org.biojava.bio.search

Class MaxMismatchPattern

java.lang.Object

org.biojava.bio.search.MaxMismatchPattern

All Implemented Interfaces:

BioPattern

public class MaxMismatchPattern
extends Object
implements BioPattern

This class permits searching a SymbolList with another SymbolList while permitting a specified number of mismatches. The search pattern can include ambiguity Symbols.

Author:

Matthew Pocock (wrote original MaxMissmatchPattern class), David Huen (debugging and extension to permit ambiguity symbols)

Constructor Summary

Constructors

Constructor and Description
MaxMismatchPattern()
MaxMismatchPattern(SymbolList pattern, int mismatches)

Method Summary

Methods

Modifier and Type	Method and Description
int	getMismatches()
SymbolList	getPattern()
BioMatcher	matcher(SymbolList symList) Get a matcher that will use these parameters to search a SymbolList.
void	setMismatches(int mismatches)
void	setPattern(SymbolList pattern)

Methods inherited from class java.lang.Object

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

Constructor Detail

MaxMismatchPattern

public MaxMismatchPattern()

MaxMismatchPattern

public MaxMismatchPattern(SymbolList pattern,
                  int mismatches)

Method Detail

getMismatches

public int getMismatches()

setMismatches

public void setMismatches(int mismatches)

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