public interface RateMatrix extends NamedParameterized, Report, java.lang.Cloneable, java.io.Serializable
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
Modifier and Type | Method and 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)