Class UnconstrainedModel

Method Details

• getCladeConstraints

  public String[][] getCladeConstraints(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(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 String getRateModelSummary()

  Specified by:

  getRateModelSummary in interface ConstraintModel