Class Taxon

java.lang.Object

org.episteme.natural.biology.Taxon

All Implemented Interfaces:

Serializable, Commented, ComprehensiveIdentification, Identified<Identification>, Named

public class Taxon
extends Object
implements ComprehensiveIdentification

Represents a taxonomic group in a phylogenetic tree. Implements ComprehensiveIdentification to support dynamic traits and consistent identity.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
double	angle
protected final Identification	id
double	radius
protected final Map<String,Object>	traits
double	x
double	y

Constructor Summary

Constructors

Constructor	Description
Taxon(String id, Object parentId, String name, Real coi, Real rna16s, Real cytb)
Taxon(String id, String parentId, String name, Real coi, Real rna16s, Real cytb)

Method Summary

Modifier and Type	Method	Description
void	addChild(Taxon t)
boolean	equals(Object o)
List<Taxon>	getChildren()
Real	getCoi()
Real	getCytb()
Identification	getId()	Returns the unique identifier of this entity.
String	getParentId()
Real	getRna16s()
Map<String,Object>	getTraits()	Returns the traits map for this entity.
int	hashCode()
String	toString()

Methods inherited from class Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface Commented

getComments, getTrait, setComments

Methods inherited from interface ComprehensiveIdentification

getName, getTrait, setName, setTrait

Field Details

id

protected final Identification id

traits

protected final Map<String,Object> traits

x

public transient double x

y

public transient double y

angle

public transient double angle

radius

public transient double radius

Constructor Details

Taxon

public Taxon(String id,
 String parentId,
 String name,
 Real coi,
 Real rna16s,
 Real cytb)

Taxon

public Taxon(String id,
 Object parentId,
 String name,
 Real coi,
 Real rna16s,
 Real cytb)

Method Details

getId

public Identification getId()

Description copied from interface: Identified

Returns the unique identifier of this entity.

Specified by:

getId in interface Identified<Identification>

Returns:

the identifier

getTraits

public Map<String,Object> getTraits()

Description copied from interface: ComprehensiveIdentification

Returns the traits map for this entity.

Specified by:

getTraits in interface Commented

Specified by:

getTraits in interface ComprehensiveIdentification

Returns:

the traits map

addChild

public void addChild(Taxon t)

getChildren

public List<Taxon> getChildren()

getParentId

public String getParentId()

getCoi

public Real getCoi()

getRna16s

public Real getRna16s()

getCytb

public Real getCytb()

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object