Uses of Interface
pal.treesearch.FreeNode
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Packages that use FreeNode Package Description pal.treesearch -
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Uses of FreeNode in pal.treesearch
Classes in pal.treesearch that implement FreeNode Modifier and Type Class Description class
FreeInternalNode
class
FreeLeafNode
class
PivotNode
Methods in pal.treesearch that return FreeNode Modifier and Type Method Description FreeNode
GeneralConstructionTool. createFreeNode(Node peer, FreeBranch parent, GeneralConstraintGroupManager.Store store)
Create an appropriate free node given a peer, and it's parent branchFreeNode
FreeBranch. getLeft()
FreeNode
FreeBranch. getOther(FreeNode caller)
FreeNode
FreeBranch. getRight()
Methods in pal.treesearch with parameters of type FreeNode Modifier and Type Method Description Node
FreeBranch. buildPALNodeBase(FreeNode caller)
Node
FreeBranch. buildPALNodeES(FreeNode caller)
void
FreeBranch. getAllComponents(java.util.ArrayList store, java.lang.Class componentType, FreeNode caller)
ConditionalProbabilityStore
FreeBranch. getExtendedConditionalProbabilities(FreeNode caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore extendedStore, GeneralConstructionTool tool)
ConditionalProbabilityStore
FreeBranch. getExtendedConditionalProbabilities(FreeNode caller, GeneralConstructionTool tool)
FreeNode
FreeBranch. getOther(FreeNode caller)
PatternInfo
FreeBranch. getPatternInfo(GeneralConstructionTool tool, FreeNode caller)
boolean
FreeBranch. hasConnection(FreeBranch c, FreeNode caller)
void
FreeBranch. setNodes(FreeNode left, FreeNode right)
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
FreeBranch. swapNode(FreeNode nodeToReplace, FreeNode replacement)
void
FreeBranch. testLikelihood(FreeNode caller, GeneralConstructionTool tool)
java.lang.String
FreeBranch. toString(FreeNode caller)
Constructors in pal.treesearch with parameters of type FreeNode Constructor Description FreeBranch(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
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