diff --git a/.metadata/.log b/.metadata/.log
index 3a2ab441..5feacfcc 100644
--- a/.metadata/.log
+++ b/.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
diff --git a/.metadata/.plugins/com.aptana.core.io/connections.1 b/.metadata/.plugins/com.aptana.core.io/connections.1
deleted file mode 100644
index 46f15223..00000000
--- a/.metadata/.plugins/com.aptana.core.io/connections.1
+++ /dev/null
@@ -1,2 +0,0 @@
-
-
\ No newline at end of file
diff --git a/.metadata/.plugins/com.aptana.syncing.core/defaultConnection.1 b/.metadata/.plugins/com.aptana.syncing.core/defaultConnection.1
deleted file mode 100644
index e6c05502..00000000
--- a/.metadata/.plugins/com.aptana.syncing.core/defaultConnection.1
+++ /dev/null
@@ -1,7 +0,0 @@
-
-
-
-Default
-file:/home/opencog
-
-
\ No newline at end of file
diff --git a/.metadata/.plugins/com.aptana.syncing.core/sites.1 b/.metadata/.plugins/com.aptana.syncing.core/sites.1
deleted file mode 100644
index dc24d7a5..00000000
--- a/.metadata/.plugins/com.aptana.syncing.core/sites.1
+++ /dev/null
@@ -1,2 +0,0 @@
-
-
\ No newline at end of file
diff --git a/.metadata/.plugins/org.eclipse.core.resources/.root/1.tree b/.metadata/.plugins/org.eclipse.core.resources/.root/1.tree
deleted file mode 100644
index c87dc296..00000000
Binary files a/.metadata/.plugins/org.eclipse.core.resources/.root/1.tree and /dev/null differ
diff --git a/.metadata/.plugins/org.eclipse.core.resources/.safetable/com.aptana.core.io.1 b/.metadata/.plugins/org.eclipse.core.resources/.safetable/com.aptana.core.io.1
deleted file mode 100644
index 0dff3f68..00000000
--- a/.metadata/.plugins/org.eclipse.core.resources/.safetable/com.aptana.core.io.1
+++ /dev/null
@@ -1,3 +0,0 @@
-#safe table
-#Thu Nov 06 10:39:19 EAT 2014
-connections=connections.1
diff --git a/.metadata/.plugins/org.eclipse.core.resources/.safetable/com.aptana.syncing.core.1 b/.metadata/.plugins/org.eclipse.core.resources/.safetable/com.aptana.syncing.core.1
deleted file mode 100644
index a769d549..00000000
--- a/.metadata/.plugins/org.eclipse.core.resources/.safetable/com.aptana.syncing.core.1
+++ /dev/null
@@ -1,4 +0,0 @@
-#safe table
-#Thu Nov 06 10:39:19 EAT 2014
-defaultConnection=defaultConnection.1
-sites=sites.1
diff --git a/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources b/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources
index 2c3abda8..b9c429fa 100644
Binary files a/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources and b/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources differ
diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/com.aptana.theme.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/com.aptana.theme.prefs
index cec0058d..a8ea562a 100644
--- a/.metadata/.plugins/org.eclipse.core.runtime/.settings/com.aptana.theme.prefs
+++ b/.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
diff --git a/.metadata/.plugins/org.eclipse.e4.workbench/workbench.xmi b/.metadata/.plugins/org.eclipse.e4.workbench/workbench.xmi
index 378bf593..a38c553d 100644
--- a/.metadata/.plugins/org.eclipse.e4.workbench/workbench.xmi
+++ b/.metadata/.plugins/org.eclipse.e4.workbench/workbench.xmi
@@ -3,7 +3,7 @@
activeSchemeId:org.eclipse.ui.defaultAcceleratorConfigurationModelMigrationProcessor.001
-
+
@@ -68,9 +68,9 @@
-
+
-
+ newtablook
@@ -159,9 +159,15 @@
ViewcategoryTag:Studio
-
+
+ ViewcategoryTag:Studio
+
+ ViewMenu
+ menuContribution:menu
+
+
@@ -184,39 +190,48 @@
Draggable
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+ toolbarSeparator
+
+ Draggable
+
+
+ Draggable
-
-
-
-
-
-
+
+
+
+
+
+
+
+ Draggable
+
+ Draggable
-
-
-
-
-
+
+
+
+
+ toolbarSeparator
@@ -224,13 +239,12 @@
Draggable
-
-
-
-
-
-
-
+
+
+
+
+
+ toolbarSeparator
@@ -242,8 +256,8 @@
Draggable
-
-
+
+ stretch
@@ -268,8 +282,19 @@
Draggable
-
-
+
+
+ TrimStack
+
+
+
+
+ TrimStack
+
+
+ TrimStack
+
+
diff --git a/.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml b/.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml
index e1c99a7f..0b1556df 100644
--- a/.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml
+++ b/.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml
@@ -1,8 +1,8 @@
-
-
+
+
@@ -12,4 +12,6 @@
+
+
diff --git a/AtomViewer/WebContent/atom_viewer.html b/AtomViewer/WebContent/atom_viewer.html
index 2e10d213..076f9f44 100755
--- a/AtomViewer/WebContent/atom_viewer.html
+++ b/AtomViewer/WebContent/atom_viewer.html
@@ -187,8 +187,8 @@
-
-
+
diff --git a/AtomViewer/WebContent/lib/atomviewer/av_main.js b/AtomViewer/WebContent/lib/atomviewer/av_main.js
index a0bdc8f6..1c042819 100755
--- a/AtomViewer/WebContent/lib/atomviewer/av_main.js
+++ b/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);
}
diff --git a/AtomViewer/WebContent/lib/atomviewer/views/av_graph_view.js b/AtomViewer/WebContent/lib/atomviewer/views/av_graph_view.js
index 85f9bcd3..55ce4b7f 100755
--- a/AtomViewer/WebContent/lib/atomviewer/views/av_graph_view.js
+++ b/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;
}
diff --git a/AtomViewer/WebContent/lib/atomviewer/views/av_views.js b/AtomViewer/WebContent/lib/atomviewer/views/av_views.js
index 6981a68c..e949b890 100755
--- a/AtomViewer/WebContent/lib/atomviewer/views/av_views.js
+++ b/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 = "
(No Data)
";
diff --git a/AtomViewer/WebContent/lib/d3/views/av_d3grahp.js b/AtomViewer/WebContent/lib/d3/views/av_d3grahp.js
index 2b2c4d0e..d67e0837 100644
--- a/AtomViewer/WebContent/lib/d3/views/av_d3grahp.js
+++ b/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;