Islandplot Demo libs

README.md

Libraries for Islandplot demos

canvg.js

/*
 * canvg.js - Javascript SVG parser and renderer on Canvas
 * MIT Licensed 
 * Gabe Lerner (gabelerner@gmail.com)
 * http://code.google.com/p/canvg/
 *
 * Requires: rgbcolor.js - http://www.phpied.com/rgb-color-parser-in-javascript/
 */
(function(){
	// canvg(target, s)
	// empty parameters: replace all 'svg' elements on page with 'canvas' elements
	// target: canvas element or the id of a canvas element
	// s: svg string, url to svg file, or xml document
	// opts: optional hash of options
	//		 ignoreMouse: true => ignore mouse events
	//		 ignoreAnimation: true => ignore animations
	//		 ignoreDimensions: true => does not try to resize canvas
	//		 ignoreClear: true => does not clear canvas
	//		 offsetX: int => draws at a x offset
	//		 offsetY: int => draws at a y offset
	//		 scaleWidth: int => scales horizontally to width
	//		 scaleHeight: int => scales vertically to height
	//		 renderCallback: function => will call the function after the first render is completed
	//		 forceRedraw: function => will call the function on every frame, if it returns true, will redraw
	this.canvg = function (target, s, opts) {
		// no parameters
		if (target == null && s == null && opts == null) {
			var svgTags = document.getElementsByTagName('svg');
			for (var i=0; i<svgTags.length; i++) {
				var svgTag = svgTags[i];
				var c = document.createElement('canvas');
				c.width = svgTag.clientWidth;
				c.height = svgTag.clientHeight;
				svgTag.parentNode.insertBefore(c, svgTag);
				svgTag.parentNode.removeChild(svgTag);
				var div = document.createElement('div');
				div.appendChild(svgTag);
				canvg(c, div.innerHTML);
			}
			return;
		}	
		opts = opts || {};
	
		if (typeof target == 'string') {
			target = document.getElementById(target);
		}
		
		// store class on canvas
		if (target.svg != null) target.svg.stop();
		var svg = build();
		// on i.e. 8 for flash canvas, we can't assign the property so check for it
		if (!(target.childNodes.length == 1 && target.childNodes[0].nodeName == 'OBJECT')) target.svg = svg;
		svg.opts = opts;
		
		var ctx = target.getContext('2d');
		if (typeof(s.documentElement) != 'undefined') {
			// load from xml doc
			svg.loadXmlDoc(ctx, s);
		}
		else if (s.substr(0,1) == '<') {
			// load from xml string
			svg.loadXml(ctx, s);
		}
		else {
			// load from url
			svg.load(ctx, s);
		}
	}

	function build() {
		var svg = { };
		
		svg.FRAMERATE = 30;
		svg.MAX_VIRTUAL_PIXELS = 30000;
		
		// globals
		svg.init = function(ctx) {
			var uniqueId = 0;
			svg.UniqueId = function () { uniqueId++; return 'canvg' + uniqueId;	};
			svg.Definitions = {};
			svg.Styles = {};
			svg.Animations = [];
			svg.Images = [];
			svg.ctx = ctx;
			svg.ViewPort = new (function () {
				this.viewPorts = [];
				this.Clear = function() { this.viewPorts = []; }
				this.SetCurrent = function(width, height) { this.viewPorts.push({ width: width, height: height }); }
				this.RemoveCurrent = function() { this.viewPorts.pop(); }
				this.Current = function() { return this.viewPorts[this.viewPorts.length - 1]; }
				this.width = function() { return this.Current().width; }
				this.height = function() { return this.Current().height; }
				this.ComputeSize = function(d) {
					if (d != null && typeof(d) == 'number') return d;
					if (d == 'x') return this.width();
					if (d == 'y') return this.height();
					return Math.sqrt(Math.pow(this.width(), 2) + Math.pow(this.height(), 2)) / Math.sqrt(2);			
				}
			});
		}
		svg.init();
		
		// images loaded
		svg.ImagesLoaded = function() { 
			for (var i=0; i<svg.Images.length; i++) {
				if (!svg.Images[i].loaded) return false;
			}
			return true;
		}

		// trim
		svg.trim = function(s) { return s.replace(/^\s+|\s+$/g, ''); }
		
		// compress spaces
		svg.compressSpaces = function(s) { return s.replace(/[\s\r\t\n]+/gm,' '); }
		
		// ajax
		svg.ajax = function(url) {
			var AJAX;
			if(window.XMLHttpRequest){AJAX=new XMLHttpRequest();}
			else{AJAX=new ActiveXObject('Microsoft.XMLHTTP');}
			if(AJAX){
			   AJAX.open('GET',url,false);
			   AJAX.send(null);
			   return AJAX.responseText;
			}
			return null;
		} 
		
		// parse xml
		svg.parseXml = function(xml) {
			if (window.DOMParser)
			{
				var parser = new DOMParser();
				return parser.parseFromString(xml, 'text/xml');
			}
			else 
			{
				xml = xml.replace(/<!DOCTYPE svg[^>]*>/, '');
				var xmlDoc = new ActiveXObject('Microsoft.XMLDOM');
				xmlDoc.async = 'false';
				xmlDoc.loadXML(xml); 
				return xmlDoc;
			}		
		}
		
		svg.Property = function(name, value) {
			this.name = name;
			this.value = value;
		}	
			svg.Property.prototype.getValue = function() {
				return this.value;
			}
		
			svg.Property.prototype.hasValue = function() {
				return (this.value != null && this.value !== '');
			}
							
			// return the numerical value of the property
			svg.Property.prototype.numValue = function() {
				if (!this.hasValue()) return 0;
				
				var n = parseFloat(this.value);
				if ((this.value + '').match(/%$/)) {
					n = n / 100.0;
				}
				return n;
			}
			
			svg.Property.prototype.valueOrDefault = function(def) {
				if (this.hasValue()) return this.value;
				return def;
			}
			
			svg.Property.prototype.numValueOrDefault = function(def) {
				if (this.hasValue()) return this.numValue();
				return def;
			}
			
			// color extensions
				// augment the current color value with the opacity
				svg.Property.prototype.addOpacity = function(opacity) {
					var newValue = this.value;
					if (opacity != null && opacity != '' && typeof(this.value)=='string') { // can only add opacity to colors, not patterns
						var color = new RGBColor(this.value);
						if (color.ok) {
							newValue = 'rgba(' + color.r + ', ' + color.g + ', ' + color.b + ', ' + opacity + ')';
						}
					}
					return new svg.Property(this.name, newValue);
				}
			
			// definition extensions
				// get the definition from the definitions table
				svg.Property.prototype.getDefinition = function() {
					var name = this.value.match(/#([^\)'"]+)/);
					if (name) { name = name[1]; }
					if (!name) { name = this.value; }
					return svg.Definitions[name];
				}
				
				svg.Property.prototype.isUrlDefinition = function() {
					return this.value.indexOf('url(') == 0
				}
				
				svg.Property.prototype.getFillStyleDefinition = function(e, opacityProp) {
					var def = this.getDefinition();
					
					// gradient
					if (def != null && def.createGradient) {
						return def.createGradient(svg.ctx, e, opacityProp);
					}
					
					// pattern
					if (def != null && def.createPattern) {
						if (def.getHrefAttribute().hasValue()) {
							var pt = def.attribute('patternTransform');
							def = def.getHrefAttribute().getDefinition();
							if (pt.hasValue()) { def.attribute('patternTransform', true).value = pt.value; }
						}
						return def.createPattern(svg.ctx, e);
					}
					
					return null;
				}
			
			// length extensions
				svg.Property.prototype.getDPI = function(viewPort) {
					return 96.0; // TODO: compute?
				}
				
				svg.Property.prototype.getEM = function(viewPort) {
					var em = 12;
					
					var fontSize = new svg.Property('fontSize', svg.Font.Parse(svg.ctx.font).fontSize);
					if (fontSize.hasValue()) em = fontSize.toPixels(viewPort);
					
					return em;
				}
				
				svg.Property.prototype.getUnits = function() {
					var s = this.value+'';
					return s.replace(/[0-9\.\-]/g,'');
				}
			
				// get the length as pixels
				svg.Property.prototype.toPixels = function(viewPort, processPercent) {
					if (!this.hasValue()) return 0;
					var s = this.value+'';
					if (s.match(/em$/)) return this.numValue() * this.getEM(viewPort);
					if (s.match(/ex$/)) return this.numValue() * this.getEM(viewPort) / 2.0;
					if (s.match(/px$/)) return this.numValue();
					if (s.match(/pt$/)) return this.numValue() * this.getDPI(viewPort) * (1.0 / 72.0);
					if (s.match(/pc$/)) return this.numValue() * 15;
					if (s.match(/cm$/)) return this.numValue() * this.getDPI(viewPort) / 2.54;
					if (s.match(/mm$/)) return this.numValue() * this.getDPI(viewPort) / 25.4;
					if (s.match(/in$/)) return this.numValue() * this.getDPI(viewPort);
					if (s.match(/%$/)) return this.numValue() * svg.ViewPort.ComputeSize(viewPort);
					var n = this.numValue();
					if (processPercent && n < 1.0) return n * svg.ViewPort.ComputeSize(viewPort);
					return n;
				}

			// time extensions
				// get the time as milliseconds
				svg.Property.prototype.toMilliseconds = function() {
					if (!this.hasValue()) return 0;
					var s = this.value+'';
					if (s.match(/s$/)) return this.numValue() * 1000;
					if (s.match(/ms$/)) return this.numValue();
					return this.numValue();
				}
			
			// angle extensions
				// get the angle as radians
				svg.Property.prototype.toRadians = function() {
					if (!this.hasValue()) return 0;
					var s = this.value+'';
					if (s.match(/deg$/)) return this.numValue() * (Math.PI / 180.0);
					if (s.match(/grad$/)) return this.numValue() * (Math.PI / 200.0);
					if (s.match(/rad$/)) return this.numValue();
					return this.numValue() * (Math.PI / 180.0);
				}
		
		// fonts
		svg.Font = new (function() {
			this.Styles = 'normal|italic|oblique|inherit';
			this.Variants = 'normal|small-caps|inherit';
			this.Weights = 'normal|bold|bolder|lighter|100|200|300|400|500|600|700|800|900|inherit';
			
			this.CreateFont = function(fontStyle, fontVariant, fontWeight, fontSize, fontFamily, inherit) { 
				var f = inherit != null ? this.Parse(inherit) : this.CreateFont('', '', '', '', '', svg.ctx.font);
				return { 
					fontFamily: fontFamily || f.fontFamily, 
					fontSize: fontSize || f.fontSize, 
					fontStyle: fontStyle || f.fontStyle, 
					fontWeight: fontWeight || f.fontWeight, 
					fontVariant: fontVariant || f.fontVariant,
					toString: function () { return [this.fontStyle, this.fontVariant, this.fontWeight, this.fontSize, this.fontFamily].join(' ') } 
				} 
			}
			
			var that = this;
			this.Parse = function(s) {
				var f = {};
				var d = svg.trim(svg.compressSpaces(s || '')).split(' ');
				var set = { fontSize: false, fontStyle: false, fontWeight: false, fontVariant: false }
				var ff = '';
				for (var i=0; i<d.length; i++) {
					if (!set.fontStyle && that.Styles.indexOf(d[i]) != -1) { if (d[i] != 'inherit') f.fontStyle = d[i]; set.fontStyle = true; }
					else if (!set.fontVariant && that.Variants.indexOf(d[i]) != -1) { if (d[i] != 'inherit') f.fontVariant = d[i]; set.fontStyle = set.fontVariant = true;	}
					else if (!set.fontWeight && that.Weights.indexOf(d[i]) != -1) {	if (d[i] != 'inherit') f.fontWeight = d[i]; set.fontStyle = set.fontVariant = set.fontWeight = true; }
					else if (!set.fontSize) { if (d[i] != 'inherit') f.fontSize = d[i].split('/')[0]; set.fontStyle = set.fontVariant = set.fontWeight = set.fontSize = true; }
					else { if (d[i] != 'inherit') ff += d[i]; }
				} if (ff != '') f.fontFamily = ff;
				return f;
			}
		});
		
		// points and paths
		svg.ToNumberArray = function(s) {
			var a = svg.trim(svg.compressSpaces((s || '').replace(/,/g, ' '))).split(' ');
			for (var i=0; i<a.length; i++) {
				a[i] = parseFloat(a[i]);
			}
			return a;
		}		
		svg.Point = function(x, y) {
			this.x = x;
			this.y = y;
		}	
			svg.Point.prototype.angleTo = function(p) {
				return Math.atan2(p.y - this.y, p.x - this.x);
			}
			
			svg.Point.prototype.applyTransform = function(v) {
				var xp = this.x * v[0] + this.y * v[2] + v[4];
				var yp = this.x * v[1] + this.y * v[3] + v[5];
				this.x = xp;
				this.y = yp;
			}

		svg.CreatePoint = function(s) {
			var a = svg.ToNumberArray(s);
			return new svg.Point(a[0], a[1]);
		}
		svg.CreatePath = function(s) {
			var a = svg.ToNumberArray(s);
			var path = [];
			for (var i=0; i<a.length; i+=2) {
				path.push(new svg.Point(a[i], a[i+1]));
			}
			return path;
		}
		
		// bounding box
		svg.BoundingBox = function(x1, y1, x2, y2) { // pass in initial points if you want
			this.x1 = Number.NaN;
			this.y1 = Number.NaN;
			this.x2 = Number.NaN;
			this.y2 = Number.NaN;
			
			this.x = function() { return this.x1; }
			this.y = function() { return this.y1; }
			this.width = function() { return this.x2 - this.x1; }
			this.height = function() { return this.y2 - this.y1; }
			
			this.addPoint = function(x, y) {	
				if (x != null) {
					if (isNaN(this.x1) || isNaN(this.x2)) {
						this.x1 = x;
						this.x2 = x;
					}
					if (x < this.x1) this.x1 = x;
					if (x > this.x2) this.x2 = x;
				}
			
				if (y != null) {
					if (isNaN(this.y1) || isNaN(this.y2)) {
						this.y1 = y;
						this.y2 = y;
					}
					if (y < this.y1) this.y1 = y;
					if (y > this.y2) this.y2 = y;
				}
			}			
			this.addX = function(x) { this.addPoint(x, null); }
			this.addY = function(y) { this.addPoint(null, y); }
			
			this.addBoundingBox = function(bb) {
				this.addPoint(bb.x1, bb.y1);
				this.addPoint(bb.x2, bb.y2);
			}
			
			this.addQuadraticCurve = function(p0x, p0y, p1x, p1y, p2x, p2y) {
				var cp1x = p0x + 2/3 * (p1x - p0x); // CP1 = QP0 + 2/3 *(QP1-QP0)
				var cp1y = p0y + 2/3 * (p1y - p0y); // CP1 = QP0 + 2/3 *(QP1-QP0)
				var cp2x = cp1x + 1/3 * (p2x - p0x); // CP2 = CP1 + 1/3 *(QP2-QP0)
				var cp2y = cp1y + 1/3 * (p2y - p0y); // CP2 = CP1 + 1/3 *(QP2-QP0)
				this.addBezierCurve(p0x, p0y, cp1x, cp2x, cp1y,	cp2y, p2x, p2y);
			}
			
			this.addBezierCurve = function(p0x, p0y, p1x, p1y, p2x, p2y, p3x, p3y) {
				// from http://blog.hackers-cafe.net/2009/06/how-to-calculate-bezier-curves-bounding.html
				var p0 = [p0x, p0y], p1 = [p1x, p1y], p2 = [p2x, p2y], p3 = [p3x, p3y];
				this.addPoint(p0[0], p0[1]);
				this.addPoint(p3[0], p3[1]);
				
				for (i=0; i<=1; i++) {
					var f = function(t) { 
						return Math.pow(1-t, 3) * p0[i]
						+ 3 * Math.pow(1-t, 2) * t * p1[i]
						+ 3 * (1-t) * Math.pow(t, 2) * p2[i]
						+ Math.pow(t, 3) * p3[i];
					}
					
					var b = 6 * p0[i] - 12 * p1[i] + 6 * p2[i];
					var a = -3 * p0[i] + 9 * p1[i] - 9 * p2[i] + 3 * p3[i];
					var c = 3 * p1[i] - 3 * p0[i];
					
					if (a == 0) {
						if (b == 0) continue;
						var t = -c / b;
						if (0 < t && t < 1) {
							if (i == 0) this.addX(f(t));
							if (i == 1) this.addY(f(t));
						}
						continue;
					}
					
					var b2ac = Math.pow(b, 2) - 4 * c * a;
					if (b2ac < 0) continue;
					var t1 = (-b + Math.sqrt(b2ac)) / (2 * a);
					if (0 < t1 && t1 < 1) {
						if (i == 0) this.addX(f(t1));
						if (i == 1) this.addY(f(t1));
					}
					var t2 = (-b - Math.sqrt(b2ac)) / (2 * a);
					if (0 < t2 && t2 < 1) {
						if (i == 0) this.addX(f(t2));
						if (i == 1) this.addY(f(t2));
					}
				}
			}
			
			this.isPointInBox = function(x, y) {
				return (this.x1 <= x && x <= this.x2 && this.y1 <= y && y <= this.y2);
			}
			
			this.addPoint(x1, y1);
			this.addPoint(x2, y2);
		}
		
		// transforms
		svg.Transform = function(v) {	
			var that = this;
			this.Type = {}
		
			// translate
			this.Type.translate = function(s) {
				this.p = svg.CreatePoint(s);			
				this.apply = function(ctx) {
					ctx.translate(this.p.x || 0.0, this.p.y || 0.0);
				}
				this.unapply = function(ctx) {
					ctx.translate(-1.0 * this.p.x || 0.0, -1.0 * this.p.y || 0.0);
				}
				this.applyToPoint = function(p) {
					p.applyTransform([1, 0, 0, 1, this.p.x || 0.0, this.p.y || 0.0]);
				}
			}
			
			// rotate
			this.Type.rotate = function(s) {
				var a = svg.ToNumberArray(s);
				this.angle = new svg.Property('angle', a[0]);
				this.cx = a[1] || 0;
				this.cy = a[2] || 0;
				this.apply = function(ctx) {
					ctx.translate(this.cx, this.cy);
					ctx.rotate(this.angle.toRadians());
					ctx.translate(-this.cx, -this.cy);
				}
				this.unapply = function(ctx) {
					ctx.translate(this.cx, this.cy);
					ctx.rotate(-1.0 * this.angle.toRadians());
					ctx.translate(-this.cx, -this.cy);
				}
				this.applyToPoint = function(p) {
					var a = this.angle.toRadians();
					p.applyTransform([1, 0, 0, 1, this.p.x || 0.0, this.p.y || 0.0]);
					p.applyTransform([Math.cos(a), Math.sin(a), -Math.sin(a), Math.cos(a), 0, 0]);
					p.applyTransform([1, 0, 0, 1, -this.p.x || 0.0, -this.p.y || 0.0]);
				}			
			}
			
			this.Type.scale = function(s) {
				this.p = svg.CreatePoint(s);
				this.apply = function(ctx) {
					ctx.scale(this.p.x || 1.0, this.p.y || this.p.x || 1.0);
				}
				this.unapply = function(ctx) {
					ctx.scale(1.0 / this.p.x || 1.0, 1.0 / this.p.y || this.p.x || 1.0);
				}
				this.applyToPoint = function(p) {
					p.applyTransform([this.p.x || 0.0, 0, 0, this.p.y || 0.0, 0, 0]);
				}				
			}
			
			this.Type.matrix = function(s) {
				this.m = svg.ToNumberArray(s);
				this.apply = function(ctx) {
					ctx.transform(this.m[0], this.m[1], this.m[2], this.m[3], this.m[4], this.m[5]);
				}
				this.applyToPoint = function(p) {
					p.applyTransform(this.m);
				}					
			}
			
			this.Type.SkewBase = function(s) {
				this.base = that.Type.matrix;
				this.base(s);
				this.angle = new svg.Property('angle', s);
			}
			this.Type.SkewBase.prototype = new this.Type.matrix;
			
			this.Type.skewX = function(s) {
				this.base = that.Type.SkewBase;
				this.base(s);
				this.m = [1, 0, Math.tan(this.angle.toRadians()), 1, 0, 0];
			}
			this.Type.skewX.prototype = new this.Type.SkewBase;
			
			this.Type.skewY = function(s) {
				this.base = that.Type.SkewBase;
				this.base(s);
				this.m = [1, Math.tan(this.angle.toRadians()), 0, 1, 0, 0];
			}
			this.Type.skewY.prototype = new this.Type.SkewBase;
		
			this.transforms = [];
			
			this.apply = function(ctx) {
				for (var i=0; i<this.transforms.length; i++) {
					this.transforms[i].apply(ctx);
				}
			}
			
			this.unapply = function(ctx) {
				for (var i=this.transforms.length-1; i>=0; i--) {
					this.transforms[i].unapply(ctx);
				}
			}
			
			this.applyToPoint = function(p) {
				for (var i=0; i<this.transforms.length; i++) {
					this.transforms[i].applyToPoint(p);
				}
			}
			
			var data = svg.trim(svg.compressSpaces(v)).replace(/\)(\s?,\s?)/g,') ').split(/\s(?=[a-z])/);
			for (var i=0; i<data.length; i++) {
				var type = svg.trim(data[i].split('(')[0]);
				var s = data[i].split('(')[1].replace(')','');
				var transform = new this.Type[type](s);
				transform.type = type;
				this.transforms.push(transform);
			}
		}
		
		// aspect ratio
		svg.AspectRatio = function(ctx, aspectRatio, width, desiredWidth, height, desiredHeight, minX, minY, refX, refY) {
			// aspect ratio - http://www.w3.org/TR/SVG/coords.html#PreserveAspectRatioAttribute
			aspectRatio = svg.compressSpaces(aspectRatio);
			aspectRatio = aspectRatio.replace(/^defer\s/,''); // ignore defer
			var align = aspectRatio.split(' ')[0] || 'xMidYMid';
			var meetOrSlice = aspectRatio.split(' ')[1] || 'meet';					
	
			// calculate scale
			var scaleX = width / desiredWidth;
			var scaleY = height / desiredHeight;
			var scaleMin = Math.min(scaleX, scaleY);
			var scaleMax = Math.max(scaleX, scaleY);
			if (meetOrSlice == 'meet') { desiredWidth *= scaleMin; desiredHeight *= scaleMin; }
			if (meetOrSlice == 'slice') { desiredWidth *= scaleMax; desiredHeight *= scaleMax; }	
			
			refX = new svg.Property('refX', refX);
			refY = new svg.Property('refY', refY);
			if (refX.hasValue() && refY.hasValue()) {				
				ctx.translate(-scaleMin * refX.toPixels('x'), -scaleMin * refY.toPixels('y'));
			} 
			else {					
				// align
				if (align.match(/^xMid/) && ((meetOrSlice == 'meet' && scaleMin == scaleY) || (meetOrSlice == 'slice' && scaleMax == scaleY))) ctx.translate(width / 2.0 - desiredWidth / 2.0, 0); 
				if (align.match(/YMid$/) && ((meetOrSlice == 'meet' && scaleMin == scaleX) || (meetOrSlice == 'slice' && scaleMax == scaleX))) ctx.translate(0, height / 2.0 - desiredHeight / 2.0); 
				if (align.match(/^xMax/) && ((meetOrSlice == 'meet' && scaleMin == scaleY) || (meetOrSlice == 'slice' && scaleMax == scaleY))) ctx.translate(width - desiredWidth, 0); 
				if (align.match(/YMax$/) && ((meetOrSlice == 'meet' && scaleMin == scaleX) || (meetOrSlice == 'slice' && scaleMax == scaleX))) ctx.translate(0, height - desiredHeight); 
			}
			
			// scale
			if (align == 'none') ctx.scale(scaleX, scaleY);
			else if (meetOrSlice == 'meet') ctx.scale(scaleMin, scaleMin); 
			else if (meetOrSlice == 'slice') ctx.scale(scaleMax, scaleMax); 	
			
			// translate
			ctx.translate(minX == null ? 0 : -minX, minY == null ? 0 : -minY);			
		}
		
		// elements
		svg.Element = {}
		
		svg.EmptyProperty = new svg.Property('EMPTY', '');
		
		svg.Element.ElementBase = function(node) {	
			this.attributes = {};
			this.styles = {};
			this.children = [];
			
			// get or create attribute
			this.attribute = function(name, createIfNotExists) {
				var a = this.attributes[name];
				if (a != null) return a;
							
				if (createIfNotExists == true) { a = new svg.Property(name, ''); this.attributes[name] = a; }
				return a || svg.EmptyProperty;
			}
			
			this.getHrefAttribute = function() {
				for (var a in this.attributes) { 
					if (a.match(/:href$/)) { 
						return this.attributes[a]; 
					} 
				}
				return svg.EmptyProperty;
			}
			
