pal.substmodel
Class SingleClassSubstitutionModel

java.lang.Object
  pal.misc.PalObjectListener.EventGenerator
      pal.misc.Parameterized.ParameterizedUser
          pal.substmodel.SingleClassSubstitutionModel

All Implemented Interfaces:

java.io.Serializable, Parameterized, Report, SubstitutionModel

public class SingleClassSubstitutionModel
extends Parameterized.ParameterizedUser
implements SubstitutionModel

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.substmodel.SubstitutionModel

SubstitutionModel.Utils

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser

Constructor Summary

SingleClassSubstitutionModel(NeoRateMatrix base, DataType dt, double[] frequencies)

Method Summary

void	addPalObjectListener(PalObjectListener l)
java.lang.Object	clone()
SubstitutionModel	getCopy()
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[][][] store) Table is organized as [transition_group][from][to]
void	getTransitionProbabilities(double branchLength, int category, double[][] store) Table is organized as [transition_group][from][to]
void	getTransitionProbabilitiesTranspose(double branchLength, double[][][] store) Table is organized as [transition_group][to][from]
void	getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] store) Table is organized as [transition_group][to][from]
void	removePalObjectListener(PalObjectListener l)
void	report(java.io.PrintWriter out) print human readable report (e.g., on parameters and associated model)
java.lang.String	toString()

Methods inherited from class pal.misc.Parameterized.ParameterizedUser

getAllParameters, getDefaultValue, getLowerLimit, getNumParameters, getParameter, getRandomParameterValue, getUpperLimit, randomiseParameters, setParameter, setParameterizedBase, setParameterSE

Methods inherited from class pal.misc.PalObjectListener.EventGenerator

fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface pal.misc.Parameterized

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

Constructor Detail

SingleClassSubstitutionModel

public SingleClassSubstitutionModel(NeoRateMatrix base,
                                    DataType dt,
                                    double[] frequencies)

Method Detail

getDataType

public DataType getDataType()

Specified by:

getDataType in interface SubstitutionModel

getNumberOfTransitionCategories

public int getNumberOfTransitionCategories()

Specified by:

getNumberOfTransitionCategories in interface SubstitutionModel

getTransitionCategoryProbability

public double getTransitionCategoryProbability(int category)

Specified by:

getTransitionCategoryProbability in interface SubstitutionModel

getTransitionCategoryProbabilities

public double[] getTransitionCategoryProbabilities()

Specified by:

getTransitionCategoryProbabilities in interface SubstitutionModel

Returns:

all the category probabilites for each category respectively.

getEquilibriumFrequencies

public double[] getEquilibriumFrequencies()

Description copied from interface: SubstitutionModel

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)

Specified by:

getEquilibriumFrequencies in interface SubstitutionModel

getTransitionProbabilities

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

Description copied from interface: SubstitutionModel

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

Specified by:

getTransitionProbabilities in interface SubstitutionModel

getTransitionProbabilities

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

Description copied from interface: SubstitutionModel

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

Specified by:

getTransitionProbabilities in interface SubstitutionModel

getTransitionProbabilitiesTranspose

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

Description copied from interface: SubstitutionModel

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

Specified by:

getTransitionProbabilitiesTranspose in interface SubstitutionModel

getTransitionProbabilitiesTranspose

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

Description copied from interface: SubstitutionModel

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

Specified by:

getTransitionProbabilitiesTranspose in interface SubstitutionModel

addPalObjectListener

public void addPalObjectListener(PalObjectListener l)

Specified by:

addPalObjectListener in interface SubstitutionModel

Overrides:

addPalObjectListener in class PalObjectListener.EventGenerator

removePalObjectListener

public void removePalObjectListener(PalObjectListener l)

Specified by:

removePalObjectListener in interface SubstitutionModel

Overrides:

removePalObjectListener in class PalObjectListener.EventGenerator

getOrthogonalHints

public OrthogonalHints getOrthogonalHints()

Description copied from interface: SubstitutionModel

May return null

Specified by:

getOrthogonalHints in interface SubstitutionModel

report

public void report(java.io.PrintWriter out)

Description copied from interface: Report

print human readable report (e.g., on parameters and associated model)

Specified by:

report in interface Report

Parameters:

out - output stream

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

clone

public java.lang.Object clone()

Specified by:

clone in interface SubstitutionModel

Overrides:

clone in class java.lang.Object

getCopy

public SubstitutionModel getCopy()