mobios.dist
Class SequenceFragmentMetric

java.lang.Object
  mobios.dist.SequenceFragmentMetric

All Implemented Interfaces:

Serializable, Metric

Direct Known Subclasses:

WHDGlobalSequenceFragmentMetric

public abstract class SequenceFragmentMetric
extends Object
implements Metric

Computes the distance between two Fragments.

Version:

2006.05.31

Author:

Jack, Rui Mao, Willard

See Also:

Serialized Form

Constructor Summary

SequenceFragmentMetric(WeightMatrix weightMatrix)
Creates a new SequenceFragmentMetric over the given WeightMatrix.

Method Summary

abstract double	getDistance(Fragment one, Fragment two) Computes the distance between two Fragments
double	getDistance(IndexObject one, IndexObject two) Computes the distance between two objects.
WeightMatrix	getWeightMatrix()

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceFragmentMetric

public SequenceFragmentMetric(WeightMatrix weightMatrix)

Creates a new SequenceFragmentMetric over the given WeightMatrix.

Parameters:

weightMatrix -

Method Detail

getWeightMatrix

public WeightMatrix getWeightMatrix()

Returns:

the WeightMatrix used when computing the distance between two fragments using this metric.

getDistance

public double getDistance(IndexObject one,
                          IndexObject two)

Description copied from interface: Metric

Computes the distance between two objects.

Specified by:

getDistance in interface Metric

Parameters:

one - the first IndexObject to compute distance on

two - the second IndexObject to compute distance on

Returns:

the distance between the two objects

getDistance

public abstract double getDistance(Fragment one,
                                   Fragment two)

Computes the distance between two Fragments

Parameters:

one - the first Fragment to compute distance on

two - the second Fragment to compute distance on

Returns:

the distance between the two Fragments