net.maizegenetics.taxa.tree

Class SimpleTree

net.maizegenetics.taxa.tree.SimpleTree

All Implemented Interfaces:

Tree, Units, UnitsProvider

Direct Known Subclasses:

NeighborJoiningTree, UPGMATree

public class SimpleTree
implements Tree

data structure for a binary/non-binary rooted/unrooted trees

Constructor Detail

SimpleTree

public SimpleTree()

constructor tree consisting solely of root node

SimpleTree

public SimpleTree(Node r)

constructor taking a root node

SimpleTree

public SimpleTree(Tree tree)

clone constructor

SimpleTree

public SimpleTree(Tree tree,
                  boolean keepIdentifiers)

clone constructor

SimpleTree

public SimpleTree(Tree tree,
                  LabelMapping lm)

clone constructor

Parameters:

lm - - a label mapping use for translating the original label names into something else

Method Detail

getUnits

public int getUnits()

Return the units that this tree is expressed in.

Returns:

org.jetbrains.dokka.NodeRenderContent@5e84de1a: the units relating to this object.

setUnits

public void setUnits(int units)

Sets the units that this tree is expressed in.

getExternalNodeCount

public int getExternalNodeCount()

Returns the number of external nodes.

Returns:

org.jetbrains.dokka.NodeRenderContent@7505a154: a count of the number of external nodes (tips) in this tree.

getExternalNode

public Node getExternalNode(int i)

Returns the ith external node.

Returns:

org.jetbrains.dokka.NodeRenderContent@75cd2834: the ith external node in the tree.

getInternalNodeCount

public int getInternalNodeCount()

Returns the number of internal nodes.

Returns:

org.jetbrains.dokka.NodeRenderContent@10408a0b: a count of the number of internal nodes (and hence clades) in this tree.

getInternalNode

public Node getInternalNode(int i)

Returns the ith internal node.

Returns:

org.jetbrains.dokka.NodeRenderContent@68ccf217: the ith internal node in the tree.

getRoot

public Node getRoot()

Returns the root node of this tree.

Returns:

org.jetbrains.dokka.NodeRenderContent@301be15b: the root node of this tree.

setRoot

public void setRoot(Node r)

Set a new node as root node.

createNodeList

public void createNodeList()

count and list external and internal nodes and compute heights of each node

toString

public java.lang.String toString()

findNode

public Node findNode(int num)

return node with number num (as displayed in ASCII tree)

Parameters:

num - number of node

Returns:

org.jetbrains.dokka.NodeRenderContent@2c8be3e4: node

setAttribute

public void setAttribute(Node node,
                         java.lang.String name,
                         java.lang.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.

whichIdNumber

public int whichIdNumber(Taxon t)

getAttribute

public java.lang.Object getAttribute(Node node,
                                     java.lang.String name)

Parameters:

node - the node being interrogated.

name - the name of the attribute of interest.

Returns:

org.jetbrains.dokka.NodeRenderContent@388f24ac: an object representing the named attributed for the numbered node.

reroot

public void reroot(int num)

make node with number num to root node

Parameters:

num - number of node

reroot

public void reroot(Node node)

make provided node the root node

Parameters:

node - the node to make the root.

report

public void report(java.io.Writer out)

getCopy

public Tree getCopy()