pal.treesearch
Class UnconstrainedModel
java.lang.Object
pal.treesearch.UnconstrainedModel
- All Implemented Interfaces:
- ConstraintModel
public class UnconstrainedModel
- extends java.lang.Object
- implements ConstraintModel
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
UnconstrainedModel
public UnconstrainedModel(UnconstrainedLikelihoodModel.Instance likelihoodModel)
getCladeConstraints
public java.lang.String[][] getCladeConstraints(java.lang.String[] allLabelSet)
- Description copied from interface:
ConstraintModel
- Obtain the permanent clade sets. That is, when randomly building the tree, and when tree searching, what labels must always
form a clade.
- Specified by:
getCladeConstraints
in interface ConstraintModel
- Parameters:
allLabelSet
- The set of all leaf labels in the tree
- Returns:
- An array of string arrays dividing up the label set
getGlobalClockConstraintGrouping
public ConstraintModel.GroupManager getGlobalClockConstraintGrouping(java.lang.String[] leafLabelSet)
- Description copied from interface:
ConstraintModel
- Enquire about the clock constraint grouping of the leaf
- Specified by:
getGlobalClockConstraintGrouping
in interface ConstraintModel
- Returns:
- the grouping of the leaf, or null if outside the leaf is unconstrained (free)
createNewFreeLeaf
public UnconstrainedLikelihoodModel.Leaf createNewFreeLeaf(int[] patternStateMatchup,
int numberOfPatterns)
- Specified by:
createNewFreeLeaf
in interface ConstraintModel
createNewFreeExternal
public UnconstrainedLikelihoodModel.External createNewFreeExternal()
- Specified by:
createNewFreeExternal
in interface ConstraintModel
createNewFreeInternal
public UnconstrainedLikelihoodModel.Internal createNewFreeInternal()
- Specified by:
createNewFreeInternal
in interface ConstraintModel
createAppropriateConditionalProbabilityStore
public ConditionalProbabilityStore createAppropriateConditionalProbabilityStore(boolean isForLeaf)
- Specified by:
createAppropriateConditionalProbabilityStore
in interface ConstraintModel
getGlobalParameterAccess
public NeoParameterized getGlobalParameterAccess()
- Specified by:
getGlobalParameterAccess
in interface ConstraintModel
getRateModelSummary
public java.lang.String getRateModelSummary()
- Specified by:
getRateModelSummary
in interface ConstraintModel