			// get or create style, crawls up node tree
			this.style = function(name, createIfNotExists) {
				var s = this.styles[name];
				if (s != null) return s;
				
				var a = this.attribute(name);
				if (a != null && a.hasValue()) {
					this.styles[name] = a; // move up to me to cache
					return a;
				}
				
				var p = this.parent;
				if (p != null) {
					var ps = p.style(name);
					if (ps != null && ps.hasValue()) {
						return ps;
					}
				}
					
				if (createIfNotExists == true) { s = new svg.Property(name, ''); this.styles[name] = s; }
				return s || svg.EmptyProperty;
			}
			
			// base render
			this.render = function(ctx) {
				// don't render display=none
				if (this.style('display').value == 'none') return;
				
				// don't render visibility=hidden
				if (this.attribute('visibility').value == 'hidden') return;
			
				ctx.save();
				if (this.attribute('mask').hasValue()) { // mask
					var mask = this.attribute('mask').getDefinition();
					if (mask != null) mask.apply(ctx, this);
				}
				else if (this.style('filter').hasValue()) { // filter
					var filter = this.style('filter').getDefinition();
					if (filter != null) filter.apply(ctx, this);
				}
				else {	
					this.setContext(ctx);
					this.renderChildren(ctx);	
					this.clearContext(ctx);							
				}
				ctx.restore();
			}
			
			// base set context
			this.setContext = function(ctx) {
				// OVERRIDE ME!
			}
			
			// base clear context
			this.clearContext = function(ctx) {
				// OVERRIDE ME!
			}			
			
			// base render children
			this.renderChildren = function(ctx) {
				for (var i=0; i<this.children.length; i++) {
					this.children[i].render(ctx);
				}
			}
			
			this.addChild = function(childNode, create) {
				var child = childNode;
				if (create) child = svg.CreateElement(childNode);
				child.parent = this;
				this.children.push(child);			
			}
				
			if (node != null && node.nodeType == 1) { //ELEMENT_NODE
				// add children
				for (var i=0; i<node.childNodes.length; i++) {
					var childNode = node.childNodes[i];
					if (childNode.nodeType == 1) this.addChild(childNode, true); //ELEMENT_NODE
					if (this.captureTextNodes && childNode.nodeType == 3) {
						var text = childNode.nodeValue || childNode.text || '';
						if (svg.trim(svg.compressSpaces(text)) != '') {
							this.addChild(new svg.Element.tspan(childNode), false); // TEXT_NODE
						}
					}
				}
				
				// add attributes
				for (var i=0; i<node.attributes.length; i++) {
					var attribute = node.attributes[i];
					this.attributes[attribute.nodeName] = new svg.Property(attribute.nodeName, attribute.nodeValue);
				}
										
				// add tag styles
				var styles = svg.Styles[node.nodeName];
				if (styles != null) {
					for (var name in styles) {
						this.styles[name] = styles[name];
					}
				}					
				
				// add class styles
				if (this.attribute('class').hasValue()) {
					var classes = svg.compressSpaces(this.attribute('class').value).split(' ');
					for (var j=0; j<classes.length; j++) {
						styles = svg.Styles['.'+classes[j]];
						if (styles != null) {
							for (var name in styles) {
								this.styles[name] = styles[name];
							}
						}
						styles = svg.Styles[node.nodeName+'.'+classes[j]];
						if (styles != null) {
							for (var name in styles) {
								this.styles[name] = styles[name];
							}
						}
					}
				}
				
				// add id styles
				if (this.attribute('id').hasValue()) {
					var styles = svg.Styles['#' + this.attribute('id').value];
					if (styles != null) {
						for (var name in styles) {
							this.styles[name] = styles[name];
						}
					}
				}
				
				// add inline styles
				if (this.attribute('style').hasValue()) {
					var styles = this.attribute('style').value.split(';');
					for (var i=0; i<styles.length; i++) {
						if (svg.trim(styles[i]) != '') {
							var style = styles[i].split(':');
							var name = svg.trim(style[0]);
							var value = svg.trim(style[1]);
							this.styles[name] = new svg.Property(name, value);
						}
					}
				}	

				// add id
				if (this.attribute('id').hasValue()) {
					if (svg.Definitions[this.attribute('id').value] == null) {
						svg.Definitions[this.attribute('id').value] = this;
					}
				}
			}
		}
		
		svg.Element.RenderedElementBase = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);
			
			this.setContext = function(ctx) {
				// fill
				if (this.style('fill').isUrlDefinition()) {
					var fs = this.style('fill').getFillStyleDefinition(this, this.style('fill-opacity'));
					if (fs != null) ctx.fillStyle = fs;
				}
				else if (this.style('fill').hasValue()) {
					var fillStyle = this.style('fill');
					if (fillStyle.value == 'currentColor') fillStyle.value = this.style('color').value;
					ctx.fillStyle = (fillStyle.value == 'none' ? 'rgba(0,0,0,0)' : fillStyle.value);
				}
				if (this.style('fill-opacity').hasValue()) {
					var fillStyle = new svg.Property('fill', ctx.fillStyle);
					fillStyle = fillStyle.addOpacity(this.style('fill-opacity').value);
					ctx.fillStyle = fillStyle.value;
				}
									
				// stroke
				if (this.style('stroke').isUrlDefinition()) {
					var fs = this.style('stroke').getFillStyleDefinition(this, this.style('stroke-opacity'));
					if (fs != null) ctx.strokeStyle = fs;
				}
				else if (this.style('stroke').hasValue()) {
					var strokeStyle = this.style('stroke');
					if (strokeStyle.value == 'currentColor') strokeStyle.value = this.style('color').value;
					ctx.strokeStyle = (strokeStyle.value == 'none' ? 'rgba(0,0,0,0)' : strokeStyle.value);
				}
				if (this.style('stroke-opacity').hasValue()) {
					var strokeStyle = new svg.Property('stroke', ctx.strokeStyle);
					strokeStyle = strokeStyle.addOpacity(this.style('stroke-opacity').value);
					ctx.strokeStyle = strokeStyle.value;
				}
				if (this.style('stroke-width').hasValue()) {
					var newLineWidth = this.style('stroke-width').toPixels();
					ctx.lineWidth = newLineWidth == 0 ? 0.001 : newLineWidth; // browsers don't respect 0
			    }
				if (this.style('stroke-linecap').hasValue()) ctx.lineCap = this.style('stroke-linecap').value;
				if (this.style('stroke-linejoin').hasValue()) ctx.lineJoin = this.style('stroke-linejoin').value;
				if (this.style('stroke-miterlimit').hasValue()) ctx.miterLimit = this.style('stroke-miterlimit').value;
				if (this.style('stroke-dasharray').hasValue()) {
					var gaps = svg.ToNumberArray(this.style('stroke-dasharray').value);
					if (typeof(ctx.setLineDash) != 'undefined') { ctx.setLineDash(gaps); }
					else if (typeof(ctx.webkitLineDash) != 'undefined') { ctx.webkitLineDash = gaps; }
					else if (typeof(ctx.mozDash ) != 'undefined') { ctx.mozDash  = gaps; }
					
					var offset = this.style('stroke-dashoffset').numValueOrDefault(1);
					if (typeof(ctx.lineDashOffset) != 'undefined') { ctx.lineDashOffset = offset; }
					else if (typeof(ctx.webkitLineDashOffset) != 'undefined') { ctx.webkitLineDashOffset = offset; }
					else if (typeof(ctx.mozDashOffset) != 'undefined') { ctx.mozDashOffset = offset; }
				}

				// font
				if (typeof(ctx.font) != 'undefined') {
					ctx.font = svg.Font.CreateFont( 
						this.style('font-style').value, 
						this.style('font-variant').value, 
						this.style('font-weight').value, 
						this.style('font-size').hasValue() ? this.style('font-size').toPixels() + 'px' : '', 
						this.style('font-family').value).toString();
				}
				
				// transform
				if (this.attribute('transform').hasValue()) { 
					var transform = new svg.Transform(this.attribute('transform').value);
					transform.apply(ctx);
				}
				
				// clip
				if (this.style('clip-path').hasValue()) {
					var clip = this.style('clip-path').getDefinition();
					if (clip != null) clip.apply(ctx);
				}
				
				// opacity
				if (this.style('opacity').hasValue()) {
					ctx.globalAlpha = this.style('opacity').numValue();
				}
			}		
		}
		svg.Element.RenderedElementBase.prototype = new svg.Element.ElementBase;
		
		svg.Element.PathElementBase = function(node) {
			this.base = svg.Element.RenderedElementBase;
			this.base(node);
			
			this.path = function(ctx) {
				if (ctx != null) ctx.beginPath();
				return new svg.BoundingBox();
			}
			
			this.renderChildren = function(ctx) {
				this.path(ctx);
				svg.Mouse.checkPath(this, ctx);
				if (ctx.fillStyle != '') {
					if (this.attribute('fill-rule').hasValue()) { ctx.fill(this.attribute('fill-rule').value); }
					else { ctx.fill(); }
				}
				if (ctx.strokeStyle != '') ctx.stroke();
				
				var markers = this.getMarkers();
				if (markers != null) {
					if (this.style('marker-start').isUrlDefinition()) {
						var marker = this.style('marker-start').getDefinition();
						marker.render(ctx, markers[0][0], markers[0][1]);
					}
					if (this.style('marker-mid').isUrlDefinition()) {
						var marker = this.style('marker-mid').getDefinition();
						for (var i=1;i<markers.length-1;i++) {
							marker.render(ctx, markers[i][0], markers[i][1]);
						}
					}
					if (this.style('marker-end').isUrlDefinition()) {
						var marker = this.style('marker-end').getDefinition();
						marker.render(ctx, markers[markers.length-1][0], markers[markers.length-1][1]);
					}
				}					
			}
			
			this.getBoundingBox = function() {
				return this.path();
			}
			
			this.getMarkers = function() {
				return null;
			}
		}
		svg.Element.PathElementBase.prototype = new svg.Element.RenderedElementBase;
		
		// svg element
		svg.Element.svg = function(node) {
			this.base = svg.Element.RenderedElementBase;
			this.base(node);
			
			this.baseClearContext = this.clearContext;
			this.clearContext = function(ctx) {
				this.baseClearContext(ctx);
				svg.ViewPort.RemoveCurrent();
			}
			
			this.baseSetContext = this.setContext;
			this.setContext = function(ctx) {
				// initial values
				ctx.strokeStyle = 'rgba(0,0,0,0)';
				ctx.lineCap = 'butt';
				ctx.lineJoin = 'miter';
				ctx.miterLimit = 4;			
			
				this.baseSetContext(ctx);
				
				// create new view port
				if (!this.attribute('x').hasValue()) this.attribute('x', true).value = 0;
				if (!this.attribute('y').hasValue()) this.attribute('y', true).value = 0;
				ctx.translate(this.attribute('x').toPixels('x'), this.attribute('y').toPixels('y'));
				
				var width = svg.ViewPort.width();
				var height = svg.ViewPort.height();
				
				if (!this.attribute('width').hasValue()) this.attribute('width', true).value = '100%';
				if (!this.attribute('height').hasValue()) this.attribute('height', true).value = '100%';
				if (typeof(this.root) == 'undefined') {
					width = this.attribute('width').toPixels('x');
					height = this.attribute('height').toPixels('y');
					
					var x = 0;
					var y = 0;
					if (this.attribute('refX').hasValue() && this.attribute('refY').hasValue()) {
						x = -this.attribute('refX').toPixels('x');
						y = -this.attribute('refY').toPixels('y');
					}
					
					ctx.beginPath();
					ctx.moveTo(x, y);
					ctx.lineTo(width, y);
					ctx.lineTo(width, height);
					ctx.lineTo(x, height);
					ctx.closePath();
					ctx.clip();
				}
				svg.ViewPort.SetCurrent(width, height);	
						
				// viewbox
				if (this.attribute('viewBox').hasValue()) {				
					var viewBox = svg.ToNumberArray(this.attribute('viewBox').value);
					var minX = viewBox[0];
					var minY = viewBox[1];
					width = viewBox[2];
					height = viewBox[3];
					
					svg.AspectRatio(ctx,
									this.attribute('preserveAspectRatio').value, 
									svg.ViewPort.width(), 
									width,
									svg.ViewPort.height(),
									height,
									minX,
									minY,
									this.attribute('refX').value,
									this.attribute('refY').value);
										
					svg.ViewPort.RemoveCurrent();	
					svg.ViewPort.SetCurrent(viewBox[2], viewBox[3]);						
				}				
			}
		}
		svg.Element.svg.prototype = new svg.Element.RenderedElementBase;

		// rect element
		svg.Element.rect = function(node) {
			this.base = svg.Element.PathElementBase;
			this.base(node);
			
			this.path = function(ctx) {
				var x = this.attribute('x').toPixels('x');
				var y = this.attribute('y').toPixels('y');
				var width = this.attribute('width').toPixels('x');
				var height = this.attribute('height').toPixels('y');
				var rx = this.attribute('rx').toPixels('x');
				var ry = this.attribute('ry').toPixels('y');
				if (this.attribute('rx').hasValue() && !this.attribute('ry').hasValue()) ry = rx;
				if (this.attribute('ry').hasValue() && !this.attribute('rx').hasValue()) rx = ry;
				rx = Math.min(rx, width / 2.0);
				ry = Math.min(ry, height / 2.0);
				if (ctx != null) {
					ctx.beginPath();
					ctx.moveTo(x + rx, y);
					ctx.lineTo(x + width - rx, y);
					ctx.quadraticCurveTo(x + width, y, x + width, y + ry)
					ctx.lineTo(x + width, y + height - ry);
					ctx.quadraticCurveTo(x + width, y + height, x + width - rx, y + height)
					ctx.lineTo(x + rx, y + height);
					ctx.quadraticCurveTo(x, y + height, x, y + height - ry)
					ctx.lineTo(x, y + ry);
					ctx.quadraticCurveTo(x, y, x + rx, y)
					ctx.closePath();
				}
				
				return new svg.BoundingBox(x, y, x + width, y + height);
			}
		}
		svg.Element.rect.prototype = new svg.Element.PathElementBase;
		
		// circle element
		svg.Element.circle = function(node) {
			this.base = svg.Element.PathElementBase;
			this.base(node);
			
			this.path = function(ctx) {
				var cx = this.attribute('cx').toPixels('x');
				var cy = this.attribute('cy').toPixels('y');
				var r = this.attribute('r').toPixels();
			
				if (ctx != null) {
					ctx.beginPath();
					ctx.arc(cx, cy, r, 0, Math.PI * 2, true); 
					ctx.closePath();
				}
				
				return new svg.BoundingBox(cx - r, cy - r, cx + r, cy + r);
			}
		}
		svg.Element.circle.prototype = new svg.Element.PathElementBase;	

		// ellipse element
		svg.Element.ellipse = function(node) {
			this.base = svg.Element.PathElementBase;
			this.base(node);
			
			this.path = function(ctx) {
				var KAPPA = 4 * ((Math.sqrt(2) - 1) / 3);
				var rx = this.attribute('rx').toPixels('x');
				var ry = this.attribute('ry').toPixels('y');
				var cx = this.attribute('cx').toPixels('x');
				var cy = this.attribute('cy').toPixels('y');
				
				if (ctx != null) {
					ctx.beginPath();
					ctx.moveTo(cx, cy - ry);
					ctx.bezierCurveTo(cx + (KAPPA * rx), cy - ry,  cx + rx, cy - (KAPPA * ry), cx + rx, cy);
					ctx.bezierCurveTo(cx + rx, cy + (KAPPA * ry), cx + (KAPPA * rx), cy + ry, cx, cy + ry);
					ctx.bezierCurveTo(cx - (KAPPA * rx), cy + ry, cx - rx, cy + (KAPPA * ry), cx - rx, cy);
					ctx.bezierCurveTo(cx - rx, cy - (KAPPA * ry), cx - (KAPPA * rx), cy - ry, cx, cy - ry);
					ctx.closePath();
				}
				
				return new svg.BoundingBox(cx - rx, cy - ry, cx + rx, cy + ry);
			}
		}
		svg.Element.ellipse.prototype = new svg.Element.PathElementBase;			
		
		// line element
		svg.Element.line = function(node) {
			this.base = svg.Element.PathElementBase;
			this.base(node);
			
			this.getPoints = function() {
				return [
					new svg.Point(this.attribute('x1').toPixels('x'), this.attribute('y1').toPixels('y')),
					new svg.Point(this.attribute('x2').toPixels('x'), this.attribute('y2').toPixels('y'))];
			}
								
			this.path = function(ctx) {
				var points = this.getPoints();
				
				if (ctx != null) {
					ctx.beginPath();
					ctx.moveTo(points[0].x, points[0].y);
					ctx.lineTo(points[1].x, points[1].y);
				}
				
				return new svg.BoundingBox(points[0].x, points[0].y, points[1].x, points[1].y);
			}
			
			this.getMarkers = function() {
				var points = this.getPoints();	
				var a = points[0].angleTo(points[1]);
				return [[points[0], a], [points[1], a]];
			}
		}
		svg.Element.line.prototype = new svg.Element.PathElementBase;		
				
		// polyline element
		svg.Element.polyline = function(node) {
			this.base = svg.Element.PathElementBase;
			this.base(node);
			
			this.points = svg.CreatePath(this.attribute('points').value);
			this.path = function(ctx) {
				var bb = new svg.BoundingBox(this.points[0].x, this.points[0].y);
				if (ctx != null) {
					ctx.beginPath();
					ctx.moveTo(this.points[0].x, this.points[0].y);
				}
				for (var i=1; i<this.points.length; i++) {
					bb.addPoint(this.points[i].x, this.points[i].y);
					if (ctx != null) ctx.lineTo(this.points[i].x, this.points[i].y);
				}
				return bb;
			}
			
			this.getMarkers = function() {
				var markers = [];
				for (var i=0; i<this.points.length - 1; i++) {
					markers.push([this.points[i], this.points[i].angleTo(this.points[i+1])]);
				}
				markers.push([this.points[this.points.length-1], markers[markers.length-1][1]]);
				return markers;
			}			
		}
		svg.Element.polyline.prototype = new svg.Element.PathElementBase;				
				
		// polygon element
		svg.Element.polygon = function(node) {
			this.base = svg.Element.polyline;
			this.base(node);
			
			this.basePath = this.path;
			this.path = function(ctx) {
				var bb = this.basePath(ctx);
				if (ctx != null) {
					ctx.lineTo(this.points[0].x, this.points[0].y);
					ctx.closePath();
				}
				return bb;
			}
		}
		svg.Element.polygon.prototype = new svg.Element.polyline;

		// path element
		svg.Element.path = function(node) {
			this.base = svg.Element.PathElementBase;
			this.base(node);
					
			var d = this.attribute('d').value;
			// TODO: convert to real lexer based on http://www.w3.org/TR/SVG11/paths.html#PathDataBNF
			d = d.replace(/,/gm,' '); // get rid of all commas
			d = d.replace(/([MmZzLlHhVvCcSsQqTtAa])([MmZzLlHhVvCcSsQqTtAa])/gm,'$1 $2'); // separate commands from commands
			d = d.replace(/([MmZzLlHhVvCcSsQqTtAa])([MmZzLlHhVvCcSsQqTtAa])/gm,'$1 $2'); // separate commands from commands
			d = d.replace(/([MmZzLlHhVvCcSsQqTtAa])([^\s])/gm,'$1 $2'); // separate commands from points
			d = d.replace(/([^\s])([MmZzLlHhVvCcSsQqTtAa])/gm,'$1 $2'); // separate commands from points
			d = d.replace(/([0-9])([+\-])/gm,'$1 $2'); // separate digits when no comma
			d = d.replace(/(\.[0-9]*)(\.)/gm,'$1 $2'); // separate digits when no comma
			d = d.replace(/([Aa](\s+[0-9]+){3})\s+([01])\s*([01])/gm,'$1 $3 $4 '); // shorthand elliptical arc path syntax
			d = svg.compressSpaces(d); // compress multiple spaces
			d = svg.trim(d);
			this.PathParser = new (function(d) {
				this.tokens = d.split(' ');
				
				this.reset = function() {
					this.i = -1;
					this.command = '';
					this.previousCommand = '';
					this.start = new svg.Point(0, 0);
					this.control = new svg.Point(0, 0);
					this.current = new svg.Point(0, 0);
					this.points = [];
					this.angles = [];
				}
								
				this.isEnd = function() {
					return this.i >= this.tokens.length - 1;
				}
				
				this.isCommandOrEnd = function() {
					if (this.isEnd()) return true;
					return this.tokens[this.i + 1].match(/^[A-Za-z]$/) != null;
				}
				
				this.isRelativeCommand = function() {
					switch(this.command)
					{
						case 'm':
						case 'l':
						case 'h':
						case 'v':
						case 'c':
						case 's':
						case 'q':
						case 't':
						case 'a':
						case 'z':
							return true;
							break;
					}
					return false;
				}
							
				this.getToken = function() {
					this.i++;
					return this.tokens[this.i];
				}
				
				this.getScalar = function() {
					return parseFloat(this.getToken());
				}
				
				this.nextCommand = function() {
					this.previousCommand = this.command;
					this.command = this.getToken();
				}				
				
				this.getPoint = function() {
					var p = new svg.Point(this.getScalar(), this.getScalar());
					return this.makeAbsolute(p);
				}
				
				this.getAsControlPoint = function() {
					var p = this.getPoint();
					this.control = p;
					return p;
				}
				
				this.getAsCurrentPoint = function() {
					var p = this.getPoint();
					this.current = p;
					return p;	
				}
				
				this.getReflectedControlPoint = function() {
					if (this.previousCommand.toLowerCase() != 'c' && 
					    this.previousCommand.toLowerCase() != 's' &&
						this.previousCommand.toLowerCase() != 'q' && 
						this.previousCommand.toLowerCase() != 't' ){
						return this.current;
					}
					
					// reflect point
					var p = new svg.Point(2 * this.current.x - this.control.x, 2 * this.current.y - this.control.y);					
					return p;
				}
				
				this.makeAbsolute = function(p) {
					if (this.isRelativeCommand()) {
						p.x += this.current.x;
						p.y += this.current.y;
					}
					return p;
				}
				
				this.addMarker = function(p, from, priorTo) {
					// if the last angle isn't filled in because we didn't have this point yet ...
					if (priorTo != null && this.angles.length > 0 && this.angles[this.angles.length-1] == null) {
						this.angles[this.angles.length-1] = this.points[this.points.length-1].angleTo(priorTo);
					}
					this.addMarkerAngle(p, from == null ? null : from.angleTo(p));
				}
				
				this.addMarkerAngle = function(p, a) {
					this.points.push(p);
					this.angles.push(a);
				}				
				
				this.getMarkerPoints = function() { return this.points; }
				this.getMarkerAngles = function() {
					for (var i=0; i<this.angles.length; i++) {
						if (this.angles[i] == null) {
							for (var j=i+1; j<this.angles.length; j++) {
								if (this.angles[j] != null) {
									this.angles[i] = this.angles[j];
									break;
								}
							}
						}
					}
					return this.angles;
				}
			})(d);

			this.path = function(ctx) {
				var pp = this.PathParser;
				pp.reset();

				var bb = new svg.BoundingBox();
				if (ctx != null) ctx.beginPath();
				while (!pp.isEnd()) {
					pp.nextCommand();
					switch (pp.command) {
					case 'M':
					case 'm':
						var p = pp.getAsCurrentPoint();
						pp.addMarker(p);
						bb.addPoint(p.x, p.y);
						if (ctx != null) ctx.moveTo(p.x, p.y);
						pp.start = pp.current;
						while (!pp.isCommandOrEnd()) {
							var p = pp.getAsCurrentPoint();
							pp.addMarker(p, pp.start);
							bb.addPoint(p.x, p.y);
							if (ctx != null) ctx.lineTo(p.x, p.y);
						}
						break;
					case 'L':
					case 'l':
						while (!pp.isCommandOrEnd()) {
							var c = pp.current;
							var p = pp.getAsCurrentPoint();
							pp.addMarker(p, c);
							bb.addPoint(p.x, p.y);
							if (ctx != null) ctx.lineTo(p.x, p.y);
						}
						break;
					case 'H':
					case 'h':
						while (!pp.isCommandOrEnd()) {
							var newP = new svg.Point((pp.isRelativeCommand() ? pp.current.x : 0) + pp.getScalar(), pp.current.y);
							pp.addMarker(newP, pp.current);
							pp.current = newP;
							bb.addPoint(pp.current.x, pp.current.y);
							if (ctx != null) ctx.lineTo(pp.current.x, pp.current.y);
						}
						break;
					case 'V':
					case 'v':
						while (!pp.isCommandOrEnd()) {
							var newP = new svg.Point(pp.current.x, (pp.isRelativeCommand() ? pp.current.y : 0) + pp.getScalar());
							pp.addMarker(newP, pp.current);
							pp.current = newP;
							bb.addPoint(pp.current.x, pp.current.y);
							if (ctx != null) ctx.lineTo(pp.current.x, pp.current.y);
						}
						break;
					case 'C':
					case 'c':
						while (!pp.isCommandOrEnd()) {
							var curr = pp.current;
							var p1 = pp.getPoint();
							var cntrl = pp.getAsControlPoint();
							var cp = pp.getAsCurrentPoint();
							pp.addMarker(cp, cntrl, p1);
							bb.addBezierCurve(curr.x, curr.y, p1.x, p1.y, cntrl.x, cntrl.y, cp.x, cp.y);
							if (ctx != null) ctx.bezierCurveTo(p1.x, p1.y, cntrl.x, cntrl.y, cp.x, cp.y);
						}
						break;
					case 'S':
					case 's':
						while (!pp.isCommandOrEnd()) {
							var curr = pp.current;
							var p1 = pp.getReflectedControlPoint();
							var cntrl = pp.getAsControlPoint();
							var cp = pp.getAsCurrentPoint();
							pp.addMarker(cp, cntrl, p1);
							bb.addBezierCurve(curr.x, curr.y, p1.x, p1.y, cntrl.x, cntrl.y, cp.x, cp.y);
							if (ctx != null) ctx.bezierCurveTo(p1.x, p1.y, cntrl.x, cntrl.y, cp.x, cp.y);
						}
						break;
					case 'Q':
					case 'q':
						while (!pp.isCommandOrEnd()) {
							var curr = pp.current;
							var cntrl = pp.getAsControlPoint();
							var cp = pp.getAsCurrentPoint();
							pp.addMarker(cp, cntrl, cntrl);
							bb.addQuadraticCurve(curr.x, curr.y, cntrl.x, cntrl.y, cp.x, cp.y);
							if (ctx != null) ctx.quadraticCurveTo(cntrl.x, cntrl.y, cp.x, cp.y);
						}
						break;
					case 'T':
					case 't':
						while (!pp.isCommandOrEnd()) {
							var curr = pp.current;
							var cntrl = pp.getReflectedControlPoint();
							pp.control = cntrl;
							var cp = pp.getAsCurrentPoint();
							pp.addMarker(cp, cntrl, cntrl);
							bb.addQuadraticCurve(curr.x, curr.y, cntrl.x, cntrl.y, cp.x, cp.y);
							if (ctx != null) ctx.quadraticCurveTo(cntrl.x, cntrl.y, cp.x, cp.y);
						}
						break;
					case 'A':
					case 'a':
						while (!pp.isCommandOrEnd()) {
						    var curr = pp.current;
							var rx = pp.getScalar();
							var ry = pp.getScalar();
							var xAxisRotation = pp.getScalar() * (Math.PI / 180.0);
							var largeArcFlag = pp.getScalar();
							var sweepFlag = pp.getScalar();
							var cp = pp.getAsCurrentPoint();

