Uses of Class
pal.treesearch.GeneralConstructionTool
Packages that use GeneralConstructionTool
-
Uses of GeneralConstructionTool in pal.treesearch
Methods in pal.treesearch with parameters of type GeneralConstructionToolModifier and TypeMethodDescriptiondoubleConstrainedInternalNode.calculateLogLikelihood(GeneralConstructionTool tool) doubleFreeBranch.calculateLogLikelihood(GeneralConstructionTool tool) doublePivotNode.calculateLogLikelihood(GeneralConstructionTool tool) doubleRootAccess.calculateLogLikelihood(GeneralConstructionTool tool) doubleFreeBranch.calculateLogLikelihood2(GeneralConstructionTool tool) FreeBranch.calculateSiteDetails(UnconstrainedLikelihoodModel.External calculator, GeneralConstructionTool tool) protected final UnconstrainedLikelihoodModel.LeafAbstractLeafNode.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 PatternInfoFreeBranch.getCenterPatternInfo(GeneralConstructionTool tool) voidFreeBranch.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 doubleAbstractParentableConstrainedNode.getDescendentLogLikelihood(GeneralConstructionTool tool, boolean allowCaching) final PatternInfoAbstractParentableConstrainedNode.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 PatternInfoAbstractParentableConstrainedNode.getLeftChildPatternInfo(GeneralConstructionTool tool) protected final ConditionalProbabilityStoreAbstractParentableConstrainedNode.getLeftDescendentExtendedConditionals(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to a particular heightprotected final ConditionalProbabilityStoreAbstractParentableConstrainedNode.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 PatternInfoFreeBranch.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 PatternInfoFreeBranch.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 PatternInfoAbstractParentableConstrainedNode.getRightChildPatternInfo(GeneralConstructionTool tool) protected final ConditionalProbabilityStoreAbstractParentableConstrainedNode.getRightDescendentExtendedConditionals(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to a particular heightprotected final ConditionalProbabilityStoreAbstractParentableConstrainedNode.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 PatternInfoFreeBranch.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) doubleConstrainedInternalNode.optimise(int optimisationType, UnivariateMinimum minimiser, GeneralConstructionTool tool, int fracDigits) doubleFreeBranch.optimise(int optimisationType, UnivariateMinimum minimiser, GeneralConstructionTool tool, int fracDigits) doubleGeneralOptimisable.optimise(int optimisationType, UnivariateMinimum minimiser, GeneralConstructionTool tool, int fracDigits) doublePivotNode.optimise(int optimisationType, UnivariateMinimum minimiser, GeneralConstructionTool tool, int fracDigits) voidFreeLeafNode.rebuildConnectionPatterns(GeneralConstructionTool tool, FreeBranch caller) final voidAbstractParentableConstrainedNode.rebuildDescendentPattern(GeneralConstructionTool tool) voidConstrainedLeafNode.rebuildDescendentPattern(GeneralConstructionTool tool) intFreeLeafNode.redirectRebuildPattern(GeneralConstructionTool tool) This should only be called by another leaf node on the other end of the connection.voidConstrainedInternalNode.testLikelihood(GeneralConstructionTool tool) voidConstrainedLeafNode.testLikelihood(GeneralConstructionTool tool) voidConstrainedNode.testLikelihood(GeneralConstructionTool tool) voidFreeBranch.testLikelihood(FreeNode caller, GeneralConstructionTool tool) voidFreeBranch.testLikelihood(GeneralConstructionTool tool) voidFreeInternalNode.testLikelihood(FreeBranch caller, GeneralConstructionTool tool) voidFreeLeafNode.testLikelihood(FreeBranch caller, GeneralConstructionTool tool) voidFreeNode.testLikelihood(FreeBranch caller, GeneralConstructionTool tool) voidPivotNode.testLikelihood(FreeBranch caller, GeneralConstructionTool tool) voidPivotNode.testLikelihood(GeneralConstructionTool tool) voidRootAccess.testLikelihood(GeneralConstructionTool tool) Constructors in pal.treesearch with parameters of type GeneralConstructionToolModifierConstructorDescriptionAbstractLeafNode(String id, GeneralConstructionTool tool) protectedAbstractParentableConstrainedNode(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