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)