pal.treesearch
Interface ConstrainedNode

All Superinterfaces:
GeneralTreeComponent
All Known Implementing Classes:
ConstrainedInternalNode, ConstrainedLeafNode

public interface ConstrainedNode
extends GeneralTreeComponent


Nested Class Summary
static interface ConstrainedNode.HeightAdjustment
           
 
Method Summary
 Node buildDescendentPALNodeBase()
          Build node model base units (eg years)
 Node buildDescendentPALNodeES(ConstraintModel.GroupManager groupConstraints)
          Build node with Expected Substitution Units
 ConditionalProbabilityStore getDescendentExtendedConditionals(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore getDescendentExtendedConditionalsWithAdjustedInternalHeights(double adjustedExtensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching)
           
 ConditionalProbabilityStore getDescendentFlatConditionals(GeneralConstructionTool tool, boolean allowCaching)
           
 PatternInfo getDescendentPatternInfo(GeneralConstructionTool tool)
           
 ConstrainedNode getLeftChild()
           
 double getMaxOriginalDescendentLeafHeight()
           
 double getMinimumChildSeperation(double currentSeperation)
           
 double getMinimumDirectChildDistance()
           
 double getMinimumLeafChildSeperation(double parentHeight)
           
 double getMinOriginalDescendentLeafHeight()
           
 double getNodeHeight()
           
 void getNonSubTreeComponents(java.util.ArrayList store, java.lang.Class componentType)
           
 ConstrainedNode getRightChild()
           
 void getSubTreeComponents(java.util.ArrayList store, java.lang.Class componentType)
           
 void obtainLeafInformation(HeightInformationUser user)
          Obtain information regarding the current state of the leaf heights (called when first constructed).
 void recursivelyAdjustNodeHeight(ConstrainedNode.HeightAdjustment heightAdjustment)
           
 void recursivelySetParentPivot(PivotNode parentPivot)
           
 void setupInternalNodeHeights(ConstraintModel.GroupManager groupConstraints)
           
 void testLikelihood(GeneralConstructionTool tool)
           
 java.lang.String toStringHeights()
           
 java.lang.String toStringLengths(double parentHeight)
           
 
Methods inherited from interface pal.treesearch.GeneralTreeComponent
getAllComponents
 

Method Detail

getLeftChild

ConstrainedNode getLeftChild()

getRightChild

ConstrainedNode getRightChild()

getMinimumDirectChildDistance

double getMinimumDirectChildDistance()
Returns:
the minum distance to a child or zero if no children

recursivelyAdjustNodeHeight

void recursivelyAdjustNodeHeight(ConstrainedNode.HeightAdjustment heightAdjustment)

recursivelySetParentPivot

void recursivelySetParentPivot(PivotNode parentPivot)

setupInternalNodeHeights

void setupInternalNodeHeights(ConstraintModel.GroupManager groupConstraints)

getMinimumChildSeperation

double getMinimumChildSeperation(double currentSeperation)

getMinimumLeafChildSeperation

double getMinimumLeafChildSeperation(double parentHeight)

getMinOriginalDescendentLeafHeight

double getMinOriginalDescendentLeafHeight()

getMaxOriginalDescendentLeafHeight

double getMaxOriginalDescendentLeafHeight()

getDescendentPatternInfo

PatternInfo getDescendentPatternInfo(GeneralConstructionTool tool)

getSubTreeComponents

void getSubTreeComponents(java.util.ArrayList store,
                          java.lang.Class componentType)

getNonSubTreeComponents

void getNonSubTreeComponents(java.util.ArrayList store,
                             java.lang.Class componentType)

getNodeHeight

double getNodeHeight()

buildDescendentPALNodeBase

Node buildDescendentPALNodeBase()
Build node model base units (eg years)

Returns:
A normal PAL node

buildDescendentPALNodeES

Node buildDescendentPALNodeES(ConstraintModel.GroupManager groupConstraints)
Build node with Expected Substitution Units

Parameters:
groupConstraints - The constraints object to do the conversion with
Returns:
A normal PAL node

obtainLeafInformation

void obtainLeafInformation(HeightInformationUser user)
Obtain information regarding the current state of the leaf heights (called when first constructed). The resulting heights will, for exampled, be averaged across components and then used as the starting height values (see setLeafHeights...())

Parameters:
user - An object that uses the height information

testLikelihood

void testLikelihood(GeneralConstructionTool tool)

toStringHeights

java.lang.String toStringHeights()

toStringLengths

java.lang.String toStringLengths(double parentHeight)

getDescendentExtendedConditionals

ConditionalProbabilityStore getDescendentExtendedConditionals(double extensionHeight,
                                                              GeneralConstructionTool tool,
                                                              boolean allowCaching)

getDescendentExtendedConditionalsWithAdjustedInternalHeights

ConditionalProbabilityStore getDescendentExtendedConditionalsWithAdjustedInternalHeights(double adjustedExtensionHeight,
                                                                                         GeneralConstructionTool tool,
                                                                                         ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster,
                                                                                         boolean allowCaching)

getDescendentFlatConditionals

ConditionalProbabilityStore getDescendentFlatConditionals(GeneralConstructionTool tool,
                                                          boolean allowCaching)