com.rubecula.darwin.domain.environment
Class Pharacter_

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

All Implemented Interfaces:

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

Direct Known Subclasses:

Pharacter_Fisherian, Pharacter_Sex

public abstract class Pharacter_
extends net.sf.tostring0.AToString
implements Pharacter

Base implementation of Pharacter (a Phenotypic Character). This class is the environmental analog to Locus_.

Author:

Robin Hillyard

Field Summary

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

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

Pharacter_(java.lang.String identifier, boolean sexLinked) Protected abstract constructor.

Method Summary

java.lang.String	addVariant(Variant variant) Add the variant to this Pharacter, set its character to be this; then return its key.
boolean	equals(java.lang.Object obj)
java.lang.String	getIdentifier() Get the identifier for this phenotypic character, for example "Eye Color".
java.lang.String	getKey(Variant variant) if _variants contains an element whose key is the variant's id, then return the key else null.
Variant	getVariant(java.lang.String key) Method to get the specific variant referred to by the key.
java.util.Set<java.lang.String>	getVariantKeys()
java.util.Collection<Variant>	getVariants()
int	hashCode()
boolean	isSexLinked()
void	setVariants(java.util.Collection<? extends Variant> variants) Clear the list of variants and add in all those from the given list.

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

Constructor Detail

Pharacter_

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

Protected abstract constructor.

Parameters:

identifier - the identifier for this character

sexLinked - XXX

Method Detail

addVariant

public java.lang.String addVariant(Variant variant)

Add the variant to this Pharacter, set its character to be this; then return its key.

Specified by:

addVariant in interface Pharacter

Parameters:

variant - A value which this character can take.

Returns:

the variant's key.

See Also:

com.rubecula.darwin.domain.helper.Pharacter#addVariant(com.rubecula .darwin.domain.helper.Variant)

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

See Also:

Object.equals(java.lang.Object)

getIdentifier

public java.lang.String getIdentifier()

Get the identifier for this phenotypic character, for example "Eye Color".

Specified by:

getIdentifier in interface net.sf.tostring0.Identifiable

See Also:

Identifiable.getIdentifier()

getKey

public java.lang.String getKey(Variant variant)

if _variants contains an element whose key is the variant's id, then return the key else null.

Specified by:

getKey in interface Pharacter

Returns:

the key of the trait for this Pharacter, otherwise null

See Also:

Pharacter.getKey(com.rubecula.darwin.domain.helper.Variant)

getVariant

public Variant getVariant(java.lang.String key)

Method to get the specific variant referred to by the key.

Specified by:

getVariant in interface Pharacter

Parameters:

key - a string which identifies the variant from among those which are legal for this character. If the key is null, then we return null as the result. This is the case when a trait is variable and there is no registered variants.

Returns:

the trait for this character indicated by key.

See Also:

Pharacter.getVariant(java.lang.String)

getVariantKeys

public java.util.Set<java.lang.String> getVariantKeys()

Specified by:

getVariantKeys in interface Pharacter

Returns:

the set of keys of the variants.

See Also:

Pharacter.getVariantKeys()

getVariants

public java.util.Collection<Variant> getVariants()

Specified by:

getVariants in interface Pharacter

Returns:

the entire list of traits for this character. Getter/setter typically used by reflection.

See Also:

Pharacter.getVariants()

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:

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()

setVariants

public void setVariants(java.util.Collection<? extends Variant> variants)

Clear the list of variants and add in all those from the given list. For each of the variants, set its character to this.

Parameters:

variants - a collection of variants which will make up the variants for this phenotypic character.