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About

info.bioinfweb.treegraph.document
Class Node

java.lang.Object
  info.bioinfweb.treegraph.document.ConcretePaintableElement
      info.bioinfweb.treegraph.document.AbstractTextElement
          info.bioinfweb.treegraph.document.Node

All Implemented Interfaces:

CornerRadiusElement, HiddenDataElement, LineElement, PaintableElement, TextElement, TreeElement, Cloneable

public class Node
extends AbstractTextElement
implements LineElement, CornerRadiusElement, HiddenDataElement, TreeElement, Cloneable

This class represents a node of a tree in the TreeGraph data structure.

Author:

Ben Stöver

Field Summary

private Branch	afferentBranch
private HashMap<String,Object>	attributeMap
private ArrayList<Node>	children
private NodeFormats	formats
private HiddenDataMap	hiddenDataMap
private Node	parent
private String	uniqueName

Fields inherited from class info.bioinfweb.treegraph.document.ConcretePaintableElement

positions

Constructor Summary

Node()

Method Summary

Node	clone() Returns a deep copy of this node not including the subtrees.
Node	clone(boolean keepUniqheNames) Returns a deep copy of this node not including the subtrees.
Node	cloneWithSubtree(boolean keepUniqueNames) Clones this object and all objects in this subtree and its afferent branch.
boolean	containedInSubtree(ConcretePaintableElement element) Tests whether an element is contained in the subtree under this node.
Branch	getAfferentBranch()
HashMap<String,Object>	getAttributeMap() The attribute map can store data that is specific to special tasks like ladderizing or tree merging.
List<Node>	getChildren()
NodeFormats	getFormats()
HiddenDataMap	getHiddenDataMap()
Node	getHighestChild() Returns the upper most subnode of this node (e.g. needed for legend positioning).
static Node	getInstanceWithBranch()
Node	getLinkedNode()
Node	getLowestChild() Returns the lowest subnode of this node (e.g. needed for legend positioning).
Node	getNext()
Node	getNextLeaf()
Node	getParent()
NodePositionData	getPosition(PositionPaintType type) Returns the stored DataPosition-object of an for an positioner- identifier.
Node	getPrevious()
Node	getPreviousLeaf()
String	getUniqueName() The unique name is used to identify nodes in the XML-file which are associated with legends.
boolean	hasAfferentBranch()
boolean	hasParent()
boolean	hasUniqueName() Test if this node has a unique name specified
boolean	isChildOf(Node ancestor) Tests if the specified node is an ancestor of this node.
boolean	isFirst()
boolean	isLast()
boolean	isLeaf() Tests if this Node is at the deepest level of the tree (has no subnodes).
boolean	isOnlySubelement() Tests if this element is the only Node under the parent node.
Vector<String>	leafNames()
private void	searchLeafNames(Node root, Vector<String> names)
void	setAfferentBranch(Branch afferentBranch) Sets the specified branch as the afferent branch of this node and additionally sets this node as the target node of the specified branch.
void	setFormats(ElementFormats formats)
void	setParent(Node node)
void	setUniqueName(String uniqueName) The unique name is used to identify nodes in the XML-file which are associated with legends.

Methods inherited from class info.bioinfweb.treegraph.document.AbstractTextElement

assignTextElementData, getData, toString

Methods inherited from class java.lang.Object

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

Field Detail

parent

private Node parent

children

private ArrayList<Node> children

afferentBranch

private Branch afferentBranch

formats

private NodeFormats formats

uniqueName

private String uniqueName

hiddenDataMap

private HiddenDataMap hiddenDataMap

attributeMap

private HashMap<String,Object> attributeMap

Constructor Detail

Node

public Node()

Method Detail

getInstanceWithBranch

public static Node getInstanceWithBranch()

getPosition

public NodePositionData getPosition(PositionPaintType type)

Description copied from interface: PaintableElement

Returns the stored DataPosition-object of an for an positioner- identifier. If no position-object has been stored for this identifier, one will be created.

