pal.treesearch
Class UnconstrainedModel

java.lang.Object
  extended by pal.treesearch.UnconstrainedModel
All Implemented Interfaces:
ConstraintModel

public class UnconstrainedModel
extends java.lang.Object
implements ConstraintModel


Nested Class Summary
 
Nested classes/interfaces inherited from interface pal.treesearch.ConstraintModel
ConstraintModel.GroupManager
 
Constructor Summary
UnconstrainedModel(UnconstrainedLikelihoodModel.Instance likelihoodModel)
           
 
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()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

UnconstrainedModel

public UnconstrainedModel(UnconstrainedLikelihoodModel.Instance likelihoodModel)
Method Detail

getCladeConstraints

public java.lang.String[][] getCladeConstraints(java.lang.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(java.lang.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 java.lang.String getRateModelSummary()
Specified by:
getRateModelSummary in interface ConstraintModel