com.rubecula.darwin.domain.genetics
Class Gene_

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

All Implemented Interfaces:

Basic, CacheSignature, Censusible, Gene, Ploidy, java.lang.Cloneable, net.sf.tostring0.Identifiable, net.sf.tostring0.IToString

Direct Known Subclasses:

Gene_Diploid, Gene_Haploid

public abstract class Gene_
extends net.sf.tostring0.AToString
implements Gene, java.lang.Cloneable, net.sf.tostring0.Identifiable

This abstract class represents a particular gene at a locus of a genome. In a diploid system there will be two genes at a locus. In most systems there is one. A gene can take as its "value" an Allele which is valid at the given locus.

Version:

$Revision: 1.36 $

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

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

DIPLOID, HAPLOID

Constructor Summary

protected

Gene_(int ploidy) Primary protected constructor to create a Gene_ which appears at a particular locus.

Method Summary

boolean	censusMe(Census census, java.lang.Object context) Method to census this object.
java.lang.Object	clone() XXX
boolean	equals(java.lang.Object obj)
Allele	getAllele(int index) Accessor method to return the indexth allele for this gene.
int	getAlleleCount()
java.lang.String	getAlleleKey(int index) Accessor method to return the key to the indexth allele for this gene.
java.lang.String	getBases()
java.util.Collection<? extends Censusible>	getCensusibleChildren() Method to return a list of censusible children of this object.
java.lang.String	getIdentifier()
Locus	getLocus()
int	getPloidy() XXX
java.lang.String	getSignature()
int	hashCode()
Gene	mutate(Mutator mutator) Method to get a mutated copy of a Gene.
void	setAllele(int index, java.lang.String allele) XXX It's the responsibility of the caller to ensure that the indicated allele is valid for the locus to which this gene will belong.
void	setLocus(Locus locus) Set the locus for this gene.

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

Field Detail

LOG

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

The logger for this class.

Constructor Detail

Gene_

protected Gene_(int ploidy)

Primary protected constructor to create a Gene_ which appears at a particular locus. The array alleles of size ploidy is initialized with no elements specified.

Parameters:

ploidy - the number of alleles at any given gene locus

Method Detail

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()

XXX

Overrides:

clone in class java.lang.Object

See Also:

Object.clone()

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

See Also:

Object.equals(java.lang.Object)

getAllele

public Allele getAllele(int index)

Description copied from interface: Gene

Accessor method to return the indexth allele for this gene.

Specified by:

getAllele in interface Gene

Parameters:

index -

Returns:

the indexth allele

getAlleleCount

public int getAlleleCount()

Specified by:

getAlleleCount in interface Gene

Returns:

the number of alleles for the locus of this gene

getAlleleKey

public java.lang.String getAlleleKey(int index)

Description copied from interface: Gene

Accessor method to return the key to the indexth allele for this gene.

Specified by:

getAlleleKey in interface Gene

Parameters:

index - which allele to get.

Returns:

key of the allele within the locus, at that index.

See Also:

Gene.getAlleleKey(int)

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()

getIdentifier

public java.lang.String getIdentifier()

Specified by:

getIdentifier in interface net.sf.tostring0.Identifiable

See Also:

Identifiable.getIdentifier()

getLocus

public Locus getLocus()

Specified by:

getLocus in interface Gene

Returns:

the locus at which this gene appears

See Also:

Gene.getLocus()

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()

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()

Overrides:

hashCode in class java.lang.Object

See Also:

Object.hashCode()

mutate

public Gene mutate(Mutator mutator)

Method to get a mutated copy of a Gene.

Specified by:

mutate in interface Gene

Parameters:

mutator -

Returns:

a mutated copy (which may be identical if no mutations have occurred)

See Also:

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

setAllele

public void setAllele(int index,
                      java.lang.String allele)

XXX It's the responsibility of the caller to ensure that the indicated allele is valid for the locus to which this gene will belong.

Specified by:

setAllele in interface Gene

Parameters:

index - which allele is to be set.

allele - the value of the allele to set.

See Also:

Gene.setAllele(int, String)

setLocus

public void setLocus(Locus locus)

Description copied from interface: Gene

Set the locus for this gene.

Specified by:

setLocus in interface Gene

See Also:

Gene.setLocus(com.rubecula.darwin.domain.helper.Locus)