							// Conversion from endpoint to center parameterization
							// http://www.w3.org/TR/SVG11/implnote.html#ArcImplementationNotes
							// x1', y1'
							var currp = new svg.Point(
								Math.cos(xAxisRotation) * (curr.x - cp.x) / 2.0 + Math.sin(xAxisRotation) * (curr.y - cp.y) / 2.0,
								-Math.sin(xAxisRotation) * (curr.x - cp.x) / 2.0 + Math.cos(xAxisRotation) * (curr.y - cp.y) / 2.0
							);
							// adjust radii
							var l = Math.pow(currp.x,2)/Math.pow(rx,2)+Math.pow(currp.y,2)/Math.pow(ry,2);
							if (l > 1) {
								rx *= Math.sqrt(l);
								ry *= Math.sqrt(l);
							}
							// cx', cy'
							var s = (largeArcFlag == sweepFlag ? -1 : 1) * Math.sqrt(
								((Math.pow(rx,2)*Math.pow(ry,2))-(Math.pow(rx,2)*Math.pow(currp.y,2))-(Math.pow(ry,2)*Math.pow(currp.x,2))) /
								(Math.pow(rx,2)*Math.pow(currp.y,2)+Math.pow(ry,2)*Math.pow(currp.x,2))
							);
							if (isNaN(s)) s = 0;
							var cpp = new svg.Point(s * rx * currp.y / ry, s * -ry * currp.x / rx);
							// cx, cy
							var centp = new svg.Point(
								(curr.x + cp.x) / 2.0 + Math.cos(xAxisRotation) * cpp.x - Math.sin(xAxisRotation) * cpp.y,
								(curr.y + cp.y) / 2.0 + Math.sin(xAxisRotation) * cpp.x + Math.cos(xAxisRotation) * cpp.y
							);
							// vector magnitude
							var m = function(v) { return Math.sqrt(Math.pow(v[0],2) + Math.pow(v[1],2)); }
							// ratio between two vectors
							var r = function(u, v) { return (u[0]*v[0]+u[1]*v[1]) / (m(u)*m(v)) }
							// angle between two vectors
							var a = function(u, v) { return (u[0]*v[1] < u[1]*v[0] ? -1 : 1) * Math.acos(r(u,v)); }
							// initial angle
							var a1 = a([1,0], [(currp.x-cpp.x)/rx,(currp.y-cpp.y)/ry]);
							// angle delta
							var u = [(currp.x-cpp.x)/rx,(currp.y-cpp.y)/ry];
							var v = [(-currp.x-cpp.x)/rx,(-currp.y-cpp.y)/ry];
							var ad = a(u, v);
							if (r(u,v) <= -1) ad = Math.PI;
							if (r(u,v) >= 1) ad = 0;

							// for markers
							var dir = 1 - sweepFlag ? 1.0 : -1.0;
							var ah = a1 + dir * (ad / 2.0);
							var halfWay = new svg.Point(
								centp.x + rx * Math.cos(ah),
								centp.y + ry * Math.sin(ah)
							);
							pp.addMarkerAngle(halfWay, ah - dir * Math.PI / 2);
							pp.addMarkerAngle(cp, ah - dir * Math.PI);

							bb.addPoint(cp.x, cp.y); // TODO: this is too naive, make it better
							if (ctx != null) {
								var r = rx > ry ? rx : ry;
								var sx = rx > ry ? 1 : rx / ry;
								var sy = rx > ry ? ry / rx : 1;

								ctx.translate(centp.x, centp.y);
								ctx.rotate(xAxisRotation);
								ctx.scale(sx, sy);
								ctx.arc(0, 0, r, a1, a1 + ad, 1 - sweepFlag);
								ctx.scale(1/sx, 1/sy);
								ctx.rotate(-xAxisRotation);
								ctx.translate(-centp.x, -centp.y);
							}
						}
						break;
					case 'Z':
					case 'z':
						if (ctx != null) ctx.closePath();
						pp.current = pp.start;
					}
				}

				return bb;
			}

			this.getMarkers = function() {
				var points = this.PathParser.getMarkerPoints();
				var angles = this.PathParser.getMarkerAngles();
				
				var markers = [];
				for (var i=0; i<points.length; i++) {
					markers.push([points[i], angles[i]]);
				}
				return markers;
			}
		}
		svg.Element.path.prototype = new svg.Element.PathElementBase;
		
		// pattern element
		svg.Element.pattern = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);
			
			this.createPattern = function(ctx, element) {
				var width = this.attribute('width').toPixels('x', true);
				var height = this.attribute('height').toPixels('y', true);
			
				// render me using a temporary svg element
				var tempSvg = new svg.Element.svg();
				tempSvg.attributes['viewBox'] = new svg.Property('viewBox', this.attribute('viewBox').value);
				tempSvg.attributes['width'] = new svg.Property('width', width + 'px');
				tempSvg.attributes['height'] = new svg.Property('height', height + 'px');
				tempSvg.attributes['transform'] = new svg.Property('transform', this.attribute('patternTransform').value);
				tempSvg.children = this.children;
				
				var c = document.createElement('canvas');
				c.width = width;
				c.height = height;
				var cctx = c.getContext('2d');
				if (this.attribute('x').hasValue() && this.attribute('y').hasValue()) {
					cctx.translate(this.attribute('x').toPixels('x', true), this.attribute('y').toPixels('y', true));
				}
				// render 3x3 grid so when we transform there's no white space on edges
				for (var x=-1; x<=1; x++) {
					for (var y=-1; y<=1; y++) {
						cctx.save();
						cctx.translate(x * c.width, y * c.height);
						tempSvg.render(cctx);
						cctx.restore();
					}
				}
				var pattern = ctx.createPattern(c, 'repeat');
				return pattern;
			}
		}
		svg.Element.pattern.prototype = new svg.Element.ElementBase;
		
		// marker element
		svg.Element.marker = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);
			
			this.baseRender = this.render;
			this.render = function(ctx, point, angle) {
				ctx.translate(point.x, point.y);
				if (this.attribute('orient').valueOrDefault('auto') == 'auto') ctx.rotate(angle);
				if (this.attribute('markerUnits').valueOrDefault('strokeWidth') == 'strokeWidth') ctx.scale(ctx.lineWidth, ctx.lineWidth);
				ctx.save();
							
				// render me using a temporary svg element
				var tempSvg = new svg.Element.svg();
				tempSvg.attributes['viewBox'] = new svg.Property('viewBox', this.attribute('viewBox').value);
				tempSvg.attributes['refX'] = new svg.Property('refX', this.attribute('refX').value);
				tempSvg.attributes['refY'] = new svg.Property('refY', this.attribute('refY').value);
				tempSvg.attributes['width'] = new svg.Property('width', this.attribute('markerWidth').value);
				tempSvg.attributes['height'] = new svg.Property('height', this.attribute('markerHeight').value);
				tempSvg.attributes['fill'] = new svg.Property('fill', this.attribute('fill').valueOrDefault('black'));
				tempSvg.attributes['stroke'] = new svg.Property('stroke', this.attribute('stroke').valueOrDefault('none'));
				tempSvg.children = this.children;
				tempSvg.render(ctx);
				
				ctx.restore();
				if (this.attribute('markerUnits').valueOrDefault('strokeWidth') == 'strokeWidth') ctx.scale(1/ctx.lineWidth, 1/ctx.lineWidth);
				if (this.attribute('orient').valueOrDefault('auto') == 'auto') ctx.rotate(-angle);
				ctx.translate(-point.x, -point.y);
			}
		}
		svg.Element.marker.prototype = new svg.Element.ElementBase;
		
		// definitions element
		svg.Element.defs = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);	
			
			this.render = function(ctx) {
				// NOOP
			}
		}
		svg.Element.defs.prototype = new svg.Element.ElementBase;
		
		// base for gradients
		svg.Element.GradientBase = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);
			
			this.gradientUnits = this.attribute('gradientUnits').valueOrDefault('objectBoundingBox');
			
			this.stops = [];			
			for (var i=0; i<this.children.length; i++) {
				var child = this.children[i];
				if (child.type == 'stop') this.stops.push(child);
			}	
			
			this.getGradient = function() {
				// OVERRIDE ME!
			}			

			this.createGradient = function(ctx, element, parentOpacityProp) {
				var stopsContainer = this;
				if (this.getHrefAttribute().hasValue()) {
					stopsContainer = this.getHrefAttribute().getDefinition();
				}
				
				var addParentOpacity = function (color) {
					if (parentOpacityProp.hasValue()) {
						var p = new svg.Property('color', color);
						return p.addOpacity(parentOpacityProp.value).value;
					}
					return color;
				};
			
				var g = this.getGradient(ctx, element);
				if (g == null) return addParentOpacity(stopsContainer.stops[stopsContainer.stops.length - 1].color);
				for (var i=0; i<stopsContainer.stops.length; i++) {
					g.addColorStop(stopsContainer.stops[i].offset, addParentOpacity(stopsContainer.stops[i].color));
				}
				
				if (this.attribute('gradientTransform').hasValue()) {
					// render as transformed pattern on temporary canvas
					var rootView = svg.ViewPort.viewPorts[0];
					
					var rect = new svg.Element.rect();
					rect.attributes['x'] = new svg.Property('x', -svg.MAX_VIRTUAL_PIXELS/3.0);
					rect.attributes['y'] = new svg.Property('y', -svg.MAX_VIRTUAL_PIXELS/3.0);
					rect.attributes['width'] = new svg.Property('width', svg.MAX_VIRTUAL_PIXELS);
					rect.attributes['height'] = new svg.Property('height', svg.MAX_VIRTUAL_PIXELS);
					
					var group = new svg.Element.g();
					group.attributes['transform'] = new svg.Property('transform', this.attribute('gradientTransform').value);
					group.children = [ rect ];
					
					var tempSvg = new svg.Element.svg();
					tempSvg.attributes['x'] = new svg.Property('x', 0);
					tempSvg.attributes['y'] = new svg.Property('y', 0);
					tempSvg.attributes['width'] = new svg.Property('width', rootView.width);
					tempSvg.attributes['height'] = new svg.Property('height', rootView.height);
					tempSvg.children = [ group ];
					
					var c = document.createElement('canvas');
					c.width = rootView.width;
					c.height = rootView.height;
					var tempCtx = c.getContext('2d');
					tempCtx.fillStyle = g;
					tempSvg.render(tempCtx);		
					return tempCtx.createPattern(c, 'no-repeat');
				}
				
				return g;				
			}
		}
		svg.Element.GradientBase.prototype = new svg.Element.ElementBase;
		
		// linear gradient element
		svg.Element.linearGradient = function(node) {
			this.base = svg.Element.GradientBase;
			this.base(node);
			
			this.getGradient = function(ctx, element) {
				var bb = element.getBoundingBox();
				
				if (!this.attribute('x1').hasValue()
				 && !this.attribute('y1').hasValue()
				 && !this.attribute('x2').hasValue()
				 && !this.attribute('y2').hasValue()) {
					this.attribute('x1', true).value = 0;
					this.attribute('y1', true).value = 0;
					this.attribute('x2', true).value = 1;
					this.attribute('y2', true).value = 0;
				 }
				
				var x1 = (this.gradientUnits == 'objectBoundingBox' 
					? bb.x() + bb.width() * this.attribute('x1').numValue() 
					: this.attribute('x1').toPixels('x'));
				var y1 = (this.gradientUnits == 'objectBoundingBox' 
					? bb.y() + bb.height() * this.attribute('y1').numValue()
					: this.attribute('y1').toPixels('y'));
				var x2 = (this.gradientUnits == 'objectBoundingBox' 
					? bb.x() + bb.width() * this.attribute('x2').numValue()
					: this.attribute('x2').toPixels('x'));
				var y2 = (this.gradientUnits == 'objectBoundingBox' 
					? bb.y() + bb.height() * this.attribute('y2').numValue()
					: this.attribute('y2').toPixels('y'));

				if (x1 == x2 && y1 == y2) return null;
				return ctx.createLinearGradient(x1, y1, x2, y2);
			}
		}
		svg.Element.linearGradient.prototype = new svg.Element.GradientBase;
		
		// radial gradient element
		svg.Element.radialGradient = function(node) {
			this.base = svg.Element.GradientBase;
			this.base(node);
			
			this.getGradient = function(ctx, element) {
				var bb = element.getBoundingBox();
				
				if (!this.attribute('cx').hasValue()) this.attribute('cx', true).value = '50%';
				if (!this.attribute('cy').hasValue()) this.attribute('cy', true).value = '50%';
				if (!this.attribute('r').hasValue()) this.attribute('r', true).value = '50%';
				
				var cx = (this.gradientUnits == 'objectBoundingBox' 
					? bb.x() + bb.width() * this.attribute('cx').numValue() 
					: this.attribute('cx').toPixels('x'));
				var cy = (this.gradientUnits == 'objectBoundingBox' 
					? bb.y() + bb.height() * this.attribute('cy').numValue() 
					: this.attribute('cy').toPixels('y'));
				
				var fx = cx;
				var fy = cy;
				if (this.attribute('fx').hasValue()) {
					fx = (this.gradientUnits == 'objectBoundingBox' 
					? bb.x() + bb.width() * this.attribute('fx').numValue() 
					: this.attribute('fx').toPixels('x'));
				}
				if (this.attribute('fy').hasValue()) {
					fy = (this.gradientUnits == 'objectBoundingBox' 
					? bb.y() + bb.height() * this.attribute('fy').numValue() 
					: this.attribute('fy').toPixels('y'));
				}
				
				var r = (this.gradientUnits == 'objectBoundingBox' 
					? (bb.width() + bb.height()) / 2.0 * this.attribute('r').numValue()
					: this.attribute('r').toPixels());
				
				return ctx.createRadialGradient(fx, fy, 0, cx, cy, r);
			}
		}
		svg.Element.radialGradient.prototype = new svg.Element.GradientBase;
		
		// gradient stop element
		svg.Element.stop = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);
			
			this.offset = this.attribute('offset').numValue();
			if (this.offset < 0) this.offset = 0;
			if (this.offset > 1) this.offset = 1;
			
			var stopColor = this.style('stop-color');
			if (this.style('stop-opacity').hasValue()) stopColor = stopColor.addOpacity(this.style('stop-opacity').value);
			this.color = stopColor.value;
		}
		svg.Element.stop.prototype = new svg.Element.ElementBase;
		
		// animation base element
		svg.Element.AnimateBase = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);
			
			svg.Animations.push(this);
			
			this.duration = 0.0;
			this.begin = this.attribute('begin').toMilliseconds();
			this.maxDuration = this.begin + this.attribute('dur').toMilliseconds();
			
			this.getProperty = function() {
				var attributeType = this.attribute('attributeType').value;
				var attributeName = this.attribute('attributeName').value;
				
				if (attributeType == 'CSS') {
					return this.parent.style(attributeName, true);
				}
				return this.parent.attribute(attributeName, true);			
			};
			
			this.initialValue = null;
			this.initialUnits = '';
			this.removed = false;			

			this.calcValue = function() {
				// OVERRIDE ME!
				return '';
			}
					
			this.update = function(delta) {	
				// set initial value
				if (this.initialValue == null) {
					this.initialValue = this.getProperty().value;
					this.initialUnits = this.getProperty().getUnits();
				}
			
				// if we're past the end time
				if (this.duration > this.maxDuration) {
					// loop for indefinitely repeating animations
					if (this.attribute('repeatCount').value == 'indefinite'
					 || this.attribute('repeatDur').value == 'indefinite') {
						this.duration = 0.0
					}
					else if (this.attribute('fill').valueOrDefault('remove') == 'remove' && !this.removed) {
						this.removed = true;
						this.getProperty().value = this.initialValue;
						return true;
					}
					else {
						return false; // no updates made
					}
				}			
				this.duration = this.duration + delta;
			
				// if we're past the begin time
				var updated = false;
				if (this.begin < this.duration) {
					var newValue = this.calcValue(); // tween
					
					if (this.attribute('type').hasValue()) {
						// for transform, etc.
						var type = this.attribute('type').value;
						newValue = type + '(' + newValue + ')';
					}
					
					this.getProperty().value = newValue;
					updated = true;
				}
				
				return updated;
			}
			
			this.from = this.attribute('from');
			this.to = this.attribute('to');
			this.values = this.attribute('values');
			if (this.values.hasValue()) this.values.value = this.values.value.split(';');
			
			// fraction of duration we've covered
			this.progress = function() {
				var ret = { progress: (this.duration - this.begin) / (this.maxDuration - this.begin) };
				if (this.values.hasValue()) {
					var p = ret.progress * (this.values.value.length - 1);
					var lb = Math.floor(p), ub = Math.ceil(p);
					ret.from = new svg.Property('from', parseFloat(this.values.value[lb]));
					ret.to = new svg.Property('to', parseFloat(this.values.value[ub]));
					ret.progress = (p - lb) / (ub - lb);
				}
				else {
					ret.from = this.from;
					ret.to = this.to;
				}
				return ret;
			}			
		}
		svg.Element.AnimateBase.prototype = new svg.Element.ElementBase;
		
		// animate element
		svg.Element.animate = function(node) {
			this.base = svg.Element.AnimateBase;
			this.base(node);
			
			this.calcValue = function() {
				var p = this.progress();
				
				// tween value linearly
				var newValue = p.from.numValue() + (p.to.numValue() - p.from.numValue()) * p.progress; 
				return newValue + this.initialUnits;
			};
		}
		svg.Element.animate.prototype = new svg.Element.AnimateBase;
			
		// animate color element
		svg.Element.animateColor = function(node) {
			this.base = svg.Element.AnimateBase;
			this.base(node);

			this.calcValue = function() {
				var p = this.progress();
				var from = new RGBColor(p.from.value);
				var to = new RGBColor(p.to.value);
				
				if (from.ok && to.ok) {
					// tween color linearly
					var r = from.r + (to.r - from.r) * p.progress;
					var g = from.g + (to.g - from.g) * p.progress;
					var b = from.b + (to.b - from.b) * p.progress;
					return 'rgb('+parseInt(r,10)+','+parseInt(g,10)+','+parseInt(b,10)+')';
				}
				return this.attribute('from').value;
			};
		}
		svg.Element.animateColor.prototype = new svg.Element.AnimateBase;
		
		// animate transform element
		svg.Element.animateTransform = function(node) {
			this.base = svg.Element.AnimateBase;
			this.base(node);
			
			this.calcValue = function() {
				var p = this.progress();
				
				// tween value linearly
				var from = svg.ToNumberArray(p.from.value);
				var to = svg.ToNumberArray(p.to.value);
				var newValue = '';
				for (var i=0; i<from.length; i++) {
					newValue += from[i] + (to[i] - from[i]) * p.progress + ' ';
				}
				return newValue;
			};
		}
		svg.Element.animateTransform.prototype = new svg.Element.animate;
		
		// font element
		svg.Element.font = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);

			this.horizAdvX = this.attribute('horiz-adv-x').numValue();			
			
			this.isRTL = false;
			this.isArabic = false;
			this.fontFace = null;
			this.missingGlyph = null;
			this.glyphs = [];			
			for (var i=0; i<this.children.length; i++) {
				var child = this.children[i];
				if (child.type == 'font-face') {
					this.fontFace = child;
					if (child.style('font-family').hasValue()) {
						svg.Definitions[child.style('font-family').value] = this;
					}
				}
				else if (child.type == 'missing-glyph') this.missingGlyph = child;
				else if (child.type == 'glyph') {
					if (child.arabicForm != '') {
						this.isRTL = true;
						this.isArabic = true;
						if (typeof(this.glyphs[child.unicode]) == 'undefined') this.glyphs[child.unicode] = [];
						this.glyphs[child.unicode][child.arabicForm] = child;
					}
					else {
						this.glyphs[child.unicode] = child;
					}
				}
			}	
		}
		svg.Element.font.prototype = new svg.Element.ElementBase;
		
		// font-face element
		svg.Element.fontface = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);	
			
			this.ascent = this.attribute('ascent').value;
			this.descent = this.attribute('descent').value;
			this.unitsPerEm = this.attribute('units-per-em').numValue();				
		}
		svg.Element.fontface.prototype = new svg.Element.ElementBase;
		
		// missing-glyph element
		svg.Element.missingglyph = function(node) {
			this.base = svg.Element.path;
			this.base(node);	
			
			this.horizAdvX = 0;
		}
		svg.Element.missingglyph.prototype = new svg.Element.path;
		
		// glyph element
		svg.Element.glyph = function(node) {
			this.base = svg.Element.path;
			this.base(node);	
			
			this.horizAdvX = this.attribute('horiz-adv-x').numValue();
			this.unicode = this.attribute('unicode').value;
			this.arabicForm = this.attribute('arabic-form').value;
		}
		svg.Element.glyph.prototype = new svg.Element.path;
		
		// text element
		svg.Element.text = function(node) {
			this.captureTextNodes = true;
			this.base = svg.Element.RenderedElementBase;
			this.base(node);
			
			this.baseSetContext = this.setContext;
			this.setContext = function(ctx) {
				this.baseSetContext(ctx);
				if (this.style('dominant-baseline').hasValue()) ctx.textBaseline = this.style('dominant-baseline').value;
				if (this.style('alignment-baseline').hasValue()) ctx.textBaseline = this.style('alignment-baseline').value;
			}
			
			this.getBoundingBox = function () {
				// TODO: implement
				return new svg.BoundingBox(this.attribute('x').toPixels('x'), this.attribute('y').toPixels('y'), 0, 0);
			}
			
			this.renderChildren = function(ctx) {
				this.x = this.attribute('x').toPixels('x');
				this.y = this.attribute('y').toPixels('y');
				this.x += this.getAnchorDelta(ctx, this, 0);
				for (var i=0; i<this.children.length; i++) {
					this.renderChild(ctx, this, i);
				}
			}
			
			this.getAnchorDelta = function (ctx, parent, startI) {
				var textAnchor = this.style('text-anchor').valueOrDefault('start');
				if (textAnchor != 'start') {
					var width = 0;
					for (var i=startI; i<parent.children.length; i++) {
						var child = parent.children[i];
						if (i > startI && child.attribute('x').hasValue()) break; // new group
						width += child.measureTextRecursive(ctx);
					}
					return -1 * (textAnchor == 'end' ? width : width / 2.0);
				}
				return 0;
			}
			
			this.renderChild = function(ctx, parent, i) {
				var child = parent.children[i];
				if (child.attribute('x').hasValue()) {
					child.x = child.attribute('x').toPixels('x') + this.getAnchorDelta(ctx, parent, i);
				}
				else {
					if (this.attribute('dx').hasValue()) this.x += this.attribute('dx').toPixels('x');
					if (child.attribute('dx').hasValue()) this.x += child.attribute('dx').toPixels('x');
					child.x = this.x;
				}
				this.x = child.x + child.measureText(ctx);
				
				if (child.attribute('y').hasValue()) {
					child.y = child.attribute('y').toPixels('y');
				}
				else {
					if (this.attribute('dy').hasValue()) this.y += this.attribute('dy').toPixels('y');
					if (child.attribute('dy').hasValue()) this.y += child.attribute('dy').toPixels('y');
					child.y = this.y;
				}
				this.y = child.y;
				
				child.render(ctx);
				
				for (var i=0; i<child.children.length; i++) {
					this.renderChild(ctx, child, i);
				}
			}
		}
		svg.Element.text.prototype = new svg.Element.RenderedElementBase;
		
