com.rubecula.darwin.domain.genetics
Class Chromosome_

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

All Implemented Interfaces:

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

Direct Known Subclasses:

Chromosome_NoSex, Chromosome_Sex

public abstract class Chromosome_
extends net.sf.tostring0.AToString
implements Chromosome

Abstract class implementing base methods for the Chromosome interface. There is no specific support for Epistasis since the ordering of the loci set that is returned by getLoci() is essentially random. If you need to allow certain genes to suppress the expression of other genes, then it would probably be best to extend this class.

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.Chromosome

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

Chromosome_(java.lang.String identifier, boolean sexLinked)

Method Summary

protected void	add(int index, Locus locus)
protected boolean	add(Locus o)
protected boolean	addAll(java.util.Collection<? extends Locus> loci)
void	addLocus(int index, Locus locus) add locus and set the locus to point to this Chromosome as its owner.
boolean	addLocus(Locus locus) Method to add a Locus at the end of this Genomic.
protected void	clear()
protected boolean	contains(java.lang.Object locus)
boolean	equals(java.lang.Object obj)
int	getCount()
Genomic	getGenomic()
java.lang.String	getIdentifier()
java.util.Collection<Locus>	getLoci() Getter/setter typically used by reflection.
Locus	getLocus(int index)
int	hashCode()
protected int	indexOf(java.lang.Object locus)
protected boolean	isEmpty()
boolean	isSexLinked()
protected int	lastIndexOf(java.lang.Object locus)
protected Locus	remove(int index) Actually remove a locus, even if it is the sex locus (unless this method is overridden by Chromosome_Sex.
protected boolean	remove(java.lang.Object locus) Actually remove a locus, even if it is the sex locus (unless this method is overridden by Chromosome_Sex.
protected boolean	retainAll(java.util.Collection<?> c)
void	setGenomic(Genomic genomic)
void	setLoci(java.util.Collection<Locus> loci) This is now the preferred method to set the loci.
protected java.lang.Object[]	toArray()
protected <T> T[]	toArray(T[] a)

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 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

Chromosome_

protected Chromosome_(java.lang.String identifier,
                      boolean sexLinked)

Parameters:

identifier - the identifier for this chromosome.

sexLinked - true if this chromosome is sex-linked

Method Detail

addLocus

public void addLocus(int index,
                     Locus locus)
              throws GeneticsException

add locus and set the locus to point to this Chromosome as its owner. Note: do not use this to add a polygenic loci, except for the first of each group.

Specified by:

addLocus in interface Chromosome

Parameters:

index -

locus -

Throws:

GeneticsException

See Also:

Chromosome.addLocus(int, com.rubecula.darwin.domain.helper.Locus)

addLocus

public boolean addLocus(Locus locus)
                 throws GeneticsException

Method to add a Locus at the end of this Genomic. Generally, we prefer to use setLoci(Collection) instead.

Specified by:

addLocus in interface Chromosome

Parameters:

locus - a locus to be inserted into this Genomic.

Returns:

true, always.

Throws:

GeneticsException

See Also:

addLocus(int, Locus)

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

See Also:

Object.equals(java.lang.Object)

getCount

public int getCount()

Specified by:

getCount in interface Chromosome

Returns:

the number of loci in this chromosome.

See Also:

Chromosome.getCount()

getGenomic

public Genomic getGenomic()

Specified by:

getGenomic in interface Chromosome

Returns:

the Genomic to which this chromosome belongs.

See Also:

Chromosome.getGenomic()

getIdentifier

public java.lang.String getIdentifier()

Specified by:

getIdentifier in interface net.sf.tostring0.Identifiable

Returns:

result of invoking Identifiable.getIdentifier() on _loci.

See Also:

Identifiable.getIdentifier()

getLoci

public java.util.Collection<Locus> getLoci()

Description copied from interface: Chromosome

Getter/setter typically used by reflection.

Specified by:

getLoci in interface Chromosome

Returns:

the loci as a collection of Locus objects.

getLocus

public Locus getLocus(int index)

Specified by:

getLocus in interface Chromosome

Returns:

the indexth locus.

See Also:

Chromosome.getLocus(int)

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

See Also:

Object.hashCode()

isSexLinked

public boolean isSexLinked()

Specified by:

isSexLinked in interface SexLinked

Returns:

value of field _sexLinked.

See Also:

SexLinked.isSexLinked()

setGenomic

public void setGenomic(Genomic genomic)

Specified by:

setGenomic in interface Chromosome

See Also:

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

setLoci

public void setLoci(java.util.Collection<Locus> loci)

This is now the preferred method to set the loci. Any prior loci will be forgotten. Note: do not include any polygenic loci, except for the first of each group.

Specified by:

setLoci in interface Chromosome

Parameters:

loci -

add

protected void add(int index,
                   Locus locus)
            throws GeneticsException

Throws:

GeneticsException

add

protected boolean add(Locus o)

addAll

protected boolean addAll(java.util.Collection<? extends Locus> loci)

clear

protected void clear()

contains

protected boolean contains(java.lang.Object locus)

indexOf

protected int indexOf(java.lang.Object locus)

isEmpty

protected boolean isEmpty()

lastIndexOf

protected int lastIndexOf(java.lang.Object locus)

remove

protected Locus remove(int index)

Actually remove a locus, even if it is the sex locus (unless this method is overridden by Chromosome_Sex.

Parameters:

index -

Returns:

the element previously at the specified position.

remove

protected boolean remove(java.lang.Object locus)

Actually remove a locus, even if it is the sex locus (unless this method is overridden by Chromosome_Sex.

Parameters:

locus -

Returns:

true if the list contained the object.

retainAll

protected boolean retainAll(java.util.Collection<?> c)

toArray

protected java.lang.Object[] toArray()

toArray

protected <T> T[] toArray(T[] a)