info.bioinfweb.treegraph.document
Class Tree

java.lang.Object
  info.bioinfweb.treegraph.document.Tree

public class Tree
extends java.lang.Object

Intances of this class provide an enviroment for the rcursive data-structure of tree-elements without their formats.

Author:

Ben Stöver

Field Summary

private GlobalFormats	formats
private Legends	legends
private java.util.EnumMap<PositionPaintType,DistanceDimension>	paintDimensions
private Node	paintStart
private ScaleBar	scaleBar
static java.lang.String	UNIQUE_NAME_CHARS
static int	UNIQUE_NAME_LENGTH

Constructor Summary

Tree()

Method Summary

void	assignUniqueNames() Assigns unique names to all nodes in the tree currently without one.
private void	assignUniqueNamesToSubtree(Node root) Assigns unique names to all nodes in the subtree under root currently without one.
void	clear() Removes all tree elements including all legends from this object.
boolean	contains(ConcretePaintableElement element) Tests if the given element is present in the tree.
boolean	containsDecimal(NodeDataAdapter adapter) Tests if the tree contains a node which would be able to return a decimal value to the given adapter.
static boolean	containsDecimal(NodeDataAdapter adapter, Node root) Tests if the subtree unter root contains a node which would be able to return a decimal value to the given adapter.
GlobalFormats	getFormats()
Legends	getLegends()
static Node	getLinkedNode(PaintableElement element) Returns the linked node to the given element.
static Node	getNodeByUniqueName(Node root, java.lang.String uniqueName) Searches for a node with the given unique name in the subtree under root.
Node	getNodeByUniqueName(java.lang.String uniqueName) Searches for a node with the given unique name in this tree.
DistanceDimension	getPaintDimension(PositionPaintType type) Returnes the stored paint dimension (the size of the document) for the given painter ID.
Node	getPaintStart()
ScaleBar	getScaleBar()
boolean	hasAllBranchLengths() Tests is there are any branches without a defined length in the tree.
static boolean	hasAllBranchLengths(Node root) Tests is there are any branches without a defined length in the subtree under root.
boolean	isEmpty() Tests if there are tree elements present.
private java.lang.String	newUniqueName() Generates a random unique name for a node which is currently not present in this tree.
void	setPaintStart(Node paintStart)
void	setScaleBar(ScaleBar scaleBar)

Methods inherited from class java.lang.Object

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

Field Detail

UNIQUE_NAME_CHARS

public static final java.lang.String UNIQUE_NAME_CHARS

See Also:

Constant Field Values

UNIQUE_NAME_LENGTH

public static final int UNIQUE_NAME_LENGTH

See Also:

Constant Field Values

paintStart

private Node paintStart

scaleBar

private ScaleBar scaleBar

legends

private Legends legends

paintDimensions

private java.util.EnumMap<PositionPaintType,DistanceDimension> paintDimensions

formats

private GlobalFormats formats

Constructor Detail

Tree

public Tree()

Method Detail

getPaintStart

public Node getPaintStart()

setPaintStart

public void setPaintStart(Node paintStart)

getScaleBar

public ScaleBar getScaleBar()

setScaleBar

public void setScaleBar(ScaleBar scaleBar)

getLegends

public Legends getLegends()

getFormats

public GlobalFormats getFormats()

isEmpty

public boolean isEmpty()

Tests if there are tree elements present. Note that it is not testet weather there are legends present even if no tree elements are.

Returns:

true if tree elements (minimal a root node) are present

clear

public void clear()

Removes all tree elements including all legends from this object.

contains

public boolean contains(ConcretePaintableElement element)

Tests if the given element is present in the tree.

Parameters:

element - the element to search for

Returns:

true, if the element is found

getPaintDimension

public DistanceDimension getPaintDimension(PositionPaintType type)

Returnes the stored paint dimension (the size of the document) for the given painter ID. If none is stored an new empty instance of Distancedimension is stored for this ID and returned.

Parameters:

id - - the painter ID

Returns:

the stored paint dimension

newUniqueName

private java.lang.String newUniqueName()

Generates a random unique name for a node which is currently not present in this tree. Currently a unique name is 10 characters long and consits of the following characters: abcdefghijklmnopqrstuvwxyz01234567890. This means that there are 27¹⁰ ≈ 2 • 10¹⁴ different names possible.

Returns:

the new unique name

assignUniqueNamesToSubtree

private void assignUniqueNamesToSubtree(Node root)

Assigns unique names to all nodes in the subtree under root currently without one.
This method is used by info.webinsel.treegraph.document.Tree.assignUniqueNames().

Parameters:

root - - the root node of the subtree

assignUniqueNames

public void assignUniqueNames()

Assigns unique names to all nodes in the tree currently without one.

getNodeByUniqueName

public Node getNodeByUniqueName(java.lang.String uniqueName)

Searches for a node with the given unique name in this tree.

Parameters:

uniqueName - - the searched unique name

Returns:

the node with the unique name or null if no node is found

getNodeByUniqueName

public static Node getNodeByUniqueName(Node root,
                                       java.lang.String uniqueName)

Searches for a node with the given unique name in the subtree under root.

Parameters:

root- - the root of the subtree to be searched

uniqueName - - the searched unique name

Returns:

the node with the unique name or null if no node is found

getLinkedNode

public static Node getLinkedNode(PaintableElement element)

Returns the linked node to the given element. The result differs by the type of PaintableElement as follows:

• Node: The node itsself
• Branch: The target node of this branch
• Label: The target node of the holding branch
• Legend: null

Parameters:

element - - the element which linked node shall be returned

Returns:

the linked node or null

hasAllBranchLengths

public static boolean hasAllBranchLengths(Node root)

Tests is there are any branches without a defined length in the subtree under root.

Returns:

true, if there a no lengths missing

hasAllBranchLengths

public boolean hasAllBranchLengths()

Tests is there are any branches without a defined length in the tree. Calling this method is equivalent to hasAllBranchLengths(getPaintStart())

Returns:

true, if there a no lengths missing

containsDecimal

public static boolean containsDecimal(NodeDataAdapter adapter,
                                      Node root)

Tests if the subtree unter root contains a node which would be able to return a decimal value to the given adapter.

Parameters:

adapter - - the adapter to obtain the decimal value

root - - the root of the subtree to be checked

Returns:

true if at least one decimal value could be returned

containsDecimal

public boolean containsDecimal(NodeDataAdapter adapter)

Tests if the tree contains a node which would be able to return a decimal value to the given adapter.

Parameters:

adapter - - the adapter to obtain the decimal value

Returns:

true if at least one decimal value could be returned