pal.treesearch
Interface FreeNode

All Superinterfaces:
GeneralTreeComponent
All Known Implementing Classes:
FreeInternalNode, FreeLeafNode, PivotNode

public interface FreeNode
extends GeneralTreeComponent


Method Summary
 Node buildPALNodeBase(double branchLength_, FreeBranch caller)
           
 Node buildPALNodeES(double branchLength_, FreeBranch caller)
           
 FreeBranch extract(FreeBranch caller)
          Instruct the node to extract itself from the two connections that aren't the caller One of the other two connections will become redunant.
 void getAllComponents(java.util.ArrayList store, java.lang.Class componentType, FreeBranch connection)
          Recurse to all neighbours but caller
 ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool)
           
 FreeBranch getLeftBranch(FreeBranch caller)
           
 PatternInfo getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 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)
           
 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)
           
 java.lang.String toString(FreeBranch caller)
           
 
Methods inherited from interface pal.treesearch.GeneralTreeComponent
getAllComponents
 

Method Detail

getPatternInfo

PatternInfo getPatternInfo(GeneralConstructionTool tool,
                           FreeBranch caller)

hasConnection

boolean hasConnection(FreeBranch c,
                      FreeBranch caller)

getLeftBranch

FreeBranch getLeftBranch(FreeBranch caller)

getRightBranch

FreeBranch getRightBranch(FreeBranch caller)

getAllComponents

void getAllComponents(java.util.ArrayList store,
                      java.lang.Class componentType,
                      FreeBranch connection)
Recurse to all neighbours but caller


testLikelihood

void testLikelihood(FreeBranch caller,
                    GeneralConstructionTool tool)

getLeftPatternInfo

PatternInfo getLeftPatternInfo(GeneralConstructionTool tool,
                               FreeBranch caller)
Parameters:
caller -
Returns:
Get the pattern info for the relative left (from the caller's perspective), or null if not left pattern info

getRightPatternInfo

PatternInfo getRightPatternInfo(GeneralConstructionTool tool,
                                FreeBranch caller)
Parameters:
caller -
Returns:
Get the pattern info for the relative right (from the caller's perspective), or null if not right pattern info

getExtendedConditionalProbabilities

ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance,
                                                                FreeBranch callingConnection,
                                                                GeneralConstructionTool tool)

getExtendedConditionalProbabilities

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

extract

FreeBranch extract(FreeBranch caller)
Instruct the node to extract itself from the two connections that aren't the caller One of the other two connections will become redunant.

Returns:
the redundant connection, or null of this node can't extract

buildPALNodeES

Node buildPALNodeES(double branchLength_,
                    FreeBranch caller)

buildPALNodeBase

Node buildPALNodeBase(double branchLength_,
                      FreeBranch caller)

getFlatConditionalProbabilities

ConditionalProbabilityStore getFlatConditionalProbabilities(FreeBranch caller,
                                                            GeneralConstructionTool tool)

toString

java.lang.String toString(FreeBranch caller)

setConnectingBranches

void setConnectingBranches(FreeBranch[] store,
                           int number)

hasDirectConnection

boolean hasDirectConnection(FreeBranch query)

swapConnection

void swapConnection(FreeBranch original,
                    FreeBranch newConnection)
Should not do anything but swap branches around


swapConnection

void swapConnection(FreeBranch original,
                    FreeNode nodeToReplace,
                    FreeBranch newConnection)
Should preserve tree integrity