A collection of candidates. More...

Inheritance diagram for denoptim.ga.Population:

Collaboration diagram for denoptim.ga.Population:

Classes
class	XoverSitesAmongCandidates
	A data structure collecting crossover-compatible sites. More...

Public Member Functions
	Population (GAParameters settings)

boolean	add (Candidate c)

void	add (int index, Candidate c)

Candidate	set (int index, Candidate c)

Candidate	remove (int index)

boolean	remove (Object c)

boolean	removeAll (Collection<?> c)

void	clear ()

boolean	retainAll (Collection<?> c)

int	getVersionID ()
	Returns an integer that represent the current status of the population. More...

Population	clone ()
	Does not clone the cross-over compatibility relations between each pairs of population members. More...

List< Candidate >	getXoverPartners (Candidate memberA, List< Candidate > eligibleParents, FragmentSpace fragSpace)
	Returns a list of population members that can do crossover with the specified member. More...

List< XoverSite >	getXoverSites (Candidate parentA, Candidate parentB)
	Returns a list of crossover sites between the two given parents. More...

void	trim (int populationSize)
	Removes all the elements exceeding the given size. More...

double	getMinFitness ()
	Gets the minimum value of the fitness in this population. More...

Candidate	getMinFitnessMember ()
	Gets the `Candidate` with minimum value of the fitness in this population. More...

double	getMaxFitness ()
	Gets the maximum value of the fitness in this population. More...

boolean	isWithinPercentile (double value, double percentile)
	Checks if a given fitness value if within the given percentile of best candidates. More...

Candidate	getCandidateNamed (String name)
	Returns the candidate with the given name, if present, or null. More...

Private Attributes
AtomicInteger	populationUpdate = new AtomicInteger()
	An integer that changes every time we change the population. More...

XoverSitesAmongCandidates	xoverCompatibilities
	Crossover compatibility between members. More...

GAParameters	settings
	Parameters controlling the GA experiment. More...

Static Private Attributes
static final long	serialVersionUID = 1L
	Version UID. More...

Detailed Description

A collection of candidates.

To speed-up operations such as the selection of parents for crossover, this class holds also compatibility relations between candidates. The latter are relevant when APClass compatibility rules are in use. Therefore, if FragmentSpace.useAPclassBasedApproach() returns false the population is just a list of candidates.

Author: Marco Foscato

Definition at line 47 of file Population.java.

Constructor & Destructor Documentation

◆ Population()

denoptim.ga.Population.Population ( GAParameters settings )

Definition at line 71 of file Population.java.

References denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.ga.Population.settings, denoptim.fragspace.FragmentSpace.useAPclassBasedApproach(), and denoptim.ga.Population.xoverCompatibilities.

Referenced by denoptim.ga.Population.clone().

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Member Function Documentation

◆ add() [1/2]

boolean denoptim.ga.Population.add ( Candidate c )

Definition at line 87 of file Population.java.

References denoptim.ga.Population.populationUpdate.

Referenced by denoptim.ga.OffspringEvaluationTask.call(), denoptim.ga.Population.clone(), denoptim.ga.EAUtilsTest.testAvoidRedundantXOver(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_FixedStructure(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_Free(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_FreeBackwards(), denoptim.ga.EAUtilsTest.testBuildByXOver_SubGraph(), denoptim.ga.PopulationTest.testClone(), denoptim.ga.PopulationTest.testGetMinMax(), denoptim.ga.PopulationTest.testIsInPercentile(), denoptim.ga.PopulationTest.testPopulationVersion(), denoptim.io.DenoptimIOTest.testReadGenerationFromSummary(), and denoptim.ga.PopulationTest.testXOverCompatibility().

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◆ add() [2/2]

void denoptim.ga.Population.add	(	int	index,
		Candidate	c
	)

Definition at line 98 of file Population.java.

References denoptim.ga.Population.populationUpdate.

◆ clear()

void denoptim.ga.Population.clear ( )

Definition at line 147 of file Population.java.

References denoptim.ga.Population.populationUpdate.

◆ clone()

Population denoptim.ga.Population.clone ( )

Does not clone the cross-over compatibility relations between each pairs of population members.

Definition at line 184 of file Population.java.

References denoptim.ga.Population.add(), denoptim.ga.Population.clone(), denoptim.ga.Population.XoverSitesAmongCandidates.clone(), denoptim.ga.Population.Population(), denoptim.ga.Population.settings, and denoptim.ga.Population.xoverCompatibilities.

