statalign.model.subst.plugins
Class Dayhoff

java.lang.Object
  extended by statalign.model.subst.SubstitutionModel
      extended by statalign.model.subst.plugins.AminoAcidModel
          extended by 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.