pal.distance

Class PairwiseDistance

java.lang.Object

pal.distance.PairwiseDistance

All Implemented Interfaces:

java.io.Serializable

public class PairwiseDistance
extends java.lang.Object
implements java.io.Serializable

determines the (observed and ML) distance between a pair of sequences

Version:

$Id: PairwiseDistance.java,v 1.10 2002/09/08 03:47:01 matt Exp $

Author:

Korbinian Strimmer

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
double	distance last estimated distance
double	distanceSE last estimate standard error of a distance

Constructor Summary

Constructors

Constructor and Description
PairwiseDistance(SitePattern sp) Constructor 1 (estimate observed distances only)
PairwiseDistance(SitePattern sp, SubstitutionModel m) Constructor 2 (uses evolutionary model)

Method Summary

Methods

Modifier and Type	Method and Description
double	getDistance(byte[] s1, byte[] s2) compute distance between two sequences (not necessarly in the given alignment but with the same weights in the site pattern)
double	getDistance(int s1, int s2) compute distance between two sequences in the given alignment
void	updateModel(SubstitutionModel m) update model of substitution
void	updateSitePattern(SitePattern sp) update site pattern

Methods inherited from class java.lang.Object

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

Field Detail

distance

public double distance

last estimated distance

distanceSE

public double distanceSE

last estimate standard error of a distance

Constructor Detail

PairwiseDistance

public PairwiseDistance(SitePattern sp)

Constructor 1 (estimate observed distances only)

Parameters:

sp - site pattern

PairwiseDistance

public PairwiseDistance(SitePattern sp,
                SubstitutionModel m)

Constructor 2 (uses evolutionary model)

Parameters:

sp - site pattern

m - evolutionary model

Method Detail

updateModel

public void updateModel(SubstitutionModel m)

update model of substitution

Parameters:

model - of substitution

updateSitePattern

public void updateSitePattern(SitePattern sp)

update site pattern

Parameters:

site - pattern

getDistance

public double getDistance(int s1,
                 int s2)

compute distance between two sequences in the given alignment

Parameters:

s1 - number of first sequence

s2 - number of second sequence

Returns:

estimated distance (observed or ML, depending on constructor used)

getDistance

public double getDistance(byte[] s1,
                 byte[] s2)

compute distance between two sequences (not necessarly in the given alignment but with the same weights in the site pattern)

Parameters:

s1 - site pattern of first sequence

s2 - site pattern of second sequence

Returns:

estimated distance (observed or ML, depending on constructor used)