pal.substmodel
public interface NeoRateMatrix extends java.io.Serializable
Modifier and Type | Method and Description |
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void |
createRelativeRates(double[][] rateStore,
double[] rateParameters,
int startIndex)
Create the relative rates array
|
void |
getDefaultRateParameters(double[] parameterStore,
int startIndex) |
int |
getDimension() |
int |
getNumberOfRateParameters() |
double |
getRateParameterLowerBound(int parameter) |
double |
getRateParameterUpperBound(int parameter) |
java.lang.String |
getUniqueName() |
boolean |
isDataTypeCompatible(DataType dt)
Check the compatibility of a data type to be used with the rate matrix
|
boolean |
isReversible()
Is the relative rate matrix described by this rate matrix meant to represent a reversible process?
If true only the upper part of the rate matrix needs to be filled in (eg in matrix[i][j], for all where j > i );
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java.lang.String getUniqueName()
boolean isReversible()
int getDimension()
boolean isDataTypeCompatible(DataType dt)
dt
- the data type to testvoid createRelativeRates(double[][] rateStore, double[] rateParameters, int startIndex)
rateStore
- The place where the relative rates are stored (should be assumed to be large enough - based on dimension)rateParameters
- The parameters to be used to construct the rate storestartIndex
- The index into the rateParameters to start reading parametersint getNumberOfRateParameters()
double getRateParameterLowerBound(int parameter)
double getRateParameterUpperBound(int parameter)
void getDefaultRateParameters(double[] parameterStore, int startIndex)