Specified by:

getPosition in interface PaintableElement

Overrides:

getPosition in class ConcretePaintableElement

Returns:

the stored position

getParent

public Node getParent()

setParent

public void setParent(Node node)

getChildren

public List<Node> getChildren()

getAfferentBranch

public Branch getAfferentBranch()

setAfferentBranch

public void setAfferentBranch(Branch afferentBranch)

Sets the specified branch as the afferent branch of this node and additionally sets this node as the target node of the specified branch.

Parameters:

afferentBranch - the new afferent branch

getAttributeMap

public HashMap<String,Object> getAttributeMap()

The attribute map can store data that is specific to special tasks like ladderizing or tree merging. Several special routines can store custom objects under their own key here.

Returns:

the attribute map

isLeaf

public boolean isLeaf()

Tests if this Node is at the deepest level of the tree (has no subnodes).

Returns:

true if there are no subnodes or branches.

hasParent

public boolean hasParent()

hasAfferentBranch

public boolean hasAfferentBranch()

isOnlySubelement

public boolean isOnlySubelement()

Tests if this element is the only Node under the parent node.

Returns:

true, if the given element is the only element in the parent node

isFirst

public boolean isFirst()

Returns:

true, if this element is the fist

isLast

public boolean isLast()

Returns:

true, if this element is the last in its parent node

getPrevious

public Node getPrevious()

getNext

public Node getNext()

getPreviousLeaf

public Node getPreviousLeaf()

getNextLeaf

public Node getNextLeaf()

isChildOf

public boolean isChildOf(Node ancestor)

Tests if the specified node is an ancestor of this node. (The result of n.isAncestor(n) is false.)

Parameters:

ancestor -

Returns:

containedInSubtree

public boolean containedInSubtree(ConcretePaintableElement element)

Tests whether an element is contained in the subtree under this node. This also includes legends which are completely anchored inside this subtree.

Parameters:

element - the element to search for (either a Node, Branch, Label or Legend)

Returns:

true, if the element is found

See Also:

TreeSerializer

getFormats

public NodeFormats getFormats()

Specified by:

getFormats in interface CornerRadiusElement

Specified by:

getFormats in interface LineElement

Specified by:

getFormats in interface PaintableElement

Specified by:

getFormats in interface TextElement

Specified by:

getFormats in class AbstractTextElement

setFormats

public void setFormats(ElementFormats formats)

Specified by:

setFormats in interface PaintableElement

getUniqueName

public String getUniqueName()

The unique name is used to identify nodes in the XML-file which are associated with legends.

Returns:

the unique name or null if none is assigned

setUniqueName

public void setUniqueName(String uniqueName)

The unique name is used to identify nodes in the XML-file which are associated with legends.

Parameters:

uniqueName - the new unique name or null if it shall be deleted

hasUniqueName

public boolean hasUniqueName()

Test if this node has a unique name specified

Returns:

true if a unique name has been specified, false if the unique name is null

getHiddenDataMap

public HiddenDataMap getHiddenDataMap()

Specified by:

getHiddenDataMap in interface HiddenDataElement

getHighestChild

public Node getHighestChild()

Returns the upper most subnode of this node (e.g. needed for legend positioning).

Returns:

the upper most subnode

getLowestChild

public Node getLowestChild()

Returns the lowest subnode of this node (e.g. needed for legend positioning).

Returns:

the lowest subnode

searchLeafNames

private void searchLeafNames(Node root,
                             Vector<String> names)

leafNames

public Vector<String> leafNames()

getLinkedNode

public Node getLinkedNode()

Specified by:

getLinkedNode in interface TreeElement

clone

public Node clone()

Returns a deep copy of this node not including the subtrees. The attribute map and the unique names are not copied. Calling this method is equivalent to clone(false).

Specified by:

clone in interface TextElement

Specified by:

clone in class AbstractTextElement

clone

public Node clone(boolean keepUniqheNames)

Returns a deep copy of this node not including the subtrees. The attribute map is not copied.

Parameters:

keepUniqheNames - defines whether the copy should have the same unique name as the original.

Returns:

the copy

cloneWithSubtree

public Node cloneWithSubtree(boolean keepUniqueNames)

Clones this object and all objects in this subtree and its afferent branch. The parent node will be set to null.

Parameters:

keepUniqueNames - defines wheather the copied nodes should have the same unique names as the originals.

Returns:

the root of the cloned tree