Constructor Detail

• FreeInternalNode

  public FreeInternalNode​(Node i,
                          FreeBranch parentFreeBranch,
                          GeneralConstructionTool tool,
                          GeneralConstraintGroupManager.Store store)

Method Detail

• mark

  public void mark​()

• undoToMark

  public void undoToMark​()

• hasDirectConnection

  public boolean hasDirectConnection​(FreeBranch c)

  Specified by:

  hasDirectConnection in interface FreeNode

• hasConnection

  public boolean hasConnection​(FreeBranch c,
                               FreeBranch caller)

  Specified by:

  hasConnection in interface FreeNode

• testLikelihood

  public void testLikelihood​(FreeBranch caller,
                             GeneralConstructionTool tool)

  Specified by:

  testLikelihood in interface FreeNode

• setConnectingBranches

  public void setConnectingBranches​(FreeBranch[] store,
                                    int number)

  Specified by:

  setConnectingBranches in interface FreeNode

• getLeftBranch

  public FreeBranch getLeftBranch​(FreeBranch caller)

  Specified by:

  getLeftBranch in interface FreeNode

• getRightBranch

  public FreeBranch getRightBranch​(FreeBranch caller)

  Specified by:

  getRightBranch in interface FreeNode

• extract

  public FreeBranch extract​(FreeBranch caller)

  Description copied from interface: FreeNode
  Instruct the node to extract itself from the two connections that aren't the caller One of the other two connections will become redunant.

  Specified by:

  extract in interface FreeNode

  Returns:

  the redundant connection, or null of this node can't extract

• swapConnection

  public void swapConnection​(FreeBranch original,
                             FreeNode nodeToReplace,
                             FreeBranch newConnection)

  Description copied from interface: FreeNode
  Should preserve tree integrity

  Specified by:

  swapConnection in interface FreeNode

• swapConnection

  public void swapConnection​(FreeBranch original,
                             FreeBranch newConnection)

  Description copied from interface: FreeNode
  Should not do anything but swap branches around

  Specified by:

  swapConnection in interface FreeNode

• getPatternInfo

  public PatternInfo getPatternInfo​(GeneralConstructionTool tool,
                                    FreeBranch caller)

  Specified by:

  getPatternInfo in interface FreeNode

• buildPALNodeES

  public Node buildPALNodeES​(double branchLength,
                             FreeBranch caller)

  Specified by:

  buildPALNodeES in interface FreeNode

• buildPALNodeBase

  public Node buildPALNodeBase​(double branchLength,
                               FreeBranch caller)

  Specified by:

  buildPALNodeBase in interface FreeNode

• toString

  public java.lang.String toString​(FreeBranch caller)

  Specified by:

  toString in interface FreeNode

• getAllComponents

  public void getAllComponents​(java.util.ArrayList store,
                               java.lang.Class componentType)

  Specified by:

  getAllComponents in interface GeneralTreeComponent

• getAllComponents

  public void getAllComponents​(java.util.ArrayList store,
                               java.lang.Class componentType,
                               FreeBranch caller)

  Description copied from interface: FreeNode
  Recurse to all neighbours but caller

  Specified by:

  getAllComponents in interface FreeNode

• getLeftExtendedConditionalProbabilities

  public ConditionalProbabilityStore getLeftExtendedConditionalProbabilities​(FreeBranch callingConnection,
                                                                             UnconstrainedLikelihoodModel.External external,
                                                                             ConditionalProbabilityStore resultStore,
                                                                             GeneralConstructionTool tool)

• getRightExtendedConditionalProbabilities

  public ConditionalProbabilityStore getRightExtendedConditionalProbabilities​(FreeBranch callingConnection,
                                                                              UnconstrainedLikelihoodModel.External external,
                                                                              ConditionalProbabilityStore resultStore,
                                                                              GeneralConstructionTool tool)

• getLeftPatternInfo

  public PatternInfo getLeftPatternInfo​(GeneralConstructionTool tool,
                                        FreeBranch caller)

  Specified by:

  getLeftPatternInfo in interface FreeNode

  Returns:

  Get the pattern info for the relative left (from the caller's perspective), or null if not left pattern info

• getRightPatternInfo

  public PatternInfo getRightPatternInfo​(GeneralConstructionTool tool,
                                         FreeBranch caller)

  Specified by:

  getRightPatternInfo in interface FreeNode

  Returns:

  Get the pattern info for the relative right (from the caller's perspective), or null if not right pattern info

• getFlatConditionalProbabilities

  public ConditionalProbabilityStore getFlatConditionalProbabilities​(FreeBranch callerConnection,
                                                                     UnconstrainedLikelihoodModel.External externalCalculator,
                                                                     ConditionalProbabilityStore resultStore,
                                                                     GeneralConstructionTool tool)

• getFlatConditionalProbabilities

  public ConditionalProbabilityStore getFlatConditionalProbabilities​(FreeBranch callerConnection,
                                                                     GeneralConstructionTool tool)

  Specified by:

  getFlatConditionalProbabilities in interface FreeNode

• getExtendedConditionalProbabilities

  public ConditionalProbabilityStore getExtendedConditionalProbabilities​(double distance,
                                                                         FreeBranch callerConnection,
                                                                         UnconstrainedLikelihoodModel.External externalCalculator,
                                                                         ConditionalProbabilityStore resultStore,
                                                                         GeneralConstructionTool tool)

  Specified by:

  getExtendedConditionalProbabilities in interface FreeNode

• getExtendedConditionalProbabilities

  public ConditionalProbabilityStore getExtendedConditionalProbabilities​(double distance,
                                                                         FreeBranch callerConnection,
                                                                         GeneralConstructionTool tool)

  Specified by:

  getExtendedConditionalProbabilities in interface FreeNode