Class Clade

java.lang.Object

org.episteme.natural.biology.evolution.Clade

All Implemented Interfaces:

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

public class Clade
extends Object
implements ComprehensiveIdentification

Represents a clade in a phylogenetic tree.

A clade is a group of organisms that consists of a common ancestor and all its lineal descendants. In a phylogenetic tree, it corresponds to a node and the subtree rooted at that node.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
Clade(String name)

Method Summary

Modifier and Type	Method	Description
void	addChild(Clade child)
Double	getBranchLength()
List<Clade>	getChildren()
Identification	getId()	Returns the unique identifier of this entity.
String	getName()
Species	getSpecies()
Map<String,Object>	getTraits()	Returns the traits map for this entity.
boolean	isLeaf()
void	setBranchLength(Double branchLength)
void	setName(String name)	Sets the name of this entity.
void	setSpecies(Species species)
String	toString()

Methods inherited from class Object

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

Methods inherited from interface Commented

getComments, getTrait, setComments

Methods inherited from interface ComprehensiveIdentification

getTrait, setTrait

Constructor Details

Clade

public Clade(String name)

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

getName

public String getName()

Specified by:

getName in interface ComprehensiveIdentification

Specified by:

getName in interface Named

setName

public void setName(String name)

Description copied from interface: ComprehensiveIdentification

Sets the name of this entity.

Specified by:

setName in interface ComprehensiveIdentification

Parameters:

name - the name to set

getBranchLength

public Double getBranchLength()

setBranchLength

public void setBranchLength(Double branchLength)

getSpecies

public Species getSpecies()

setSpecies

public void setSpecies(Species species)

addChild

public void addChild(Clade child)

getChildren

public List<Clade> getChildren()

isLeaf

public boolean isLeaf()

toString

public String toString()

Overrides:

toString in class Object