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 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.