Package | Description |
---|---|
pal.treesearch |
Modifier and Type | Class | Description |
---|---|---|
class |
FreeInternalNode |
|
class |
FreeLeafNode |
|
class |
PivotNode |
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 branch
|
FreeNode |
FreeBranch.getLeft() |
|
FreeNode |
FreeBranch.getOther(FreeNode caller) |
|
FreeNode |
FreeBranch.getRight() |
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 structure
|
void |
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 integrity
|
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 | Description |
---|---|
FreeBranch(Node n,
FreeNode parent,
GeneralConstructionTool tool,
GeneralConstraintGroupManager.Store store) |
Continuing recurison constructor for a given tree
|
FreeBranch(FreeNode left,
FreeNode right,
double branchLength,
GeneralConstructionTool tool) |
A generic constructor given two already defined left and right children
|