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