com.rubecula.darwin.domain.genetics
Class Genomic_

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

All Implemented Interfaces:

Genomic, Ploidy, Replicator, Countable, net.sf.tostring0.Identifiable, net.sf.tostring0.IToString

Direct Known Subclasses:

Genomic_Diploid, Genomic_Haploid

public abstract class Genomic_
extends net.sf.tostring0.AToString
implements Genomic

Abstract class implementing base methods for the Genomic interface.

Author:

Robin Hillyard

Field Summary

protected AuditableList<Chromosome>	_chromosomes
protected Expresser	expresserCommon
protected java.util.Map<Locus,Expresser>	expressers
protected static org.apache.commons.logging.Log	LOG The logger for this class.

Fields inherited from interface com.rubecula.darwin.domain.helper.Ploidy

DIPLOID, HAPLOID

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	Genomic_(java.lang.String identifier, int ploidy, Meiosis meiosis) TEST Constructor for a new Genomic_ instance.
protected	Genomic_(java.lang.String identifier, int ploidy, Meiosis meiosis, Mutator mutator) Constructor for a new Genomic_ instance.

Method Summary

boolean	addChromosome(Chromosome chromosome) Method to add a chromosome at the end of this Genomic.
void	addChromosome(int index, Chromosome chromosome) Method to add a chromosome at the specified index.
protected void	clearChromosomes()
Genome	createGamete(Genes genes) XXX This is very similar to the way SeedGenome works.
boolean	equals(java.lang.Object obj)
void	express(Phenotype phenotype, Colony colony, Genes genes) Standard implementation of express for this Genomic.
void	express(Phenotype phenotype, Genes genes) Standard implementation of this method simply calls express(Phenotype, Colony, Genes) with null population.
java.lang.String	getAlphabet() Override this method if not using the standard alphabet of bases.
Chromosome	getChromosome(int index)
java.util.Collection<Chromosome>	getChromosomes() Getter/setter typically used by reflection.
int	getCount()
Expresser	getExpresser(Locus locus) Get the expresser for the specific locus.
java.util.Map<Locus,Expresser>	getExpressers() This is a bean property (not part of an interface).
java.lang.String	getIdentifier()
Locus	getLocus(int n) method to step through each chromosome and get the nth locus relative to this genom object.
int	getLocusCount() Get the total number of locus by cycling through the chromosomes.
Meiosis	getMeiosis() XXX
Mutator	getMutator() XXX
int	getPloidy() XXX
int	hashCode()
Genome	mutate(Genome genome) Non-mutating method to mutate this Genome and return a mutated copy.
void	normalize(Genome genome, Genome reference) Normalize the given genome with respect to the reference genome.
Expresser	putExpresser(Locus locus, Expresser expresser) Register an expresser.
void	setChromosomes(java.util.Collection<Chromosome> chromosomes) This is the preferred method to set the chromosomes.
void	setExpresser(Expresser expresser) Set the common expresser (for all loci).
void	setExpressers(java.util.Map<Locus,Expresser> expressers) Used by dependency injection: sets the expresser map.
boolean	simplify(Genome genome) Repeatedly invoke the simplify method of the mutator on the genome until there are no further changes.

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

expresserCommon

protected transient Expresser expresserCommon

expressers

protected transient java.util.Map<Locus,Expresser> expressers

_chromosomes

protected final transient AuditableList<Chromosome> _chromosomes

LOG

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

The logger for this class.

Constructor Detail

Genomic_

protected Genomic_(java.lang.String identifier,
                   int ploidy,
                   Meiosis meiosis)

TEST Constructor for a new Genomic_ instance. This type of Genomic undergoes no mutations.

Parameters:

identifier - the identifier for this Genomic.

ploidy - the ploidy (haploid/diploid/etc).

meiosis - the implementer of Meiosis.

Genomic_

protected Genomic_(java.lang.String identifier,
                   int ploidy,
                   Meiosis meiosis,
                   Mutator mutator)

Constructor for a new Genomic_ instance.

