## 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
BlastLikeSearchFilter: A SearchContentHandler class that implements filtering in chains of SearchContentHandler instances.
BlastLikeSearchFilter.Node
FilterTest: Class for implementing tests with BlastLikeSearchFilter objects.
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
BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
BlastLikeSearchFilter.And
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.Not
BlastLikeSearchFilter.Or
FilteringContentHandler
FilterTest.Equals: Tests that the value associated with the specified key is equal to the value supplied here by whatever criterion of equality appropriate to those objects.
FilterTest.FindRegex: Tests that the value associated with the specified key contains a part matched by the supplied regex.
FilterTest.GreaterThan: Tests that the value associated with the specified key is greater than the specified threshold.
FilterTest.LessThan: Tests that the value associated with the specified key is less than the specified threshold.
FilterTest.MatchRegex: Tests that the value associated with the specified key is matched in its entirety by the supplied regex.
KnuthMorrisPrattSearch: An object to find exact subsequences within a sequence.
MaxMismatchMatcher: A BioMatcher class returned by MaxMismatchPattern.matcher() that implements searching of a SymbolList.
MaxMismatchPattern: This class permits searching a SymbolList with another SymbolList while permitting a specified number of mismatches.
SearchContentAdapter: An adapter for SearchContentHandler.
SearchContentFilter: Filtering implementation of SearchContentHandler that by default passes all messages on to the next delegate in the chain.
SearchContentHandlerDebugger: This class prints to a PrintStream calls to the SearchContentHandler interface in human readable form.
SeqContentPattern: A pattern that can be used to find regions with given sequence content.
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.