Package pal.eval
Interface UnconstrainedLikelihoodModel.Instance
- All Superinterfaces:
Serializable
- Enclosing interface:
- UnconstrainedLikelihoodModel
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Method Summary
Modifier and TypeMethodDescriptioncreateAppropriateConditionalProbabilityStore
(boolean isForLeaf) createNewLeaf
(int[] patternStateMatchup, int numberOfPatterns) Create anew leaf calculatorboolean
If true, then user can assume that areas of trees that haven't changed, and the model parameters haven't be altered, can have their conditionals cached.
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Method Details
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createNewLeaf
Create anew leaf calculator- Parameters:
patternStateMatchup
- The sequence as reduced to patterns. This should just be one state per pattern. For example given a sequence [ 0, 1,0,1,3,0] a patternMatchup may be [0,1,3] (the first element is the first pattern, which is state 0, the second element is the second pattern which is 1, and the third element is the third pattern (novel pattern) which is state 3)numberOfPatterns
- The number of patterns in the patternStateMatchup array- Returns:
- a leaf calculator object
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createNewExternal
UnconstrainedLikelihoodModel.External createNewExternal() -
createNewInternal
UnconstrainedLikelihoodModel.Internal createNewInternal() -
isAllowCaching
boolean isAllowCaching()If true, then user can assume that areas of trees that haven't changed, and the model parameters haven't be altered, can have their conditionals cached.- Returns:
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createAppropriateConditionalProbabilityStore
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getSubstitutionModelSummary
String getSubstitutionModelSummary() -
getParameterAccess
NeoParameterized getParameterAccess()
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