ConstraintModel
public class UnconstrainedModel extends java.lang.Object implements ConstraintModel
ConstraintModel.GroupManager
Constructor | Description |
---|---|
UnconstrainedModel(UnconstrainedLikelihoodModel.Instance likelihoodModel) |
Modifier and Type | Method | Description |
---|---|---|
ConditionalProbabilityStore |
createAppropriateConditionalProbabilityStore(boolean isForLeaf) |
|
UnconstrainedLikelihoodModel.External |
createNewFreeExternal() |
|
UnconstrainedLikelihoodModel.Internal |
createNewFreeInternal() |
|
UnconstrainedLikelihoodModel.Leaf |
createNewFreeLeaf(int[] patternStateMatchup,
int numberOfPatterns) |
|
java.lang.String[][] |
getCladeConstraints(java.lang.String[] allLabelSet) |
Obtain the permanent clade sets.
|
ConstraintModel.GroupManager |
getGlobalClockConstraintGrouping(java.lang.String[] leafLabelSet) |
Enquire about the clock constraint grouping of the leaf
|
NeoParameterized |
getGlobalParameterAccess() |
|
java.lang.String |
getRateModelSummary() |
public UnconstrainedModel(UnconstrainedLikelihoodModel.Instance likelihoodModel)
public java.lang.String[][] getCladeConstraints(java.lang.String[] allLabelSet)
ConstraintModel
getCladeConstraints
in interface ConstraintModel
allLabelSet
- The set of all leaf labels in the treepublic ConstraintModel.GroupManager getGlobalClockConstraintGrouping(java.lang.String[] leafLabelSet)
ConstraintModel
getGlobalClockConstraintGrouping
in interface ConstraintModel
public UnconstrainedLikelihoodModel.Leaf createNewFreeLeaf(int[] patternStateMatchup, int numberOfPatterns)
createNewFreeLeaf
in interface ConstraintModel
public UnconstrainedLikelihoodModel.External createNewFreeExternal()
createNewFreeExternal
in interface ConstraintModel
public UnconstrainedLikelihoodModel.Internal createNewFreeInternal()
createNewFreeInternal
in interface ConstraintModel
public ConditionalProbabilityStore createAppropriateConditionalProbabilityStore(boolean isForLeaf)
createAppropriateConditionalProbabilityStore
in interface ConstraintModel
public NeoParameterized getGlobalParameterAccess()
getGlobalParameterAccess
in interface ConstraintModel
public java.lang.String getRateModelSummary()
getRateModelSummary
in interface ConstraintModel