Connector (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
        
        ini.trakem2.display.Connector

All Implemented Interfaces:

Paintable, VectorData
```
public class Connector
extends Treeline
```
A one-to-many connection, represented by one source point and one or more target points. The connector is drawn by click+drag+release, defining the origin at click and the target at release. By clicking anywhere else, the connector can be given another target. Points can be dragged and removed. Connectors are meant to represent synapses, in particular polyadic synapses.

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Connector.ConnectorNode
- Nested classes/interfaces inherited from class ini.trakem2.display.Treeline
  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`	`Connector.ConnectorNode`

Field Summary
- Fields inherited from class ini.trakem2.display.Treeline
  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

Constructor Summary

Constructors
Constructor and Description
`Connector(Project project, long id, HashMap<String,String> ht_attr, HashMap<Displayable,String> ht_links)` Reconstruct from XML.
`Connector(Project project, long id, String title, float width, float height, float alpha, boolean visible, Color color, boolean locked, AffineTransform at)`
`Connector(Project project, String title)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`addTarget(double x, double y, long layer_id, double r)`
`int`	`addTarget(float x, float y, long layer_id, float r)`
`Connector`	`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.
`boolean`	`crop(List<Layer> range)` If the root node (the origin) does not remain within the range, this Connector is left empty.
`static void`	`exportDTD(StringBuilder sb_header, HashSet<String> hs, String indent)`
`protected Rectangle`	`getBounds(Collection<? extends Node<Float>> nodes)`
`Coordinate<Node<Float>>`	`getCoordinate(int i)` Get a coordinate for target i.
`Coordinate<Node<Float>>`	`getCoordinateAtOrigin()`
`String`	`getInfo()` Returns id and project name; this method is meant to be overriden by any of the subclasses.
`Set<Displayable>`	`getOrigins()` Returns the set of Displayable objects under the origin point, or an empty set if none.
`Set<Displayable>`	`getOrigins(Class<?> c)` Returns the set of Displayable objects under the origin point, or an empty set if none.
`Set<Displayable>`	`getOrigins(Class<?> c, boolean instance_of)`
`int`	`getTargetCount()`
`List<Point3f>`	`getTargetPoints(boolean calibrated)`
`List<Set<Displayable>>`	`getTargets()` Returns the list of sets of visible Displayable objects under each target, or an empty list if none.
`List<Set<Displayable>>`	`getTargets(Class<?> c)` Returns the list of sets of visible Displayable objects under each target, or an empty list if none.
`List<Set<Displayable>>`	`getTargets(Class<?> c, boolean instance_of)`
`boolean`	`intersectsOrigin(Area area, Layer la)`
`boolean`	`intersectsOrigin(double wx, double wy, Layer la)` Whether the area of the root node intersects the world coordinates `wx`, `wy` at `Layer` `la`.
`protected boolean`	`layerRemoved(Layer la)` If the root node is in Layer @param la, then all nodes are removed.
`ij.measure.ResultsTable`	`measure(ij.measure.ResultsTable rt)` Measures number of branch points and end points, and total cable length.
`static Connector`	`merge(List<Connector> col)` Takes the List of Connector instances and adds the targets of all to the first one.
`protected void`	`mergeTargets(Connector c)`
`void`	`mousePressed(MouseEvent me, Layer layer, int x_p, int y_p, double mag)` Add a root or child nodes to root.
`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.
`void`	`readLegacyXML(LayerSet ls, HashMap<String,String> ht_attr, HashMap<Displayable,String> ht_links)`
`protected boolean`	`requireAltDownToEditRadius()`

Methods inherited from class ini.trakem2.display.Treeline
adjustNodeRadius, askAdjustRadius, createMeasurementPair, exportXMLNodeAttributes, exportXMLNodeData, generateMesh, keyPressed, mouseDragged, mouseReleased, mouseWheelMoved

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, 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, linkPatches, markNear, 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, getProject, getUniqueIdentifier, removeFromDatabase, updateInDatabase

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

Constructor Detail

Connector

public Connector(Project project,
                 String title)

Connector

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

Connector

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

Reconstruct from XML.

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.).

Overrides:

newInstance in class Treeline

newNode

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

Overrides:: newNode in class Treeline

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

To reconstruct from XML.