		// text base
		svg.Element.TextElementBase = function(node) {
			this.base = svg.Element.RenderedElementBase;
			this.base(node);
			
			this.getGlyph = function(font, text, i) {
				var c = text[i];
				var glyph = null;
				if (font.isArabic) {
					var arabicForm = 'isolated';
					if ((i==0 || text[i-1]==' ') && i<text.length-2 && text[i+1]!=' ') arabicForm = 'terminal'; 
					if (i>0 && text[i-1]!=' ' && i<text.length-2 && text[i+1]!=' ') arabicForm = 'medial';
					if (i>0 && text[i-1]!=' ' && (i == text.length-1 || text[i+1]==' ')) arabicForm = 'initial';
					if (typeof(font.glyphs[c]) != 'undefined') {
						glyph = font.glyphs[c][arabicForm];
						if (glyph == null && font.glyphs[c].type == 'glyph') glyph = font.glyphs[c];
					}
				}
				else {
					glyph = font.glyphs[c];
				}
				if (glyph == null) glyph = font.missingGlyph;
				return glyph;
			}
			
			this.renderChildren = function(ctx) {
				var customFont = this.parent.style('font-family').getDefinition();
				if (customFont != null) {
					var fontSize = this.parent.style('font-size').numValueOrDefault(svg.Font.Parse(svg.ctx.font).fontSize);
					var fontStyle = this.parent.style('font-style').valueOrDefault(svg.Font.Parse(svg.ctx.font).fontStyle);
					var text = this.getText();
					if (customFont.isRTL) text = text.split("").reverse().join("");
					
					var dx = svg.ToNumberArray(this.parent.attribute('dx').value);
					for (var i=0; i<text.length; i++) {
						var glyph = this.getGlyph(customFont, text, i);
						var scale = fontSize / customFont.fontFace.unitsPerEm;
						ctx.translate(this.x, this.y);
						ctx.scale(scale, -scale);
						var lw = ctx.lineWidth;
						ctx.lineWidth = ctx.lineWidth * customFont.fontFace.unitsPerEm / fontSize;
						if (fontStyle == 'italic') ctx.transform(1, 0, .4, 1, 0, 0);
						glyph.render(ctx);
						if (fontStyle == 'italic') ctx.transform(1, 0, -.4, 1, 0, 0);
						ctx.lineWidth = lw;
						ctx.scale(1/scale, -1/scale);
						ctx.translate(-this.x, -this.y);	
						
						this.x += fontSize * (glyph.horizAdvX || customFont.horizAdvX) / customFont.fontFace.unitsPerEm;
						if (typeof(dx[i]) != 'undefined' && !isNaN(dx[i])) {
							this.x += dx[i];
						}
					}
					return;
				}
			
				if (ctx.fillStyle != '') ctx.fillText(svg.compressSpaces(this.getText()), this.x, this.y);
				if (ctx.strokeStyle != '') ctx.strokeText(svg.compressSpaces(this.getText()), this.x, this.y);
			}
			
			this.getText = function() {
				// OVERRIDE ME
			}
			
			this.measureTextRecursive = function(ctx) {
				var width = this.measureText(ctx);
				for (var i=0; i<this.children.length; i++) {
					width += this.children[i].measureTextRecursive(ctx);
				}
				return width;
			}
			
			this.measureText = function(ctx) {
				var customFont = this.parent.style('font-family').getDefinition();
				if (customFont != null) {
					var fontSize = this.parent.style('font-size').numValueOrDefault(svg.Font.Parse(svg.ctx.font).fontSize);
					var measure = 0;
					var text = this.getText();
					if (customFont.isRTL) text = text.split("").reverse().join("");
					var dx = svg.ToNumberArray(this.parent.attribute('dx').value);
					for (var i=0; i<text.length; i++) {
						var glyph = this.getGlyph(customFont, text, i);
						measure += (glyph.horizAdvX || customFont.horizAdvX) * fontSize / customFont.fontFace.unitsPerEm;
						if (typeof(dx[i]) != 'undefined' && !isNaN(dx[i])) {
							measure += dx[i];
						}
					}
					return measure;
				}
			
				var textToMeasure = svg.compressSpaces(this.getText());
				if (!ctx.measureText) return textToMeasure.length * 10;
				
				ctx.save();
				this.setContext(ctx);
				var width = ctx.measureText(textToMeasure).width;
				ctx.restore();
				return width;
			}
		}
		svg.Element.TextElementBase.prototype = new svg.Element.RenderedElementBase;
		
		// tspan 
		svg.Element.tspan = function(node) {
			this.captureTextNodes = true;
			this.base = svg.Element.TextElementBase;
			this.base(node);
			
			this.text = node.nodeValue || node.text || '';
			this.getText = function() {
				return this.text;
			}
		}
		svg.Element.tspan.prototype = new svg.Element.TextElementBase;
		
		// tref
		svg.Element.tref = function(node) {
			this.base = svg.Element.TextElementBase;
			this.base(node);
			
			this.getText = function() {
				var element = this.getHrefAttribute().getDefinition();
				if (element != null) return element.children[0].getText();
			}
		}
		svg.Element.tref.prototype = new svg.Element.TextElementBase;		
		
		// a element
		svg.Element.a = function(node) {
			this.base = svg.Element.TextElementBase;
			this.base(node);
			
			this.hasText = true;
			for (var i=0; i<node.childNodes.length; i++) {
				if (node.childNodes[i].nodeType != 3) this.hasText = false;
			}
			
			// this might contain text
			this.text = this.hasText ? node.childNodes[0].nodeValue : '';
			this.getText = function() {
				return this.text;
			}		

			this.baseRenderChildren = this.renderChildren;
			this.renderChildren = function(ctx) {
				if (this.hasText) {
					// render as text element
					this.baseRenderChildren(ctx);
					var fontSize = new svg.Property('fontSize', svg.Font.Parse(svg.ctx.font).fontSize);
					svg.Mouse.checkBoundingBox(this, new svg.BoundingBox(this.x, this.y - fontSize.toPixels('y'), this.x + this.measureText(ctx), this.y));					
				}
				else {
					// render as temporary group
					var g = new svg.Element.g();
					g.children = this.children;
					g.parent = this;
					g.render(ctx);
				}
			}
			
			this.onclick = function() {
				window.open(this.getHrefAttribute().value);
			}
			
			this.onmousemove = function() {
				svg.ctx.canvas.style.cursor = 'pointer';
			}
		}
		svg.Element.a.prototype = new svg.Element.TextElementBase;		
		
		// image element
		svg.Element.image = function(node) {
			this.base = svg.Element.RenderedElementBase;
			this.base(node);
			
			var href = this.getHrefAttribute().value;
			var isSvg = href.match(/\.svg$/)
			
			svg.Images.push(this);
			this.loaded = false;
			if (!isSvg) {
				this.img = document.createElement('img');
				var self = this;
				this.img.onload = function() { self.loaded = true; }
				this.img.onerror = function() { if (typeof(console) != 'undefined') { console.log('ERROR: image "' + href + '" not found'); self.loaded = true; } }
				this.img.src = href;
			}
			else {
				this.img = svg.ajax(href);
				this.loaded = true;
			}
			
			this.renderChildren = function(ctx) {
				var x = this.attribute('x').toPixels('x');
				var y = this.attribute('y').toPixels('y');
				
				var width = this.attribute('width').toPixels('x');
				var height = this.attribute('height').toPixels('y');			
				if (width == 0 || height == 0) return;
			
				ctx.save();
				if (isSvg) {
					ctx.drawSvg(this.img, x, y, width, height);
				}
				else {
					ctx.translate(x, y);
					svg.AspectRatio(ctx,
									this.attribute('preserveAspectRatio').value,
									width,
									this.img.width,
									height,
									this.img.height,
									0,
									0);	
					ctx.drawImage(this.img, 0, 0);		
				}
				ctx.restore();
			}
			
			this.getBoundingBox = function() {
				var x = this.attribute('x').toPixels('x');
				var y = this.attribute('y').toPixels('y');
				var width = this.attribute('width').toPixels('x');
				var height = this.attribute('height').toPixels('y');
				return new svg.BoundingBox(x, y, x + width, y + height);
			}
		}
		svg.Element.image.prototype = new svg.Element.RenderedElementBase;
		
		// group element
		svg.Element.g = function(node) {
			this.base = svg.Element.RenderedElementBase;
			this.base(node);
			
			this.getBoundingBox = function() {
				var bb = new svg.BoundingBox();
				for (var i=0; i<this.children.length; i++) {
					bb.addBoundingBox(this.children[i].getBoundingBox());
				}
				return bb;
			};
		}
		svg.Element.g.prototype = new svg.Element.RenderedElementBase;

		// symbol element
		svg.Element.symbol = function(node) {
			this.base = svg.Element.RenderedElementBase;
			this.base(node);
			
			this.baseSetContext = this.setContext;
			this.setContext = function(ctx) {		
				this.baseSetContext(ctx);
				
				// viewbox
				if (this.attribute('viewBox').hasValue()) {				
					var viewBox = svg.ToNumberArray(this.attribute('viewBox').value);
					var minX = viewBox[0];
					var minY = viewBox[1];
					width = viewBox[2];
					height = viewBox[3];
					
					svg.AspectRatio(ctx,
									this.attribute('preserveAspectRatio').value, 
									this.attribute('width').toPixels('x'),
									width,
									this.attribute('height').toPixels('y'),
									height,
									minX,
									minY);

					svg.ViewPort.SetCurrent(viewBox[2], viewBox[3]);						
				}
			}			
		}
		svg.Element.symbol.prototype = new svg.Element.RenderedElementBase;		
			
		// style element
		svg.Element.style = function(node) { 
			this.base = svg.Element.ElementBase;
			this.base(node);
			
			// text, or spaces then CDATA
			var css = ''
			for (var i=0; i<node.childNodes.length; i++) {
			  css += node.childNodes[i].nodeValue;
			}
			css = css.replace(/(\/\*([^*]|[\r\n]|(\*+([^*\/]|[\r\n])))*\*+\/)|(^[\s]*\/\/.*)/gm, ''); // remove comments
			css = svg.compressSpaces(css); // replace whitespace
			var cssDefs = css.split('}');
			for (var i=0; i<cssDefs.length; i++) {
				if (svg.trim(cssDefs[i]) != '') {
					var cssDef = cssDefs[i].split('{');
					var cssClasses = cssDef[0].split(',');
					var cssProps = cssDef[1].split(';');
					for (var j=0; j<cssClasses.length; j++) {
						var cssClass = svg.trim(cssClasses[j]);
						if (cssClass != '') {
							var props = {};
							for (var k=0; k<cssProps.length; k++) {
								var prop = cssProps[k].indexOf(':');
								var name = cssProps[k].substr(0, prop);
								var value = cssProps[k].substr(prop + 1, cssProps[k].length - prop);
								if (name != null && value != null) {
									props[svg.trim(name)] = new svg.Property(svg.trim(name), svg.trim(value));
								}
							}
							svg.Styles[cssClass] = props;
							if (cssClass == '@font-face') {
								var fontFamily = props['font-family'].value.replace(/"/g,'');
								var srcs = props['src'].value.split(',');
								for (var s=0; s<srcs.length; s++) {
									if (srcs[s].indexOf('format("svg")') > 0) {
										var urlStart = srcs[s].indexOf('url');
										var urlEnd = srcs[s].indexOf(')', urlStart);
										var url = srcs[s].substr(urlStart + 5, urlEnd - urlStart - 6);
										var doc = svg.parseXml(svg.ajax(url));
										var fonts = doc.getElementsByTagName('font');
										for (var f=0; f<fonts.length; f++) {
											var font = svg.CreateElement(fonts[f]);
											svg.Definitions[fontFamily] = font;
										}
									}
								}
							}
						}
					}
				}
			}
		}
		svg.Element.style.prototype = new svg.Element.ElementBase;
		
		// use element 
		svg.Element.use = function(node) {
			this.base = svg.Element.RenderedElementBase;
			this.base(node);
			
			this.baseSetContext = this.setContext;
			this.setContext = function(ctx) {
				this.baseSetContext(ctx);
				if (this.attribute('x').hasValue()) ctx.translate(this.attribute('x').toPixels('x'), 0);
				if (this.attribute('y').hasValue()) ctx.translate(0, this.attribute('y').toPixels('y'));
			}
			
			this.getDefinition = function() {
				var element = this.getHrefAttribute().getDefinition();
				if (this.attribute('width').hasValue()) element.attribute('width', true).value = this.attribute('width').value;
				if (this.attribute('height').hasValue()) element.attribute('height', true).value = this.attribute('height').value;
				return element;
			}
			
			this.path = function(ctx) {
				var element = this.getDefinition();
				if (element != null) element.path(ctx);
			}
			
			this.getBoundingBox = function() {
				var element = this.getDefinition();
				if (element != null) return element.getBoundingBox();
			}
			
			this.renderChildren = function(ctx) {
				var element = this.getDefinition();
				if (element != null) {
					// temporarily detach from parent and render
					var oldParent = element.parent;
					element.parent = null;
					element.render(ctx);
					element.parent = oldParent;
				}
			}
		}
		svg.Element.use.prototype = new svg.Element.RenderedElementBase;
		
		// mask element
		svg.Element.mask = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);
						
			this.apply = function(ctx, element) {
				// render as temp svg	
				var x = this.attribute('x').toPixels('x');
				var y = this.attribute('y').toPixels('y');
				var width = this.attribute('width').toPixels('x');
				var height = this.attribute('height').toPixels('y');
				
				if (width == 0 && height == 0) {
					var bb = new svg.BoundingBox();
					for (var i=0; i<this.children.length; i++) {
						bb.addBoundingBox(this.children[i].getBoundingBox());
					}
					var x = Math.floor(bb.x1);
					var y = Math.floor(bb.y1);
					var width = Math.floor(bb.width());
					var	height = Math.floor(bb.height());
				}
				
				// temporarily remove mask to avoid recursion
				var mask = element.attribute('mask').value;
				element.attribute('mask').value = '';
				
					var cMask = document.createElement('canvas');
					cMask.width = x + width;
					cMask.height = y + height;
					var maskCtx = cMask.getContext('2d');
					this.renderChildren(maskCtx);
				
					var c = document.createElement('canvas');
					c.width = x + width;
					c.height = y + height;
					var tempCtx = c.getContext('2d');
					element.render(tempCtx);
					tempCtx.globalCompositeOperation = 'destination-in';
					tempCtx.fillStyle = maskCtx.createPattern(cMask, 'no-repeat');
					tempCtx.fillRect(0, 0, x + width, y + height);
					
					ctx.fillStyle = tempCtx.createPattern(c, 'no-repeat');
					ctx.fillRect(0, 0, x + width, y + height);
					
				// reassign mask
				element.attribute('mask').value = mask;	
			}
			
			this.render = function(ctx) {
				// NO RENDER
			}
		}
		svg.Element.mask.prototype = new svg.Element.ElementBase;
		
		// clip element
		svg.Element.clipPath = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);
			
			this.apply = function(ctx) {
				for (var i=0; i<this.children.length; i++) {
					var child = this.children[i];
					if (typeof(child.path) != 'undefined') {
						var transform = null;
						if (child.attribute('transform').hasValue()) { 
							transform = new svg.Transform(child.attribute('transform').value);
							transform.apply(ctx);
						}
						child.path(ctx);
						ctx.clip();
						if (transform) { transform.unapply(ctx); }
					}
				}
			}
			
			this.render = function(ctx) {
				// NO RENDER
			}
		}
		svg.Element.clipPath.prototype = new svg.Element.ElementBase;

		// filters
		svg.Element.filter = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);
						
			this.apply = function(ctx, element) {
				// render as temp svg	
				var bb = element.getBoundingBox();
				var x = Math.floor(bb.x1);
				var y = Math.floor(bb.y1);
				var width = Math.floor(bb.width());
				var	height = Math.floor(bb.height());

				// temporarily remove filter to avoid recursion
				var filter = element.style('filter').value;
				element.style('filter').value = '';
				
				var px = 0, py = 0;
				for (var i=0; i<this.children.length; i++) {
					var efd = this.children[i].extraFilterDistance || 0;
					px = Math.max(px, efd);
					py = Math.max(py, efd);
				}
				
				var c = document.createElement('canvas');
				c.width = width + 2*px;
				c.height = height + 2*py;
				var tempCtx = c.getContext('2d');
				tempCtx.translate(-x + px, -y + py);
				element.render(tempCtx);
			
				// apply filters
				for (var i=0; i<this.children.length; i++) {
					this.children[i].apply(tempCtx, 0, 0, width + 2*px, height + 2*py);
				}
				
				// render on me
				ctx.drawImage(c, 0, 0, width + 2*px, height + 2*py, x - px, y - py, width + 2*px, height + 2*py);
				
				// reassign filter
				element.style('filter', true).value = filter;	
			}
			
			this.render = function(ctx) {
				// NO RENDER
			}		
		}
		svg.Element.filter.prototype = new svg.Element.ElementBase;
		
		svg.Element.feMorphology = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);
			
			this.apply = function(ctx, x, y, width, height) {
				// TODO: implement
			}
		}
		svg.Element.feMorphology.prototype = new svg.Element.ElementBase;
		
		svg.Element.feColorMatrix = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);
			
			function imGet(img, x, y, width, height, rgba) {
				return img[y*width*4 + x*4 + rgba];
			}
			
			function imSet(img, x, y, width, height, rgba, val) {
				img[y*width*4 + x*4 + rgba] = val;
			}
			
			this.apply = function(ctx, x, y, width, height) {
				// only supporting grayscale for now per Issue 195, need to extend to all matrix
				// assuming x==0 && y==0 for now
				var srcData = ctx.getImageData(0, 0, width, height);
				for (var y = 0; y < height; y++) {
					for (var x = 0; x < width; x++) {
						var r = imGet(srcData.data, x, y, width, height, 0);
						var g = imGet(srcData.data, x, y, width, height, 1);
						var b = imGet(srcData.data, x, y, width, height, 2);
						var gray = (r + g + b) / 3;
						imSet(srcData.data, x, y, width, height, 0, gray);
						imSet(srcData.data, x, y, width, height, 1, gray);
						imSet(srcData.data, x, y, width, height, 2, gray);
					}
				}
				ctx.clearRect(0, 0, width, height);
				ctx.putImageData(srcData, 0, 0);
			}
		}
		svg.Element.feColorMatrix.prototype = new svg.Element.ElementBase;
		
		svg.Element.feGaussianBlur = function(node) {
			this.base = svg.Element.ElementBase;
			this.base(node);

			this.blurRadius = Math.floor(this.attribute('stdDeviation').numValue());
			this.extraFilterDistance = this.blurRadius;
			
			this.apply = function(ctx, x, y, width, height) {
				if (typeof(stackBlurCanvasRGBA) == 'undefined') {
					if (typeof(console) != 'undefined') { console.log('ERROR: StackBlur.js must be included for blur to work'); }
					return;
				}
				
				// StackBlur requires canvas be on document
				ctx.canvas.id = svg.UniqueId();
				ctx.canvas.style.display = 'none';
				document.body.appendChild(ctx.canvas);
				stackBlurCanvasRGBA(ctx.canvas.id, x, y, width, height, this.blurRadius);
				document.body.removeChild(ctx.canvas);
			}
		}
		svg.Element.feGaussianBlur.prototype = new svg.Element.ElementBase;
		
		// title element, do nothing
		svg.Element.title = function(node) {
		}
		svg.Element.title.prototype = new svg.Element.ElementBase;

		// desc element, do nothing
		svg.Element.desc = function(node) {
		}
		svg.Element.desc.prototype = new svg.Element.ElementBase;		
		
		svg.Element.MISSING = function(node) {
			if (typeof(console) != 'undefined') { console.log('ERROR: Element \'' + node.nodeName + '\' not yet implemented.'); }
		}
		svg.Element.MISSING.prototype = new svg.Element.ElementBase;
		
		// element factory
		svg.CreateElement = function(node) {	
			var className = node.nodeName.replace(/^[^:]+:/,''); // remove namespace
			className = className.replace(/\-/g,''); // remove dashes
			var e = null;
			if (typeof(svg.Element[className]) != 'undefined') {
				e = new svg.Element[className](node);
			}
			else {
				e = new svg.Element.MISSING(node);
			}

			e.type = node.nodeName;
			return e;
		}
				
		// load from url
		svg.load = function(ctx, url) {
			svg.loadXml(ctx, svg.ajax(url));
		}
		
		// load from xml
		svg.loadXml = function(ctx, xml) {
			svg.loadXmlDoc(ctx, svg.parseXml(xml));
		}
		
		svg.loadXmlDoc = function(ctx, dom) {
			svg.init(ctx);
			
			var mapXY = function(p) {
				var e = ctx.canvas;
				while (e) {
					p.x -= e.offsetLeft;
					p.y -= e.offsetTop;
					e = e.offsetParent;
				}
				if (window.scrollX) p.x += window.scrollX;
				if (window.scrollY) p.y += window.scrollY;
				return p;
			}
			
			// bind mouse
			if (svg.opts['ignoreMouse'] != true) {
				ctx.canvas.onclick = function(e) {
					var p = mapXY(new svg.Point(e != null ? e.clientX : event.clientX, e != null ? e.clientY : event.clientY));
					svg.Mouse.onclick(p.x, p.y);
				};
				ctx.canvas.onmousemove = function(e) {
					var p = mapXY(new svg.Point(e != null ? e.clientX : event.clientX, e != null ? e.clientY : event.clientY));
					svg.Mouse.onmousemove(p.x, p.y);
				};
			}
		
			var e = svg.CreateElement(dom.documentElement);
			e.root = true;
					
			// render loop
			var isFirstRender = true;
			var draw = function() {
				svg.ViewPort.Clear();
				if (ctx.canvas.parentNode) svg.ViewPort.SetCurrent(ctx.canvas.parentNode.clientWidth, ctx.canvas.parentNode.clientHeight);
			
				if (svg.opts['ignoreDimensions'] != true) {
					// set canvas size
					if (e.style('width').hasValue()) {
						ctx.canvas.width = e.style('width').toPixels('x');
						ctx.canvas.style.width = ctx.canvas.width + 'px';
					}
					if (e.style('height').hasValue()) {
						ctx.canvas.height = e.style('height').toPixels('y');
						ctx.canvas.style.height = ctx.canvas.height + 'px';
					}
				}
				var cWidth = ctx.canvas.clientWidth || ctx.canvas.width;
				var cHeight = ctx.canvas.clientHeight || ctx.canvas.height;
				if (svg.opts['ignoreDimensions'] == true && e.style('width').hasValue() && e.style('height').hasValue()) {
					cWidth = e.style('width').toPixels('x');
					cHeight = e.style('height').toPixels('y');
				}
				svg.ViewPort.SetCurrent(cWidth, cHeight);		
				
				if (svg.opts['offsetX'] != null) e.attribute('x', true).value = svg.opts['offsetX'];
				if (svg.opts['offsetY'] != null) e.attribute('y', true).value = svg.opts['offsetY'];
				if (svg.opts['scaleWidth'] != null && svg.opts['scaleHeight'] != null) {
					var xRatio = 1, yRatio = 1, viewBox = svg.ToNumberArray(e.attribute('viewBox').value);
					if (e.attribute('width').hasValue()) xRatio = e.attribute('width').toPixels('x') / svg.opts['scaleWidth'];
					else if (!isNaN(viewBox[2])) xRatio = viewBox[2] / svg.opts['scaleWidth'];
					if (e.attribute('height').hasValue()) yRatio = e.attribute('height').toPixels('y') / svg.opts['scaleHeight'];
					else if (!isNaN(viewBox[3])) yRatio = viewBox[3] / svg.opts['scaleHeight'];
					
					e.attribute('width', true).value = svg.opts['scaleWidth'];
					e.attribute('height', true).value = svg.opts['scaleHeight'];			
					e.attribute('viewBox', true).value = '0 0 ' + (cWidth * xRatio) + ' ' + (cHeight * yRatio);
					e.attribute('preserveAspectRatio', true).value = 'none';
				}
			
				// clear and render
				if (svg.opts['ignoreClear'] != true) {
					ctx.clearRect(0, 0, cWidth, cHeight);
				}
				e.render(ctx);
				if (isFirstRender) {
					isFirstRender = false;
					if (typeof(svg.opts['renderCallback']) == 'function') svg.opts['renderCallback'](dom);
				}			
			}
			
			var waitingForImages = true;
			if (svg.ImagesLoaded()) {
				waitingForImages = false;
				draw();
			}
			svg.intervalID = setInterval(function() { 
				var needUpdate = false;
				
				if (waitingForImages && svg.ImagesLoaded()) {
					waitingForImages = false;
					needUpdate = true;
				}
			
