pal.substmodel
Interface SubstitutionModel

All Superinterfaces:

Parameterized, Report, java.io.Serializable

All Known Implementing Classes:

GeneralRateDistributionSubstitutionModel, SingleClassSubstitutionModel, YangCodonModel.SimpleNeutralSelection, YangCodonModel.SimplePositiveSelection

public interface SubstitutionModel

extends Parameterized, Report, java.io.Serializable

model of sequence substitution (rate matrix + rate variation). provides a convenient interface for the computation of transition probabilities

Nested Class Summary

static class

SubstitutionModel.Utils A small Utility class for things relating to Substitution Models in general

Nested classes inherited from class pal.misc.Parameterized

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser

Method Summary

void	addPalObjectListener(PalObjectListener l)
java.lang.Object	clone()
DataType	getDataType()
double[]	getEquilibriumFrequencies() Should return a double[] array of the related equilibrium frequencies.
int	getNumberOfTransitionCategories()
OrthogonalHints	getOrthogonalHints() May return null
double[]	getTransitionCategoryProbabilities()
double	getTransitionCategoryProbability(int category)
void	getTransitionProbabilities(double branchLength, double[][][] tableStore) Table is organized as [transition_group][from][to]
void	getTransitionProbabilities(double branchLength, int category, double[][] tableStore) Table is organized as [transition_group][from][to]
void	getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore) Table is organized as [transition_group][to][from]
void	getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore) Table is organized as [transition_group][to][from]
void	removePalObjectListener(PalObjectListener l)

Methods inherited from interface pal.misc.Parameterized

getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE

Methods inherited from interface pal.misc.Report

report

Method Detail

getDataType

public DataType getDataType()

getNumberOfTransitionCategories

public int getNumberOfTransitionCategories()

getTransitionCategoryProbability

public double getTransitionCategoryProbability(int category)

getTransitionCategoryProbabilities

public double[] getTransitionCategoryProbabilities()

Returns:

all the category probabilites for each category respectively.

getTransitionProbabilities

public void getTransitionProbabilities(double branchLength,
                                       double[][][] tableStore)

Table is organized as [transition_group][from][to]

getTransitionProbabilitiesTranspose

public void getTransitionProbabilitiesTranspose(double branchLength,
                                                double[][][] tableStore)

Table is organized as [transition_group][to][from]

getTransitionProbabilities

public void getTransitionProbabilities(double branchLength,
                                       int category,
                                       double[][] tableStore)

Table is organized as [transition_group][from][to]

getTransitionProbabilitiesTranspose

public void getTransitionProbabilitiesTranspose(double branchLength,
                                                int category,
                                                double[][] tableStore)

Table is organized as [transition_group][to][from]

getEquilibriumFrequencies

public double[] getEquilibriumFrequencies()

Should return a double[] array of the related equilibrium frequencies. As a rule, callers should not alter the returned array (it may be used internally)

addPalObjectListener

public void addPalObjectListener(PalObjectListener l)

removePalObjectListener

public void removePalObjectListener(PalObjectListener l)

getOrthogonalHints

public OrthogonalHints getOrthogonalHints()

May return null

clone

public java.lang.Object clone()