org.biojava.bio.program.ssaha
Class SearchListener.Wrapper

java.lang.Object
  extended by org.biojava.bio.program.ssaha.SearchListener.Wrapper
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.

Since:
1.4
Author:
Matthew Pocock
For advanced users:
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.

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojava.bio.program.ssaha.SearchListener
SearchListener.Echo, SearchListener.FilterByLength, SearchListener.Tee, SearchListener.Wrapper
 
Constructor Summary
SearchListener.Wrapper(SearchListener delegate)
           
 
Method Summary
 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.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SearchListener.Wrapper

public SearchListener.Wrapper(SearchListener delegate)
Method Detail

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 interface SearchListener
Parameters:
seqID - the id of the sequence to be searched

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 interface SearchListener
Parameters:
seqID - the id of the sequence to be searched

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 interface SearchListener
Parameters:
hitID - the number of the sequence hit; resolvable by String id = DataStore.seqNameForID(hitID)
queryOffset - the offset into the query sequence
hitOffset - the offset into the sequence hit in the database
hitLength - the number of symbols hit