java.lang.Object
- pal.treesearch.GlobalClockModel

All Implemented Interfaces:: MolecularClockLikelihoodModel.HeightConverter, NeoParameterized, ConstraintModel, ConstraintModel.GroupManager

public class GlobalClockModel
extends java.lang.Object
implements ConstraintModel, ConstraintModel.GroupManager, MolecularClockLikelihoodModel.HeightConverter, NeoParameterized

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

Constructor Summary

Constructors
Constructor Description

GlobalClockModel(MolecularClockLikelihoodModel.Instance likelihoodModel)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`ConditionalProbabilityStore`	`createAppropriateConditionalProbabilityStore(boolean isForLeaf)`
`MolecularClockLikelihoodModel.External`	`createNewClockExternal()`
`MolecularClockLikelihoodModel.Internal`	`createNewClockInternal()`
`MolecularClockLikelihoodModel.Leaf`	`createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup)`
`UnconstrainedLikelihoodModel.External`	`createNewFreeExternal()`
`UnconstrainedLikelihoodModel.Internal`	`createNewFreeInternal()`
`UnconstrainedLikelihoodModel.Leaf`	`createNewFreeLeaf(int[] patternStateMatchup, int numberOfPatterns)`
`NeoParameterized`	`getAllGroupRelatedParameterAccess()`
`double`	`getBaseHeight(double originalExpectSubstitutionHeight)`
`int`	`getBaseHeightUnits()`
`java.lang.String[][]`	`getCladeConstraints(java.lang.String[] allLabelSet)`	Obtain the permanent clade sets.
`void`	`getDefaultValues(double[] store, int startIndex)`	get default value parameter values
`double`	`getExpectedSubstitutionDistance(double lowerBaseHeight, double upperBaseHeight)`
`double`	`getExpectedSubstitutionHeight(double baseHeight)`
`ConstraintModel.GroupManager`	`getGlobalClockConstraintGrouping(java.lang.String[] leafLabelSet)`	Enquire about the clock constraint grouping of the leaf
`NeoParameterized`	`getGlobalParameterAccess()`
`double`	`getLeafBaseHeight(java.lang.String leafLabel)`
`double`	`getLowerLimit(int n)`	get lower parameter limit
`int`	`getNumberOfParameters()`	get number of parameters
`void`	`getParameters(double[] store, int startIndex)`	get model parameter
`NeoParameterized`	`getPrimaryGroupRelatedParameterAccess()`
`java.lang.String`	`getRateModelSummary()`
`NeoParameterized`	`getSecondaryGroupRelatedParameterAccess()`
`double`	`getUpperLimit(int n)`	get upper parameter limit
`void`	`initialiseParameters(java.lang.String[] leafNames, double[] leafHeights)`
`void`	`setParameters(double[] parameters, int startIndex)`	set model parameter

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

- Constructor Detail
  - GlobalClockModel
```
public GlobalClockModel(MolecularClockLikelihoodModel.Instance likelihoodModel)
```
- Method Detail
  - getRateModelSummary
```
public java.lang.String getRateModelSummary()
```
    Specified by:
    
    getRateModelSummary in interface ConstraintModel
  - 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)
  - 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
  - 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
  - getLeafBaseHeight
```
public double getLeafBaseHeight(java.lang.String leafLabel)
```
    Specified by:
    
    getLeafBaseHeight in interface ConstraintModel.GroupManager
  - getBaseHeight
```
public double getBaseHeight(double originalExpectSubstitutionHeight)
```
    Specified by:
    
    getBaseHeight in interface ConstraintModel.GroupManager
  - getBaseHeightUnits
```
public int getBaseHeightUnits()
```
    Specified by:
    
    getBaseHeightUnits in interface ConstraintModel.GroupManager
  - initialiseParameters
```
public void initialiseParameters(java.lang.String[] leafNames,
                                 double[] leafHeights)
```
    Specified by:
    
    initialiseParameters in interface ConstraintModel.GroupManager
  - getAllGroupRelatedParameterAccess
```
public NeoParameterized getAllGroupRelatedParameterAccess()
```
    Specified by:
    
    getAllGroupRelatedParameterAccess in interface ConstraintModel.GroupManager
  - getPrimaryGroupRelatedParameterAccess
```
public NeoParameterized getPrimaryGroupRelatedParameterAccess()
```
    Specified by:
    
