public class SequencePairLikelihood extends java.lang.Object implements UnivariateFunction, java.io.Serializable
Constructor and Description |
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SequencePairLikelihood(SitePattern sp,
SubstitutionModel m)
initialisation
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Modifier and Type | Method and Description |
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double |
evaluate(double arc)
compute function value
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double |
getLowerBound()
get lower bound of argument
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double |
getUpperBound()
get upper bound of argument
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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)
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void |
setSequences(int s1,
int s2)
specification of two sequences in the given alignment
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void |
updateModel(SubstitutionModel m)
update model of substitution
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void |
updateSitePattern(SitePattern sp)
update site pattern
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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