|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
public interface NeoRateMatrix
The new RateMatrix class. Replaces the old RateMatrix, and will in turn be renamed to RateMatrix at a later point. A NeoRateMatix object should be stateless (with regard to parameters used in likelihood searching). State is given by the parameter values which are administered externally.
Method Summary | |
---|---|
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 ); |
Method Detail |
---|
java.lang.String getUniqueName()
boolean isReversible()
int getDimension()
boolean isDataTypeCompatible(DataType dt)
dt
- the data type to test
void 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)
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |