net.sourceforge.cilib.bioinf.rnaprediction
Class Efn2RNAFitness

java.lang.Object
  net.sourceforge.cilib.measurement.single.Fitness
      net.sourceforge.cilib.bioinf.rnaprediction.RNAFitness
          net.sourceforge.cilib.bioinf.rnaprediction.Efn2RNAFitness

All Implemented Interfaces:

Serializable, Measurement, Cloneable

public class Efn2RNAFitness
extends RNAFitness

Author:

mneethling This class computes the Free Energy (dG) of an RNA conformation by calling an external program (efn2). efn2 is the enrgy calculation function supplied with mfold from Michael Zuker.

See Also:

Serialized Form

Field Summary

Fields inherited from class net.sourceforge.cilib.bioinf.rnaprediction.RNAFitness

nucleotides

Constructor Summary

Efn2RNAFitness()

Efn2RNAFitness(Efn2RNAFitness copy)

Method Summary

Efn2RNAFitness	getClone() Create a cloned copy of the current object and return it.
Double	getRNAFitness(RNAConformation stems)

Methods inherited from class net.sourceforge.cilib.measurement.single.Fitness

getDomain, getValue

Methods inherited from class java.lang.Object

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

Constructor Detail

Efn2RNAFitness

public Efn2RNAFitness()

Efn2RNAFitness

public Efn2RNAFitness(Efn2RNAFitness copy)

Method Detail

getClone

public Efn2RNAFitness getClone()

Description copied from class: Fitness

Create a cloned copy of the current object and return it. In general the created copy will be a deep copy of the provided instance. As a result this operation an be quite expensive if used incorrectly.

Specified by:

getClone in interface Measurement

Specified by:

getClone in interface Cloneable

Specified by:

getClone in class RNAFitness

Returns:

An exact clone of the current object instance.

See Also:

Object.clone()

getRNAFitness

public Double getRNAFitness(RNAConformation stems)

Specified by:

getRNAFitness in class RNAFitness