Author: clopes
Date: 2011-09-20 13:56:51 -0700 (Tue, 20 Sep 2011)
New Revision: 26889
Modified:
cytoscapeweb/trunk/cytoscapeweb/default.properties
cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test1.graphml
cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test2.xgmml
cytoscapeweb/trunk/cytoscapeweb/html-template/js/cytoscapeweb.js
cytoscapeweb/trunk/cytoscapeweb/html-template/js/tests.js
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/model/converters/SIFConverterTest.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/GraphProxy.as
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/converters/SIFConverter.as
Log:
Implemented #2463: Add "nodeAttr" option to sif function.
Updated API doc.
Modified: cytoscapeweb/trunk/cytoscapeweb/default.properties
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/default.properties 2011-09-20 20:53:22 UTC
(rev 26888)
+++ cytoscapeweb/trunk/cytoscapeweb/default.properties 2011-09-20 20:56:51 UTC
(rev 26889)
@@ -1,3 +1,3 @@
-build.version=0.7.5
+build.version=0.8
FLEX_HOME=/Applications/Adobe Flex Builder 3 Plug-in/sdks/3.2.0/
\ No newline at end of file
Modified: cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test1.graphml
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test1.graphml
2011-09-20 20:53:22 UTC (rev 26888)
+++ cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test1.graphml
2011-09-20 20:56:51 UTC (rev 26889)
@@ -1,5 +1,6 @@
<graphml>
<key id="label" for="all" attr.name="label" attr.type="string"/>
+ <key id="name" for="all" attr.name="name" attr.type="string"/>
<key id="weight" for="node" attr.name="weight" attr.type="double"/>
<key id="ranking" for="node" attr.name="ranking" attr.type="int"/>
@@ -20,6 +21,7 @@
<data key="weight">0.45</data>
<data key="ranking">1</data>
<data key="label">n1
TEST LINE BREAK</data>
+ <data key="name">Node 1</data>
<data key="type">1</data>
<data key="shape">ELLIPSE</data>
<data key="special">false</data>
@@ -28,6 +30,7 @@
<data key="weight">0.22</data>
<data key="ranking">2</data>
<data key="label">n2</data>
+ <data key="name">Node 2</data>
<data key="type">2</data>
<data key="shape">TRIANGLE</data>
<data key="special">true</data>
@@ -36,6 +39,7 @@
<data key="weight">0.09</data>
<data key="ranking">3</data>
<data key="label">n3</data>
+ <data key="name">Node 3</data>
<data key="type">1</data>
<data key="shape">OCTAGON</data>
<data key="special">false</data>
@@ -44,6 +48,7 @@
<data key="weight">0.03</data>
<data key="ranking">4</data>
<data key="label">n4</data>
+ <data key="name">Node 4</data>
<data key="type">1</data>
<data key="shape">DIAMOND</data>
<data key="special">false</data>
@@ -51,6 +56,7 @@
<node id="5">
<data key="weight">0.10</data>
<data key="ranking">5</data>
+ <data key="name">Node 5</data>
<data key="label">n5</data>
<data key="type">3</data>
<data key="shape">PARALLELOGRAM</data>
Modified: cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test2.xgmml
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test2.xgmml
2011-09-20 20:53:22 UTC (rev 26888)
+++ cytoscapeweb/trunk/cytoscapeweb/html-template/fixtures/test2.xgmml
2011-09-20 20:56:51 UTC (rev 26889)
@@ -6,6 +6,7 @@
<att type="real" name="GRAPH_VIEW_CENTER_Y" value="0"/>
<node id="101" weight="0.45" label="A01">
+ <att type="string" name="name" value="Node 1"/>
<att type="string" name="type" value="1"/>
<att type="integer" name="ranking" value="1"/>
<att type="string" name="shape" value="ELLIPSE"/>
@@ -13,6 +14,7 @@
<graphics x="387.25" y="304" fill="#cccccc" outline="#333333" w="36"
