Author: tomithy
Date: 2010-09-04 18:46:25 -0700 (Sat, 04 Sep 2010)
New Revision: 21700
Modified:
cytoscapeweb/branches/gsoc2010/gbeb/src/GBEBView.as
Log:
Cleaned up version of GBEB code.
Modified: cytoscapeweb/branches/gsoc2010/gbeb/src/GBEBView.as
===================================================================
--- cytoscapeweb/branches/gsoc2010/gbeb/src/GBEBView.as 2010-09-03 23:43:04 UTC
(rev 21699)
+++ cytoscapeweb/branches/gsoc2010/gbeb/src/GBEBView.as 2010-09-05 01:46:25 UTC
(rev 21700)
@@ -7,42 +7,43 @@
import flare.data.DataSet;
import flare.data.converters.GraphMLConverter;
import flare.display.DirtySprite;
- import flare.util.Displays;
+ import flare.scale.ScaleType;
import flare.util.Shapes;
+ import flare.util.palette.ColorPalette;
import flare.vis.Visualization;
- import flare.vis.controls.DragControl;
import flare.vis.data.Data;
import flare.vis.data.EdgeSprite;
import flare.vis.data.NodeSprite;
import flare.vis.data.Tree;
- import flare.vis.data.render.EdgeRenderer;
import flare.vis.events.SelectionEvent;
+ import flare.vis.operator.encoder.ColorEncoder;
import flare.vis.operator.layout.CircleLayout;
- import flare.vis.operator.layout.Layout;
+ import flare.vis.operator.layout.RadialTreeLayout;
import flash.display.Sprite;
import flash.display.StageAlign;
import flash.display.StageScaleMode;
import flash.events.Event;
import flash.events.MouseEvent;
- import flash.external.ExternalInterface;
import flash.geom.Rectangle;
import flash.net.URLLoader;
import flash.net.URLRequest;
import flash.text.TextFormat;
import flash.utils.Dictionary;
- import gbeb.util.converters.XGMMLConverter;
import gbeb.view.components.ProgressBar;
- import gbeb.view.layout.PresetLayout;
import gbeb.view.operator.router.GBEBRouter;
import gbeb.view.render.BundleRenderer;
[SWF(width="800",height="600", backgroundColor="#ffffff", frameRate="30")]
public class GBEBView extends Sprite
- {
+ {
+ //private var _url:String = "data/sample1.xml";
private var _url:String =
"http://flare.prefuse.org/data/flare.json.txt";;
+ //private var _url:String
="/Users/Tomithy/Desktop/GSOC/Datasets/flare.json.txt";
+ //private var _url:String
="/Users/Tomithy/Desktop/GSOC/Datasets/flare_reduced.json.txt";
+ //private var _url:String
="/Users/Tomithy/Desktop/GSOC/Datasets/socialnet.xml";
private var _vis:Visualization;
private var _bar:ProgressBar;
private var _bounds:Rectangle;
@@ -50,8 +51,6 @@
private var _fmt:TextFormat = new TextFormat("_sans", 7);
private var _focus:NodeSprite;
private var _appBounds:Rectangle;
- private var _layout:Layout;
- private var _bundler:GBEBRouter;
//testing Variables
private var addEventCounter:int = 0;
@@ -64,19 +63,18 @@
protected function init():void {
// create progress bar
addChild(_bar = new ProgressBar());
- var url:String = stage.loaderInfo.parameters["url"];
- if (url == null) url = _url;
-
+
// load data file
- var ldr:URLLoader = new URLLoader(new URLRequest(url));
+ // TODO: load Graphml:
+
+ var ldr:URLLoader = new URLLoader(new URLRequest(_url));
_bar.loadURL(
ldr,
function():void {
var obj:String = ldr.data as String;
- var data:Data = buildData(obj);
+ var data:Data = buildData(obj);
visualize(data);
_bar = null;
- trace("GBEBView: Checking URL Loader!");
});
}
@@ -85,49 +83,57 @@
data.nodes.setProperties({
shape: Shapes.CIRCLE,
alpha: 0.2,
- buttonMode: true
+ //visible: eq("childDegree",0), // only show leaf nodes
