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See:
Description
Interface Summary | |
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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 | |
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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. |
Interfaces and classes for representing sequence similarity search results.
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