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

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

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	Description
Wrapper(SearchListener delegate)

Method Summary

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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Wrapper

public 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