Uses of Class
pal.treesearch.FreeBranch
Packages that use FreeBranch
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Uses of FreeBranch in pal.treesearch
Methods in pal.treesearch that return FreeBranchModifier and TypeMethodDescriptionFreeBranch.attachTo
(FreeBranch attachmentPoint, FreeBranch[] store) FreeInternalNode.extract
(FreeBranch caller) FreeLeafNode.extract
(FreeBranch caller) 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.PivotNode.extract
(FreeBranch caller) We can't extractFreeInternalNode.getLeftBranch
(FreeBranch caller) FreeLeafNode.getLeftBranch
(FreeBranch caller) FreeNode.getLeftBranch
(FreeBranch caller) PivotNode.getLeftBranch
(FreeBranch caller) FreeBranch.getLeftLeftBranch()
FreeBranch.getLeftRightBranch()
FreeInternalNode.getRightBranch
(FreeBranch caller) FreeLeafNode.getRightBranch
(FreeBranch caller) FreeNode.getRightBranch
(FreeBranch caller) PivotNode.getRightBranch
(FreeBranch caller) FreeBranch.getRightLeftBranch()
FreeBranch.getRightRightBranch()
Methods in pal.treesearch with parameters of type FreeBranchModifier and TypeMethodDescriptionFreeBranch.attachTo
(FreeBranch attachmentPoint, FreeBranch[] store) final Node
FreeLeafNode.buildPALNode
(double branchLength, FreeBranch caller) FreeInternalNode.buildPALNodeBase
(double branchLength, FreeBranch caller) final Node
FreeLeafNode.buildPALNodeBase
(double branchLength, FreeBranch caller) FreeNode.buildPALNodeBase
(double branchLength_, FreeBranch caller) PivotNode.buildPALNodeBase
(double branchLength_, FreeBranch caller) FreeInternalNode.buildPALNodeES
(double branchLength, FreeBranch caller) final Node
FreeLeafNode.buildPALNodeES
(double branchLength, FreeBranch caller) FreeNode.buildPALNodeES
(double branchLength_, FreeBranch caller) PivotNode.buildPALNodeES
(double branchLength_, FreeBranch caller) GeneralConstructionTool.createFreeNode
(Node peer, FreeBranch parent, GeneralConstraintGroupManager.Store store) Create an appropriate free node given a peer, and it's parent branchFreeInternalNode.extract
(FreeBranch caller) FreeLeafNode.extract
(FreeBranch caller) 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.PivotNode.extract
(FreeBranch caller) We can't extractvoid
FreeInternalNode.getAllComponents
(ArrayList store, Class componentType, FreeBranch caller) void
FreeLeafNode.getAllComponents
(ArrayList store, Class componentType, FreeBranch caller) void
FreeNode.getAllComponents
(ArrayList store, Class componentType, FreeBranch connection) Recurse to all neighbours but callervoid
PivotNode.getAllComponents
(ArrayList store, Class componentType, FreeBranch caller) void
FreeLeafNode.getAllConnections
(ArrayList store, FreeBranch caller) FreeInternalNode.getExtendedConditionalProbabilities
(double distance, FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeInternalNode.getExtendedConditionalProbabilities
(double distance, FreeBranch callerConnection, GeneralConstructionTool tool) FreeLeafNode.getExtendedConditionalProbabilities
(double distance, FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getExtendedConditionalProbabilities
(double distance, FreeBranch callingBranch, GeneralConstructionTool tool) FreeNode.getExtendedConditionalProbabilities
(double distance, FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeNode.getExtendedConditionalProbabilities
(double distance, FreeBranch callingConnection, GeneralConstructionTool tool) PivotNode.getExtendedConditionalProbabilities
(double distance, FreeBranch caller, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) PivotNode.getExtendedConditionalProbabilities
(double distance, FreeBranch caller, GeneralConstructionTool tool) FreeInternalNode.getFlatConditionalProbabilities
(FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeInternalNode.getFlatConditionalProbabilities
(FreeBranch callerConnection, GeneralConstructionTool tool) FreeLeafNode.getFlatConditionalProbabilities
(FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getFlatConditionalProbabilities
(FreeBranch caller, GeneralConstructionTool tool) FreeNode.getFlatConditionalProbabilities
(FreeBranch caller, GeneralConstructionTool tool) PivotNode.getFlatConditionalProbabilities
(FreeBranch caller, GeneralConstructionTool tool) FreeInternalNode.getLeftBranch
