Uses of Interface
pal.treesearch.FreeNode
Packages that use FreeNode
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Uses of FreeNode in pal.treesearch
Classes in pal.treesearch that implement FreeNodeMethods in pal.treesearch that return FreeNodeModifier and TypeMethodDescriptionGeneralConstructionTool.createFreeNode(Node peer, FreeBranch parent, GeneralConstraintGroupManager.Store store) Create an appropriate free node given a peer, and it's parent branchfinal FreeNodeFreeBranch.getLeft()final FreeNodeFreeBranch.getRight()Methods in pal.treesearch with parameters of type FreeNodeModifier and TypeMethodDescriptionFreeBranch.buildPALNodeBase(FreeNode caller) FreeBranch.buildPALNodeES(FreeNode caller) voidFreeBranch.getAllComponents(ArrayList store, Class componentType, FreeNode caller) FreeBranch.getExtendedConditionalProbabilities(FreeNode caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore extendedStore, GeneralConstructionTool tool) FreeBranch.getExtendedConditionalProbabilities(FreeNode caller, GeneralConstructionTool tool) final PatternInfoFreeBranch.getPatternInfo(GeneralConstructionTool tool, FreeNode caller) booleanFreeBranch.hasConnection(FreeBranch c, FreeNode caller) voidDoes nothing to fix up tree structurevoidFreeInternalNode.swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) voidFreeLeafNode.swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) voidFreeNode.swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) Should preserve tree integrityvoidPivotNode.swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) Should preserve tree integrityvoidvoidFreeBranch.testLikelihood(FreeNode caller, GeneralConstructionTool tool) Constructors in pal.treesearch with parameters of type FreeNodeModifierConstructorDescriptionFreeBranch(Node n, FreeNode parent, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store) Continuing recurison constructor for a given treeFreeBranch(FreeNode left, FreeNode right, double branchLength, GeneralConstructionTool tool) A generic constructor given two already defined left and right children