net.maizegenetics.taxa.tree

Interface Tree

All Superinterfaces:

Serializable, Units, UnitsProvider

All Known Implementing Classes:

NeighborJoiningTree, SimpleTree, UPGMATree

public interface Tree
extends Serializable, UnitsProvider

Interface for a phylogenetic or genealogical tree.

Author:

Alexei Drummond

Field Summary

Fields inherited from interface net.maizegenetics.taxa.tree.Units

DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS

Method Summary

Modifier and Type	Method and Description
void	createNodeList() This method is called to ensure that the calls to other methods in this interface are valid.
Object	getAttribute(Node node, String name)
Tree	getCopy()
Node	getExternalNode(int i)
int	getExternalNodeCount()
Node	getInternalNode(int i)
int	getInternalNodeCount()
Node	getRoot()
int	getUnits() Gets the units that this tree's branch lengths and node heights are expressed in.
void	setAttribute(Node node, String name, Object value) Sets an named attribute for a given node.
void	setRoot(Node root) This method constructs a tree from the given root node.
int	whichIdNumber(Taxon t)

Method Detail

getRoot

Node getRoot()

Returns:

the root node of this tree.

setRoot

void setRoot(Node root)

This method constructs a tree from the given root node.

Parameters:

root - the root node of the tree to construct.

getExternalNodeCount

int getExternalNodeCount()

Returns:

a count of the number of external nodes (tips) in this tree.

getInternalNodeCount

int getInternalNodeCount()

Returns:

a count of the number of internal nodes (and hence clades) in this tree.

getExternalNode

Node getExternalNode(int i)

Returns:

the ith external node in the tree.

getInternalNode

Node getInternalNode(int i)

Returns:

the ith internal node in the tree.

createNodeList

void createNodeList()

This method is called to ensure that the calls to other methods in this interface are valid.

getUnits

int getUnits()

Gets the units that this tree's branch lengths and node heights are expressed in.

Specified by:

getUnits in interface UnitsProvider

Returns:

the units relating to this object.

whichIdNumber

int whichIdNumber(Taxon t)

setAttribute

void setAttribute(Node node,
                  String name,
                  Object value)

Sets an named attribute for a given node.

Parameters:

node - the node whose attribute is being set.

name - the name of the attribute.

value - the new value of the attribute.

getAttribute

Object getAttribute(Node node,
                    String name)

Parameters:

node - the node being interrogated.

name - the name of the attribute of interest.

Returns:

an object representing the named attributed for the numbered node.

getCopy

Tree getCopy()

Returns:

a clone of this tree