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

  • 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)