filter atom first

.metadata/.log

@@ -20,3 +20,30 @@ java.util.ConcurrentModificationException
 
 !ENTRY org.eclipse.core.jobs 2 2 2014-11-06 10:39:20.691
 !MESSAGE Job found still running after platform shutdown.  Jobs should be canceled by the plugin that scheduled them during shutdown: com.aptana.usage.internal.DefaultAnalyticsEventHandler$1
+!SESSION 2015-01-20 12:03:23.026 -----------------------------------------------
+eclipse.buildId=3.6.0.201407100658
+java.version=1.7.0_72
+java.vendor=Oracle Corporation
+BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_US
+Command-line arguments:  -os linux -ws gtk -arch x86_64
+
+!ENTRY org.eclipse.core.jobs 2 2 2015-01-20 12:03:48.806
+!MESSAGE Job found still running after platform shutdown.  Jobs should be canceled by the plugin that scheduled them during shutdown: com.aptana.usage.internal.DefaultAnalyticsEventHandler$1
+!SESSION 2015-01-21 14:37:00.194 -----------------------------------------------
+eclipse.buildId=3.6.0.201407100658
+java.version=1.7.0_72
+java.vendor=Oracle Corporation
+BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_US
+Command-line arguments:  -os linux -ws gtk -arch x86_64
+
+!ENTRY org.eclipse.core.jobs 2 2 2015-01-21 14:39:22.033
+!MESSAGE Job found still running after platform shutdown.  Jobs should be canceled by the plugin that scheduled them during shutdown: com.aptana.usage.internal.DefaultAnalyticsEventHandler$1
+!SESSION 2015-01-21 15:21:35.536 -----------------------------------------------
+eclipse.buildId=3.6.0.201407100658
+java.version=1.7.0_72
+java.vendor=Oracle Corporation
+BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_US
+Command-line arguments:  -os linux -ws gtk -arch x86_64
+
+!ENTRY org.eclipse.core.jobs 2 2 2015-01-21 15:22:31.149
+!MESSAGE Job found still running after platform shutdown.  Jobs should be canceled by the plugin that scheduled them during shutdown: com.aptana.usage.internal.DefaultAnalyticsEventHandler$1

.metadata/.plugins/org.eclipse.core.runtime/.settings/com.aptana.theme.prefs

@@ -1,7 +1,7 @@
 ACTIVE_HYPERLINK_COLOR=13,17,113
 ACTIVE_THEME=Light Studio
 HYPERLINK_COLOR=13,17,113
-THEME_CHANGED=1415259489309
+THEME_CHANGED=1421842901048
 eclipse.preferences.version=1
 hyperlinkColor=13,17,113
 hyperlinkColor.SystemDefault=false

.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml

@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <section name="Workbench">
 	<section name="org.eclipse.ui.internal.QuickAccess">
-		<item value="1000" key="dialogWidth"/>
-		<item value="562" key="dialogHeight"/>
+		<item value="1200" key="dialogWidth"/>
+		<item value="675" key="dialogHeight"/>
 		<list key="orderedProviders">
 		</list>
 		<list key="textArray">
@@ -12,4 +12,6 @@
 		<list key="textEntries">
 		</list>
 	</section>
+	<section name="NewWizardAction">
+	</section>
 </section>

AtomViewer/WebContent/atom_viewer.html

@@ -187,8 +187,8 @@
 					<br/>
 					<br/>
 					<div style="text-align: center;">
-						<!--<input type="button" data-dojo-type="dijit/form/Button" id="idBtnCtrlRefresh" intermediateChanges="false" label="Connect/Refresh..." iconClass="dijitNoIcon" onclick=onclickfuncalls()>-->
-						<input type="button" data-dojo-type="dijit/form/Button" id="idBtnCtrlRefresh" intermediateChanges="false" label="Connect/Refresh..." iconClass="dijitNoIcon" onclick=onClickRefresh()>
+						<!--<input type="button" data-dojo-type="dijit/form/Button" id="idBtnCtrlRefresh" intermediateChanges="false" label="Connect/Refresh..." iconClass="dijitNoIcon" onclick=onclickfuncalls()>
+						<input type="button" data-dojo-type="dijit/form/Button" id="idBtnCtrlRefresh" intermediateChanges="false" label="Connect/Refresh..." iconClass="dijitNoIcon" onclick=onClickRefresh()>-->
 
 						</input>
 					</div>

AtomViewer/WebContent/lib/atomviewer/av_main.js

@@ -408,7 +408,7 @@ function resetQueryParameters()
  */
 function disableDataButtons(disabled)
 {
-    av.Registry.byId("idBtnCtrlRefresh").setDisabled(disabled);
+    //av.Registry.byId("idBtnCtrlRefresh").setDisabled(disabled);
     av.Registry.byId("idBtnApplyFilters").setDisabled(disabled);
     av.Registry.byId("idBtnClearFilters").setDisabled(disabled);
 }