cy:nodeTransparency="0.8" cy:nodeLabelFont="SansSerif-0-11" type="ELLIPSE"
h="36" width="1"/>
</node>
<node id="102" weight="0.22" label="A02">
+ <att type="string" name="name" value="Node 2"/>
<att type="string" name="type" value="2"/>
<att type="integer" name="ranking" value="2"/>
<att type="string" name="shape" value="TRIANGLE"/>
@@ -20,6 +22,7 @@
<graphics x="324.85" y="340" fill="#cccccc" outline="#333333"
w="22.857142857142854" cy:nodeTransparency="0.8"
cy:nodeLabelFont="SansSerif-0-11" type="ELLIPSE" h="22.857142857142854"
width="1"/>
</node>
<node id="103" weight="0.09" label="A03">
+ <att type="string" name="name" value="Node 3"/>
<att type="string" name="type" value="2"/>
<att type="integer" name="ranking" value="3"/>
<att type="string" name="shape" value="OCTAGON"/>
@@ -27,6 +30,7 @@
<graphics x="324.85" y="412" fill="#cccccc" outline="#333333"
w="15.428571428571429" cy:nodeTransparency="0.8"
cy:nodeLabelFont="SansSerif-0-11" type="ELLIPSE" h="15.428571428571429"
width="1"/>
</node>
<node id="104" weight="0.03" label="A04">
+ <att type="string" name="name" value="Node 4"/>
<att type="string" name="type" value="1"/>
<att type="integer" name="ranking" value="4"/>
<att type="string" name="shape" value="DIAMOND"/>
@@ -34,6 +38,7 @@
<graphics x="387.25" y="448" fill="#cccccc" outline="#333333" w="12"
cy:nodeTransparency="0.8" cy:nodeLabelFont="SansSerif-0-11" type="ELLIPSE"
h="12" width="1"/>
</node>
<node id="105" weight="0.1" label="A05">
+ <att type="string" name="name" value="Node 5"/>
<att type="string" name="type" value="3"/>
<att type="integer" name="ranking" value="5"/>
<att type="string" name="shape" value="PARALLELOGRAM"/>
Modified: cytoscapeweb/trunk/cytoscapeweb/html-template/js/cytoscapeweb.js
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/html-template/js/cytoscapeweb.js
2011-09-20 20:53:22 UTC (rev 26888)
+++ cytoscapeweb/trunk/cytoscapeweb/html-template/js/cytoscapeweb.js
2011-09-20 20:56:51 UTC (rev 26889)
@@ -196,20 +196,20 @@
* <ul class="options">
* <li><code>network</code>: The model that
describes the network. Only this option is mandatory. It can be one of the
following formats:
* <ul><li>{@link
org.cytoscapeweb.NetworkModel}: A simple JavaScript object that defines the raw
data from which to build a network.</li>
- * <li><a
href="http://graphml.graphdrawing.org/primer/graphml-primer.html";
target="_blank">GraphML</a>: An XML format for graphs.</li>
- * <li><a
href="http://www.cs.rpi.edu/~puninj/XGMML/"; target="_blank">XGMML</a>: This XML
format allows you to define
+ * <li><a
href="http://graphml.graphdrawing.org/primer/graphml-primer.html";
rel="external">GraphML</a>: An XML format for graphs.</li>
+ * <li><a
href="http://www.cs.rpi.edu/~puninj/XGMML/"; rel="external">XGMML</a>: This XML
format allows you to define
* visual
properties (e.g. colors and shapes) and nodes positioning, if you want to,
* although using
the <code>visualStyle</code> and <code>layout</code> options is usually
better.</li>
- * <li><a
href="http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/Network_Formats/";
target="_blank">SIF</a>: A simpler text format
+ * <li><a
href="http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/Network_Formats/";
rel="external">SIF</a>: A simpler text format
* that can be
very useful if you do not need to set custom nodes/edges attributes.</li>
* </ul></li>
* <li><code>visualStyle</code>: an optional {@link
org.cytoscapeweb.VisualStyle} object to be applied on this network.</li>
* <li><code>layout</code>: an optional {@link
org.cytoscapeweb.Layout} object, or just the layout name.
