pal.treesearch
Class FreeLeafNode
java.lang.Object
pal.treesearch.AbstractLeafNode
pal.treesearch.FreeLeafNode
- All Implemented Interfaces:
- FreeNode, GeneralTreeComponent
public class FreeLeafNode
- extends AbstractLeafNode
- implements FreeNode
Method Summary |
Node |
buildPALNode(double branchLength,
FreeBranch caller)
|
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)
|
void |
getAllComponents(java.util.ArrayList store,
java.lang.Class componentType,
FreeBranch caller)
Recurse to all neighbours but caller |
void |
getAllConnections(java.util.ArrayList store,
FreeBranch caller)
|
ConditionalProbabilityStore |
getExtendedConditionalProbabilities(double distance,
FreeBranch callingBranch,
GeneralConstructionTool tool)
|
ConditionalProbabilityStore |
getExtendedConditionalProbabilities(double distance,
FreeBranch callingBranch,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool)
|
ConditionalProbabilityStore |
getFlatConditionalProbabilities(FreeBranch caller,
GeneralConstructionTool tool)
|
ConditionalProbabilityStore |
getFlatConditionalProbabilities(FreeBranch callingBranch,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool)
|
FreeBranch |
getLeftBranch(FreeBranch caller)
|
ConditionalProbabilityStore |
getLeftExtendedConditionalProbabilities(FreeBranch caller,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore resultStore)
|
PatternInfo |
getLeftPatternInfo(GeneralConstructionTool tool,
FreeBranch caller)
|
PatternInfo |
getPatternInfo(GeneralConstructionTool tool,
FreeBranch caller)
|
FreeBranch |
getRightBranch(FreeBranch caller)
|
ConditionalProbabilityStore |
getRightExtendedConditionalProbabilities(FreeBranch caller,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore resultStore)
|
PatternInfo |
getRightPatternInfo(GeneralConstructionTool tool,
FreeBranch caller)
|
boolean |
hasConnection(FreeBranch fb,
FreeBranch caller)
|
boolean |
hasDirectConnection(FreeBranch fb)
|
void |
mark()
|
void |
rebuildConnectionPatterns(GeneralConstructionTool tool,
FreeBranch caller)
|
int |
redirectRebuildPattern(GeneralConstructionTool tool)
This should only be called by another leaf node on the other end of the connection. |
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)
|
void |
undoToMark()
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
FreeLeafNode
public FreeLeafNode(FreeBranch parentBranch,
java.lang.String id,
GeneralConstructionTool tool)
hasDirectConnection
public boolean hasDirectConnection(FreeBranch fb)
- Specified by:
hasDirectConnection
in interface FreeNode
mark
public void mark()
undoToMark
public void undoToMark()
hasConnection
public boolean hasConnection(FreeBranch fb,
FreeBranch caller)
- Specified by:
hasConnection
in interface FreeNode
extract
public FreeBranch extract(FreeBranch caller)
- Description copied from interface:
FreeNode
- Instruct the node to extract itself from the two connections that aren't the caller
One of the other two connections will become redunant.
- Specified by:
extract
in interface FreeNode
- Returns:
- the redundant connection, or null of this node can't extract
getLeftExtendedConditionalProbabilities
public ConditionalProbabilityStore getLeftExtendedConditionalProbabilities(FreeBranch caller,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore resultStore)
getRightExtendedConditionalProbabilities
public ConditionalProbabilityStore getRightExtendedConditionalProbabilities(FreeBranch caller,
UnconstrainedLikelihoodModel.External externalCalculator,
ConditionalProbabilityStore resultStore)
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
setConnectingBranches
public void setConnectingBranches(FreeBranch[] store,
int number)
- Specified by:
setConnectingBranches
in interface FreeNode
testLikelihood
public void testLikelihood(FreeBranch caller,
GeneralConstructionTool tool)
- Specified by:
testLikelihood
in interface FreeNode
swapConnection
public void swapConnection(FreeBranch original,
FreeBranch newConnection)
- Description copied from interface:
FreeNode
- Should not do anything but swap branches around
- Specified by:
swapConnection
in interface FreeNode
swapConnection
public void swapConnection(FreeBranch original,
FreeNode nodeToReplace,
FreeBranch newConnection)
- Description copied from interface:
FreeNode
- Should preserve tree integrity
- Specified by:
swapConnection
in interface FreeNode
getLeftBranch
public FreeBranch getLeftBranch(FreeBranch caller)
- Specified by:
getLeftBranch
in interface FreeNode
- Returns:
- null (as not possible)
getRightBranch
public FreeBranch getRightBranch(FreeBranch caller)
- Specified by:
getRightBranch
in interface FreeNode
- Returns:
- null (as not possible)
getAllConnections
public void getAllConnections(java.util.ArrayList store,
FreeBranch caller)
getPatternInfo
public PatternInfo getPatternInfo(GeneralConstructionTool tool,
FreeBranch caller)
- Specified by:
getPatternInfo
in interface FreeNode
rebuildConnectionPatterns
public void rebuildConnectionPatterns(GeneralConstructionTool tool,
FreeBranch caller)
redirectRebuildPattern
public int redirectRebuildPattern(GeneralConstructionTool tool)
- This should only be called by another leaf node on the other end of the connection.
In this case we don't have to do much (tree is two node tree)
getFlatConditionalProbabilities
public final ConditionalProbabilityStore getFlatConditionalProbabilities(FreeBranch callingBranch,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool)
getFlatConditionalProbabilities
public final ConditionalProbabilityStore getFlatConditionalProbabilities(FreeBranch caller,
GeneralConstructionTool tool)
- Specified by:
getFlatConditionalProbabilities
in interface FreeNode
getExtendedConditionalProbabilities
public ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance,
FreeBranch callingBranch,
UnconstrainedLikelihoodModel.External external,
ConditionalProbabilityStore resultStore,
GeneralConstructionTool tool)
- Specified by:
getExtendedConditionalProbabilities
in interface FreeNode
getExtendedConditionalProbabilities
public ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance,
FreeBranch callingBranch,
GeneralConstructionTool tool)
- Specified by:
getExtendedConditionalProbabilities
in interface FreeNode
buildPALNode
public final Node buildPALNode(double branchLength,
FreeBranch caller)
buildPALNodeES
public final Node buildPALNodeES(double branchLength,
FreeBranch caller)
- Specified by:
buildPALNodeES
in interface FreeNode
buildPALNodeBase
public final Node buildPALNodeBase(double branchLength,
FreeBranch caller)
- Specified by:
buildPALNodeBase
in interface FreeNode
toString
public java.lang.String toString(FreeBranch caller)
- Specified by:
toString
in interface FreeNode
getAllComponents
public void getAllComponents(java.util.ArrayList store,
java.lang.Class componentType,
FreeBranch caller)
- Description copied from interface:
FreeNode
- Recurse to all neighbours but caller
- Specified by:
getAllComponents
in interface FreeNode
getAllComponents
public final void getAllComponents(java.util.ArrayList store,
java.lang.Class componentType)
- Specified by:
getAllComponents
in interface GeneralTreeComponent