DeltaModel.Instance
, NamedParameterized
, ParameterizedTree
, RateMatrix
, SubstitutionModel
AbstractRateMatrix
, AminoAcidModel
, BLOSUM62
, CachedRateMatrix
, ClockTree
, CodonModel
, ConstantMutationRate
, ConstantPopulation
, ConstExpConst
, ConstExpGrowth
, CPREV
, Dayhoff
, DemographicClockTree
, DemographicModel
, ExpandingPopulation
, ExponentialGrowth
, F81
, F84
, GammaRates
, GeneralRateDistributionSubstitutionModel
, GTR
, HKY
, InvariableSites
, JTT
, LogParameterizedTree
, MTREV24
, MultiParameterized
, MutationRateModel
, MutationRateModelTree
, NucleotideModel
, Parameterized.Null
, ParameterizedTree.ParameterizedTreeBase
, RateDistribution
, RateMatrixHandler
, SingleClassSubstitutionModel
, SteppedMutationRate
, TN
, TwoStateModel
, UnconstrainedTree
, UniformRate
, VT
, WAG
, WindowedMutationRate
, YangCodonModel
, YangCodonModel.SimpleNeutralSelection
, YangCodonModel.SimplePositiveSelection
public interface Parameterized
Modifier and Type | Interface | Description |
---|---|---|
static class |
Parameterized.Null |
NullParameterized Object
Can be used by subclasses to implement parameterized without actually having paramters
|
static class |
Parameterized.ParameterizedBase |
A Utility class for using as the superclass to subclasses which are based on double arrays
|
static class |
Parameterized.ParameterizedUser |
A Utility class for using as the superclass to subclasses which work by adding functionality to
a general Parameterized object (the base Parameterized object)
|
static class |
Parameterized.Utils |
Modifier and Type | Method | Description |
---|---|---|
double |
getDefaultValue(int n) |
get default value of parameter
|
double |
getLowerLimit(int n) |
get lower parameter limit
|
int |
getNumParameters() |
get number of parameters
|
double |
getParameter(int n) |
get model parameter
|
double |
getUpperLimit(int n) |
get upper parameter limit
|
void |
setParameter(double param,
int n) |
set model parameter
|
void |
setParameterSE(double paramSE,
int n) |
set standard errors for model parameter
|
int getNumParameters()
void setParameter(double param, int n)
param
- parameter valuen
- parameter numberdouble getParameter(int n)
n
- parameter numbervoid setParameterSE(double paramSE, int n)
paramSE
- standard error of parameter valuen
- parameter numberdouble getLowerLimit(int n)
n
- parameter numberdouble getUpperLimit(int n)
n
- parameter numberdouble getDefaultValue(int n)
n
- parameter number