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See:
Description
Interface Summary | |
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 | |
KnuthMorrisPrattSearch | An object to find exact subsequences within a sequence. |
SearchContentAdapter | An adapter for SearchContentHandler. |
SearchContentFilter | Filtering implementation of SearchContentHandler that by default passes all messages on to the next delegate in the chain. |
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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