FreeNode
, GeneralTreeComponent
public class FreeInternalNode extends java.lang.Object implements FreeNode
Constructor | Description |
---|---|
FreeInternalNode(Node i,
FreeBranch parentFreeBranch,
GeneralConstructionTool tool,
GeneralConstraintGroupManager.Store store) |
public FreeInternalNode(Node i, FreeBranch parentFreeBranch, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store)
public void mark()
public void undoToMark()
public boolean hasDirectConnection(FreeBranch c)
hasDirectConnection
in interface FreeNode
public boolean hasConnection(FreeBranch c, FreeBranch caller)
hasConnection
in interface FreeNode
public void testLikelihood(FreeBranch caller, GeneralConstructionTool tool)
testLikelihood
in interface FreeNode
public void setConnectingBranches(FreeBranch[] store, int number)
setConnectingBranches
in interface FreeNode
public FreeBranch getLeftBranch(FreeBranch caller)
getLeftBranch
in interface FreeNode
public FreeBranch getRightBranch(FreeBranch caller)
getRightBranch
in interface FreeNode
public FreeBranch extract(FreeBranch caller)
FreeNode
public void swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection)
FreeNode
swapConnection
in interface FreeNode
public void swapConnection(FreeBranch original, FreeBranch newConnection)
FreeNode
swapConnection
in interface FreeNode
public PatternInfo getPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
getPatternInfo
in interface FreeNode
public Node buildPALNodeES(double branchLength, FreeBranch caller)
buildPALNodeES
in interface FreeNode
public Node buildPALNodeBase(double branchLength, FreeBranch caller)
buildPALNodeBase
in interface FreeNode
public java.lang.String toString(FreeBranch caller)
public void getAllComponents(java.util.ArrayList store, java.lang.Class componentType)
getAllComponents
in interface GeneralTreeComponent
public void getAllComponents(java.util.ArrayList store, java.lang.Class componentType, FreeBranch caller)
FreeNode
getAllComponents
in interface FreeNode
public ConditionalProbabilityStore getLeftExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
public ConditionalProbabilityStore getRightExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
public PatternInfo getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
getLeftPatternInfo
in interface FreeNode
public PatternInfo getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
getRightPatternInfo
in interface FreeNode
public ConditionalProbabilityStore getFlatConditionalProbabilities(FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
public ConditionalProbabilityStore getFlatConditionalProbabilities(FreeBranch callerConnection, GeneralConstructionTool tool)
getFlatConditionalProbabilities
in interface FreeNode
public ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance, FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
getExtendedConditionalProbabilities
in interface FreeNode
public ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance, FreeBranch callerConnection, GeneralConstructionTool tool)
getExtendedConditionalProbabilities
in interface FreeNode