AtomViewer/WebContent/lib/atomviewer/views/av_graph_view.js

@@ -286,6 +286,30 @@ function generateGraphJSON()
 
         graph_json.push(graph_node);
     }
+	console.log("Jit implemntation",graph_json);
+    return graph_json;
+}
+
+
+function generateGraphJSONForD3()
+{
+    var graph_json = new Array();
+
+    var node_limit = av.atom_data.length;
+    if (node_limit > MAX_GRAPH_NODES)
+    {
+        // Must cap the number of nodes so Jit graph doesn't crash:
+        node_limit = MAX_GRAPH_NODES;
+
+        // TODO: a better idea is to change to a different graph type that can
+        // show all the nodes as points or something (like a galaxy of stars).
+    }
+
+    for (var i = 0; i < node_limit; i++)
+    {
+        var graph_node =av.atom_data[i];
+        graph_json.push(graph_node);
+    }
 
     return graph_json;
 }

AtomViewer/WebContent/lib/atomviewer/views/av_views.js

@@ -49,7 +49,7 @@ function updateAllViews()
 
 }
 
-var jsonobj={};
+//var jsonobj={};
 function updateD3Graph(){
 
 	  //av_graph.fdGraph = null;
@@ -58,8 +58,9 @@ function updateD3Graph(){
      	//Clearing what ever in html idTestTab div and redrow the d3 graph 
      	av.DOM.byId("idTestTab").innerHTML = "";
 
-    	jsonobj=av.atom_data;
-        updateD3GraphView(jsonobj);
+    	//jsonobj=generateGraphJSONForD3();
+    	//jsonobj=av.atom_data;
+        updateD3GraphView(generateGraphJSONForD3());
      }else
      {
         av.DOM.byId("idTestTab").innerHTML = "<h1 align='center'>(No Data)</h1>";

AtomViewer/WebContent/lib/d3/views/av_d3grahp.js

@@ -39,24 +39,43 @@ function updateD3GraphView(json) {
 	var gui;
 	var links = [];
 	var index = 0;
-
+	
 	// determing the source and destination of the the link
 	for (var n = 0; n < json.length; n++) {
+		//console.log(json[n]);
 		if (json[n].outgoing.length > 0) {
 			for (var outindex = 0; outindex < json[n].outgoing.length; outindex++) {
 				var templink = {};
-
+				
 				for (var i = 0; i < json.length; i++) {
 					if (json[i].handle == json[n].outgoing[outindex]) {
 						templink["source"] = n;
 						templink["target"] = i;
 						links[index] = templink;
+						index++;
+						break;
+					}
+				}
+
+			}
+		}
+		/*
+		if (json[n].incoming.length > 0) {
+			for (var inindex = 0; inindex < json[n].incoming.length; inindex++) {
+				var templink = {};
+				
+				for (var i = 0; i < json.length; i++) {
+					if (json[i].handle == json[n].ingoing[inindex]) {
+						templink["source"] = n;
+						templink["target"] = i;
+						links[index] = templink;
+						index++;
 						break;
 					}
 				}
-				index++;
 			}
 		}
+		*/
 	}
 	console.log(links);
 
@@ -215,7 +234,6 @@ function updateD3GraphView(json) {
 					if (!arrycontain(currentNde)) {
 						connectedNode[connectedNode.length] = currentNde;
 						recurse(currentNde);
-						console.log("out true");
 					}
 				});
 			//return connectedNode;
@@ -238,15 +256,17 @@ function updateD3GraphView(json) {
 
 
 	node.on("mouseover", function(d) {
-
+		
 		node.classed("node-active", function(o) {
 			thisOpacity = isConnected(d, o) ? true : false;
 			this.setAttribute('fill-opacity', thisOpacity);
 			return thisOpacity;
 		});
+
 		link.classed("link-active", function(o) {
 			return o.source === d || o.target === d ? true : false;
 		});
+
 		d3.select(this).classed("node-active", true);
 		d3.select(this).select("circle").transition().duration(750).attr("r", function(d) {
 			if (d.name == "")
@@ -276,12 +296,12 @@ function updateD3GraphView(json) {
 		zoom.translate([dcx, dcy]);
 		container.transition().duration(750).attr("transform", "translate(" + dcx + "," + dcy + ")scale(" + zoom.scale() + ")");
 		showSelectedAtom(d);
-		/*
+
 		 d3.select(this).select("circle")
 		 .transition()
 		 .duration(500)
 		 .attr("r", function(d){ return 1.4 * node_radius(d);});
-		 */
+
 		node.transition(5000).duration(1000).style("opacity", function(o) {
 			//console.log(d);
 			return isConnected(d, o) ? 1.0 : 1e-6;