public class UnconstrainedModel extends java.lang.Object implements ConstraintModel
ConstraintModel.GroupManager
Constructor and Description |
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UnconstrainedModel(UnconstrainedLikelihoodModel.Instance likelihoodModel) |
Modifier and Type | Method and Description |
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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