Node (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ini.trakem2.display.Node<T>

All Implemented Interfaces:

Taggable

Direct Known Subclasses:

AreaTree.AreaNode, Treeline.RadiusNode
```
public abstract class Node<T>
extends Object
implements Taggable
```
Can only have one parent, so there aren't cyclic graphs.

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`Node.BranchAndEndNodeIterator<I>`
`static class`	`Node.BranchNodeIterator<I>`
`static class`	`Node.BreadthFirstSubtreeIterator<I>` For a given starting node, iterates over the complete set of children nodes, recursively and breadth-first.
`static class`	`Node.EndNodeIterator<I>`
`static class`	`Node.FilteredIterator<I>`
`static class`	`Node.NodeCollection<I>` Read-only Collection with a very expensive size().
`static class`	`Node.NodeIterator<I>` Stateful abstract Node iterator.
`static interface`	`Node.Operation<I>` An operation to be applied to a specific Node.
`static class`	`Node.SlabIterator<I>` For a given starting node, iterates all the way to the next end node or branch node, inclusive.
`static class`	`Node.SubtreeIterator<I>`

Field Summary

Fields
Modifier and Type	Field and Description
`protected Node<T>[]`	`children`
`protected Color`	`color`
`protected byte`	`confidence` The confidence value of the edge towards the parent; in other words, how much this node can be trusted to continue from its parent node.
`protected Layer`	`la`
`static byte`	`MAX_EDGE_CONFIDENCE` Maximum possible confidence in an edge (ranges from 0 to 5, inclusive).
`protected Node<T>`	`parent`
`protected float`	`x`
`protected float`	`y`

Fields inherited from interface ini.trakem2.display.Taggable
DASHED_STROKE, TAG_BACKGROUND

Constructor Summary

Constructors
Constructor and Description

Node(float x, float y, Layer la)

Node(HashMap<String,String> attr)
To reconstruct from XML, without a layer.

Constructors
Constructor and Description
`Node(float x, float y, Layer la)`
`Node(HashMap<String,String> attr)` To reconstruct from XML, without a layer.

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`add(Node<T> child, byte conf)` Returns -1 when not added (e.g.
`boolean`	`addTag(Tag tag)`
`boolean`	`adjustConfidence(int inc)` Adjust the confidence value of this node with its parent.
`void`	`apply(CoordinateTransform ct, Area roi)`
`protected void`	`apply(Node.Operation<T> op, Iterator<Node<T>> nodes)`
`void`	`apply(VectorDataTransform vlocal)`
`void`	`applyToSlab(Node.Operation<T> op)` Apply @param op to this Node and all its subtree nodes until reaching a branch node or end node, inclusive.
`void`	`applyToSubtree(Node.Operation<T> op)` Apply @param op to this Node and all its subtree nodes.
`Point3f`	`asPoint()`
`Node<T>`	`clone(Project pr)` Returns a recursive copy of this Node subtree, where the copy of this Node is the root.
`HashMap<Node<T>,Integer>`	`computeAllDegrees()` Return a map of node vs degree of that node, for the entire subtree (including this node).
`int`	`computeDegree()` Traverse the tree from this node all the way to the root node, and count how many nodes apart this node is from the root node: that is the degree.
`protected void`	`copyProperties(Node<?> nd)`
`Collection<Displayable>`	`findLinkTargets(AffineTransform to_world)` Returns a list of Patch to link, which lay under the node.
`Node<T>`	`findNextBranchOrEndPoint()` Assumes there aren't any cycles.
`static <I> List<Node<I>>`	`findPath(Node<I> a, Node<I> b)` Obtain the (only) list from node a to node b, including both a (the first element) and b (the last element).
`Node<T>`	`findPreviousBranchOrRootPoint()`
`Area`	`getArea()` Returns area in local coords.
`Collection<Node<T>>`	`getBranchAndEndNodes()` Returns a lazy read-only Collection of all branch and end nodes under this node.
`Collection<Node<T>>`	`getBranchNodes()` Returns a lazy read-only Collection of all branch nodes under this node.
`Map<Node<T>,Byte>`	`getChildren()`
`int`	`getChildrenCount()`
`ArrayList<Node<T>>`	`getChildrenNodes()`
`Color`	`getColor()`
`byte`	`getConfidence()`
`abstract T`	`getData()`
`abstract T`	`getDataCopy()`
`List<Byte>`	`getEdgeConfidence()`
`byte`	`getEdgeConfidence(Node<T> child)`
`Collection<Node<T>>`	`getEndNodes()` Returns a lazy read-only Collection of all end nodes under this node.
`Layer`	`getLayer()`
`Node<T>`	`getParent()`
`Collection<Node<T>>`	`getSlabNodes()` Returns a lazy read-only Collection of the nodes from this node up to the next branch node or end node, inclusive.
`Collection<Node<T>>`	`getSubtreeNodes()` Returns a lazy read-only Collection of the nodes belonging to the subtree of this node, including the node itself as the root.
`Set<Tag>`	`getTags()`
`float`	`getX()`
`float`	`getY()`
`boolean`	`hasChildren()`
`boolean`	`hasSameTags(Node<?> other)`
`boolean`	`hasTag(Tag t)`
`abstract boolean`	`intersects(Area a)` Expects Area in local coords.
`boolean`	`isRoughlyInside(Rectangle localbox)` May return a false positive but never a false negative.
`abstract Node<T>`	`newInstance(float x, float y, Layer layer)`
`abstract void`	`paintData(Graphics2D g, Rectangle srcRect, Tree<T> tree, AffineTransform to_screen, Color cc, Layer active_layer)`
`protected void`	`paintHandle(Graphics2D g, Rectangle srcRect, double magnification, Tree<T> t)`
`protected void`	`paintHandle(Graphics2D g, Rectangle srcRect, double magnification, Tree<T> t, boolean paint_background)` Paint in the context of offscreen space, without transformations.
`boolean`	`remove(Node<T> child)`
`Set<Tag>`	`removeAllTags()`
`boolean`	`removeTag(Tag tag)`
`void`	`setColor(Color c)`
`boolean`	`setConfidence(byte conf)` Set the confidence value of this node with its parent.
`abstract boolean`	`setData(T t)`
`void`	`setLayer(Layer la)`
`void`	`setPosition(float[] p)` Expects two dimensions.
`void`	`setPosition(float x, float y)`
`String`	`toString()`
`protected void`	`transformData(AffineTransform aff)` Apply @param aff to the data, not to the x,y position.
`void`	`translate(float dx, float dy)` Only this node, not any of its children.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail
- MAX_EDGE_CONFIDENCE
```
public static final byte MAX_EDGE_CONFIDENCE
```
  Maximum possible confidence in an edge (ranges from 0 to 5, inclusive).
  
