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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--pal.distance.SequencePairLikelihood
computation of the (negative) log-likelihood for a pair of sequences
Constructor Summary | |
SequencePairLikelihood(SitePattern sp,
SubstitutionModel m)
initialisation |
Method Summary | |
double |
evaluate(double arc)
compute (negative) log-likelihood for a given distance between the two sequences |
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 |
public SequencePairLikelihood(SitePattern sp, SubstitutionModel m)
sp
- site patternm
- model of substitutionMethod Detail |
public 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 double evaluate(double arc)
evaluate
in interface UnivariateFunction
arc
- expected distancepublic double getLowerBound()
UnivariateFunction
getLowerBound
in interface UnivariateFunction
pal.math.UnivariateFunction
public double getUpperBound()
UnivariateFunction
getUpperBound
in interface UnivariateFunction
pal.math.UnivariateFunction
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