Uses of Class
pal.treesearch.GeneralConstructionTool
Packages that use GeneralConstructionTool
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Uses of GeneralConstructionTool in pal.treesearch
Methods in pal.treesearch with parameters of type GeneralConstructionToolModifier and TypeMethodDescriptiondouble
ConstrainedInternalNode.calculateLogLikelihood
(GeneralConstructionTool tool) double
FreeBranch.calculateLogLikelihood
(GeneralConstructionTool tool) double
PivotNode.calculateLogLikelihood
(GeneralConstructionTool tool) double
RootAccess.calculateLogLikelihood
(GeneralConstructionTool tool) double
FreeBranch.calculateLogLikelihood2
(GeneralConstructionTool tool) FreeBranch.calculateSiteDetails
(UnconstrainedLikelihoodModel.External calculator, GeneralConstructionTool tool) protected final UnconstrainedLikelihoodModel.Leaf
AbstractLeafNode.createNewFreeLeafCalculator
(GeneralConstructionTool tool) ConstrainedInternalNode.getAscendentExtended
(double baseHeight, ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching) ParentableConstrainedNode.getAscendentExtended
(double baseHeight, ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching) PivotNode.getAscendentExtended
(double baseHeight, ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching) ConstrainedInternalNode.getAscendentFlat
(ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching) ParentableConstrainedNode.getAscendentFlat
(ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching) PivotNode.getAscendentFlat
(ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching) ConstrainedInternalNode.getAscendentPatternInfo
(ConstrainedNode childCaller, GeneralConstructionTool tool) ParentableConstrainedNode.getAscendentPatternInfo
(ConstrainedNode childCaller, GeneralConstructionTool tool) PivotNode.getAscendentPatternInfo
(ConstrainedNode childCaller, GeneralConstructionTool tool) ConstrainedInternalNode.getCenterPattern
(GeneralConstructionTool tool) For center pattern, left is ascendent component, right is descendent componentfinal PatternInfo
FreeBranch.getCenterPatternInfo
(GeneralConstructionTool tool) void
FreeBranch.getCenterPatternInfo
(GeneralConstructionTool tool, PatternInfo store) AbstractParentableConstrainedNode.getDescendentExtendedConditionals
(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching) ConstrainedLeafNode.getDescendentExtendedConditionals
(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching) ConstrainedNode.getDescendentExtendedConditionals
(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching) AbstractParentableConstrainedNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights
(double adjustedExtensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching) ConstrainedLeafNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights
(double extensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching) ConstrainedNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights
(double adjustedExtensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching) AbstractParentableConstrainedNode.getDescendentFlatConditionals
(GeneralConstructionTool tool, boolean allowCaching) ConstrainedLeafNode.getDescendentFlatConditionals
(GeneralConstructionTool tool, boolean allowCaching) ConstrainedNode.getDescendentFlatConditionals
(GeneralConstructionTool tool, boolean allowCaching) protected final double
AbstractParentableConstrainedNode.getDescendentLogLikelihood
(GeneralConstructionTool tool, boolean allowCaching) final PatternInfo
AbstractParentableConstrainedNode.getDescendentPatternInfo
(GeneralConstructionTool tool) ConstrainedLeafNode.getDescendentPatternInfo
(GeneralConstructionTool tool) ConstrainedNode.getDescendentPatternInfo
(GeneralConstructionTool tool) FreeBranch.getExtendedConditionalProbabilities
(FreeNode caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore extendedStore, GeneralConstructionTool tool) FreeBranch.getExtendedConditionalProbabilities
(FreeNode caller, GeneralConstructionTool tool) FreeInternalNode.getExtendedConditionalProbabilities
(double distance, FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeInternalNode.getExtendedConditionalProbabilities
(double distance, FreeBranch callerConnection, GeneralConstructionTool tool) FreeLeafNode.getExtendedConditionalProbabilities
(double distance, FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getExtendedConditionalProbabilities
(double distance, FreeBranch callingBranch, GeneralConstructionTool tool) FreeNode.getExtendedConditionalProbabilities
(double distance, FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeNode.getExtendedConditionalProbabilities
(double distance, FreeBranch callingConnection, GeneralConstructionTool tool) PivotNode.getExtendedConditionalProbabilities
(double distance, FreeBranch caller, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) PivotNode.getExtendedConditionalProbabilities
