pal.distance
Class SequencePairLikelihood

java.lang.Object
  pal.distance.SequencePairLikelihood

All Implemented Interfaces:

java.io.Serializable, UnivariateFunction

public class SequencePairLikelihood
extends java.lang.Object
implements UnivariateFunction, java.io.Serializable

computation of the (negative) log-likelihood for a pair of sequences

Version:

$Id: SequencePairLikelihood.java,v 1.11 2002/12/05 04:27:28 matt Exp $

Author:

Korbinian Strimmer

See Also:

Serialized Form

Constructor Summary

SequencePairLikelihood(SitePattern sp, SubstitutionModel m)
initialisation

Method Summary

double	evaluate(double arc) compute function value
double	getLowerBound() get lower bound of argument
double	getUpperBound() get upper bound of argument
void	setSequences(byte[] s1, byte[] s2) specification of two sequences (not necessarily in the given alignment but with the same weights in the site pattern)
void	setSequences(int s1, int s2) specification of 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

Constructor Detail

SequencePairLikelihood

public SequencePairLikelihood(SitePattern sp,
                              SubstitutionModel m)

initialisation

Parameters:

sp - site pattern

m - model of substitution

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

setSequences

public void setSequences(int s1,
                         int s2)

specification of two sequences in the given alignment

Parameters:

s1 - number of first sequence

s2 - number of second sequence

setSequences

public void setSequences(byte[] s1,
                         byte[] s2)

specification of two sequences (not necessarily 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

evaluate

public final double evaluate(double arc)

Description copied from interface: UnivariateFunction

compute function value

Specified by:

evaluate in interface UnivariateFunction

Returns:

function value

getLowerBound

public double getLowerBound()

Description copied from interface: UnivariateFunction

get lower bound of argument

Specified by:

getLowerBound in interface UnivariateFunction

Returns:

lower bound

getUpperBound

public double getUpperBound()

Description copied from interface: UnivariateFunction

get upper bound of argument

Specified by:

getUpperBound in interface UnivariateFunction

Returns:

upper bound