Referenced by denoptim.ga.Population.clone(), and denoptim.ga.PopulationTest.testClone().

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◆ getCandidateNamed()

Candidate denoptim.ga.Population.getCandidateNamed ( String name )

Returns the candidate with the given name, if present, or null.

Parameters

name	the name of the candidate to retrieve

Returns: the candidate with the given name, if present, or null.

Definition at line 515 of file Population.java.

◆ getMaxFitness()

double denoptim.ga.Population.getMaxFitness ( )

Gets the maximum value of the fitness in this population.

Returns: the maximum fitness value in this population

Definition at line 477 of file Population.java.

References denoptim.graph.Candidate.getFitness().

Referenced by denoptim.ga.Population.isWithinPercentile(), and denoptim.ga.PopulationTest.testGetMinMax().

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◆ getMinFitness()

double denoptim.ga.Population.getMinFitness ( )

Gets the minimum value of the fitness in this population.

Returns: the minimum fitness value in this population, or the Double#MIN_VALUE

Definition at line 452 of file Population.java.

References denoptim.graph.Candidate.getFitness(), and denoptim.ga.Population.getMinFitnessMember().

Referenced by denoptim.ga.OffspringEvaluationTask.call(), denoptim.ga.Population.isWithinPercentile(), and denoptim.ga.PopulationTest.testGetMinMax().

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◆ getMinFitnessMember()

Candidate denoptim.ga.Population.getMinFitnessMember ( )

Gets the Candidate with minimum value of the fitness in this population.

Returns: the population member with minimum fitness value.

Definition at line 464 of file Population.java.

References denoptim.graph.Candidate.getFitness().

Referenced by denoptim.ga.OffspringEvaluationTask.call(), and denoptim.ga.Population.getMinFitness().

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◆ getVersionID()

int denoptim.ga.Population.getVersionID ( )

Returns an integer that represent the current status of the population.

Additions, removal or change of a population member triggers change of the returned value. The integer is a good way to check for population changes without looking at the actual population content.

Returns: an integer representing the version of the population.

Definition at line 173 of file Population.java.

References denoptim.ga.Population.populationUpdate.

Referenced by denoptim.ga.PopulationTest.testPopulationVersion().

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◆ getXoverPartners()

List< Candidate > denoptim.ga.Population.getXoverPartners	(	Candidate	memberA,
		List< Candidate >	eligibleParents,
		FragmentSpace	fragSpace
	)

Returns a list of population members that can do crossover with the specified member.

Parameters

memberA	a member that wants to do crossover and searches for a partner.
the	subset of population members we can consider as eligible parents.

Returns: the list of crossover-compatible population members.

Definition at line 370 of file Population.java.

References denoptim.ga.Population.XoverSitesAmongCandidates.contains(), denoptim.graph.Candidate.getGraph(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.ga.Population.XoverSitesAmongCandidates.getMembersCompatibleWith(), denoptim.graph.Candidate.getName(), denoptim.ga.GraphOperations.locateCompatibleXOverPoints(), denoptim.programs.denovo.GAParameters.maxXOverableSubGraphSize, denoptim.ga.Population.XoverSitesAmongCandidates.put(), denoptim.graph.DGraph.sameAs(), denoptim.ga.Population.settings, and denoptim.ga.Population.xoverCompatibilities.

Referenced by denoptim.ga.EAUtils.performFBCC(), denoptim.ga.PopulationTest.testClone(), and denoptim.ga.PopulationTest.testXOverCompatibility().

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◆ getXoverSites()

List< XoverSite > denoptim.ga.Population.getXoverSites	(	Candidate	parentA,
		Candidate	parentB
	)

Returns a list of crossover sites between the two given parents.

The crossover sites are given using the same order used to specify the parents. This method should always be run after the Population#getXoverPartners(Candidate, ArrayList), which populated the crossover compatibility data.

Parameters

parentA
parentB

Returns: the list crossover sites.

Definition at line 423 of file Population.java.

References denoptim.ga.Population.XoverSitesAmongCandidates.get(), and denoptim.ga.Population.xoverCompatibilities.

Referenced by denoptim.ga.PopulationTest.compareSizeOfSites(), denoptim.ga.EAUtils.performFBCC(), and denoptim.ga.PopulationTest.testClone().

