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## 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.

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