Treeline (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ini.trakem2.persistence.DBObject
- - ini.trakem2.display.Displayable
  - - ini.trakem2.display.ZDisplayable
    - - ini.trakem2.display.Tree<Float>
      - ini.trakem2.display.Treeline

All Implemented Interfaces:

Paintable, VectorData

Direct Known Subclasses:

Connector
```
public class Treeline
extends Tree<Float>
```

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Treeline.RadiusNode
- Nested classes/interfaces inherited from class ini.trakem2.display.Tree
  Tree.MeasurementPair, Tree.MeasurePathDistance<I>, Tree.MeshData, Tree.NodePath, Tree.Pair
- Nested classes/interfaces inherited from class ini.trakem2.display.Displayable
  Displayable.DataPackage, Displayable.DoEdit, Displayable.DoEdits, Displayable.DoTransforms, Displayable.SliderListener

Nested Classes
Modifier and Type	Class and Description
`static class`	`Treeline.RadiusNode`

Field Summary

Fields
Modifier and Type Field and Description

protected static float last_radius
- Fields inherited from class ini.trakem2.display.Tree
  end_nodes, node_layer_map, root
- Fields inherited from class ini.trakem2.display.ZDisplayable
  layer_set
- Fields inherited from class ini.trakem2.display.Displayable
  alpha, annotation, at, color, COMPOSITE_ADD, COMPOSITE_COLOR_YCBCR, COMPOSITE_DIFFERENCE, COMPOSITE_MULTIPLY, COMPOSITE_NORMAL, COMPOSITE_SUBTRACT, compositeModes, height, hs_linked, last_color, layer, linked_props, linked_props_origins, locked, props, TAG_ATTR1, TAG_ATTR2, title, visible, width
- Fields inherited from class ini.trakem2.persistence.DBObject
  id, project

Fields
Modifier and Type	Field and Description
`protected static float`	`last_radius`

Constructor Summary

Constructors
Constructor and Description
`Treeline(Project project, long id, HashMap<String,String> ht_attr, HashMap<Displayable,String> ht_links)` Reconstruct from XML.
`Treeline(Project project, long id, String title, float width, float height, float alpha, boolean visible, Color color, boolean locked, AffineTransform at)` For cloning purposes, does not call addToDatabase()
`Treeline(Project project, String title)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected Node<Float>`	`adjustNodeRadius(float inc, float x, float y, Layer layer, DisplayCanvas dc)`
`protected boolean`	`askAdjustRadius(Node<Float> nd)`
`Treeline`	`clone(Project pr, boolean copy_id)` Performs a deep copy of this object, obtaining its unique id either from the given project or the exact same as this object's id.
`protected Tree.MeasurementPair`	`createMeasurementPair(Tree.NodePath np)`
`static void`	`exportDTD(StringBuilder sb_header, HashSet<String> hs, String indent)`
`protected boolean`	`exportXMLNodeAttributes(StringBuilder indent, StringBuilder sb, Node<Float> node)` Export the radius only if it is larger than zero.
`protected boolean`	`exportXMLNodeData(StringBuilder indent, StringBuilder sb, Node<Float> node)`
`Tree.MeshData`	`generateMesh(double scale_, int parallels)` Returns a list of two lists: the `List<Point3f>` and the corresponding `List<Color3f>`.
`protected Rectangle`	`getBounds(Collection<? extends Node<Float>> nodes)`
`void`	`keyPressed(KeyEvent ke)`
`void`	`mouseDragged(MouseEvent me, Layer la, int x_p, int y_p, int x_d, int y_d, int x_d_old, int y_d_old)`
`void`	`mousePressed(MouseEvent me, Layer la, int x_p, int y_p, double mag)`
`void`	`mouseReleased(MouseEvent me, Layer la, int x_p, int y_p, int x_d, int y_d, int x_r, int y_r)`
`void`	`mouseWheelMoved(MouseWheelEvent mwe)` Does nothing unless overriden.
`Tree<Float>`	`newInstance()` Create a new instance, intialized with same ZDisplayable-level parameters (affine, color, title, etc.).
`Node<Float>`	`newNode(float lx, float ly, Layer la, Node<?> modelNode)`
`Node<Float>`	`newNode(HashMap<String,String> ht_attr)` To reconstruct from XML.
`protected boolean`	`requireAltDownToEditRadius()`

