Methods
Modifier and Type |
Method and Description |
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,
FreeBranch connection)
Recurse to all neighbours but caller
|
ConditionalProbabilityStore |
getExtendedConditionalProbabilities(double distance,
FreeBranch callingConnection,
GeneralConstructionTool tool) |
ConditionalProbabilityStore |
getExtendedConditionalProbabilities(double distance,
FreeBranch callingConnection,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool) |
ConditionalProbabilityStore |
getFlatConditionalProbabilities(FreeBranch caller,
GeneralConstructionTool tool) |
FreeBranch |
getLeftBranch(FreeBranch caller) |
PatternInfo |
getLeftPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
PatternInfo |
getPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
FreeBranch |
getRightBranch(FreeBranch caller) |
PatternInfo |
getRightPatternInfo(GeneralConstructionTool tool,
FreeBranch caller) |
boolean |
hasConnection(FreeBranch c,
FreeBranch caller) |
boolean |
hasDirectConnection(FreeBranch query) |
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) |