Uses of Class
pal.treesearch.GeneralConstructionTool

Packages that use GeneralConstructionTool
pal.treesearch   
 

Uses of GeneralConstructionTool in pal.treesearch
 

Methods in pal.treesearch with parameters of type GeneralConstructionTool
 double PivotNode.calculateLogLikelihood(GeneralConstructionTool tool)
           
 double RootAccess.calculateLogLikelihood(GeneralConstructionTool tool)
           
 double ConstrainedInternalNode.calculateLogLikelihood(GeneralConstructionTool tool)
           
 double FreeBranch.calculateLogLikelihood(GeneralConstructionTool tool)
           
 double FreeBranch.calculateLogLikelihood2(GeneralConstructionTool tool)
           
 SiteDetails FreeBranch.calculateSiteDetails(UnconstrainedLikelihoodModel.External calculator, GeneralConstructionTool tool)
           
protected  UnconstrainedLikelihoodModel.Leaf AbstractLeafNode.createNewFreeLeafCalculator(GeneralConstructionTool tool)
           
 ConditionalProbabilityStore PivotNode.getAscendentExtended(double baseHeight, ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ParentableConstrainedNode.getAscendentExtended(double baseHeight, ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedInternalNode.getAscendentExtended(double baseHeight, ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore PivotNode.getAscendentFlat(ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ParentableConstrainedNode.getAscendentFlat(ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedInternalNode.getAscendentFlat(ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)
           
 PatternInfo PivotNode.getAscendentPatternInfo(ConstrainedNode childCaller, GeneralConstructionTool tool)
           
 PatternInfo ParentableConstrainedNode.getAscendentPatternInfo(ConstrainedNode childCaller, GeneralConstructionTool tool)
           
 PatternInfo ConstrainedInternalNode.getAscendentPatternInfo(ConstrainedNode childCaller, GeneralConstructionTool tool)
           
 PatternInfo ConstrainedInternalNode.getCenterPattern(GeneralConstructionTool tool)
          For center pattern, left is ascendent component, right is descendent component
 PatternInfo FreeBranch.getCenterPatternInfo(GeneralConstructionTool tool)
           
 void FreeBranch.getCenterPatternInfo(GeneralConstructionTool tool, PatternInfo store)
           
 ConditionalProbabilityStore ConstrainedLeafNode.getDescendentExtendedConditionals(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedNode.getDescendentExtendedConditionals(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore AbstractParentableConstrainedNode.getDescendentExtendedConditionals(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedLeafNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights(double extensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights(double adjustedExtensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching)
           
 ConditionalProbabilityStore AbstractParentableConstrainedNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights(double adjustedExtensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedLeafNode.getDescendentFlatConditionals(GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedNode.getDescendentFlatConditionals(GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore AbstractParentableConstrainedNode.getDescendentFlatConditionals(GeneralConstructionTool tool, boolean allowCaching)
           
protected  double AbstractParentableConstrainedNode.getDescendentLogLikelihood(GeneralConstructionTool tool, boolean allowCaching)
           
 PatternInfo ConstrainedLeafNode.getDescendentPatternInfo(GeneralConstructionTool tool)
           
 PatternInfo ConstrainedNode.getDescendentPatternInfo(GeneralConstructionTool tool)
           
 PatternInfo AbstractParentableConstrainedNode.getDescendentPatternInfo(GeneralConstructionTool tool)
           
 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 FreeBranch.getExtendedConditionalProbabilities(FreeNode caller, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeBranch.getExtendedConditionalProbabilities(FreeNode caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore extendedStore, 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)
           
protected  PatternInfo AbstractParentableConstrainedNode.getLeftChildPatternInfo(GeneralConstructionTool tool)
           
protected  ConditionalProbabilityStore AbstractParentableConstrainedNode.getLeftDescendentExtendedConditionals(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching)
          Obtain conditionals by extended left child conditionals to a particular height
protected  ConditionalProbabilityStore AbstractParentableConstrainedNode.getLeftDescendentExtendedConditionals(GeneralConstructionTool tool, boolean allowCaching)
          Obtain conditionals by extended left child conditionals to height of this node
 ConditionalProbabilityStore FreeInternalNode.getLeftExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeBranch.getLeftFlatConditionalProbabilities(GeneralConstructionTool tool)
           
