com.rubecula.darwin.domain.genetics
Class Genotype_

java.lang.Object
  net.sf.tostring0.AToString
      com.rubecula.darwin.foundation.AuditableList<Gene>
          com.rubecula.darwin.domain.genetics.Genotype_

All Implemented Interfaces:

Basic, CacheSignature, Censusible, Genes, Genotype, Ploidy, java.lang.Cloneable, java.lang.Iterable<Gene>, java.util.Collection<Gene>, java.util.List<Gene>, net.sf.tostring0.Identifiable, net.sf.tostring0.IToString

Direct Known Subclasses:

Genome_

public abstract class Genotype_
extends AuditableList<Gene>
implements Genotype, java.lang.Cloneable

This abstract class provides base definitions for implementers of Genome, the genetic information contained in an Organism belonging to a Taxon. A Genome may contain any number of Genes, though in practice the number is determined by the Genomic which defines this Genome. The structure of Genome is approximately parallel to that of Genomic .

Version:

$Revision: 1.48 $

Author:

Robin Hillyard

Field Summary

protected int	_ploidy The "ploidy" (or "oid") is the genetic "form" of the this genome.
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

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

DIPLOID, HAPLOID

Constructor Summary

protected

Genotype_(int ploidy) Constructor which creates a Genome instance with the given "ploidy".

Method Summary

boolean	addGene(Gene gene) Add gene to this Genotype at its end.
void	addGene(int locus, Gene gene) Add a Gene to this Genotype at a specific index.
void	addGenes(Genes genes) Iteratively call addGene(Gene) for each of the genes provided.
boolean	censusMe(Census census, java.lang.Object context) Method to census this object.
java.lang.Object	clone()
void	doCensus(FrequencyMap<Allele> alleleFrequencies)
boolean	equals(java.lang.Object obj) Determine equality based on the value of getBases().
java.lang.String	getBases()
java.util.Collection<? extends Censusible>	getCensusibleChildren() Method to return a list of censusible children of this object.
Gene	getGene(int locus)
java.lang.String	getIdentifier()
protected java.util.Collection<Gene>	getList()
int	getPloidy() The "ploidy" of this Genome.
java.lang.String	getSignature()
int	hashCode() return the hashcode of the bases.

Methods inherited from class com.rubecula.darwin.foundation.AuditableList

add, add, addAll, addAll, clear, contains, containsAll, get, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, retainAll, set, setList, size, subList, toArray, toArray

Methods inherited from class net.sf.tostring0.AToString

toString, toString, toStringBrief, toStringId

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.sf.tostring0.IToString

toString, toStringBrief, toStringId

Methods inherited from interface java.util.List

add, add, addAll, addAll, clear, contains, containsAll, get, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, retainAll, set, size, subList, toArray, toArray

Field Detail

_ploidy

protected final int _ploidy

The "ploidy" (or "oid") is the genetic "form" of the this genome. It is the number of alleles that are carried at any locus by this genome. Note that an organism has its ploidy determined by its genome. However, gametes of that organism are always haploid.
For a haploid system, the Ode is 1; for a diploid system, the Ode is 2, etc.

LOG

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

The logger for this class.

Constructor Detail

Genotype_

protected Genotype_(int ploidy)

Constructor which creates a Genome instance with the given "ploidy".

Parameters:

ploidy - the ploidy (haploid, diploid) of the genome.

Method Detail

addGene

public boolean addGene(Gene gene)

Description copied from interface: Genotype

Add gene to this Genotype at its end.

Specified by:

addGene in interface Genotype

Parameters:

gene - the gene to add

Returns:

true.

See Also:

AuditableList.add(net.sf.tostring0.IToString)

addGene

public void addGene(int locus,
                    Gene gene)

Description copied from interface: Genotype

Add a Gene to this Genotype at a specific index.

Specified by:

addGene in interface Genotype

Parameters:

locus -

gene -

See Also:

Genotype.addGene(int, com.rubecula.darwin.domain.helper.Gene)

addGenes

public void addGenes(Genes genes)

Iteratively call addGene(Gene) for each of the genes provided.

Specified by:

addGenes in interface Genotype

Parameters:

genes -

See Also:

Genotype.addGenes(com.rubecula.darwin.domain.helper.Genes)

censusMe

public boolean censusMe(Census census,
                        java.lang.Object context)

Description copied from interface: Censusible

Method to census this object.

Specified by:

censusMe in interface Censusible

Parameters:

census - the census object which will present the results of taking this census

context - an arbitrary object which can be used by the census object to provide appropriate context for this object.

Returns:

true if we should continue censusing this object at deeper levels. If the result is false, then we do not call Censusible.getCensusibleChildren().

See Also:

Censusible.censusMe(com.rubecula.darwin.domain.helper.Census, java.lang.Object)

clone

public java.lang.Object clone()

Overrides:

clone in class java.lang.Object

See Also:

Object.clone()

doCensus

public void doCensus(FrequencyMap<Allele> alleleFrequencies)

Specified by:

doCensus in interface Genotype

Parameters:

alleleFrequencies -

equals

public boolean equals(java.lang.Object obj)

Determine equality based on the value of getBases(). Ignore the super-class.

Specified by:

equals in interface java.util.Collection<Gene>

Specified by:

equals in interface java.util.List<Gene>

Overrides:

equals in class AuditableList<Gene>

See Also:

AuditableList.equals(java.lang.Object)

getBases

public java.lang.String getBases()

Specified by:

getBases in interface Basic

Returns:

a set of bases in the base alphabet of the genome (e.g. "CAGT") which correspond to this genetic object. These bases are used to determine certain mutations and crossover situations.

See Also:

Basic.getBases()

getCensusibleChildren

public java.util.Collection<? extends Censusible> getCensusibleChildren()

Description copied from interface: Censusible

Method to return a list of censusible children of this object.

Specified by:

getCensusibleChildren in interface Censusible

Returns:

either null or an ArrayList of censusible objects.

See Also:

Censusible.getCensusibleChildren()

getGene

public Gene getGene(int locus)

Specified by:

getGene in interface Genes

Parameters:

locus - an integer from 0...

Returns:

the Gene at the specified locus position.

See Also:

Genes.getGene(int)

getIdentifier

public java.lang.String getIdentifier()

Specified by:

getIdentifier in interface net.sf.tostring0.Identifiable

Overrides:

getIdentifier in class AuditableList<Gene>

Returns:

the signature for this TraitMap

See Also:

AuditableList.getIdentifier()

getPloidy

public int getPloidy()

The "ploidy" of this Genome. It may not match that of the Genomic to which the genes belong.

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()

getSignature

public java.lang.String getSignature()

Specified by:

getSignature in interface CacheSignature

Returns:

a "signature" for this object which can be used to form part of a cache key. The signature is similar in a sense to the hash code but typically, it is based more on mutable components of an object than is the hash code.

See Also:

CacheSignature.getSignature()

hashCode

public int hashCode()

return the hashcode of the bases. We ignore the super method.

Specified by:

hashCode in interface java.util.Collection<Gene>

Specified by:

hashCode in interface java.util.List<Gene>

Overrides:

hashCode in class AuditableList<Gene>

See Also:

AuditableList.hashCode()

getList

protected java.util.Collection<Gene> getList()

Overrides:

getList in class AuditableList<Gene>

Returns:

the actual list as a Collection