pal.substmodel

Class SubstitutionModel.Utils

java.lang.Object

pal.substmodel.SubstitutionModel.Utils

Enclosing interface:

SubstitutionModel

public static class SubstitutionModel.Utils
extends java.lang.Object

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

Constructor Summary

Constructors

Constructor and Description
SubstitutionModel.Utils()

Method Summary

Methods

Modifier and Type	Method and Description
static SubstitutionModel	createSubstitutionModel(NeoRateMatrix rm, DataType dt, double[] equilibriumFrequencies)
static SubstitutionModel	createSubstitutionModel(RateMatrix rm)
static SubstitutionModel	createSubstitutionModel(RateMatrix rm, RateDistribution rd)
static SubstitutionModel	createSubstitutionModel(RateMatrix rm, RateDistribution rd, boolean parameteriseDistribution)
static double[][][]	generateTransitionProbabilityTables(SubstitutionModel model)

Methods inherited from class java.lang.Object

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

Constructor Detail

SubstitutionModel.Utils

public SubstitutionModel.Utils()

Method Detail

generateTransitionProbabilityTables

public static final double[][][] generateTransitionProbabilityTables(SubstitutionModel model)

createSubstitutionModel

public static final SubstitutionModel createSubstitutionModel(RateMatrix rm)

Returns:

a substitution model base on a rate matrix. There is only one transition category. There is no independent distribution access (as not distribution across one transition category)

createSubstitutionModel

public static final SubstitutionModel createSubstitutionModel(NeoRateMatrix rm,
                                        DataType dt,
                                        double[] equilibriumFrequencies)

Returns:

a substitution model base on a rate matrix. There is only one transition category. There is no independent distribution access (as not distribution across one transition category)

createSubstitutionModel

public static final SubstitutionModel createSubstitutionModel(RateMatrix rm,
                                        RateDistribution rd)

Returns:

a substitution model base on a rate matrix, and a rate distribution. There are as many transition categories as there are rate categories in the rate distribution. There is no independent distribution access (as rate distributions don't normally allow changing of probabilities for a category without changing the rate of a category - at least none in pal do)

createSubstitutionModel

public static final SubstitutionModel createSubstitutionModel(RateMatrix rm,
                                        RateDistribution rd,
                                        boolean parameteriseDistribution)

Parameters:

parameteriseDistribution - If true will include the distribution parameters as part of the substitution modle parameters, if false then the distribution parameters are set from the point of view of the substitution model.

Returns:

a substitution model base on a rate matrix, and a rate distribution. There are as many transition categories as there are rate categories in the rate distribution. There is no independent distribution access (as rate distributions don't normally allow changing of probabilities for a category without changing the rate of a category - at least none in pal do)