Package | Description |
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pal.treesearch |
Modifier and Type | Class and Description |
---|---|
class |
FreeInternalNode |
class |
FreeLeafNode |
class |
PivotNode |
Modifier and Type | Method and Description |
---|---|
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() |
Modifier and Type | Method and 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,
GeneralConstructionTool tool) |
ConditionalProbabilityStore |
FreeBranch.getExtendedConditionalProbabilities(FreeNode caller,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore extendedStore,
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 structure
|
void |
FreeNode.swapConnection(FreeBranch original,
FreeNode nodeToReplace,
FreeBranch newConnection)
Should preserve tree integrity
|
void |
FreeLeafNode.swapConnection(FreeBranch original,
FreeNode nodeToReplace,
FreeBranch newConnection) |
void |
FreeInternalNode.swapConnection(FreeBranch original,
FreeNode nodeToReplace,
FreeBranch newConnection) |
void |
PivotNode.swapConnection(FreeBranch original,
FreeNode nodeToReplace,
FreeBranch newConnection)
Should preserve tree integrity
|
void |
FreeBranch.swapNode(FreeNode nodeToReplace,
FreeNode replacement) |
void |
FreeBranch.testLikelihood(FreeNode caller,
GeneralConstructionTool tool) |
java.lang.String |
FreeBranch.toString(FreeNode caller) |
Constructor and Description |
---|
FreeBranch(FreeNode left,
FreeNode right,
double branchLength,
GeneralConstructionTool tool)
A generic constructor given two already defined left and right children
|
FreeBranch(Node n,
FreeNode parent,
GeneralConstructionTool tool,
GeneralConstraintGroupManager.Store store)
Continuing recurison constructor for a given tree
|