 PatternInfo FreeBranch.getLeftPatternInfo(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)
           
 PatternInfo FreeBranch.getPatternInfo(GeneralConstructionTool tool, FreeNode caller)
           
protected  PatternInfo AbstractParentableConstrainedNode.getRightChildPatternInfo(GeneralConstructionTool tool)
           
protected  ConditionalProbabilityStore AbstractParentableConstrainedNode.getRightDescendentExtendedConditionals(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching)
          Obtain conditionals by extended left child conditionals to a particular height
protected  ConditionalProbabilityStore AbstractParentableConstrainedNode.getRightDescendentExtendedConditionals(GeneralConstructionTool tool, boolean allowCaching)
          Obtain conditionals by extended right child conditionals to height of this node
 ConditionalProbabilityStore FreeInternalNode.getRightExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeBranch.getRightFlatConditionalProbabilities(GeneralConstructionTool tool)
           
 PatternInfo FreeBranch.getRightPatternInfo(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)
           
 double PivotNode.optimise(int optimisationType, UnivariateMinimum minimiser, GeneralConstructionTool tool, int fracDigits)
           
 double GeneralOptimisable.optimise(int optimisationType, UnivariateMinimum minimiser, GeneralConstructionTool tool, int fracDigits)
           
 double ConstrainedInternalNode.optimise(int optimisationType, UnivariateMinimum minimiser, GeneralConstructionTool tool, int fracDigits)
           
 double FreeBranch.optimise(int optimisationType, UnivariateMinimum minimiser, GeneralConstructionTool tool, int fracDigits)
           
 void FreeLeafNode.rebuildConnectionPatterns(GeneralConstructionTool tool, FreeBranch caller)
           
 void ConstrainedLeafNode.rebuildDescendentPattern(GeneralConstructionTool tool)
           
 void AbstractParentableConstrainedNode.rebuildDescendentPattern(GeneralConstructionTool tool)
           
 int FreeLeafNode.redirectRebuildPattern(GeneralConstructionTool tool)
          This should only be called by another leaf node on the other end of the connection.
 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)
           
 void FreeBranch.testLikelihood(FreeNode caller, GeneralConstructionTool tool)
           
 void PivotNode.testLikelihood(GeneralConstructionTool tool)
           
 void ConstrainedLeafNode.testLikelihood(GeneralConstructionTool tool)
           
 void RootAccess.testLikelihood(GeneralConstructionTool tool)
           
 void ConstrainedInternalNode.testLikelihood(GeneralConstructionTool tool)
           
 void ConstrainedNode.testLikelihood(GeneralConstructionTool tool)
           
 void FreeBranch.testLikelihood(GeneralConstructionTool tool)
           
 

Constructors in pal.treesearch with parameters of type GeneralConstructionTool
AbstractLeafNode(java.lang.String id, GeneralConstructionTool tool)
           
AbstractParentableConstrainedNode(Node peer, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager)
           
ConstrainedInternalNode(Node peer, ParentableConstrainedNode parentNode, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager)
           
ConstrainedLeafNode(ParentableConstrainedNode parentNode, Node peer, double height, GeneralConstructionTool tool, ConstraintModel.GroupManager parentGroup)
           
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
FreeBranch(Node n, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store)
          The starting constructor for building from a given tree
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
PivotNode(Node subTree, GeneralConstructionTool tool, GeneralConstraintGroupManager groupManager, GeneralConstraintGroupManager.Store store)
          The root constructor, only used when the whole tree is constrained