java.lang.Object
- pal.treesearch.AbstractLeafNode
- - pal.treesearch.FreeLeafNode

All Implemented Interfaces:: FreeNode, GeneralTreeComponent

public class FreeLeafNode
extends AbstractLeafNode
implements FreeNode

Constructor Summary

Constructors
Constructor Description

FreeLeafNode(FreeBranch parentBranch, java.lang.String id, GeneralConstructionTool tool)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)`
`ConditionalProbabilityStore`	`getExtendedConditionalProbabilities(double distance, FreeBranch callingBranch, GeneralConstructionTool tool)`
`ConditionalProbabilityStore`	`getFlatConditionalProbabilities(FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)`
`ConditionalProbabilityStore`	`getFlatConditionalProbabilities(FreeBranch caller, 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 pal.treesearch.AbstractLeafNode
createNewConstrainedLeafCalculator, createNewFreeLeafCalculator, getLabel, getNumberOfPatterns, getPatternInfo

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

Constructor Detail

FreeLeafNode

public FreeLeafNode(FreeBranch parentBranch,
                    java.lang.String id,
                    GeneralConstructionTool tool)

Method Detail

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

Class FreeLeafNode

Constructor Summary

Method Summary

Methods inherited from class pal.treesearch.AbstractLeafNode

Methods inherited from class java.lang.Object

Constructor Detail

FreeLeafNode

Method Detail

hasDirectConnection

mark

undoToMark

hasConnection

extract

getLeftExtendedConditionalProbabilities

getRightExtendedConditionalProbabilities

getLeftPatternInfo

getRightPatternInfo

setConnectingBranches

testLikelihood

swapConnection

swapConnection

getLeftBranch

getRightBranch

getAllConnections

getPatternInfo

rebuildConnectionPatterns

redirectRebuildPattern

getFlatConditionalProbabilities

getFlatConditionalProbabilities

getExtendedConditionalProbabilities

getExtendedConditionalProbabilities

buildPALNode

buildPALNodeES

buildPALNodeBase

toString

getAllComponents

getAllComponents