mobios.dist
Class SymmetricSubstitutionWeightMatrix

java.lang.Object
  mobios.dist.SymmetricSubstitutionWeightMatrix

All Implemented Interfaces:

Serializable, WeightMatrix

public class SymmetricSubstitutionWeightMatrix
extends Object
implements WeightMatrix

Implements a WeightMatrix by providing a symmetric substitution matrix of double distances for a given Alphabet. Thus, this class defines a weighted edit distance on an Alphabet.

Version:

2004.03.02

Author:

Rui Mao, Willard

See Also:

Serialized Form

Constructor Summary

SymmetricSubstitutionWeightMatrix(Alphabet alphabet, double[][] distances)
Constructor.

Method Summary

Alphabet	getAlphabet()
double	getDistance(Symbol one, Symbol two)

Methods inherited from class java.lang.Object

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

Constructor Detail

SymmetricSubstitutionWeightMatrix

public SymmetricSubstitutionWeightMatrix(Alphabet alphabet,
                                         double[][] distances)

Constructor.

Parameters:

alphabet - the Alphabet that this SymmetricSubstitionWeightMatrix is defined over.

distances - a two-dimensional array of double distances between the Symbol objects of the alphabet.

Method Detail

getDistance

public double getDistance(Symbol one,
                          Symbol two)

Specified by:

getDistance in interface WeightMatrix

Returns:

the distance between two Symbol objects in the Alphabet over which this matrix is defined.

getAlphabet

public Alphabet getAlphabet()

Specified by:

getAlphabet in interface WeightMatrix

Returns:

the Alphabet over which this matrix is defined.