* The default is
"ForceDirected", unless the network data is an
- * <a
href="http://www.cs.rpi.edu/~puninj/XGMML/"; target="_blank">XGMML</a>, whose
- * <code><a
href="http://www.cs.rpi.edu/~puninj/XGMML/draft-xgmml-20010628.html#NodeE";
target="_blank">node</a></code>
+ * <a
href="http://www.cs.rpi.edu/~puninj/XGMML/"; rel="external">XGMML</a>, whose
+ * <code><a
href="http://www.cs.rpi.edu/research/groups/pb/punin/public_html/XGMML/draft-xgmml-20010628.html#NodeE";
rel="external">node</a></code>
* elements contain
- * <code><a
href="http://www.cs.rpi.edu/~puninj/XGMML/draft-xgmml-20010628.html#GraphicsA";
target="_blank">graphics</a></code>
+ * <code><a
href="http://www.cs.rpi.edu/research/groups/pb/punin/public_html/XGMML/draft-xgmml-20010628.html#GLCPE";
rel="external">graphics</a></code>
* tags with defined
<code>x</code> and <code>y</code> attributes. In that case, the "Preset" layout
is applied by default.</li>
* <li><code>nodeLabelsVisible</code>: Boolean that
defines whether or not the node labels will be visible.
* The default
value is <code>true</code>.
@@ -651,8 +651,18 @@
},
/**
- * TODO: DOCUMENT ME
- *
+ * <p>Add new nodes and/or edges to the network.</p>
+ * <p>The rules described in {@link
org.cytoscapeweb.Visualization#addNode} and {@link
org.cytoscapeweb.Visualization#addEdge}
+ * are still valid here.</p>
+ * <p>You can add nodes and edges together and, when doing so, the
order of the elements in
+ * the array do not matter, because Cytoscape Web will first add all
the nodes, and then
+ * the edges.</p>
+ * <p>The new element must have a <code>group</code> field set to
either <code>"nodes"</code> or <code>"edges"</code>,
+ * because {@link org.cytoscapeweb.Node} and {@link
org.cytoscapeweb.Edge} objects are untype objects and Cytoscape Web
+ * has no other safe way of making the distinction between the two
types.</p>
+ * <p>If the new elements contain visual properties (e.g. color,
opacity), they are simply ignored and Cytoscape Web applies
+ * new visual property values according to the current {@link
org.cytoscapeweb.VisualStyle} and {@link org.cytoscapeweb.VisualStyleBypass}.
+ * The node positions (x, y), if specified, are respected, though.</p>
* @example
* // 1. Add two nodes with no data (IDs will be created
automatically):
* var nodesArray = [ { group: "nodes", x: 10, y: 35 },
@@ -663,7 +673,15 @@
* var array = [ { group: "nodes", x: 10, y: 35, data: { id: "n01" } },
* { group: "nodes", x: 20, y: 70, data: { id: "n02" } },
* { group: "edges", data: { source: "n01", target:
"n02" } } ];
- * vis.addElements(array, true);
+ * var elements = vis.addElements(array, true);
+ * @param {Array} [items] The nodes and edges to be added to the
network.
+ * The array must contain {@link
org.cytoscapeweb.Node} and/or {@link org.cytoscapeweb.Edge} objects.
+ * @param {Boolean} [updateVisualMappers] It tells Cytoscape Web to
reapply the visual mappers
+ * to the network view after
removing the elements.
+ * @return {Array} The new created elements ({@link
org.cytoscapeweb.Node} and {@link org.cytoscapeweb.Edge} objects).
+ * @see org.cytoscapeweb.Visualization#removeElements
+ * @see org.cytoscapeweb.Visualization#addNode
+ * @see org.cytoscapeweb.Visualization#addEdge
*/
addElements: function(/*items, updateVisualMappers*/) {
var items, updateVisualMappers = false;
@@ -680,9 +698,11 @@
/**
* <p>Create a new node and add it to the network view.<p>
* <p>If the node <code>id</code> is not specified, Cytoscape Web
creates a new one automatically.</p>
- * <p>If you try to add data attributes that have not been previously
defined,
- * Cytoscape Web will automatically add the necessary field
definitions, although it might be safer to always add the
- * fields to the schema first, by calling {@link
org.cytoscapeweb.Visualization#addDataField}.</p>
+ * <p>If the data contains attributes that have not been previously
defined in the {@link org.cytoscapeweb.DataSchema},
+ * Cytoscape Web will throw an error. To prevent that, you simply add
the new fields to the schema first,
+ * by calling {@link org.cytoscapeweb.Visualization#addDataField}.</p>
+ * <p>Keep in mind that {@link
org.cytoscapeweb.Visualization#addElements} is much faster if you have to
+ * add more than one element at once.</p>
* @example
* var data = { id: "n4",
* label: "MYO2 (Yeast)",
@@ -698,6 +718,7 @@
* The default value is
<code>false</code>.
