statalign.model.subst.plugins
Class Wag

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

public class Wag
extends AminoAcidModel

Implements the WAG (Whelan & Goldman model) substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/11319253

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

Wag()
Constructor used when instantiation is necessary.

Method Summary

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

Wag

public Wag()
    throws java.io.IOException

Constructor used when instantiation is necessary.

Throws:

java.io.IOException