pal.eval
Interface UnconstrainedLikelihoodModel.Instance

All Superinterfaces:
java.io.Serializable
Enclosing interface:
UnconstrainedLikelihoodModel

public static interface UnconstrainedLikelihoodModel.Instance
extends java.io.Serializable


Method Summary
 ConditionalProbabilityStore createAppropriateConditionalProbabilityStore(boolean isForLeaf)
           
 UnconstrainedLikelihoodModel.External createNewExternal()
           
 UnconstrainedLikelihoodModel.Internal createNewInternal()
           
 UnconstrainedLikelihoodModel.Leaf createNewLeaf(int[] patternStateMatchup, int numberOfPatterns)
          Create anew leaf calculator
 NeoParameterized 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.
 

Method Detail

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

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:

createAppropriateConditionalProbabilityStore

ConditionalProbabilityStore createAppropriateConditionalProbabilityStore(boolean isForLeaf)

getSubstitutionModelSummary

java.lang.String getSubstitutionModelSummary()

getParameterAccess

NeoParameterized getParameterAccess()