Overrides:

newNode in class Treeline

readLegacyXML

public void readLegacyXML(LayerSet ls,
                          HashMap<String,String> ht_attr,
                          HashMap<Displayable,String> ht_links)

addTarget

public int addTarget(float x,
                     float y,
                     long layer_id,
                     float r)

addTarget

public int addTarget(double x,
                     double y,
                     long layer_id,
                     double r)

mergeTargets

protected void mergeTargets(Connector c)
                     throws NoninvertibleTransformException

Throws:: NoninvertibleTransformException

intersectsOrigin

public boolean intersectsOrigin(Area area,
                                Layer la)

intersectsOrigin

public boolean intersectsOrigin(double wx,
                                double wy,
                                Layer la)

Whether the area of the root node intersects the world coordinates wx, wy at Layer la.

getOrigins
```
public Set<Displayable> getOrigins(Class<?> c)
```
Returns the set of Displayable objects under the origin point, or an empty set if none.

getOrigins

public Set<Displayable> getOrigins(Class<?> c,
                                   boolean instance_of)

getOrigins
```
public Set<Displayable> getOrigins()
```
Returns the set of Displayable objects under the origin point, or an empty set if none.

getTargets

public List<Set<Displayable>> getTargets(Class<?> c,
                                         boolean instance_of)

getTargets
```
public List<Set<Displayable>> getTargets(Class<?> c)
```
Returns the list of sets of visible Displayable objects under each target, or an empty list if none.

getTargets
```
public List<Set<Displayable>> getTargets()
```
Returns the list of sets of visible Displayable objects under each target, or an empty list if none.

getTargetCount
```
public int getTargetCount()
```

exportDTD

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

clone
```
public Connector 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.

Overrides:

clone in class Treeline

measure
```
public ij.measure.ResultsTable measure(ij.measure.ResultsTable rt)
```
Description copied from class: Tree

Measures number of branch points and end points, and total cable length. Cable length is measured as: Cable length: the sum of all distances between all consecutive pairs of nodes. Lower-bound cable length: the sum of all distances between all end points to branch points, branch points to other branch points, and first branch point to root.

Overrides:

measure in class Tree<Float>

getTargetPoints

public List<Point3f> getTargetPoints(boolean calibrated)

getCoordinateAtOrigin

public Coordinate<Node<Float>> getCoordinateAtOrigin()

getCoordinate

public Coordinate<Node<Float>> getCoordinate(int i)

Get a coordinate for target i.

getInfo
```
public String getInfo()
```
Description copied from class: DBObject

Returns id and project name; this method is meant to be overriden by any of the subclasses.

Overrides:

getInfo in class DBObject

layerRemoved
```
protected boolean layerRemoved(Layer la)
```
If the root node is in Layer @param la, then all nodes are removed.

Overrides:

layerRemoved in class Tree<Float>

merge
```
public static Connector merge(List<Connector> col)
                       throws NoninvertibleTransformException
```
Takes the List of Connector instances and adds the targets of all to the first one. Removes the others from the LayerSet and from the Project. If any of the Connector instances cannot be removed, returns null.

Throws:

NoninvertibleTransformException

mousePressed

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

Add a root or child nodes to root.

Overrides:: mousePressed in class Treeline

requireAltDownToEditRadius
```
protected boolean requireAltDownToEditRadius()
```
Overrides:

requireAltDownToEditRadius in class Treeline

getBounds

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

Overrides:: getBounds in class Treeline

crop
```
public boolean crop(List<Layer> range)
```
If the root node (the origin) does not remain within the range, this Connector is left empty.

Overrides:

crop in class Tree<Float>

Class Connector

Nested Class Summary

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

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.Treeline

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.Treeline

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

Constructor Detail

Connector

Connector

Connector

Method Detail

newInstance

newNode

newNode

readLegacyXML

addTarget

addTarget

mergeTargets

intersectsOrigin

intersectsOrigin

getOrigins

getOrigins

getOrigins

getTargets

getTargets

getTargets

getTargetCount

exportDTD

clone

measure

getTargetPoints

getCoordinateAtOrigin

getCoordinate

getInfo

layerRemoved

merge

mousePressed

requireAltDownToEditRadius

getBounds

crop