|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectpal.substmodel.GeneralPoissonRateMatrix
public class GeneralPoissonRateMatrix
A general rate matrix class for JC69/F81 style rate matrices (but for all data types)
Constructor Summary | |
---|---|
GeneralPoissonRateMatrix(int dimension)
|
Method Summary | |
---|---|
void |
createRelativeRates(double[][] rateStore,
double[] rateParameters,
int startIndex)
Create the relative rates array |
void |
getDefaultRateParameters(double[] store,
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 ); |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public GeneralPoissonRateMatrix(int dimension)
Method Detail |
---|
public java.lang.String getUniqueName()
getUniqueName
in interface NeoRateMatrix
public boolean isReversible()
NeoRateMatrix
isReversible
in interface NeoRateMatrix
public int getDimension()
getDimension
in interface NeoRateMatrix
public boolean isDataTypeCompatible(DataType dt)
isDataTypeCompatible
in interface NeoRateMatrix
dt
- the data type to test
public void createRelativeRates(double[][] rateStore, double[] rateParameters, int startIndex)
NeoRateMatrix
createRelativeRates
in interface NeoRateMatrix
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 parameterspublic int getNumberOfRateParameters()
getNumberOfRateParameters
in interface NeoRateMatrix
public double getRateParameterLowerBound(int parameter)
getRateParameterLowerBound
in interface NeoRateMatrix
public double getRateParameterUpperBound(int parameter)
getRateParameterUpperBound
in interface NeoRateMatrix
public void getDefaultRateParameters(double[] store, int startIndex)
getDefaultRateParameters
in interface NeoRateMatrix
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |