Class PhylogeneticTree.Node

java.lang.Object

org.episteme.natural.biology.phylogeny.PhylogeneticTree.Node

Enclosing class:

PhylogeneticTree

public static class PhylogeneticTree.Node
extends Object

Node in a phylogenetic tree with branch length support.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

Field Summary

Fields

Modifier and Type	Field	Description
final Real	branchLength
final Real	height
final PhylogeneticTree.Node	left
final String	name
final PhylogeneticTree.Node	right
final Species	species

Constructor Summary

Constructors

Constructor	Description
Node(String name)	Leaf node constructor from Name
Node(String name, PhylogeneticTree.Node left, PhylogeneticTree.Node right, Real branchLength)	Internal node constructor with branch length
Node(PhylogeneticTree.Node left, PhylogeneticTree.Node right, Real height)	Internal node constructor for UPGMA
Node(Species species)	Leaf node constructor from Species

Method Summary

Modifier and Type	Method	Description
boolean	isLeaf()
String	toNewick()
String	toString()

Methods inherited from class Object

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

Field Details

name

public final String name

species

public final Species species

height

public final Real height

branchLength

public final Real branchLength

left

public final PhylogeneticTree.Node left

right

public final PhylogeneticTree.Node right

Constructor Details

Node

public Node(String name)

Leaf node constructor from Name

Node

public Node(Species species)

Leaf node constructor from Species

Node

public Node(PhylogeneticTree.Node left,
 PhylogeneticTree.Node right,
 Real height)

Internal node constructor for UPGMA

Node

public Node(String name,
 PhylogeneticTree.Node left,
 PhylogeneticTree.Node right,
 Real branchLength)

Internal node constructor with branch length

Method Details

isLeaf

public boolean isLeaf()

toString

public String toString()

Overrides:

toString in class Object

toNewick

public String toNewick()