Interfaces and classes for representing sequence similarity search results.
Interface Summary Interface Description BioMatcherInterface for things that perform matches. BioPattern BlastLikeSearchFilterA SearchContentHandler class that implements filtering in chains of SearchContentHandler instances. BlastLikeSearchFilter.Node FilterTestClass for implementing tests with BlastLikeSearchFilter objects. SearchBuilderThe
SearchBuilderinterface is to be used by objects which accumulate state via a
SearchContentHandlerand then construct a
SearchContentHandleris a notification interface for objects which listen to search stream parsers.
SeqSimilaritySearcherObjects of this type represent one particular installation (not just implementation) of a sequence similarity searcher such as BLASTP. SeqSimilaritySearchHitObjects of this type represent one particular hit (sequence and associated information) from a sequence similarity search. SeqSimilaritySearchResultObjects of this type represent one particular result of a sequence similarity search. SeqSimilaritySearchSubHitObjects 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.ByHitPropertyApplies test to the value specified by the key in hit properties. BlastLikeSearchFilter.BySearchPropertyApplies test to the value specified by the key in search properties. BlastLikeSearchFilter.BySubHitPropertyApplies test to the value specified by the key in subhit properties. BlastLikeSearchFilter.Not BlastLikeSearchFilter.Or FilteringContentHandler FilterTest.EqualsTests 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.FindRegexTests that the value associated with the specified key contains a part matched by the supplied regex. FilterTest.GreaterThanTests that the value associated with the specified key is greater than the specified threshold. FilterTest.LessThanTests that the value associated with the specified key is less than the specified threshold. FilterTest.MatchRegexTests that the value associated with the specified key is matched in its entirety by the supplied regex. KnuthMorrisPrattSearchAn object to find exact subsequences within a sequence. MaxMismatchMatcherA BioMatcher class returned by MaxMismatchPattern.matcher() that implements searching of a SymbolList. MaxMismatchPatternThis class permits searching a SymbolList with another SymbolList while permitting a specified number of mismatches. SearchContentAdapterAn adapter for SearchContentHandler. SearchContentFilterFiltering implementation of SearchContentHandler that by default passes all messages on to the next delegate in the chain. SearchContentHandlerDebuggerThis class prints to a PrintStream calls to the SearchContentHandler interface in human readable form. SeqContentPatternA pattern that can be used to find regions with given sequence content. SeqSimilaritySearchHit.ByScoreComparator
SeqSimilaritySearchHits by their score.
SeqSimilaritySearchHits by their number of sub-hits.
SeqSimilaritySearchSubHits by their score.
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
SimpleSeqSimilaritySearchHitobjects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.
SimpleSeqSimilaritySearchResultobjects represent a result of a search of a
SymbolListagainst the sequences within a
SimpleSeqSimilaritySearchSubHitobjects represent sub-hits which make up a hit.