Package pal.treesearch
Class AbstractParentableConstrainedNode
java.lang.Object
pal.treesearch.AbstractParentableConstrainedNode
- All Implemented Interfaces:
ParentableConstrainedNode
- Direct Known Subclasses:
ConstrainedInternalNode
,PivotNode
public abstract class AbstractParentableConstrainedNode
extends Object
implements ParentableConstrainedNode
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Constructor Summary
ConstructorsModifierConstructorDescriptionprotected
AbstractParentableConstrainedNode
(Node peer, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager) -
Method Summary
Modifier and TypeMethodDescriptionprotected final void
adjustNodeHeight
(double heightDelta) final Node
final Node
buildDescendentPALNodeES
(ConstraintModel.GroupManager groupManager) protected final Node
protected final Node
final void
getAllComponents
(ArrayList store, Class componentType) protected final MolecularClockLikelihoodModel.Internal
getDescendentExtendedConditionals
(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching) getDescendentExtendedConditionalsWithAdjustedInternalHeights
(double adjustedExtensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching) getDescendentFlatConditionals
(GeneralConstructionTool tool, boolean allowCaching) protected final double
getDescendentLogLikelihood
(GeneralConstructionTool tool, boolean allowCaching) final PatternInfo
final ConstrainedNode
protected final PatternInfo
protected final ConditionalProbabilityStore
getLeftDescendentExtendedConditionals
(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to a particular heightprotected final ConditionalProbabilityStore
getLeftDescendentExtendedConditionals
(GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to height of this nodeprotected final double
double
double
double
getMinimumChildSeperation
(double currentSeparation) double
protected final double
final double
getMinimumLeafChildSeperation
(double parentHeight) double
final double
abstract void
getNonSubTreeComponents
(ArrayList store, Class componentType) void
getNonSubTreeOfChildComponents
(ArrayList store, Class componentType, ConstrainedNode childCaller) final ConstrainedNode
protected final PatternInfo
protected final ConditionalProbabilityStore
getRightDescendentExtendedConditionals
(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to a particular heightprotected final ConditionalProbabilityStore
getRightDescendentExtendedConditionals
(GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended right child conditionals to height of this nodefinal void
getSubTreeComponents
(ArrayList store, Class componentType) boolean
isLeftChild
(ConstrainedNode node) Investigate if given node is left node (and not right)void
final void
void
protected final void
recursivelySetChildrenParentPivot
(PivotNode parentPivot) protected final void
setNodeHeight
(double nodeHeight) final void
setupInternalNodeHeights
(ConstraintModel.GroupManager groupConstraints) final String
protected final String
final String
toStringLengths
(double parentHeight) Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface pal.treesearch.ParentableConstrainedNode
getAscendentExtended, getAscendentFlat, getAscendentPatternInfo
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Constructor Details
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AbstractParentableConstrainedNode
protected AbstractParentableConstrainedNode(Node peer, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager)
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Method Details
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obtainConstrainedExternalCalculator
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getMinOriginalDescendentLeafHeight
public double getMinOriginalDescendentLeafHeight() -
getMaxOriginalDescendentLeafHeight
public double getMaxOriginalDescendentLeafHeight() -
getMinimumDirectChildDistance
public double getMinimumDirectChildDistance() -
toStringHeights
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toStringLengths
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toStringLengths
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getNodeHeight
public final double getNodeHeight()- Specified by:
getNodeHeight
in interfaceParentableConstrainedNode
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getMinimumChildSeperation
public double getMinimumChildSeperation() -
getMinimumChildSeperation
public double getMinimumChildSeperation(double currentSeparation) -
getMinimumLeafChildSeperation
protected final double getMinimumLeafChildSeperation() -
getMinimumLeafChildSeperation
public final double getMinimumLeafChildSeperation(double parentHeight) -
setupInternalNodeHeights
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getDescendentPatternInfo
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rebuildDescendentPattern
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getRightChildPatternInfo
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getLeftChildPatternInfo
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setNodeHeight
protected final void setNodeHeight(double nodeHeight) -
adjustNodeHeight
protected final void adjustNodeHeight(double heightDelta) -
recursivelyAdjustNodeHeight
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getLeftChild
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getRightChild
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buildLeftDecendentPALNodeBase
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buildRightDecendentPALNodeBase
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buildDescendentPALNodeBase
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buildDescendentPALNodeES
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recursivelySetChildrenParentPivot
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getLeftDescendentExtendedConditionals
protected final ConditionalProbabilityStore getLeftDescendentExtendedConditionals(GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to height of this node- Parameters:
tool
- The construction tool- Returns:
- the extended conditionals
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getLeftDescendentExtendedConditionals
protected final ConditionalProbabilityStore getLeftDescendentExtendedConditionals(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to a particular height- Parameters:
specifiedHeight
- The desired height of extensiontool
- The construction tool- Returns:
- the extended conditionals
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getRightDescendentExtendedConditionals
protected final ConditionalProbabilityStore getRightDescendentExtendedConditionals(GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended right child conditionals to height of this node- Parameters:
tool
- The construction tool- Returns:
- the extended conditionals
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getRightDescendentExtendedConditionals
protected final ConditionalProbabilityStore getRightDescendentExtendedConditionals(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to a particular height- Parameters:
specifiedHeight
- The desired height of extensiontool
- The construction tool- Returns:
- the extended conditionals
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getConstrainedInternal
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getDescendentLogLikelihood
protected final double getDescendentLogLikelihood(GeneralConstructionTool tool, boolean allowCaching) -
getMaxChildHeight
protected final double getMaxChildHeight() -
getDescendentExtendedConditionals
public ConditionalProbabilityStore getDescendentExtendedConditionals(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching) -
getDescendentExtendedConditionalsWithAdjustedInternalHeights
public ConditionalProbabilityStore getDescendentExtendedConditionalsWithAdjustedInternalHeights(double adjustedExtensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching) -
getDescendentFlatConditionals
public ConditionalProbabilityStore getDescendentFlatConditionals(GeneralConstructionTool tool, boolean allowCaching) -
getSubTreeComponents
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getAllComponents
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getNonSubTreeOfChildComponents
public void getNonSubTreeOfChildComponents(ArrayList store, Class componentType, ConstrainedNode childCaller) - Specified by:
getNonSubTreeOfChildComponents
in interfaceParentableConstrainedNode
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isLeftChild
Investigate if given node is left node (and not right)- Parameters:
node
- the node to investigate- Returns:
- true if left, false if right
- Throws:
IllegalArgumentException
- if node is neither left nor right
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obtainLeafInformation
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getNonSubTreeComponents
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