pal.treesearch
Interface ConstraintModel
- All Known Implementing Classes:
- FixedBSRDTGlobalClockModel, FixedSRDTGlobalClockModel, GlobalClockModel, MRDTGlobalClockModel, SRDTGlobalClockModel, UnconstrainedModel
public interface ConstraintModel
getGlobalClockConstraintGrouping
ConstraintModel.GroupManager getGlobalClockConstraintGrouping(java.lang.String[] leafLabelSet)
- Enquire about the clock constraint grouping of the leaf
- Parameters:
leafLabel
- the label of the leaf
- Returns:
- the grouping of the leaf, or null if outside the leaf is unconstrained (free)
getCladeConstraints
java.lang.String[][] getCladeConstraints(java.lang.String[] allLabelSet)
- Obtain the permanent clade sets. That is, when randomly building the tree, and when tree searching, what labels must always
form a clade.
- Parameters:
allLabelSet
- The set of all leaf labels in the tree
- Returns:
- An array of string arrays dividing up the label set
createNewFreeLeaf
UnconstrainedLikelihoodModel.Leaf createNewFreeLeaf(int[] patternStateMatchup,
int numberOfPatterns)
createNewFreeExternal
UnconstrainedLikelihoodModel.External createNewFreeExternal()
createNewFreeInternal
UnconstrainedLikelihoodModel.Internal createNewFreeInternal()
createAppropriateConditionalProbabilityStore
ConditionalProbabilityStore createAppropriateConditionalProbabilityStore(boolean isForLeaf)
getGlobalParameterAccess
NeoParameterized getGlobalParameterAccess()
getRateModelSummary
java.lang.String getRateModelSummary()