Package pal.eval
Interface UnconstrainedLikelihoodModel.Instance
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- All Superinterfaces:
java.io.Serializable
- Enclosing interface:
- UnconstrainedLikelihoodModel
public static interface UnconstrainedLikelihoodModel.Instance extends java.io.Serializable
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description ConditionalProbabilityStore
createAppropriateConditionalProbabilityStore(boolean isForLeaf)
UnconstrainedLikelihoodModel.External
createNewExternal()
UnconstrainedLikelihoodModel.Internal
createNewInternal()
UnconstrainedLikelihoodModel.Leaf
createNewLeaf(int[] patternStateMatchup, int numberOfPatterns)
Create anew leaf calculatorNeoParameterized
getParameterAccess()
java.lang.String
getSubstitutionModelSummary()
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.
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Method Detail
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createNewLeaf
UnconstrainedLikelihoodModel.Leaf createNewLeaf(int[] patternStateMatchup, int numberOfPatterns)
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()
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createNewInternal
UnconstrainedLikelihoodModel.Internal createNewInternal()
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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
ConditionalProbabilityStore createAppropriateConditionalProbabilityStore(boolean isForLeaf)
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getSubstitutionModelSummary
java.lang.String getSubstitutionModelSummary()
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getParameterAccess
NeoParameterized getParameterAccess()
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