Add drawrna, with existing code until npm dependency works

config/plugins/visualizations/drawrna/config/drawrna.xml

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
+<visualization name="RNA Structure Viewer">
+    <description>Renders RNA structures hosted at https://github.com/bene200/drawrnajs.</description>
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test test_attr="ext" result_type="datatype">dbn</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+    </data_sources>
+    <params>
+        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+    <entry_point entry_point_type="chart" src="static/script.js" func="func"/>
+</visualization>

config/plugins/visualizations/drawrna/package.json

@@ -0,0 +1,20 @@
+{
+    "name": "visualization",
+    "version": "0.1.0",
+    "keywords": [
+        "galaxy",
+        "visualization"
+    ],
+    "license": "AFL-3.0",
+    "dependencies": {
+        "babel-preset-env": "^1.6.1",
+        "backbone": "^1.3.3",
+        "bootstrap": "^3.3.7",
+        "drawrnajs": "^1.2.6",
+        "jquery": "^3.1.1",
+        "parcel-bundler": "^1.4.1"
+    },
+    "scripts": {
+        "build": "parcel build src/script.js -d static"
+    }
+}

config/plugins/visualizations/drawrna/src/drawrnajs/drawrna.js

@@ -0,0 +1,15 @@
+var Backbone = require("backbone");
+var Structure = require("./models/structure");
+var Vispanel = require("./views/vispanel");
+
+var Drawrnajs = Backbone.View.extend({
+    initialize: function(opts){
+        this.struct = new Structure(opts.seq, opts.dotbr, 'naview');
+        this.vis = new Vispanel({ el: opts.el, struct: this.struct, resindex: opts.resindex });
+    },
+    render: function(){
+        this.vis.render();
+    }
+});
+
+module.exports = Drawrnajs;

config/plugins/visualizations/drawrna/src/drawrnajs/layouts/layout.js

@@ -0,0 +1,24 @@
+var radiate = require("./radiate/getradiate");
+var naview = require("./naview/getnaview");
+
+var Layout = function(layout, nodes, links){
+    this.layout = layout;
+    this.nodes = nodes;
+    this.links = links;
+}
+
+Layout.prototype.getCoords = function(){
+    var coords = null;
+    if(this.layout === "radiate"){
+        coords = radiate(this.nodes, this.links);
+    }
+    else if(this.layout === "naview"){
+        coords = naview(this.nodes, this.links);
+    }
+    else {
+        throw new Error("Invalid layout");
+    }
+    return coords;
+}
+
+module.exports = Layout;

config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/base.js

@@ -0,0 +1,49 @@
+var Region = require("./region");
+
+var Base = module.exports = function(){
+	this.mate = null;
+	this.x = null;
+    this.y = null;
+	this.extracted = null;
+	this.region = new Region();
+}
+
+Base.prototype.getMate = function(){
+	return this.mate;
+}
+
+Base.prototype.setMate = function(mate){
+	this.mate = mate;
+}
+
+Base.prototype.getX = function(){
+	return this.x;
+}
+
+Base.prototype.setX = function(x){
+	this.x = x;
+}
+
+Base.prototype.getY = function(){
+	return this.y;
+}
+
+Base.prototype.setY = function(y){
+	this.y = y;
+}
+
+Base.prototype.isExtracted = function(){
+	return this.extracted;
+}
+
+Base.prototype.setExtracted = function(extracted){
+	this.extracted = extracted;
+}
+
+Base.prototype.getRegion = function(){
+	return this.region;
+}
+
+Base.prototype.setRegion = function(region){
+	this.region = region;
+}

