statalign.model.subst.plugins
Class Kimura3

java.lang.Object
  statalign.model.subst.SubstitutionModel
      statalign.model.subst.plugins.NucleotideModel
          statalign.model.subst.plugins.Kimura3

public class Kimura3
extends NucleotideModel

Implements the Kimura 3 parameter model.

Author:

miklos

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

Kimura3()
This constructor reads transition rates from the file data/kimura3_rate.dat, the alphabet from data/DNAalphabet.dat, and the equilibrium distribution from data/kimura3_equilibrium.dat.

Method Summary

java.lang.String	print() Prints the parameters of the model
double	sampleParameter() This function implements a proposal for new parameter values.

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

acceptable, getColor, mostLikely, restoreParameter, 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

Kimura3

public Kimura3()
        throws java.io.IOException

This constructor reads transition rates from the file data/kimura3_rate.dat, the alphabet from data/DNAalphabet.dat, and the equilibrium distribution from data/kimura3_equilibrium.dat.

Throws:

java.io.IOException

Method Detail

print

public java.lang.String print()

Prints the parameters of the model

Overrides:

print in class NucleotideModel

Returns:

the resulting String

sampleParameter

public double sampleParameter()

This function implements a proposal for new parameter values. Returns with the logarithm of the Metropolis-Hastings ratio.

Specified by:

sampleParameter in class SubstitutionModel

Returns:

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