Class FreeInternalNode

Method Details

• 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 String toString(FreeBranch caller)

  Specified by:

  toString in interface FreeNode

• getAllComponents

  public void getAllComponents(ArrayList store, Class componentType)

  Specified by:

  getAllComponents in interface GeneralTreeComponent

• getAllComponents

  public void getAllComponents(ArrayList store, 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