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