config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/connection.js

@@ -0,0 +1,100 @@
+var Loop = require("./loop");
+var Region = require("./region");
+
+var Connection = module.exports = function(){
+	this.loop = new Loop();
+	this.region = new Region();
+	// Start and end form the 1st base pair of the region.
+	this.start = null;
+    this.end = null;
+	this.xrad = null;
+    this.yrad = null;
+    this.angle = null;
+	// True if segment between this connection and the
+	// next must be extruded out of the circle
+	this.extruded = null;
+	// True if the extruded segment must be drawn long.
+	this.broken = null;
+
+	this._isNull = false;
+}
+
+Connection.prototype.isNull = function(){
+	return this._isNull;
+}
+
+Connection.prototype.setNull = function(isNull){
+	this._isNull = isNull;
+}
+
+Connection.prototype.getLoop = function(){
+	return this.loop;
+}
+
+Connection.prototype.setLoop = function(loop) {
+	this.loop = loop;
+}
+
+Connection.prototype.getRegion = function(){
+	return this.region;
+}
+
+Connection.prototype.setRegion = function(region){
+	this.region = region;
+}
+
+Connection.prototype.getStart = function(){
+	return this.start;
+}
+
+Connection.prototype.setStart = function(start) {
+	this.start = start;
+}
+
+Connection.prototype.getEnd = function(){
+	return this.end;
+}
+
+Connection.prototype.setEnd = function(end){
+	this.end = end;
+}
+
+Connection.prototype.getXrad = function(){
+	return this.xrad;
+}
+
+Connection.prototype.setXrad = function(xrad){
+	this.xrad = xrad;
+}
+
+Connection.prototype.getYrad = function(){
+	return this.yrad;
+}
+
+Connection.prototype.setYrad = function(yrad) {
+	this.yrad = yrad;
+}
+
+Connection.prototype.getAngle = function(){
+	return this.angle;
+}
+
+Connection.prototype.setAngle = function(angle){
+	this.angle = angle;
+}
+
+Connection.prototype.isExtruded = function(){
+	return this.extruded;
+}
+
+Connection.prototype.setExtruded = function(extruded){
+	this.extruded = extruded;
+}
+
+Connection.prototype.isBroken = function(){
+	return this.broken;
+}
+
+Connection.prototype.setBroken = function(broken){
+	this.broken = broken;
+}

config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/getnaview.js

@@ -0,0 +1,44 @@
+var NAView = require("./naview");
+
+getCoordsNAVIEW = module.exports = function(nodes, links){
+	//Calculates coordinates according to the NAView layout
+	var pairTable = [];
+
+	for(var i=0; i<nodes.length; i++){
+		pairTable.push(getPartner(i, links));
+	}
+	var naView = new NAView();
+	var xy = naView.naview_xy_coordinates(pairTable);
+
+	// Updating individual base positions
+	var coords = []
+	for (var i = 0; i < nodes.length; i++) {
+		coords.push({
+			x: Math.round(xy.x[i] * 2.5),
+			y: Math.round(xy.y[i] * 2.5)
+		});
+	}
+	return coords;
+}
+
+function getPartner(srcIndex, links){
+	//Returns the partner of a nucleotide:
+	//-1 means there is no partner
+	var partner = -1;
+	for(var i = 0; i < links.length; i++){
+		if(links[i].type !== "phosphodiester" && links[i].type !== "index"){
+			if(links[i].source === srcIndex){
+				partner = links[i].target;
+				break;
+			}
+			else if(links[i].target === srcIndex){
+				partner = links[i].source;
+				break;
+			}
+			else {
+				continue;
+			}
+		}
+	}
+	return partner;
+}

config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/loop.js

@@ -0,0 +1,98 @@
+var Loop = module.exports = function(){
+	this.nconnection = null;
+	this.connections = [];
+	this._connections = [];
+	this.number = null;
+	this.depth = null;
+	this.mark = null;
+	this.x = null;
+    this.y = null;
+    this.radius = null;
+}
+
+Loop.prototype.getNconnection = function() {
+	return this.nconnection;
+}
+
+Loop.prototype.setNconnection = function(nconnection) {
+	this.nconnection = nconnection;
+}
+
+Loop.prototype.setConnection = function(i, c){
+	var Connection = require("./connection");
+	if (c != null){
+		this._connections[i] = c;
+    }
+	else {
+		if (!this._connections[i]){
+			this._connections[i] = new Connection();
+		}
+		this._connections[i].setNull(true);
+	}
+}
+
+Loop.prototype.getConnection = function(i){
+	var Connection = require("./connection");
+	if (!this._connections[i]){
+        this._connections[i] = new Connection();
+    }
+	var c = this._connections[i];
+	if (c.isNull()){
+		return null;
+    }
+	else {
+		return c;
+    }
+}
+
+Loop.prototype.addConnection = function(i, c){
+	this._connections.push(c);
+}
+
+Loop.prototype.getNumber = function(){
+	return this.number;
+}
+
+Loop.prototype.setNumber = function(number){
+	this.number = number;
+}
+
+Loop.prototype.getDepth = function(){
+	return this.depth;
+}
+
+Loop.prototype.setDepth = function(depth){
+	this.depth = depth;
+}
+
+Loop.prototype.isMark = function(){
+	return this.mark;
+}
+
+Loop.prototype.setMark = function(mark){
+	this.mark = mark;
+}
+
+Loop.prototype.getX = function(){
+	return this.x;
+}
+
+Loop.prototype.setX = function(x){
+	this.x = x;
+}
+
+Loop.prototype.getY = function(){
+	return this.y;
+}
+
+Loop.prototype.setY = function(y){
+	this.y = y;
+}
+
+Loop.prototype.getRadius = function(){
+	return this.radius;
+}
+
+Loop.prototype.setRadius = function(radius){
+	this.radius = radius;
+}