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Packages that use org.biojava.bio.search | |
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 | |
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 | |
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 | |
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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