Parameters:

identifier - the identifier for this Genomic.

ploidy - the ploidy (haploid/diploid/etc).

meiosis - the implementer of Meiosis.

mutator - the implementer of Mutator which will be applied to all new genomes.

Method Detail

addChromosome

public boolean addChromosome(Chromosome chromosome)

Description copied from interface: Genomic

Method to add a chromosome at the end of this Genomic.

Specified by:

addChromosome in interface Genomic

Parameters:

chromosome - a chromosome to be inserted into this Genomic.

Returns:

true if the chromosome was added.

See Also:

Genomic.addChromosome(com.rubecula.darwin.domain.helper.Chromosome)

addChromosome

public void addChromosome(int index,
                          Chromosome chromosome)

Description copied from interface: Genomic

Method to add a chromosome at the specified index.

Specified by:

addChromosome in interface Genomic

Parameters:

index - the index at which the new object will appear.

chromosome - a chromosome to be inserted into this Genomic.

See Also:

Genomic.addChromosome(int, com.rubecula.darwin.domain.helper.Chromosome)

createGamete

public Genome createGamete(Genes genes)

XXX This is very similar to the way SeedGenome works. Probably they should be combined.

Specified by:

createGamete in interface Replicator

Parameters:

genes - the Genome from which the gamete will be created via a process of meiosis.

Returns:

a newly constructed gamete in the form of a genome.

See Also:

Replicator.createGamete(com.rubecula.darwin.domain.helper.Genes)

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

See Also:

Object.equals(java.lang.Object)

express

public void express(Phenotype phenotype,
                    Colony colony,
                    Genes genes)

Standard implementation of express for this Genomic. Construct a new empty phenotype (the result), then for each gene passed in, express it and add the resulting trait to the result.

Specified by:

express in interface Genomic

Parameters:

phenotype - the phenotype to which we will add any traits resulting from the expression of the given genes

colony - the population to which our genome belongs, usually ignored but referenced if population and/or environment affect gene expression.

genes - the genes to express

See Also:

Genomic.express(Phenotype, Colony, com.rubecula.darwin.domain.helper.Genes)

express

public void express(Phenotype phenotype,
                    Genes genes)

Standard implementation of this method simply calls express(Phenotype, Colony, Genes) with null population. TODO consider checking the cache here (although this implementation is never called other than by unit tests).

Specified by:

express in interface Genomic

Parameters:

phenotype - the phenotype to which the expressions will be added.

See Also:

Genomic.express(Phenotype, com.rubecula.darwin.domain.helper.Genes)

getAlphabet

public java.lang.String getAlphabet()

Override this method if not using the standard alphabet of bases.

Specified by:

getAlphabet in interface Genomic

Returns:

"CGAT".

See Also:

Genomic.getAlphabet()

getChromosome

public Chromosome getChromosome(int index)

Specified by:

getChromosome in interface Genomic

Returns:

the chromosome defined by index (0..N). Note that sex chromosomes are never counted in the index. Thus the first non-sex chromosome in the genomic is at index 0, etc.

See Also:

Genomic.getChromosome(int)

getChromosomes

public java.util.Collection<Chromosome> getChromosomes()

Description copied from interface: Genomic

Getter/setter typically used by reflection.

Specified by:

getChromosomes in interface Genomic

Returns:

the chromosomes as a collection of Chromosome objects.

See Also:

XXX showIdentifer=false has no effect because it uses an either/or rule.

getCount

public int getCount()

Specified by:

getCount in interface Countable

Returns:

the number of chromosomes in this Genomic.

getExpresser

public Expresser getExpresser(Locus locus)

Get the expresser for the specific locus. If the locus is null, then we return the common expresser. If the locus is not null, then we return the expresser for that locus. If there is no such expresser, then we return the expresser for the parent locus, if such exists. If there is still no expresser for this locus, then we return the common expresser.

Specified by:

getExpresser in interface Genomic

Parameters:

locus - the locus (or null) for which we want the expresser

Returns:

the appropriate expresser for the given locus else (see above for rules).

