ec.vector.breed

Class GeneDuplicationPipeline

java.lang.Object

ec.BreedingSource

ec.BreedingPipeline

ec.vector.breed.GeneDuplicationPipeline

All Implemented Interfaces:

Prototype, Setup, SteadyStateBSourceForm, RandomChoiceChooserD, java.io.Serializable, java.lang.Cloneable

public class GeneDuplicationPipeline
extends BreedingPipeline

GeneDuplicationPipeline is designed to duplicate a sequence of genes from the chromosome and append them to the end of the chromosome. The sequence of genes copied are randomly determined. That is to say, a random begining index is selected and a random ending index is selected from the chromosome. Then this area is copied (begining inclusive, ending exclusive) and appended to the end of the chromosome. Since randomness is a factor several checks are performed to make sure the begining and ending indicies are valid. For example, since the ending index is exclusive, the ending index cannot equal the begining index (a new ending index would be randomly seleceted in this case). Likewise the begining index cannot be larger than the ending index (they would be swapped in this case).

Default Base
ec.vector.breed.GeneDuplicationPipeline

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	NUM_SOURCES
static java.lang.String	P_DUPLICATION

Fields inherited from class ec.BreedingPipeline

DYNAMIC_SOURCES, likelihood, mybase, P_LIKELIHOOD, P_NUMSOURCES, P_SOURCE, sources, V_SAME

Fields inherited from class ec.BreedingSource

NO_PROBABILITY, P_PROB, probability

Constructor Summary

Constructors

Constructor and Description
GeneDuplicationPipeline()

Method Summary

Modifier and Type	Method and Description
Parameter	defaultBase() Returns the default base for this prototype.
int	numSources() Returns the number of sources to this pipeline.
int	produce(int min, int max, int start, int subpopulation, Individual[] inds, EvolutionState state, int thread) Produces n individuals from the given subpopulation and puts them into inds[start...start+n-1], where n = Min(Max(q,min),max), where q is the "typical" number of individuals the BreedingSource produces in one shot, and returns n.

Methods inherited from class ec.BreedingPipeline

clone, finishProducing, individualReplaced, maxChildProduction, minChildProduction, preparePipeline, prepareToProduce, produces, reproduce, setup, sourcesAreProperForm, typicalIndsProduced

Methods inherited from class ec.BreedingSource

getProbability, pickRandom, setProbability, setupProbabilities

Methods inherited from class java.lang.Object

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

Field Detail

P_DUPLICATION

public static final java.lang.String P_DUPLICATION

See Also:

Constant Field Values

NUM_SOURCES

public static final int NUM_SOURCES

See Also:

Constant Field Values

Constructor Detail

GeneDuplicationPipeline

public GeneDuplicationPipeline()

Method Detail

defaultBase

public Parameter defaultBase()

Description copied from interface: Prototype

Returns the default base for this prototype. This should generally be implemented by building off of the static base() method on the DefaultsForm object for the prototype's package. This should be callable during setup(...).

numSources

public int numSources()

Description copied from class: BreedingPipeline

Returns the number of sources to this pipeline. Called during BreedingPipeline's setup. Be sure to return a value > 0, or DYNAMIC_SOURCES which indicates that setup should check the parameter file for the parameter "num-sources" to make its determination.

Specified by:

numSources in class BreedingPipeline

produce

public int produce(int min,
                   int max,
                   int start,
                   int subpopulation,
                   Individual[] inds,
                   EvolutionState state,
                   int thread)

Description copied from class: BreedingSource

Produces n individuals from the given subpopulation and puts them into inds[start...start+n-1], where n = Min(Max(q,min),max), where q is the "typical" number of individuals the BreedingSource produces in one shot, and returns n. max must be >= min, and min must be >= 1. For example, crossover might typically produce two individuals, tournament selection might typically produce a single individual, etc.

Specified by:

produce in class BreedingSource