				// need update from mouse events?
				if (svg.opts['ignoreMouse'] != true) {
					needUpdate = needUpdate | svg.Mouse.hasEvents();
				}
			
				// need update from animations?
				if (svg.opts['ignoreAnimation'] != true) {
					for (var i=0; i<svg.Animations.length; i++) {
						needUpdate = needUpdate | svg.Animations[i].update(1000 / svg.FRAMERATE);
					}
				}
				
				// need update from redraw?
				if (typeof(svg.opts['forceRedraw']) == 'function') {
					if (svg.opts['forceRedraw']() == true) needUpdate = true;
				}
				
				// render if needed
				if (needUpdate) {
					draw();				
					svg.Mouse.runEvents(); // run and clear our events
				}
			}, 1000 / svg.FRAMERATE);
		}
		
		svg.stop = function() {
			if (svg.intervalID) {
				clearInterval(svg.intervalID);
			}
		}
		
		svg.Mouse = new (function() {
			this.events = [];
			this.hasEvents = function() { return this.events.length != 0; }
		
			this.onclick = function(x, y) {
				this.events.push({ type: 'onclick', x: x, y: y, 
					run: function(e) { if (e.onclick) e.onclick(); }
				});
			}
			
			this.onmousemove = function(x, y) {
				this.events.push({ type: 'onmousemove', x: x, y: y,
					run: function(e) { if (e.onmousemove) e.onmousemove(); }
				});
			}			
			
			this.eventElements = [];
			
			this.checkPath = function(element, ctx) {
				for (var i=0; i<this.events.length; i++) {
					var e = this.events[i];
					if (ctx.isPointInPath && ctx.isPointInPath(e.x, e.y)) this.eventElements[i] = element;
				}
			}
			
			this.checkBoundingBox = function(element, bb) {
				for (var i=0; i<this.events.length; i++) {
					var e = this.events[i];
					if (bb.isPointInBox(e.x, e.y)) this.eventElements[i] = element;
				}			
			}
			
			this.runEvents = function() {
				svg.ctx.canvas.style.cursor = '';
				
				for (var i=0; i<this.events.length; i++) {
					var e = this.events[i];
					var element = this.eventElements[i];
					while (element) {
						e.run(element);
						element = element.parent;
					}
				}		
			
				// done running, clear
				this.events = []; 
				this.eventElements = [];
			}
		});
		
		return svg;
	}
})();

if (typeof(CanvasRenderingContext2D) != 'undefined') {
	CanvasRenderingContext2D.prototype.drawSvg = function(s, dx, dy, dw, dh) {
		canvg(this.canvas, s, { 
			ignoreMouse: true, 
			ignoreAnimation: true, 
			ignoreDimensions: true, 
			ignoreClear: true, 
			offsetX: dx, 
			offsetY: dy, 
			scaleWidth: dw, 
			scaleHeight: dh
		});
	}
}

circularplot.js

var circularTrackDefaults = {
    radius: 5,
    w: 600,
    h: 600,
    factor: 1,
    factorLegend: .85,
    TranslateX: 80,
    TranslateY: 30,
    ExtraWidthX: 100,
    ExtraWidthY: 100,
    radians: 2 * Math.PI,
    spacing: 100000,
    legend_spacing: 5,
    min_radians: .02 * Math.PI,
    dragresize: true,
    movecursor: false
}

function circularTrack(layout,tracks) {

    this.tracks = tracks;
    this.layout = layout;
    this.numTracks = tracks.length;

    if('undefined' !== typeof layout) {
	    // Copy over any defaults not passed in
	    // by the user
	    for(var i in circularTrackDefaults) {
		if('undefined' == typeof layout[i]) {
		    this.layout[i] = circularTrackDefaults[i];
		}
	    }
	}

    if('undefined' == typeof layout.plotid) {
	this.layout.plotid = layout.container.slice(1);
    }

    this.layout.containerid =  layout.container.slice(1);

    // Some constants for later so we don't have to keep recalculating
    this.layout.w2 = this.layout.w / 2;
    this.layout.h2 = this.layout.h / 2;
    this.layout.PI2 = Math.PI/2;

    // Setup some constants we'll need and build the canvas
    this.layout.radians_pre_bp = this.layout.radians/this.layout.genomesize;
    this.layout.min_bp_per_slice = this.layout.min_radians / this.layout.radians_pre_bp;
    this.layout.min_bp_per_slice_half = this.layout.min_bp_per_slice/2;
    this.layout.radius = this.layout.factor*Math.min(this.layout.w2, this.layout.h2);
    this.xScale = d3.scale.linear()
	.range([0,this.layout.radians])
	.domain([0, layout.genomesize]);
    var xScale = this.xScale;
    d3.select(layout.container).select("svg").remove();

    this.container = d3.select(layout.container)
	.append("svg")	
	.attr("id", function() { return layout.container.slice(1) + "_svg"; })
	.attr("width", this.layout.w+this.layout.ExtraWidthX)
	.attr("height", this.layout.h+this.layout.ExtraWidthY); 
   
    this.g = this.container
	.append("g")
	.attr("id", function() { return layout.container.slice(1) + "_g"; })
	.attr("transform", "translate(" + this.layout.TranslateX + "," + this.layout.TranslateY + ")");

    // Add the double click functionality, but we needed to define g first
    this.container.on("dblclick", function(d,i) {
	    if('undefined' !== typeof this.layout.dblclick) {
		var node = this.g.node();
		var curBP = calcRadBPfromXY((d3.mouse(node)[0] - (this.layout.w2)),
						  -(d3.mouse(node)[1] - (this.layout.h2)),
						  xScale)[1];
		var fn = window[this.layout.dblclick];

		if('object' ==  typeof fn) {
		    return fn.ondblclick(this.layout.plotid, curBP);
		} else if('function' == typeof fn) {
		    return fn(this.layout.plotid, curBP);
		}

	    } else {
		null;
	    }
	}.bind(this));

    this.defs = this.g.append("defs");

    this.defs.append('svg:marker')
	.attr('id', 'end-arrow')
	.attr('viewBox', '0 -5 10 10')
	.attr('refX', 6)
	.attr('markerWidth', 7)
	.attr('markerHeight', 7)
	.attr('orient', 'auto')
	.append('svg:path')
	.attr('d', 'M0,-5L10,0L0,5')
	.attr('class', "move-cross");

    this.defs.append('svg:marker')
	.attr('id', 'start-arrow')
	.attr('viewBox', '0 -5 10 10')
	.attr('refX', 4)
	.attr('markerWidth', 7)
	.attr('markerHeight', 7)
	.attr('orient', 'auto')
	.append('svg:path')
	.attr('d', 'M10,-5L0,0L10,5')
	.attr('class', "move-cross");
	//    .attr('fill', '#000');

    // Display the dragging cross if needed
    if(this.layout.movecursor == true) {
	this.g.append("rect")
	    .attr("width", 18)
	    .attr("height", 18)
	    .attr("fill-opacity", 0)
	    .attr("class", "move-shadow move_" + this.layout.containerid);

	this.g.append("line")
	    .attr("x1", 0)
	    .attr("x2", 18)
	    .attr("y1", 9)
	    .attr("y2", 9)
	    .style('marker-start', 'url(#start-arrow)')
	    .style('marker-end', 'url(#end-arrow)')
	    .attr("class", "move-cross move_" + this.layout.containerid);

	this.g.append("line")
	    .attr("x1", 9)
	    .attr("x2", 9)
	    .attr("y1", 0)
	    .attr("y2", 18)
	    .style('marker-start', 'url(#start-arrow)')
	    .style('marker-end', 'url(#end-arrow)')
	    .attr("class", "move-cross move_" + this.layout.containerid);
    }

    // Resize drag shadow
    if(this.layout.dragresize == true) {
	this.drag_shadow = this.container.append("rect")
	    .attr("width", (this.layout.w+this.layout.ExtraWidthX))
	    .attr("height", (this.layout.h+this.layout.ExtraWidthY))
	    .attr("class", "dragbar-shadow linear_hidden");
    }

    // Now we can start drawing the plots, first the basic axis...
    this.drawAxis();

    this.tip = d3.tip()
	.attr('class', 'd3-tip')
	.offset([-10, 0])
	.html(function(d) {
		return "<strong>Name:</strong> <span style='color:red'>" + d.name + "</span>";
	    });

    this.container.call(this.tip);

    // Draw the plots
    for(var i=0; i < this.tracks.length; i++) {

	if('undefined' !== typeof this.tracks[i].visible) {
	    if(! this.tracks[i].visible) {
		continue;
	    }
	} else {
	    // If the user didn't set visible,
	    // then it's visible.
	    this.tracks[i].visible = true;
	}

	// We're going to see what type of tracks we have
	// and dispatch them appropriately

	switch(this.tracks[i].trackType) {
	case "plot":
	    tracks[i].rad_per_elem = tracks[i].bp_per_element*this.layout.radians_pre_bp;
	    this.drawPlot(i);
	    break;
	case "track":
	    this.drawTrack(i);
	    break;
	case "stranded":
	    this.drawTrack(i);
	    break;
	case "gap":
	    this.drawGap(i);
	    break;
	case "glyph":
	    this.findGlyphTypes(i);

	    if('undefined' !== typeof this.tracks[i].hideTypes) {
		this.maskGlyphTypes(i, this.tracks[i].hideTypes)
	    }
	    //	    this.tracks[i].container = 
	    //	this.g.append("g")
	    //	.attr("class", this.tracks[i].trackName + "_glyph_container")
	    this.drawGlyphTrack(i);
	    break;
	default:
	    // Do nothing for an unknown track type
	}
    }

    // Resize dragger
    if(this.layout.dragresize == true) {
	var dragright = d3.behavior.drag()
	.on("dragstart", this.dragresize_start.bind(this))
	    .on("drag", this.dragresize.bind(this))
	    .on("dragend", this.dragresize_end.bind(this));

	this.dragbar_y_mid = this.layout.h/2;
	this.dragbar = this.container.append("g")
	    .attr("transform", "translate(" + (this.layout.w+this.layout.ExtraWidthX-25) + "," +  (this.layout.h+this.layout.ExtraWidthY-25) + ")")
	    .attr("width", 25)
	    .attr("height", 20)
	    .attr("fill", "lightblue")
	    .attr("fill-opacity", .2)
	    .attr("cursor", "ew-resize")
	    .call(dragright);

	this.dragbar.append("rect")
	    .attr("width", 25)
	    .attr("height", 20)
	    .attr("fill-opacity", 0);

	this.dragbar.append("line")
	    .attr("x1", 16)
	    .attr("x2", 16)
	    .attr("y1", 0)
	    .attr("y2", 14)
	    .attr("class", "dragbar-line");
	this.dragbar.append("line")
	    .attr("x1", 2)
	    .attr("x2", 16)
	    .attr("y1", 14)
	    .attr("y2", 14)
	    .attr("class", "dragbar-line");
	this.dragbar.append("line")
	    .attr("x1", 19)
	    .attr("x2", 19)
	    .attr("y1", 0)
	    .attr("y2", 17)
	    .attr("class", "dragbar-line");
	this.dragbar.append("line")
	    .attr("x1", 2)
	    .attr("x2", 19)
	    .attr("y1", 17)
	    .attr("y2", 17)
	    .attr("class", "dragbar-line");
	this.dragbar.append("line")
	    .attr("x1", 22)
	    .attr("x2", 22)
	    .attr("y1", 0)
	    .attr("y2", 20)
	    .attr("class", "dragbar-line");
	this.dragbar.append("line")
	    .attr("x1", 2)
	    .attr("x2", 22)
	    .attr("y1", 20)
	    .attr("y2", 20)
	    .attr("class", "dragbar-line");
    }

}

circularTrack.prototype.drawAxis = function() {
    var cfg = this.layout;
    var g = this.g;

    this.axis_container = this.g
	.append("g")
	.attr("id", "axis_container");

    var axis = this.axis_container.selectAll(".axis")
    .data(d3.range(0,cfg.genomesize, cfg.spacing))
    .enter()
    .append("g")
    .attr("class", "axis");

    axis.append("line")
    .attr("x1", function(d, i){return cfg.w2 + (20*Math.cos((d*cfg.radians_pre_bp)-cfg.PI2));})
    .attr("y1", function(d, i){return cfg.h2 + (20*Math.sin((d*cfg.radians_pre_bp)-cfg.PI2));})
    .attr("x2", function(d, i){return cfg.w2 + (cfg.radius*Math.cos((d*cfg.radians_pre_bp)-cfg.PI2));})
    .attr("y2", function(d, i){return cfg.h2 + (cfg.radius*Math.sin((d*cfg.radians_pre_bp)-cfg.PI2));})
    .attr("class", "line")
    .style("stroke", "grey")
    .style("stroke-width", "1px");

    var axis_label = this.axis_container.selectAll(".axislabel")
    .data(d3.range(0,cfg.genomesize, cfg.spacing*cfg.legend_spacing))
    .enter()
    .append("g")
    .attr("class", "axislabel");
      
    axis_label.append("text")
    .attr("class", "legend")
    .text(function(d){ var prefix = d3.formatPrefix(d);
	    return prefix.scale(d) + prefix.symbol;
	})
    .style("font-family", "sans-serif")
    .style("font-size", "11px")
    .attr("text-anchor", "middle")
    .attr("dy", "1.5em")
    .attr("transform", function(d, i){return "translate(0, -10)"})
    .attr("x", function(d, i){return cfg.w2 + ((cfg.radius+10)*Math.cos((d*cfg.radians_pre_bp)-cfg.PI2));})
    .attr("y", function(d, i){return cfg.h2 + ((cfg.radius+10)*Math.sin((d*cfg.radians_pre_bp)-cfg.PI2));});

    // And draw the pretty outer circle for the axis
    this.drawCircle("outerAxis", cfg.radius-10, 'grey');
}

circularTrack.prototype.moveAxis = function() {
    var cfg = this.layout;

    this.axis_container
	.selectAll("line")
	.data(d3.range(0,cfg.genomesize, cfg.spacing))
        .transition()
        .duration(1000)
	.attr("x1", function(d, i){return cfg.w2 + (20*Math.cos((d*cfg.radians_pre_bp)-cfg.PI2));})
	.attr("y1", function(d, i){return cfg.h2 + (20*Math.sin((d*cfg.radians_pre_bp)-cfg.PI2));})
	.attr("x2", function(d, i){return cfg.w2 + (cfg.radius*Math.cos((d*cfg.radians_pre_bp)-cfg.PI2));})
	.attr("y2", function(d, i){return cfg.h2 + (cfg.radius*Math.sin((d*cfg.radians_pre_bp)-cfg.PI2));});

    this.axis_container
	.selectAll("text")
	.data(d3.range(0,cfg.genomesize, cfg.spacing*cfg.legend_spacing))
        .transition()
        .duration(1000)
	.attr("x", function(d, i){return cfg.w2 + ((cfg.radius+10)*Math.cos((d*cfg.radians_pre_bp)-cfg.PI2));})
	.attr("y", function(d, i){return cfg.h2 + ((cfg.radius+10)*Math.sin((d*cfg.radians_pre_bp)-cfg.PI2));});

    // And draw the pretty outer circle for the axis
    this.moveCircle("outerAxis", cfg.radius-10);

}
// Helper function for drawing needed circles such
// as in stranded tracks
// Can be called standalone in setting up the look
// of your genome

circularTrack.prototype.drawCircle = function(name, radius, line_stroke, animate) {
    var g = this.g;
    var cfg = this.layout;

    g.append("circle")
    .attr("r", (('undefined' == typeof animate) ? radius : 1 ))
    .attr("class", name + "_circle")
    .style("fill", "none")
    .style("stroke", line_stroke)
    .attr("cx", cfg.w2)
    .attr("cy", cfg.h2);

    // An animated entrance
    if('undefined' !== typeof animate) {
	this.moveCircle(name, radius);
    }

}

// Change the radius of an inscribed circle

circularTrack.prototype.moveCircle = function(name, radius) {
    var g = this.g;
    var cfg = this.layout;

    g.selectAll("." + name + "_circle")
    .transition()
    .duration(1000)
    .attr("r", radius)
    .attr("cx", cfg.w2)
    .attr("cy", cfg.h2);

}

// Remove a drawn circle, in a pretty animated way

circularTrack.prototype.removeCircle = function(name) {
    var g = this.g;

    g.selectAll("." + name + "_circle")
    .transition()
    .duration(1000)
    .attr("r", 1)
    .style("opacity", 0)
    .remove();
}

/////////////////////////////////////////
//
// Plot type tracks (as in line graphs)
//
/////////////////////////////////////////

circularTrack.prototype.drawPlot = function(i, animate) {
    var g = this.g;
    var cfg = this.layout;
    var track = this.tracks[i];

    this.tracks[i].plotRange = d3.scale.linear()
    .domain([track.plot_min, track.plot_max])
    .range([track.plot_radius-(track.plot_width/2), track.plot_radius+(track.plot_width/2)]);

    var plotRange = this.tracks[i].plotRange;

    var lineFunction = d3.svg.line()
    .x(function(d, i) { return cfg.w2 + ((('undefined' == typeof animate) ? plotRange(d) : 1 )*Math.cos((i*track.rad_per_elem)-(cfg.PI2))); })
    .y(function(d, i) { return cfg.h2 + ((('undefined' == typeof animate) ? plotRange(d) : 1 )*Math.sin((i*track.rad_per_elem)-(cfg.PI2))); })
    .interpolate("linear");

    g.append("path")
    .attr("d", lineFunction(track.items))
    .attr("class", track.trackName)
    .attr("id", track.trackName)
    .attr("stroke-width", 1)
    .attr("fill", "none");

    // Now do the mean circle if we have one
    if('undefined' !== typeof track.plot_mean) {
	this.drawCircle(track.trackName,  this.tracks[i].plotRange(track.plot_mean), "grey", animate);
    }  

    // And if we're doing an animated entrance...
    if('undefined' !== typeof animate) {
	this.movePlot(i, track.plot_radius);
    }

    // Mark the track as visible, if not already
    this.tracks[i].visible = true;
}

circularTrack.prototype.movePlot = function(i, radius) {
    var g = this.g;
    var cfg = this.layout;
    var track = this.tracks[i];

    // Save this in case this is a change of radius
    // ratherthan an animated entrance
    if('undefined' !== typeof this.tracks[i].plot_radius) {
	this.tracks[i].plot_radius = radius;
    }

    // We needed to save the new radius but if this
    // track isn't visible, do nothing
    if(! this.tracks[i].visible) {
	return;
    }

    this.tracks[i].plotRange
	.range([track.plot_radius-(track.plot_width/2), track.plot_radius+(track.plot_width/2)]);

    var plotRange = this.tracks[i].plotRange;

    var lineFunction = d3.svg.line()
    .x(function(d, i, j) { return cfg.w2 + (plotRange(d)*Math.cos((i*track.rad_per_elem)-(cfg.PI2))); })
    .y(function(d, i) { return cfg.h2 + (plotRange(d)*Math.sin((i*track.rad_per_elem)-(cfg.PI2))); })
    .interpolate("linear");

    var plot = g.selectAll("." + track.trackName)

    plot.transition()
    .duration(1000)
    .attr("d", function(d,i) { return lineFunction(track.items)});

    // Now move the mean circle if we have one
    if('undefined' !== typeof track.plot_mean) {
	this.moveCircle(track.trackName, this.tracks[i].plotRange(track.plot_mean));
    }  
}

circularTrack.prototype.removePlot = function(i) {
    var g = this.g;
    var cfg = this.layout;
    var track = this.tracks[i];

    var plotRange = d3.scale.linear()
    .domain([track.plot_min, track.plot_max])
    .range([1-(track.plot_width/2), 1+(track.plot_width/2)]);

    var lineFunction = d3.svg.line()
    .x(function(d, i) { return cfg.w2 + (plotRange(d)*Math.cos((i*track.rad_per_elem)-(cfg.PI2))); })
    .y(function(d, i) { return cfg.h2 + (plotRange(d)*Math.sin((i*track.rad_per_elem)-(cfg.PI2))); })
    .interpolate("linear");

    g.selectAll("." + track.trackName)
    .transition()
    .duration(1000)
    .attr("d", lineFunction(track.items))
    .style("opacity", 0)
    .remove();

      if('undefined' !== typeof track.plot_mean) {
	  this.removeCircle(track.trackName);
      }

    // Mark the track as not visible
    this.tracks[i].visible = false;
}


////////////////////////////////////////////////
//
// Track type tracks (as blocks without strands)
//
////////////////////////////////////////////////

circularTrack.prototype.drawTrack = function(i, animate) {
    var g = this.g;
    var cfg = this.layout;
    var track = this.tracks[i];

    // Because of how the tooltip library binds to the SVG object we have to turn it
    // on or off here rather than in the .on() call, we'll redirect the calls to
    // a dummy do-nothing object if we're not showing tips in this context.
    var tip = {show: function() {}, hide: function() {} };
    if(('undefined' !== typeof track.showTooltip) && track.showTooltip) {
	tip = this.tip;
    }

    // The arc object which will be passed in to each
    // set of data
    var arc = d3.svg.arc()
    .innerRadius(function(d){ return (('undefined' == typeof animate) ? 
				      calcInnerRadius(track.inner_radius, track.outer_radius, d.strand) 
				      : 1);})
    .outerRadius(function(d){ return (('undefined' == typeof animate) ? 
				      calcOuterRadius(track.inner_radius, track.outer_radius, d.strand)
				      : 2);})
    .startAngle(function(d){if(track.min_slice && (d.end - d.start) < cfg.min_bp_per_slice) {
		return (d.start - ((d.end - d.start - cfg.min_bp_per_slice_half) / 2))*cfg.radians_pre_bp;
	    } else {
		return cfg.radians_pre_bp*d.start;
	    }
	})
    .endAngle(function(d){if(track.min_slice && (d.end - d.start) < cfg.min_bp_per_slice) {
		return (d.end + ((d.end - d.start - cfg.min_bp_per_slice_half)/2))*cfg.radians_pre_bp;
	    } else {
		return cfg.radians_pre_bp*d.end;
	    }
	});
      
    // Draw the track, putting in elements such as hover colour change
    // if one exists, click events, etc
    g.selectAll(".tracks."+track.trackName)
    .data(track.items)
    .enter()
    .append("path")
    .attr("d", arc)
    .attr("class", function(d) { return track.trackName + ('undefined' !== typeof d.strand ? '_' + (d.strand == 1 ? 'pos' : 'neg') : '') + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '') })
    .attr("transform", "translate("+cfg.w2+","+cfg.h2+")")
    .on("click", function(d,i) {
	    if('undefined' !== typeof track.mouseclick) {
		var fn = window[track.mouseclick];
		if('object' ==  typeof fn) {
//		    console.log(fn);
		    return fn.onclick(track.trackName, d, cfg.plotid);
		} else if('function' == typeof fn) {
		    return fn(track.trackName, d, cfg.plotid);
		}

	    } else {
		null;
	    }
	})
    .on("mouseover", function(d, i) {
	    tip.show(d);
	    if('undefined' !== typeof track.mouseover_callback) {
		var fn = window[track.mouseover_callback];
		if('object' ==  typeof fn) {
		    fn.mouseover(track.trackName, d, cfg.plotid);
		    return true;
		} else if('function' == typeof fn) {
		    return fn(track.trackNamed, cfg.plotid);
		}

	    } else {
		return null;
	    }
	})
    .on("mouseout", function(d, i) {
	    tip.hide(d);
    	    if('undefined' !== typeof track.mouseout_callback) {
		var fn = window[track.mouseout_callback];
		if('object' ==  typeof fn) {
		    return fn.mouseout(track.trackName, d, cfg.plotid);
		} else if('function' == typeof fn) {
		    return fn(track.trackNamed, cfg.plotid);
		}

    	    } else {
		return null;
	    }
    	});

    // If we're doing an animated addition, move the track out to its
    // new spot
    if('undefined' !== typeof animate) {
	this.moveTrack(i, track.inner_radius, track.outer_radius);
    }

    // And check if we've been asked to do a centre line
    if('undefined' !== typeof track.centre_line_stroke) {
	this.drawCircle(track.trackName, (track.inner_radius + track.outer_radius)/2, track.centre_line_stroke, animate);
      }

    this.tracks[i].visible = true;

}

circularTrack.prototype.moveTrack = function(i, innerRadius, outerRadius) {
    var g = this.g;
    var cfg = this.layout;
    var track = this.tracks[i];

    // Just record the new radii in case we need them later
    if('undefined' !== typeof this.tracks[i].inner_radius) {
	this.tracks[i].inner_radius = innerRadius;
    }
    if('undefined' !== typeof this.tracks[i].outer_radius) {
	this.tracks[i].outer_radius = outerRadius;
    }

