Uses of Interface
pal.mep.MutationRateModel.Factory
Packages that use MutationRateModel.Factory
Package
Description
Classes for the analysis of "measurably evolving populations" (mep).
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
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Uses of MutationRateModel.Factory in pal.mep
Methods in pal.mep that return MutationRateModel.FactoryModifier and TypeMethodDescriptionConstantMutationRate.generateFactory()
abstract MutationRateModel.Factory
MutationRateModel.generateFactory()
SteppedMutationRate.generateFactory()
WindowedMutationRate.generateFactory()
static final MutationRateModel.Factory
SteppedMutationRate.getFactory
(double[] rates, double[] muChanges, int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a SteppedMutationRatestatic final MutationRateModel.Factory
SteppedMutationRate.getFactory
(double[] muChanges, int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a SteppedMutationRatestatic final MutationRateModel.Factory
SteppedMutationRate.getFactory
(double[] muChanges, TimeOrderCharacterData tocd) Generate a MutationRateModel.Factory class for a SteppedMutationRatestatic final MutationRateModel.Factory
WindowedMutationRate.getFactory
(double muWindow, double muBackground, double windowCenter, double windowWidth, int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a WindowedMutationRatestatic final MutationRateModel.Factory
ConstantMutationRate.getFixedFactory
(double rate, int units) Generate a MutationRateModel.Factory class for a ConstantMutationRatestatic final MutationRateModel.Factory
ConstantMutationRate.getFreeFactory
(double initialRate, int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a ConstantMutationRatestatic final MutationRateModel.Factory
ConstantMutationRate.getFreeFactory
(double initialRate, int units, double minimumRate, double maximumRate) Generate a MutationRateModel.Factory class for a ConstantMutationRatestatic final MutationRateModel.Factory
ConstantMutationRate.getFreeFactory
(int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a ConstantMutationRateMethods in pal.mep with parameters of type MutationRateModel.FactoryModifier and TypeMethodDescriptionstatic final DeltaModel
DeltaModel.Utils.getMutationRateModelBased
(MutationRateModel.Factory mepFactory) For interfacing with time based mutation rate models -
Uses of MutationRateModel.Factory in pal.supgma
Methods in pal.supgma that return MutationRateModel.FactoryModifier and TypeMethodDescriptionRateHandler.generateRateModelFactory
(double[] deltas, TimeOrderCharacterData tocd) -
Uses of MutationRateModel.Factory in pal.tree
Methods in pal.tree with parameters of type MutationRateModel.FactoryModifier and TypeMethodDescriptionstatic final ParameterizedTree.Factory
MutationRateModelTree.getParameterizedTreeFactory
(MutationRateModel.Factory rateModel, TimeOrderCharacterData tocd) Obtain a ParameterizedTree.Factory for generating Unconstrained trees