statalign.model.subst.plugins
Class JukesCantor

java.lang.Object
  statalign.model.subst.SubstitutionModel
      statalign.model.subst.plugins.NucleotideModel
          statalign.model.subst.plugins.JukesCantor

public class JukesCantor
extends NucleotideModel

Implements the Jukes-Cantor model for nucleic acids.

Author:

miklos, novak

Field Summary

static java.lang.String

menuName

Fields inherited from class statalign.model.subst.plugins.NucleotideModel

type

Fields inherited from class statalign.model.subst.SubstitutionModel

alphabet, attachedScoringScheme, d, e, params, v, w

Constructor Summary

JukesCantor()
This constructor reads transition rates from the file data/jukescantor_rate.dat, the alphabet from data/DNAalphabet.dat, and the equilibrium distribution from data/jukescantor_equilibrium.dat.

Method Summary

void	restoreParameter() Empty function (no model parameters)
double	sampleParameter() It does nothing, and always return with 0, namely, log-probability 1.

Methods inherited from class statalign.model.subst.plugins.NucleotideModel

acceptable, getColor, mostLikely, print, setPrintRNA

Methods inherited from class statalign.model.subst.SubstitutionModel

getMenuName, getMenuName, getPrior, getType, getType, updateSpan, updateTransitionMatrix

Methods inherited from class java.lang.Object

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

Field Detail

menuName

public static final java.lang.String menuName

See Also:

Constant Field Values

Constructor Detail

JukesCantor

public JukesCantor()
            throws java.io.IOException

This constructor reads transition rates from the file data/jukescantor_rate.dat, the alphabet from data/DNAalphabet.dat, and the equilibrium distribution from data/jukescantor_equilibrium.dat.

Throws:

java.io.IOException

Method Detail

restoreParameter

public void restoreParameter()

Empty function (no model parameters)

Overrides:

restoreParameter in class NucleotideModel

sampleParameter

public double sampleParameter()

It does nothing, and always return with 0, namely, log-probability 1.

Specified by:

sampleParameter in class SubstitutionModel

Returns:

log(fwd proposal probability/bwd proposal probability) [i.e. inverse Hastings ratio]