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java.lang.Objectpal.eval.FastLikelihoodCalculator
public class FastLikelihoodCalculator
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.
This class should be avoided if the underlying tree doesn't change (use GeneralLikelihoodCalculator).
A new framework will be added one day to accomodate optimising tree topologies.
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.PalObjectListener |
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PalObjectListener.EventGenerator |
Constructor Summary | |
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FastLikelihoodCalculator(SitePattern pattern)
Constructor taking only site pattern. |
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FastLikelihoodCalculator(SitePattern pattern,
Tree tree,
RateMatrix model)
Constructor taking site pattern, tree and model. |
Method Summary | |
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double |
calculateLogLikelihood()
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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)
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void |
setTree(Tree t)
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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)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public FastLikelihoodCalculator(SitePattern pattern)
public FastLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)
Method Detail |
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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
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