Package org.biojava.bio.program.ssaha
Interface SearchListener
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- All Known Implementing Classes:
HitMerger
,SearchListener.Echo
,SearchListener.FilterByLength
,SearchListener.Tee
,SearchListener.Wrapper
public interface SearchListener
The interface used to inform interested parties that some sequence has been searched and something found.The callbacks will always be called in the order startSearch, hit, endSearch, during which time there may be multiple hit calls. The seqID of startSearch and endSearch will match. After this, a new startSearch may begin. These events will usually originate from the search method of DataStore.
- Author:
- Matthew Pocock
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Nested Class Summary
Nested Classes Modifier and Type Interface Description static class
SearchListener.Echo
A SearchListener that prints events out to a PrintStream.static class
SearchListener.FilterByLength
A simple listener that filters out all hits that are too short.static class
SearchListener.Tee
A SearchListener that passes events on to two delegate listeners.static class
SearchListener.Wrapper
A simple wrapper implementation.
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
endSearch(String seqID)
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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Method Detail
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startSearch
void startSearch(String seqID)
Indicates that a sequence is about to be searched against a DataStore.- Parameters:
seqID
- the id of the sequence to be searched
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endSearch
void endSearch(String seqID)
Indicates that a sequence has been searched against a DataStore.- Parameters:
seqID
- the id of the sequence to be searched
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hit
void hit(int hitID, int queryOffset, int hitOffset, int hitLength)
There has been a hit between the query sequence and a database sequence.- 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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