Class FreeBranch

Method Details

• setAnnotation

  public void setAnnotation(Object annotation)

• getLeft

  public final FreeNode getLeft()

  Returns:

  The "right" node of this connection.

• getRight

  public final FreeNode getRight()

  Returns:

  The "left" node of this connection.

• mark

  public final void mark()

  Mark this node, or in other words store information on left and right nodes and branch length for later retreival (via undoToMark())

• getLeftPatternInfo

  public final PatternInfo getLeftPatternInfo(GeneralConstructionTool tool)

  Returns:

  The pattern info object for the left node leading to this connection

• getRightPatternInfo

  public final PatternInfo getRightPatternInfo(GeneralConstructionTool tool)

  Returns:

  The pattern info object for the right node leading to this connection

• getPatternInfo

  public final PatternInfo getPatternInfo(GeneralConstructionTool tool, FreeNode caller)

• getCenterPatternInfo

  public final PatternInfo getCenterPatternInfo(GeneralConstructionTool tool)

  Returns:

  The pattern info across this connection (for use if this connection is the "root" of the likelihood calculation)

• undoToMark

  public final void undoToMark()

• toString

  public String toString()

  Overrides:

  toString in class Object

• hasConnection

  public boolean hasConnection(FreeBranch c, FreeNode caller)

• getLeftLeftBranch

  public FreeBranch getLeftLeftBranch()

  Returns:

  the "left" connection of the left node

• getLeftRightBranch

  public FreeBranch getLeftRightBranch()

  Returns:

  the "right" connection of the left node

• getRightLeftBranch

  public FreeBranch getRightLeftBranch()

  Returns:

  the "left" connection of the right node

• getRightRightBranch

  public FreeBranch getRightRightBranch()

  Returns:

  the "right" connection of the left node

• attachTo

  public FreeBranch attachTo(FreeBranch attachmentPoint, FreeBranch[] store)

  Returns:

  connection that by attaching to we would undo this operation, null if operation no successful

• buildPALNodeBase

  public Node buildPALNodeBase()

  Specified by:

  buildPALNodeBase in interface RootAccess

• buildPALNodeES

  public Node buildPALNodeES()

  Specified by:

  buildPALNodeES in interface RootAccess

• buildPALNodeBase

  public Node buildPALNodeBase(FreeNode caller)

• buildPALNodeES

  public Node buildPALNodeES(FreeNode caller)

• setNodes

  public void setNodes(FreeNode left, FreeNode right)

  Does nothing to fix up tree structure

• swapNode

  public void swapNode(FreeNode nodeToReplace, FreeNode replacement)

• getLeftFlatConditionalProbabilities

  public final ConditionalProbabilityStore getLeftFlatConditionalProbabilities(GeneralConstructionTool tool)

• getRightFlatConditionalProbabilities

  public final ConditionalProbabilityStore getRightFlatConditionalProbabilities(GeneralConstructionTool tool)

• getBranchLength

  public final double getBranchLength()

• setBranchLength

  public final void setBranchLength(double x)

• toString

  public String toString(FreeNode caller)

• testLikelihood

  public void testLikelihood(GeneralConstructionTool tool)

  Specified by:

  testLikelihood in interface RootAccess

• testLikelihood

  public void testLikelihood(FreeNode caller, GeneralConstructionTool tool)

• getExtendedConditionalProbabilities

  public ConditionalProbabilityStore getExtendedConditionalProbabilities(FreeNode caller, GeneralConstructionTool tool)

• getExtendedConditionalProbabilities

  public ConditionalProbabilityStore getExtendedConditionalProbabilities(FreeNode caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore extendedStore, GeneralConstructionTool tool)

• getNumberOfOptimisationTypes

  public final int getNumberOfOptimisationTypes()

  Specified by:

  getNumberOfOptimisationTypes in interface GeneralOptimisable

• optimise

  public double optimise(int optimisationType, UnivariateMinimum minimiser, GeneralConstructionTool tool, int fracDigits)

  Specified by:

  optimise in interface GeneralOptimisable

  minimiser - The single dimensional minimisation tool

  tool - The construction tool

  fracDigits - the number of fractional digits to converge to

  Returns:

  The optimised log likelihood, or >0 if not optimisation occured

• getAllComponents

  public void getAllComponents(ArrayList store, Class componentType)

  Specified by:

  getAllComponents in interface RootAccess

• getAllComponents

  public void getAllComponents(ArrayList store, Class componentType, FreeNode caller)

• getCenterPatternInfo

  public void getCenterPatternInfo(GeneralConstructionTool tool, PatternInfo store)

• getOther

  public FreeNode getOther(FreeNode caller)

• doNNI

  public final void doNNI(MersenneTwisterFast r)

• doNNI

  public boolean doNNI(boolean leftSwapLeft, boolean rightSwapLeft)

  Does not reconstruct patterns

• calculateLogLikelihood

  public double calculateLogLikelihood(GeneralConstructionTool tool)

  Specified by:

  calculateLogLikelihood in interface RootAccess

• calculateLogLikelihood2

  public double calculateLogLikelihood2(GeneralConstructionTool tool)

• calculateSiteDetails

  public SiteDetails calculateSiteDetails(UnconstrainedLikelihoodModel.External calculator, GeneralConstructionTool tool)