Package org.biojava.bio.program.ssaha
Class SearchListener.Wrapper
- java.lang.Object
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- org.biojava.bio.program.ssaha.SearchListener.Wrapper
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- All Implemented Interfaces:
SearchListener
- Direct Known Subclasses:
SearchListener.FilterByLength
- Enclosing interface:
- SearchListener
public abstract static class SearchListener.Wrapper extends Object implements SearchListener
A simple wrapper implementation.Extend this and over-ride any of the interface methods to implement SearchListeners that filter hits before passing them on to an underlying listener.
You can modify the search events the delegate sees by over-riding any of the SearchListener methods, modify the arguments and then call the method on super with the new arguments. You can drop hits by just not passing them onto the delegate using super.hits(). Note: Be sure to maintain the nesting of start/stop search and hit, or you will confuse the delegate.- Since:
- 1.4
- Author:
- Matthew Pocock
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Nested Class Summary
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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
Constructors Constructor Description Wrapper(SearchListener delegate)
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Method Summary
All Methods Instance Methods Concrete 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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Constructor Detail
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Wrapper
public Wrapper(SearchListener delegate)
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Method Detail
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startSearch
public void startSearch(String seqID)
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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endSearch
public void endSearch(String seqID)
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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hit
public void hit(int hitID, int queryOffset, int hitOffset, int hitLength)
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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