LikelihoodCalculator
, PalObjectListener
public class FastLikelihoodCalculator extends java.lang.Object implements PalObjectListener, LikelihoodCalculator
PalObjectListener.EventGenerator
Constructor | Description |
---|---|
FastLikelihoodCalculator(SitePattern pattern) |
Constructor taking only site pattern.
|
FastLikelihoodCalculator(SitePattern pattern,
Tree tree,
RateMatrix model) |
Constructor taking site pattern, tree and model.
|
Modifier and Type | Method | Description |
---|---|---|
double |
calculateLogLikelihood() |
|
void |
parametersChanged(PalObjectEvent pe) |
Signifies that parametric valued governing the state of this Object have changed.
|
void |
release() |
This method should be called when the user is through using this calculator
to inform it to release any resources it has allocated.
|
void |
setRateMatrix(RateMatrix rateMatrix) |
|
void |
setTree(Tree t) |
|
void |
structureChanged(PalObjectEvent pe) |
Signifies that the structure of the object has changed (for example in trees to topology
has changed)
|
void |
updateSitePattern(SitePattern pattern) |
public FastLikelihoodCalculator(SitePattern pattern)
public FastLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)
public void parametersChanged(PalObjectEvent pe)
PalObjectListener
parametersChanged
in interface PalObjectListener
public void structureChanged(PalObjectEvent pe)
PalObjectListener
structureChanged
in interface PalObjectListener
public final void setRateMatrix(RateMatrix rateMatrix)
public void release()
LikelihoodCalculator
release
in interface LikelihoodCalculator
public final void setTree(Tree t)
public final void updateSitePattern(SitePattern pattern)
public double calculateLogLikelihood()
calculateLogLikelihood
in interface LikelihoodCalculator