* @return {org.cytoscapeweb.Node} The new created node object.
* @see org.cytoscapeweb.Visualization#addEdge
+ * @see org.cytoscapeweb.Visualization#addElements
* @see org.cytoscapeweb.Visualization#removeElements
*/
addNode: function (x, y/*, data, updateVisualMappers*/) {
@@ -710,10 +731,13 @@
/**
* <p>Create a new edge linking two nodes and add it to the network
view.<p>
* <p>If the edge <code>id</code> is not specified, Cytoscape Web
creates a new one automatically.</p>
- * <p>Throws exception if missing <code>source</code> or
<code>target</code>.</p>
- * <p>If you try to add data attributes that have not been previously
defined,
- * Cytoscape Web will automatically add the necessary field
definitions, although it might be safer to always add the
- * fields to the schema first, by calling {@link
org.cytoscapeweb.Visualization#addDataField}.</p>
+ * <p>However the <code>source</code> and <code>target</code> data
fields are mandatory, and Cytoscape Web
+ * throws an error if any of them is missing.</p>
+ * <p>If the data contains attributes that have not been previously
defined in the {@link org.cytoscapeweb.DataSchema},
+ * Cytoscape Web will throw an error. To prevent that, just add the
new fields to the schema first,
+ * by calling {@link org.cytoscapeweb.Visualization#addDataField}.</p>
+ * <p>You might also want to take a look at {@link
org.cytoscapeweb.Visualization#addElements}, which is much faster
+ * when adding more than one element at once.</p>
* @example
* var data = { id: "e10",
* source: "n1",
@@ -729,6 +753,7 @@
* to the network view after
adding the edge.
* @return {org.cytoscapeweb.Edge} The new created edge object.
* @see org.cytoscapeweb.Visualization#addNode
+ * @see org.cytoscapeweb.Visualization#addElements
* @see org.cytoscapeweb.Visualization#removeElements
*/
addEdge: function (data/*, updateVisualMappers*/) {
@@ -1153,7 +1178,7 @@
* return a boolean value indicating the
visibility of that element.
* So, if it returns false, that node or edge
will be hidden.
* If the argument is an array, it must contain
the IDs or the Node/Edge objects
- * you want to make visible.
+ * you want to make or keep visible.
* @param {Boolean} [updateVisualMappers] It tells Cytoscape Web to
update and reapply the visual mappers
* to the network view after
the filtering action is done.
* Remember that continuous
mappers ignore filtered out elements
@@ -1245,7 +1270,7 @@
},
/**
- * <p>Return the network data as <a
href="http://graphml.graphdrawing.org/primer/graphml-primer.html";
target="_blank">GraphML</a>.</p>
+ * <p>Return the network data as <a
href="http://graphml.graphdrawing.org/primer/graphml-primer.html";
rel="external">GraphML</a>.</p>
* @return {String} The XML text.
* @see org.cytoscapeweb.Visualization#xgmml
* @see org.cytoscapeweb.Visualization#sif
@@ -1256,7 +1281,7 @@
},
/**
- * <p>Return the network data as <a
href="http://www.cs.rpi.edu/~puninj/XGMML/"; target="_blank">XGMML</a>.</p>
+ * <p>Return the network data as <a
href="http://www.cs.rpi.edu/~puninj/XGMML/"; rel="external">XGMML</a>.</p>
* @return {String} The XML text.
* @see org.cytoscapeweb.Visualization#graphml
* @see org.cytoscapeweb.Visualization#sif
@@ -1267,19 +1292,27 @@
},
/**
- * <p>Return the network data as <a
href="http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/Network_Formats/";
target="_blank">Simple Interaction Format (SIF)</a>.</p>
+ * <p>Return the network data as <a
href="http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/Network_Formats/";
rel="external">Simple Interaction Format (SIF)</a>.</p>
* <p>Cytoscape Web uses tab characters to delimit the fields, because
the node and interaction names may contain spaces.</p>
- * <p>The node name in the SIF text is taken from the node's
<code>data.id</code> attribute.</p>
+ * <p>By default, the node name in the SIF text is taken from the
node's <code>data.id</code> attribute.
