com.rubecula.darwin.domain.genetics
Class Mutator_

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

All Implemented Interfaces:

Mutator, net.sf.tostring0.Identifiable, net.sf.tostring0.IToString

Direct Known Subclasses:

Mutator_Null, Mutator_Random

public abstract class Mutator_
extends net.sf.tostring0.AToString
implements Mutator

Abstract class to define the base methods and fields for instances of Mutator interface.

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	Mutator_() Protected constructor for a mutating Mutator.
protected	Mutator_(boolean identity) Protected constructor.

Method Summary

protected static void	addToLocusIfUnknown(Allele allele)
boolean	equals(java.lang.Object obj)
java.lang.String	getIdentifier() Return the class's simple name (since these are normally singleton instances we don't really need to distinguish them).
int	hashCode()
protected boolean	isComplementary(Gene prior, Gene gene) Method to test whether two genes are complimentary.
boolean	isIdentity() XXX
Allele	mutate(Allele allele) By default, the allele is returned unchanged.
Genome	mutate(Genome genome) By default, the copy of the genome is returned, such that the individual genes have been processed using the mutate(Allele) method.
void	normalize(Genome genome, Genome reference) Normalize the given genome with respect to the reference genome.
boolean	simplify(Genome genome) Do nothing.

Methods inherited from class net.sf.tostring0.AToString

toString, toString, toStringBrief, toStringId

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

LOG

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

The logger for this class.

Constructor Detail

Mutator_

protected Mutator_()

Protected constructor for a mutating Mutator.

Mutator_

protected Mutator_(boolean identity)

Protected constructor.

Parameters:

identity - true only if the new Mutator does not change anything

Method Detail

addToLocusIfUnknown

protected static void addToLocusIfUnknown(Allele allele)

Parameters:

allele -

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

See Also:

Object.equals(java.lang.Object)

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()

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

See Also:

Object.hashCode()

isIdentity

public boolean isIdentity()

XXX

Specified by:

isIdentity in interface Mutator

Returns:

true if this mutator does not actually change anything

See Also:

Mutator.isIdentity()

mutate

public Allele mutate(Allele allele)

By default, the allele is returned unchanged. TEST

Specified by:

mutate in interface Mutator

Parameters:

allele - the original allele

Returns:

either the original allele or a mutated version of it. TODO it seems to me now that this mutation should operate on a Gene, not on an Allele, but there again we have to remember that the word "gene" is used in two different ways in common parlance.

See Also:

Mutator.mutate(com.rubecula.darwin.domain.helper.Allele)

mutate

public Genome mutate(Genome genome)

By default, the copy of the genome is returned, such that the individual genes have been processed using the mutate(Allele) method. To be precise, the result is the result of invoking Genome.mutate(Mutator). This implementation of the method never returns a reference to the genome, it is always a copy (although result.equals(genome) may still be true).

Specified by:

mutate in interface Mutator

Parameters:

genome - the original genome

Returns:

either the original genome or a mutated version of it.

See Also:

Mutator.mutate(com.rubecula.darwin.domain.helper.Genome)

normalize

public void normalize(Genome genome,
                      Genome reference)

Description copied from interface: Mutator

Normalize the given genome with respect to the reference genome. For example, if genome and reference are identical to start with, genome will be modified such that it is now empty. This is particularly useful in asexual systems.

Specified by:

normalize in interface Mutator

See Also:

Mutator.normalize(com.rubecula.darwin.domain.helper.Genome, com.rubecula.darwin.domain.helper.Genome)

simplify

public boolean simplify(Genome genome)

Do nothing. In order to do something useful, a class must override this method.

Specified by:

simplify in interface Mutator

Parameters:

genome - TODO consider narrowing to Genotype

Returns:

true if the genome has changed as a result of simplification.

See Also:

Mutator.simplify(com.rubecula.darwin.domain.helper.Genome)

isComplementary

protected boolean isComplementary(Gene prior,
                                  Gene gene)

Method to test whether two genes are complimentary. The two genes must belong to the same locus. XXX this doesn't truly make sense genetically (two genes don't generally belong to the same locus). But it makes some sense in the context of mutation because genes can be repeated.

Parameters:

prior -

gene -

Returns:

true if the genes are complimentary.

Throws:

DarwinException - if the loci are different