com.rubecula.darwin.domain.genetics
Class Meiosis_

java.lang.Object
  net.sf.tostring0.AToString
      com.rubecula.darwin.domain.genetics.Meiosis_

All Implemented Interfaces:

Meiosis, net.sf.tostring0.Identifiable, net.sf.tostring0.IToString

Direct Known Subclasses:

Meiosis_Chromosome, Meiosis_Clone, Meiosis_Locus

public abstract class Meiosis_
extends net.sf.tostring0.AToString
implements Meiosis

Abstract class which defines the base operations for an implementation of Meiosis.

Author:

Robin Hillyard

Field Summary

protected static org.apache.commons.logging.Log

LOG The logger for this class.

Fields inherited from interface net.sf.tostring0.IToString

ANGBR_OPEN, ANGBRA_CLSE, BRA_CLSE, BRA_OPEN, BRCE_OPEN, BRCS_CLSE, COLON, LIST_SEPARATOR, MAX_ELEMENTS_DEFAULT, S_MT, S_PERCENT, SEPARATOR, SPACE

Constructor Summary

protected

Meiosis_(org.apache.commons.math.random.RandomGenerator random) Protected constructor for an implementer of Meiosis

Method Summary

java.lang.String	doMeiosis(Gene gene, int index) Choose an allele at random for the given locus.
protected Genome	doMeiosisChromosome(Genomic genomic, Genes genes, Chromosome chromosome, int index)
java.lang.String	getIdentifier() Return the class's simple name (since these are normally singleton instances we don't really need to distinguish them).
protected org.apache.commons.math.random.RandomGenerator	getRandom()

Methods inherited from class net.sf.tostring0.AToString

toString, toString, toStringBrief, toStringId

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.rubecula.darwin.domain.helper.Meiosis

doMeiosis

Field Detail

LOG

protected static final org.apache.commons.logging.Log LOG

The logger for this class.

Constructor Detail

Meiosis_

protected Meiosis_(org.apache.commons.math.random.RandomGenerator random)

Protected constructor for an implementer of Meiosis

Parameters:

random - a random number source.

Method Detail

doMeiosis

public java.lang.String doMeiosis(Gene gene,
                                  int index)

Choose an allele at random for the given locus.

Specified by:

doMeiosis in interface Meiosis

Parameters:

gene - the gene on which we are doing the meiosis.

index - if index >=0 then we use it, otherwise we generate a random number between 0 and the gene's ploidy less one.

Returns:

the key of the allele chosen.

getIdentifier

public java.lang.String getIdentifier()

Return the class's simple name (since these are normally singleton instances we don't really need to distinguish them).

Specified by:

getIdentifier in interface net.sf.tostring0.Identifiable

See Also:

Identifiable.getIdentifier()

doMeiosisChromosome

protected Genome doMeiosisChromosome(Genomic genomic,
                                     Genes genes,
                                     Chromosome chromosome,
                                     int index)

Parameters:

genomic -

genes -

chromosome -

index - the index to use to choose the allele for a given gene (if < 0 then we use a random number)

Returns:

a newly constructed Genome

getRandom

protected org.apache.commons.math.random.RandomGenerator getRandom()

Returns:

the random number generator