double |
ConstrainedInternalNode.calculateLogLikelihood(GeneralConstructionTool tool) |
|
double |
FreeBranch.calculateLogLikelihood(GeneralConstructionTool tool) |
|
double |
PivotNode.calculateLogLikelihood(GeneralConstructionTool tool) |
|
double |
RootAccess.calculateLogLikelihood(GeneralConstructionTool tool) |
|
double |
FreeBranch.calculateLogLikelihood2(GeneralConstructionTool tool) |
|
SiteDetails |
FreeBranch.calculateSiteDetails(UnconstrainedLikelihoodModel.External calculator,
GeneralConstructionTool tool) |
|
protected UnconstrainedLikelihoodModel.Leaf |
AbstractLeafNode.createNewFreeLeafCalculator(GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
ConstrainedInternalNode.getAscendentExtended(double baseHeight,
ConstrainedNode childCaller,
GeneralConstructionTool tool,
boolean allowCaching) |
|
ConditionalProbabilityStore |
ParentableConstrainedNode.getAscendentExtended(double baseHeight,
ConstrainedNode childCaller,
GeneralConstructionTool tool,
boolean allowCaching) |
|
ConditionalProbabilityStore |
PivotNode.getAscendentExtended(double baseHeight,
ConstrainedNode childCaller,
GeneralConstructionTool tool,
boolean allowCaching) |
|
ConditionalProbabilityStore |
ConstrainedInternalNode.getAscendentFlat(ConstrainedNode childCaller,
GeneralConstructionTool tool,
boolean allowCaching) |
|
ConditionalProbabilityStore |
ParentableConstrainedNode.getAscendentFlat(ConstrainedNode childCaller,
GeneralConstructionTool tool,
boolean allowCaching) |
|
ConditionalProbabilityStore |
PivotNode.getAscendentFlat(ConstrainedNode childCaller,
GeneralConstructionTool tool,
boolean allowCaching) |
|
PatternInfo |
ConstrainedInternalNode.getAscendentPatternInfo(ConstrainedNode childCaller,
GeneralConstructionTool tool) |
|
PatternInfo |
ParentableConstrainedNode.getAscendentPatternInfo(ConstrainedNode childCaller,
GeneralConstructionTool tool) |
|
PatternInfo |
PivotNode.getAscendentPatternInfo(ConstrainedNode childCaller,
GeneralConstructionTool tool) |
|
PatternInfo |
ConstrainedInternalNode.getCenterPattern(GeneralConstructionTool tool) |
For center pattern, left is ascendent component, right is descendent component
|
PatternInfo |
FreeBranch.getCenterPatternInfo(GeneralConstructionTool tool) |
|
void |
FreeBranch.getCenterPatternInfo(GeneralConstructionTool tool,
PatternInfo store) |
|
ConditionalProbabilityStore |
AbstractParentableConstrainedNode.getDescendentExtendedConditionals(double extensionHeight,
GeneralConstructionTool tool,
boolean allowCaching) |
|
ConditionalProbabilityStore |
ConstrainedLeafNode.getDescendentExtendedConditionals(double extensionHeight,
GeneralConstructionTool tool,
boolean allowCaching) |
|
ConditionalProbabilityStore |
ConstrainedNode.getDescendentExtendedConditionals(double extensionHeight,
GeneralConstructionTool tool,
boolean allowCaching) |
|
ConditionalProbabilityStore |
AbstractParentableConstrainedNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights(double adjustedExtensionHeight,
GeneralConstructionTool tool,
ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster,
boolean allowCaching) |
|
ConditionalProbabilityStore |
ConstrainedLeafNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights(double extensionHeight,
GeneralConstructionTool tool,
ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster,
boolean allowCaching) |
|
ConditionalProbabilityStore |
ConstrainedNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights(double adjustedExtensionHeight,
GeneralConstructionTool tool,
ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster,
boolean allowCaching) |
|
ConditionalProbabilityStore |
AbstractParentableConstrainedNode.getDescendentFlatConditionals(GeneralConstructionTool tool,
boolean allowCaching) |
|
ConditionalProbabilityStore |
ConstrainedLeafNode.getDescendentFlatConditionals(GeneralConstructionTool tool,
boolean allowCaching) |
|
ConditionalProbabilityStore |
ConstrainedNode.getDescendentFlatConditionals(GeneralConstructionTool tool,
boolean allowCaching) |
|
protected double |
AbstractParentableConstrainedNode.getDescendentLogLikelihood(GeneralConstructionTool tool,
boolean allowCaching) |
|
PatternInfo |
AbstractParentableConstrainedNode.getDescendentPatternInfo(GeneralConstructionTool tool) |
|
PatternInfo |
ConstrainedLeafNode.getDescendentPatternInfo(GeneralConstructionTool tool) |
|
PatternInfo |
ConstrainedNode.getDescendentPatternInfo(GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeBranch.getExtendedConditionalProbabilities(FreeNode caller,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore extendedStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeBranch.getExtendedConditionalProbabilities(FreeNode caller,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeInternalNode.getExtendedConditionalProbabilities(double distance,
FreeBranch callerConnection,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeInternalNode.getExtendedConditionalProbabilities(double distance,
FreeBranch callerConnection,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeLeafNode.getExtendedConditionalProbabilities(double distance,
FreeBranch callingBranch,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeLeafNode.getExtendedConditionalProbabilities(double distance,
FreeBranch callingBranch,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeNode.getExtendedConditionalProbabilities(double distance,
FreeBranch callingConnection,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeNode.getExtendedConditionalProbabilities(double distance,
FreeBranch callingConnection,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
PivotNode.getExtendedConditionalProbabilities(double distance,
