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Packages that use FreeNode | |
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pal.treesearch |
Uses of FreeNode in pal.treesearch |
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Classes in pal.treesearch that implement FreeNode | |
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class |
FreeInternalNode
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class |
FreeLeafNode
|
class |
PivotNode
|
Methods in pal.treesearch that return FreeNode | |
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FreeNode |
GeneralConstructionTool.createFreeNode(Node peer,
FreeBranch parent,
GeneralConstraintGroupManager.Store store)
Create an appropriate free node given a peer, and it's parent branch |
FreeNode |
FreeBranch.getLeft()
|
FreeNode |
FreeBranch.getOther(FreeNode caller)
|
FreeNode |
FreeBranch.getRight()
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Methods in pal.treesearch with parameters of type FreeNode | |
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Node |
FreeBranch.buildPALNodeBase(FreeNode caller)
|
Node |
FreeBranch.buildPALNodeES(FreeNode caller)
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void |
FreeBranch.getAllComponents(java.util.ArrayList store,
java.lang.Class componentType,
FreeNode caller)
|
ConditionalProbabilityStore |
FreeBranch.getExtendedConditionalProbabilities(FreeNode caller,
GeneralConstructionTool tool)
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ConditionalProbabilityStore |
FreeBranch.getExtendedConditionalProbabilities(FreeNode caller,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore extendedStore,
GeneralConstructionTool tool)
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FreeNode |
FreeBranch.getOther(FreeNode caller)
|
PatternInfo |
FreeBranch.getPatternInfo(GeneralConstructionTool tool,
FreeNode caller)
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boolean |
FreeBranch.hasConnection(FreeBranch c,
FreeNode caller)
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void |
FreeBranch.setNodes(FreeNode left,
FreeNode right)
Does nothing to fix up tree structure |
void |
FreeNode.swapConnection(FreeBranch original,
FreeNode nodeToReplace,
FreeBranch newConnection)
Should preserve tree integrity |
void |
PivotNode.swapConnection(FreeBranch original,
FreeNode nodeToReplace,
FreeBranch newConnection)
Should preserve tree integrity |
void |
FreeLeafNode.swapConnection(FreeBranch original,
FreeNode nodeToReplace,
FreeBranch newConnection)
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void |
FreeInternalNode.swapConnection(FreeBranch original,
FreeNode nodeToReplace,
FreeBranch newConnection)
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void |
FreeBranch.swapNode(FreeNode nodeToReplace,
FreeNode replacement)
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void |
FreeBranch.testLikelihood(FreeNode caller,
GeneralConstructionTool tool)
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java.lang.String |
FreeBranch.toString(FreeNode caller)
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Constructors in pal.treesearch with parameters of type FreeNode | |
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FreeBranch(FreeNode left,
FreeNode right,
double branchLength,
GeneralConstructionTool tool)
A generic constructor given two already defined left and right children |
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FreeBranch(Node n,
FreeNode parent,
GeneralConstructionTool tool,
GeneralConstraintGroupManager.Store store)
Continuing recurison constructor for a given tree |
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