pal.supgma
Interface RateHandler


public interface RateHandler


Nested Class Summary
static class RateHandler.Utils
           
 
Method Summary
 void adjustDistances(double[][] matrix, TimeOrderCharacterData tocd)
           
 void fillInLSInfo(double[] mRow, int startingIndex, int minSample, int maxSample, double[] sampleTimes)
           
 MutationRateModel.Factory generateRateModelFactory(double[] deltas, TimeOrderCharacterData tocd)
           
 java.lang.String getInfo()
           
 int getNumberOfParameters(TimeOrderCharacterData tocd)
           
 boolean isCICompatible()
           
 

Method Detail

getNumberOfParameters

int getNumberOfParameters(TimeOrderCharacterData tocd)

adjustDistances

void adjustDistances(double[][] matrix,
                     TimeOrderCharacterData tocd)

isCICompatible

boolean isCICompatible()

getInfo

java.lang.String getInfo()

fillInLSInfo

void fillInLSInfo(double[] mRow,
                  int startingIndex,
                  int minSample,
                  int maxSample,
                  double[] sampleTimes)

generateRateModelFactory

MutationRateModel.Factory generateRateModelFactory(double[] deltas,
                                                   TimeOrderCharacterData tocd)