FreeBranch caller,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
PivotNode.getExtendedConditionalProbabilities(double distance,
FreeBranch caller,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeInternalNode.getFlatConditionalProbabilities(FreeBranch callerConnection,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeInternalNode.getFlatConditionalProbabilities(FreeBranch callerConnection,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeLeafNode.getFlatConditionalProbabilities(FreeBranch callingBranch,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeLeafNode.getFlatConditionalProbabilities(FreeBranch caller,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeNode.getFlatConditionalProbabilities(FreeBranch caller,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
PivotNode.getFlatConditionalProbabilities(FreeBranch caller,
GeneralConstructionTool tool) |
|
protected PatternInfo |
AbstractParentableConstrainedNode.getLeftChildPatternInfo(GeneralConstructionTool tool) |
|
protected ConditionalProbabilityStore |
AbstractParentableConstrainedNode.getLeftDescendentExtendedConditionals(double specifiedHeight,
GeneralConstructionTool tool,
boolean allowCaching) |
Obtain conditionals by extended left child conditionals to a particular height
|
protected ConditionalProbabilityStore |
AbstractParentableConstrainedNode.getLeftDescendentExtendedConditionals(GeneralConstructionTool tool,
boolean allowCaching) |
Obtain conditionals by extended left child conditionals to height of this node
|
ConditionalProbabilityStore |
FreeInternalNode.getLeftExtendedConditionalProbabilities(FreeBranch callingConnection,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeBranch.getLeftFlatConditionalProbabilities(GeneralConstructionTool tool) |
|
PatternInfo |
FreeBranch.getLeftPatternInfo(GeneralConstructionTool tool) |
|
PatternInfo |
FreeInternalNode.getLeftPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
FreeLeafNode.getLeftPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
FreeNode.getLeftPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
PivotNode.getLeftPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
FreeBranch.getPatternInfo(GeneralConstructionTool tool,
FreeNode caller) |
|
PatternInfo |
FreeInternalNode.getPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
FreeLeafNode.getPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
FreeNode.getPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
PivotNode.getPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
protected PatternInfo |
AbstractParentableConstrainedNode.getRightChildPatternInfo(GeneralConstructionTool tool) |
|
protected ConditionalProbabilityStore |
AbstractParentableConstrainedNode.getRightDescendentExtendedConditionals(double specifiedHeight,
GeneralConstructionTool tool,
boolean allowCaching) |
Obtain conditionals by extended left child conditionals to a particular height
|
protected ConditionalProbabilityStore |
AbstractParentableConstrainedNode.getRightDescendentExtendedConditionals(GeneralConstructionTool tool,
boolean allowCaching) |
Obtain conditionals by extended right child conditionals to height of this node
|
ConditionalProbabilityStore |
FreeInternalNode.getRightExtendedConditionalProbabilities(FreeBranch callingConnection,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeBranch.getRightFlatConditionalProbabilities(GeneralConstructionTool tool) |
|
PatternInfo |
FreeBranch.getRightPatternInfo(GeneralConstructionTool tool) |
|
PatternInfo |
FreeInternalNode.getRightPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
FreeLeafNode.getRightPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
FreeNode.getRightPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
PivotNode.getRightPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
double |
ConstrainedInternalNode.optimise(int optimisationType,
UnivariateMinimum minimiser,
GeneralConstructionTool tool,
int fracDigits) |
|
double |
FreeBranch.optimise(int optimisationType,
UnivariateMinimum minimiser,
GeneralConstructionTool tool,
int fracDigits) |
|
double |
GeneralOptimisable.optimise(int optimisationType,
UnivariateMinimum minimiser,
GeneralConstructionTool tool,
int fracDigits) |
|
double |
PivotNode.optimise(int optimisationType,
UnivariateMinimum minimiser,
GeneralConstructionTool tool,
int fracDigits) |
|
void |
FreeLeafNode.rebuildConnectionPatterns(GeneralConstructionTool tool,
FreeBranch caller) |
|
void |
AbstractParentableConstrainedNode.rebuildDescendentPattern(GeneralConstructionTool tool) |
|
void |
ConstrainedLeafNode.rebuildDescendentPattern(GeneralConstructionTool tool) |
|
int |
FreeLeafNode.redirectRebuildPattern(GeneralConstructionTool tool) |
This should only be called by another leaf node on the other end of the connection.
|
void |
ConstrainedInternalNode.testLikelihood(GeneralConstructionTool tool) |
|
void |
ConstrainedLeafNode.testLikelihood(GeneralConstructionTool tool) |
|
void |
ConstrainedNode.testLikelihood(GeneralConstructionTool tool) |
|
void |
FreeBranch.testLikelihood(FreeNode caller,
GeneralConstructionTool tool) |
|
void |
FreeBranch.testLikelihood(GeneralConstructionTool tool) |
|
void |
FreeInternalNode.testLikelihood(FreeBranch caller,
GeneralConstructionTool tool) |
|
void |
FreeLeafNode.testLikelihood(FreeBranch caller,
GeneralConstructionTool tool) |
|
void |
FreeNode.testLikelihood(FreeBranch caller,
GeneralConstructionTool tool) |
|
void |
PivotNode.testLikelihood(FreeBranch caller,
GeneralConstructionTool tool) |
|
void |
PivotNode.testLikelihood(GeneralConstructionTool tool) |
|
void |
RootAccess.testLikelihood(GeneralConstructionTool tool) |
|