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Packages that use MutationRateModel.Factory | |
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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 |
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Methods in pal.mep that return MutationRateModel.Factory | |
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MutationRateModel.Factory |
SteppedMutationRate.generateFactory()
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abstract MutationRateModel.Factory |
MutationRateModel.generateFactory()
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MutationRateModel.Factory |
ConstantMutationRate.generateFactory()
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MutationRateModel.Factory |
WindowedMutationRate.generateFactory()
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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 | |
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static DeltaModel |
DeltaModel.Utils.getMutationRateModelBased(MutationRateModel.Factory mepFactory)
For interfacing with time based mutation rate models |
Uses of MutationRateModel.Factory in pal.supgma |
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Methods in pal.supgma that return MutationRateModel.Factory | |
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MutationRateModel.Factory |
RateHandler.generateRateModelFactory(double[] deltas,
TimeOrderCharacterData tocd)
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Uses of MutationRateModel.Factory in pal.tree |
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Methods in pal.tree with parameters of type MutationRateModel.Factory | |
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static ParameterizedTree.Factory |
MutationRateModelTree.getParameterizedTreeFactory(MutationRateModel.Factory rateModel,
TimeOrderCharacterData tocd)
Obtain a ParameterizedTree.Factory for generating Unconstrained trees |
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