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

java.lang.Object
  extended by org.biojava.bio.program.ssaha.SearchListener.Echo
All Implemented Interfaces:
SearchListener
Enclosing interface:
SearchListener

public static final class SearchListener.Echo
extends Object
implements SearchListener

A SearchListener that prints events out to a PrintStream.

Use this for debugging purposes.

Since:
1.4
Author:
Matthew Pocock

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.Echo(PrintStream out)
           
 
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.Echo

public SearchListener.Echo(PrintStream out)
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