statalign.model.subst.plugins
Class Dayhoff

java.lang.Object
  statalign.model.subst.SubstitutionModel
      statalign.model.subst.plugins.AminoAcidModel
          statalign.model.subst.plugins.Dayhoff

public class Dayhoff
extends AminoAcidModel

Implements the classic Dayhoff substitution model.

Author:

miklos, novak

Field Summary

static java.lang.String

menuName

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

type

Fields inherited from class statalign.model.subst.SubstitutionModel

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

Constructor Summary

Dayhoff()
Constructor used when instantiation is necessary.

Method Summary

static void

main(java.lang.String[] args) Only for testing.

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

acceptable, getColor, mostLikely, print, restoreParameter, sampleParameter

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

Dayhoff

public Dayhoff()
        throws java.io.IOException

Constructor used when instantiation is necessary.

Throws:

java.io.IOException

Method Detail

main

public static void main(java.lang.String[] args)

Only for testing.

Parameters:

args - No argument is used.