Interface ConstraintModel

All Known Implementing Classes:
FixedBSRDTGlobalClockModel, FixedSRDTGlobalClockModel, GlobalClockModel, MRDTGlobalClockModel, SRDTGlobalClockModel, UnconstrainedModel

public interface ConstraintModel
  • Method Details

    • getGlobalClockConstraintGrouping

      ConstraintModel.GroupManager getGlobalClockConstraintGrouping(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

      String[][] getCladeConstraints(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

      String getRateModelSummary()