statalign.model.subst.plugins
Class CpRev

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

public class CpRev
extends AminoAcidModel

This class implements the Chloroplast reversible substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/10795826

Author:
miklos, novak

Field Summary
 
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
CpRev()
          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
 

Constructor Detail

CpRev

public CpRev()
      throws java.io.IOException
Constructor used when instantiation is necessary.

Throws:
java.io.IOException