All Implemented Interfaces:

BioPattern

public class MaxMismatchPattern
extends Object
implements BioPattern 

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

  All 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