Package org.biojava.bio.search

Interfaces and classes for representing sequence similarity search results.

See:
          Description

Interface Summary
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.
SearchContentAdapter An adapter for SearchContentHandler.
SearchContentFilter Filtering implementation of SearchContentHandler that by default passes all messages on to the next delegate in the chain.
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.