FreeBranch |
FreeBranch.attachTo(FreeBranch attachmentPoint,
FreeBranch[] store) |
|
Node |
FreeLeafNode.buildPALNode(double branchLength,
FreeBranch caller) |
|
Node |
FreeInternalNode.buildPALNodeBase(double branchLength,
FreeBranch caller) |
|
Node |
FreeLeafNode.buildPALNodeBase(double branchLength,
FreeBranch caller) |
|
Node |
FreeNode.buildPALNodeBase(double branchLength_,
FreeBranch caller) |
|
Node |
PivotNode.buildPALNodeBase(double branchLength_,
FreeBranch caller) |
|
Node |
FreeInternalNode.buildPALNodeES(double branchLength,
FreeBranch caller) |
|
Node |
FreeLeafNode.buildPALNodeES(double branchLength,
FreeBranch caller) |
|
Node |
FreeNode.buildPALNodeES(double branchLength_,
FreeBranch caller) |
|
Node |
PivotNode.buildPALNodeES(double branchLength_,
FreeBranch caller) |
|
FreeNode |
GeneralConstructionTool.createFreeNode(Node peer,
FreeBranch parent,
GeneralConstraintGroupManager.Store store) |
Create an appropriate free node given a peer, and it's parent branch
|
FreeBranch |
FreeInternalNode.extract(FreeBranch caller) |
|
FreeBranch |
FreeLeafNode.extract(FreeBranch caller) |
|
FreeBranch |
FreeNode.extract(FreeBranch caller) |
Instruct the node to extract itself from the two connections that aren't the caller
One of the other two connections will become redunant.
|
FreeBranch |
PivotNode.extract(FreeBranch caller) |
We can't extract
|
void |
FreeInternalNode.getAllComponents(java.util.ArrayList store,
java.lang.Class componentType,
FreeBranch caller) |
|
void |
FreeLeafNode.getAllComponents(java.util.ArrayList store,
java.lang.Class componentType,
FreeBranch caller) |
|
void |
FreeNode.getAllComponents(java.util.ArrayList store,
java.lang.Class componentType,
FreeBranch connection) |
Recurse to all neighbours but caller
|
void |
PivotNode.getAllComponents(java.util.ArrayList store,
java.lang.Class componentType,
FreeBranch caller) |
|
void |
FreeLeafNode.getAllConnections(java.util.ArrayList store,
FreeBranch caller) |
|
ConditionalProbabilityStore |
FreeInternalNode.getExtendedConditionalProbabilities(double distance,
FreeBranch callerConnection,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeInternalNode.getExtendedConditionalProbabilities(double distance,
FreeBranch callerConnection,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeLeafNode.getExtendedConditionalProbabilities(double distance,
FreeBranch callingBranch,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeLeafNode.getExtendedConditionalProbabilities(double distance,
FreeBranch callingBranch,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeNode.getExtendedConditionalProbabilities(double distance,
FreeBranch callingConnection,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeNode.getExtendedConditionalProbabilities(double distance,
FreeBranch callingConnection,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
PivotNode.getExtendedConditionalProbabilities(double distance,
FreeBranch caller,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
PivotNode.getExtendedConditionalProbabilities(double distance,
FreeBranch caller,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeInternalNode.getFlatConditionalProbabilities(FreeBranch callerConnection,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeInternalNode.getFlatConditionalProbabilities(FreeBranch callerConnection,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeLeafNode.getFlatConditionalProbabilities(FreeBranch callingBranch,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeLeafNode.getFlatConditionalProbabilities(FreeBranch caller,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeNode.getFlatConditionalProbabilities(FreeBranch caller,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
PivotNode.getFlatConditionalProbabilities(FreeBranch caller,
GeneralConstructionTool tool) |
|
FreeBranch |
FreeInternalNode.getLeftBranch(FreeBranch caller) |
|
FreeBranch |
FreeLeafNode.getLeftBranch(FreeBranch caller) |
|
FreeBranch |
FreeNode.getLeftBranch(FreeBranch caller) |
|
FreeBranch |
PivotNode.getLeftBranch(FreeBranch caller) |
|
ConditionalProbabilityStore |
FreeInternalNode.getLeftExtendedConditionalProbabilities(FreeBranch callingConnection,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeLeafNode.getLeftExtendedConditionalProbabilities(FreeBranch caller,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore resultStore) |
