pal.tree

Class Tree.TreeBase

java.lang.Object

pal.tree.Tree.TreeBase

All Implemented Interfaces:

java.io.Serializable, IdGroup, Report, Units, UnitsProvider, Tree

Enclosing interface:

Tree

public abstract static class Tree.TreeBase
extends java.lang.Object
implements Tree, Report, Units, java.io.Serializable

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.tree.Tree

Tree.TreeBase

Nested classes/interfaces inherited from interface pal.misc.IdGroup

IdGroup.Utils

Field Summary

Fields inherited from interface pal.misc.Units

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

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	Tree.TreeBase() constructor
protected	Tree.TreeBase(Node theRoot) constructor
protected	Tree.TreeBase(Tree.TreeBase tree, Node newRoot) clone constructor

Method Summary

Methods

Modifier and Type	Method and Description
void	createNodeList() count and list external and internal nodes and compute heights of each node
Node	findNode(int num) return node with number num (as displayed in ASCII tree)
java.lang.Object	getAttribute(Node node, java.lang.String name)
Node	getExternalNode(int i) Returns the ith external node.
int	getExternalNodeCount() Returns the number of external nodes.
int	getIdCount() Returns the number of identifiers in this group
Identifier	getIdentifier(int i) Returns the ith identifier.
Node	getInternalNode(int i) Returns the ith internal node.
int	getInternalNodeCount() Returns the number of internal nodes.
Node	getRoot() Returns the root node of this tree.
int	getUnits() Return the units that this tree is expressed in.
void	report(java.io.PrintWriter out) print human readable report (e.g., on parameters and associated model)
void	reroot(int num) make node with number num to root node
void	reroot(Node node) make provided node the root node
void	setAttribute(Node node, java.lang.String name, java.lang.Object value) Sets an named attribute for a given node.
void	setIdentifier(int i, Identifier id) Sets the ith identifier.
void	setRoot(Node theRoot) Called by subclasses that can't give root at time of construction (of this class)
protected void	setSetupLengthsAndHeights(boolean value) Set whether or not this class should call methods to adjust either heights or lengths automatically
void	setUnits(int units) Sets the units that this tree is expressed in.
java.lang.String	toString()
int	whichIdNumber(java.lang.String s) returns the index of the identifier with the given name.

Methods inherited from class java.lang.Object

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

Methods inherited from interface pal.tree.Tree

getCopy

Constructor Detail

Tree.TreeBase

protected Tree.TreeBase(Node theRoot)

constructor

Parameters:

theRoot - the node to base tree on

Tree.TreeBase

protected Tree.TreeBase()

constructor

Tree.TreeBase

protected Tree.TreeBase(Tree.TreeBase tree,
             Node newRoot)

clone constructor

Method Detail

setRoot

public void setRoot(Node theRoot)

Called by subclasses that can't give root at time of construction (of this class)

Specified by:

setRoot in interface Tree

Parameters:

theRoot - the root node of the tree to construct.

getUnits

public final int getUnits()

Return the units that this tree is expressed in.

Specified by:

getUnits in interface UnitsProvider

Specified by:

getUnits in interface Tree

Returns:

the units relating to this object.

setUnits

public final void setUnits(int units)

Sets the units that this tree is expressed in.

getExternalNodeCount

public final int getExternalNodeCount()

Returns the number of external nodes.

Specified by:

getExternalNodeCount in interface Tree

Returns:

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

getExternalNode

public final Node getExternalNode(int i)

Returns the ith external node.

Specified by:

getExternalNode in interface Tree

Returns:

the ith external node in the tree.

getInternalNodeCount

public final int getInternalNodeCount()

Returns the number of internal nodes.

Specified by:

getInternalNodeCount in interface Tree

Returns:

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

getInternalNode

public final Node getInternalNode(int i)

Returns the ith internal node.

Specified by:

getInternalNode in interface Tree

Returns:

the ith internal node in the tree.

getRoot

public final Node getRoot()

Returns the root node of this tree.

Specified by:

getRoot in interface Tree

Returns:

the root node of this tree.

findNode

public Node findNode(int num)

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

Parameters:

num - number of node

Returns:

node

createNodeList

public void createNodeList()

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

Specified by:

createNodeList in interface Tree

setSetupLengthsAndHeights

protected void setSetupLengthsAndHeights(boolean value)

Set whether or not this class should call methods to adjust either heights or lengths automatically

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

setAttribute

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

Sets an named attribute for a given node.

Specified by:

setAttribute in interface Tree

Parameters:

node - the node whose attribute is being set.

name - the name of the attribute.

value - the new value of the attribute.

getAttribute

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

Specified by:

getAttribute in interface Tree

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.

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.

getIdCount

public int getIdCount()

Description copied from interface: IdGroup

Returns the number of identifiers in this group

Specified by:

getIdCount in interface IdGroup

getIdentifier

public Identifier getIdentifier(int i)

Description copied from interface: IdGroup

Returns the ith identifier.

Specified by:

getIdentifier in interface IdGroup

setIdentifier

public void setIdentifier(int i,
                 Identifier id)

Description copied from interface: IdGroup

Sets the ith identifier.

Specified by:

setIdentifier in interface IdGroup

whichIdNumber

public int whichIdNumber(java.lang.String s)

Description copied from interface: IdGroup

returns the index of the identifier with the given name.

Specified by:

whichIdNumber in interface IdGroup

report

public void report(java.io.PrintWriter out)

Description copied from interface: Report

print human readable report (e.g., on parameters and associated model)

Specified by:

report in interface Report

Parameters:

out - output stream