All Methods Instance Methods Concrete Methods
Modifier and Type |
Method and Description |
Node |
buildPALNode(double branchLength,
FreeBranch caller) |
Node |
buildPALNodeBase(double branchLength,
FreeBranch caller) |
Node |
buildPALNodeES(double branchLength,
FreeBranch caller) |
FreeBranch |
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.
|
void |
getAllComponents(java.util.ArrayList store,
java.lang.Class componentType) |
void |
getAllComponents(java.util.ArrayList store,
java.lang.Class componentType,
FreeBranch caller)
Recurse to all neighbours but caller
|
void |
getAllConnections(java.util.ArrayList store,
FreeBranch caller) |
ConditionalProbabilityStore |
getExtendedConditionalProbabilities(double distance,
FreeBranch callingBranch,
GeneralConstructionTool tool) |
ConditionalProbabilityStore |
getExtendedConditionalProbabilities(double distance,
FreeBranch callingBranch,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
ConditionalProbabilityStore |
getFlatConditionalProbabilities(FreeBranch caller,
GeneralConstructionTool tool) |
ConditionalProbabilityStore |
getFlatConditionalProbabilities(FreeBranch callingBranch,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
FreeBranch |
getLeftBranch(FreeBranch caller) |
ConditionalProbabilityStore |
getLeftExtendedConditionalProbabilities(FreeBranch caller,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore resultStore) |
PatternInfo |
getLeftPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
PatternInfo |
getPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
FreeBranch |
getRightBranch(FreeBranch caller) |
ConditionalProbabilityStore |
getRightExtendedConditionalProbabilities(FreeBranch caller,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore resultStore) |
PatternInfo |
getRightPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
boolean |
hasConnection(FreeBranch fb,
FreeBranch caller) |
boolean |
hasDirectConnection(FreeBranch fb) |
void |
mark() |
void |
rebuildConnectionPatterns(GeneralConstructionTool tool,
FreeBranch caller) |
int |
redirectRebuildPattern(GeneralConstructionTool tool)
This should only be called by another leaf node on the other end of the connection.
|
void |
setConnectingBranches(FreeBranch[] store,
int number) |
void |
swapConnection(FreeBranch original,
FreeBranch newConnection)
Should not do anything but swap branches around
|
void |
swapConnection(FreeBranch original,
FreeNode nodeToReplace,
FreeBranch newConnection)
Should preserve tree integrity
|
void |
testLikelihood(FreeBranch caller,
GeneralConstructionTool tool) |
java.lang.String |
toString(FreeBranch caller) |
void |
undoToMark() |