pal.treesearch
Class AbstractParentableConstrainedNode
java.lang.Object
pal.treesearch.AbstractParentableConstrainedNode
- All Implemented Interfaces:
- ParentableConstrainedNode
- Direct Known Subclasses:
- ConstrainedInternalNode, PivotNode
public abstract class AbstractParentableConstrainedNode
- extends java.lang.Object
- implements ParentableConstrainedNode
Method Summary |
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)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
AbstractParentableConstrainedNode
protected AbstractParentableConstrainedNode(Node peer,
GeneralConstructionTool tool,
GeneralConstraintGroupManager.Store store,
GeneralConstraintGroupManager groupManager)
obtainConstrainedExternalCalculator
public MolecularClockLikelihoodModel.External obtainConstrainedExternalCalculator()
getMinOriginalDescendentLeafHeight
public double getMinOriginalDescendentLeafHeight()
getMaxOriginalDescendentLeafHeight
public double getMaxOriginalDescendentLeafHeight()
getMinimumDirectChildDistance
public double getMinimumDirectChildDistance()
toStringHeights
public final java.lang.String toStringHeights()
toStringLengths
protected final java.lang.String toStringLengths()
toStringLengths
public final java.lang.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 extensiontool
- 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 extensiontool
- 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(java.util.ArrayList store,
java.lang.Class componentType)
getAllComponents
public final void getAllComponents(java.util.ArrayList store,
java.lang.Class componentType)
getNonSubTreeOfChildComponents
public void getNonSubTreeOfChildComponents(java.util.ArrayList store,
java.lang.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:
java.lang.IllegalArgumentException
- if node is neither left nor right
obtainLeafInformation
public void obtainLeafInformation(HeightInformationUser user)
getNonSubTreeComponents
public abstract void getNonSubTreeComponents(java.util.ArrayList store,
java.lang.Class componentType)