pal.treesearch
public interface FreeNode extends GeneralTreeComponent
getAllComponents
PatternInfo getPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
boolean hasConnection(FreeBranch c, FreeBranch caller)
FreeBranch getLeftBranch(FreeBranch caller)
FreeBranch getRightBranch(FreeBranch caller)
void getAllComponents(java.util.ArrayList store, java.lang.Class componentType, FreeBranch connection)
void testLikelihood(FreeBranch caller, GeneralConstructionTool tool)
PatternInfo getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
caller
- PatternInfo getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
caller
- ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, GeneralConstructionTool tool)
ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
FreeBranch extract(FreeBranch caller)
Node buildPALNodeES(double branchLength_, FreeBranch caller)
Node buildPALNodeBase(double branchLength_, FreeBranch caller)
ConditionalProbabilityStore getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool)
java.lang.String toString(FreeBranch caller)
void setConnectingBranches(FreeBranch[] store, int number)
boolean hasDirectConnection(FreeBranch query)
void swapConnection(FreeBranch original, FreeBranch newConnection)
void swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection)