Uses of Class
pal.treesearch.FreeBranch

Packages that use FreeBranch
pal.treesearch   
 

Uses of FreeBranch in pal.treesearch
 

Methods in pal.treesearch that return FreeBranch
 FreeBranch FreeBranch.attachTo(FreeBranch attachmentPoint, FreeBranch[] store)
           
 FreeBranch FreeNode.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.
 FreeBranch PivotNode.extract(FreeBranch caller)
          We can't extract
 FreeBranch FreeLeafNode.extract(FreeBranch caller)
           
 FreeBranch FreeInternalNode.extract(FreeBranch caller)
           
 FreeBranch FreeNode.getLeftBranch(FreeBranch caller)
           
 FreeBranch PivotNode.getLeftBranch(FreeBranch caller)
           
 FreeBranch FreeLeafNode.getLeftBranch(FreeBranch caller)
           
 FreeBranch FreeInternalNode.getLeftBranch(FreeBranch caller)
           
 FreeBranch FreeBranch.getLeftLeftBranch()
           
 FreeBranch FreeBranch.getLeftRightBranch()
           
 FreeBranch FreeNode.getRightBranch(FreeBranch caller)
           
 FreeBranch PivotNode.getRightBranch(FreeBranch caller)
           
 FreeBranch FreeLeafNode.getRightBranch(FreeBranch caller)
           
 FreeBranch FreeInternalNode.getRightBranch(FreeBranch caller)
           
 FreeBranch FreeBranch.getRightLeftBranch()
           
 FreeBranch FreeBranch.getRightRightBranch()
           
 

Methods in pal.treesearch with parameters of type FreeBranch
 FreeBranch FreeBranch.attachTo(FreeBranch attachmentPoint, FreeBranch[] store)
           
 FreeBranch FreeBranch.attachTo(FreeBranch attachmentPoint, FreeBranch[] store)
           
 Node FreeLeafNode.buildPALNode(double branchLength, FreeBranch caller)
           
 Node FreeNode.buildPALNodeBase(double branchLength_, FreeBranch caller)
           
 Node PivotNode.buildPALNodeBase(double branchLength_, FreeBranch caller)
           
 Node FreeLeafNode.buildPALNodeBase(double branchLength, FreeBranch caller)
           
 Node FreeInternalNode.buildPALNodeBase(double branchLength, FreeBranch caller)
           
 Node FreeNode.buildPALNodeES(double branchLength_, FreeBranch caller)
           
 Node PivotNode.buildPALNodeES(double branchLength_, FreeBranch caller)
           
 Node FreeLeafNode.buildPALNodeES(double branchLength, FreeBranch caller)
           
 Node FreeInternalNode.buildPALNodeES(double branchLength, FreeBranch caller)
           
 FreeNode GeneralConstructionTool.createFreeNode(Node peer, FreeBranch parent, GeneralConstraintGroupManager.Store store)
          Create an appropriate free node given a peer, and it's parent branch
 FreeBranch FreeNode.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.
 FreeBranch PivotNode.extract(FreeBranch caller)
          We can't extract
 FreeBranch FreeLeafNode.extract(FreeBranch caller)
           
 FreeBranch FreeInternalNode.extract(FreeBranch caller)
           
 void FreeNode.getAllComponents(java.util.ArrayList store, java.lang.Class componentType, FreeBranch connection)
          Recurse to all neighbours but caller
 void PivotNode.getAllComponents(java.util.ArrayList store, java.lang.Class componentType, FreeBranch caller)
           
 void FreeLeafNode.getAllComponents(java.util.ArrayList store, java.lang.Class componentType, FreeBranch caller)
           
 void FreeInternalNode.getAllComponents(java.util.ArrayList store, java.lang.Class componentType, FreeBranch caller)
           
 void FreeLeafNode.getAllConnections(java.util.ArrayList store, FreeBranch caller)
           
 ConditionalProbabilityStore FreeNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore PivotNode.getExtendedConditionalProbabilities(double distance, FreeBranch caller, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingBranch, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeInternalNode.getExtendedConditionalProbabilities(double distance, FreeBranch callerConnection, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore PivotNode.getExtendedConditionalProbabilities(double distance, FreeBranch caller, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeInternalNode.getExtendedConditionalProbabilities(double distance, FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeNode.getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore PivotNode.getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeInternalNode.getFlatConditionalProbabilities(FreeBranch callerConnection, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getFlatConditionalProbabilities(FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeInternalNode.getFlatConditionalProbabilities(FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 FreeBranch FreeNode.getLeftBranch(FreeBranch caller)
           
 FreeBranch PivotNode.getLeftBranch(FreeBranch caller)
           
 FreeBranch FreeLeafNode.getLeftBranch(FreeBranch caller)
           
 FreeBranch FreeInternalNode.getLeftBranch(FreeBranch caller)
           
 ConditionalProbabilityStore FreeLeafNode.getLeftExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore)
           
 ConditionalProbabilityStore FreeInternalNode.getLeftExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 PatternInfo FreeNode.getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo PivotNode.getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo FreeLeafNode.getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo FreeInternalNode.getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo FreeNode.getPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo PivotNode.getPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo FreeLeafNode.getPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo FreeInternalNode.getPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 FreeBranch FreeNode.getRightBranch(FreeBranch caller)
           
 FreeBranch PivotNode.getRightBranch(FreeBranch caller)
           
 FreeBranch FreeLeafNode.getRightBranch(FreeBranch caller)
           
 FreeBranch FreeInternalNode.getRightBranch(FreeBranch caller)
           
 ConditionalProbabilityStore FreeLeafNode.getRightExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore)
           
 ConditionalProbabilityStore FreeInternalNode.getRightExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 PatternInfo FreeNode.getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo PivotNode.getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo FreeLeafNode.getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo FreeInternalNode.getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 boolean FreeNode.hasConnection(FreeBranch c, FreeBranch caller)
           
 boolean PivotNode.hasConnection(FreeBranch c, FreeBranch caller)
           
 boolean FreeLeafNode.hasConnection(FreeBranch fb, FreeBranch caller)
           
 boolean FreeInternalNode.hasConnection(FreeBranch c, FreeBranch caller)
           
 boolean FreeBranch.hasConnection(FreeBranch c, FreeNode caller)
           
 boolean FreeNode.hasDirectConnection(FreeBranch query)
           
 boolean PivotNode.hasDirectConnection(FreeBranch query)
           
 boolean FreeLeafNode.hasDirectConnection(FreeBranch fb)
           
 boolean FreeInternalNode.hasDirectConnection(FreeBranch c)
           
 void FreeLeafNode.rebuildConnectionPatterns(GeneralConstructionTool tool, FreeBranch caller)
           
 void FreeNode.setConnectingBranches(FreeBranch[] store, int number)
           
 void PivotNode.setConnectingBranches(FreeBranch[] store, int number)
           
 void FreeLeafNode.setConnectingBranches(FreeBranch[] store, int number)
           
 void FreeInternalNode.setConnectingBranches(FreeBranch[] store, int number)
           
 void FreeNode.swapConnection(FreeBranch original, FreeBranch newConnection)
          Should not do anything but swap branches around
 void PivotNode.swapConnection(FreeBranch original, FreeBranch newConnection)
          Should not do anything but swap branches around
 void FreeLeafNode.swapConnection(FreeBranch original, FreeBranch newConnection)
           
 void FreeInternalNode.swapConnection(FreeBranch original, FreeBranch newConnection)
           
 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 FreeNode.testLikelihood(FreeBranch caller, GeneralConstructionTool tool)
           
 void PivotNode.testLikelihood(FreeBranch caller, GeneralConstructionTool tool)
           
 void FreeLeafNode.testLikelihood(FreeBranch caller, GeneralConstructionTool tool)
           
 void FreeInternalNode.testLikelihood(FreeBranch caller, GeneralConstructionTool tool)
           
 java.lang.String FreeNode.toString(FreeBranch caller)
           
 java.lang.String PivotNode.toString(FreeBranch caller)
           
 java.lang.String ConstrainedLeafNode.toString(FreeBranch caller)
           
 java.lang.String FreeLeafNode.toString(FreeBranch caller)
           
 java.lang.String FreeInternalNode.toString(FreeBranch caller)
           
 

Constructors in pal.treesearch with parameters of type FreeBranch
FreeInternalNode(Node i, FreeBranch parentFreeBranch, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store)
           
FreeLeafNode(FreeBranch parentBranch, java.lang.String id, GeneralConstructionTool tool)
           
PivotNode(Node tree, FreeBranch parentConnection, GeneralConstructionTool tool, GeneralConstraintGroupManager constraintGroupManager, GeneralConstraintGroupManager.Store store)
          The subtree constructor with a connection to the rest of the tree