  See Also:
  
  Constant Field Values
- parent
```
protected Node<T> parent
```
- x
```
protected float x
```
- y
```
protected float y
```
- color
```
protected Color color
```
- confidence
```
protected byte confidence
```
  The confidence value of the edge towards the parent; in other words, how much this node can be trusted to continue from its parent node. Defaults to MAX_EDGE_CONFIDENCE for full trust, and 0 for none.
- la
```
protected Layer la
```
- children
```
protected Node<T>[] children
```

Constructor Detail
- Node
```
public Node(float x,
            float y,
            Layer la)
```
  Parameters:
  
  x - The X in local coordinates.
  
  y - The Y in local coordinates.
  
  la - The Layer where the point represented by this Node sits.
- Node
```
public Node(HashMap<String,String> attr)
```
  To reconstruct from XML, without a layer. WARNING this method doesn't do any error checking. If "x" or "y" are not present in @param attr, it will simply fail with a NumberFormatException.

Method Detail

getParent
```
public Node<T> getParent()
```

getX
```
public float getX()
```

getY
```
public float getY()
```

getColor
```
public Color getColor()
```

setColor
```
public void setColor(Color c)
```

setPosition

public void setPosition(float x,
                        float y)

setPosition
```
public void setPosition(float[] p)
```
Expects two dimensions.

getConfidence
```
public byte getConfidence()
```

getLayer
```
public Layer getLayer()
```

getChildrenNodes

public ArrayList<Node<T>> getChildrenNodes()

getChildren
```
public Map<Node<T>,Byte> getChildren()
```
Returns:

a map of child node vs edge confidence to that child.

getEdgeConfidence
```
public List<Byte> getEdgeConfidence()
```

getEdgeConfidence

public byte getEdgeConfidence(Node<T> child)

toString
```
public String toString()
```
Overrides:

toString in class Object

setLayer
```
public void setLayer(Layer la)
```

add

public final int add(Node<T> child,
                     byte conf)

Returns -1 when not added (e.g. if child is null).

remove

public final boolean remove(Node<T> child)

paintHandle

protected void paintHandle(Graphics2D g,
                           Rectangle srcRect,
                           double magnification,
                           Tree<T> t)

paintHandle

protected void paintHandle(Graphics2D g,
                           Rectangle srcRect,
                           double magnification,
                           Tree<T> t,
                           boolean paint_background)

Paint in the context of offscreen space, without transformations.

getSubtreeNodes
```
public final Collection<Node<T>> getSubtreeNodes()
```
Returns a lazy read-only Collection of the nodes belonging to the subtree of this node, including the node itself as the root. Non-recursive, avoids potential stack overflow.

getSlabNodes
```
public final Collection<Node<T>> getSlabNodes()
```
Returns a lazy read-only Collection of the nodes from this node up to the next branch node or end node, inclusive.

getBranchAndEndNodes
```
public final Collection<Node<T>> getBranchAndEndNodes()
```
Returns a lazy read-only Collection of all branch and end nodes under this node.

getBranchNodes
```
public final Collection<Node<T>> getBranchNodes()
```
Returns a lazy read-only Collection of all branch nodes under this node.

getEndNodes
```
public final Collection<Node<T>> getEndNodes()
```
Returns a lazy read-only Collection of all end nodes under this node.

translate

public final void translate(float dx,
                            float dy)