    // We needed to save the new radius but if this
    // track isn't visible, do nothing
    if(! this.tracks[i].visible) {
	return;
    }

    var arcShrink = d3.svg.arc()
    .innerRadius(function(d){return calcInnerRadius(innerRadius, outerRadius, d.strand);})
    .outerRadius(function(d){return calcOuterRadius(innerRadius, outerRadius, d.strand);})
    .startAngle(function(d){if(track.min_slice && (d.end - d.start) < cfg.min_bp_per_slice) {
		return (d.start - ((d.end - d.start - cfg.min_bp_per_slice_half) / 2))*cfg.radians_pre_bp;
	    } else {
		return cfg.radians_pre_bp*d.start;
	    }
	})
    .endAngle(function(d){if(track.min_slice && (d.end - d.start) < cfg.min_bp_per_slice) {
		return (d.end + ((d.end - d.start - cfg.min_bp_per_slice_half)/2))*cfg.radians_pre_bp;
	    } else {
		return cfg.radians_pre_bp*d.end;
	    }
	});
 

    //   .endAngle(function(d){return cfg.radians_pre_bp*d.start;})
    //    .startAngle(function(d){return cfg.radians_pre_bp*d.end;});

    g.selectAll("." + track.trackName + ", ." + track.trackName + "_pos, ." + track.trackName + "_neg")
    .transition()
    .duration(1000)
    .attr("d", arcShrink)
    .attr("transform", "translate("+cfg.w2+","+cfg.h2+")")

    // And check if we've been asked to do a centre line
    if('undefined' !== typeof track.centre_line_stroke) {
	this.moveCircle(track.trackName, (track.inner_radius + track.outer_radius)/2);
      }

}

circularTrack.prototype.removeTrack = function(i) {
    var g = this.g;
    var cfg = this.layout;
    var track = this.tracks[i];

    var arcShrink = d3.svg.arc()
    .innerRadius(1)
    .outerRadius(2)
    .endAngle(function(d){return cfg.radians_pre_bp*d.start;})
    .startAngle(function(d){return cfg.radians_pre_bp*d.end;});

    g.selectAll("." + track.trackName + ", ." + track.trackName + "_pos, ." + track.trackName + "_neg")
    .transition()
    .duration(1000)
    .attr("d", arcShrink)
    .style("opacity", 0)
    .remove();

    if('undefined' !== track.centre_line_stroke) {
	this.removeCircle(track.trackName);
    }

    this.tracks[i].visible = false;

}

////////////////////////////////////////////////
//
// Gap type tracks
//
////////////////////////////////////////////////

circularTrack.prototype.drawGap = function(i, animate) {
    var g = this.g;
    var cfg = this.layout;
    var track = this.tracks[i];
    var self = this;

    var gap_range = ('undefined' == typeof animate) ? d3.range(track.inner_radius, track.outer_radius, 8) : [1,2];

    // Draw the track, putting in elements such as hover colour change
    // if one exists, click events, etc
    var gaps = g.selectAll(".tracks."+track.trackName)
    .data(track.items)
    .enter()
    .append("g")
    .attr("class", function(d) { return track.trackName + ' ' + track.trackName + '_g ' + track.trackName + '_' + d.name + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '') })
    .attr("transform", "translate("+cfg.w2+","+cfg.h2+")")
    .each(function(d) {
	    d3.select(this)
	    .append("path")
	    .attr("d", self.jaggedLineGenerator(d.start, gap_range))
	    .attr("class", function(d2) { return track.trackName + ' ' + track.trackName + '_line' + ('undefined' !== typeof d.extraclass ? d.extraclass : '') })
	    .attr("stroke-width", 1)
	    .attr("fill", "none");

	    d3.select(this)
	    .append("path")
	    .attr("d", self.jaggedLineGenerator(d.end, gap_range))
	    .attr("class", function(d2) { return track.trackName + ' ' + track.trackName + '_line' + ('undefined' !== typeof d.extraclass ? d.extraclass : '') })
	    .attr("stroke-width", 1)
	    .attr("fill", "none");
	});

    // If we're doing an animated addition, move the track out to its
    // new spot
    if('undefined' !== typeof animate) {
	this.moveGap(i, track.inner_radius, track.outer_radius);
    }

}

circularTrack.prototype.moveGap = function(i, innerRadius, outerRadius) {
    var g = this.g;
    var cfg = this.layout;
    var track = this.tracks[i];
    var self = this;

    // Just record the new radii in case we need them later
    if('undefined' !== typeof this.tracks[i].inner_radius) {
	this.tracks[i].inner_radius = innerRadius;
    }
    if('undefined' !== typeof this.tracks[i].outer_radius) {
	this.tracks[i].outer_radius = outerRadius;
    }

    // We needed to save the new radius but if this
    // track isn't visible, do nothing
    if(! this.tracks[i].visible) {
	return;
    }

    var gap_range = d3.range(innerRadius, outerRadius, 8);

    g.selectAll("." + track.trackName + '_g') 
    .transition()
    .duration(1000)
    .attr("transform", "translate("+cfg.w2+","+cfg.h2+")")

    g.selectAll('.' + track.trackName + '_line')
    .transition()
    .duration(1000)
    .attrTween("d", function(d) { return pathTween(this, self.jaggedLineGenerator(d.start, gap_range), 4) });

    
}

circularTrack.prototype.removeGap = function(i) {
    var g = this.g;
    var cfg = this.layout;
    var track = this.tracks[i];
    var self = this;

    g.selectAll('.' + track.trackName + '_line')
    .transition()
    .duration(1000)
    .attrTween("d", function(d) { return pathTween(this, self.jaggedLineGenerator(d.start, [1,2]), 4) })
    .remove();

    g.selectAll("." + track.trackName + '_g') 
    .transition()
    .duration(1000)
    .style('opacity', 0)
    .remove()

    this.tracks[i].visible = false;

}

// Jagged line path generator for the gap track type

circularTrack.prototype.jaggedLineGenerator = function(bp, data) {
    var cfg = this.layout;

    var generator = d3.svg.line()
	.x(function(d, i) { var offset = ((i % 2 === 0) ? 0.02 : -0.02); return d * Math.cos((bp*cfg.radians_pre_bp)-cfg.PI2+(i ? offset : 0) ); } )
	.y(function(d, i) { var offset = ((i % 2 === 0) ? 0.02 : -0.02); return d * Math.sin((bp*cfg.radians_pre_bp)-cfg.PI2+ (i ? offset : 0) ); } )
	.interpolate("linear");

    return generator(data);
}

function pathTween(path, d1, precision) {
    //  return function() {
      //    var path0 = this,
    var path0 = path,
        path1 = path0.cloneNode(),
        n0 = path0.getTotalLength(),
        n1 = (path1.setAttribute("d", d1), path1).getTotalLength();

    // Uniform sampling of distance based on specified precision.
    var distances = [0], i = 0, dt = precision / Math.max(n0, n1);
    while ((i += dt) < 1) distances.push(i);
    distances.push(1);

    // Compute point-interpolators at each distance.
    var points = distances.map(function(t) {
      var p0 = path0.getPointAtLength(t * n0),
          p1 = path1.getPointAtLength(t * n1);
      return d3.interpolate([p0.x, p0.y], [p1.x, p1.y]);
    });

    return function(t) {
      return t < 1 ? "M" + points.map(function(p) { return p(t); }).join("L") : d1;
    };
    //  };
}

////////////////////////////////////////////////
//
// Glyph type tracks
//
////////////////////////////////////////////////

// We will probably need to send a localized
// version of the data so the update works
// properly

circularTrack.prototype.drawGlyphTrack = function(i) {
    var g = this.g;
    var cfg = this.layout;
    var track = this.tracks[i];
    var stack_count = 0;

    var items = track.items.filter(function(d) { return track.visTypes.contains(d.type) } );

    // Because on update the order of processing changes we need
    // to recompute the stacking order manually each time
    for(var i = 0; i < items.length; i++) {
	if(i < 1) {
	    items[i].stackCount = 0;
	    continue;
	}

	xs = (cfg.h/2 + (track.radius*Math.sin((items[i].bp*cfg.radians_pre_bp)-cfg.PI2))) -
	(cfg.h/2 + (track.radius*Math.sin((items[i-1].bp*cfg.radians_pre_bp)-cfg.PI2)));
	ys = (cfg.h/2 + (track.radius*Math.cos((items[i].bp*cfg.radians_pre_bp)-cfg.PI2))) -
	(cfg.h/2 + (track.radius*Math.cos((items[i-1].bp*cfg.radians_pre_bp)-cfg.PI2)));
	xs = xs * xs;
	ys = ys * ys;
	var dist = Math.sqrt(xs + ys);

	if(dist < track.pixel_spacing) { 
	    items[i].stackCount = items[i-1].stackCount + 1; 
	    continue;
	}

	items[i].stackCount = 0;
    }

    var x = function(d,i) { return cfg.w2 + (((track.glyph_buffer * d.stackCount) + track.radius)*Math.cos((d.bp*cfg.radians_pre_bp)-cfg.PI2)); };
    var y = function(d,i) { return cfg.h2 + (((track.glyph_buffer * d.stackCount) + track.radius)*Math.sin((d.bp*cfg.radians_pre_bp)-cfg.PI2)); };

    var trackPath = g.selectAll("." + track.trackName)
    //    var trackPath = track.container.selectAll("." + track.trackName)
    .data(items, function(d) { return d.id; });

    trackPath.transition()
    .duration(1000)
    .attr("transform", function(d,i) { return "translate(" + x(d,i) + ","
		+ y(d,i) + ")" })
    .style("opacity", 1);    

    trackPath.exit()
    .transition()
    .duration(1000)
    .attr("transform", "translate(" + cfg.h2 + "," + cfg.w2 + ")")
    .style("opacity", 0)
    .remove();

    trackPath.enter()
    .append('path')
    .attr('id', function(d,i) { return track.trackName + "_glyph" + d.id; })
    .attr('class', function(d) {return track.trackName + '_' + d.type + ' ' + track.trackName})
    .attr("d", d3.svg.symbol().type(track.glyphType).size(track.glyphSize))
    .attr("transform", "translate(" + cfg.h2 + "," + cfg.w2 + ")")
    .style("opacity", 0)
    .transition()
    .duration(1000)
    .attr("transform", function(d,i) { return "translate(" + x(d,i) + ","
				       + y(d,i) + ")" })
    .style("opacity", 1);


}

circularTrack.prototype.updateGlyphTrack = function(i) {
    var g = this.g;
    var cfg = this.layout;
    var track = this.tracks[i];
    var stack_count = 0;

    
}

////////////////////////////////////////////////
//
// Brush functionality
//
////////////////////////////////////////////////

circularTrack.prototype.attachBrush = function(callbackObj) {
    if('undefined' !== typeof this.callbackObj) {

	if( Object.prototype.toString.call( callbackObj ) === '[object Array]' ) { 
	    this.callbackObj.push(callbackObj);
	} else {
	    var tmpobj = this.callbackObj;
	    this.callbackObj = [tmpobj, callbackObj];
	}
    } else {
	this.callbackObj = callbackObj;
	this.createBrush();
    }

}

circularTrack.prototype.redrawBrush = function(startRad, endRad) {
    var cfg = this.layout;

    if('undefined' !== typeof this.brush) {

	this.brushArc
	    .outerRadius(cfg.radius-10);

	this.brush
	    .transition()
	    .duration(1000)
	    .attr("transform", "translate("+cfg.w2+","+cfg.h2+")");

	this.moveBrush(startRad, endRad);

	d3.select("#brushStart_" + cfg.containerid)		
	    .transition()
	    .duration(1000)
	    .attr("cx", cfg.h/2 + ((cfg.radius-10)*Math.cos(startRad-cfg.PI2)))
	    .attr("cy", cfg.h/2 + ((cfg.radius-10)*Math.sin(startRad-cfg.PI2)));

	d3.select("#brushEnd_" + cfg.containerid)		
	    .transition()
	    .duration(1000)
	    .attr("cx", cfg.w2 + ((cfg.radius-10)*Math.cos(endRad-cfg.PI2)))
	    .attr("cy", cfg.h2 + ((cfg.radius-10)*Math.sin(endRad-cfg.PI2)));

    }
}

circularTrack.prototype.createBrush = function() {
    var g = this.g;
    var cfg = this.layout;
    var xScale = this.xScale;
    var self = this;

    this.brushStart = 0;
    this.brushEnd = 0;
    this.brushStartBP = 0;
    this.brushEndBP = 0;

    this.brushArc = d3.svg.arc()
    .innerRadius(20)
    .outerRadius(cfg.radius-10)
    .endAngle(function(d){return xScale(0);})
    .startAngle(function(d){return xScale(0);});

    this.brush = g.insert("path", "defs")
    .attr("d", this.brushArc)
    .attr("id", "polarbrush_" + cfg.containerid)
    .attr("class", "polarbrush circularbrush")
    .attr("transform", "translate("+cfg.w2+","+cfg.h2+")")

    var dragStart = d3.behavior.drag()
    .on("drag", function(d) {
	    var mx = d3.mouse(this)[0];
	    var my = d3.mouse(this)[1];

	    var curRadandBP = calcRadBPfromXY((d3.mouse(this)[0] - (cfg.w2)),
					      -(d3.mouse(this)[1] - (cfg.h2)),
					      xScale);

	    // Don't allow the brush to go beyond the other
	    if(curRadandBP[0] >= self.brushEnd) {
		return;
	    }

	    g.select("#brushStart_" + cfg.containerid)		
	    .attr("cx", function(d, i){return cfg.h/2 + (cfg.radius-10)*Math.cos((curRadandBP[0])-cfg.PI2);})
	    .attr("cy", function(d, i){return cfg.h/2 + (cfg.radius-10)*Math.sin((curRadandBP[0])-cfg.PI2); });
		
	    self.brushStart = curRadandBP[0];
	    self.brushStartBP = curRadandBP[1];
	    self.moveBrush(self.brushStart, self.brushEnd);
	    if('undefined' !== typeof self.callbackObj) {
		self.doBrushCallback(self.brushStartBP, self.brushEndBP);
		//		self.callbackObj.update(self.brushStartBP, self.brushEndBP);
	    }
	})
    .on("dragend", function(d) {
	    self.doBrushFinishedCallback(self.brushStartBP, self.brushEndBP);
	});

    var dragEnd = d3.behavior.drag()
    .on("drag", function(d) {
	    var mx = d3.mouse(this)[0];
	    var my = d3.mouse(this)[1];

	    var curRadandBP = calcRadBPfromXY((d3.mouse(this)[0] - (cfg.w2)),
					      -(d3.mouse(this)[1] - (cfg.h2)),
					      xScale);

	    // Don't allow the brush to go beyond the other
	    if(curRadandBP[0] <= self.brushStart) {
		return;
	    }

	    g.select("#brushEnd_" + cfg.containerid)		
	    .attr("cx", function(d, i){return cfg.h/2 + (cfg.radius-10)*Math.cos((curRadandBP[0])-cfg.PI2);})
	    .attr("cy", function(d, i){return cfg.h/2 + (cfg.radius-10)*Math.sin((curRadandBP[0])-cfg.PI2); });
		
	    self.brushEnd = curRadandBP[0];
	    self.brushEndBP = curRadandBP[1];
	    self.moveBrush(self.brushStart, self.brushEnd);
	    if('undefined' !== typeof self.callbackObj) {
		self.doBrushCallback(self.brushStartBP, self.brushEndBP);
		//		self.callbackObj.update(self.brushStartBP, self.brushEndBP);
	    }
	})
    .on("dragend", function(d) {
	    self.doBrushFinishedCallback(self.brushStartBP, self.brushEndBP);
	});

    this.endBrushObj = g.append("circle")
    .attr({
	    id: 'brushEnd_' + cfg.containerid,
	    class: 'brushEnd circularbrush',
		cx: (cfg.w2 + ((cfg.radius-10)*Math.cos((this.xScale(0))-cfg.PI2))),
		cy: (cfg.h2 + ((cfg.radius-10)*Math.sin((this.xScale(0))-cfg.PI2))),
		r: 5
	    })
            .call(dragEnd);

    this.startBrushObj = g.append("circle")
    .attr({
	    id: 'brushStart_' + cfg.containerid,
	    class: 'brushStart circularbrush',
		cx: (cfg.w2 + ((cfg.radius-10)*Math.cos((this.xScale(0))-cfg.PI2))),
		cy: (cfg.h2 + ((cfg.radius-10)*Math.sin((this.xScale(0))-cfg.PI2))),
		r: 5
		})
    .call(dragStart);

    // Create the start and stop pointers

}

circularTrack.prototype.doBrushCallback = function(startBP, endBP) {
    var cfg = this.layout;

    if( Object.prototype.toString.call( this.callbackObj ) === '[object Array]' ) { 
	for(var obj in this.callbackObj) {
	    if(this.callbackObj.hasOwnProperty(obj)) {
		this.callbackObj[obj].update(startBP, endBP, { plotid: cfg.plotid } );
	    }
	}
    } else {
	this.callbackObj.update(startBP, endBP, { plotid: cfg.plotid });
    }

}

circularTrack.prototype.doBrushFinishedCallback = function(startBP, endBP) {
    var cfg = this.layout;

    if( Object.prototype.toString.call( this.callbackObj ) === '[object Array]' ) { 
	for(var obj in this.callbackObj) {
	    if(this.callbackObj.hasOwnProperty(obj)) {
		this.callbackObj[obj].update_finished(startBP, endBP, { plotid: cfg.plotid });
	    }
	}
    } else {
	this.callbackObj.update_finished(startBP, endBP, { plotid: cfg.plotid });
    }

}

circularTrack.prototype.moveBrush = function(startRad, endRad) {
    var g = this.g;
    var cfg = this.layout;

    //    console.log("moving brush to " + startRad, endRad);

    this.brushArc
    .startAngle(startRad)
    .endAngle(endRad);

    d3.select('#polarbrush_' + cfg.containerid)
    .attr("d", this.brushArc);

    this.currentStart = startRad;
    this.currentEnd = endRad;
    
}

circularTrack.prototype.moveBrushbyBP = function(startbp, endbp) {
    var cfg = this.layout;

    var startRad = startbp*this.layout.radians_pre_bp;
    var endRad = endbp*this.layout.radians_pre_bp;
    this.moveBrush(startRad,endRad);

    this.brushStart = startRad;
    this.brushStartBP = startbp;
    this.currentStart = startRad;
    this.currentEnd = endRad;
    d3.select("#brushStart_" + cfg.containerid)		
    .attr("cx", cfg.h/2 + ((cfg.radius-10)*Math.cos(startRad-cfg.PI2)))
    .attr("cy", cfg.h/2 + ((cfg.radius-10)*Math.sin(startRad-cfg.PI2)));

    this.brushEnd = endRad;
    this.brushEndBP = endbp;
    d3.select("#brushEnd_" + cfg.containerid)		
    .attr("cx", cfg.w2 + ((cfg.radius-10)*Math.cos(endRad-cfg.PI2)))
    .attr("cy", cfg.h2 + ((cfg.radius-10)*Math.sin(endRad-cfg.PI2)));


}

circularTrack.prototype.hideBrush = function() {
    var cfg = this.layout;

    d3.select("#brushStart_" + cfg.containerid)
    .style("visibility", "hidden");

    d3.select("#brushEnd_" + cfg.containerid)
    .style("visibility", "hidden");

    d3.select('#polarbrush_' + cfg.containerid)
    .style("visibility", "hidden");
}

circularTrack.prototype.showBrush = function() {
    var cfg = this.layout;

    d3.select("#brushStart_" + cfg.containerid)
    .style("visibility", "visible");

    d3.select("#brushEnd_" + cfg.containerid)
    .style("visibility", "visible");

    d3.select('#polarbrush_' + cfg.containerid)
    .style("visibility", "visible");
}

    circularTrack.prototype.update = function(startBP, endBP, params) {
    this.moveBrushbyBP(startBP, endBP);
}

	circularTrack.prototype.update_finished = function(startBP, endBP, params) {
    //    console.log("Thank you, got: " + startBP, endBP);
}

////////////////////////////////////////////////
//
// Export functionality
//
////////////////////////////////////////////////

// Allowed export formats are 'png' and 'svg'
// The extension will be added, just summply the base
// filename.

// Saving to raster format is dependent on FileSaver.js
// and canvg.js (which include rgbcolor.js & StackBlur.js),
// they must be loaded before circularplot.js

circularTrack.prototype.savePlot = function(scaling, filename, stylesheetfile, format) {

    // First lets get the stylesheet
    var sheetlength = stylesheetfile.length;
    var style = document.createElementNS("http://www.w3.org/1999/xhtml", "style");
	style.textContent += "<![CDATA[\n";
    for (var i=0;i<document.styleSheets.length; i++) {
	str = document.styleSheets[i].href;
	if(null == str) continue;

	if (str.substr(str.length-sheetlength)==stylesheetfile){
            var rules;
            if(document.styleSheets[i].cssRules) {
                rules = document.styleSheets[i].cssRules;
            } else if (document.styleSheets[i].rules) {
                rules = document.styleSheets[i].rules;
            }
            if(rules) {
                for (var j=0; j<rules.length;j++){
                    style.textContent += (rules[j].cssText + "\n");
                }
            }
            break;
    	}
    }
    style.textContent += "]]>";

    // Now we clone the SVG element, resize and scale it up
    var container = this.layout.container.slice(1);
    var containertag = document.getElementById(container);
    var clonedSVG = containertag.cloneNode(true);
    var svg = clonedSVG.getElementsByTagName("svg")[0];

    // Remove drag-resize shadow element
    var tags = svg.getElementsByClassName("dragbar-shadow")
    for(var i=0; i<tags.length; i++) {
	if(tags[i].getAttributeNS(null, "name") === name) {
	    tags[i].parentNode.removeChild(tags[i]);
        }
    }

    // Remove the brush if it's on the chart
    var tags = svg.getElementsByClassName("circularbrush")
    for(var i=tags.length-1; i>=0; i--) {
//	if(tags[i].getAttributeNS(null, "name") === name) {
	    tags[i].parentNode.removeChild(tags[i]);
//        }
    }

    // Remove the move croshairs if on the chart
    var tags = svg.getElementsByClassName("move_circularchart")
    for(var i=tags.length-1; i>=0; i--) {
//	if(tags[i].getAttributeNS(null, "name") === name) {
	    tags[i].parentNode.removeChild(tags[i]);
//        }
    }

    // We need to resize the svg with the new canvas size
    svg.removeAttribute('width');
    svg.removeAttribute('height');
    svg.setAttribute('width', this.layout.w*scaling +  this.layout.TranslateX*scaling);
    svg.setAttribute('height', this.layout.h*scaling +  this.layout.TranslateY*scaling);

    // Update first g tag with the scaling
    g = svg.getElementsByTagName("g")[0];
    transform = g.getAttribute("transform");
    g.setAttribute("transform", transform + " scale(" + scaling + ")");

    // Append the stylehsheet to the cloned svg element
    // so when we export it the style are inline and 
    // get rendered
    svg.getElementsByTagName("defs")[0].appendChild(style);

    // Fetch the actual SVG tag and convert it to a canvas
    // element
    var content = clonedSVG.innerHTML.trim();

    if(format == 'svg') {
	var a = document.createElement('a');
	a.href = "data:application/octet-stream;base64;attachment," + btoa(content);
	a.download = filename + ".svg";
	a.click();

    } else if(format == 'png') {
	var canvas = document.createElement('canvas');
	canvg(canvas, content);

	// Convert the canvas to a data url (this could
	// be displayed inline by inserting it in to an 
	// <img> tag in the src attribute, ie
	// <img src="'+imgData+'">
	var theImage = canvas.toDataURL('image/png');

	// Convert to a blob
	var blob = this.dataURLtoBlob(theImage);

	// Prompt to save
	saveAs(blob, filename);
    }
}

// Saving to raster format is dependent on FileSaver.js
// and canvg.js (which include rgbcolor.js & StackBlur.js),
// they must be loaded before circularplot.js

circularTrack.prototype.saveRaster = function(scaling, filename, stylesheetfile) {
    // First lets get the stylesheet
    var sheetlength = stylesheetfile.length;
    var style = document.createElementNS("http://www.w3.org/1999/xhtml", "style");
	style.textContent += "<![CDATA[\n";
    for (var i=0;i<document.styleSheets.length; i++) {
	str = document.styleSheets[i].href;
	if(null == str) continue;

	if (str.substr(str.length-sheetlength)==stylesheetfile){
      	    var rules = document.styleSheets[i].rules;
            for (var j=0; j<rules.length;j++){
		style.textContent += (rules[j].cssText + "\n");
            }
            break;
    	}
    }
    style.textContent += "]]>";

    // Now we clone the SVG element, resize and scale it up
    var container = this.layout.container.slice(1);
    var containertag = document.getElementById(container);
    var clonedSVG = containertag.cloneNode(true);
    var svg = clonedSVG.getElementsByTagName("svg")[0];

    // We need to resize the svg with the new canvas size
    svg.removeAttribute('width');
    svg.removeAttribute('height');
    svg.setAttribute('width', this.layout.w*scaling +  this.layout.TranslateX*scaling);
    svg.setAttribute('height', this.layout.h*scaling +  this.layout.TranslateY*scaling);

    // Update first g tag with the scaling
    g = svg.getElementsByTagName("g")[0];
    transform = g.getAttribute("transform");
    g.setAttribute("transform", transform + " scale(" + scaling + ")");