Methods inherited from class ini.trakem2.display.Tree
addNode, addToLinkLater, adjustEdgeConfidence, adjustNodeColors, apply, apply, asPoint, asVertices, cacheSubtree, calculateBoundingBox, canJoin, clearCache, clearState, colorizeByBranchBetweennessCentrality, colorizeByNodeBetweennessCentrality, computeAllDegrees, computeCentrality, contains, copyAs, createCoordinate, createMultiTableView, createNewNode, createReviewStack, crop, deselect, destroy, dropAllTags, duplicateAs, exportXML, findClosestNode, findClosestNodeW, findClosestNodeW, findConnectors, findFirstIntersectingNode, findIntersecting, findNearAndGetNext, findNearAndGetPrevious, findNearestEdge, findNearestEndNode, findNearestNode, findNextBranchOrEndPoint, findNode, findNodeNear, findNodeNear, findPreviousBranchOrRootPoint, findTaggedPairs, findTags, fireNodeRemoved, firstIntersectingNode, fix, flyThrough, flyThroughMarked, generateAllReviewStacks, generateRegions, generateReviewStackForSlab, generateReviewStackForSlab, generateSkeleton, generateSubtreeReviewStacks, generateSubtreeReviewStacks, generateTriangles, getActive, getAreaAt, getBounds, getBranchAndEndNodes, getBranchNodes, getEndNodes, getFirstLayer, getLastAdded, getLastEdited, getLastVisited, getLayerIds, getLayersWithData, getMarked, getNodesAt, getNodesToPaint, getNodesToPaint, getOriginPoint, getPaintingBounds, getRoot, getShortTitle, insertNode, intersects, intersects, intersects, isAnyNear, isDeletable, isRoughlyInside, isTagging, join, layerRemoved, linkPatches, markNear, measure, measurePathDistance, measurePathDistance, measureTaggedPairs, paint, paint, paintsAt, paintSnapshot, popNode, remove2, removeFromLinkLater, removeNode, removeReviews, repaint, reRoot, reRoot, setActive, setEdgeConfidence, setLastAdded, setLastEdited, setLastMarked, setLastVisited, setRoot, splitAt, splitNear, toClosestPaintedNode, unmark, updateCache, updateView, updateViewData

Methods inherited from class ini.trakem2.display.ZDisplayable
exportDTD, getBucketable, getLayerSet, remove, setColor, setLayer, setLayerSet, setLayerSet, setVisible, softRemove, transformPoints, updateBucket, updateBucket

Methods inherited from class ini.trakem2.display.Displayable
adjustProperties, areThereLayerCrossLinks, canSendTo, clone, clone, commonDTDChildren, contains, displacePoints, exportSVG, findById, findNearestPoint, findNearestPoint, getAffineTransform, getAffineTransformCopy, getAlpha, getAnnotation, getArea, getAreaForBucket, getBoundingBox, getBoundingBox, getBoundingBox, getBounds, getColor, getComposite, getComposite, getCompositeMode, getHeight, getIntersection, getLayer, getLinked, getLinked, getLinkedBox, getLinkedGroup, getLinkedProperties, getLinkedProperties, getLinkedProperty, getLinkedProperty, getMinimalBoundingBox, getNameId, getPerimeter, getPerimeter, getProperties, getProperty, getProperty, getTitle, getWidth, getX, getXMLSafeValue, getXMLSafeValue, getY, hasLinkedGroupWithinLayer, hasProperties, intersects, intersects, inverseTransformPoint, isLinked, isLinked, isLinked, isLocked, isLocked2, isOnlyLinkedTo, isOnlyLinkedTo, isOutOfRepaintingClip, isOutOfRepaintingClip, isVisible, link, link, makeAdjustPropertiesDialog, paintAsBox, paintOffscreen, preConcatenate, prePaint, preTransform, processAdjustPropertiesDialog, removeLinkedProperties, removeLinkedPropertiesFromOrigins, repaint, restXML, rotate, rotate, rotatePoints, scale, scale, scalePoints, setAffineTransform, setAlpha, setAlpha, setAnnotation, setCompositeMode, setDimensions, setDimensions, setLayer, setLinkedProperties, setLinkedProperty, setLocation, setLocked, setProperty, setTitle, setVisible, snapTo, toString, transform, transformPoint, transformPoint, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformRectangle, translate, translate, unlink, unlink, unlinkAll, updateInDatabase, xmlError, xmlError

Methods inherited from class ini.trakem2.persistence.DBObject
addToDatabase, getId, getInfo, getProject, getUniqueIdentifier, removeFromDatabase, updateInDatabase

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

Field Detail
- last_radius
```
protected static float last_radius
```

Constructor Detail

Treeline

public Treeline(Project project,
                String title)

Treeline

public Treeline(Project project,
                long id,
                HashMap<String,String> ht_attr,
                HashMap<Displayable,String> ht_links)

Reconstruct from XML.

