Package org.biojava.bio.search
package org.biojava.bio.search
Interfaces and classes for representing sequence similarity search results.
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ClassDescriptionInterface for things that perform matches.A SearchContentHandler class that implements filtering in chains of SearchContentHandler instances.Applies test to the value specified by the key in hit properties.Applies test to the value specified by the key in search properties.Applies test to the value specified by the key in subhit properties.Class for implementing tests with BlastLikeSearchFilter objects.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.Tests that the value associated with the specified key contains a part matched by the supplied regex.Tests that the value associated with the specified key is greater than the specified threshold.Tests that the value associated with the specified key is less than the specified threshold.Tests that the value associated with the specified key is matched in its entirety by the supplied regex.An object to find exact subsequences within a sequence.A BioMatcher class returned by MaxMismatchPattern.matcher() that implements searching of a SymbolList.This class permits searching a SymbolList with another SymbolList while permitting a specified number of mismatches.The
SearchBuilder
interface is to be used by objects which accumulate state via aSearchContentHandler
and then construct aSeqSimilaritySearchResult
object.An adapter for SearchContentHandler.Filtering implementation of SearchContentHandler that by default passes all messages on to the next delegate in the chain.SearchContentHandler
is a notification interface for objects which listen to search stream parsers.This class prints to a PrintStream calls to the SearchContentHandler interface in human readable form.A pattern that can be used to find regions with given sequence content.Objects of this type represent one particular installation (not just implementation) of a sequence similarity searcher such as BLASTP.Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.ByScoreComparator
comparesSeqSimilaritySearchHit
s by their score.BySubHitCountComparator
comparesSeqSimilaritySearchHit
s by their number of sub-hits.Objects of this type represent one particular result of a sequence similarity search.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.ByScoreComparator
comparesSeqSimilaritySearchSubHit
s by their score.BySubjectStartComparator
comparesSeqSimilaritySearchSubHit
s by their start position on the subject sequence.Deprecated.SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.Deprecated.SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.Deprecated.SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.SimpleSeqSimilaritySearchHit
objects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.SimpleSeqSimilaritySearchResult
objects represent a result of a search of aSymbolList
against the sequences within aSequenceDB
object.SimpleSeqSimilaritySearchSubHit
objects represent sub-hits which make up a hit.