pal.eval
Class FastLikelihoodCalculator
java.lang.Object
|
+--pal.eval.FastLikelihoodCalculator
- All Implemented Interfaces:
- LikelihoodCalculator, PalObjectListener
- public class FastLikelihoodCalculator
- extends java.lang.Object
- implements PalObjectListener, LikelihoodCalculator
Title: Fast Likelihood Calculator
Description: A fast likelihood calculator
Original code by Matthew Goode. This calculates the likelihood of similar trees
(or a single changing tree) on the same site pattern fast by remembering
partial likelihoods of invariant subtrees.
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
FastLikelihoodCalculator
public FastLikelihoodCalculator(SitePattern pattern)
- Constructor taking only site pattern.
NOTE: setTree and setRateMatrix must both be called (in that order) before
computeLikelihood.
FastLikelihoodCalculator
public FastLikelihoodCalculator(SitePattern pattern,
Tree tree,
RateMatrix model)
- Constructor taking site pattern, tree and model.
parametersChanged
public void parametersChanged(PalObjectEvent pe)
- Description copied from interface:
PalObjectListener
- Signifies that parametric valued governing the state of this Object have changed.
Parameters don't have to be visible ones
For example, in trees the branch lengths have changed.
- Specified by:
parametersChanged
in interface PalObjectListener
structureChanged
public void structureChanged(PalObjectEvent pe)
- Description copied from interface:
PalObjectListener
- Signifies that the structure of the object has changed (for example in trees to topology
has changed)
- Specified by:
structureChanged
in interface PalObjectListener
setRateMatrix
public final void setRateMatrix(RateMatrix rateMatrix)
setTree
public final void setTree(Tree t)
updateSitePattern
public final void updateSitePattern(SitePattern pattern)
calculateLogLikelihood
public double calculateLogLikelihood()
- Specified by:
calculateLogLikelihood
in interface LikelihoodCalculator
- Returns:
- the likelihood of this tree under the given model and data.