Package pal.treesearch
Interface FreeNode
-
- All Superinterfaces:
GeneralTreeComponent
- All Known Implementing Classes:
FreeInternalNode
,FreeLeafNode
,PivotNode
public interface FreeNode extends GeneralTreeComponent
-
-
Method Summary
-
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
-
-