    // Append the stylehsheet to the cloned svg element
    // so when we export it the style are inline and 
    // get rendered
    svg.getElementsByTagName("defs")[0].appendChild(style);

    // Fetch the actual SVG tag and convert it to a canvas
    // element
    var content = clonedSVG.innerHTML.trim();
    var canvas = document.createElement('canvas');
    canvg(canvas, content);

    // Convert the canvas to a data url (this could
    // be displayed inline by inserting it in to an 
    // <img> tag in the src attribute, ie
    // <img src="'+imgData+'">
    var theImage = canvas.toDataURL('image/png');

    // Convert to a blob
    var blob = this.dataURLtoBlob(theImage);

    // Prompt to save
    saveAs(blob, filename);

}

circularTrack.prototype.dataURLtoBlob = function(dataURL) {
  // Decode the dataURL    
  var binary = atob(dataURL.split(',')[1]);
  // Create 8-bit unsigned array
  var array = [];
  for(var i = 0; i < binary.length; i++) {
      array.push(binary.charCodeAt(i));
  }
  // Return our Blob object
  return new Blob([new Uint8Array(array)], {type: 'image/png'});
}

////////////////////////////////////////////////
//
// Utility functions
//
////////////////////////////////////////////////

circularTrack.prototype.showTrack = function(name) {
    var i = this.findTrackbyName(name);

    // We didn't find the track by that name
    if(i < 0) {
	return;
    }

    // Is it already visible? Do nothing
    if(this.tracks[i].visible) {
	return;
    } else {
	this.tracks[i].visible = true;
    }

    switch(this.tracks[i].trackType) {
    case "plot":
    this.drawPlot(i, true);
        break;
    case "track":
    this.drawTrack(i, true);
        break;
    case "stranded":
        this.drawTrack(i, true);
        break;
    case "gap":
        this.drawGap(i, true);
        break;
    case "glyph":
        // Do nothing for a glyph type, special case
        // but leave this as a placeholder for now
        break;
    default:
    // Do nothing for an unknown track type
    }

}

circularTrack.prototype.hideTrack = function(name) {
    var i = this.findTrackbyName(name);

    // We didn't find the track by that name
    if(i < 0) {
	return;
    }

    // Is it already not visible? Do nothing
    if(! this.tracks[i].visible) {
	return;
    }

    switch(this.tracks[i].trackType) {
    case "plot":
        this.removePlot(i);
        break;
    case "track":
        this.removeTrack(i);
        break;
    case "stranded":
        this.removeTrack(i);
        break;
    case "gap":
        this.removeGap(i);
        break;
    case "glyph":
        // Do nothing for a glyph type, special case
        // but leave this as a placeholder for now
        break;
    default:
    // Do nothing for an unknown track type
    }

}

circularTrack.prototype.hideGlyphTrackType = function(name, type) {
    var i = this.findTrackbyName(name);

    // We didn't find the track by that name
    if(i < 0) {
	return;
    }

    if(this.tracks[i].trackType !== "glyph") {
	// Wrong track type, bail
	return;
    }

    // Don't try to show if already visible
    if(! this.isvisibleGlyphTrackType(name, type)) {
	return;
    }

    for(var j = 0; j < this.tracks[i].visTypes.length; j++) {
	if(this.tracks[i].visTypes[j] == type) {
	    this.tracks[i].visTypes.splice(j, 1);
	    j--;
	}
    }

    this.drawGlyphTrack(i);

}

circularTrack.prototype.showGlyphTrackType = function(name, type) {
    var i = this.findTrackbyName(name);

    // We didn't find the track by that name
    if(i < 0) {
	return;
    }

    if(this.tracks[i].trackType !== "glyph") {
	// Wrong track type, bail
	return;
    }

    // Don't try to show if already visible
    if(this.isvisibleGlyphTrackType(name, type)) {
	return;
    }

    if(! this.tracks[i].visTypes.contains(type) ) {
	this.tracks[i].visTypes.push(type);
    }

    this.drawGlyphTrack(i);

}

circularTrack.prototype.isvisibleGlyphTrackType = function(name, type) {
    var i = this.findTrackbyName(name);

    // We didn't find the track by that name
    if(i < 0) {
	return;
    }

    if(this.tracks[i].trackType !== "glyph") {
	// Wrong track type, bail
	return;
    }

    for(var j = 0; j < this.tracks[i].visTypes.length; j++) {
	if(this.tracks[i].visTypes[j] == type) {
	    return true;
	}
    }

    return false;
}

circularTrack.prototype.dragresize = function() {
    var newWidth = d3.event.x - this.layout.ExtraWidthX;
    var newHeight = d3.event.y - this.layout.ExtraWidthY;

    var newSize = Math.max(newWidth, newHeight);

    // Don't allow going below 25px in size
    if(newSize <= 25) {
        return;
    }

//    console.log(this.layout.w);
//    console.log("x " + newWidth);
//    console.log("y " + newHeight);

    this.layout.newSize = newSize
//    this.layout.w = newSize;
//    this.layout.h = newSize;

    this.dragbar
	.attr("transform", "translate(" + (newSize+this.layout.ExtraWidthX-25) + "," +  (newSize+this.layout.ExtraWidthY-25) + ")")

    this.drag_shadow
	.attr("width", (newSize+this.layout.ExtraWidthX))
	.attr("height", (newSize+this.layout.ExtraWidthY));

    if((newSize >= this.layout.w) || (newSize >= this.layout.h)) {
	this.container
	    .attr("width", newSize+this.layout.ExtraWidthX)
	    .attr("height", newSize+this.layout.ExtraWidthY)
    }
//    this.resize(newSize);

}

circularTrack.prototype.dragresize_start = function() {
    d3.event.sourceEvent.stopPropagation();

    this.drag_shadow
	.attr("class", "dragbar-shadow");
}

circularTrack.prototype.dragresize_end = function() {
    var newSize = this.layout.newSize;

    this.resize(this.layout.w);

    this.layout.w = newSize;
    this.layout.w2 = newSize / 2;
    this.layout.h = newSize;
    this.layout.h2 = this.layout.w2;

    this.drag_shadow
	.attr("class", "linear_hidden dragbar-shadow");

    this.resize(newSize);

}

circularTrack.prototype.resize = function(newWidth) {
    
    var resize_ratio = newWidth / this.layout.radius / 2;

    this.layout.radius = this.layout.factor*Math.min(newWidth/2, newWidth/2);

    this.layout.w = newWidth;
    this.layout.w2 = newWidth / 2;
    this.layout.h = newWidth;
    this.layout.h2 = this.layout.w2;

    this.moveAxis();

    // Resize the plots
    for(var i=0; i < this.tracks.length; i++) {

	//	if('undefined' !== typeof this.tracks[i].visible) {
	//	    if(! this.tracks[i].visible) {
	//		continue;
	//	    }
	//	}

	// We're going to see what type of tracks we have
	// and dispatch them appropriately

	switch(this.tracks[i].trackType) {
	case "plot":
	    this.movePlot(i, (this.tracks[i].plot_radius*resize_ratio));
	    break;
	case "track":
	    this.moveTrack(i, (this.tracks[i].inner_radius*resize_ratio), (this.tracks[i].outer_radius*resize_ratio));
	    break;
	case "stranded":
	    this.moveTrack(i, (this.tracks[i].inner_radius*resize_ratio), (this.tracks[i].outer_radius*resize_ratio));
	    break;
	case "gap":
	    this.moveGap(i, (this.tracks[i].inner_radius*resize_ratio), (this.tracks[i].outer_radius*resize_ratio));
	    break;
	case "glyph":
	    this.tracks[i].radius = this.tracks[i].radius * resize_ratio;
	    // We needed to save the new radius but if this
	    // track isn't visible, do nothing
	    if(this.tracks[i].visible) {
		this.drawGlyphTrack(i);
	    }
	    break;
	default:
	    // Do nothing for an unknown track type
	}
    }

    this.container
	.attr("width", newWidth+this.layout.ExtraWidthX)
	.attr("height", newWidth+this.layout.ExtraWidthY)

    this.redrawBrush(this.currentStart, this.currentEnd);

    this.dragbar
	.attr("transform", "translate(" + (newWidth+this.layout.ExtraWidthX-25) + "," +  (newWidth+this.layout.ExtraWidthY-25) + ")")

}

////////////////////////////////////////////////
//
// Helper functions
//
////////////////////////////////////////////////

circularTrack.prototype.findTrackbyName = function(name) {
    var tracks = this.tracks;

    for(var i=0; i < tracks.length; i++) {
	if(tracks[i].trackName == name) {
	    return i;
	}
    }

    return -1;

}

circularTrack.prototype.findGlyphTypes = function(i) {

    var classes = [];

    if('undefined' == typeof this.tracks[i].visItems) {
	this.tracks[i].visTypes = [];
    }

    for(var j=0; j < this.tracks[i].items.length; j++) {
	if(! this.tracks[i].visTypes.contains(this.tracks[i].items[j].type)) {
	    this.tracks[i].visTypes.push(this.tracks[i].items[j].type);
	    classes.push(this.tracks[i].trackName + "_" + this.tracks[i].items[j].type);
	}
    }

    this.tracks[i].visClasses = classes.join(' ');

}

circularTrack.prototype.maskGlyphTypes = function(i, types) {

    for(var j = this.tracks[i].visTypes.length - 1; j >= 0; j--) {
	if(types.contains(this.tracks[i].visTypes[j])) {
	    this.tracks[i].visTypes.splice(j, 1);
	}
    }

}

Array.prototype.contains = function(obj) {
    var i = this.length;
    while (i--) {
        if (this[i] == obj) {
            return true;
        }
    }
    return false;
}

// If we're displaying a stranded track, calculate
// the inner radius depending on which strand the 
// gene is on.

function calcInnerRadius(inner, outer, strand) {
    if('undefined' == typeof strand) {
	return inner;
    } else if(strand == -1) {
	return inner;
    } else {
	return (inner+outer)/2;
    }
}

// If we're displaying a stranded track, calculate
// the outer radius depending on which strand the 
// gene is on.
    
function calcOuterRadius (inner, outer, strand) {
    if('undefined' == typeof strand) {
	return outer;
    } else if(strand == -1) {
	return (inner+outer)/2;
    } else {
	return outer;
    }
}

function calcRadBPfromXY (x,y,xScale) {
    var rad = Math.PI/2 - Math.atan(y/x);
    if(x < 0) {
	// II & III quadrant
	rad = rad + Math.PI;
    }

    return [rad,Math.floor(xScale.invert(rad))];
}

function calcMinSliceSize () {
    var cfg = this.layout;

    
    //cfg.radians_pre_bp
}

d3-tip.js

// d3.tip
// Copyright (c) 2013 Justin Palmer
//
// Tooltips for d3.js SVG visualizations

(function (root, factory) {
  if (typeof define === 'function' && define.amd) {
    // AMD. Register as an anonymous module with d3 as a dependency.
    define(['d3'], factory)
  } else {
    // Browser global.
    root.d3.tip = factory(root.d3)
  }
}(this, function (d3) {

  // Public - contructs a new tooltip
  //
  // Returns a tip
  return function() {
    var direction = d3_tip_direction,
        offset    = d3_tip_offset,
        html      = d3_tip_html,
        node      = initNode(),
        svg       = null,
        point     = null,
        target    = null
  
    function tip(vis) {
      svg = getSVGNode(vis)
      point = svg.createSVGPoint()
      document.body.appendChild(node)
    }
  
    // Public - show the tooltip on the screen
    //
    // Returns a tip
    tip.show = function() {
      var args = Array.prototype.slice.call(arguments)
      if(args[args.length - 1] instanceof SVGElement) target = args.pop()
  
      var content = html.apply(this, args),
          poffset = offset.apply(this, args),
          dir     = direction.apply(this, args),
          nodel   = d3.select(node),
          i       = directions.length,
          coords
  
      nodel.html(content)
        .style({ opacity: 1, 'pointer-events': 'all' })
  
      while(i--) nodel.classed(directions[i], false)
      coords = direction_callbacks.get(dir).apply(this)
      nodel.classed(dir, true).style({
        top: (coords.top +  poffset[0]) + 'px',
        left: (coords.left + poffset[1]) + 'px'
      })
  
      return tip
    }
  
    // Public - hide the tooltip
    //
    // Returns a tip
    tip.hide = function() {
      nodel = d3.select(node)
      nodel.style({ opacity: 0, 'pointer-events': 'none' })
      return tip
    }
  
    // Public: Proxy attr calls to the d3 tip container.  Sets or gets attribute value.
    //
    // n - name of the attribute
    // v - value of the attribute
    //
    // Returns tip or attribute value
    tip.attr = function(n, v) {
      if (arguments.length < 2 && typeof n === 'string') {
        return d3.select(node).attr(n)
      } else {
        var args =  Array.prototype.slice.call(arguments)
        d3.selection.prototype.attr.apply(d3.select(node), args)
      }
  
      return tip
    }
  
    // Public: Proxy style calls to the d3 tip container.  Sets or gets a style value.
    //
    // n - name of the property
    // v - value of the property
    //
    // Returns tip or style property value
    tip.style = function(n, v) {
      if (arguments.length < 2 && typeof n === 'string') {
        return d3.select(node).style(n)
      } else {
        var args =  Array.prototype.slice.call(arguments)
        d3.selection.prototype.style.apply(d3.select(node), args)
      }
  
      return tip
    }
  
    // Public: Set or get the direction of the tooltip
    //
    // v - One of n(north), s(south), e(east), or w(west), nw(northwest),
    //     sw(southwest), ne(northeast) or se(southeast)
    //
    // Returns tip or direction
    tip.direction = function(v) {
      if (!arguments.length) return direction
      direction = v == null ? v : d3.functor(v)
  
      return tip
    }
  
    // Public: Sets or gets the offset of the tip
    //
    // v - Array of [x, y] offset
    //
    // Returns offset or
    tip.offset = function(v) {
      if (!arguments.length) return offset
      offset = v == null ? v : d3.functor(v)
  
      return tip
    }
  
    // Public: sets or gets the html value of the tooltip
    //
    // v - String value of the tip
    //
    // Returns html value or tip
    tip.html = function(v) {
      if (!arguments.length) return html
      html = v == null ? v : d3.functor(v)
  
      return tip
    }
  
    function d3_tip_direction() { return 'n' }
    function d3_tip_offset() { return [0, 0] }
    function d3_tip_html() { return ' ' }
  
    var direction_callbacks = d3.map({
      n:  direction_n,
      s:  direction_s,
      e:  direction_e,
      w:  direction_w,
      nw: direction_nw,
      ne: direction_ne,
      sw: direction_sw,
      se: direction_se
    }),
  
    directions = direction_callbacks.keys()
  
    function direction_n() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.n.y - node.offsetHeight,
        left: bbox.n.x - node.offsetWidth / 2
      }
    }
  
    function direction_s() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.s.y,
        left: bbox.s.x - node.offsetWidth / 2
      }
    }
  
    function direction_e() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.e.y - node.offsetHeight / 2,
        left: bbox.e.x
      }
    }
  
    function direction_w() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.w.y - node.offsetHeight / 2,
        left: bbox.w.x - node.offsetWidth
      }
    }
  
    function direction_nw() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.nw.y - node.offsetHeight,
        left: bbox.nw.x - node.offsetWidth
      }
    }
  
    function direction_ne() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.ne.y - node.offsetHeight,
        left: bbox.ne.x
      }
    }
  
    function direction_sw() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.sw.y,
        left: bbox.sw.x - node.offsetWidth
      }
    }
  
    function direction_se() {
      var bbox = getScreenBBox()
      return {
        top:  bbox.se.y,
        left: bbox.e.x
      }
    }
  
    function initNode() {
      var node = d3.select(document.createElement('div'))
      node.style({
        position: 'absolute',
        top: 0,
        opacity: 0,
        'pointer-events': 'none',
        'box-sizing': 'border-box'
      })
  
      return node.node()
    }
  
    function getSVGNode(el) {
      el = el.node()
      if(el.tagName.toLowerCase() == 'svg')
        return el
  
      return el.ownerSVGElement
    }
  
    // Private - gets the screen coordinates of a shape
    //
    // Given a shape on the screen, will return an SVGPoint for the directions
    // n(north), s(south), e(east), w(west), ne(northeast), se(southeast), nw(northwest),
    // sw(southwest).
    //
    //    +-+-+
    //    |   |
    //    +   +
    //    |   |
    //    +-+-+
    //
    // Returns an Object {n, s, e, w, nw, sw, ne, se}
    function getScreenBBox() {
      var targetel   = target || d3.event.target,
          bbox       = {},
          matrix     = targetel.getScreenCTM(),
          tbbox      = targetel.getBBox(),
          width      = tbbox.width,
          height     = tbbox.height,
          x          = tbbox.x,
          y          = tbbox.y,
          scrollEl   = document.documentElement? document.documentElement : document.body,
          scrollTop  = scrollEl.scrollTop,
          scrollLeft = scrollEl.scrollLeft
  
  
      point.x = x + scrollLeft
      point.y = y + scrollTop
      bbox.nw = point.matrixTransform(matrix)
      point.x += width
      bbox.ne = point.matrixTransform(matrix)
      point.y += height
      bbox.se = point.matrixTransform(matrix)
      point.x -= width
      bbox.sw = point.matrixTransform(matrix)
      point.y -= height / 2
      bbox.w  = point.matrixTransform(matrix)
      point.x += width
      bbox.e = point.matrixTransform(matrix)
      point.x -= width / 2
      point.y -= height / 2
      bbox.n = point.matrixTransform(matrix)
      point.y += height
      bbox.s = point.matrixTransform(matrix)
  
      return bbox
    }
  
    return tip
  };

}));

d3.min.js

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data.js

var tracks = [
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		trackType: "stranded",
		visible: true,
		inner_radius: 80,
		outer_radius: 120,
		trackFeatures: "complex",
		featureThreshold: 7000000,
		mouseover_callback: 'islandPopup',
		mouseout_callback: 'islandPopupClear',
		linear_mouseclick: 'linearPopup',
		showLabels: true,
		showTooltip: true,
		linear_mouseclick: 'linearClick',
		items: [
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                         {id: 2, start:60000,end:100000, name:"island1", strand: 1},
                         {id: 3, start:800000,end:1000000, name:"island2withavery long name", strand: 1},
                         {id: 4, start:1200000,end:1500000, name:"island3", strand: 1},
                         {id: 5, start:1500000,end:1700000, name:"island4",strand: -1, extraclass: "cellwall"},
                         {id: 6, start:2000000,end:2100000, name:"is", strand: -1, extraclass: "innermembrane"},
                         {id: 8, start:142000,end:149000, name:"cheeky gene", strand: -1, extraclass: "outermembrane"},
                         {id: 9, start:3000000,end:3100000, name:"meow meow", strand: 1, extraclass: "innermembrane"},
                         {id: 10, start:120000,end:136000, name:"turtle power", strand: -1, extraclass: "extrashelluar"},
                         {id: 11, start:3200000,end:3300000, name:"out of ideas", strand: -1, extraclass: "lostinspace"},
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                         {id: 21, start: 45000, end:50000, name:"promoter", strand: -1, feature:"arrow"},
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                         {id: 23, start:136000 , end: 139000, name: "promoter", strand: -1, feature: "arrow"},
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                         {id: 31, start:149000 , end: 162000, name: "promoter", strand: -1, feature: "arrow"},
                         {id: 27, start:1000000,end:1200000, name:"intergenic", strand: 0},
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			]
	      },
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		visible: true,
		trackType: "stranded",
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		outer_radius: 234,
		centre_line_stroke: "grey",
		showLabels: true,

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{id: 8, start:10434, end:12488, name:"PA0008", strand:-1},
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{id: 13, start:15620, end:16273, name:"PA0013", strand:1},
{id: 14, start:16335, end:16607, name:"PA0014", strand:-1},
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{id: 16, start:17366, end:18739, name:"PA0016", strand:-1},
{id: 17, start:18767, end:20071, name:"PA0017", strand:-1},
{id: 18, start:20068, end:21012, name:"PA0018", strand:-1},
{id: 19, start:21067, end:21573, name:"PA0019", strand:-1},
{id: 20, start:21712, end:22737, name:"PA0020", strand:1},
{id: 21, start:22872, end:23960, name:"PA0021", strand:1},
{id: 22, start:24001, end:24558, name:"PA0022", strand:1},
{id: 23, start:24568, end:25545, name:"PA0023", strand:-1},
{id: 24, start:25736, end:26653, name:"PA0024", strand:1},
{id: 25, start:26711, end:27535, name:"PA0025", strand:1},
{id: 26, start:27646, end:28632, name:"PA0026", strand:1},
{id: 27, start:28613, end:29899, name:"PA0027", strand:1},
{id: 28, start:29896, end:30498, name:"PA0028", strand:1},
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{id: 37, start:39202, end:40089, name:"PA0037", strand:1},
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{id: 84, start:101778, end:103274, name:"PA0084", strand:1},
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{id: 382, start:783012, end:792990, name:"PA0711"},
{id: 383, start:783012, end:792990, name:"PA0712"},
{id: 384, start:783012, end:792990, name:"PA0713"},
{id: 385, start:783012, end:792990, name:"PA0714"},
{id: 386, start:783012, end:792990, name:"PA0714.1"},
{id: 387, start:783012, end:792990, name:"PA0715"},
{id: 388, start:783012, end:792990, name:"PA0716"},
{id: 389, start:783012, end:792990, name:"PA0717"},
{id: 390, start:783012, end:792990, name:"PA0718"},
{id: 391, start:783012, end:792990, name:"PA0719"},
{id: 392, start:783012, end:792990, name:"PA0720"},
{id: 393, start:783012, end:792990, name:"PA0721"},
{id: 394, start:783012, end:792990, name:"PA0722"},
{id: 395, start:783012, end:792990, name:"PA0723"},
{id: 396, start:783012, end:792990, name:"PA0724"},
{id: 397, start:783012, end:792990, name:"PA0725"},
{id: 398, start:1060510, end:1080015, name:"PA0977"},
{id: 399, start:1060510, end:1080015, name:"PA0978"},
{id: 400, start:1060510, end:1080015, name:"PA0979"},
{id: 401, start:1060510, end:1080015, name:"PA0980"},
{id: 402, start:1060510, end:1080015, name:"PA0981"},
{id: 403, start:1060510, end:1080015, name:"PA0982"},
{id: 404, start:1060510, end:1080015, name:"PA0983"},
{id: 405, start:1060510, end:1080015, name:"PA0984"},
{id: 406, start:1060510, end:1080015, name:"PA0985"},
{id: 407, start:1060510, end:1080015, name:"PA0986"},
{id: 408, start:1060510, end:1080015, name:"PA0987"},
{id: 409, start:1060510, end:1080015, name:"PA0988"},
{id: 410, start:1060510, end:1080015, name:"PA0989"},
{id: 411, start:1060510, end:1080015, name:"PA0990"},
{id: 412, start:1060510, end:1080015, name:"PA0991"},
{id: 413, start:1060510, end:1080015, name:"PA0992"},
{id: 414, start:1060510, end:1080015, name:"PA0993"},
{id: 415, start:1060510, end:1080015, name:"PA0994"},
{id: 416, start:1060510, end:1080015, name:"PA0995"},
{id: 417, start:1060510, end:1080015, name:"PA0996"},
{id: 418, start:1060510, end:1080015, name:"PA0997"},
{id: 419, start:1060513, end:1080012, name:"PA0977"},
{id: 420, start:1060513, end:1080012, name:"PA0978"},
{id: 421, start:1060513, end:1080012, name:"PA0979"},
{id: 422, start:1060513, end:1080012, name:"PA0980"},
{id: 423, start:1060513, end:1080012, name:"PA0981"},
{id: 424, start:1060513, end:1080012, name:"PA0982"},
{id: 425, start:1060513, end:1080012, name:"PA0983"},
{id: 426, start:1060513, end:1080012, name:"PA0984"},
{id: 427, start:1060513, end:1080012, name:"PA0985"},
{id: 428, start:1060513, end:1080012, name:"PA0986"},
{id: 429, start:1060513, end:1080012, name:"PA0987"},
{id: 430, start:1060513, end:1080012, name:"PA0988"},
{id: 431, start:1060513, end:1080012, name:"PA0989"},
{id: 432, start:1060513, end:1080012, name:"PA0990"},
{id: 433, start:1060513, end:1080012, name:"PA0991"},
{id: 434, start:1060513, end:1080012, name:"PA0992"},
{id: 435, start:1060513, end:1080012, name:"PA0993"},
{id: 436, start:1060513, end:1080012, name:"PA0994"},
{id: 437, start:1060513, end:1080012, name:"PA0995"},
{id: 438, start:1060513, end:1080012, name:"PA0996"},
{id: 439, start:1060513, end:1080012, name:"PA0997"},
{id: 440, start:1480215, end:1495492, name:"PA1367"},
{id: 441, start:1480215, end:1495492, name:"PA1368"},
{id: 442, start:1480215, end:1495492, name:"PA1369"},
{id: 443, start:1480215, end:1495492, name:"PA1370"},
{id: 444, start:1480215, end:1495492, name:"PA1371"},
{id: 445, start:1480215, end:1495492, name:"PA1372"},
{id: 446, start:1480215, end:1495492, name:"PA1373"},
{id: 447, start:1480215, end:1495492, name:"PA1374"},
{id: 448, start:1480215, end:1495492, name:"PA1375"},
{id: 449, start:1480215, end:1495492, name:"PA1376"},
{id: 450, start:1480215, end:1495492, name:"PA1377"},
{id: 451, start:1480218, end:1495489, name:"PA1367"},
{id: 452, start:1480218, end:1495489, name:"PA1368"},
{id: 453, start:1480218, end:1495489, name:"PA1369"},
{id: 454, start:1480218, end:1495489, name:"PA1370"},
{id: 455, start:1480218, end:1495489, name:"PA1371"},
{id: 456, start:1480218, end:1495489, name:"PA1372"},
{id: 457, start:1480218, end:1495489, name:"PA1373"},
{id: 458, start:1480218, end:1495489, name:"PA1374"},
{id: 459, start:1480218, end:1495489, name:"PA1375"},
{id: 460, start:1480218, end:1495489, name:"PA1376"},
{id: 461, start:1480218, end:1495489, name:"PA1377"},
{id: 500, start: 1409000, end: 1503991, name: "terminator2", feature: "terminator"},
{id: 501, start:1550000 , end: 2250000, name: "promoter", feature: "arrow"},
{id: 502, start:1700000 , end: 2250000, name: "promoter", feature: "arrow"},
			]
		    },
	      { trackName: "track4",
		trackType: "plot",
		visible: true,
		plot_min: 0.4891,
		plot_max: 0.7274,
		plot_mean: 0.66558768401076,
		bp_per_element: 10000,
	        plot_width: 75,
		plot_radius: 130,
	        linear_plot_width: 100,
		linear_plot_height: 285,
		items: [
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			]
	      },
	      { trackName: "track5",
		trackType: 'glyph',
		glyphType: 'circle',
		radius: 155,
		pixel_spacing: 5,
		linear_pixel_spacing: 5,
	        glyph_buffer: 5,
	        linear_glyph_buffer: 5,
		glyphSize: 20,
		linear_glyphSize: 20,
		linear_height: 100,
		showTooltip: true,
		items: [
			{id: 1, bp: 1000, type: 'vfdb', name: 'vfdb1'},
			{id: 2, bp: 50000, type: 'adb', name: 'adb1'},
			{id: 3, bp: 51000, type: 'adb', name: 'adb2'},
			{id: 4, bp: 52000, type: 'vfdb', name: 'vfdb2'},
			{id: 5, bp: 53000, type: 'adb', name: 'adb3'},
			{id: 6, bp: 54000, type: 'vfdb', name: 'vfdb4'},
			{id: 7, bp: 55000, type: 'adb', name: 'adb4'},
			{id: 8, bp: 56000, type: 'adb', name: 'adb5'},
			{id: 9, bp: 156000, type: 'adb', name: 'adb6'},
			{id: 10, bp: 256000, type: 'adb', name: 'adb7'},
			{id: 11, bp: 3560000, type: 'adb', name: 'db8'},
			{id: 12, bp: 3560005, type: 'adb', name: 'adb9'},
			{id: 13, bp: 556000, type: 'adb', name: 'adb10'},
			{id: 14, bp: 556000, type: 'adb', name: 'adb11'},
			{id: 15, bp: 5560000, type: 'adb', name: 'db12'},
			{id: 16, bp: 5560005, type: 'adb', name: 'adb13'},
			{id: 14, bp: 557000, type: 'adb', name: 'adb14'},
			{id: 15, bp: 5560000, type: 'adb', name: 'db15'},
			{id: 16, bp: 100000, type: 'adb', name: 'adb16'},
			{id: 17, bp: 101000, type: 'vfdb', name: 'adb17'},
			{id: 18, bp: 5000000, type: 'adb', name: 'adb18'},
			{id: 19, bp: 5005000, type: 'vfdb', name: 'db19'},
			{id: 20, bp: 5006005, type: 'vfdb', name: 'adb20'},
	           ]
		      },
		  {
		      trackName: "gapTrack",
		      trackType: "gap",
		      inner_radius: 25,
		      outer_radius: 235,
		      showTooltip: true,
		      items: [
			      {id: 1, start: 6150000, end: 6160000, name: 'contig_gap1'},
			      {id: 2, start: 5350000, end: 5360000, name: 'contig_gap2'},
			      {id: 3, start: 2050000, end: 2060000, name: 'contig_gap3'},
			      {id: 4, start: 3250000, end: 3260000, name: 'contig_gap4'},
		     ]
                  }
      ];

