Interface ConstraintModel

    • Method Detail

      • 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
      • createAppropriateConditionalProbabilityStore

        ConditionalProbabilityStore createAppropriateConditionalProbabilityStore​(boolean isForLeaf)
      • getRateModelSummary

        java.lang.String getRateModelSummary()