org.biojava.bio.program.ssaha

Class HitMerger

java.lang.Object

org.biojava.bio.program.ssaha.HitMerger

All Implemented Interfaces:

SearchListener

public class HitMerger
extends Object
implements SearchListener

A listener that merges overlapping hits and culls all hits under a given length.

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
HitMerger(SearchListener delegate, int minLength) Build a new HitMerger that will pass events on to a delegate.

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

HitMerger

public HitMerger(SearchListener delegate,
         int minLength)

Build a new HitMerger that will pass events on to a delegate.

Parameters:

delegate - the SearchListener to inform of all merged and filtered hits

minLength - the minimum length a hit must reach to be passed on

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

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

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