net.sourceforge.cilib.bioinf.rnaprediction
Class RNAOptimisationProblem

java.lang.Object
  net.sourceforge.cilib.problem.OptimisationProblemAdapter
      net.sourceforge.cilib.bioinf.rnaprediction.RNAOptimisationProblem

All Implemented Interfaces:

Serializable, OptimisationProblem, Problem, Cloneable

public class RNAOptimisationProblem
extends OptimisationProblemAdapter

Author:

mneethling

See Also:

Serialized Form

Field Summary

protected int

fitnessEvaluations

Constructor Summary

RNAOptimisationProblem()

RNAOptimisationProblem(RNAOptimisationProblem copy)
Copy constructor.

Method Summary

protected Fitness	calculateFitness(Type solution) Determine the Fitness of the current Problem instance based on the provided solution.
DomainRegistry	getBehaviouralDomain() Returns the domain component that describes the search space of the needed behavioral characteristics of the problem.
RNAOptimisationProblem	getClone() Create a cloned copy of the current object and return it.
DataSetBuilder	getDataSetBuilder() Get the associated DataSetBuilder.
DomainRegistry	getDomain() Returns the domain component that describes the search space for this problem.
RNAFitness	getFitnessCalculator()
void	setDataSetBuilder(DataSetBuilder dataSetBuilder) Set the DataSetBuilder for this optimistion problem.
void	setFitnessCalculator(RNAFitness fit)

Methods inherited from class net.sourceforge.cilib.problem.OptimisationProblemAdapter

accept, changeEnvironment, getChangeStrategy, getFitness, getFitnessEvaluations, setChangeStrategy

Methods inherited from class java.lang.Object

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

Field Detail

fitnessEvaluations

protected int fitnessEvaluations

Constructor Detail

RNAOptimisationProblem

public RNAOptimisationProblem()

RNAOptimisationProblem

public RNAOptimisationProblem(RNAOptimisationProblem copy)

Copy constructor. Create a copy of the provided instance.

Parameters:

copy - The instance to copy.

Method Detail

getClone

public RNAOptimisationProblem getClone()

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 OptimisationProblem

Specified by:

getClone in interface Problem

Specified by:

getClone in interface Cloneable

Specified by:

getClone in class OptimisationProblemAdapter

Returns:

An exact clone of the current object instance.

See Also:

Object.clone()

getFitnessCalculator

public RNAFitness getFitnessCalculator()

Returns:

Returns the fit.

setFitnessCalculator

public void setFitnessCalculator(RNAFitness fit)

Parameters:

fit - The fit to set.

calculateFitness

protected Fitness calculateFitness(Type solution)

Determine the Fitness of the current Problem instance based on the provided solution.

Specified by:

calculateFitness in class OptimisationProblemAdapter

Parameters:

solution - The Type representing the candidate solution.

Returns:

The Fitness of the solution in the current Problem.

See Also:

OptimisationProblemAdapter.getFitness(Type, boolean)

setDataSetBuilder

public void setDataSetBuilder(DataSetBuilder dataSetBuilder)

Set the DataSetBuilder for this optimistion problem.

Specified by:

setDataSetBuilder in interface OptimisationProblem

Overrides:

setDataSetBuilder in class OptimisationProblemAdapter

Parameters:

dataSetBuilder - The DataSetBuilder to be set on the current OptimisationProblem.

getDataSetBuilder

public DataSetBuilder getDataSetBuilder()

Get the associated DataSetBuilder.

Specified by:

getDataSetBuilder in interface OptimisationProblem

Overrides:

getDataSetBuilder in class OptimisationProblemAdapter

Returns:

The currently associated DataSetBuilder.

getDomain

public DomainRegistry getDomain()

Returns the domain component that describes the search space for this problem.

Returns:

A DomainRegistry object representing the search space.

getBehaviouralDomain

public DomainRegistry getBehaviouralDomain()

Returns the domain component that describes the search space of the needed behavioral characteristics of the problem. This is mainly used for ECs, however, the use of behavioral parameters with PSO will be investigated.

Returns:

The domain of the behavioral component