com.rubecula.darwin.domain.environment
Class Phenotype_

java.lang.Object
  net.sf.tostring0.AToString
      com.rubecula.darwin.domain.environment.TraitMap_
          com.rubecula.darwin.domain.environment.Phenotype_

All Implemented Interfaces:

CacheSignature, Censusible, Fit, Phenotype, TraitMap, net.sf.tostring0.Identifiable, net.sf.tostring0.IToString

Direct Known Subclasses:

Phenotype_Dawkinsian, Phenotype_TS

public abstract class Phenotype_
extends TraitMap_
implements Phenotype

Abstract class to define the base methods and fields for an implementation of Phenotype.

Author:

Robin Hillyard

Field Summary

java.util.List<ExPhen>	_extendedPhenotypes the list of extended phenotypes for this phenotype.
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

Constructor Summary

protected

Phenotype_(java.lang.String id) Constructor to create an identified empty Phenotype.

Method Summary

void	addExtended(ExPhen expression)
java.lang.String	addTrait(java.lang.String key, Trait trait) Add a trait and set it to "belong" to this Phenotype.
java.lang.String	addTrait(Trait trait) Add a trait using for its key the id of the character to which this trait belongs.
void	doCensus(Pharacter character, FrequencyMap<Trait> traitFrequencies)
boolean	equals(java.lang.Object obj)
java.util.Collection<ExPhen>	getExtendedPhenotypes()
java.lang.String	getIdentifier()
TraitMap	getSexTraits()
int	hashCode()

Methods inherited from class com.rubecula.darwin.domain.environment.TraitMap_

censusMe, getCensusibleChildren, getKeys, getSignature, getTrait, getTraits, put, 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 net.sf.tostring0.IToString

toString, toStringBrief, toStringId

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

getKeys, getTrait, getTraits, size

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

getSignature

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

censusMe, getCensusibleChildren

Field Detail

_extendedPhenotypes

public final java.util.List<ExPhen> _extendedPhenotypes

the list of extended phenotypes for this phenotype.

LOG

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

The logger for this class.

Constructor Detail

Phenotype_

protected Phenotype_(java.lang.String id)

Constructor to create an identified empty Phenotype.

Parameters:

id - the identifier for this Phenotype

Method Detail

addExtended

public void addExtended(ExPhen expression)

Specified by:

addExtended in interface Phenotype

See Also:

Phenotype.addExtended(com.rubecula.darwin.domain.helper.ExPhen)

addTrait

public java.lang.String addTrait(java.lang.String key,
                                 Trait trait)

Add a trait and set it to "belong" to this Phenotype.

Specified by:

addTrait in interface Phenotype

Parameters:

key -

trait -

Returns:

the key to the new trait (so it can be found in the trait map).

See Also:

Phenotype.addTrait(java.lang.String, com.rubecula.darwin.domain.helper.Trait)

addTrait

public java.lang.String addTrait(Trait trait)

Add a trait using for its key the id of the character to which this trait belongs.

Specified by:

addTrait in interface Phenotype

Parameters:

trait - the trait.

Returns:

the key that this trait is indexed under.

See Also:

Phenotype.addTrait(com.rubecula.darwin.domain.helper.Trait)

doCensus

public void doCensus(Pharacter character,
                     FrequencyMap<Trait> traitFrequencies)

Specified by:

doCensus in interface Phenotype

Parameters:

character -

traitFrequencies -

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class TraitMap_

See Also:

TraitMap_.equals(java.lang.Object)

getExtendedPhenotypes

public java.util.Collection<ExPhen> getExtendedPhenotypes()

Specified by:

getExtendedPhenotypes in interface Phenotype

Returns:

a collection of extended phenotype, ExPhen, objects.

See Also:

Phenotype.getExtendedPhenotypes()

getIdentifier

public java.lang.String getIdentifier()

Specified by:

getIdentifier in interface net.sf.tostring0.Identifiable

Overrides:

getIdentifier in class TraitMap_

Returns:

_id.

See Also:

TraitMap_.getIdentifier()

getSexTraits

public TraitMap getSexTraits()

Specified by:

getSexTraits in interface Phenotype

Returns:

the sex-linked traits as a TraitMap

See Also:

Phenotype.getSexTraits()

hashCode

public int hashCode()

Overrides:

hashCode in class TraitMap_

See Also:

TraitMap_.hashCode()