Author: Christian Lopes
Date: 2010-09-03 14:54:37 -0700 (Fri, 03 Sep 2010)
New Revision: 21694
Modified:
cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/weighted1.graphml
cytoscapeweb/trunk/cytoscapeweb/html-template/js/cytoscapeweb.js
cytoscapeweb/trunk/cytoscapeweb/html-template/sample.html
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/data/ContinuousVizMapperVO.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/GraphMediator.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/controls/EnclosingSelectionControl.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/layout/ForceDirectedLayout.as
Log:
Implemented feature #2288: Continuous mapper should allow user-custom scales
(it needs more tests).
Added LOG normalization option to the weighted force directed layout.
Fixed bug that would prevent and element from being drag-selected when it was
previously shift-clicked.
Modified:
cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/weighted1.graphml
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/weighted1.graphml
2010-09-03 21:23:07 UTC (rev 21693)
+++ cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/weighted1.graphml
2010-09-03 21:54:37 UTC (rev 21694)
@@ -57,8 +57,9 @@
<data key="shape">HEXAGON</data>
<data key="label">A08</data>
</node>
- <node id="n1">
+ <node id="a09">
<data key="weight">0.6234616006258875</data>
+ <data key="label">A09</data>
</node>
<edge id="e3" source="a01" directed="true" target="a02">
@@ -123,7 +124,7 @@
<edge id="e15" source="a07" target="a04">
<data key="weight">5000</data>
</edge>
- <edge id="e16" source="a07" target="n1">
+ <edge id="e16" source="a07" target="a09">
<data key="weight">7000</data>
</edge>
</graph>
Modified: cytoscapeweb/trunk/cytoscapeweb/html-template/js/cytoscapeweb.js
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/html-template/js/cytoscapeweb.js
2010-09-03 21:23:07 UTC (rev 21693)
+++ cytoscapeweb/trunk/cytoscapeweb/html-template/js/cytoscapeweb.js
2010-09-03 21:54:37 UTC (rev 21694)
@@ -2260,7 +2260,7 @@
* The default value is
<code>null</code>, which means that the layout is unweighted.
* If you want to generate
an edge-weighted layout, you just need to provide the name of the data
attribute that should be used as weight.</li>
* <li><code>weightNorm</code> {String}: The normalization method
that is applied to the weight values when using a weighted layout.
- * Possible values are:
<code>"linear"</code>, <code>"inverselinear"</code> and <code>"log"</code>.
+ * Possible values are:
<code>"linear"</code>, <code>"invlinear"</code> and <code>"log"</code>.
* The default value is
<code>"linear"</code>.</li>
* <li><code>minWeight</code> {Number}: The minimum edge weight to
consider, if the layout is set to be weighted.
* Do not specify any value
if you want the layout to get the minimum weight from the rendered edges data
(filtered-out edges are ignored).
@@ -2588,8 +2588,16 @@
* <li>The mapping algorithm uses a linear interpolation to calculate
the values.</li>
* <li>Continuous mappers ignore filtered out elements.</li>
* </ul>
+ *
* @example
+ * // A mapper that could be used to set the sizes of the nodes, for
example:
* var sizeMapper = { attrName: "weight", minValue: 12, maxValue: 36 };
+ *
+ * // This one could be used to create a color gradient:
+ * var colorMapper = { attrName: "score", minValue: "#ffff00", maxValue:
"#00ff00" };
+ *
+ * // In this example we want to specify the minimum and maximum data
values for the scale:
+ * var widthMapper = { attrName: "weight", minValue: 1, maxValue: 4,
minAttrValue: 0.1, maxAttrValue: 1.0 };
* @class
* @name ContinuousMapper
* @type Object
@@ -2600,6 +2608,46 @@
* @see org.cytoscapeweb.VisualStyle
*/
/**
+ * The name of the data attribute that will be mapped to a visual style's
property.
+ * @property
+ * @name attrName
+ * @type String
+ * @memberOf org.cytoscapeweb.ContinuousMapper#
+ */
+ /**
+ * The minimum value of the visual style's property. It is usually a
number (e.g. edge width),
+ * but accepts strings if the visual property is a color.
+ * @property
+ * @name minValue
+ * @memberOf org.cytoscapeweb.ContinuousMapper#
+ */
+ /**
+ * The maximum value of the visual style's property. It is usually a
number (e.g. edge width),
+ * but accepts strings if the visual property is a color.
