statalign.model.subst.plugins
Class CpRev

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