Add context menu, and the functionality to reverse especially one contig

js/BootstrapMenu.min.js

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+	  Copyright (c) 2016 Jed Watson.
+	  Licensed under the MIT License (MIT), see
+	  http://jedwatson.github.io/classnames
+	*/
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+	 * jQuery UI Position 1.12.0
+	 * http://jqueryui.com
+	 *
+	 * Copyright jQuery Foundation and other contributors
+	 * Released under the MIT license.
+	 * http://jquery.org/license
+	 *
+	 * http://api.jqueryui.com/position/
+	 */
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\ No newline at end of file

js/d3.boxplot.events.js

@@ -21,6 +21,32 @@ d3.boxplot.events.init = function () {
     });
 };
 
+d3.boxplot.events.init_context_menu = function () {
+    d3.boxplot.svgcontainer.on("mousedown", function() {
+        let event = d3.event;
+        let rect = $("g.container")[0].getBoundingClientRect();
+        let posY = rect.top + window.scrollY,
+            height_c = rect.height;
+        let y = d3.boxplot.scale - ((event.pageY - posY) / height_c * d3.boxplot.scale);
+        d3.boxplot.query_selected = d3.boxplot.select_query(y);
+        console.log(d3.boxplot.query_selected)
+    });
+
+    let menu = new BootstrapMenu("svg.svgcontainer", {
+        actions: [{
+            name: 'Export SVG',
+            onClick: dgenies.result.export.export_svg
+        },{
+            name: 'Export PNG',
+            onClick: dgenies.result.export.export_png
+        },{
+            name: 'Reverse query',
+            isShown: function() {return d3.boxplot.name_x !== d3.boxplot.name_y},
+            onClick: dgenies.result.controls.launch_reverse_contig
+        }]
+    });
+};
+
 d3.boxplot.events.set_break_lines_visibility = function(value) {
     if (value === "0") {
         d3.boxplot.break_lines_show = false;

js/d3.boxplot.js

@@ -18,6 +18,7 @@ d3.boxplot.zoom_enabled = true;
 d3.boxplot.min_idy = 0;
 d3.boxplot.max_idy = 0;
 d3.boxplot.zone_selected = false;
+d3.boxplot.query_selected = null;
 
 //For translations:
 d3.boxplot.translate_start = null;
@@ -119,6 +120,24 @@ d3.boxplot.launch = function(res, update=false) {
     d3.boxplot.mousetip.init();
 };
 
+d3.boxplot.select_target = function (x) {
+    for (let zone in d3.boxplot.x_zones) {
+        if (d3.boxplot.x_zones[zone][0] < x && x <= d3.boxplot.x_zones[zone][1]) {
+            return zone;
+        }
+    }
+    return null;
+};
+
+d3.boxplot.select_query = function(y) {
+    for (let zone in d3.boxplot.y_zones) {
+        if (d3.boxplot.y_zones[zone][0] < y && y <= d3.boxplot.y_zones[zone][1]) {
+            return zone;
+        }
+    }
+    return null;
+}
+
 d3.boxplot.select_zone = function (x=null, y=null, x_zone=null, y_zone=null, force=false) {
     d3.boxplot.mousetip.hide();
     dgenies.show_loading();
@@ -127,22 +146,12 @@ d3.boxplot.select_zone = function (x=null, y=null, x_zone=null, y_zone=null, for
 
             if (x_zone === null) {
                 //Search zone for X axis:
-                for (let zone in d3.boxplot.x_zones) {
-                    if (d3.boxplot.x_zones[zone][0] < x && x <= d3.boxplot.x_zones[zone][1]) {
-                        x_zone = zone;
-                        break;
-                    }
-                }
+                x_zone = d3.boxplot.select_target(x)
             }
 
             if (y_zone === null) {
                 //Search zone for Y axis:
-                for (let zone in d3.boxplot.y_zones) {
-                    if (d3.boxplot.y_zones[zone][0] < y && y <= d3.boxplot.y_zones[zone][1]) {
-                        y_zone = zone;
-                        break;
-                    }
-                }
+                y_zone = d3.boxplot.select_query(y);
             }
 
             d3.boxplot.zone_selected = [x_zone, y_zone];
@@ -847,4 +856,6 @@ d3.boxplot.draw = function (x_contigs, x_order, y_contigs, y_order) {
     }, 0);
 
     d3.boxplot.zoom.init();
+
+    d3.boxplot.events.init_context_menu();
 };

js/dgenies.result.controls.js

@@ -34,6 +34,35 @@ dgenies.result.controls.launch_sort_contigs = function () {
     }, 0);
 };
 
