Class PhylogeneticTree

java.lang.Object

org.episteme.natural.biology.evolution.PhylogeneticTree

All Implemented Interfaces:

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

public class PhylogeneticTree
extends Object
implements ComprehensiveIdentification

Represents a phylogenetic tree.

This class serves as the container for the root of a phylogenetic tree and provides access to tree-level metadata and construction algorithms.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
PhylogeneticTree(String name)

Method Summary

Modifier and Type	Method	Description
static Clade	buildUPGMA(Real[][] distanceMatrix, List<Species> speciesList)
Identification	getId()	Returns the unique identifier of this entity.
String	getName()
Clade	getRoot()
Map<String,Object>	getTraits()	Returns the traits map for this entity.
void	setName(String name)	Sets the name of this entity.
void	setRoot(Clade root)
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

PhylogeneticTree

public PhylogeneticTree(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

getRoot

public Clade getRoot()

setRoot

public void setRoot(Clade root)

buildUPGMA

public static Clade buildUPGMA(Real[][] distanceMatrix,
 List<Species> speciesList)

toString

public String toString()

Overrides:

toString in class Object