pal.treesearch

Class SRDTGlobalClockModel

java.lang.Object

pal.treesearch.SRDTGlobalClockModel

All Implemented Interfaces:

MolecularClockLikelihoodModel.HeightConverter, NeoParameterized, ConstraintModel, ConstraintModel.GroupManager

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

Nested Class Summary

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

ConstraintModel.GroupManager

Constructor Summary

Constructors

Constructor and Description
SRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel)
SRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel, boolean allowMetaRate)

Method Summary

Methods

Modifier and Type	Method and 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	getSubstitutionRate()
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
void	setSubstitutionRate(double rate)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SRDTGlobalClockModel

public SRDTGlobalClockModel(SampleInformation sampleInformation,
                    MolecularClockLikelihoodModel.Instance likelihoodModel)

SRDTGlobalClockModel

public SRDTGlobalClockModel(SampleInformation sampleInformation,
                    MolecularClockLikelihoodModel.Instance likelihoodModel,
                    boolean allowMetaRate)

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

getSubstitutionRate

public double getSubstitutionRate()

setSubstitutionRate

public void setSubstitutionRate(double rate)

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 MolecularClockLikelihoodModel.HeightConverter

Specified by:

getExpectedSubstitutionHeight in interface ConstraintModel.GroupManager

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