+dgenies.result.controls.launch_reverse_contig = function () {
+    if (d3.boxplot.query_selected !== null) {
+        d3.boxplot.zoom.reset_scale();
+        window.setTimeout(() => {
+            dgenies.show_loading("Building...");
+            window.setTimeout(() => {
+                dgenies.post(`/reverse-contig/${dgenies.result.id_res}`,
+                    {"contig": d3.boxplot.query_selected},
+                    function (data) {
+                        if (data["success"]) {
+                            dgenies.reset_loading_message();
+                            window.setTimeout(() => {
+                                d3.boxplot.launch(data, true);
+                            }, 0);
+                        }
+                        else {
+                            dgenies.hide_loading();
+                            dgenies.notify(data["message"] || "An error occurred! Please contact us to report the bug", "danger");
+                        }
+                    }
+                );
+            }, 0);
+        }, 0);
+    }
+    else {
+        dgenies.notify("Error: no query selected. Please contact us to report the bug", "danger");
+    }
+};
+
 dgenies.result.controls.launch_hide_noise = function () {
     d3.boxplot.zoom.reset_scale();
     window.setTimeout(() => {

js/dgenies.result.js

@@ -7,6 +7,6 @@ dgenies.result = {};
 dgenies.result.id_res = null;
 
 dgenies.result.init = function(id_res) {
-    dgenies.result.id_res = id_res
+    dgenies.result.id_res = id_res;
     d3.boxplot.init();
 };

lib/paf.py

@@ -310,7 +310,11 @@ class Paf:
                     parts[2] = str(len_q - x2_q)
                     parts[3] = str(len_q - x1_q)
                 target.write("\t".join(parts) + "\n")
-        self.paf = sorted_file
+        if self.paf.endswith(".sorted"):
+            os.remove(self.paf)
+            shutil.move(sorted_file, self.paf)
+        else:
+            self.paf = sorted_file
         return True
 
     def _update_query_index(self, contigs_reoriented):
@@ -442,6 +446,15 @@ class Paf:
         self.parsed = False
         self.parse_paf()
 
+    def reverse_contig(self, contig_name):
+        self.parse_paf(False)
+        reorient_contigs = [contig_name]
+        self.reorient_contigs_in_paf(reorient_contigs)
+        self._update_query_index(reorient_contigs)
+        self.set_sorted(True)
+        self.parsed = False
+        self.parse_paf()
+
     def get_query_on_target_association(self):
         """
         For each query, get the best matching chromosome

srv/main.py

@@ -261,6 +261,23 @@ def sort_graph(id_res):
     return jsonify({"success": False, "message": "Sort is not available for All-vs-All mode"})
 
 
+@app.route('/reverse-contig/<id_res>', methods=['POST'])
+def reverse_contig(id_res):
+    contig_name = request.form["contig"]
+    if not os.path.exists(os.path.join(APP_DATA, id_res, ".all-vs-all")):
+        paf_file = os.path.join(app_data, id_res, "map.paf")
+        idx1 = os.path.join(app_data, id_res, "query.idx")
+        idx2 = os.path.join(app_data, id_res, "target.idx")
+        paf = Paf(paf_file, idx1, idx2, False)
+        paf.reverse_contig(contig_name)
+        if paf.parsed:
+            res = paf.get_d3js_data()
+            res["success"] = True
+            return jsonify(res)
+        return jsonify({"success": False, "message": paf.error})
+    return jsonify({"success": False, "message": "Sort is not available for All-vs-All mode"})
+
+
 @app.route('/freenoise/<id_res>', methods=['POST'])
 def free_noise(id_res):
     paf_file = os.path.join(app_data, id_res, "map.paf")

srv/templates/results.html

@@ -12,6 +12,7 @@
     <script src="{{ url_for('static', filename='js/d3.boxplot.zoom.js') }}" type="text/JavaScript"></script>
     <script src="{{ url_for('static', filename='js/d3.boxplot.events.js') }}" type="text/JavaScript"></script>
     <script src="{{ url_for('static', filename='js/d3.boxplot.mousetip.js') }}" type="text/JavaScript"></script>
+    <script src="{{ url_for('static', filename='js/BootstrapMenu.min.js') }}" type="text/JavaScript"></script>
     <link rel="stylesheet" href="{{ url_for('static', filename='css/chosen.min.css') }}" type="text/css">
 {% endblock %}
 {% block onload %}dgenies.result.init('{{ id }}');{% endblock %}