pal.distance
Class SequencePairLikelihood

java.lang.Object
  extended by 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