+ * You can choose any other node attribute to be the node name by
passing the <code>nodeAttr</code> option.
+ * Of course the custom node field should have unique values.</p>
* <p>Cytoscape Web tries to get the interaction name from the edge's
<code>data.interaction</code> attribute.
- * You can choose any other edge attribute to be the interaction name
by passing an <code>interactionAttr</code> parameter.
+ * You can choose any other edge attribute to be the interaction name
by passing the <code>interactionAttr</code> option.
* If the edge data does not have the defined interaction field,
Cytoscape Web just uses the edge <code>id</code>.</p>
* @example
* var xml = '<graphml>' +
- * // Create a custom "type" attribute:
+ * // Create a custom node "label" attribute:
+ * '<key id="label" for="node" attr.name="label"
attr.type="string"/>' +
+ * // Create a custom edge "type" attribute:
* '<key id="type" for="edge" attr.name="type"
attr.type="string"/>' +
* '<graph>' +
- * '<node id="1"/>' +
- * '<node id="2"/>' +
+ * '<node id="1">' +
+ * '<data key="label">Node 1</data>'
+
+ * '</node>' +
+ * '<node id="2">' +
+ * '<data key="label">Node 2</data>'
+
+ * '</node>' +
* '<edge source="1" target="2">' +
* '<data
key="type">co-expression</data>' +
* '</edge>' +
@@ -1292,23 +1325,27 @@
* var vis = new org.cytoscapeweb.Visualization("container_id");
*
* vis.ready(function() {
- * // Export to SIF, using the "type" attribute as edge
interaction:
- * var text = vis.sif('type');
+ * // Export to SIF, using the "label" as node ID and edge "type"
as edge interaction:
+ * var text = vis.sif({ nodeAttr: 'label', interactionAttr:
'type'});
*
- * // text == '1\tco-expression\t2\n' +
- * // '2\tco-localization\t1\n'
+ * // text == 'Node 1\tco-expression\tNode 2\n' +
+ * // 'Node 2\tco-localization\Node 1\n'
* });
*
* vis.draw({ network: xml });
*
- * @param {String} [interactionAttr] Optional edge attribute name to
be used as the SIF interaction name.
+ * @param {Object} [options] Non-mandatory settings:
+ * <ul class="options">
+ * <li><code>nodeAttr</code>:</strong>
Optional node attribute name to be used as node name.</li>
+ *
<li><code>interactionAttr</code>:</strong> Optional edge attribute name to be
used as interaction name.</li>
+ * </ul>
* @return {String} The SIF text.
* @see org.cytoscapeweb.Visualization#graphml
* @see org.cytoscapeweb.Visualization#xgmml
* @see org.cytoscapeweb.Visualization#networkModel
*/
- sif: function (interactionAttr) {
- return this.swf().getNetworkAsText("sif", { interactionAttr:
interactionAttr });
+ sif: function (options) {
+ return this.swf().getNetworkAsText("sif", options);
},
/**
@@ -1552,6 +1589,8 @@
* the new one and only one menu item will be displayed.</p>
* <p>It is possible to add more than one menu item with the same
label, but only if they are added to
* different groups.</p>
+ * <p><b>Important:</b> Since the context menu is rendered by Flash,
be aware of these
+ * <a
href="http://help.adobe.com/en_US/FlashPlatform/reference/actionscript/3/flash/ui/ContextMenuItem.html";
rel="external">restrictions</a>.</p>
*
* @example
* // We will use the context menu to select the first neighbors of the
@@ -1681,7 +1720,7 @@
/**
* <p>Redefine this function if you want to use another method to
detect the Flash Player version
* and embed the SWF file (e.g. SWFObject).</p>
- * <p>By default, Adobe's <a
href="http://www.adobe.com/products/flashplayer/download/detection_kit/";
target="_blank">Flash Player Detection Kit</a>
+ * <p>By default, Adobe's <a
href="http://www.adobe.com/products/flashplayer/download/detection_kit/";
rel="external">Flash Player Detection Kit</a>
* is used.</p>
* @requires <code>AC_OETags.js</code> and
