Package org.biojava.bio.program.ssaha

Class SearchListener.FilterByLength

java.lang.Object

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

org.biojava.bio.program.ssaha.SearchListener.FilterByLength

All Implemented Interfaces:

SearchListener

Enclosing interface:

SearchListener

public static final class SearchListener.FilterByLength
extends SearchListener.Wrapper

A simple listener that filters out all hits that are too short.

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
FilterByLength(SearchListener delegate, int minLength)

Method Summary

Modifier and Type	Method	Description
void	hit(int hitID, int queryOffset, int hitOffset, int hitLength)	There has been a hit between the query sequence and a database sequence.

Methods inherited from class org.biojava.bio.program.ssaha.SearchListener.Wrapper

endSearch, startSearch

Methods inherited from class java.lang.Object

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

Constructor Detail

FilterByLength

public FilterByLength(SearchListener delegate,
                      int minLength)

Method Detail

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

Overrides:

hit in class SearchListener.Wrapper

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