## 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 `SeqSimilaritySearchHit`s by their score.
SeqSimilaritySearchHit.BySubHitCountComparator: `BySubHitCountComparator` compares `SeqSimilaritySearchHit`s by their number of sub-hits.
SeqSimilaritySearchSubHit.ByScoreComparator: `ByScoreComparator` compares `SeqSimilaritySearchSubHit`s by their score.
SeqSimilaritySearchSubHit.BySubjectStartComparator: `BySubjectStartComparator` compares `SeqSimilaritySearchSubHit`s 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.