|
PatternInfo |
FreeInternalNode.getLeftPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
FreeLeafNode.getLeftPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
FreeNode.getLeftPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
PivotNode.getLeftPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
FreeInternalNode.getPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
FreeLeafNode.getPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
FreeNode.getPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
PivotNode.getPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
FreeBranch |
FreeInternalNode.getRightBranch(FreeBranch caller) |
|
FreeBranch |
FreeLeafNode.getRightBranch(FreeBranch caller) |
|
FreeBranch |
FreeNode.getRightBranch(FreeBranch caller) |
|
FreeBranch |
PivotNode.getRightBranch(FreeBranch caller) |
|
ConditionalProbabilityStore |
FreeInternalNode.getRightExtendedConditionalProbabilities(FreeBranch callingConnection,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
|
ConditionalProbabilityStore |
FreeLeafNode.getRightExtendedConditionalProbabilities(FreeBranch caller,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore resultStore) |
|
PatternInfo |
FreeInternalNode.getRightPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
FreeLeafNode.getRightPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
FreeNode.getRightPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
PatternInfo |
PivotNode.getRightPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
|
boolean |
FreeBranch.hasConnection(FreeBranch c,
FreeNode caller) |
|
boolean |
FreeInternalNode.hasConnection(FreeBranch c,
FreeBranch caller) |
|
boolean |
FreeLeafNode.hasConnection(FreeBranch fb,
FreeBranch caller) |
|
boolean |
FreeNode.hasConnection(FreeBranch c,
FreeBranch caller) |
|
boolean |
PivotNode.hasConnection(FreeBranch c,
FreeBranch caller) |
|
boolean |
FreeInternalNode.hasDirectConnection(FreeBranch c) |
|
boolean |
FreeLeafNode.hasDirectConnection(FreeBranch fb) |
|
boolean |
FreeNode.hasDirectConnection(FreeBranch query) |
|
boolean |
PivotNode.hasDirectConnection(FreeBranch query) |
|
void |
FreeLeafNode.rebuildConnectionPatterns(GeneralConstructionTool tool,
FreeBranch caller) |
|
void |
FreeInternalNode.setConnectingBranches(FreeBranch[] store,
int number) |
|
void |
FreeLeafNode.setConnectingBranches(FreeBranch[] store,
int number) |
|
void |
FreeNode.setConnectingBranches(FreeBranch[] store,
int number) |
|
void |
PivotNode.setConnectingBranches(FreeBranch[] store,
int number) |
|
void |
FreeInternalNode.swapConnection(FreeBranch original,
FreeBranch newConnection) |
|
void |
FreeInternalNode.swapConnection(FreeBranch original,
FreeNode nodeToReplace,
FreeBranch newConnection) |
|
void |
FreeLeafNode.swapConnection(FreeBranch original,
FreeBranch newConnection) |
|
void |
FreeLeafNode.swapConnection(FreeBranch original,
FreeNode nodeToReplace,
FreeBranch newConnection) |
|
void |
FreeNode.swapConnection(FreeBranch original,
FreeBranch newConnection) |
Should not do anything but swap branches around
|
void |
FreeNode.swapConnection(FreeBranch original,
FreeNode nodeToReplace,
FreeBranch newConnection) |
Should preserve tree integrity
|
void |
PivotNode.swapConnection(FreeBranch original,
FreeBranch newConnection) |
Should not do anything but swap branches around
|
void |
PivotNode.swapConnection(FreeBranch original,
FreeNode nodeToReplace,
FreeBranch newConnection) |
Should preserve tree integrity
|
void |
FreeInternalNode.testLikelihood(FreeBranch caller,
GeneralConstructionTool tool) |
|
void |
FreeLeafNode.testLikelihood(FreeBranch caller,
GeneralConstructionTool tool) |
|
void |
FreeNode.testLikelihood(FreeBranch caller,
GeneralConstructionTool tool) |
|
void |
PivotNode.testLikelihood(FreeBranch caller,
GeneralConstructionTool tool) |
|
java.lang.String |
ConstrainedLeafNode.toString(FreeBranch caller) |
|
java.lang.String |
FreeInternalNode.toString(FreeBranch caller) |
|
java.lang.String |
FreeLeafNode.toString(FreeBranch caller) |
|
java.lang.String |
FreeNode.toString(FreeBranch caller) |
|
java.lang.String |
PivotNode.toString(FreeBranch caller) |
|