org.biojava.bio.search

Class MaxMismatchMatcher

java.lang.Object

org.biojava.bio.search.MaxMismatchMatcher

All Implemented Interfaces:

BioMatcher

public class MaxMismatchMatcher
extends Object
implements BioMatcher

A BioMatcher class returned by MaxMismatchPattern.matcher() that implements searching of a SymbolList.

This class is public only to allow access to the mismatchCount() method.

Author:

Matthew Pocock (wrote original MaxMissmatchMatcher class), David Huen (debugging and extension of functionality)

Method Summary

Methods

Modifier and Type	Method and Description
int	end() Get the last symbol index that matches the pattern.
boolean	find() Attempt to find the next match.
SymbolList	group() Get the matching region as a SymbolList.
int	mismatchCount() Returns number of mismatches
int	start() Get the first symbol index that matches the pattern.

Methods inherited from class java.lang.Object

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

Method Detail

find

public boolean find()

Description copied from interface: BioMatcher

Attempt to find the next match.

If the pattern can be found, then this will return true. If it could not, then it will return false. This is convenient within for or while loops.

Each time this is called, the next match will be found. The start() and end() values will increase each time, regardless of wether you called any other methods.

Specified by:

find in interface BioMatcher

Returns:

true if there is another match

start

public int start()

Description copied from interface: BioMatcher

Get the first symbol index that matches the pattern.

Specified by:

start in interface BioMatcher

Returns:

the start of the current match

end

public int end()

Description copied from interface: BioMatcher

Get the last symbol index that matches the pattern.

Specified by:

end in interface BioMatcher

Returns:

the end of the current match

group

public SymbolList group()

Description copied from interface: BioMatcher

Get the matching region as a SymbolList.

Specified by:

group in interface BioMatcher

Returns:

the matching symbols

mismatchCount

public int mismatchCount()

Returns number of mismatches