net.sourceforge.cilib.bioinf.rnaprediction
Class RNAParticle

java.lang.Object
  net.sourceforge.cilib.entity.AbstractEntity
      net.sourceforge.cilib.pso.particle.AbstractParticle
          net.sourceforge.cilib.bioinf.rnaprediction.RNAParticle

All Implemented Interfaces:

Serializable, Comparable<Entity>, CandidateSolution, Entity, Particle, SocialEntity, Cloneable

public class RNAParticle
extends AbstractParticle

Author:

marais

See Also:

Serialized Form

Field Summary

Fields inherited from class net.sourceforge.cilib.pso.particle.AbstractParticle

neighbourhoodBestUpdateStrategy, personalBestUpdateStrategy, positionInitialisationStrategy, positionUpdateStrategy, velocityInitialisationStrategy, velocityUpdateStrategy

Constructor Summary

RNAParticle()
Create a new RNAParticle instance.

RNAParticle(RNAParticle copy)
Copy constructor.

Method Summary

void	calculateFitness(boolean count) Calculate the fitness of the Entity.
boolean	equals(Object object) It doesn;t make sense to compare the meta data of the entity.
Fitness	getBestFitness() Return the best fitness associated with this Entity, provided a best fitness is defined on the Entity.
StructuredType	getBestPosition() Get the best position of the Particle.
RNAParticle	getClone() Make a clone of the Entity the exact semantics of the clone method will be defined by the classes that implements this interface.
int	getDimension() Returns the dimension of the Entity.
RNAFitness	getFitnessCalc()
Particle	getNeighbourhoodBest() Get the current Particle's neighbourhood best.
StructuredType	getPosition() Get the position of the Particle.
StructuredType	getVelocity() Get the velocity representation of the Particle.
int	hashCode()
void	initialise(OptimisationProblem problem) Intialise the Entity to something meaningful and within the problem space.
void	reinitialise() Re-initialise the given Entity within the defined domain.
void	setBestPosition(Type bestPosition) Set the best position for the current RNAParticle.
void	setFitness(Fitness fitness) Explicitly set the current fitness value.
void	setFitnessCalc(RNAFitness fitnessCalc)
void	setNeighbourhoodBest(Particle particle) Set the neighbourhood best particle for the current Particle based on the topology of the current particle.
void	setRNAFolder(RNAFolder folder) Set the RNAFolder to use.
void	updateControlParameters() Update all the ControlParameters that are maintained within the Particle.
void	updatePosition() Update the position of the Particle.
void	updateVelocity() Update the velocity of the Particle.

Methods inherited from class net.sourceforge.cilib.pso.particle.AbstractParticle

calculateFitness, compareTo, getNeighbourhoodBestUpdateStrategy, getPersonalBestUpdateStrategy, getPositionInitialisationStrategy, getPositionUpdateStrategy, getSocialBestFitness, getVelocityInitialisationStrategy, getVelocityUpdateStrategy, setNeighbourhoodBestUpdateStrategy, setPersonalBestUpdateStrategy, setPositionInitialisationStrategy, setPositionUpdateStrategy, setVelocityInitialisationStrategy, setVelocityUpdateStrategy

Methods inherited from class net.sourceforge.cilib.entity.AbstractEntity

getCandidateSolution, getFitness, getFitnessCalculator, getId, getProperties, setCandidateSolution, setFitnessCalculator, setProperties

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.sourceforge.cilib.entity.Particle

getFitness

Methods inherited from interface net.sourceforge.cilib.entity.Entity

getCandidateSolution, getFitnessCalculator, getId, getProperties, setCandidateSolution, setProperties

Constructor Detail

RNAParticle

public RNAParticle()

Create a new RNAParticle instance.

RNAParticle

public RNAParticle(RNAParticle copy)

Copy constructor. Create a copy of the provided instance.

Parameters:

copy - The instance to copy.

Method Detail

getClone

public RNAParticle getClone()

Make a clone of the Entity the exact semantics of the clone method will be defined by the classes that implements this interface.

Specified by:

getClone in interface Entity

Specified by:

getClone in interface Particle

Specified by:

getClone in interface Cloneable

Specified by:

getClone in class AbstractParticle

Returns:

the cloned object

See Also:

Object.clone()

equals

public boolean equals(Object object)

It doesn;t make sense to compare the meta data of the entity. In other words, the properties of the entity may vary, but the entity is still the same entity.

