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About

info.bioinfweb.treegraph.document
Class Tree

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

public class Tree
extends Object

Instances of this class provide an environment for the recursive data-structure of tree-elements without their formats.

Author:

Ben Stöver

Field Summary

static float	DEFAULT_LONGEST_PATH_LENGTH The default length of the longest path from the root to a leaf in millimeters.
private HashSet<ConcretePaintableElement>	elementSet
private GlobalFormats	formats
private Legends	legends
private EnumMap<PositionPaintType,DistanceDimension>	paintDimensions
private Node	paintStart
private ScaleBar	scaleBar
static String	UNIQUE_NAME_CHARS
static int	UNIQUE_NAME_LENGTH
private TreeMap<String,Node>	uniqueNameMap

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(NodeBranchDataAdapter adapter) Tests if the tree contains a node which would be able to return a decimal value to the given adapter.
static boolean	containsDecimal(NodeBranchDataAdapter adapter, Node root) Tests if the subtree under 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.
Node	getNodeByUniqueName(String uniqueName) Searches for a node with the given unique name in this tree.
DistanceDimension	getPaintDimension(PositionPaintType type) Returns 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, boolean needsRootLength) Tests is there are any branches without a defined length in the subtree under root.
boolean	isEmpty() Tests if there are tree elements present.
double	longestPath() Returns the longest path to a terminal in this tree.
static double	longestPath(Node root, boolean includeRootBranch) Returns the longest path to a terminal in the subtree of root.
static Node	mostRecentCommonAncestor(Node n1, Node n2)
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)
void	updateElementSet()

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_LONGEST_PATH_LENGTH

public static final float DEFAULT_LONGEST_PATH_LENGTH

The default length of the longest path from the root to a leaf in millimeters. (Used by NewickReader and NexusReader).)

See Also:

Constant Field Values

UNIQUE_NAME_CHARS

public static final 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 EnumMap<PositionPaintType,DistanceDimension> paintDimensions

formats

private GlobalFormats formats

uniqueNameMap

private TreeMap<String,Node> uniqueNameMap

elementSet

private HashSet<ConcretePaintableElement> elementSet

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)

Returns 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

public 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 consists of the following characters: abcdefghijklmnopqrstuvwxyz01234567890. This means that there are 27¹⁰ ≈ 2 • 10¹⁴ different possible names.

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.

updateElementSet

public void updateElementSet()

getNodeByUniqueName

public Node getNodeByUniqueName(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

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 itself
• 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

mostRecentCommonAncestor

public static Node mostRecentCommonAncestor(Node n1,
                                            Node n2)

hasAllBranchLengths

public static boolean hasAllBranchLengths(Node root,
                                          boolean needsRootLength)

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

Parameters:

root - the root node of the tree

needsRootLength - specifies whether the root node needs a defined branch length

Returns:

true, if there a no lengths missing or root was null.

hasAllBranchLengths

public boolean hasAllBranchLengths()

Tests is there are any branches without a defined length in the tree. The root branch only needs to have a length if it is displayed. Calling this method is equivalent to hasAllBranchLengths(getPaintStart(), getFormats().getShowRooted()).

Returns:

true, if there a no necessary lengths missing

longestPath

public static double longestPath(Node root,
                                 boolean includeRootBranch)

Returns the longest path to a terminal in the subtree of root. All branch lengths of the subtree under root must be defined except that of the root branch if includeRootBranch is false.

Parameters:

root - the root node of the tree

includeRootBranch - indicates whether the length of the afferent branch of the root node shall be included

Returns:

the lengths in branch length units or Double.NaN if not all branch lengths are defined

longestPath

public double longestPath()

Returns the longest path to a terminal in this tree. All branch lengths must be defined except that of the root branch if getFormats().getShowRooted() is false. If this tree is empty 0 is returned.

Returns:

the lengths in branch length units or Double.NaN if not all branch lengths are defined

containsDecimal

public static boolean containsDecimal(NodeBranchDataAdapter adapter,
                                      Node root)

Tests if the subtree under 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(NodeBranchDataAdapter 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