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)
|
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