Updated to have the flower type vis

gnvweb/eneg/src/main/resources/public/js/vis/ajaxCalls.js

@@ -14,7 +14,7 @@ function getNetworksFromBedFile() {
 		data : {request: "status"},
 		success : function(data) {
 			   run_networks_in_bed(JSON.parse(data));
-               data['threeD_attr'] = set_up_3D_attr();
+               //data['threeD_attr'] = set_up_3D_attr();
 		},
 		error : function(e) {
 			console.log("ERROR: ", e);
@@ -42,11 +42,15 @@ function getNetworkByChromAndPosition(chrom, start, end) {
 		data : data,
 		success : function(data) {
 		        // Run the two D version
-                dna_attr.data = JSON.parse(data)[0];
-                run_dna_visualisation();
+                dna_attr.data = JSON.parse(data);
+                // Set up the facts for the data so we can easily filter
+                // in dataProcessing we create a crossfilter instance.
+                process_networks();
+                // Always run the vis with the default network
+                run_dna_visualisation(0);
                 // Run the 3D version
                 // Clear the inner HTML first
-                threeD_attr = set_up_3D_attr();
+                //threeD_attr = set_up_3D_attr();
 
 		},
 		error : function(e) {

gnvweb/eneg/src/main/resources/public/js/vis/dataProcessing.js

@@ -198,3 +198,139 @@ var filter_on_gene = function(gene) {
 
 
 
+
+
+
+
+
+
+/**
+ * ====================================================================================================================
+ *                              Create a new crossfilter instance for each network range
+ * ====================================================================================================================
+ */
+
+var set_up_network_data = function (data) {
+     // Set up the crossfilter facts. --> use a JSON object i.e. data
+     // that contains elements (array) these get translated to facts.
+     // Data contains the following:
+     //      1.start     2.end   3. Array of networks that have that start and end.
+     var network_facts = crossfilter(data);
+
+     // Store globally
+     processed_data["network_facts"] = network_facts;
+}
+
+
+// Need to remove the facts when we get a new network
+var remove_network_data = function() {
+    if (processed_data.network_facts != []) {
+        processed_data.network_facts.remove();
+    }
+}
+
+/**
+ * ============================================================================
+ *                        Create interaction dimensions
+ * ============================================================================
+ */
+
+/**
+ * Make a dimension on the network ID to make it quick to filter on that ID.
+ */
+var create_network_dimension = function() {
+    // Create a dimesnsion on the chromosone of the gene or network
+    var network_dimension = processed_data.network_facts.dimension(function (d) {
+        return d.network_id;
+    });
+
+    // Store Globally
+    processed_data["network_dimension"] = network_dimension;
+};
+
+/**
+ * Make a dimension tpo easily filter between edges and interactions
+ */
+var create_network_type_dimension = function() {
+    // Create a dimesnsion on the chromosone of the gene or network
+    var network_type_dimension = processed_data.network_facts.dimension(function (d) {
+        return d.type;
+    });
+
+    // Store Globally
+    processed_data["network_type_dimension"] = network_type_dimension;
+};
+
+
+/**
+ * Make a dimension on the start to make it easy to filter.
+ */
+var create_interaction_start_dimension = function() {
+    // Create a dimesnsion on the chromosone of the gene or network
+    var interaction_start_dimension = processed_data.network_facts.dimension(function (d) {
+        return d.start;
+    });
+
+    // Store Globally
+    processed_data["interaction_start_dimension"] = interaction_start_dimension;
+};
+
+
+/**
+ * Make a dimension on the start to make it easy to filter.
+ */
+var create_interaction_end_dimension = function() {
+    // Create a dimesnsion on the chromosone of the gene or network
+    var interaction_end_dimension = processed_data.network_facts.dimension(function (d) {
+        return d.end;
+    });
+
+    // Store Globally
+    processed_data["interaction_end_dimension"] = interaction_end_dimension;
+}
+
+/**
+ *  ===================================================================================================================
+ *                           Want filters: 1. Networks (need to check if in array)
+ *  ===================================================================================================================
+ */
+
+var remove_network_filters = function() {
+    processed_data.network_dimension.filterAll();
+    processed_data.network_type_dimension.filterAll();
+    processed_data.interaction_start_dimension.filterAll();
+    processed_data.interaction_end_dimension.filterAll();
+}
+
+ var filter_on_network = function(network_id) {
+    processed_data.network_dimension.filterAll();
+
+    // want the interactions with that network
+    processed_data.network_dimension.filterExact(network_id);
+
+    return processed_data.network_type_dimension.top(Infinity);
+ }
+
+// Either returns all interactions or all egdes
+var filter_on_network_type = function(type) {
+    processed_data.network_type_dimension.filterAll();
+
+    // Only want interactions not edges
+    type_filter = processed_data.network_type_dimension.filterExact(type);
+
+    return processed_data.network_dimension.top(Infinity);
+ }
+
+ var filter_interactions_on_position = function(start, end) {
+    // Clear the associated filters.
+    processed_data.interaction_start_dimension.filterAll();
+    processed_data.interaction_end_dimension.filterAll();
+
+    // Filters the data based on the start and end positions
+    // filterRange([>=min, <max]); Can also do on strings
+    processed_data.interaction_start_dimension.filterRange([start, end]);
+    processed_data.interaction_end_dimension.filterRange([start, end]);
+
+    // Now the underlying data has changed (will need to redraw)
+    return get_filter(processed_data.network_facts);
+ }
\ No newline at end of file

gnvweb/eneg/src/main/resources/templates/fragments/form.html

@@ -34,7 +34,9 @@
                     </div>
                 </div>
 
-                <div class="form-group row col-sm-offset-1 col-sm-8 pad-top-bottom" style="padding-top:30px;"><button type="submit" name="submitGnv" class="btn btn-default col-xs-12" style="background-color: #C8D3BB;" id="submit-btn" onclick="javascript:displayLoad();">Perform reconstruction</button></div>            </form>
+                <div class="form-group row col-sm-offset-1 col-sm-8 pad-top-bottom" style="padding-top:30px;">
+                </div>
+            </form>
         </div>
         </div>
     </div>

gnvweb/eneg/src/main/resources/templates/fragments/results.html

@@ -41,7 +41,7 @@
                     <div id="genomevis-div">
                         <button id="diff-dna-view" onclick="diff_dna_view();" >change stand view</button>
                         <!--   Contains the D3 strand vis.   -->
-                        <svg id="strandvis" width="1200" height="400"></svg>
+                        <svg id="strandvis" width="1200" height="800"></svg>
                     </div>
                     <div id="interactionvis-div">
                         <svg id="interactionvis" width="200" height="300"></svg>