Package org.biojava.bio.program.ssaha
Class HitMerger
java.lang.Object
org.biojava.bio.program.ssaha.HitMerger
- All Implemented Interfaces:
SearchListener
A listener that merges overlapping hits and culls all hits under a given
length.
- Author:
- Matthew Pocock
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.program.ssaha.SearchListener
SearchListener.Echo, SearchListener.FilterByLength, SearchListener.Tee, SearchListener.Wrapper
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Constructor Summary
ConstructorsConstructorDescriptionHitMerger
(SearchListener delegate, int minLength) Build a new HitMerger that will pass events on to a delegate. -
Method Summary
Modifier and TypeMethodDescriptionvoid
Indicates that a sequence has been searched against a DataStore.void
hit
(int hitID, int queryOffset, int hitOffset, int hitLength) There has been a hit between the query sequence and a database sequence.void
startSearch
(String seqID) Indicates that a sequence is about to be searched against a DataStore.
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Constructor Details
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HitMerger
Build a new HitMerger that will pass events on to a delegate.- Parameters:
delegate
- the SearchListener to inform of all merged and filtered hitsminLength
- the minimum length a hit must reach to be passed on
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Method Details
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startSearch
Description copied from interface:SearchListener
Indicates that a sequence is about to be searched against a DataStore.- Specified by:
startSearch
in interfaceSearchListener
- Parameters:
seqID
- the id of the sequence to be searched
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hit
Description copied from interface:SearchListener
There has been a hit between the query sequence and a database sequence.- Specified by:
hit
in interfaceSearchListener
- Parameters:
hitID
- the number of the sequence hit; resolvable by String id = DataStore.seqNameForID(hitID)queryOffset
- the offset into the query sequencehitOffset
- the offset into the sequence hit in the databasehitLength
- the number of symbols hit
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endSearch
Description copied from interface:SearchListener
Indicates that a sequence has been searched against a DataStore.- Specified by:
endSearch
in interfaceSearchListener
- Parameters:
seqID
- the id of the sequence to be searched
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