Uses of Interface
pal.mep.MutationRateModel.Factory

Packages that use MutationRateModel.Factory

pal.mep	Classes for the analysis of "measurably evolving populations" (mep).
pal.supgma
pal.tree	Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).

Uses of MutationRateModel.Factory in pal.mep

Methods in pal.mep that return MutationRateModel.Factory

MutationRateModel.Factory	SteppedMutationRate.generateFactory()
abstract MutationRateModel.Factory	MutationRateModel.generateFactory()
MutationRateModel.Factory	ConstantMutationRate.generateFactory()
MutationRateModel.Factory	WindowedMutationRate.generateFactory()
static MutationRateModel.Factory	SteppedMutationRate.getFactory(double[] rates, double[] muChanges, int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a SteppedMutationRate
static MutationRateModel.Factory	SteppedMutationRate.getFactory(double[] muChanges, int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a SteppedMutationRate
static MutationRateModel.Factory	SteppedMutationRate.getFactory(double[] muChanges, TimeOrderCharacterData tocd) Generate a MutationRateModel.Factory class for a SteppedMutationRate
static MutationRateModel.Factory	WindowedMutationRate.getFactory(double muWindow, double muBackground, double windowCenter, double windowWidth, int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a WindowedMutationRate
static MutationRateModel.Factory	ConstantMutationRate.getFixedFactory(double rate, int units) Generate a MutationRateModel.Factory class for a ConstantMutationRate
static MutationRateModel.Factory	ConstantMutationRate.getFreeFactory(double initialRate, int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a ConstantMutationRate
static MutationRateModel.Factory	ConstantMutationRate.getFreeFactory(double initialRate, int units, double minimumRate, double maximumRate) Generate a MutationRateModel.Factory class for a ConstantMutationRate
static MutationRateModel.Factory	ConstantMutationRate.getFreeFactory(int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a ConstantMutationRate

Methods in pal.mep with parameters of type MutationRateModel.Factory

static 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.Factory

MutationRateModel.Factory

RateHandler.generateRateModelFactory(double[] deltas, TimeOrderCharacterData tocd)

Uses of MutationRateModel.Factory in pal.tree

Methods in pal.tree with parameters of type MutationRateModel.Factory

static ParameterizedTree.Factory

MutationRateModelTree.getParameterizedTreeFactory(MutationRateModel.Factory rateModel, TimeOrderCharacterData tocd) Obtain a ParameterizedTree.Factory for generating Unconstrained trees