    getPrimaryGroupRelatedParameterAccess in interface ConstraintModel.GroupManager
  - getSecondaryGroupRelatedParameterAccess
```
public NeoParameterized getSecondaryGroupRelatedParameterAccess()
```
    Specified by:
    
    getSecondaryGroupRelatedParameterAccess in interface ConstraintModel.GroupManager
  - createNewClockLeaf
```
public MolecularClockLikelihoodModel.Leaf createNewClockLeaf(PatternInfo pattern,
                                                             int[] patternStateMatchup)
```
    Specified by:
    
    createNewClockLeaf in interface ConstraintModel.GroupManager
  - createNewClockExternal
```
public MolecularClockLikelihoodModel.External createNewClockExternal()
```
    Specified by:
    
    createNewClockExternal in interface ConstraintModel.GroupManager
  - createNewClockInternal
```
public MolecularClockLikelihoodModel.Internal createNewClockInternal()
```
    Specified by:
    
    createNewClockInternal in interface ConstraintModel.GroupManager
  - getExpectedSubstitutionHeight
```
public double getExpectedSubstitutionHeight(double baseHeight)
```
    Specified by:
    
    getExpectedSubstitutionHeight in interface ConstraintModel.GroupManager
    
    Specified by:
    
    getExpectedSubstitutionHeight in interface MolecularClockLikelihoodModel.HeightConverter
  - getExpectedSubstitutionDistance
```
public double getExpectedSubstitutionDistance(double lowerBaseHeight,
                                              double upperBaseHeight)
```
    Specified by:
    
    getExpectedSubstitutionDistance in interface MolecularClockLikelihoodModel.HeightConverter
  - getNumberOfParameters
```
public int getNumberOfParameters()
```
    Description copied from interface: NeoParameterized
    
    get number of parameters
    
    Specified by:
    
    getNumberOfParameters in interface NeoParameterized
    
    Returns:
    
    number of parameters
  - setParameters
```
public void setParameters(double[] parameters,
                          int startIndex)
```
    Description copied from interface: NeoParameterized
    
    set model parameter
    
    Specified by:
    
    setParameters in interface NeoParameterized
    
    Parameters:
    
    parameters - the array holding the parameters
    
    startIndex - the index into the array that the related parameters start at
  - getParameters
```
public void getParameters(double[] store,
                          int startIndex)
```
    Description copied from interface: NeoParameterized
    
    get model parameter
    
    Specified by:
    
    getParameters in interface NeoParameterized
    
    startIndex - the index into the array that the related parameters start at
  - getLowerLimit
```
public double getLowerLimit(int n)
```
    Description copied from interface: NeoParameterized
    
    get lower parameter limit
    
    Specified by:
    
    getLowerLimit in interface NeoParameterized
    
    Parameters:
    
    n - parameter number
    
    Returns:
    
    lower bound
  - getUpperLimit
```
public double getUpperLimit(int n)
```
    Description copied from interface: NeoParameterized
    
    get upper parameter limit
    
    Specified by:
    
    getUpperLimit in interface NeoParameterized
    
    Parameters:
    
    n - parameter number
    
    Returns:
    
    upper bound
  - getDefaultValues
```
public void getDefaultValues(double[] store,
                             int startIndex)
```
    Description copied from interface: NeoParameterized
    
    get default value parameter values
    
    Specified by:
    
    getDefaultValues in interface NeoParameterized

Class GlobalClockModel

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

GlobalClockModel

Method Detail

getRateModelSummary

getGlobalClockConstraintGrouping

getCladeConstraints

createNewFreeLeaf

createNewFreeExternal

createNewFreeInternal

createAppropriateConditionalProbabilityStore

getGlobalParameterAccess

getLeafBaseHeight

getBaseHeight

getBaseHeightUnits

initialiseParameters

getAllGroupRelatedParameterAccess

getPrimaryGroupRelatedParameterAccess

getSecondaryGroupRelatedParameterAccess

createNewClockLeaf

createNewClockExternal

createNewClockInternal

getExpectedSubstitutionHeight

getExpectedSubstitutionDistance

getNumberOfParameters

setParameters

getParameters

getLowerLimit

getUpperLimit

getDefaultValues