Constructor Detail

• FreeLeafNode

  public FreeLeafNode​(FreeBranch parentBranch,
                      java.lang.String id,
                      GeneralConstructionTool tool)

Method Detail

• hasDirectConnection

  public boolean hasDirectConnection​(FreeBranch fb)

  Specified by:

  hasDirectConnection in interface FreeNode

• mark

  public void mark​()

• undoToMark

  public void undoToMark​()

• hasConnection

  public boolean hasConnection​(FreeBranch fb,
                               FreeBranch caller)

  Specified by:

  hasConnection 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

• getLeftExtendedConditionalProbabilities

  public ConditionalProbabilityStore getLeftExtendedConditionalProbabilities​(FreeBranch caller,
                                                                             UnconstrainedLikelihoodModel.External externalCalculator,
                                                                             ConditionalProbabilityStore resultStore)

• getRightExtendedConditionalProbabilities

  public ConditionalProbabilityStore getRightExtendedConditionalProbabilities​(FreeBranch caller,
                                                                              UnconstrainedLikelihoodModel.External externalCalculator,
                                                                              ConditionalProbabilityStore resultStore)

• 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

• setConnectingBranches

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

  Specified by:

  setConnectingBranches in interface FreeNode

• testLikelihood

  public void testLikelihood​(FreeBranch caller,
                             GeneralConstructionTool tool)

  Specified by:

  testLikelihood 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

• 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

• getLeftBranch

  public FreeBranch getLeftBranch​(FreeBranch caller)

  Specified by:

  getLeftBranch in interface FreeNode

  Returns:

  null (as not possible)

• getRightBranch

  public FreeBranch getRightBranch​(FreeBranch caller)

  Specified by:

  getRightBranch in interface FreeNode

  Returns:

  null (as not possible)

• getAllConnections

  public void getAllConnections​(java.util.ArrayList store,
                                FreeBranch caller)

• getPatternInfo

  public PatternInfo getPatternInfo​(GeneralConstructionTool tool,
                                    FreeBranch caller)

  Specified by:

  getPatternInfo in interface FreeNode

• rebuildConnectionPatterns

  public void rebuildConnectionPatterns​(GeneralConstructionTool tool,
                                        FreeBranch caller)

• redirectRebuildPattern

  public int redirectRebuildPattern​(GeneralConstructionTool tool)

  This should only be called by another leaf node on the other end of the connection. In this case we don't have to do much (tree is two node tree)

• getFlatConditionalProbabilities

  public final ConditionalProbabilityStore getFlatConditionalProbabilities​(FreeBranch callingBranch,
                                                                           UnconstrainedLikelihoodModel.External external,
                                                                           ConditionalProbabilityStore resultStore,
                                                                           GeneralConstructionTool tool)

• getFlatConditionalProbabilities

  public final ConditionalProbabilityStore getFlatConditionalProbabilities​(FreeBranch caller,
                                                                           GeneralConstructionTool tool)

  Specified by:

  getFlatConditionalProbabilities in interface FreeNode

• getExtendedConditionalProbabilities

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

  Specified by:

  getExtendedConditionalProbabilities in interface FreeNode

• getExtendedConditionalProbabilities

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

  Specified by:

  getExtendedConditionalProbabilities in interface FreeNode

• buildPALNode

  public final Node buildPALNode​(double branchLength,
                                 FreeBranch caller)

• buildPALNodeES

  public final Node buildPALNodeES​(double branchLength,
                                   FreeBranch caller)

  Specified by:

  buildPALNodeES in interface FreeNode

• buildPALNodeBase

  public final 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,
                               FreeBranch caller)

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

  Specified by:

  getAllComponents in interface FreeNode

• getAllComponents

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

  Specified by:

  getAllComponents in interface GeneralTreeComponent