Package pal.treesearch
Class FreeInternalNode
java.lang.Object
pal.treesearch.FreeInternalNode
- All Implemented Interfaces:
FreeNode
,GeneralTreeComponent
-
Constructor Summary
ConstructorsConstructorDescriptionFreeInternalNode
(Node i, FreeBranch parentFreeBranch, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store) -
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) void
getAllComponents
(ArrayList store, Class componentType, FreeBranch caller) Recurse to all neighbours but callergetExtendedConditionalProbabilities
(double distance, FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) getExtendedConditionalProbabilities
(double distance, FreeBranch callerConnection, GeneralConstructionTool tool) getFlatConditionalProbabilities
(FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) getFlatConditionalProbabilities
(FreeBranch callerConnection, GeneralConstructionTool tool) getLeftBranch
(FreeBranch caller) getLeftExtendedConditionalProbabilities
(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) getLeftPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) getPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) getRightBranch
(FreeBranch caller) getRightExtendedConditionalProbabilities
(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) getRightPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) boolean
hasConnection
(FreeBranch c, FreeBranch caller) boolean
void
mark()
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) void
-
Constructor Details
-
FreeInternalNode
public FreeInternalNode(Node i, FreeBranch parentFreeBranch, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store)
-
-
Method Details
-
mark
public void mark() -
undoToMark
public void undoToMark() -
hasDirectConnection
- Specified by:
hasDirectConnection
in interfaceFreeNode
-
hasConnection
- Specified by:
hasConnection
in interfaceFreeNode
-
testLikelihood
- Specified by:
testLikelihood
in interfaceFreeNode
-
setConnectingBranches
- Specified by:
setConnectingBranches
in interfaceFreeNode
-
getLeftBranch
- Specified by:
getLeftBranch
in interfaceFreeNode
-
getRightBranch
- Specified by:
getRightBranch
in interfaceFreeNode
-
extract
Description copied from interface:FreeNode
Instruct the node to extract itself from the two connections that aren't the caller One of the other two connections will become redunant. -
swapConnection
Description copied from interface:FreeNode
Should preserve tree integrity- Specified by:
swapConnection
in interfaceFreeNode
-
swapConnection
Description copied from interface:FreeNode
Should not do anything but swap branches around- Specified by:
swapConnection
in interfaceFreeNode
-
getPatternInfo
- Specified by:
getPatternInfo
in interfaceFreeNode
-
buildPALNodeES
- Specified by:
buildPALNodeES
in interfaceFreeNode
-
buildPALNodeBase
- Specified by:
buildPALNodeBase
in interfaceFreeNode
-
toString
-
getAllComponents
- Specified by:
getAllComponents
in interfaceGeneralTreeComponent
-
getAllComponents
Description copied from interface:FreeNode
Recurse to all neighbours but caller- Specified by:
getAllComponents
in interfaceFreeNode
-
getLeftExtendedConditionalProbabilities
public ConditionalProbabilityStore getLeftExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) -
getRightExtendedConditionalProbabilities
public ConditionalProbabilityStore getRightExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) -
getLeftPatternInfo
- Specified by:
getLeftPatternInfo
in interfaceFreeNode
- Parameters:
caller
-- Returns:
- Get the pattern info for the relative left (from the caller's perspective), or null if not left pattern info
-
getRightPatternInfo
- Specified by:
getRightPatternInfo
in interfaceFreeNode
- Parameters:
caller
-- Returns:
- Get the pattern info for the relative right (from the caller's perspective), or null if not right pattern info
-
getFlatConditionalProbabilities
public ConditionalProbabilityStore getFlatConditionalProbabilities(FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) -
getFlatConditionalProbabilities
public ConditionalProbabilityStore getFlatConditionalProbabilities(FreeBranch callerConnection, GeneralConstructionTool tool) - Specified by:
getFlatConditionalProbabilities
in interfaceFreeNode
-
getExtendedConditionalProbabilities
public ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance, FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) - Specified by:
getExtendedConditionalProbabilities
in interfaceFreeNode
-
getExtendedConditionalProbabilities
public ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance, FreeBranch callerConnection, GeneralConstructionTool tool) - Specified by:
getExtendedConditionalProbabilities
in interfaceFreeNode
-