java.lang.Cloneable
, NamedParameterized
, Parameterized
, Report
, java.io.Serializable
AbstractRateMatrix
, AminoAcidModel
, BLOSUM62
, CachedRateMatrix
, CodonModel
, CPREV
, Dayhoff
, F81
, F84
, GTR
, HKY
, JTT
, MTREV24
, NucleotideModel
, TN
, TwoStateModel
, VT
, WAG
, YangCodonModel
public interface RateMatrix extends NamedParameterized, Report, java.lang.Cloneable, java.io.Serializable
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
Modifier and Type | Method | Description |
---|---|---|
void |
addPalObjectListener(PalObjectListener pol) |
Add a PalObjectListener to be notified of changes to the model.
|
java.lang.Object |
clone() |
|
DataType |
getDataType() |
Get the data type of this rate matrix
|
int |
getDimension() |
|
double[] |
getEquilibriumFrequencies() |
|
double |
getEquilibriumFrequency(int i) |
|
int |
getModelID() |
get numerical code describing the model type
|
OrthogonalHints |
getOrthogonalHints() |
|
double[][] |
getRelativeRates() |
Deprecated.
try not to use.
|
void |
getTransitionProbabilities(double[][] probabilityStore) |
A utility method for speed, transfers trans prob information quickly
into store
|
double |
getTransitionProbability(int fromState,
int toState) |
|
int |
getTypeID() |
get numerical code describing the data type
|
java.lang.String |
getUniqueName() |
|
void |
removePalObjectListener(PalObjectListener pol) |
|
void |
scale(double scaleValue) |
|
void |
setDistance(double distance) |
Sets the distance (such as time/branch length) used when calculating
the probabilities.
|
void |
setDistanceTranspose(double distance) |
Sets the distance (such as time/branch length) used when calculating
the probabilities.
|
double |
setParametersNoScale(double[] parameters) |
getParameterName
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
int getTypeID()
int getModelID()
java.lang.String getUniqueName()
int getDimension()
double[] getEquilibriumFrequencies()
double getEquilibriumFrequency(int i)
DataType getDataType()
double[][] getRelativeRates()
double getTransitionProbability(int fromState, int toState)
fromState
- The state from which we are startingtoState
- The resulting statevoid getTransitionProbabilities(double[][] probabilityStore)
void setDistance(double distance)
void setDistanceTranspose(double distance)
void addPalObjectListener(PalObjectListener pol)
void removePalObjectListener(PalObjectListener pol)
OrthogonalHints getOrthogonalHints()
java.lang.Object clone()
double setParametersNoScale(double[] parameters)
void scale(double scaleValue)