+ buttonMode: true // show hand cursor
});
data.edges.setProperties({
lineWidth: 2,
- lineColor: 0xff0b94b1,
+ lineColor: 0xff0055cc,
mouseEnabled: true,
- buttonMode: true
+ buttonMode: true,
+// visible: neq("source.parentNode","target.parentNode"),
+ renderer: BundleRenderer.instance
});
_vis = new Visualization(data);
+ //_vis.continuousUpdates = false;
addChild(_vis);
-
+
if (_bounds) resize(_bounds);
+
+
+
+
+
- if (_layout == null) {
+ // place around circle by tree structure, radius mapped to
depth
+// _vis.operators.add(new CircleLayout(null, null, true));
+// CircleLayout(_vis.operators.last).angleWidth = 2 * Math.PI;
+
// _vis.operators.add(new RadialTreeLayout(80));
// RadialTreeLayout(_vis.operators.last).autoScale = true;
- _vis.operators.add(new CircleLayout());
-// _vis.operators.add(new
NodeLinkTreeLayout("topToBottom", 50, 50, 50));
- } else {
- _vis.operators.add(_layout);
- }
+ _vis.operators.add(new CircleLayout());
+
+ //_vis.operators.add(new
NodeLinkTreeLayout("topToBottom", 50, 50, 50));
+
+
+ // set the edge alpha values
+ // longer edge, lighter alpha: 1/(2*numCtrlPoints)
+// _vis.operators.add(new PropertyEncoder({ alpha: edgeAlpha },
Data.EDGES));
- _vis.controls.add( new DragControl(function(o:*):Boolean { return
o is NodeSprite; }) );
-
+ // TODO: replace by GBEB Router:
//
##############################################################
-// var bounds:Rectangle = new Rectangle(0, 0, width, height);
-// _vis.operators.add(new ColorEncoder("index",
"edges", "lineColour"))
+ // bundle edges to route along the tree structure
+ //_vis.operators.add(new BundledEdgeRouter(0.95));
+
+ //var bounds:Rectangle = new Rectangle(0, 0, width, height);
+
//_vis.operators.add(new ColorEncoder("index", "edges", "lineColour"))
// _vis.operators.add(new Labeler("data.name"));
- trace("GBEBView: how many times GBEBView called the
GBEBRouter? " + addEventCounter++);
+ _vis.operators.add(new GBEBRouter(_bounds, 30 , 0.95));
+ trace("GBEBView: No. of times View calls router: " +
addEventCounter++);
//
##############################################################
-
- var t:Transitioner = _vis.update(0.1);
- t.addEventListener(TransitionEvent.END,
function(evt:TransitionEvent):void {
- centerGraph(_vis);
-
- // bundle edges to route along the tree
structure
-// var bundler:BundledEdgeRouter = new
BundledEdgeRouter(0.95);
-// _vis.operators.add(bundler);
-// bundler.operate();
- });
- t.play();
+ _vis.update();
// show all dependencies on single-click
// var linkType:int = NodeSprite.OUT_LINKS;
@@ -182,11 +188,12 @@
/** Remove highlight from a node and connected edges/nodes */
private function unhighlight(n:*):void
{
- var node:NodeSprite = n is NodeSprite ? NodeSprite(n) :
SelectionEvent(n).node;
+ var node:NodeSprite = n is NodeSprite ?
+ NodeSprite(n) : SelectionEvent(n).node;
// set everything back to normal
node.setEdgeProperties({
- alpha: 0.8,
- lineColor: 0xff0b94b1
+ alpha: edgeAlpha,
+ lineColor: 0xff0055cc
}, NodeSprite.GRAPH_LINKS);
}
@@ -236,13 +243,6 @@
private function onStageAdd(evt:Event):void {
removeEventListener(Event.ADDED_TO_STAGE, onStageAdd);
-
- try {
- ExternalInterface.addCallback("bundleEdges", bundleEdges);
- } catch(err:Error) {
- trace("Error [addFunction]: " + err);
- }
-
initStage();
init();
onResize();
@@ -271,163 +271,84 @@
/**
* Creates the visualized data.
