Package pal.eval
Class SimpleLikelihoodCalculator
java.lang.Object
pal.eval.SimpleLikelihoodCalculator
- All Implemented Interfaces:
LikelihoodCalculator
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Constructor Summary
ConstructorsConstructorDescriptionSimpleLikelihoodCalculator
(SitePattern pattern) Need to use setTree(), and setModel() before using compute() if you use this constructorSimpleLikelihoodCalculator
(SitePattern pattern, Tree tree, RateMatrix model) -
Method Summary
Modifier and TypeMethodDescriptiondouble
compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihoodprotected Node
getNextBranch
(Node branch, Node center) get next branch around a center node (center may be root, but root is never returned)protected double[][]
getPartial
(Node branch) get partial likelihood of a branchgetTree()
final void
protected void
partialsExternal
(Node branch) compute partials for external branchprotected void
partialsInternal
(Node center) compute partials for branch around center node (it is assumed that multiplied partials are available in the neighbor branch)protected void
productPartials
(Node center) multiply partials into the neighbour of branchvoid
release()
Doesn't do anything...void
define model (a site pattern must have been set before calling this method)void
define tree ,(must only be called only after a site pattern has been defined).final void
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Constructor Details
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SimpleLikelihoodCalculator
Need to use setTree(), and setModel() before using compute() if you use this constructor -
SimpleLikelihoodCalculator
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Method Details
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release
public void release()Doesn't do anything...- Specified by:
release
in interfaceLikelihoodCalculator
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calculateLogLikelihood
public double calculateLogLikelihood()compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihood- Specified by:
calculateLogLikelihood
in interfaceLikelihoodCalculator
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getSitePattern
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getTree
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setRateMatrix
define model (a site pattern must have been set before calling this method)- Parameters:
m
- model of substitution (rate matrix + rate distribution)
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setTree
define tree ,(must only be called only after a site pattern has been defined).- Parameters:
t
- tree
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modelUpdated
public final void modelUpdated() -
treeUpdated
public final void treeUpdated() -
getPartial
get partial likelihood of a branch -
getNextBranch
get next branch around a center node (center may be root, but root is never returned) -
productPartials
multiply partials into the neighbour of branch -
partialsInternal
compute partials for branch around center node (it is assumed that multiplied partials are available in the neighbor branch) -
partialsExternal
compute partials for external branch
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