartComparator compares SeqSimilaritySearchSubHits by their start position on the subject sequence.
SequenceDBSearchHit	Deprecated. SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.
SequenceDBSearchResult	Deprecated. SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.
SequenceDBSearchSubHit	Deprecated. SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.
SimpleSeqSimilaritySearchHit	SimpleSeqSimilaritySearchHit objects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.
SimpleSeqSimilaritySearchResult	SimpleSeqSimilaritySearchResult objects represent a result of a search of a SymbolList against the sequences within a SequenceDB object.
SimpleSeqSimilaritySearchSubHit	SimpleSeqSimilaritySearchSubHit objects represent sub-hits which make up a hit.

Package org.biojava.bio.search Description

Interfaces and classes for representing sequence similarity search results.