Package pal.treesearch

Class GeneralConstraintGroupManager

java.lang.Object
pal.treesearch.GeneralConstraintGroupManager
public class GeneralConstraintGroupManager extends Object

  • Constructor Details

  • Method Details

    • 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