java.lang.Object

pal.treesearch.AbstractParentableConstrainedNode

pal.treesearch.PivotNode

All Implemented Interfaces:: FreeNode, GeneralOptimisable, GeneralTreeComponent, GroupLeader, ParentableConstrainedNode, RootAccess

public class PivotNode extends AbstractParentableConstrainedNode implements GeneralOptimisable, ParentableConstrainedNode, FreeNode, RootAccess, GroupLeader

Constructor Summary

Constructors

Constructor

Description

PivotNode(Node tree, FreeBranch parentConnection, GeneralConstructionTool tool, GeneralConstraintGroupManager constraintGroupManager, GeneralConstraintGroupManager.Store store)

The subtree constructor with a connection to the rest of the tree

PivotNode(Node subTree, GeneralConstructionTool tool, GeneralConstraintGroupManager groupManager, GeneralConstraintGroupManager.Store store)

The root constructor, only used when the whole tree is constrained
Method Summary

Modifier and Type

Method

Description

Node

buildPALNodeBase()

Node

buildPALNodeBase(double branchLength_, FreeBranch caller)

Node

buildPALNodeES()

Node

buildPALNodeES(double branchLength_, FreeBranch caller)

double

calculateLogLikelihood(GeneralConstructionTool tool)

FreeBranch

extract(FreeBranch caller)

We can't extract

void

getAllComponents(ArrayList store, Class componentType, FreeBranch caller)

Recurse to all neighbours but caller

ConditionalProbabilityStore

getAscendentExtended(double baseHeight, ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)

ConditionalProbabilityStore

getAscendentFlat(ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)

PatternInfo

getAscendentPatternInfo(ConstrainedNode childCaller, GeneralConstructionTool tool)

ConditionalProbabilityStore

getExtendedConditionalProbabilities(double distance, FreeBranch caller, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)

ConditionalProbabilityStore

getExtendedConditionalProbabilities(double distance, FreeBranch caller, GeneralConstructionTool tool)

ConditionalProbabilityStore

getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool)

FreeBranch

getLeftBranch(FreeBranch caller)

PatternInfo

getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller)

void

getNonSubTreeComponents(ArrayList store, Class componentType)

int

getNumberOfOptimisationTypes()

PatternInfo

getPatternInfo(GeneralConstructionTool tool, FreeBranch caller)

FreeBranch

getRightBranch(FreeBranch caller)

PatternInfo

getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller)

boolean

hasConnection(FreeBranch c, FreeBranch caller)

boolean

hasDirectConnection(FreeBranch query)

double

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

void

postSetupNotify(ConstraintModel.GroupManager groupConstraints)

Tell the group leader that the groupConstraints have been set up (parameter wise), and that internal node heights for example may be calculated

void

setConnectingBranches(FreeBranch[] store, int number)

void

swapConnection(FreeBranch original, FreeBranch newConnection)

Should not do anything but swap branches around

void

swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection)

Should preserve tree integrity

void

testLikelihood(FreeBranch caller, GeneralConstructionTool tool)

void

testLikelihood(GeneralConstructionTool tool)

String

toString()

String

toString(FreeBranch caller)

Methods inherited from class pal.treesearch.AbstractParentableConstrainedNode
adjustNodeHeight, buildDescendentPALNodeBase, buildDescendentPALNodeES, buildLeftDecendentPALNodeBase, buildRightDecendentPALNodeBase, getAllComponents, getConstrainedInternal, getDescendentExtendedConditionals, getDescendentExtendedConditionalsWithAdjustedInternalHeights, getDescendentFlatConditionals, getDescendentLogLikelihood, getDescendentPatternInfo, getLeftChild, getLeftChildPatternInfo, getLeftDescendentExtendedConditionals, getLeftDescendentExtendedConditionals, getMaxChildHeight, getMaxOriginalDescendentLeafHeight, getMinimumChildSeperation, getMinimumChildSeperation, getMinimumDirectChildDistance, getMinimumLeafChildSeperation, getMinimumLeafChildSeperation, getMinOriginalDescendentLeafHeight, getNodeHeight, getNonSubTreeOfChildComponents, getRightChild, getRightChildPatternInfo, getRightDescendentExtendedConditionals, getRightDescendentExtendedConditionals, getSubTreeComponents, isLeftChild, obtainConstrainedExternalCalculator, obtainLeafInformation, rebuildDescendentPattern, recursivelyAdjustNodeHeight, recursivelySetChildrenParentPivot, setNodeHeight, setupInternalNodeHeights, toStringHeights, toStringLengths, toStringLengths

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface pal.treesearch.GeneralTreeComponent
getAllComponents

Methods inherited from interface pal.treesearch.GroupLeader
obtainLeafInformation

Methods inherited from interface pal.treesearch.ParentableConstrainedNode
getNodeHeight, getNonSubTreeOfChildComponents

Methods inherited from interface pal.treesearch.RootAccess
getAllComponents

Constructor Details
- PivotNode
  
  public PivotNode(Node tree, FreeBranch parentConnection, GeneralConstructionTool tool, GeneralConstraintGroupManager constraintGroupManager, GeneralConstraintGroupManager.Store store)
  
  The subtree constructor with a connection to the rest of the tree
  
  Parameters:
  
  tree - the PAL node tree to base this tree on
  
  parentConnection - The connection with the rest of tree (must be free, otherwise this shouldn't be the pivot)
  
  tool - A general construction tool object for objtaining/building various components
  
  groupConstraints - The constraints object that manages the leaf constraints
- PivotNode
  
  public PivotNode(Node subTree, GeneralConstructionTool tool, GeneralConstraintGroupManager groupManager, GeneralConstraintGroupManager.Store store)
  