*/
- private function buildData(network:String):Data
+ public static function buildData(network:String):Data
{
var data:Data;
var tree:Tree;
var xml:XML = new XML(network as String);
- try {
- if (xml != null && xml.name() != null) {
- var isGraphml:Boolean = xml.name().localName === "graphml";
-
- if (isGraphml) {
- // convert from GraphML
- var ds:DataSet = new GraphMLConverter().parse(xml);
- data = Data.fromDataSet(ds);
- } else {
- // XGMML:
- var xgmmlConverter:XGMMLConverter = new
XGMMLConverter();
- ds = xgmmlConverter.parse(xml);
- data = Data.fromDataSet(ds)
-
- var points:Object = xgmmlConverter.points;
- if (points != null) {
- _layout = new PresetLayout(points);
+ if (xml != null && xml.name() != null) {
+ // convert from GraphML
+ var ds:DataSet = new GraphMLConverter().parse(xml);
+ data = Data.fromDataSet(ds);
+ tree = data.tree;
+ } else {
+ // build from tuples
+ var tuples:Array = JSON.decode(network) as Array;
+ data = new Data();
+ tree = new Tree();
+ tree.root = data.addNode({name:"flare", size:0});
+ var map:Object = {};
+ map.flare = tree.root;
+
+ var t:Object, u:NodeSprite, v:NodeSprite;
+ var path:Array, p:String, pp:String, i:uint;
+
+ // build data set and tree edges
+ tuples.sortOn("name");
+ for each (t in tuples) {
+ path = String(t.name).split(".");
+ for (i=0, p=""; i<path.length-1; ++i) {
+ pp = p;
+ p += (i?".":"") + path[i];
+ if (!map[p]) {
+ u = data.addNode({name:p, size:0});
+ tree.addChild(map[pp], u);
+ map[p] = u;
}
}
+ t["package"] = p;
+ u = data.addNode(t);
+ tree.addChild(map[p], u);
+ map[t.name] = u;
+ }
+
+ // create graph links
+ for each (t in tuples) {
+ u = map[t.name];
- tree = data.tree;
-
- } else {
- // build from tuples
- var tuples:Array = JSON.decode(network) as Array;
- data = new Data();
- tree = new Tree();
- tree.root = data.addNode({name:"flare", size:0});
- var map:Object = {};
- map.flare = tree.root;
-
- var t:Object, u:NodeSprite, v:NodeSprite;
- var path:Array, p:String, pp:String, i:uint;
-
- // build data set and tree edges
- tuples.sortOn("name");
- for each (t in tuples) {
- path = String(t.name).split(".");
- for (i=0, p=""; i<path.length-1; ++i) {
- pp = p;
- p += (i?".":"") + path[i];
- if (!map[p]) {
- u = data.addNode({name:p, size:0});
- tree.addChild(map[pp], u);
- map[p] = u;
- }
- }
- t["package"] = p;
- u = data.addNode(t);
- tree.addChild(map[p], u);
- map[t.name] = u;
+ var count:int = 0;
+ for each (var name:String in t.imports) {
+ v = map[name];
+ if (v && count%4 === 0) data.addEdgeFor(u, v);
+ else trace ("Missing node: "+name);
+ count++;
}
-
- // create graph links
- for each (t in tuples) {
- u = map[t.name];
-
- var count:int = 0;
- for each (var name:String in t.imports) {
- v = map[name];
- if (v && count%4 === 0) data.addEdgeFor(u, v);
- else trace ("Missing node: "+name);
- count++;
- }
- }
-
- // sort the list of children alphabetically by name
- for each (u in tree.nodes) {
- u.sortEdgesBy(NodeSprite.CHILD_LINKS,
"target.data.name");
- }
-
- data.tree = tree;
}
- // DEBUG ******
- for each (var e:EdgeSprite in data.edges) {
- e.addEventListener(MouseEvent.CLICK,
