Uses of Interface
pal.eval.LHCalculator.Factory
Packages that use LHCalculator.Factory
Package
Description
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
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Uses of LHCalculator.Factory in pal.eval
Methods in pal.eval that return LHCalculator.FactoryModifier and TypeMethodDescriptionstatic final LHCalculator.FactoryFastFourStateLHCalculator.getFactory()static final LHCalculator.FactoryFastFourStateLHCalculator.getFactory(LHCalculator.Factory fallbackFactory) static final LHCalculator.FactorySimpleLHCalculator.getFactory()static final LHCalculator.FactorySimpleModelFastFourStateLHCalculator.getFactory()static final LHCalculator.FactorySimpleModelFastFourStateLHCalculator.getFactory(LHCalculator.Factory fallbackFactory) Methods in pal.eval with parameters of type LHCalculator.FactoryModifier and TypeMethodDescriptionstatic final MolecularClockLikelihoodModel.InstanceSimpleMolecularClockLikelihoodModel.createInstance(LHCalculator.Factory baseFactory, SubstitutionModel model) static final UnconstrainedLikelihoodModel.InstanceSimpleUnconstrainedLikelihoodModel.createInstance(LHCalculator.Factory base, SubstitutionModel model) Create a SimpleUnconstrainedLikelihoodModel instancestatic final MolecularClockLikelihoodModel.InstanceSingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, LHCalculator.Factory baseFactory, double splitTime) static final LHCalculator.FactoryFastFourStateLHCalculator.getFactory(LHCalculator.Factory fallbackFactory) static final LHCalculator.FactorySimpleModelFastFourStateLHCalculator.getFactory(LHCalculator.Factory fallbackFactory) -
Uses of LHCalculator.Factory in pal.treesearch
Constructors in pal.treesearch with parameters of type LHCalculator.FactoryModifierConstructorDescriptionUnrootedMLSearcher(Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory) UnrootedMLSearcher(Node root, Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory)