net.sourceforge.cilib.bioinf.sequencealignment
Class BinaryMSAProblem

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

All Implemented Interfaces:

Serializable, OptimisationProblem, Problem, Cloneable

public class BinaryMSAProblem
extends OptimisationProblemAdapter

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

See Also:

Serialized Form

Field Summary

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

dataSetBuilder, fitnessEvaluations

Constructor Summary

BinaryMSAProblem()
Create an instance of the class.

Method Summary

protected Fitness	calculateFitness(Type solution) Determine the Fitness of the current Problem instance based on the provided solution.
BinaryAlignmentCreator	getAlignmentCreator() Get the alignment creator.
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() Get the current gap penelization method.
double	getWeight1() Get the value of weight1.
void	setAlignmentCreator(BinaryAlignmentCreator alignmentCreator) Set the AlignmentCreator.
void	setGapPenaltyMethod(GapPenaltiesMethod gapPenaltyMethod) Set the strategy to penalize gaps.
void	setMaxSequenceGapsAllowed(int number) Set the maximm number of allowable gaps.
void	setWeight1(double weight1) Set the value of weight1.
void	setWeight2(double weight2) Set the value of 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

BinaryMSAProblem

public BinaryMSAProblem()

Create an instance of the class.

Method Detail

getClone

public OptimisationProblemAdapter 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()

setWeight1

public void setWeight1(double weight1)

Set the value of weight1.

Parameters:

weight1 - The value to set.

getWeight1

public double getWeight1()

Get the value of weight1.

Returns:

The value of weight1.

getAlignmentCreator

public BinaryAlignmentCreator getAlignmentCreator()

Get the alignment creator.

Returns:

The AlignmentCreator.

setAlignmentCreator

public void setAlignmentCreator(BinaryAlignmentCreator alignmentCreator)

Set the AlignmentCreator.

Parameters:

alignmentCreator - The AlignmentCreator to set.

setWeight2

public void setWeight2(double weight2)

Set the value of weight2.

Parameters:

weight2 - The value to set.

setGapPenaltyMethod

public void setGapPenaltyMethod(GapPenaltiesMethod gapPenaltyMethod)

Set the strategy to penalize gaps.

Parameters:

gapPenaltyMethod - The strategy to set.

getGapPenaltyMethod

public GapPenaltiesMethod getGapPenaltyMethod()

Get the current gap penelization method.

Returns:

The current GapPenaltiesMethod.

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

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)

setMaxSequenceGapsAllowed

public void setMaxSequenceGapsAllowed(int number)

Set the maximm number of allowable gaps.

Parameters:

number - The maximum number allowable.

getDomain

public DomainRegistry getDomain()

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

Returns:

A DomainRegistry object representing the search space.