java.lang.Object
- pal.treesearch.UnconstrainedModel

All Implemented Interfaces:: ConstraintModel

public class UnconstrainedModel
extends java.lang.Object
implements ConstraintModel

Nested Class Summary
- Nested classes/interfaces inherited from interface pal.treesearch.ConstraintModel
  ConstraintModel.GroupManager

Constructor Summary

Constructors
Constructor Description

UnconstrainedModel(UnconstrainedLikelihoodModel.Instance likelihoodModel)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`ConditionalProbabilityStore`	`createAppropriateConditionalProbabilityStore(boolean isForLeaf)`
`UnconstrainedLikelihoodModel.External`	`createNewFreeExternal()`
`UnconstrainedLikelihoodModel.Internal`	`createNewFreeInternal()`
`UnconstrainedLikelihoodModel.Leaf`	`createNewFreeLeaf(int[] patternStateMatchup, int numberOfPatterns)`
`java.lang.String[][]`	`getCladeConstraints(java.lang.String[] allLabelSet)`	Obtain the permanent clade sets.
`ConstraintModel.GroupManager`	`getGlobalClockConstraintGrouping(java.lang.String[] leafLabelSet)`	Enquire about the clock constraint grouping of the leaf
`NeoParameterized`	`getGlobalParameterAccess()`
`java.lang.String`	`getRateModelSummary()`

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

- Constructor Detail
  - UnconstrainedModel
```
public UnconstrainedModel(UnconstrainedLikelihoodModel.Instance likelihoodModel)
```
- Method Detail
  - getCladeConstraints
```
public java.lang.String[][] getCladeConstraints(java.lang.String[] allLabelSet)
```
    Description copied from interface: ConstraintModel
    
    Obtain the permanent clade sets. That is, when randomly building the tree, and when tree searching, what labels must always form a clade.
    
    Specified by:
    
    getCladeConstraints in interface ConstraintModel
    
    Parameters:
    
    allLabelSet - The set of all leaf labels in the tree
    
    Returns:
    
    An array of string arrays dividing up the label set
  - getGlobalClockConstraintGrouping
```
public ConstraintModel.GroupManager getGlobalClockConstraintGrouping(java.lang.String[] leafLabelSet)
```
    Description copied from interface: ConstraintModel
    
    Enquire about the clock constraint grouping of the leaf
    
    Specified by:
    
    getGlobalClockConstraintGrouping in interface ConstraintModel
    
    Returns:
    
    the grouping of the leaf, or null if outside the leaf is unconstrained (free)
  - createNewFreeLeaf
```
public UnconstrainedLikelihoodModel.Leaf createNewFreeLeaf(int[] patternStateMatchup,
                                                           int numberOfPatterns)
```
    Specified by:
    
    createNewFreeLeaf in interface ConstraintModel
  - createNewFreeExternal
```
public UnconstrainedLikelihoodModel.External createNewFreeExternal()
```
    Specified by:
    
    createNewFreeExternal in interface ConstraintModel
  - createNewFreeInternal
```
public UnconstrainedLikelihoodModel.Internal createNewFreeInternal()
```
    Specified by:
    
    createNewFreeInternal in interface ConstraintModel
  - createAppropriateConditionalProbabilityStore
```
public ConditionalProbabilityStore createAppropriateConditionalProbabilityStore(boolean isForLeaf)
```
    Specified by:
    
    createAppropriateConditionalProbabilityStore in interface ConstraintModel
  - getGlobalParameterAccess
```
public NeoParameterized getGlobalParameterAccess()
```
    Specified by:
    
    getGlobalParameterAccess in interface ConstraintModel
  - getRateModelSummary
```
public java.lang.String getRateModelSummary()
```
    Specified by:
    
    getRateModelSummary in interface ConstraintModel

Class UnconstrainedModel

Nested Class Summary

Nested classes/interfaces inherited from interface pal.treesearch.ConstraintModel

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

UnconstrainedModel

Method Detail

getCladeConstraints

getGlobalClockConstraintGrouping

createNewFreeLeaf

createNewFreeExternal

createNewFreeInternal

createAppropriateConditionalProbabilityStore

getGlobalParameterAccess

getRateModelSummary