com.rubecula.darwin.core
Class Factory_Abstract

java.lang.Object
  com.rubecula.darwin.core.Factory_Abstract

All Implemented Interfaces:

Factory

Direct Known Subclasses:

Factory_Default

public abstract class Factory_Abstract
extends Object
implements Factory

Abstract Factory.

Author:

Robin

Field Summary

static String	P_ALLELE0 allele0
static String	P_ALLELE1 allele1
static String	P_SEX sex

Constructor Summary

protected

Factory_Abstract()

Method Summary

Allele	makeAllele(Object value) Factory method to instantiate a new Allele of the appropriate class, with an auto-generated key.
Allele	makeAllele(Object key, Object value) Factory method to instantiate a new Allele of the appropriate class.
static Map<String,Object>	makeDiploidAlleleMap(Allele x, Allele y) Class convenience method to create a map suitable for calling makeGene().
Gene	makeGene(int ode) Factory method to instantiate a new Gene of the appropriate class.
Genotype	makeGenotype(int ode) Factory method to instantiate a new genotype of the appropriate class.
static Map<String,Object>	makeHaploidAlleleMap(Allele x) Class convenience method to create a map suitable for calling makeGene().
Organism	makeOrganism(Population population, Genotype genotype) Factory method to instantiate a new organism of the appropriate class, with a population-specific auto-generated identifier.
Organism	makeOrganism(Population population, Genotype genotype, Map<String,Object> properties) Factory method to instantiate a new organism of the appropriate class, with a population-specific auto-generated identifier.
Organism	makeOrganism(String identifier, Population population, Genotype genotype) Factory method to instantiate a new organism of the appropriate class.
Phenotype	makePhenotype() Factory method to instantiate a new phenotype of the appropriate class.
static Map<String,Object>	makeSexMap(boolean female) Class convenience method to create a map suitable for calling makeOrganism().
Trait	makeTrait(String identifier) Factory method to instantiate a new Trait of the appropriate class, without an initial value.
Trait	makeTrait(String identifier, Map<String,Object> properties) Factory method to instantiate a new Trait of the appropriate class, without an initial value.
Trait	makeTrait(String identifier, Object value) Factory method to instantiate a new Trait of the appropriate class.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface com.rubecula.darwin.core.Factory

makeAllele, makeAllele, makeGene, makeGenotype, makeOrganism, makePhenotype, makeTrait

Field Detail

P_ALLELE1

public static final String P_ALLELE1

allele1

See Also:

Constant Field Values

P_ALLELE0

public static final String P_ALLELE0

allele0

See Also:

Constant Field Values

P_SEX

public static final String P_SEX

sex

See Also:

Constant Field Values

Constructor Detail

Factory_Abstract

protected Factory_Abstract()

Method Detail

makeDiploidAlleleMap

public static Map<String,Object> makeDiploidAlleleMap(Allele x,
                                                      Allele y)

Class convenience method to create a map suitable for calling makeGene().

Parameters:

x - allele for position P_ALLELE0

y - allele for position P_ALLELE1

Returns:

a instance of Map objects

makeHaploidAlleleMap

public static Map<String,Object> makeHaploidAlleleMap(Allele x)

Class convenience method to create a map suitable for calling makeGene().

Parameters:

x - an allele for position P_ALLELE0

Returns:

a instance of Map objects

makeSexMap

public static Map<String,Object> makeSexMap(boolean female)

Class convenience method to create a map suitable for calling makeOrganism().

Parameters:

female - a boolean for the sex (true for female).

Returns:

a instance of Map objects with one element with the key P_SEX and the value (as a Boolean) female.

makeAllele

public Allele makeAllele(Object value)

Description copied from interface: Factory

Factory method to instantiate a new Allele of the appropriate class, with an auto-generated key.

Specified by:

makeAllele in interface Factory

Parameters:

value - the value of the new allele.

Returns:

a newly constructed instance of Allele.

makeAllele

public Allele makeAllele(Object key,
                         Object value)

Description copied from interface: Factory

Factory method to instantiate a new Allele of the appropriate class.

Specified by:

makeAllele in interface Factory

Parameters:

key - the key of the new allele.

value - the value of the new allele.

Returns:

a newly constructed instance of Allele.

makeGene

public Gene makeGene(int ode)

Description copied from interface: Factory

Factory method to instantiate a new Gene of the appropriate class.

Specified by:

makeGene in interface Factory

Parameters:

ode - the number of alleles to be found at a particular locus (1 if haploid, 2 if diploid).

Returns:

a newly constructed instance of Gene.

makeGenotype

public Genotype makeGenotype(int ode)

Description copied from interface: Factory

Factory method to instantiate a new genotype of the appropriate class.

Specified by:

makeGenotype in interface Factory

Parameters:

ode - the number of alleles to be found at a particular locus (1 if haploid, 2 if diploid).

Returns:

a newly constructed instance of Genotype.

makeOrganism

public Organism makeOrganism(Population population,
                             Genotype genotype)

Description copied from interface: Factory

Factory method to instantiate a new organism of the appropriate class, with a population-specific auto-generated identifier.

Specified by:

makeOrganism in interface Factory

Parameters:

population - the population into which the new organism will be "born".

genotype - the genotype which defines the new organism.

Returns:

a newly constructed instance of Organism.

makeOrganism

public Organism makeOrganism(Population population,
                             Genotype genotype,
                             Map<String,Object> properties)

Description copied from interface: Factory

Factory method to instantiate a new organism of the appropriate class, with a population-specific auto-generated identifier.

Specified by:

makeOrganism in interface Factory

Parameters:

population - the population into which the new organism will be "born".

genotype - the genotype which defines the new organism.

properties - a map which specifies any additional properties required at instantation time.

Returns:

a newly constructed instance of Organism.

makeOrganism

public Organism makeOrganism(String identifier,
                             Population population,
                             Genotype genotype)

Description copied from interface: Factory

Factory method to instantiate a new organism of the appropriate class.

Specified by:

makeOrganism in interface Factory

Parameters:

identifier - the identifier for the new organism.

population - the population into which the new organism will be "born".

genotype - the genotype which defines the new organism.

Returns:

a newly constructed instance of Organism.

makePhenotype

public Phenotype makePhenotype()

Description copied from interface: Factory

Factory method to instantiate a new phenotype of the appropriate class.

Specified by:

makePhenotype in interface Factory

Returns:

a newly constructed instance of Phenotype.

makeTrait

public Trait makeTrait(String identifier)

Description copied from interface: Factory

Factory method to instantiate a new Trait of the appropriate class, without an initial value.

Specified by:

makeTrait in interface Factory

Parameters:

identifier - the identifier of the new trait.

Returns:

a newly constructed instance of Trait.

makeTrait

public Trait makeTrait(String identifier,
                       Map<String,Object> properties)

Description copied from interface: Factory

Factory method to instantiate a new Trait of the appropriate class, without an initial value.

Specified by:

makeTrait in interface Factory

Parameters:

identifier - the identifier of the new trait.

properties - a map which specifies any additional properties required at instantation time.

Returns:

a newly constructed instance of Trait.

makeTrait

public Trait makeTrait(String identifier,
                       Object value)

Description copied from interface: Factory

Factory method to instantiate a new Trait of the appropriate class.

Specified by:

makeTrait in interface Factory

Parameters:

identifier - the identifier of the new trait.

value - the initial value of the new trait.

Returns:

a newly constructed instance of Trait.