mobios.dist
Class WHDGlobalSequenceFragmentMetric

java.lang.Object
  mobios.dist.SequenceFragmentMetric
      mobios.dist.WHDGlobalSequenceFragmentMetric

All Implemented Interfaces:

Serializable, Metric

public class WHDGlobalSequenceFragmentMetric
extends SequenceFragmentMetric

Computes global alignment on Fragments with Weighted Hamming Distance. The fragments must be the same length.

Version:

2004.03.02

Author:

Weijia Xu, Rui Mao, Willard

See Also:

Serialized Form

Constructor Summary

WHDGlobalSequenceFragmentMetric(WeightMatrix weightMatrix)
Constructor.

Method Summary

double	getDistance(Fragment one, Fragment two) Computes the distance between two Fragments
WeightMatrix	getWeightMatrix()

Methods inherited from class mobios.dist.SequenceFragmentMetric

getDistance

Methods inherited from class java.lang.Object

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

Constructor Detail

WHDGlobalSequenceFragmentMetric

public WHDGlobalSequenceFragmentMetric(WeightMatrix weightMatrix)

Constructor. Defines a new WHDGlobalSequenceFragmentMetric over the given WeightMatrix

Parameters:

weightMatrix -

Method Detail

getDistance

public double getDistance(Fragment one,
                          Fragment two)

Description copied from class: SequenceFragmentMetric

Computes the distance between two Fragments

Specified by:

getDistance in class SequenceFragmentMetric

Parameters:

one - the first Fragment to compute distance on

two - the second Fragment to compute distance on

Returns:

the distance between the two Fragments

getWeightMatrix

public WeightMatrix getWeightMatrix()

Overrides:

getWeightMatrix in class SequenceFragmentMetric

Returns:

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