pal.treesearch
public abstract class AbstractParentableConstrainedNode extends java.lang.Object implements ParentableConstrainedNode
Modifier | Constructor and Description |
---|---|
protected |
AbstractParentableConstrainedNode(Node peer,
GeneralConstructionTool tool,
GeneralConstraintGroupManager.Store store,
GeneralConstraintGroupManager groupManager) |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getAscendentExtended, getAscendentFlat, getAscendentPatternInfo
protected AbstractParentableConstrainedNode(Node peer, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager)
public MolecularClockLikelihoodModel.External obtainConstrainedExternalCalculator()
public double getMinOriginalDescendentLeafHeight()
public double getMaxOriginalDescendentLeafHeight()
public double getMinimumDirectChildDistance()
public final java.lang.String toStringHeights()
protected final java.lang.String toStringLengths()
public final java.lang.String toStringLengths(double parentHeight)
public final double getNodeHeight()
getNodeHeight
in interface ParentableConstrainedNode
public double getMinimumChildSeperation()
public double getMinimumChildSeperation(double currentSeparation)
protected final double getMinimumLeafChildSeperation()
public final double getMinimumLeafChildSeperation(double parentHeight)
public final void setupInternalNodeHeights(ConstraintModel.GroupManager groupConstraints)
public final PatternInfo getDescendentPatternInfo(GeneralConstructionTool tool)
public final void rebuildDescendentPattern(GeneralConstructionTool tool)
protected final PatternInfo getRightChildPatternInfo(GeneralConstructionTool tool)
protected final PatternInfo getLeftChildPatternInfo(GeneralConstructionTool tool)
protected final void setNodeHeight(double nodeHeight)
protected final void adjustNodeHeight(double heightDelta)
public void recursivelyAdjustNodeHeight(ConstrainedNode.HeightAdjustment height)
public final ConstrainedNode getLeftChild()
public final ConstrainedNode getRightChild()
protected final Node buildLeftDecendentPALNodeBase()
protected final Node buildRightDecendentPALNodeBase()
public final Node buildDescendentPALNodeBase()
public final Node buildDescendentPALNodeES(ConstraintModel.GroupManager groupManager)
protected final void recursivelySetChildrenParentPivot(PivotNode parentPivot)
protected final ConditionalProbabilityStore getLeftDescendentExtendedConditionals(GeneralConstructionTool tool, boolean allowCaching)
tool
- The construction toolprotected final ConditionalProbabilityStore getLeftDescendentExtendedConditionals(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching)
specifiedHeight
- The desired height of extensiontool
- The construction toolprotected final ConditionalProbabilityStore getRightDescendentExtendedConditionals(GeneralConstructionTool tool, boolean allowCaching)
tool
- The construction toolprotected final ConditionalProbabilityStore getRightDescendentExtendedConditionals(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching)
specifiedHeight
- The desired height of extensiontool
- The construction toolprotected final MolecularClockLikelihoodModel.Internal getConstrainedInternal()
protected final double getDescendentLogLikelihood(GeneralConstructionTool tool, boolean allowCaching)
protected final double getMaxChildHeight()
public ConditionalProbabilityStore getDescendentExtendedConditionals(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching)
public ConditionalProbabilityStore getDescendentExtendedConditionalsWithAdjustedInternalHeights(double adjustedExtensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching)
public ConditionalProbabilityStore getDescendentFlatConditionals(GeneralConstructionTool tool, boolean allowCaching)
public final void getSubTreeComponents(java.util.ArrayList store, java.lang.Class componentType)
public final void getAllComponents(java.util.ArrayList store, java.lang.Class componentType)
public void getNonSubTreeOfChildComponents(java.util.ArrayList store, java.lang.Class componentType, ConstrainedNode childCaller)
getNonSubTreeOfChildComponents
in interface ParentableConstrainedNode
public boolean isLeftChild(ConstrainedNode node)
node
- the node to investigatejava.lang.IllegalArgumentException
- if node is neither left nor rightpublic void obtainLeafInformation(HeightInformationUser user)
public abstract void getNonSubTreeComponents(java.util.ArrayList store, java.lang.Class componentType)