(FreeBranch caller) FreeLeafNode.getLeftBranch
(FreeBranch caller) FreeNode.getLeftBranch
(FreeBranch caller) PivotNode.getLeftBranch
(FreeBranch caller) FreeInternalNode.getLeftExtendedConditionalProbabilities
(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getLeftExtendedConditionalProbabilities
(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore) FreeInternalNode.getLeftPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) FreeLeafNode.getLeftPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) FreeNode.getLeftPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) PivotNode.getLeftPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) FreeInternalNode.getPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) FreeLeafNode.getPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) FreeNode.getPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) PivotNode.getPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) FreeInternalNode.getRightBranch
(FreeBranch caller) FreeLeafNode.getRightBranch
(FreeBranch caller) FreeNode.getRightBranch
(FreeBranch caller) PivotNode.getRightBranch
(FreeBranch caller) FreeInternalNode.getRightExtendedConditionalProbabilities
(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getRightExtendedConditionalProbabilities
(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore) FreeInternalNode.getRightPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) FreeLeafNode.getRightPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) FreeNode.getRightPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) PivotNode.getRightPatternInfo
(GeneralConstructionTool tool, FreeBranch caller) boolean
FreeBranch.hasConnection
(FreeBranch c, FreeNode caller) boolean
FreeInternalNode.hasConnection
(FreeBranch c, FreeBranch caller) boolean
FreeLeafNode.hasConnection
(FreeBranch fb, FreeBranch caller) boolean
FreeNode.hasConnection
(FreeBranch c, FreeBranch caller) boolean
PivotNode.hasConnection
(FreeBranch c, FreeBranch caller) boolean
FreeInternalNode.hasDirectConnection
(FreeBranch c) boolean
FreeLeafNode.hasDirectConnection
(FreeBranch fb) boolean
FreeNode.hasDirectConnection
(FreeBranch query) boolean
PivotNode.hasDirectConnection
(FreeBranch query) void
FreeLeafNode.rebuildConnectionPatterns
(GeneralConstructionTool tool, FreeBranch caller) void
FreeInternalNode.setConnectingBranches
(FreeBranch[] store, int number) void
FreeLeafNode.setConnectingBranches
(FreeBranch[] store, int number) void
FreeNode.setConnectingBranches
(FreeBranch[] store, int number) void
PivotNode.setConnectingBranches
(FreeBranch[] store, int number) void
FreeInternalNode.swapConnection
(FreeBranch original, FreeBranch newConnection) void
FreeInternalNode.swapConnection
(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) void
FreeLeafNode.swapConnection
(FreeBranch original, FreeBranch newConnection) void
FreeLeafNode.swapConnection
(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) void
FreeNode.swapConnection
(FreeBranch original, FreeBranch newConnection) Should not do anything but swap branches aroundvoid
FreeNode.swapConnection
(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) Should preserve tree integrityvoid
PivotNode.swapConnection
(FreeBranch original, FreeBranch newConnection) Should not do anything but swap branches aroundvoid
PivotNode.swapConnection
(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) Should preserve tree integrityvoid
FreeInternalNode.testLikelihood
(FreeBranch caller, GeneralConstructionTool tool) void
FreeLeafNode.testLikelihood
(FreeBranch caller, GeneralConstructionTool tool) void
FreeNode.testLikelihood
(FreeBranch caller, GeneralConstructionTool tool) void
PivotNode.testLikelihood
(FreeBranch caller, GeneralConstructionTool tool) ConstrainedLeafNode.toString
(FreeBranch caller) FreeInternalNode.toString
(FreeBranch caller) FreeLeafNode.toString
(FreeBranch caller) FreeNode.toString
(FreeBranch caller) PivotNode.toString
(FreeBranch caller) Constructors in pal.treesearch with parameters of type FreeBranchModifierConstructorDescriptionFreeInternalNode
(Node i, FreeBranch parentFreeBranch, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store) FreeLeafNode
(FreeBranch parentBranch, 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