statalign.model.subst.plugins
Class ReversibleNucleotide

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

public class ReversibleNucleotide
extends NucleotideModel

This class implements the general time reversible parameter model.

Author:

lyngsoe

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

ReversibleNucleotide()
This constructor uses numerical methods to diagonalise the rate matrix and to set diagonalising matrices.

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

ReversibleNucleotide

public ReversibleNucleotide()
                     throws java.io.IOException

This constructor uses numerical methods to diagonalise the rate matrix and to set diagonalising matrices.

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]