Package pal.treesearch
Interface FreeNode
- All Superinterfaces:
GeneralTreeComponent
- All Known Implementing Classes:
FreeInternalNode
,FreeLeafNode
,PivotNode
-
Method Summary
Modifier and TypeMethodDescriptionbuildPALNodeBase
(double branchLength_, FreeBranch caller) buildPALNodeES
(double branchLength_, FreeBranch caller) 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
(ArrayList store, Class componentType, FreeBranch connection) Recurse to all neighbours but callergetExtendedConditionalProbabilities
(double distance, FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) getExtendedConditionalProbabilities
(double distance, FreeBranch callingConnection, GeneralConstructionTool tool) getFlatConditionalProbabilities
(FreeBranch caller, GeneralConstructionTool tool) getLeftBranch
(FreeBranch caller) getLeftPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) getPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) getRightBranch
(FreeBranch caller) 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 aroundvoid
swapConnection
(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) Should preserve tree integrityvoid
testLikelihood
(FreeBranch caller, GeneralConstructionTool tool) toString
(FreeBranch caller) Methods inherited from interface pal.treesearch.GeneralTreeComponent
getAllComponents
-
Method Details
-
getPatternInfo
-
hasConnection
-
getLeftBranch
-
getRightBranch
-
getAllComponents
Recurse to all neighbours but caller -
testLikelihood
-
getLeftPatternInfo
- Parameters:
caller
-- Returns:
- Get the pattern info for the relative left (from the caller's perspective), or null if not left pattern info
-
getRightPatternInfo
- Parameters:
caller
-- Returns:
- Get the pattern info for the relative right (from the caller's perspective), or null if not right pattern info
-
getExtendedConditionalProbabilities
ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, GeneralConstructionTool tool) -
getExtendedConditionalProbabilities
ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) -
extract
Instruct the node to extract itself from the two connections that aren't the caller One of the other two connections will become redunant.- Returns:
- the redundant connection, or null of this node can't extract
-
buildPALNodeES
-
buildPALNodeBase
-
getFlatConditionalProbabilities
ConditionalProbabilityStore getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool) -
toString
-
setConnectingBranches
-
hasDirectConnection
-
swapConnection
Should not do anything but swap branches around -
swapConnection
Should preserve tree integrity
-