pal.treesearch
Interface ConstraintModel

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

public interface ConstraintModel


Nested Class Summary
static interface ConstraintModel.GroupManager
           
 
Method Summary
 ConditionalProbabilityStore createAppropriateConditionalProbabilityStore(boolean isForLeaf)
           
 UnconstrainedLikelihoodModel.External createNewFreeExternal()
           
 UnconstrainedLikelihoodModel.Internal createNewFreeInternal()
           
 UnconstrainedLikelihoodModel.Leaf createNewFreeLeaf(int[] patternStateMatchup, int numberOfPatterns)
           
 java.lang.String[][] getCladeConstraints(java.lang.String[] allLabelSet)
          Obtain the permanent clade sets.
 ConstraintModel.GroupManager getGlobalClockConstraintGrouping(java.lang.String[] leafLabelSet)
          Enquire about the clock constraint grouping of the leaf
 NeoParameterized getGlobalParameterAccess()
           
 java.lang.String getRateModelSummary()
           
 

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

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()