+ * @property
+ * @name maxValue
+ * @memberOf org.cytoscapeweb.ContinuousMapper#
+ */
+ /**
+ * An optional minimum value for the linear scale. If you don't specify it,
+ * Cytoscape Web gets the lowest attribute value from the rendered nodes
or edges (filtered-out elements are ignored).
+ * And if an element's data value is lower than the specified minimum,
that element's visual property is simply scaled up to the minimum value.
+ * @property
+ * @name minAttrValue
+ * @type Number
+ * @memberOf org.cytoscapeweb.ContinuousMapper#
+ */
+ /**
+ * An optional maximum value for the linear scale. If you don't specify it,
+ * Cytoscape Web gets the highest attribute value from the rendered nodes
or edges (filtered-out elements are ignored).
+ * And if an element's data value is higher than the specified maximum,
that element's visual property is simply scaled down to the maximum value.
+ * @property
+ * @name maxAttrValue
+ * @type Number
+ * @memberOf org.cytoscapeweb.ContinuousMapper#
+ */
+
+ /**
* <p>This object represents a Discrete Mapper type, but is just an
untyped object.</p>
* <p>Discrete network attributes are mapped to discrete visual
attributes.</p>
* <p>For example, a discrete mapper can map node colors to gene
annotations.</p>
Modified: cytoscapeweb/trunk/cytoscapeweb/html-template/sample.html
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/html-template/sample.html 2010-09-03
21:23:07 UTC (rev 21693)
+++ cytoscapeweb/trunk/cytoscapeweb/html-template/sample.html 2010-09-03
21:54:37 UTC (rev 21694)
@@ -28,7 +28,7 @@
},
nodes: {
shape: "ELLIPSE",
- color: { defaultValue: "#cccccc", continuousMapper: {
attrName: "weight", minValue: "#ffffff", maxValue: "#0b94b1" } },
+ color: { defaultValue: "#cccccc", continuousMapper: {
attrName: "weight", minValue: "#ffffff", maxValue: "#0b94b1" } },
opacity: 0.9,
size: { defaultValue: 20, continuousMapper: {
attrName: "weight", minValue: 20, maxValue: 40 } },
borderWidth: 2,
@@ -41,7 +41,7 @@
},
edges: {
color: "#0b94b1",
- width: { defaultValue: 2, continuousMapper: {
attrName: "weight", minValue: 2, maxValue: 8 } },
+ width: { defaultValue: 2, continuousMapper: {
attrName: "weight", minValue: 2, maxValue: 8, minAttrValue: 4000,
maxAttrValue: 6000 } },
mergeWidth: { defaultValue: 2, continuousMapper: {
attrName: "weight", minValue: 2, maxValue: 8 } },
mergeColor: "#0b94b1",
opacity: 0.7,
@@ -70,7 +70,7 @@
layout = { name: "Preset", options: { fitToScreen: true
} };
} else { // GraphML or SIF
if ($("#layouts").val() !== "Preset") {
- layout = { name: $("#layouts").val(), options: {
weightAttr: "weight", weightNorm: "linear", restLength: 50, autoStabilize:
false } };
+ layout = { name: $("#layouts").val(), options: {
weightAttr: "weight", weightNorm: "log", restLength: 50, autoStabilize: false }
};
}
}
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/data/ContinuousVizMapperVO.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/data/ContinuousVizMapperVO.as
2010-09-03 21:23:07 UTC (rev 21693)
+++
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/data/ContinuousVizMapperVO.as
2010-09-03 21:54:37 UTC (rev 21694)
@@ -46,6 +46,8 @@
// Attribute values:
private var _minAttrValue:Number;
private var _maxAttrValue:Number;
+ private var _dynamicMin:Boolean = true;
+ private var _dynamicMax:Boolean = true;
// ========[ PUBLIC PROPERTIES
]============================================================
@@ -58,7 +60,7 @@
*/
public function set dataList(list:Array):void {
_dataList = list;
- buildScale();
+ if (_dynamicMin || _dynamicMax) buildScale();
}
public function get minValue():Number {
@@ -69,15 +71,29 @@
return _maxValue;
}
+ public function get minAttrValue():Number {
+ return _minAttrValue;
+ }
+
+ public function get maxAttrValue():Number {
