calhoun.analysis.crf.features.supporting.phylogenetic
Class NucleotideSubstitutionModel

java.lang.Object
  calhoun.analysis.crf.features.supporting.phylogenetic.NucleotideSubstitutionModel

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

HKY85Model, Kimura80Model

public abstract class NucleotideSubstitutionModel
extends java.lang.Object
implements java.io.Serializable

See Also:

Serialized Form

Constructor Summary

NucleotideSubstitutionModel()

Method Summary

abstract java.lang.String	getEvolutionaryModelName()
abstract double[]	getParameters()
cern.colt.matrix.DoubleMatrix2D	getRateMatrix()
abstract void	setParameters(double[] parms)
abstract void	summarize()
cern.colt.matrix.DoubleMatrix2D	transitionMatrix(double t)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

NucleotideSubstitutionModel

public NucleotideSubstitutionModel()

Method Detail

getEvolutionaryModelName

public abstract java.lang.String getEvolutionaryModelName()

getParameters

public abstract double[] getParameters()

setParameters

public abstract void setParameters(double[] parms)

getRateMatrix

public cern.colt.matrix.DoubleMatrix2D getRateMatrix()

transitionMatrix

public cern.colt.matrix.DoubleMatrix2D transitionMatrix(double t)

summarize

public abstract void summarize()