Package org.biojava.bio.program.ssaha
Class SearchListener.Wrapper
java.lang.Object
org.biojava.bio.program.ssaha.SearchListener.Wrapper
- All Implemented Interfaces:
SearchListener
- Direct Known Subclasses:
SearchListener.FilterByLength
- Enclosing interface:
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
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 -
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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Wrapper
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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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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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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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