Package pal.treesearch
Class GeneralConstraintGroupManager
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- pal.treesearch.GeneralConstraintGroupManager
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public class GeneralConstraintGroupManager extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static interface
GeneralConstraintGroupManager.LikelihoodScoreAccess
static class
GeneralConstraintGroupManager.Store
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Constructor Summary
Constructors Constructor Description GeneralConstraintGroupManager(ConstraintModel.GroupManager relatedGroup)
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Method Summary
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Constructor Detail
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GeneralConstraintGroupManager
public GeneralConstraintGroupManager(ConstraintModel.GroupManager relatedGroup)
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Method Detail
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isOptimisable
public boolean isOptimisable()
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isPrimaryOptimisable
public boolean isPrimaryOptimisable()
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isSecondarOptimisable
public boolean isSecondarOptimisable()
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obtainConstrainedExternalCalculator
public MolecularClockLikelihoodModel.External obtainConstrainedExternalCalculator()
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getRelatedGroup
public ConstraintModel.GroupManager getRelatedGroup()
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setup
public void setup()
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isSameGroup
public boolean isSameGroup(ConstraintModel.GroupManager queryGroup)
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addGroupLeader
public void addGroupLeader(GroupLeader gl)
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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 optimisationscoreAccess
- A means for assessing a set of parametersfxFracDigits
- Accuracy for the likelihoodxFracDigits
- Accruracy for the parametersrateMonitor
- A monitor for our progress- Returns:
- the optimised log likelihood or >0 if cannot do any optimisation
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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 optimisationscoreAccess
- A means for assessing a set of parametersfxFracDigits
- Accuracy for the likelihoodxFracDigits
- Accruracy for the parametersrateMonitor
- A monitor for our progress- Returns:
- the optimised log likelihood or >0 if cannot do any optimisation
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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 optimisationscoreAccess
- A means for assessing a set of parametersfxFracDigits
- Accuracy for the likelihoodxFracDigits
- Accruracy for the parametersrateMonitor
- A monitor for our progress- Returns:
- the optimised log likelihood or >0 if cannot do any optimisation
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