org.biojava.bio.program.ssaha

Class SearchListener.Echo

java.lang.Object

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

Constructors

Constructor and Description
SearchListener.Echo(PrintStream out)

Method Summary

Methods

Modifier and Type	Method and 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.

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