Package pal.treesearch
Class GeneralLikelihoodSearcher
java.lang.Object
pal.treesearch.GeneralLikelihoodSearcher
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
static final int
static final int
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Constructor Summary
ConstructorsConstructorDescriptionGeneralLikelihoodSearcher
(Node baseTopology, Alignment baseAlignment, ConstraintModel constraintModel) -
Method Summary
Modifier and TypeMethodDescriptiondouble
double
optimiseAllFullHeirarchy
(StoppingCriteria mainStopper, StoppingCriteria subStopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor) double
optimiseAllPlusSubstitutionModel
(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, MultivariateMinimum substitutionModelMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, int substitutionModelOptimiseFrequency, MinimiserMonitor substitutionModelMonitor, MinimiserMonitor rateMonitor) double
optimiseAllSimple
(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback) double
optimiseAllSimple
(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor) double
optimiseAllSimple
(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor, int groupOptimistionType) double
optimiseAllSimpleHeirarchy
(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor) double
optimiseConstraintRateModels
(MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor rateMonitor) double
optimiseGeneral
(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback) double
optimiseGeneral
(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback, SearchMonitor monitor) double
optimiseSubstitutionModels
(MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor) void
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Field Details
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OPTIMISE_ALL
public static final int OPTIMISE_ALL- See Also:
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OPTIMISE_PRIMARY
public static final int OPTIMISE_PRIMARY- See Also:
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OPTIMISE_SECONDARY
public static final int OPTIMISE_SECONDARY- See Also:
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NO_OPTIMISE
public static final int NO_OPTIMISE- See Also:
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Constructor Details
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GeneralLikelihoodSearcher
public GeneralLikelihoodSearcher(Node baseTopology, Alignment baseAlignment, ConstraintModel constraintModel)
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Method Details
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optimiseGeneral
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optimiseGeneral
public double optimiseGeneral(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback, SearchMonitor monitor) -
optimiseConstraintRateModels
public double optimiseConstraintRateModels(MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor rateMonitor) -
optimiseSubstitutionModels
public double optimiseSubstitutionModels(MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor) -
optimiseAllSimple
public double optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback) -
optimiseAllSimple
public double optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor) -
optimiseAllSimple
public double optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor, int groupOptimistionType) -
optimiseAllSimpleHeirarchy
public double optimiseAllSimpleHeirarchy(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor) -
optimiseAllFullHeirarchy
public double optimiseAllFullHeirarchy(StoppingCriteria mainStopper, StoppingCriteria subStopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor) -
optimiseAllPlusSubstitutionModel
public double optimiseAllPlusSubstitutionModel(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, MultivariateMinimum substitutionModelMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, int substitutionModelOptimiseFrequency, MinimiserMonitor substitutionModelMonitor, MinimiserMonitor rateMonitor) -
buildPALNodeBase
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buildPALTreeBase
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buildPALNodeES
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buildPALTreeES
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calculatedLogLikelihood
public double calculatedLogLikelihood() -
testLikelihood
public void testLikelihood()
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