+ return _maxAttrValue;
+ }
+
// ========[ CONSTRUCTOR
]==================================================================
public function ContinuousVizMapperVO(attrName:String,
propName:String,
minValue:Number,
- maxValue:Number) {
+ maxValue:Number,
+ minAttrValue:Number=NaN,
+ maxAttrValue:Number=NaN) {
super(attrName, propName, this);
- this._minValue = minValue;
- this._maxValue = maxValue;
+ _minValue = minValue;
+ _maxValue = maxValue;
+ _minAttrValue = minAttrValue;
+ _maxAttrValue = maxAttrValue;
+ _dynamicMin = isNaN(minAttrValue);
+ _dynamicMax = isNaN(maxAttrValue);
}
// ========[ PUBLIC METHODS
]===============================================================
@@ -107,6 +123,8 @@
obj.attrName = attrName;
obj.minValue = VisualProperties.toExportValue(propName, minValue);
obj.maxValue = VisualProperties.toExportValue(propName, maxValue);
+ if (!_dynamicMin) obj.minAttrValue = minAttrValue;
+ if (!_dynamicMax) obj.maxAttrValue = maxAttrValue;
return obj;
}
@@ -116,23 +134,29 @@
var min:Number = VisualProperties.parseValue(propName,
obj.minValue) as Number;
var max:Number = VisualProperties.parseValue(propName,
obj.maxValue) as Number;
- return new ContinuousVizMapperVO(attrName, propName, min, max);
+ var minAttr:Number, maxAttr:Number;
+ if (!isNaN(obj.minAttrValue)) minAttr = Number(obj.minAttrValue);
+ if (!isNaN(obj.maxAttrValue)) maxAttr = Number(obj.maxAttrValue);
+
+ return new ContinuousVizMapperVO(attrName, propName, min, max,
minAttr, maxAttr);
}
// ========[ PRIVATE METHODS
]==============================================================
private function buildScale():void {
- _maxAttrValue = _minAttrValue = 0;
+// _maxAttrValue = _minAttrValue = 0;
if (dataList != null && dataList.length > 0) {
- _maxAttrValue = Number.NEGATIVE_INFINITY;
- _minAttrValue = Number.POSITIVE_INFINITY;
+ if (_dynamicMin) _minAttrValue = Number.POSITIVE_INFINITY;
+ if (_dynamicMax) _maxAttrValue = Number.NEGATIVE_INFINITY;
- for each (var dt:Object in dataList) {
- var value:Number = dt[attrName] as Number;
- _maxAttrValue = Math.max(_maxAttrValue, value);
- _minAttrValue = Math.min(_minAttrValue, value);
- }
+ if (_dynamicMin || _dynamicMax) {
+ for each (var dt:Object in dataList) {
+ var value:Number = dt[attrName] as Number;
+ if (_dynamicMin) _minAttrValue =
Math.min(_minAttrValue, value);
+ if (_dynamicMax) _maxAttrValue =
Math.max(_maxAttrValue, value);
+ }
+ }
}
}
}
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/GraphMediator.as
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/GraphMediator.as
2010-09-03 21:23:07 UTC (rev 21693)
+++ cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/GraphMediator.as
2010-09-03 21:54:37 UTC (rev 21694)
@@ -548,7 +548,7 @@
if (configProxy.mouseDownToDragDelay >= 0) {
_dragAllTimer = new Timer(configProxy.mouseDownToDragDelay, 1);
_dragAllTimer.addEventListener(TimerEvent.TIMER,
function(te:TimerEvent):void {
- trace("* Hold Mouse DOWN - will drag part...");
+ trace("* Hold Mouse DOWN - will drag part...");
_draggingComponent = true;
updateCursor();
vis.showDragRectangle(n);
@@ -573,6 +573,7 @@
evt.currentTarget.removeEventListener(evt.type, arguments.callee);
var n:NodeSprite = evt.target as NodeSprite;
_draggingGraph = false;
+ _selectionControl.enabled = true;
updateCursor();
// Return the MOUSE DOWN to the View, so panning is possible again:
graphView.stage.addEventListener(MouseEvent.MOUSE_DOWN,
onMouseDownView, false, 0, true);
@@ -675,12 +676,12 @@
if (_draggingComponent) vis.updateDragRectangle(amountX, amountY);
}
- private function onSelect(evt:SelectionEvent):void {
+ private function onSelect(evt:SelectionEvent):void {for each (var item
in evt.items) { trace(" S---> " + item.data.label); }
if (evt.items != null && evt.items.length > 0)