(double distance, FreeBranch caller, GeneralConstructionTool tool) FreeInternalNode.getFlatConditionalProbabilities
(FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeInternalNode.getFlatConditionalProbabilities
(FreeBranch callerConnection, GeneralConstructionTool tool) FreeLeafNode.getFlatConditionalProbabilities
(FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getFlatConditionalProbabilities
(FreeBranch caller, GeneralConstructionTool tool) FreeNode.getFlatConditionalProbabilities
(FreeBranch caller, GeneralConstructionTool tool) PivotNode.getFlatConditionalProbabilities
(FreeBranch caller, GeneralConstructionTool tool) protected final PatternInfo
AbstractParentableConstrainedNode.getLeftChildPatternInfo
(GeneralConstructionTool tool) protected final ConditionalProbabilityStore
AbstractParentableConstrainedNode.getLeftDescendentExtendedConditionals
(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to a particular heightprotected final ConditionalProbabilityStore
AbstractParentableConstrainedNode.getLeftDescendentExtendedConditionals
(GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to height of this nodeFreeInternalNode.getLeftExtendedConditionalProbabilities
(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeBranch.getLeftFlatConditionalProbabilities
(GeneralConstructionTool tool) final PatternInfo
FreeBranch.getLeftPatternInfo
(GeneralConstructionTool tool) FreeInternalNode.getLeftPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) FreeLeafNode.getLeftPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) FreeNode.getLeftPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) PivotNode.getLeftPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) final PatternInfo
FreeBranch.getPatternInfo
(GeneralConstructionTool tool, FreeNode caller) FreeInternalNode.getPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) FreeLeafNode.getPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) FreeNode.getPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) PivotNode.getPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) protected final PatternInfo
AbstractParentableConstrainedNode.getRightChildPatternInfo
(GeneralConstructionTool tool) protected final ConditionalProbabilityStore
AbstractParentableConstrainedNode.getRightDescendentExtendedConditionals
(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to a particular heightprotected final ConditionalProbabilityStore
AbstractParentableConstrainedNode.getRightDescendentExtendedConditionals
(GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended right child conditionals to height of this nodeFreeInternalNode.getRightExtendedConditionalProbabilities
(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeBranch.getRightFlatConditionalProbabilities
(GeneralConstructionTool tool) final PatternInfo
FreeBranch.getRightPatternInfo
(GeneralConstructionTool tool) FreeInternalNode.getRightPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) FreeLeafNode.getRightPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) FreeNode.getRightPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) 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) final 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) Constructors in pal.treesearch with parameters of type GeneralConstructionToolModifierConstructorDescriptionAbstractLeafNode
(String id, GeneralConstructionTool tool) protected
AbstractParentableConstrainedNode
(Node peer, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager) ConstrainedInternalNode
(Node peer, ParentableConstrainedNode parentNode, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager) ConstrainedLeafNode
(ParentableConstrainedNode parentNode, Node peer, double height, GeneralConstructionTool tool, ConstraintModel.GroupManager parentGroup) FreeBranch
(Node n, FreeNode parent, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store) Continuing recurison constructor for a given treeFreeBranch
(Node n, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store) The starting constructor for building from a given treeFreeBranch
(FreeNode left, FreeNode right, double branchLength, GeneralConstructionTool tool) A generic constructor given two already defined left and right childrenFreeInternalNode
(Node i, FreeBranch parentFreeBranch, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store) FreeLeafNode
(FreeBranch parentBranch, String id, GeneralConstructionTool tool) PivotNode
(Node tree, FreeBranch parentConnection, GeneralConstructionTool tool, GeneralConstraintGroupManager constraintGroupManager, GeneralConstraintGroupManager.Store store) The subtree constructor with a connection to the rest of the treePivotNode
(Node subTree, GeneralConstructionTool tool, GeneralConstraintGroupManager groupManager, GeneralConstraintGroupManager.Store store) The root constructor, only used when the whole tree is constrained