java.io.Serializable
, UnivariateFunction
public class SequencePairLikelihood extends java.lang.Object implements UnivariateFunction, java.io.Serializable
Constructor | Description |
---|---|
SequencePairLikelihood(SitePattern sp,
SubstitutionModel m) |
initialisation
|
Modifier and Type | Method | Description |
---|---|---|
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
|
public SequencePairLikelihood(SitePattern sp, SubstitutionModel m)
sp
- site patternm
- model of substitutionpublic void updateModel(SubstitutionModel m)
model
- of substitutionpublic void updateSitePattern(SitePattern sp)
site
- patternpublic void setSequences(int s1, int s2)
s1
- number of first sequences2
- number of second sequencepublic void setSequences(byte[] s1, byte[] s2)
s1
- site pattern of first sequences2
- site pattern of second sequencepublic final double evaluate(double arc)
UnivariateFunction
evaluate
in interface UnivariateFunction
public double getLowerBound()
UnivariateFunction
getLowerBound
in interface UnivariateFunction
public double getUpperBound()
UnivariateFunction
getUpperBound
in interface UnivariateFunction