com.rubecula.darwin.domain.genetics
Class Locus_

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

All Implemented Interfaces:

Locus, Progenitor, SexLinked, net.sf.tostring0.Identifiable, net.sf.tostring0.IToString

Direct Known Subclasses:

Locus_Random

public abstract class Locus_
extends net.sf.tostring0.AToString
implements Locus, SexLinked

Abstract class defining the base methods and fields for an implementer of Locus.

Author:

Robin Hillyard

Field Summary

protected static org.apache.commons.logging.Log

LOG The logger for this class.

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

ID_SEX

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

Locus_(java.lang.String identifier) Protected method to construct a plain vanilla implementer of Locus.

Method Summary

java.lang.String	addAllele(Allele allele) Incrementally add the given allele to this Locus.
boolean	equals(java.lang.Object obj)
Allele	getAllele(java.lang.String key)
java.util.Map<java.lang.String,Allele>	getAlleleMap()
java.util.Map<Allele,java.lang.Integer>	getAlleles() TODO reduce to default scope.
java.util.Collection<Allele>	getAlleleValues()
Chromosome	getChromosome()
protected java.util.Map<java.lang.String,java.lang.Integer>	getFrequencies()
java.lang.String	getIdentifier()
java.lang.String	getKey(Allele allele)
Progenitor	getParent()
Locus	getPolygenic()
int	hashCode()
boolean	isLegal(java.lang.String allele) Method to determine if the given allele is legal at this Locus.
boolean	isSexLinked()
Gene	makeGene(java.lang.String... alleles) Make a gene with the alleles specified by the variable number of allele indexes.
protected void	onChange() This method is invoked whenever the set of alleles or their frequencies changes
java.lang.String	putAllele(Allele allele, int frequency)
void	setAlleles(java.util.Map<? extends Allele,java.lang.Integer> map) Preferred method of setting up the allele/frequency map (rather than using add()).
void	setParent(Progenitor parent) Set the parent for this locus.
void	setPolygenic(Locus locus) Bean method to set the next locus in a chain of polygenic loci.
int	size()

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

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

add, pickAllele

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

Locus_

protected Locus_(java.lang.String identifier)

Protected method to construct a plain vanilla implementer of Locus.

Parameters:

identifier - the identifier for this locus.

Method Detail

addAllele

public java.lang.String addAllele(Allele allele)

Incrementally add the given allele to this Locus. The frequency value for the allele will be 1. This is an alternative to the preferred method of setting the alleles: setAlleles(Map).

Specified by:

addAllele in interface Locus

Parameters:

allele - an allele which is possible at this locus.

Returns:

the result of invoking Locus.add(Allele, int) with allele and 1 as the parameters.

See Also:

Locus.addAllele(com.rubecula.darwin.domain.helper.Allele)

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(java.lang.String key)

Specified by:

getAllele in interface Locus

Returns:

the allele from this locus corresponding to key.

See Also:

Locus.getAllele(java.lang.String)

getAlleleMap

public java.util.Map<java.lang.String,Allele> getAlleleMap()

Specified by:

getAlleleMap in interface Locus

Returns:

the map of alleles for this locus. Getter/setter typically used by reflection.

See Also:

Locus.getAlleleMap()

getAlleles

public java.util.Map<Allele,java.lang.Integer> getAlleles()

TODO reduce to default scope.

Returns:

a map of alleles and their frequencies Note that the returned values is essentially a join of two maps, _alleleMap and _frequencies, and so updating the result is just updating a temporary copy.

getAlleleValues

public java.util.Collection<Allele> getAlleleValues()

Specified by:

getAlleleValues in interface Locus

Returns:

a list of allele values for this locus.

See Also:

Locus.getAlleleValues()

getChromosome

public Chromosome getChromosome()

Specified by:

getChromosome in interface Locus

Returns:

the value of the field parent.

See Also:

Locus.getChromosome()

getIdentifier

public java.lang.String getIdentifier()

Specified by:

getIdentifier in interface net.sf.tostring0.Identifiable

Returns:

the _identifier

See Also:

Identifiable.getIdentifier()

getKey

public java.lang.String getKey(Allele allele)

Specified by:

getKey in interface Locus

Parameters:

allele -

Returns:

result of invoking List.indexOf(Object) on the #list with the parameter allele. Will return -1 if the allele is not found.

getParent

public Progenitor getParent()

Specified by:

getParent in interface Locus

Returns:

the owning Chromosome for a non-polygenic locus (or the first such), otherwise get the polygenic locus which in turn points to this one.

See Also:

Locus.getParent()

getPolygenic

public Locus getPolygenic()

Specified by:

getPolygenic in interface Locus

Returns:

null if there is no polygenic locus to which this locus is linked, i.e. this locus is either non-polygenic or it is at the end of a polygenic chain.

See Also:

Locus.getPolygenic()

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

See Also:

Object.hashCode()

isLegal

public boolean isLegal(java.lang.String allele)

Method to determine if the given allele is legal at this Locus.

Specified by:

isLegal in interface Locus

Parameters:

allele - the allele to be tested

Returns:

true if this allele is defined for (known at) this locus and if its frequency is greater than zero.

See Also:

Locus.isLegal(java.lang.String)

isSexLinked

public boolean isSexLinked()

Specified by:

isSexLinked in interface SexLinked

Returns:

true if this object is sex-linked, that is to say it is a sex chromosome, a locus on a sex chromosome, or a phenotypic character which derives from one/more sex-linked gene(s).

See Also:

SexLinked.isSexLinked()

makeGene

public Gene makeGene(java.lang.String... alleles)

Make a gene with the alleles specified by the variable number of allele indexes.

Specified by:

makeGene in interface Locus

Parameters:

alleles - variable number of alleles indexes.

Returns:

the new Gene.

See Also:

Locus.makeGene(java.lang.String[])

putAllele

public java.lang.String putAllele(Allele allele,
                                  int frequency)

Parameters:

allele -

frequency -

Returns:

the index of the new allele

setAlleles

public void setAlleles(java.util.Map<? extends Allele,java.lang.Integer> map)

Preferred method of setting up the allele/frequency map (rather than using add()).

Parameters:

map -

setParent

public void setParent(Progenitor parent)

Set the parent for this locus.

Specified by:

setParent in interface Locus

Parameters:

parent - either the preceding locus if this locus is polygenic, or the chromosome that this locus belongs to.

See Also:

Locus.setParent(com.rubecula.darwin.domain.helper.Progenitor)

setPolygenic

public void setPolygenic(Locus locus)

Bean method to set the next locus in a chain of polygenic loci.

Parameters:

locus -

size

public int size()

Specified by:

size in interface Locus

Returns:

the number of alleles in this Locus

getFrequencies

protected java.util.Map<java.lang.String,java.lang.Integer> getFrequencies()

Returns:

the frequencies

onChange

protected void onChange()

This method is invoked whenever the set of alleles or their frequencies changes