pal.treesearch
Class ConstrainedLeafNode

java.lang.Object
  pal.treesearch.AbstractLeafNode
      pal.treesearch.ConstrainedLeafNode

All Implemented Interfaces:

ConstrainedNode, GeneralTreeComponent

public class ConstrainedLeafNode
extends AbstractLeafNode
implements ConstrainedNode

Nested Class Summary

Nested classes/interfaces inherited from interface pal.treesearch.ConstrainedNode

ConstrainedNode.HeightAdjustment

Constructor Summary

ConstrainedLeafNode(ParentableConstrainedNode parentNode, Node peer, double height, GeneralConstructionTool tool, ConstraintModel.GroupManager parentGroup)

Method Summary

Node	buildDescendentPALNodeBase() Build node model base units (eg years)
Node	buildDescendentPALNodeES(ConstraintModel.GroupManager groupManager) Build node with Expected Substitution Units
void	getAllComponents(java.util.ArrayList store, java.lang.Class componentType)
ConditionalProbabilityStore	getDescendentExtendedConditionals(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching)
ConditionalProbabilityStore	getDescendentExtendedConditionalsWithAdjustedInternalHeights(double extensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching)
ConditionalProbabilityStore	getDescendentFlatConditionals(GeneralConstructionTool tool, boolean allowCaching)
PatternInfo	getDescendentPatternInfo(GeneralConstructionTool tool)
ConstrainedNode	getLeftChild() Returns null as we can't have children...
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	rebuildDescendentPattern(GeneralConstructionTool tool)
void	recursivelyAdjustNodeHeight(ConstrainedNode.HeightAdjustment heightDelta)
void	recursivelySetParentPivot(PivotNode parentPivot)
void	setupInternalNodeHeights(ConstraintModel.GroupManager groupConstraints)
void	testLikelihood(GeneralConstructionTool tool)
java.lang.String	toString(FreeBranch caller)
java.lang.String	toStringHeights()
java.lang.String	toStringLengths(double parentHeight)

Methods inherited from class pal.treesearch.AbstractLeafNode

createNewConstrainedLeafCalculator, createNewFreeLeafCalculator, getLabel, getNumberOfPatterns, getPatternInfo

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ConstrainedLeafNode

public ConstrainedLeafNode(ParentableConstrainedNode parentNode,
                           Node peer,
                           double height,
                           GeneralConstructionTool tool,
                           ConstraintModel.GroupManager parentGroup)

Method Detail

recursivelySetParentPivot

public void recursivelySetParentPivot(PivotNode parentPivot)

Specified by:

recursivelySetParentPivot in interface ConstrainedNode

setupInternalNodeHeights

public void setupInternalNodeHeights(ConstraintModel.GroupManager groupConstraints)

Specified by:

setupInternalNodeHeights in interface ConstrainedNode

getMinOriginalDescendentLeafHeight

public double getMinOriginalDescendentLeafHeight()

Specified by:

getMinOriginalDescendentLeafHeight in interface ConstrainedNode

getMaxOriginalDescendentLeafHeight

public double getMaxOriginalDescendentLeafHeight()

Specified by:

getMaxOriginalDescendentLeafHeight in interface ConstrainedNode

getLeftChild

public ConstrainedNode getLeftChild()

Returns null as we can't have children...

Specified by:

getLeftChild in interface ConstrainedNode

Returns:

null

getRightChild

public ConstrainedNode getRightChild()

Specified by:

getRightChild in interface ConstrainedNode

recursivelyAdjustNodeHeight

public void recursivelyAdjustNodeHeight(ConstrainedNode.HeightAdjustment heightDelta)

Specified by:

recursivelyAdjustNodeHeight in interface ConstrainedNode

toStringHeights

public java.lang.String toStringHeights()

Specified by:

toStringHeights in interface ConstrainedNode

toStringLengths

public java.lang.String toStringLengths(double parentHeight)

Specified by:

toStringLengths in interface ConstrainedNode

getMinimumDirectChildDistance

public double getMinimumDirectChildDistance()

Specified by:

getMinimumDirectChildDistance in interface ConstrainedNode

Returns:

the minum distance to a child or zero if no children

buildDescendentPALNodeBase

public Node buildDescendentPALNodeBase()

Description copied from interface: ConstrainedNode

Build node model base units (eg years)

Specified by:

buildDescendentPALNodeBase in interface ConstrainedNode

Returns:

A normal PAL node

buildDescendentPALNodeES

public final Node buildDescendentPALNodeES(ConstraintModel.GroupManager groupManager)

Description copied from interface: ConstrainedNode

Build node with Expected Substitution Units

Specified by:

buildDescendentPALNodeES in interface ConstrainedNode

Parameters:

groupManager - The constraints object to do the conversion with

Returns:

A normal PAL node

getMinimumLeafChildSeperation

public final double getMinimumLeafChildSeperation(double parentHeight)

Specified by:

getMinimumLeafChildSeperation in interface ConstrainedNode

rebuildDescendentPattern

public void rebuildDescendentPattern(GeneralConstructionTool tool)

getDescendentPatternInfo

public PatternInfo getDescendentPatternInfo(GeneralConstructionTool tool)

Specified by:

getDescendentPatternInfo in interface ConstrainedNode

getSubTreeComponents

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

Specified by:

getSubTreeComponents in interface ConstrainedNode

getNonSubTreeComponents

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

Specified by:

getNonSubTreeComponents in interface ConstrainedNode

getAllComponents

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

Specified by:

getAllComponents in interface GeneralTreeComponent

getNodeHeight

public final double getNodeHeight()

Specified by:

getNodeHeight in interface ConstrainedNode

getMinimumChildSeperation

public double getMinimumChildSeperation(double currentSeperation)

Specified by:

getMinimumChildSeperation in interface ConstrainedNode

obtainLeafInformation

public void obtainLeafInformation(HeightInformationUser user)

Description copied from interface: ConstrainedNode

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...())

Specified by:

obtainLeafInformation in interface ConstrainedNode

Parameters:

user - An object that uses the height information

getDescendentExtendedConditionals

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

Specified by:

getDescendentExtendedConditionals in interface ConstrainedNode

getDescendentExtendedConditionalsWithAdjustedInternalHeights

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

Specified by:

getDescendentExtendedConditionalsWithAdjustedInternalHeights in interface ConstrainedNode

getDescendentFlatConditionals

public ConditionalProbabilityStore getDescendentFlatConditionals(GeneralConstructionTool tool,
                                                                 boolean allowCaching)

Specified by:

getDescendentFlatConditionals in interface ConstrainedNode

testLikelihood

public void testLikelihood(GeneralConstructionTool tool)

Specified by:

testLikelihood in interface ConstrainedNode

toString

public java.lang.String toString(FreeBranch caller)