<code>playerProductInstall.swf</code>
*/
Modified: cytoscapeweb/trunk/cytoscapeweb/html-template/js/tests.js
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/html-template/js/tests.js 2011-09-20
20:53:22 UTC (rev 26888)
+++ cytoscapeweb/trunk/cytoscapeweb/html-template/js/tests.js 2011-09-20
20:56:51 UTC (rev 26889)
@@ -1344,16 +1344,19 @@
test("SIF", function() {
var sif = vis.sif();
var edges = vis.edges();
+ // Default fields:
$.each(edges, function(i, e) {
var inter = e.data.interaction ? e.data.interaction : e.data.id;
var line = e.data.source + "\t" + inter + "\t" + e.data.target;
ok(sif.indexOf(line) > -1, "SIF text should have the line:
'"+line+"'");
});
- // Now replace the default interaction field:
- var sif = vis.sif("type");
+ // Now replace the default node and interaction fields:
+ var sif = vis.sif({ nodeAttr: "name", interactionAttr: "type" });
var edges = vis.edges();
$.each(edges, function(i, e) {
- var line = e.data.source + "\t" + e.data.type + "\t" +
e.data.target;
+ var src = vis.node(e.data.source).data.name;
+ var tgt = vis.node(e.data.target).data.name;
+ var line = src + "\t" + e.data.type + "\t" + tgt;
ok(sif.indexOf(line) > -1, "SIF text should have the line:
'"+line+"'");
});
});
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/GraphProxy.as
===================================================================
--- cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/GraphProxy.as
2011-09-20 20:53:22 UTC (rev 26888)
+++ cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/GraphProxy.as
2011-09-20 20:56:51 UTC (rev 26889)
@@ -765,8 +765,7 @@
if (format === "graphml") {
out = new GraphMLConverter().write(dtSet);
} else {
- var interaction:String = options != null ?
options.interactionAttr : null;
- out = new SIFConverter(interaction).write(dtSet);
+ out = new SIFConverter(options).write(dtSet);
}
}
Modified:
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/converters/SIFConverter.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/converters/SIFConverter.as
2011-09-20 20:53:22 UTC (rev 26888)
+++
cytoscapeweb/trunk/cytoscapeweb/src/org/cytoscapeweb/model/converters/SIFConverter.as
2011-09-20 20:56:51 UTC (rev 26889)
@@ -95,13 +95,15 @@
// ========[ PRIVATE PROPERTIES
]===========================================================
- private var _interaction:String;
+ private var _nodeAttr:String;
+ private var _interactionAttr:String;
// ========[ CONSTRUCTOR
]==================================================================
- public function SIFConverter(interactionAttr:String=null) {
+ public function SIFConverter(options:Object=null) {
super();
- _interaction = interactionAttr != null ? interactionAttr :
INTERACTION;
+ _nodeAttr = options != null ? options.nodeAttr : ID;
+ _interactionAttr = options != null ? options.interactionAttr :
INTERACTION;
}
// ========[ PUBLIC PROPERTIES
]============================================================
@@ -117,23 +119,34 @@
var sif:String = "";
if (ds != null) {
- var lookup:Object = {};
+ var nodeIds:Object = {/*id -> sif_id*/};
+ var writtenNodes:Object = {/*id -> boolean*/};
var nodes:Array = ds.nodes.data;
var edges:Array = ds.edges.data;
-
- for each (var e:Object in edges) {
- var src:String = e[SOURCE];
- var tgt:String = e[TARGET];
- var inter:String = e.hasOwnProperty(_interaction) ?
e[_interaction] : e.id;
+ var n:Object, e:Object;
+ var id:*, src:String, tgt:String, inter:String;
+
+ for each (n in nodes) {
+ id = n.hasOwnProperty(_nodeAttr) ? n[_nodeAttr] : n.id;
+ nodeIds[n.id] = id;
+ }
+
+ for each (e in edges) {
+ src = nodeIds[e[SOURCE]];
+ tgt = nodeIds[e[TARGET]];
+ inter = e.hasOwnProperty(_interactionAttr) ?
