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Packages that use org.biojava.bio.search | |
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org.biojava.bio.program.sax | Parsers which offer XML representations of the output from common bioinformatics tools. |
org.biojava.bio.program.ssbind | Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD. |
org.biojava.bio.search | Interfaces and classes for representing sequence similarity search results. |
Classes in org.biojava.bio.search used by org.biojava.bio.program.sax | |
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SearchContentHandler
SearchContentHandler is a notification interface for
objects which listen to search stream parsers. |
Classes in org.biojava.bio.search used by org.biojava.bio.program.ssbind | |
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SearchBuilder
The SearchBuilder interface is to be used by objects
which accumulate state via a SearchContentHandler and
then construct a SeqSimilaritySearchResult object. |
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SearchContentHandler
SearchContentHandler is a notification interface for
objects which listen to search stream parsers. |
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SeqSimilaritySearchResult
Objects of this type represent one particular result of a sequence similarity search. |
Classes in org.biojava.bio.search used by org.biojava.bio.search | |
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BioMatcher
Interface for things that perform matches. |
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BioPattern
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BlastLikeSearchFilter
A SearchContentHandler class that implements filtering in chains of SearchContentHandler instances. |
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BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
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BlastLikeSearchFilter.ByHitProperty
Applies test to the value specified by the key in hit properties. |
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BlastLikeSearchFilter.BySearchProperty
Applies test to the value specified by the key in search properties. |
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BlastLikeSearchFilter.BySubHitProperty
Applies test to the value specified by the key in subhit properties. |
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BlastLikeSearchFilter.Node
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FilterTest
Class for implementing tests with BlastLikeSearchFilter objects. |
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SearchContentAdapter
An adapter for SearchContentHandler. |
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SearchContentHandler
SearchContentHandler is a notification interface for
objects which listen to search stream parsers. |
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SeqSimilaritySearchHit
Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search. |
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SeqSimilaritySearchHit.ByScoreComparator
ByScoreComparator compares
SeqSimilaritySearchHit s by their score. |
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SeqSimilaritySearchHit.BySubHitCountComparator
BySubHitCountComparator compares
SeqSimilaritySearchHit s by their number of
sub-hits. |
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SeqSimilaritySearchResult
Objects of this type represent one particular result of a sequence similarity search. |
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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. |
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SeqSimilaritySearchSubHit.ByScoreComparator
ByScoreComparator compares
SeqSimilaritySearchSubHit s by their score. |
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SeqSimilaritySearchSubHit.BySubjectStartComparator
BySubjectStartComparator compares
SeqSimilaritySearchSubHit s by their start position
on the subject sequence. |
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