pal.substmodel
Class SimpleRateMatrixGroup
java.lang.Object
pal.substmodel.SimpleRateMatrixGroup
- All Implemented Interfaces:
- java.io.Serializable, RateMatrixGroup
public abstract class SimpleRateMatrixGroup
- extends java.lang.Object
- implements RateMatrixGroup
- See Also:
- Serialized Form
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SimpleRateMatrixGroup
public SimpleRateMatrixGroup(NeoRateMatrix[] baseMatrices,
double[] equilibriumFrequencies,
double[] initialClassProbabilities,
DataType dataType)
getNumberOfParameters
public int getNumberOfParameters()
getLowerLimit
public double getLowerLimit(int n)
getUpperLimit
public double getUpperLimit(int n)
getDefaultValue
public double getDefaultValue(int n)
setParameters
public void setParameters(double[] parameters,
double[] categoryProbabilities)
getEquilibriumFrequencies
public double[] getEquilibriumFrequencies()
- Specified by:
getEquilibriumFrequencies
in interface RateMatrixGroup
getDataType
public DataType getDataType()
- Specified by:
getDataType
in interface RateMatrixGroup
getNumberOfTransitionCategories
public int getNumberOfTransitionCategories()
- Specified by:
getNumberOfTransitionCategories
in interface RateMatrixGroup
getTransitionProbabilities
public void getTransitionProbabilities(double branchLength,
double[][][] tableStore)
- Specified by:
getTransitionProbabilities
in interface RateMatrixGroup
getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double branchLength,
double[][][] tableStore)
- Specified by:
getTransitionProbabilitiesTranspose
in interface RateMatrixGroup
getTransitionProbabilities
public void getTransitionProbabilities(double branchLength,
int category,
double[][] tableStore)
- Specified by:
getTransitionProbabilities
in interface RateMatrixGroup
getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double branchLength,
int category,
double[][] tableStore)
- Specified by:
getTransitionProbabilitiesTranspose
in interface RateMatrixGroup
getSummary
public java.lang.String getSummary(double[] parameters,
double[] categoryProbabilities)