e[_interactionAttr] : e.id;
sif += (src + "\t" + inter + "\t" + tgt + "\n");
- lookup[src] = true;
- lookup[tgt] = true;
+ writtenNodes[src] = true;
+ writtenNodes[tgt] = true;
}
- for each (var n:Object in nodes) {
- if (!lookup[n.id]) {
- sif += n.id + "\n";
- lookup[n.id] = true;
+
+ for each (n in nodes) {
+ id = nodeIds[n.id];
+
+ if (!writtenNodes[id]) {
+ sif += id + "\n";
+ writtenNodes[id] = true;
}
}
@@ -158,7 +171,7 @@
edgeSchema.addField(new DataField(ID, DataUtil.STRING));
edgeSchema.addField(new DataField(LABEL, DataUtil.STRING));
- edgeSchema.addField(new DataField(_interaction, DataUtil.STRING));
+ edgeSchema.addField(new DataField(_interactionAttr,
DataUtil.STRING));
edgeSchema.addField(new DataField(SOURCE, DataUtil.STRING));
edgeSchema.addField(new DataField(TARGET, DataUtil.STRING));
edgeSchema.addField(new DataField(DIRECTED, DataUtil.BOOLEAN,
false));
@@ -230,7 +243,7 @@
protected function createEdgeData(interaction:String, source:String,
target:String):Object {
var data:Object = {};
data[ID] = source + " (" + interaction + ") " + target;
- data[_interaction] = data[LABEL] = interaction;
+ data[_interactionAttr] = data[LABEL] = interaction;
data[SOURCE] = source;
data[TARGET] = target;
data[DIRECTED] = false;
Modified:
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/model/converters/SIFConverterTest.as
===================================================================
---
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/model/converters/SIFConverterTest.as
2011-09-20 20:53:22 UTC (rev 26888)
+++
cytoscapeweb/trunk/cytoscapeweb/src-test/org/cytoscapeweb/model/converters/SIFConverterTest.as
2011-09-20 20:56:51 UTC (rev 26889)
@@ -99,7 +99,7 @@
}
}
- public function testWrite():void {
+ public function testWriteWithDefaultFields():void {
var ds:DataSet = Fixtures.getDataSet(Fixtures.GRAPHML_SIMPLE);
var data:Data = Data.fromDataSet(ds);
var nodes:Array = data.nodes.toDataArray();
@@ -115,7 +115,8 @@
}
for each (e in edges) {
var inter:String = e.hasOwnProperty("interaction") ?
e.interaction : e.id;
- assertTrue("Missing interaction: " + inter, sif.indexOf(inter)
> -1);
+ var line:String = e.source + "\t" + inter + "\t" + e.target;
+ assertTrue("Missing line: " + line, sif.indexOf(line) > -1);
}
// If we parse the SIF file again, will it generate the same graph?
@@ -126,14 +127,31 @@
assertEquals(nodes.length, nodes2.length);
assertEquals(edges.length, edges2.length);
+ }
+
+ public function testWriteWithCustomFields():void {
+ var ds:DataSet = Fixtures.getDataSet(Fixtures.GRAPHML_SIMPLE);
+ var data:Data = Data.fromDataSet(ds);
+ var nodes:Array = data.nodes.toDataArray();
+ var edges:Array = data.edges.toDataArray();
+ var n:Object, e:Object;
+
+ var out:IDataOutput = new SIFConverter().write(ds);
+ var sif:String = "" + out;
- // Test again, this time replacing the default "interaction" field:
- out = new SIFConverter("label").write(ds);
- sif = "" + out;
-
- for each (e in edges) {
- assertTrue("Missing interaction: " + e.label,
sif.indexOf(e.label) > -1);
+ // Does the generated SIF contain all nodes and edges?
+ for each (n in nodes) {
+ assertTrue("Missing node: " + n.id, sif.indexOf(n.id) > -1);
}
+
+ // If we parse the SIF file again, will it generate the same graph?
+ var ds2:DataSet = new SIFConverter().parse(sif);
+ var data2:Data = Data.fromDataSet(ds2);
+ var nodes2:Array = data2.nodes.toDataArray();
+ var edges2:Array = data2.edges.toDataArray();
+
+ assertEquals(nodes.length, nodes2.length);
+ assertEquals(edges.length, edges2.length);
}
// ========[ PRIVATE METHODS
]==============================================================
--
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