org.biojava.bio.search
Class MaxMissmatchPattern

java.lang.Object
  org.biojava.bio.search.MaxMissmatchPattern

All Implemented Interfaces:

BioPattern

public class MaxMissmatchPattern

extends Object

implements BioPattern

Author:

Matthew Pocock

Constructor Summary

MaxMissmatchPattern()

MaxMissmatchPattern(SymbolList pattern, int missmatches)

Method Summary

int	getMissmatches()
SymbolList	getPattern()
BioMatcher	matcher(SymbolList symList) Get a matcher that will use these parameters to search a SymbolList.
void	setMissmatches(int missmatches)
void	setPattern(SymbolList pattern)

Methods inherited from class java.lang.Object

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

Constructor Detail

MaxMissmatchPattern

public MaxMissmatchPattern()

MaxMissmatchPattern

public MaxMissmatchPattern(SymbolList pattern,
                           int missmatches)

Method Detail

getMissmatches

public int getMissmatches()

setMissmatches

public void setMissmatches(int missmatches)

getPattern

public SymbolList getPattern()

setPattern

public void setPattern(SymbolList pattern)

matcher

public BioMatcher matcher(SymbolList symList)
                   throws IllegalAlphabetException

Description copied from interface: BioPattern

Get a matcher that will use these parameters to search a SymbolList.

The resulting BioMatcher is independant of this BioPattern. In particular, calling any mutator methods on this pattern will not affect the matcher.

Specified by:

matcher in interface BioPattern

Parameters:

symList - the SymbolList to match against

Returns:

a BioMatcher that will perform the search

Throws:

IllegalAlphabetException - if symList is not over the right alphabet