sendNotification(ApplicationFacade.SELECT, evt.items);
}
- private function onDeselect(evt:SelectionEvent):void {
+ private function onDeselect(evt:SelectionEvent):void {for each (var
item in evt.items) { trace(" D---> " + item.data.label); }
if (evt.items != null && evt.items.length > 0)
sendNotification(ApplicationFacade.DESELECT, evt.items);
}
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/controls/EnclosingSelectionControl.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/controls/EnclosingSelectionControl.as
2010-09-03 21:23:07 UTC (rev 21693)
+++
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/controls/EnclosingSelectionControl.as
2010-09-03 21:54:37 UTC (rev 21694)
@@ -182,7 +182,7 @@
}
}
- private function mouseDown(evt:MouseEvent):void {
+ private function mouseDown(evt:MouseEvent):void {trace("--DOWN--");
if (_stage == null) return;
_stage.addEventListener(MouseEvent.MOUSE_UP, mouseUp);
_stage.addEventListener(MouseEvent.MOUSE_MOVE, mouseMove);
@@ -195,11 +195,11 @@
DisplayObjectContainer(_object).addChild(_shape);
renderShape(_shape.graphics);
-
+ trace(_enabled);
if (_enabled) {
if (fireImmediately) {
selectionTest(evt);
- } else if (!evt.shiftKey) {
+ } else {
// ALTERED: if SHIFT key is not pressed, it should reset
everything first:
_rem = _add = null;
_rem0 = _add0 = null;
@@ -219,14 +219,14 @@
}
}
- private function mouseUp(evt:MouseEvent):void {
+ private function mouseUp(evt:MouseEvent):void {trace("--UP--");
if (!enabled) return;
if (!fireImmediately)
selectionTest(evt);
stopSelection();
}
- private function stopSelection():void {
+ private function stopSelection():void {trace("--stop sel");
if (_drag) {
DisplayObjectContainer(_object).removeChild(_shape);
}
@@ -247,7 +247,7 @@
}
}
- private function selectionTest(evt:MouseEvent):void {
+ private function selectionTest(evt:MouseEvent):void { trace("-->sel
TEST");
var con:DisplayObjectContainer = DisplayObjectContainer(_object);
for (var i:uint=0; i<con.numChildren; ++i) {
walkTree(con.getChildAt(i), test);
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/layout/ForceDirectedLayout.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/layout/ForceDirectedLayout.as
2010-09-03 21:23:07 UTC (rev 21693)
+++
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/view/layout/ForceDirectedLayout.as
2010-09-03 21:54:37 UTC (rev 21694)
@@ -59,7 +59,7 @@
// ========[ CONSTANTS
]====================================================================
public static const NORMALIZED_WEIGHT:String = "linear";
- public static const INV_NORMALIZED_WEIGHT:String = "inverselinear";
+ public static const INV_NORMALIZED_WEIGHT:String = "invlinear";
public static const LOG_WEIGHT:String = "log";
protected static const MIN_SPRING_WEIGHT:Number = 0.1;
@@ -135,9 +135,7 @@
switch (edgeWeightNormalization) {
case INV_NORMALIZED_WEIGHT:
rl /= (MIN_SPRING_WEIGHT + MAX_SPRING_WEIGHT -
sw); break;
- case LOG_WEIGHT:
- // TODO...
- default: // normalized...
+ default:
if (sw !== 0) rl /= sw;
}
}
@@ -322,6 +320,11 @@
}
});
+ if (weightNormalization === LOG_WEIGHT) {
+ minWeight = Math.log(minWeight);
+ maxWeight = Math.log(maxWeight);
+ }
+
// set up simulation parameters
// this needs to be kept separate from the above initialization
// to ensure all simulation items are created first
@@ -340,6 +343,7 @@
if (weighted) {
ew = e.data[weightAttr];
+ if (weightNormalization === LOG_WEIGHT) ew = Math.log(ew);
// Normalize min and max weights for better visual results
(always between 0 and 1):
if (minWeight === maxWeight) {
@@ -353,7 +357,7 @@
sw = Maths.linearInterp(f, MIN_SPRING_WEIGHT,
MAX_SPRING_WEIGHT);
}
}
-
+
e.props.springWeight = sw;
if (restLength != null)
--
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