Package | Description |
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pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
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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).
|
Modifier and Type | Method | Description |
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MutationRateModel.Factory |
ConstantMutationRate.generateFactory() |
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abstract MutationRateModel.Factory |
MutationRateModel.generateFactory() |
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MutationRateModel.Factory |
SteppedMutationRate.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
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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
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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
|
Modifier and Type | Method | Description |
---|---|---|
static DeltaModel |
DeltaModel.Utils.getMutationRateModelBased(MutationRateModel.Factory mepFactory) |
For interfacing with time based mutation rate models
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Modifier and Type | Method | Description |
---|---|---|
MutationRateModel.Factory |
RateHandler.generateRateModelFactory(double[] deltas,
TimeOrderCharacterData tocd) |
Modifier and Type | Method | Description |
---|---|---|
static ParameterizedTree.Factory |
MutationRateModelTree.getParameterizedTreeFactory(MutationRateModel.Factory rateModel,
TimeOrderCharacterData tocd) |
Obtain a ParameterizedTree.Factory for generating Unconstrained trees
|