pal.treesearch
Class GeneralConstraintGroupManager

java.lang.Object
  pal.treesearch.GeneralConstraintGroupManager

public class GeneralConstraintGroupManager

extends java.lang.Object

Nested Class Summary

static interface	GeneralConstraintGroupManager.LikelihoodScoreAccess
static class	GeneralConstraintGroupManager.Store

Constructor Summary

GeneralConstraintGroupManager(ConstraintModel.GroupManager relatedGroup)

Method Summary

void	addGroupLeader(GroupLeader gl)
ConstraintModel.GroupManager	getRelatedGroup()
boolean	isOptimisable()
boolean	isPrimaryOptimisable()
boolean	isSameGroup(ConstraintModel.GroupManager queryGroup)
boolean	isSecondarOptimisable()
MolecularClockLikelihoodModel.External	obtainConstrainedExternalCalculator()
double	optimiseAllGlobalClockConstraints(MultivariateMinimum minimiser, GeneralConstraintGroupManager.LikelihoodScoreAccess scoreAccess, int fxFracDigits, int xFracDigits, MinimiserMonitor rateMonitor) Optimise all the global clock parameters related to this group
double	optimisePrimaryGlobalClockConstraints(MultivariateMinimum minimiser, GeneralConstraintGroupManager.LikelihoodScoreAccess scoreAccess, int fxFracDigits, int xFracDigits, MinimiserMonitor rateMonitor) Optimise the global clock parameters marked as primary related to this group
double	optimiseSecondaryGlobalClockConstraints(MultivariateMinimum minimiser, GeneralConstraintGroupManager.LikelihoodScoreAccess scoreAccess, int fxFracDigits, int xFracDigits, MinimiserMonitor rateMonitor) Optimise the global clock parameters marked as secondary related to this group
void	setup()

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneralConstraintGroupManager

public GeneralConstraintGroupManager(ConstraintModel.GroupManager relatedGroup)

Method Detail

isOptimisable

public boolean isOptimisable()

isPrimaryOptimisable

public boolean isPrimaryOptimisable()

isSecondarOptimisable

public boolean isSecondarOptimisable()

obtainConstrainedExternalCalculator

public MolecularClockLikelihoodModel.External obtainConstrainedExternalCalculator()

getRelatedGroup

public ConstraintModel.GroupManager getRelatedGroup()

setup

public void setup()

isSameGroup

public boolean isSameGroup(ConstraintModel.GroupManager queryGroup)

addGroupLeader

public void addGroupLeader(GroupLeader gl)

optimiseAllGlobalClockConstraints

public final double optimiseAllGlobalClockConstraints(MultivariateMinimum minimiser,
                                                      GeneralConstraintGroupManager.LikelihoodScoreAccess scoreAccess,
                                                      int fxFracDigits,
                                                      int xFracDigits,
                                                      MinimiserMonitor rateMonitor)

Optimise all the global clock parameters related to this group

Parameters:

minimiser - The minimiser used for optimisation

scoreAccess - A means for assessing a set of parameters

fxFracDigits - Accuracy for the likelihood

xFracDigits - Accruracy for the parameters

rateMonitor - A monitor for our progress

Returns:

the optimised log likelihood or >0 if cannot do any optimisation

optimisePrimaryGlobalClockConstraints

public final double optimisePrimaryGlobalClockConstraints(MultivariateMinimum minimiser,
                                                          GeneralConstraintGroupManager.LikelihoodScoreAccess scoreAccess,
                                                          int fxFracDigits,
                                                          int xFracDigits,
                                                          MinimiserMonitor rateMonitor)

Optimise the global clock parameters marked as primary related to this group

Parameters:

minimiser - The minimiser used for optimisation

scoreAccess - A means for assessing a set of parameters

fxFracDigits - Accuracy for the likelihood

xFracDigits - Accruracy for the parameters

rateMonitor - A monitor for our progress

Returns:

the optimised log likelihood or >0 if cannot do any optimisation

optimiseSecondaryGlobalClockConstraints

public final double optimiseSecondaryGlobalClockConstraints(MultivariateMinimum minimiser,
                                                            GeneralConstraintGroupManager.LikelihoodScoreAccess scoreAccess,
                                                            int fxFracDigits,
                                                            int xFracDigits,
                                                            MinimiserMonitor rateMonitor)

Optimise the global clock parameters marked as secondary related to this group

Parameters:

minimiser - The minimiser used for optimisation

scoreAccess - A means for assessing a set of parameters

fxFracDigits - Accuracy for the likelihood

xFracDigits - Accruracy for the parameters

rateMonitor - A monitor for our progress

Returns:

the optimised log likelihood or >0 if cannot do any optimisation