function(evt:MouseEvent):void {
- var clicked:EdgeSprite = evt.target as
EdgeSprite;
- trace("CLICK >> " + clicked.source.data.name +
" - " + clicked.target.data.name);
- data.edges.setProperty("lineColor", 0xff0b94b1);
- data.edges.setProperty("props.$debug", false);
- clicked.lineColor = 0xffff0000;
- clicked.props.$debug = true;
- });
+ // sort the list of children alphabetically by name
+ for each (u in tree.nodes) {
+ u.sortEdgesBy(NodeSprite.CHILD_LINKS, "target.data.name");
}
- // ************
- } catch (err:Error) {
- trace(err);
- throw err;
- }
-
- return data;
- }
-
- private function bundleEdges(value:Boolean):void {
- if (value === true) {
- _bundler = new GBEBRouter(getRealBounds(_vis.data), 30 , 0.95);
- _vis.operators.add(_bundler);
- _vis.data.edges.setProperty("renderer",
BundleRenderer.instance);
- _bundler.operate();
- } else if (_bundler != null) {
- _bundler.enabled = false;
- _vis.operators.remove(_bundler);
- _vis.data.edges.setProperty("shape", Shapes.LINE);
- _vis.data.edges.setProperty("renderer", EdgeRenderer.instance);
- }
- }
-
- private function centerGraph(vis:Visualization):void {
- var b:Rectangle = getRealBounds(vis.data);
-
- if (b != null && b.width > 0 && b.height > 0) {
- // The new coordinates:
- var newX:Number = (stage.stageWidth - b.width) / 2;
- var newY:Number = (stage.stageHeight - b.height) / 2;
- // The amount to move, considering the new coordinates and the
current position:
- var panX:Number = newX - b.x;
- var panY:Number = newY - b.y;
-
- Displays.panBy(vis, panX, panY);
+ data.tree = tree;
}
- }
-
- private static function getRealBounds(data:Data):Rectangle {
-
- var bounds:Rectangle = new Rectangle();
- if (data != null && data.nodes.length > 0) {
- var minX:Number = Number.POSITIVE_INFINITY, minY:Number =
Number.POSITIVE_INFINITY;
- var maxX:Number = Number.NEGATIVE_INFINITY, maxY:Number =
Number.NEGATIVE_INFINITY;
-
- // First, consider the NODES bounds:
- for each (var n:NodeSprite in data.nodes) {
- // The node size (its shape must have the same height and
width; e.g. a circle)
- var ns:Number = n.height;
- // Verify MIN and MAX x/y again:
- minX = Math.min(minX, (n.x - ns/2));
- minY = Math.min(minY, (n.y - ns/2));
- maxX = Math.max(maxX, (n.x + ns/2));
- maxY = Math.max(maxY, (n.y + ns/2));
- }
-
- const PAD:Number = 2;
- bounds.x = minX - PAD;
- bounds.y = minY - PAD;
- bounds.width = maxX - bounds.x + PAD;
- bounds.height = maxY - bounds.y + PAD;
+ // DEBUG ******
+ for each (var e:EdgeSprite in data.edges) {
+ e.addEventListener(MouseEvent.CLICK,
function(evt:MouseEvent):void {
+ var clicked:EdgeSprite = evt.target as EdgeSprite;
+ trace("CLICK >> " + clicked.source.data.name + " - " +
clicked.target.data.name);
+// trace("CLICK >> " + clicked.source.data.id + " - " +
clicked.target.data.id);
+ data.edges.setProperty("lineColor", clicked.lineColor);
+ data.edges.setProperty("props.$debug", false);
+ clicked.lineColor = 0xffff0000;
+ clicked.props.$debug = true;
+ });
}
+ // ************
- return bounds;
+ return data;
}
} // end of class DependencyGraph
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