Uses of Interface
pal.treesearch.FreeNode

Packages that use FreeNode
pal.treesearch   
 

Uses of FreeNode in pal.treesearch
 

Classes in pal.treesearch that implement FreeNode
 class FreeInternalNode
           
 class FreeLeafNode
           
 class PivotNode
           
 

Methods in pal.treesearch that return FreeNode
 FreeNode GeneralConstructionTool.createFreeNode(Node peer, FreeBranch parent, GeneralConstraintGroupManager.Store store)
          Create an appropriate free node given a peer, and it's parent branch
 FreeNode FreeBranch.getLeft()
           
 FreeNode FreeBranch.getOther(FreeNode caller)
           
 FreeNode FreeBranch.getRight()
           
 

Methods in pal.treesearch with parameters of type FreeNode
 Node FreeBranch.buildPALNodeBase(FreeNode caller)
           
 Node FreeBranch.buildPALNodeES(FreeNode caller)
           
 void FreeBranch.getAllComponents(java.util.ArrayList store, java.lang.Class componentType, FreeNode caller)
           
 ConditionalProbabilityStore FreeBranch.getExtendedConditionalProbabilities(FreeNode caller, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeBranch.getExtendedConditionalProbabilities(FreeNode caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore extendedStore, GeneralConstructionTool tool)
           
 FreeNode FreeBranch.getOther(FreeNode caller)
           
 PatternInfo FreeBranch.getPatternInfo(GeneralConstructionTool tool, FreeNode caller)
           
 boolean FreeBranch.hasConnection(FreeBranch c, FreeNode caller)
           
 void FreeBranch.setNodes(FreeNode left, FreeNode right)
          Does nothing to fix up tree structure
 void FreeNode.swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection)
          Should preserve tree integrity
 void PivotNode.swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection)
          Should preserve tree integrity
 void FreeLeafNode.swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection)
           
 void FreeInternalNode.swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection)
           
 void FreeBranch.swapNode(FreeNode nodeToReplace, FreeNode replacement)
           
 void FreeBranch.testLikelihood(FreeNode caller, GeneralConstructionTool tool)
           
 java.lang.String FreeBranch.toString(FreeNode caller)
           
 

Constructors in pal.treesearch with parameters of type FreeNode
FreeBranch(FreeNode left, FreeNode right, double branchLength, GeneralConstructionTool tool)
          A generic constructor given two already defined left and right children
FreeBranch(Node n, FreeNode parent, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store)
          Continuing recurison constructor for a given tree