Uses of Class
org.episteme.natural.biology.phylogeny.PhylogeneticTree.Node

Packages that use PhylogeneticTree.Node

Package	Description
org.episteme.natural.biology.phylogeny	Biological modeling, genetics, and life science simulations.

Uses of PhylogeneticTree.Node in org.episteme.natural.biology.phylogeny

Fields in org.episteme.natural.biology.phylogeny declared as PhylogeneticTree.Node

Modifier and Type	Field	Description
final PhylogeneticTree.Node	PhylogeneticTree.Node.left
final PhylogeneticTree.Node	PhylogeneticTree.Node.right

Methods in org.episteme.natural.biology.phylogeny that return PhylogeneticTree.Node

Modifier and Type	Method	Description
static PhylogeneticTree.Node	PhylogeneticTree.buildNeighborJoining(Real[][] distanceMatrix, List<Species> speciesList)
static PhylogeneticTree.Node	PhylogeneticTree.buildNeighborJoiningFromLabels(Real[][] distanceMatrix, List<String> labels)	Builds a phylogenetic tree using Neighbor-Joining algorithm (String labels).
static PhylogeneticTree.Node	PhylogeneticTree.buildUPGMA(Real[][] distanceMatrix, List<Species> speciesList)
static PhylogeneticTree.Node	PhylogeneticTree.buildUPGMAFromLabels(Real[][] distanceMatrix, List<String> labels)	Builds a phylogenetic tree using UPGMA algorithm (String labels).
static PhylogeneticTree.Node	PhylogeneticTree.parseNewick(String newick)	Parses a Newick format string into a phylogenetic tree.

Methods in org.episteme.natural.biology.phylogeny that return types with arguments of type PhylogeneticTree.Node

Modifier and Type	Method	Description
static Tree<PhylogeneticTree.Node>	PhylogeneticTree.asTree(PhylogeneticTree.Node root)	Converts a phylogenetic tree to a Tree interface for graph operations.

Methods in org.episteme.natural.biology.phylogeny with parameters of type PhylogeneticTree.Node

Modifier and Type	Method	Description
static Tree<PhylogeneticTree.Node>	PhylogeneticTree.asTree(PhylogeneticTree.Node root)	Converts a phylogenetic tree to a Tree interface for graph operations.
static int	PhylogeneticTree.countLeaves(PhylogeneticTree.Node node)	Counts the number of leaves in the tree.
static List<String>	PhylogeneticTree.getLeafNames(PhylogeneticTree.Node node)	Gets all leaf names from the tree.

Constructors in org.episteme.natural.biology.phylogeny with parameters of type PhylogeneticTree.Node

Modifier	Constructor	Description
	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