Package pal.distance
Class SequencePairLikelihood
java.lang.Object
pal.distance.SequencePairLikelihood
- All Implemented Interfaces:
Serializable
,UnivariateFunction
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:
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionfinal double
evaluate
(double arc) compute function valuedouble
get lower bound of argumentdouble
get upper bound of argumentvoid
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 alignmentvoid
update model of substitutionvoid
update site pattern
-
Constructor Details
-
SequencePairLikelihood
initialisation- Parameters:
sp
- site patternm
- model of substitution
-
-
Method Details
-
updateModel
update model of substitution- Parameters:
model
- of substitution
-
updateSitePattern
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 sequences2
- 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 sequences2
- site pattern of second sequence
-
evaluate
public final double evaluate(double arc) Description copied from interface:UnivariateFunction
compute function value- Specified by:
evaluate
in interfaceUnivariateFunction
- Returns:
- function value
-
getLowerBound
public double getLowerBound()Description copied from interface:UnivariateFunction
get lower bound of argument- Specified by:
getLowerBound
in interfaceUnivariateFunction
- Returns:
- lower bound
-
getUpperBound
public double getUpperBound()Description copied from interface:UnivariateFunction
get upper bound of argument- Specified by:
getUpperBound
in interfaceUnivariateFunction
- Returns:
- upper bound
-