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.Factory
FastFourStateLHCalculator.getFactory()
static final LHCalculator.Factory
FastFourStateLHCalculator.getFactory
(LHCalculator.Factory fallbackFactory) static final LHCalculator.Factory
SimpleLHCalculator.getFactory()
static final LHCalculator.Factory
SimpleModelFastFourStateLHCalculator.getFactory()
static final LHCalculator.Factory
SimpleModelFastFourStateLHCalculator.getFactory
(LHCalculator.Factory fallbackFactory) Methods in pal.eval with parameters of type LHCalculator.FactoryModifier and TypeMethodDescriptionstatic final MolecularClockLikelihoodModel.Instance
SimpleMolecularClockLikelihoodModel.createInstance
(LHCalculator.Factory baseFactory, SubstitutionModel model) static final UnconstrainedLikelihoodModel.Instance
SimpleUnconstrainedLikelihoodModel.createInstance
(LHCalculator.Factory base, SubstitutionModel model) Create a SimpleUnconstrainedLikelihoodModel instancestatic final MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel.createInstance
(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, LHCalculator.Factory baseFactory, double splitTime) static final LHCalculator.Factory
FastFourStateLHCalculator.getFactory
(LHCalculator.Factory fallbackFactory) static final LHCalculator.Factory
SimpleModelFastFourStateLHCalculator.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)