com.rubecula.darwin.domain.helper
Interface Chromosome

All Superinterfaces:

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

All Known Implementing Classes:

Chromosome_, Chromosome_NoSex, Chromosome_Sex, Genomic_Asexual

public interface Chromosome
extends net.sf.tostring0.IToString, SexLinked, Progenitor, net.sf.tostring0.Identifiable

Defines part of a Genomic.

Version:

$Revision: 1.9 $

Author:

Robin Hillyard

Field Summary

static java.lang.String

SEX 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

Method Summary

void	addLocus(int index, Locus locus) Method to add a Locus at the specified index.
boolean	addLocus(Locus locus) Method to add a Locus at the end of this Genomic.
int	getCount()
Genomic	getGenomic()
java.util.Collection<Locus>	getLoci() Getter/setter typically used by reflection.
Locus	getLocus(int index)
void	setGenomic(Genomic genomic)
void	setLoci(java.util.Collection<Locus> loci) This is now the preferred method to set the loci.

Methods inherited from interface net.sf.tostring0.IToString

toString, toStringBrief, toStringId

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

isSexLinked

Methods inherited from interface net.sf.tostring0.Identifiable

getIdentifier

Field Detail

SEX

static final java.lang.String SEX

sex

See Also:

Constant Field Values

Method Detail

addLocus

void addLocus(int index,
              Locus locus)
              throws GeneticsException

Method to add a Locus at the specified index.

Parameters:

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

locus - a locus to be inserted into this Genomic.

Throws:

GeneticsException

See Also:

List.add(int, java.lang.Object)

addLocus

boolean addLocus(Locus locus)
                 throws GeneticsException

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

Parameters:

locus - a locus to be inserted into this Genomic.

Returns:

true if the locus is added successfully.

Throws:

GeneticsException

See Also:

addLocus(int, Locus)

getCount

int getCount()

Returns:

the number of loci in this chromosome

getGenomic

Genomic getGenomic()

Returns:

the Genomic to which this chromosome belongs.

getLoci

java.util.Collection<Locus> getLoci()

Getter/setter typically used by reflection.

Returns:

the loci as a collection of Locus objects.

getLocus

Locus getLocus(int index)

Parameters:

index -

Returns:

the locus defined by index (0..N)

setGenomic

void setGenomic(Genomic genomic)

Parameters:

genomic -

setLoci

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

This is now the preferred method to set the loci. Any prior loci will be forgotten. Getter/setter typically used by reflection.

Parameters:

loci -