Methods
Modifier and Type |
Method and Description |
protected void |
adjustNodeHeight(double heightDelta) |
Node |
buildDescendentPALNodeBase() |
Node |
buildDescendentPALNodeES(ConstraintModel.GroupManager groupManager) |
protected Node |
buildLeftDecendentPALNodeBase() |
protected Node |
buildRightDecendentPALNodeBase() |
void |
getAllComponents(java.util.ArrayList store,
java.lang.Class componentType) |
protected MolecularClockLikelihoodModel.Internal |
getConstrainedInternal() |
ConditionalProbabilityStore |
getDescendentExtendedConditionals(double extensionHeight,
GeneralConstructionTool tool,
boolean allowCaching) |
ConditionalProbabilityStore |
getDescendentExtendedConditionalsWithAdjustedInternalHeights(double adjustedExtensionHeight,
GeneralConstructionTool tool,
ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster,
boolean allowCaching) |
ConditionalProbabilityStore |
getDescendentFlatConditionals(GeneralConstructionTool tool,
boolean allowCaching) |
protected double |
getDescendentLogLikelihood(GeneralConstructionTool tool,
boolean allowCaching) |
PatternInfo |
getDescendentPatternInfo(GeneralConstructionTool tool) |
ConstrainedNode |
getLeftChild() |
protected PatternInfo |
getLeftChildPatternInfo(GeneralConstructionTool tool) |
protected ConditionalProbabilityStore |
getLeftDescendentExtendedConditionals(double specifiedHeight,
GeneralConstructionTool tool,
boolean allowCaching)
Obtain conditionals by extended left child conditionals to a particular height
|
protected ConditionalProbabilityStore |
getLeftDescendentExtendedConditionals(GeneralConstructionTool tool,
boolean allowCaching)
Obtain conditionals by extended left child conditionals to height of this node
|
protected double |
getMaxChildHeight() |
double |
getMaxOriginalDescendentLeafHeight() |
double |
getMinimumChildSeperation() |
double |
getMinimumChildSeperation(double currentSeparation) |
double |
getMinimumDirectChildDistance() |
protected double |
getMinimumLeafChildSeperation() |
double |
getMinimumLeafChildSeperation(double parentHeight) |
double |
getMinOriginalDescendentLeafHeight() |
double |
getNodeHeight() |
abstract void |
getNonSubTreeComponents(java.util.ArrayList store,
java.lang.Class componentType) |
void |
getNonSubTreeOfChildComponents(java.util.ArrayList store,
java.lang.Class componentType,
ConstrainedNode childCaller) |
ConstrainedNode |
getRightChild() |
protected PatternInfo |
getRightChildPatternInfo(GeneralConstructionTool tool) |
protected ConditionalProbabilityStore |
getRightDescendentExtendedConditionals(double specifiedHeight,
GeneralConstructionTool tool,
boolean allowCaching)
Obtain conditionals by extended left child conditionals to a particular height
|
protected ConditionalProbabilityStore |
getRightDescendentExtendedConditionals(GeneralConstructionTool tool,
boolean allowCaching)
Obtain conditionals by extended right child conditionals to height of this node
|
void |
getSubTreeComponents(java.util.ArrayList store,
java.lang.Class componentType) |
boolean |
isLeftChild(ConstrainedNode node)
Investigate if given node is left node (and not right)
|
MolecularClockLikelihoodModel.External |
obtainConstrainedExternalCalculator() |
void |
obtainLeafInformation(HeightInformationUser user) |
void |
rebuildDescendentPattern(GeneralConstructionTool tool) |
void |
recursivelyAdjustNodeHeight(ConstrainedNode.HeightAdjustment height) |
protected void |
recursivelySetChildrenParentPivot(PivotNode parentPivot) |
protected void |
setNodeHeight(double nodeHeight) |
void |
setupInternalNodeHeights(ConstraintModel.GroupManager groupConstraints) |
java.lang.String |
toStringHeights() |
protected java.lang.String |
toStringLengths() |
java.lang.String |
toStringLengths(double parentHeight) |