Overrides:

equals in class AbstractParticle

Parameters:

object - The object to compare equality.

hashCode

public int hashCode()

Overrides:

hashCode in class AbstractParticle

setFitness

public void setFitness(Fitness fitness)

Explicitly set the current fitness value.

Parameters:

fitness - The Fitness to set.

getBestFitness

public Fitness getBestFitness()

Return the best fitness associated with this Entity, provided a best fitness is defined on the Entity. If a best fitness is not defined, the current fitness is returned as it is the best current fitness. Entity objects that need to use this method need to override it in their implementation, for example with Particle objects.

Specified by:

getBestFitness in interface Entity

Specified by:

getBestFitness in interface Particle

Specified by:

getBestFitness in class AbstractParticle

Returns:

The associated best Fitness value.

getDimension

public int getDimension()

Returns the dimension of the Entity.

Specified by:

getDimension in interface Entity

Specified by:

getDimension in interface Particle

Specified by:

getDimension in class AbstractParticle

Returns:

The dimension of the Entity.

initialise

public void initialise(OptimisationProblem problem)

Intialise the Entity to something meaningful and within the problem space. The exact semantics of this method is defined by the classes that implements this interface. Take note. The Intialiser is obsolete the new Type System handles it now. Init can be left out now.

Parameters:

problem - The OptimisationProblem to based the initialisation on.

getPosition

public StructuredType getPosition()

Get the position of the Particle.

Specified by:

getPosition in interface Particle

Specified by:

getPosition in class AbstractParticle

Returns:

A Type representing the Particle's position.

getBestPosition

public StructuredType getBestPosition()

Get the best position of the Particle.

Specified by:

getBestPosition in interface Particle

Specified by:

getBestPosition in class AbstractParticle

Returns:

A Type representng the Particle's best position.

setBestPosition

public void setBestPosition(Type bestPosition)

Set the best position for the current RNAParticle.

Parameters:

bestPosition - The best position to be set.

getVelocity

public StructuredType getVelocity()

Get the velocity representation of the Particle.

Specified by:

getVelocity in interface Particle

Specified by:

getVelocity in class AbstractParticle

Returns:

A Type representing the Particle's velocity.

setNeighbourhoodBest

public void setNeighbourhoodBest(Particle particle)

Set the neighbourhood best particle for the current Particle based on the topology of the current particle.

Specified by:

setNeighbourhoodBest in interface Particle

Specified by:

setNeighbourhoodBest in class AbstractParticle

Parameters:

particle - The particle to use as the current particle's neighhod best particle

getNeighbourhoodBest

public Particle getNeighbourhoodBest()

Get the current Particle's neighbourhood best.

Specified by:

getNeighbourhoodBest in interface Particle

Specified by:

getNeighbourhoodBest in class AbstractParticle

Returns:

The neighbourhood best of the Particle

updatePosition

public void updatePosition()

Update the position of the Particle.

Specified by:

updatePosition in interface Particle

Specified by:

updatePosition in class AbstractParticle

updateVelocity

public void updateVelocity()

Update the velocity of the Particle.

Specified by:

updateVelocity in interface Particle

Specified by:

updateVelocity in class AbstractParticle

updateControlParameters

public void updateControlParameters()

Update all the ControlParameters that are maintained within the Particle.

Specified by:

updateControlParameters in interface Particle

Specified by:

updateControlParameters in class AbstractParticle

setRNAFolder

public void setRNAFolder(RNAFolder folder)

Set the RNAFolder to use.

Parameters:

folder - The RNAFolder to be used by the current RNAParticle.

setFitnessCalc

public void setFitnessCalc(RNAFitness fitnessCalc)

Parameters:

fitnessCalc - The fitnessCalc to set.

getFitnessCalc

public RNAFitness getFitnessCalc()

Returns:

Returns the fitnessCalc.

reinitialise

public void reinitialise()

Re-initialise the given Entity within the defined domain.

calculateFitness

public void calculateFitness(boolean count)

Calculate the fitness of the Entity. This method may or may not increment the number of fitness evaluations of the algorithm.

Specified by:

calculateFitness in interface Entity

Specified by:

calculateFitness in class AbstractParticle

Parameters:

count - Add or do not add this fitness evaluation to the algorithm global count.