Package org.biojava.bio.search

Interfaces and classes for representing sequence similarity search results.

Interface Summary

Interface	Description
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

Class	Description
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 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.