  The root constructor, only used when the whole tree is constrained
  
  Parameters:
  
  tool - A general construction tool object for objtaining/building various components
  
  subTree - The subtree
  
  groupConstraints - The constraints object that manages the leaf constraints
Method Details
- postSetupNotify
  
  public void postSetupNotify(ConstraintModel.GroupManager groupConstraints)
  
  Description copied from interface: GroupLeader
  
  Tell the group leader that the groupConstraints have been set up (parameter wise), and that internal node heights for example may be calculated
  
  Specified by:
  
  postSetupNotify in interface GroupLeader
- buildPALNodeBase
  
  public Node buildPALNodeBase()
  
  Specified by:
  
  buildPALNodeBase in interface RootAccess
- buildPALNodeES
  
  public Node buildPALNodeES()
  
  Specified by:
  
  buildPALNodeES in interface RootAccess
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class Object
- getAscendentExtended
  
  public ConditionalProbabilityStore getAscendentExtended(double baseHeight, ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)
  
  Specified by:
  
  getAscendentExtended in interface ParentableConstrainedNode
- getAscendentFlat
  
  public ConditionalProbabilityStore getAscendentFlat(ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)
  
  Specified by:
  
  getAscendentFlat in interface ParentableConstrainedNode
- getAscendentPatternInfo
  
  public PatternInfo getAscendentPatternInfo(ConstrainedNode childCaller, GeneralConstructionTool tool)
  
  Specified by:
  
  getAscendentPatternInfo in interface ParentableConstrainedNode
- calculateLogLikelihood
  
  public double calculateLogLikelihood(GeneralConstructionTool tool)
  
  Specified by:
  
  calculateLogLikelihood in interface RootAccess
- getPatternInfo
  
  public PatternInfo getPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
  
  Specified by:
  
  getPatternInfo in interface FreeNode
- hasConnection
  
  public boolean hasConnection(FreeBranch c, FreeBranch caller)
  
  Specified by:
  
  hasConnection 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
- 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
- testLikelihood
  
  public void testLikelihood(FreeBranch caller, GeneralConstructionTool tool)
  
  Specified by:
  
  testLikelihood in interface FreeNode
- testLikelihood
  
  public void testLikelihood(GeneralConstructionTool tool)
  
  Specified by:
  
  testLikelihood in interface RootAccess
- 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
- getExtendedConditionalProbabilities
  
  public ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance, FreeBranch caller, GeneralConstructionTool tool)
  
  Specified by:
  
  getExtendedConditionalProbabilities in interface FreeNode
- getExtendedConditionalProbabilities
  
  public ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance, FreeBranch caller, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
  
  Specified by:
  
  getExtendedConditionalProbabilities in interface FreeNode
- extract
  
  public FreeBranch extract(FreeBranch caller)
  
  We can't extract
  
  Specified by:
  
  extract in interface FreeNode
  
  Parameters:
  
  caller - should be the same as free connection!
  
  Returns:
  
  null
- 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
- getFlatConditionalProbabilities
  
  public ConditionalProbabilityStore getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool)
  
  Specified by:
  
  getFlatConditionalProbabilities in interface FreeNode
- toString
  
  public String toString(FreeBranch caller)
  
  Specified by:
  
  toString in interface FreeNode
- setConnectingBranches
  
  public void setConnectingBranches(FreeBranch[] store, int number)
  
  Specified by:
  
  setConnectingBranches in interface FreeNode
- hasDirectConnection
  
  public boolean hasDirectConnection(FreeBranch query)
  
  Specified by:
  
  hasDirectConnection in interface FreeNode
- swapConnection
  
  public void swapConnection(FreeBranch original, FreeBranch newConnection)
  
  Should not do anything but swap branches around
  
  Specified by:
  
  swapConnection in interface FreeNode
- swapConnection
  
  public void swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection)
  
  Should preserve tree integrity
  
  Specified by:
  
  swapConnection in interface FreeNode
- getNonSubTreeComponents
  
  public void getNonSubTreeComponents(ArrayList store, Class componentType)
  
  Specified by:
  
  getNonSubTreeComponents in class AbstractParentableConstrainedNode
- getNumberOfOptimisationTypes
  
  public 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

Class PivotNode

Constructor Summary

Method Summary

Methods inherited from class pal.treesearch.AbstractParentableConstrainedNode

Methods inherited from class java.lang.Object

Methods inherited from interface pal.treesearch.GeneralTreeComponent

Methods inherited from interface pal.treesearch.GroupLeader

Methods inherited from interface pal.treesearch.ParentableConstrainedNode

Methods inherited from interface pal.treesearch.RootAccess

Constructor Details

PivotNode

PivotNode

Method Details

postSetupNotify

buildPALNodeBase

buildPALNodeES

toString

getAscendentExtended

getAscendentFlat

getAscendentPatternInfo

calculateLogLikelihood

getPatternInfo

hasConnection

getLeftBranch

getRightBranch

getAllComponents

testLikelihood

testLikelihood

getLeftPatternInfo

getRightPatternInfo

getExtendedConditionalProbabilities

getExtendedConditionalProbabilities

extract

buildPALNodeES

buildPALNodeBase

getFlatConditionalProbabilities

toString

setConnectingBranches

hasDirectConnection

swapConnection

swapConnection

getNonSubTreeComponents

getNumberOfOptimisationTypes

optimise