Treeline

public Treeline(Project project,
                long id,
                String title,
                float width,
                float height,
                float alpha,
                boolean visible,
                Color color,
                boolean locked,
                AffineTransform at)

For cloning purposes, does not call addToDatabase()

Method Detail

newInstance
```
public Tree<Float> newInstance()
```
Description copied from class: Tree

Create a new instance, intialized with same ZDisplayable-level parameters (affine, color, title, etc.).

Specified by:

newInstance in class Tree<Float>

newNode

public Node<Float> newNode(float lx,
                           float ly,
                           Layer la,
                           Node<?> modelNode)

Specified by:: newNode in class Tree<Float>

newNode
```
public Node<Float> newNode(HashMap<String,String> ht_attr)
```
Description copied from class: Tree

To reconstruct from XML.

Specified by:

newNode in class Tree<Float>

clone
```
public Treeline clone(Project pr,
                      boolean copy_id)
```
Description copied from class: Displayable

Performs a deep copy of this object, obtaining its unique id either from the given project or the exact same as this object's id. The visibility, though, is set to true at all times.

Specified by:

clone in class Displayable

mousePressed

public void mousePressed(MouseEvent me,
                         Layer la,
                         int x_p,
                         int y_p,
                         double mag)

Overrides:: mousePressed in class Tree<Float>

requireAltDownToEditRadius

protected boolean requireAltDownToEditRadius()

mouseDragged

public void mouseDragged(MouseEvent me,
                         Layer la,
                         int x_p,
                         int y_p,
                         int x_d,
                         int y_d,
                         int x_d_old,
                         int y_d_old)

Overrides:: mouseDragged in class Tree<Float>

mouseReleased

public void mouseReleased(MouseEvent me,
                          Layer la,
                          int x_p,
                          int y_p,
                          int x_d,
                          int y_d,
                          int x_r,
                          int y_r)

Overrides:: mouseReleased in class Tree<Float>

mouseWheelMoved
```
public void mouseWheelMoved(MouseWheelEvent mwe)
```
Description copied from class: Displayable

Does nothing unless overriden.

Overrides:

mouseWheelMoved in class Tree<Float>

adjustNodeRadius

protected Node<Float> adjustNodeRadius(float inc,
                                       float x,
                                       float y,
                                       Layer layer,
                                       DisplayCanvas dc)

exportDTD

public static void exportDTD(StringBuilder sb_header,
                             HashSet<String> hs,
                             String indent)

exportXMLNodeAttributes

protected boolean exportXMLNodeAttributes(StringBuilder indent,
                                          StringBuilder sb,
                                          Node<Float> node)

Export the radius only if it is larger than zero.

Specified by:: exportXMLNodeAttributes in class Tree<Float>

exportXMLNodeData

protected boolean exportXMLNodeData(StringBuilder indent,
                                    StringBuilder sb,
                                    Node<Float> node)

Specified by:: exportXMLNodeData in class Tree<Float>

generateMesh

public Tree.MeshData generateMesh(double scale_,
                                  int parallels)

Returns a list of two lists: the List<Point3f> and the corresponding List<Color3f>.

keyPressed
```
public void keyPressed(KeyEvent ke)
```
Overrides:

keyPressed in class Tree<Float>

askAdjustRadius

protected boolean askAdjustRadius(Node<Float> nd)

getBounds

protected Rectangle getBounds(Collection<? extends Node<Float>> nodes)

Overrides:: getBounds in class Tree<Float>

createMeasurementPair

protected Tree.MeasurementPair createMeasurementPair(Tree.NodePath np)

Specified by:: createMeasurementPair in class Tree<Float>

Class Treeline

Nested Class Summary

Nested classes/interfaces inherited from class ini.trakem2.display.Tree

Nested classes/interfaces inherited from class ini.trakem2.display.Displayable

Field Summary

Fields inherited from class ini.trakem2.display.Tree

Fields inherited from class ini.trakem2.display.ZDisplayable

Fields inherited from class ini.trakem2.display.Displayable

Fields inherited from class ini.trakem2.persistence.DBObject

Constructor Summary

Method Summary

Methods inherited from class ini.trakem2.display.Tree

Methods inherited from class ini.trakem2.display.ZDisplayable

Methods inherited from class ini.trakem2.display.Displayable

Methods inherited from class ini.trakem2.persistence.DBObject

Methods inherited from class java.lang.Object

Field Detail

last_radius

Constructor Detail

Treeline

Treeline

Treeline

Method Detail

newInstance

newNode

newNode

clone

mousePressed

requireAltDownToEditRadius

mouseDragged

mouseReleased

mouseWheelMoved

adjustNodeRadius

exportDTD

exportXMLNodeAttributes

exportXMLNodeData

generateMesh

keyPressed

askAdjustRadius

getBounds

createMeasurementPair