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
  • Constructor Details

  • Method Details

    • obtainConstrainedExternalCalculator

      public MolecularClockLikelihoodModel.External obtainConstrainedExternalCalculator()
    • getMinOriginalDescendentLeafHeight

      public double getMinOriginalDescendentLeafHeight()
    • getMaxOriginalDescendentLeafHeight

      public double getMaxOriginalDescendentLeafHeight()
    • getMinimumDirectChildDistance

      public double getMinimumDirectChildDistance()
    • toStringHeights

      public final String toStringHeights()
    • toStringLengths

      protected final String toStringLengths()
    • toStringLengths

      public final String toStringLengths(double parentHeight)
    • getNodeHeight

      public final double getNodeHeight()
      Specified by:
      getNodeHeight in interface ParentableConstrainedNode
    • getMinimumChildSeperation

      public double getMinimumChildSeperation()
    • getMinimumChildSeperation

      public double getMinimumChildSeperation(double currentSeparation)
    • getMinimumLeafChildSeperation

      protected final double getMinimumLeafChildSeperation()
    • getMinimumLeafChildSeperation

      public final double getMinimumLeafChildSeperation(double parentHeight)
    • setupInternalNodeHeights

      public final void setupInternalNodeHeights(ConstraintModel.GroupManager groupConstraints)
    • getDescendentPatternInfo

      public final PatternInfo getDescendentPatternInfo(GeneralConstructionTool tool)
    • rebuildDescendentPattern

      public final void rebuildDescendentPattern(GeneralConstructionTool tool)
    • getRightChildPatternInfo

      protected final PatternInfo getRightChildPatternInfo(GeneralConstructionTool tool)
    • getLeftChildPatternInfo

      protected final PatternInfo getLeftChildPatternInfo(GeneralConstructionTool tool)
    • setNodeHeight

      protected final void setNodeHeight(double nodeHeight)
    • adjustNodeHeight

      protected final void adjustNodeHeight(double heightDelta)
    • recursivelyAdjustNodeHeight

      public void recursivelyAdjustNodeHeight(ConstrainedNode.HeightAdjustment height)
    • getLeftChild

      public final ConstrainedNode getLeftChild()
    • getRightChild

      public final ConstrainedNode getRightChild()
    • buildLeftDecendentPALNodeBase

      protected final Node buildLeftDecendentPALNodeBase()
    • buildRightDecendentPALNodeBase

      protected final Node buildRightDecendentPALNodeBase()
    • buildDescendentPALNodeBase

      public final Node buildDescendentPALNodeBase()
    • buildDescendentPALNodeES

      public final Node buildDescendentPALNodeES(ConstraintModel.GroupManager groupManager)
    • recursivelySetChildrenParentPivot

      protected final void recursivelySetChildrenParentPivot(PivotNode parentPivot)
    • 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
    • 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 extension
      tool - The construction tool
      Returns:
      the extended conditionals
    • 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
    • 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 extension
      tool - The construction tool
      Returns:
      the extended conditionals
    • getConstrainedInternal

      protected final MolecularClockLikelihoodModel.Internal getConstrainedInternal()
    • 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

      public final void getSubTreeComponents(ArrayList store, Class componentType)
    • getAllComponents

      public final void getAllComponents(ArrayList store, Class componentType)
    • getNonSubTreeOfChildComponents

      public void getNonSubTreeOfChildComponents(ArrayList store, Class componentType, ConstrainedNode childCaller)
      Specified by:
      getNonSubTreeOfChildComponents in interface ParentableConstrainedNode
    • 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:
      IllegalArgumentException - if node is neither left nor right
    • obtainLeafInformation

      public void obtainLeafInformation(HeightInformationUser user)
    • getNonSubTreeComponents

      public abstract void getNonSubTreeComponents(ArrayList store, Class componentType)