See Also:

Genomic.getExpresser(com.rubecula.darwin.domain.helper.Locus)

getExpressers

public java.util.Map<Locus,Expresser> getExpressers()

This is a bean property (not part of an interface).

Returns:

the mapping for Locus => Expresser for this Genomic.

getIdentifier

public java.lang.String getIdentifier()

Specified by:

getIdentifier in interface net.sf.tostring0.Identifiable

Returns:

the identifier for the set of chromosomes

See Also:

XXX omit=true has no effect because identifiers are not treated like normal ToString-annotation objects.

getLocus

public final Locus getLocus(int n)

method to step through each chromosome and get the nth locus relative to this genom object. Take care: this final method returns even the sex locus.

Specified by:

getLocus in interface Genomic

Parameters:

n - which must be greater than or equal to 0 and less than Genomic.getLocusCount().

Returns:

the nth locus or null if no such locus

See Also:

Genomic.getLocus(int)

getLocusCount

public int getLocusCount()

Get the total number of locus by cycling through the chromosomes.

Specified by:

getLocusCount in interface Genomic

Returns:

the total number of loci, over all chromosomes.

See Also:

Genomic.getLocusCount()

getMeiosis

public Meiosis getMeiosis()

XXX

Specified by:

getMeiosis in interface Genomic

Returns:

the application-specified implementer of Meiosis

See Also:

Genomic.getMeiosis()

getMutator

public Mutator getMutator()

XXX

Specified by:

getMutator in interface Genomic

Returns:

the mutator

See Also:

Genomic.getMutator()

getPloidy

public int getPloidy()

XXX

Specified by:

getPloidy in interface Ploidy

Returns:

the "ploidy" which will normally be either Ploidy.HAPLOID, i.e. simple or Ploidy.DIPLOID, i.e. double.

See Also:

Ploidy.getPloidy()

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

See Also:

Object.hashCode()

mutate

public Genome mutate(Genome genome)

Non-mutating method to mutate this Genome and return a mutated copy. XXX consider changing the parameter (and result) to Genes. TODO consider reworking the callers of this method -- the usage is inconsistent between sexual and asexual situations.

Specified by:

mutate in interface Genomic

Parameters:

genome -

Returns:

either this Genome or a mutated copy.

See Also:

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

normalize

public void normalize(Genome genome,
                      Genome reference)

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 Genomic

Parameters:

genome -

reference -

putExpresser

public Expresser putExpresser(Locus locus,
                              Expresser expresser)

Register an expresser.

Specified by:

putExpresser in interface Genomic

Returns:

the previous version of expresser, if any.

See Also:

Genomic.putExpresser(com.rubecula.darwin.domain.helper.Locus, com.rubecula.darwin.domain.helper.Expresser)

setChromosomes

public void setChromosomes(java.util.Collection<Chromosome> chromosomes)

Description copied from interface: Genomic

This is the preferred method to set the chromosomes. Any prior chromosomes will be discarded. Getter/setter typically used by reflection.

Specified by:

setChromosomes in interface Genomic

See Also:

Genomic.setChromosomes(java.util.Collection)

setExpresser

public void setExpresser(Expresser expresser)

Set the common expresser (for all loci). Note that the expresser map is used in preference to this expresser.

Specified by:

setExpresser in interface Genomic

Parameters:

expresser -

setExpressers

public void setExpressers(java.util.Map<Locus,Expresser> expressers)

Used by dependency injection: sets the expresser map. Note that this expresser map is used in preference to the common expresser.

Parameters:

expressers -

simplify

public boolean simplify(Genome genome)

Repeatedly invoke the simplify method of the mutator on the genome until there are no further changes.

Specified by:

simplify in interface Genomic

Parameters:

genome - the genome to be simplified TODO consider narrowing genome to Genotype.

Returns:

true if any simplifications have been made to genome.

See Also:

Genomic.simplify(Genome)

clearChromosomes

protected void clearChromosomes()