Only this node, not any of its children.

clone
```
public final Node<T> clone(Project pr)
```
Returns a recursive copy of this Node subtree, where the copy of this Node is the root. Non-recursive to avoid stack overflow.

hasChildren
```
public final boolean hasChildren()
```

getChildrenCount
```
public final int getChildrenCount()
```

computeDegree
```
public final int computeDegree()
```
Traverse the tree from this node all the way to the root node, and count how many nodes apart this node is from the root node: that is the degree. Thanks to Johannes Schindelin.

findPath

public static <I> List<Node<I>> findPath(Node<I> a,
                                         Node<I> b)

Obtain the (only) list from node a to node b, including both a (the first element) and b (the last element). Thanks to Johannes Schindelin.

computeAllDegrees
```
public HashMap<Node<T>,Integer> computeAllDegrees()
```
Return a map of node vs degree of that node, for the entire subtree (including this node).

setConfidence
```
public final boolean setConfidence(byte conf)
```
Set the confidence value of this node with its parent.

adjustConfidence
```
public final boolean adjustConfidence(int inc)
```
Adjust the confidence value of this node with its parent.

findPreviousBranchOrRootPoint

public final Node<T> findPreviousBranchOrRootPoint()

findNextBranchOrEndPoint
```
public final Node<T> findNextBranchOrEndPoint()
```
Assumes there aren't any cycles.

setData
```
public abstract boolean setData(T t)
```

getData
```
public abstract T getData()
```

getDataCopy
```
public abstract T getDataCopy()
```

newInstance

public abstract Node<T> newInstance(float x,
                                    float y,
                                    Layer layer)

paintData

public abstract void paintData(Graphics2D g,
                               Rectangle srcRect,
                               Tree<T> tree,
                               AffineTransform to_screen,
                               Color cc,
                               Layer active_layer)

intersects

public abstract boolean intersects(Area a)

Expects Area in local coords.

isRoughlyInside
```
public boolean isRoughlyInside(Rectangle localbox)
```
May return a false positive but never a false negative. Checks only for itself and towards its parent.

getArea
```
public Area getArea()
```
Returns area in local coords.

findLinkTargets
```
public Collection<Displayable> findLinkTargets(AffineTransform to_world)
```
Returns a list of Patch to link, which lay under the node. Use the given @param aff to transform the Node data before looking up targets.

addTag
```
public boolean addTag(Tag tag)
```
Specified by:

addTag in interface Taggable

Returns:

true if the tag wasn't there already.

removeTag
```
public boolean removeTag(Tag tag)
```
Specified by:

removeTag in interface Taggable

Returns:

true if the tag was there.

copyProperties

protected final void copyProperties(Node<?> nd)

hasTag
```
public boolean hasTag(Tag t)
```

getTags
```
public Set<Tag> getTags()
```
Specified by:

getTags in interface Taggable

Returns:

a shallow copy of the tags set, if any, or null.

removeAllTags
```
public Set<Tag> removeAllTags()
```
Specified by:

removeAllTags in interface Taggable

Returns:

the tags, if any, or null.

apply

public void apply(CoordinateTransform ct,
                  Area roi)

apply

public void apply(VectorDataTransform vlocal)

asPoint
```
public Point3f asPoint()
```

transformData
```
protected void transformData(AffineTransform aff)
```
Apply @param aff to the data, not to the x,y position.

apply

protected final void apply(Node.Operation<T> op,
                           Iterator<Node<T>> nodes)
                    throws Exception

Throws:: Exception

applyToSubtree

public void applyToSubtree(Node.Operation<T> op)
                    throws Exception

Apply @param op to this Node and all its subtree nodes.

Throws:: Exception

applyToSlab
```
public void applyToSlab(Node.Operation<T> op)
                 throws Exception
```
Apply @param op to this Node and all its subtree nodes until reaching a branch node or end node, inclusive.

Throws:

Exception

hasSameTags

public boolean hasSameTags(Node<?> other)

Class Node<T>

Nested Class Summary

Field Summary

Fields inherited from interface ini.trakem2.display.Taggable

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MAX_EDGE_CONFIDENCE

parent

x

y

color

confidence

la

children

Constructor Detail

Node

Node

Method Detail

getParent

getX

getY

getColor

setColor

setPosition

setPosition

getConfidence

getLayer

getChildrenNodes

getChildren

getEdgeConfidence

getEdgeConfidence

toString

setLayer

add

remove

paintHandle

paintHandle

getSubtreeNodes

getSlabNodes

getBranchAndEndNodes

getBranchNodes

getEndNodes

translate

clone

hasChildren

getChildrenCount

computeDegree

findPath

computeAllDegrees

setConfidence

adjustConfidence

findPreviousBranchOrRootPoint

findNextBranchOrEndPoint

setData

getData

getDataCopy

newInstance

paintData

intersects

isRoughlyInside

getArea

findLinkTargets

addTag

removeTag

copyProperties

hasTag

getTags

removeAllTags

apply

apply

asPoint

transformData

apply

applyToSubtree

applyToSlab

hasSameTags