pal.treesearch
Class FreeBranch

java.lang.Object
  pal.treesearch.FreeBranch

All Implemented Interfaces:

GeneralOptimisable, RootAccess

public final class FreeBranch
extends java.lang.Object
implements RootAccess, GeneralOptimisable

Constructor Summary

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

Method Summary

FreeBranch	attachTo(FreeBranch attachmentPoint, FreeBranch[] store)
Node	buildPALNodeBase()
Node	buildPALNodeBase(FreeNode caller)
Node	buildPALNodeES()
Node	buildPALNodeES(FreeNode caller)
double	calculateLogLikelihood(GeneralConstructionTool tool)
double	calculateLogLikelihood2(GeneralConstructionTool tool)
SiteDetails	calculateSiteDetails(UnconstrainedLikelihoodModel.External calculator, GeneralConstructionTool tool)
boolean	doNNI(boolean leftSwapLeft, boolean rightSwapLeft) Does not reconstruct patterns
void	doNNI(MersenneTwisterFast r)
void	getAllComponents(java.util.ArrayList store, java.lang.Class componentType)
void	getAllComponents(java.util.ArrayList store, java.lang.Class componentType, FreeNode caller)
double	getBranchLength()
PatternInfo	getCenterPatternInfo(GeneralConstructionTool tool)
void	getCenterPatternInfo(GeneralConstructionTool tool, PatternInfo store)
ConditionalProbabilityStore	getExtendedConditionalProbabilities(FreeNode caller, GeneralConstructionTool tool)
ConditionalProbabilityStore	getExtendedConditionalProbabilities(FreeNode caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore extendedStore, GeneralConstructionTool tool)
FreeNode	getLeft()
ConditionalProbabilityStore	getLeftFlatConditionalProbabilities(GeneralConstructionTool tool)
FreeBranch	getLeftLeftBranch()
PatternInfo	getLeftPatternInfo(GeneralConstructionTool tool)
FreeBranch	getLeftRightBranch()
int	getNumberOfOptimisationTypes()
FreeNode	getOther(FreeNode caller)
PatternInfo	getPatternInfo(GeneralConstructionTool tool, FreeNode caller)
FreeNode	getRight()
ConditionalProbabilityStore	getRightFlatConditionalProbabilities(GeneralConstructionTool tool)
FreeBranch	getRightLeftBranch()
PatternInfo	getRightPatternInfo(GeneralConstructionTool tool)
FreeBranch	getRightRightBranch()
boolean	hasConnection(FreeBranch c, FreeNode caller)
void	mark() Mark this node, or in other words store information on left and right nodes and branch length for later retreival (via undoToMark())
double	optimise(int optimisationType, UnivariateMinimum minimiser, GeneralConstructionTool tool, int fracDigits)
void	setAnnotation(java.lang.Object annotation)
void	setBranchLength(double x)
void	setNodes(FreeNode left, FreeNode right) Does nothing to fix up tree structure
void	swapNode(FreeNode nodeToReplace, FreeNode replacement)
void	testLikelihood(FreeNode caller, GeneralConstructionTool tool)
void	testLikelihood(GeneralConstructionTool tool)
java.lang.String	toString()
java.lang.String	toString(FreeNode caller)
void	undoToMark()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

FreeBranch

public FreeBranch(Node n,
                  GeneralConstructionTool tool,
                  GeneralConstraintGroupManager.Store store)

The starting constructor for building from a given tree

Parameters:

n - The normal PAL node structure to base this tree on

tool - to aid in construction

FreeBranch

public FreeBranch(Node n,
                  FreeNode parent,
                  GeneralConstructionTool tool,
                  GeneralConstraintGroupManager.Store store)

Continuing recurison constructor for a given tree

Parameters:

n - The PAL node structure to base sub tree on

parent - The parent node (sub tree in other direction)

tool - to aid in construction

FreeBranch

public FreeBranch(FreeNode left,
                  FreeNode right,
                  double branchLength,
                  GeneralConstructionTool tool)

A generic constructor given two already defined left and right children

Parameters:

left - The left node

right - The right node

branchLength - The length of connection

tool - to aid in construction

Method Detail

setAnnotation

public void setAnnotation(java.lang.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 java.lang.String toString()

Overrides:

toString in class java.lang.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 java.lang.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(java.util.ArrayList store,
                             java.lang.Class componentType)

Specified by:

getAllComponents in interface RootAccess

getAllComponents

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