FreeNode
, GeneralTreeComponent
public class FreeLeafNode extends AbstractLeafNode implements FreeNode
Constructor | Description |
---|---|
FreeLeafNode(FreeBranch parentBranch,
java.lang.String id,
GeneralConstructionTool tool) |
createNewConstrainedLeafCalculator, createNewFreeLeafCalculator, getLabel, getNumberOfPatterns, getPatternInfo
public FreeLeafNode(FreeBranch parentBranch, java.lang.String id, GeneralConstructionTool tool)
public boolean hasDirectConnection(FreeBranch fb)
hasDirectConnection
in interface FreeNode
public void mark()
public void undoToMark()
public boolean hasConnection(FreeBranch fb, FreeBranch caller)
hasConnection
in interface FreeNode
public FreeBranch extract(FreeBranch caller)
FreeNode
public ConditionalProbabilityStore getLeftExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore)
public ConditionalProbabilityStore getRightExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore)
public PatternInfo getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
getLeftPatternInfo
in interface FreeNode
public PatternInfo getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
getRightPatternInfo
in interface FreeNode
public void setConnectingBranches(FreeBranch[] store, int number)
setConnectingBranches
in interface FreeNode
public void testLikelihood(FreeBranch caller, GeneralConstructionTool tool)
testLikelihood
in interface FreeNode
public void swapConnection(FreeBranch original, FreeBranch newConnection)
FreeNode
swapConnection
in interface FreeNode
public void swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection)
FreeNode
swapConnection
in interface FreeNode
public FreeBranch getLeftBranch(FreeBranch caller)
getLeftBranch
in interface FreeNode
public FreeBranch getRightBranch(FreeBranch caller)
getRightBranch
in interface FreeNode
public void getAllConnections(java.util.ArrayList store, FreeBranch caller)
public PatternInfo getPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
getPatternInfo
in interface FreeNode
public void rebuildConnectionPatterns(GeneralConstructionTool tool, FreeBranch caller)
public int redirectRebuildPattern(GeneralConstructionTool tool)
public final ConditionalProbabilityStore getFlatConditionalProbabilities(FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
public final ConditionalProbabilityStore getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool)
getFlatConditionalProbabilities
in interface FreeNode
public ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance, FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
getExtendedConditionalProbabilities
in interface FreeNode
public ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance, FreeBranch callingBranch, GeneralConstructionTool tool)
getExtendedConditionalProbabilities
in interface FreeNode
public final Node buildPALNode(double branchLength, FreeBranch caller)
public final Node buildPALNodeES(double branchLength, FreeBranch caller)
buildPALNodeES
in interface FreeNode
public final 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, FreeBranch caller)
FreeNode
getAllComponents
in interface FreeNode
public final void getAllComponents(java.util.ArrayList store, java.lang.Class componentType)
getAllComponents
in interface GeneralTreeComponent