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 FreeNode
FreeBranch.getLeft()
final FreeNode
FreeBranch.getRight()
Methods in pal.treesearch with parameters of type FreeNodeModifier and TypeMethodDescriptionFreeBranch.buildPALNodeBase
(FreeNode caller) FreeBranch.buildPALNodeES
(FreeNode caller) void
FreeBranch.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 PatternInfo
FreeBranch.getPatternInfo
(GeneralConstructionTool tool, FreeNode caller) boolean
FreeBranch.hasConnection
(FreeBranch c, FreeNode caller) void
Does nothing to fix up tree structurevoid
FreeInternalNode.swapConnection
(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) void
FreeLeafNode.swapConnection
(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) void
FreeNode.swapConnection
(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) Should preserve tree integrityvoid
PivotNode.swapConnection
(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) Should preserve tree integrityvoid
void
FreeBranch.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