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◆ isWithinPercentile()

boolean denoptim.ga.Population.isWithinPercentile	(	double	value,
		double	percentile
	)

Checks if a given fitness value if within the given percentile of best candidates.

Parameters

value	the value of fitness to compare with the population.
percentile	number in 0-1 range defining the desired percentile.

Returns: true is the value is among the best percentile% values in the current population, i.e., is larger than min + (100-percentile% * (max-min)).

Definition at line 496 of file Population.java.

References denoptim.ga.Population.getMaxFitness(), and denoptim.ga.Population.getMinFitness().

Referenced by denoptim.ga.OffspringEvaluationTask.call(), and denoptim.ga.PopulationTest.testIsInPercentile().

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◆ remove() [1/2]

Candidate denoptim.ga.Population.remove ( int index )

Definition at line 116 of file Population.java.

References denoptim.ga.Population.populationUpdate.

Referenced by denoptim.ga.OffspringEvaluationTask.call(), and denoptim.ga.PopulationTest.testPopulationVersion().

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◆ remove() [2/2]

boolean denoptim.ga.Population.remove ( Object c )

Definition at line 125 of file Population.java.

References denoptim.ga.Population.populationUpdate.

◆ removeAll()

boolean denoptim.ga.Population.removeAll ( Collection<?> c )

Definition at line 136 of file Population.java.

References denoptim.ga.Population.populationUpdate.

◆ retainAll()

boolean denoptim.ga.Population.retainAll ( Collection<?> c )

Definition at line 156 of file Population.java.

References denoptim.ga.Population.populationUpdate.

◆ set()

Candidate denoptim.ga.Population.set	(	int	index,
		Candidate	c
	)

Definition at line 107 of file Population.java.

References denoptim.ga.Population.populationUpdate.

Referenced by denoptim.ga.PopulationTest.testPopulationVersion().

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◆ trim()

void denoptim.ga.Population.trim ( int populationSize )

Removes all the elements exceeding the given size.

Does not reorder the population prior to trimming!

Parameters

populationSize size to trim down to.

Definition at line 435 of file Population.java.

References denoptim.programs.denovo.GAParameters.getPopulationSize(), denoptim.ga.Population.XoverSitesAmongCandidates.remove(), denoptim.ga.Population.settings, and denoptim.ga.Population.xoverCompatibilities.

Referenced by denoptim.ga.EvolutionaryAlgorithm.run().

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Member Data Documentation

◆ populationUpdate

AtomicInteger denoptim.ga.Population.populationUpdate = new AtomicInteger()

private

An integer that changes every time we change the population.

Definition at line 57 of file Population.java.

Referenced by denoptim.ga.Population.add(), denoptim.ga.Population.clear(), denoptim.ga.Population.getVersionID(), denoptim.ga.Population.remove(), denoptim.ga.Population.removeAll(), denoptim.ga.Population.retainAll(), and denoptim.ga.Population.set().

◆ serialVersionUID

final long denoptim.ga.Population.serialVersionUID = 1L

staticprivate

Version UID.

Definition at line 52 of file Population.java.

◆ settings

GAParameters denoptim.ga.Population.settings

private

Parameters controlling the GA experiment.

Definition at line 67 of file Population.java.

Referenced by denoptim.ga.Population.clone(), denoptim.ga.Population.getXoverPartners(), denoptim.ga.Population.Population(), and denoptim.ga.Population.trim().

◆ xoverCompatibilities

XoverSitesAmongCandidates denoptim.ga.Population.xoverCompatibilities

private

Crossover compatibility between members.

Definition at line 62 of file Population.java.

Referenced by denoptim.ga.Population.clone(), denoptim.ga.Population.getXoverPartners(), denoptim.ga.Population.getXoverSites(), denoptim.ga.Population.Population(), and denoptim.ga.Population.trim().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/ga/Population.java

Classes

Public Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Population()

Member Function Documentation

◆ add() [1/2]

◆ add() [2/2]

◆ clear()

◆ clone()

◆ getCandidateNamed()

◆ getMaxFitness()

◆ getMinFitness()

◆ getMinFitnessMember()

◆ getVersionID()

◆ getXoverPartners()

◆ getXoverSites()

◆ isWithinPercentile()

◆ remove() [1/2]

◆ remove() [2/2]

◆ removeAll()

◆ retainAll()

◆ set()

◆ trim()

Member Data Documentation

◆ populationUpdate

◆ serialVersionUID

◆ settings

◆ xoverCompatibilities