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 NodeFreeLeafNode.buildPALNode(double branchLength, FreeBranch caller) FreeInternalNode.buildPALNodeBase(double branchLength, FreeBranch caller) final NodeFreeLeafNode.buildPALNodeBase(double branchLength, FreeBranch caller) FreeNode.buildPALNodeBase(double branchLength_, FreeBranch caller) PivotNode.buildPALNodeBase(double branchLength_, FreeBranch caller) FreeInternalNode.buildPALNodeES(double branchLength, FreeBranch caller) final NodeFreeLeafNode.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 extractvoidFreeInternalNode.getAllComponents(ArrayList store, Class componentType, FreeBranch caller) voidFreeLeafNode.getAllComponents(ArrayList store, Class componentType, FreeBranch caller) voidFreeNode.getAllComponents(ArrayList store, Class componentType, FreeBranch connection) Recurse to all neighbours but callervoidPivotNode.getAllComponents(ArrayList store, Class componentType, FreeBranch caller) voidFreeLeafNode.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) booleanFreeBranch.hasConnection(FreeBranch c, FreeNode caller) booleanFreeInternalNode.hasConnection(FreeBranch c, FreeBranch caller) booleanFreeLeafNode.hasConnection(FreeBranch fb, FreeBranch caller) booleanFreeNode.hasConnection(FreeBranch c, FreeBranch caller) booleanPivotNode.hasConnection(FreeBranch c, FreeBranch caller) booleanFreeInternalNode.hasDirectConnection(FreeBranch c) booleanFreeLeafNode.hasDirectConnection(FreeBranch fb) booleanFreeNode.hasDirectConnection(FreeBranch query) booleanPivotNode.hasDirectConnection(FreeBranch query) voidFreeLeafNode.rebuildConnectionPatterns(GeneralConstructionTool tool, FreeBranch caller) voidFreeInternalNode.setConnectingBranches(FreeBranch[] store, int number) voidFreeLeafNode.setConnectingBranches(FreeBranch[] store, int number) voidFreeNode.setConnectingBranches(FreeBranch[] store, int number) voidPivotNode.setConnectingBranches(FreeBranch[] store, int number) voidFreeInternalNode.swapConnection(FreeBranch original, FreeBranch newConnection) voidFreeInternalNode.swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) voidFreeLeafNode.swapConnection(FreeBranch original, FreeBranch newConnection) voidFreeLeafNode.swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) voidFreeNode.swapConnection(FreeBranch original, FreeBranch newConnection) Should not do anything but swap branches aroundvoidFreeNode.swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) Should preserve tree integrityvoidPivotNode.swapConnection(FreeBranch original, FreeBranch newConnection) Should not do anything but swap branches aroundvoidPivotNode.swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) Should preserve tree integrityvoidFreeInternalNode.testLikelihood(FreeBranch caller, GeneralConstructionTool tool) voidFreeLeafNode.testLikelihood(FreeBranch caller, GeneralConstructionTool tool) voidFreeNode.testLikelihood(FreeBranch caller, GeneralConstructionTool tool) voidPivotNode.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