public static interface UnconstrainedLikelihoodModel.Instance
extends java.io.Serializable
Modifier and Type | Method and Description |
---|---|
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.
|
UnconstrainedLikelihoodModel.Leaf createNewLeaf(int[] patternStateMatchup, int numberOfPatterns)
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 arrayUnconstrainedLikelihoodModel.External createNewExternal()
UnconstrainedLikelihoodModel.Internal createNewInternal()
boolean isAllowCaching()
ConditionalProbabilityStore createAppropriateConditionalProbabilityStore(boolean isForLeaf)
java.lang.String getSubstitutionModelSummary()
NeoParameterized getParameterAccess()