net.sourceforge.cilib.bioinf.sequencealignment
Class MSAProblem

java.lang.Object
  net.sourceforge.cilib.problem.OptimisationProblemAdapter
      net.sourceforge.cilib.bioinf.sequencealignment.MSAProblem

All Implemented Interfaces:

Serializable, OptimisationProblem, Problem, Cloneable

public class MSAProblem
extends OptimisationProblemAdapter

This class represents the Optimization Problem to be solved for the MSA (Real representation).

Author:

gpampara, fzablocki

See Also:

Serialized Form

Field Summary

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

dataSetBuilder, fitnessEvaluations

Constructor Summary

MSAProblem()

Method Summary

protected Fitness	calculateFitness(Type solution) Determine the Fitness of the current Problem instance based on the provided solution.
AlignmentCreator	getAlignmentCreator()
DomainRegistry	getBehaviouralDomain() Returns the domain component that describes the search space of the needed behavioral characteristics of the problem.
OptimisationProblemAdapter	getClone() Create a cloned copy of the current object and return it.
DomainRegistry	getDomain() Returns the domain component that describes the search space for this problem.
GapPenaltiesMethod	getGapPenaltyMethod()
double	getWeight1()
void	setAlignmentCreator(AlignmentCreator alignmentCreator)
void	setGapPenaltyMethod(GapPenaltiesMethod gapPenaltyMethod)
void	setMaxSequenceGapsAllowed(int number)
void	setWeight1(double weight1)
void	setWeight2(double weight2)

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

accept, changeEnvironment, getChangeStrategy, getDataSetBuilder, getFitness, getFitnessEvaluations, setChangeStrategy, setDataSetBuilder

Methods inherited from class java.lang.Object

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

Constructor Detail

MSAProblem

public MSAProblem()

Method Detail

setWeight1

public void setWeight1(double weight1)

getWeight1

public double getWeight1()

getAlignmentCreator

public AlignmentCreator getAlignmentCreator()

setAlignmentCreator

public void setAlignmentCreator(AlignmentCreator alignmentCreator)

setWeight2

public void setWeight2(double weight2)

setGapPenaltyMethod

public void setGapPenaltyMethod(GapPenaltiesMethod gapPenaltyMethod)

getGapPenaltyMethod

public GapPenaltiesMethod getGapPenaltyMethod()

getBehaviouralDomain

public DomainRegistry getBehaviouralDomain()

Description copied from interface: OptimisationProblem

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

getClone

public OptimisationProblemAdapter getClone()

Description copied from interface: OptimisationProblem

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()

calculateFitness

protected Fitness calculateFitness(Type solution)

Description copied from class: OptimisationProblemAdapter

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)

setMaxSequenceGapsAllowed

public void setMaxSequenceGapsAllowed(int number)

getDomain

public DomainRegistry getDomain()

Description copied from interface: OptimisationProblem

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

Returns:

A DomainRegistry object representing the search space.