FileSaver.js

/* FileSaver.js
 * A saveAs() FileSaver implementation.
 * 2013-10-21
 *
 * By Eli Grey, http://eligrey.com
 * License: X11/MIT
 *   See LICENSE.md
 */

/*global self */
/*jslint bitwise: true, regexp: true, confusion: true, es5: true, vars: true, white: true,
  plusplus: true */

/*! @source http://purl.eligrey.com/github/FileSaver.js/blob/master/FileSaver.js */

var saveAs = saveAs
  || (typeof navigator !== 'undefined' && navigator.msSaveOrOpenBlob && navigator.msSaveOrOpenBlob.bind(navigator))
  || (function(view) {
	"use strict";
	var
		  doc = view.document
		  // only get URL when necessary in case BlobBuilder.js hasn't overridden it yet
		, get_URL = function() {
			return view.URL || view.webkitURL || view;
		}
		, URL = view.URL || view.webkitURL || view
		, save_link = doc.createElementNS("http://www.w3.org/1999/xhtml", "a")
		, can_use_save_link =  !view.externalHost && "download" in save_link
		, click = function(node) {
			var event = doc.createEvent("MouseEvents");
			event.initMouseEvent(
				"click", true, false, view, 0, 0, 0, 0, 0
				, false, false, false, false, 0, null
			);
			node.dispatchEvent(event);
		}
		, webkit_req_fs = view.webkitRequestFileSystem
		, req_fs = view.requestFileSystem || webkit_req_fs || view.mozRequestFileSystem
		, throw_outside = function (ex) {
			(view.setImmediate || view.setTimeout)(function() {
				throw ex;
			}, 0);
		}
		, force_saveable_type = "application/octet-stream"
		, fs_min_size = 0
		, deletion_queue = []
		, process_deletion_queue = function() {
			var i = deletion_queue.length;
			while (i--) {
				var file = deletion_queue[i];
				if (typeof file === "string") { // file is an object URL
					URL.revokeObjectURL(file);
				} else { // file is a File
					file.remove();
				}
			}
			deletion_queue.length = 0; // clear queue
		}
		, dispatch = function(filesaver, event_types, event) {
			event_types = [].concat(event_types);
			var i = event_types.length;
			while (i--) {
				var listener = filesaver["on" + event_types[i]];
				if (typeof listener === "function") {
					try {
						listener.call(filesaver, event || filesaver);
					} catch (ex) {
						throw_outside(ex);
					}
				}
			}
		}
		, FileSaver = function(blob, name) {
			// First try a.download, then web filesystem, then object URLs
			var
				  filesaver = this
				, type = blob.type
				, blob_changed = false
				, object_url
				, target_view
				, get_object_url = function() {
					var object_url = get_URL().createObjectURL(blob);
					deletion_queue.push(object_url);
					return object_url;
				}
				, dispatch_all = function() {
					dispatch(filesaver, "writestart progress write writeend".split(" "));
				}
				// on any filesys errors revert to saving with object URLs
				, fs_error = function() {
					// don't create more object URLs than needed
					if (blob_changed || !object_url) {
						object_url = get_object_url(blob);
					}
					if (target_view) {
						target_view.location.href = object_url;
					} else {
                        window.open(object_url, "_blank");
                    }
					filesaver.readyState = filesaver.DONE;
					dispatch_all();
				}
				, abortable = function(func) {
					return function() {
						if (filesaver.readyState !== filesaver.DONE) {
							return func.apply(this, arguments);
						}
					};
				}
				, create_if_not_found = {create: true, exclusive: false}
				, slice
			;
			filesaver.readyState = filesaver.INIT;
			if (!name) {
				name = "download";
			}
			if (can_use_save_link) {
				object_url = get_object_url(blob);
				// FF for Android has a nasty garbage collection mechanism
				// that turns all objects that are not pure javascript into 'deadObject'
				// this means `doc` and `save_link` are unusable and need to be recreated
				// `view` is usable though:
				doc = view.document;
				save_link = doc.createElementNS("http://www.w3.org/1999/xhtml", "a");
				save_link.href = object_url;
				save_link.download = name;
				var event = doc.createEvent("MouseEvents");
				event.initMouseEvent(
					"click", true, false, view, 0, 0, 0, 0, 0
					, false, false, false, false, 0, null
				);
				save_link.dispatchEvent(event);
				filesaver.readyState = filesaver.DONE;
				dispatch_all();
				return;
			}
			// Object and web filesystem URLs have a problem saving in Google Chrome when
			// viewed in a tab, so I force save with application/octet-stream
			// http://code.google.com/p/chromium/issues/detail?id=91158
			if (view.chrome && type && type !== force_saveable_type) {
				slice = blob.slice || blob.webkitSlice;
				blob = slice.call(blob, 0, blob.size, force_saveable_type);
				blob_changed = true;
			}
			// Since I can't be sure that the guessed media type will trigger a download
			// in WebKit, I append .download to the filename.
			// https://bugs.webkit.org/show_bug.cgi?id=65440
			if (webkit_req_fs && name !== "download") {
				name += ".download";
			}
			if (type === force_saveable_type || webkit_req_fs) {
				target_view = view;
			}
			if (!req_fs) {
				fs_error();
				return;
			}
			fs_min_size += blob.size;
			req_fs(view.TEMPORARY, fs_min_size, abortable(function(fs) {
				fs.root.getDirectory("saved", create_if_not_found, abortable(function(dir) {
					var save = function() {
						dir.getFile(name, create_if_not_found, abortable(function(file) {
							file.createWriter(abortable(function(writer) {
								writer.onwriteend = function(event) {
									target_view.location.href = file.toURL();
									deletion_queue.push(file);
									filesaver.readyState = filesaver.DONE;
									dispatch(filesaver, "writeend", event);
								};
								writer.onerror = function() {
									var error = writer.error;
									if (error.code !== error.ABORT_ERR) {
										fs_error();
									}
								};
								"writestart progress write abort".split(" ").forEach(function(event) {
									writer["on" + event] = filesaver["on" + event];
								});
								writer.write(blob);
								filesaver.abort = function() {
									writer.abort();
									filesaver.readyState = filesaver.DONE;
								};
								filesaver.readyState = filesaver.WRITING;
							}), fs_error);
						}), fs_error);
					};
					dir.getFile(name, {create: false}, abortable(function(file) {
						// delete file if it already exists
						file.remove();
						save();
					}), abortable(function(ex) {
						if (ex.code === ex.NOT_FOUND_ERR) {
							save();
						} else {
							fs_error();
						}
					}));
				}), fs_error);
			}), fs_error);
		}
		, FS_proto = FileSaver.prototype
		, saveAs = function(blob, name) {
			return new FileSaver(blob, name);
		}
	;
	FS_proto.abort = function() {
		var filesaver = this;
		filesaver.readyState = filesaver.DONE;
		dispatch(filesaver, "abort");
	};
	FS_proto.readyState = FS_proto.INIT = 0;
	FS_proto.WRITING = 1;
	FS_proto.DONE = 2;

	FS_proto.error =
	FS_proto.onwritestart =
	FS_proto.onprogress =
	FS_proto.onwrite =
	FS_proto.onabort =
	FS_proto.onerror =
	FS_proto.onwriteend =
		null;

	view.addEventListener("unload", process_deletion_queue, false);
	return saveAs;
}(this.self || this.window || this.content));
// `self` is undefined in Firefox for Android content script context
// while `this` is nsIContentFrameMessageManager
// with an attribute `content` that corresponds to the window

if (typeof module !== 'undefined') module.exports = saveAs;

StackBlur.js

/*

StackBlur - a fast almost Gaussian Blur For Canvas

Version: 	0.5
Author:		Mario Klingemann
Contact: 	mario@quasimondo.com
Website:	http://www.quasimondo.com/StackBlurForCanvas
Twitter:	@quasimondo

In case you find this class useful - especially in commercial projects -
I am not totally unhappy for a small donation to my PayPal account
mario@quasimondo.de

Or support me on flattr: 
https://flattr.com/thing/72791/StackBlur-a-fast-almost-Gaussian-Blur-Effect-for-CanvasJavascript

Copyright (c) 2010 Mario Klingemann

Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use,
copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following
conditions:

The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
OTHER DEALINGS IN THE SOFTWARE.
*/

var mul_table = [
        512,512,456,512,328,456,335,512,405,328,271,456,388,335,292,512,
        454,405,364,328,298,271,496,456,420,388,360,335,312,292,273,512,
        482,454,428,405,383,364,345,328,312,298,284,271,259,496,475,456,
        437,420,404,388,374,360,347,335,323,312,302,292,282,273,265,512,
        497,482,468,454,441,428,417,405,394,383,373,364,354,345,337,328,
        320,312,305,298,291,284,278,271,265,259,507,496,485,475,465,456,
        446,437,428,420,412,404,396,388,381,374,367,360,354,347,341,335,
        329,323,318,312,307,302,297,292,287,282,278,273,269,265,261,512,
        505,497,489,482,475,468,461,454,447,441,435,428,422,417,411,405,
        399,394,389,383,378,373,368,364,359,354,350,345,341,337,332,328,
        324,320,316,312,309,305,301,298,294,291,287,284,281,278,274,271,
        268,265,262,259,257,507,501,496,491,485,480,475,470,465,460,456,
        451,446,442,437,433,428,424,420,416,412,408,404,400,396,392,388,
        385,381,377,374,370,367,363,360,357,354,350,347,344,341,338,335,
        332,329,326,323,320,318,315,312,310,307,304,302,299,297,294,292,
        289,287,285,282,280,278,275,273,271,269,267,265,263,261,259];
        
   
var shg_table = [
	     9, 11, 12, 13, 13, 14, 14, 15, 15, 15, 15, 16, 16, 16, 16, 17, 
		17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 19, 
		19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 20,
		20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 21,
		21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
		21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 
		22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22,
		22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 
		23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
		23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
		23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 
		23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 
		24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
		24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
		24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
		24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24 ];

function stackBlurImage( imageID, canvasID, radius, blurAlphaChannel )
{
			
 	var img = document.getElementById( imageID );
	var w = img.naturalWidth;
    var h = img.naturalHeight;
       
	var canvas = document.getElementById( canvasID );
      
    canvas.style.width  = w + "px";
    canvas.style.height = h + "px";
    canvas.width = w;
    canvas.height = h;
    
    var context = canvas.getContext("2d");
    context.clearRect( 0, 0, w, h );
    context.drawImage( img, 0, 0 );

	if ( isNaN(radius) || radius < 1 ) return;
	
	if ( blurAlphaChannel )
		stackBlurCanvasRGBA( canvasID, 0, 0, w, h, radius );
	else 
		stackBlurCanvasRGB( canvasID, 0, 0, w, h, radius );
}


function stackBlurCanvasRGBA( id, top_x, top_y, width, height, radius )
{
	if ( isNaN(radius) || radius < 1 ) return;
	radius |= 0;
	
	var canvas  = document.getElementById( id );
	var context = canvas.getContext("2d");
	var imageData;
	
	try {
	  try {
		imageData = context.getImageData( top_x, top_y, width, height );
	  } catch(e) {
	  
		// NOTE: this part is supposedly only needed if you want to work with local files
		// so it might be okay to remove the whole try/catch block and just use
		// imageData = context.getImageData( top_x, top_y, width, height );
		try {
			netscape.security.PrivilegeManager.enablePrivilege("UniversalBrowserRead");
			imageData = context.getImageData( top_x, top_y, width, height );
		} catch(e) {
			alert("Cannot access local image");
			throw new Error("unable to access local image data: " + e);
			return;
		}
	  }
	} catch(e) {
	  alert("Cannot access image");
	  throw new Error("unable to access image data: " + e);
	}
			
	var pixels = imageData.data;
			
	var x, y, i, p, yp, yi, yw, r_sum, g_sum, b_sum, a_sum, 
	r_out_sum, g_out_sum, b_out_sum, a_out_sum,
	r_in_sum, g_in_sum, b_in_sum, a_in_sum, 
	pr, pg, pb, pa, rbs;
			
	var div = radius + radius + 1;
	var w4 = width << 2;
	var widthMinus1  = width - 1;
	var heightMinus1 = height - 1;
	var radiusPlus1  = radius + 1;
	var sumFactor = radiusPlus1 * ( radiusPlus1 + 1 ) / 2;
	
	var stackStart = new BlurStack();
	var stack = stackStart;
	for ( i = 1; i < div; i++ )
	{
		stack = stack.next = new BlurStack();
		if ( i == radiusPlus1 ) var stackEnd = stack;
	}
	stack.next = stackStart;
	var stackIn = null;
	var stackOut = null;
	
	yw = yi = 0;
	
	var mul_sum = mul_table[radius];
	var shg_sum = shg_table[radius];
	
	for ( y = 0; y < height; y++ )
	{
		r_in_sum = g_in_sum = b_in_sum = a_in_sum = r_sum = g_sum = b_sum = a_sum = 0;
		
		r_out_sum = radiusPlus1 * ( pr = pixels[yi] );
		g_out_sum = radiusPlus1 * ( pg = pixels[yi+1] );
		b_out_sum = radiusPlus1 * ( pb = pixels[yi+2] );
		a_out_sum = radiusPlus1 * ( pa = pixels[yi+3] );
		
		r_sum += sumFactor * pr;
		g_sum += sumFactor * pg;
		b_sum += sumFactor * pb;
		a_sum += sumFactor * pa;
		
		stack = stackStart;
		
		for( i = 0; i < radiusPlus1; i++ )
		{
			stack.r = pr;
			stack.g = pg;
			stack.b = pb;
			stack.a = pa;
			stack = stack.next;
		}
		
		for( i = 1; i < radiusPlus1; i++ )
		{
			p = yi + (( widthMinus1 < i ? widthMinus1 : i ) << 2 );
			r_sum += ( stack.r = ( pr = pixels[p])) * ( rbs = radiusPlus1 - i );
			g_sum += ( stack.g = ( pg = pixels[p+1])) * rbs;
			b_sum += ( stack.b = ( pb = pixels[p+2])) * rbs;
			a_sum += ( stack.a = ( pa = pixels[p+3])) * rbs;
			
			r_in_sum += pr;
			g_in_sum += pg;
			b_in_sum += pb;
			a_in_sum += pa;
			
			stack = stack.next;
		}
		
		
		stackIn = stackStart;
		stackOut = stackEnd;
		for ( x = 0; x < width; x++ )
		{
			pixels[yi+3] = pa = (a_sum * mul_sum) >> shg_sum;
			if ( pa != 0 )
			{
				pa = 255 / pa;
				pixels[yi]   = ((r_sum * mul_sum) >> shg_sum) * pa;
				pixels[yi+1] = ((g_sum * mul_sum) >> shg_sum) * pa;
				pixels[yi+2] = ((b_sum * mul_sum) >> shg_sum) * pa;
			} else {
				pixels[yi] = pixels[yi+1] = pixels[yi+2] = 0;
			}
			
			r_sum -= r_out_sum;
			g_sum -= g_out_sum;
			b_sum -= b_out_sum;
			a_sum -= a_out_sum;
			
			r_out_sum -= stackIn.r;
			g_out_sum -= stackIn.g;
			b_out_sum -= stackIn.b;
			a_out_sum -= stackIn.a;
			
			p =  ( yw + ( ( p = x + radius + 1 ) < widthMinus1 ? p : widthMinus1 ) ) << 2;
			
			r_in_sum += ( stackIn.r = pixels[p]);
			g_in_sum += ( stackIn.g = pixels[p+1]);
			b_in_sum += ( stackIn.b = pixels[p+2]);
			a_in_sum += ( stackIn.a = pixels[p+3]);
			
			r_sum += r_in_sum;
			g_sum += g_in_sum;
			b_sum += b_in_sum;
			a_sum += a_in_sum;
			
			stackIn = stackIn.next;
			
			r_out_sum += ( pr = stackOut.r );
			g_out_sum += ( pg = stackOut.g );
			b_out_sum += ( pb = stackOut.b );
			a_out_sum += ( pa = stackOut.a );
			
			r_in_sum -= pr;
			g_in_sum -= pg;
			b_in_sum -= pb;
			a_in_sum -= pa;
			
			stackOut = stackOut.next;

			yi += 4;
		}
		yw += width;
	}

	
	for ( x = 0; x < width; x++ )
	{
		g_in_sum = b_in_sum = a_in_sum = r_in_sum = g_sum = b_sum = a_sum = r_sum = 0;
		
		yi = x << 2;
		r_out_sum = radiusPlus1 * ( pr = pixels[yi]);
		g_out_sum = radiusPlus1 * ( pg = pixels[yi+1]);
		b_out_sum = radiusPlus1 * ( pb = pixels[yi+2]);
		a_out_sum = radiusPlus1 * ( pa = pixels[yi+3]);
		
		r_sum += sumFactor * pr;
		g_sum += sumFactor * pg;
		b_sum += sumFactor * pb;
		a_sum += sumFactor * pa;
		
		stack = stackStart;
		
		for( i = 0; i < radiusPlus1; i++ )
		{
			stack.r = pr;
			stack.g = pg;
			stack.b = pb;
			stack.a = pa;
			stack = stack.next;
		}
		
		yp = width;
		
		for( i = 1; i <= radius; i++ )
		{
			yi = ( yp + x ) << 2;
			
			r_sum += ( stack.r = ( pr = pixels[yi])) * ( rbs = radiusPlus1 - i );
			g_sum += ( stack.g = ( pg = pixels[yi+1])) * rbs;
			b_sum += ( stack.b = ( pb = pixels[yi+2])) * rbs;
			a_sum += ( stack.a = ( pa = pixels[yi+3])) * rbs;
		   
			r_in_sum += pr;
			g_in_sum += pg;
			b_in_sum += pb;
			a_in_sum += pa;
			
			stack = stack.next;
		
			if( i < heightMinus1 )
			{
				yp += width;
			}
		}
		
		yi = x;
		stackIn = stackStart;
		stackOut = stackEnd;
		for ( y = 0; y < height; y++ )
		{
			p = yi << 2;
			pixels[p+3] = pa = (a_sum * mul_sum) >> shg_sum;
			if ( pa > 0 )
			{
				pa = 255 / pa;
				pixels[p]   = ((r_sum * mul_sum) >> shg_sum ) * pa;
				pixels[p+1] = ((g_sum * mul_sum) >> shg_sum ) * pa;
				pixels[p+2] = ((b_sum * mul_sum) >> shg_sum ) * pa;
			} else {
				pixels[p] = pixels[p+1] = pixels[p+2] = 0;
			}
			
			r_sum -= r_out_sum;
			g_sum -= g_out_sum;
			b_sum -= b_out_sum;
			a_sum -= a_out_sum;
		   
			r_out_sum -= stackIn.r;
			g_out_sum -= stackIn.g;
			b_out_sum -= stackIn.b;
			a_out_sum -= stackIn.a;
			
			p = ( x + (( ( p = y + radiusPlus1) < heightMinus1 ? p : heightMinus1 ) * width )) << 2;
			
			r_sum += ( r_in_sum += ( stackIn.r = pixels[p]));
			g_sum += ( g_in_sum += ( stackIn.g = pixels[p+1]));
			b_sum += ( b_in_sum += ( stackIn.b = pixels[p+2]));
			a_sum += ( a_in_sum += ( stackIn.a = pixels[p+3]));
		   
			stackIn = stackIn.next;
			
			r_out_sum += ( pr = stackOut.r );
			g_out_sum += ( pg = stackOut.g );
			b_out_sum += ( pb = stackOut.b );
			a_out_sum += ( pa = stackOut.a );
			
			r_in_sum -= pr;
			g_in_sum -= pg;
			b_in_sum -= pb;
			a_in_sum -= pa;
			
			stackOut = stackOut.next;
			
			yi += width;
		}
	}
	
	context.putImageData( imageData, top_x, top_y );
	
}


function stackBlurCanvasRGB( id, top_x, top_y, width, height, radius )
{
	if ( isNaN(radius) || radius < 1 ) return;
	radius |= 0;
	
	var canvas  = document.getElementById( id );
	var context = canvas.getContext("2d");
	var imageData;
	
	try {
	  try {
		imageData = context.getImageData( top_x, top_y, width, height );
	  } catch(e) {
	  
		// NOTE: this part is supposedly only needed if you want to work with local files
		// so it might be okay to remove the whole try/catch block and just use
		// imageData = context.getImageData( top_x, top_y, width, height );
		try {
			netscape.security.PrivilegeManager.enablePrivilege("UniversalBrowserRead");
			imageData = context.getImageData( top_x, top_y, width, height );
		} catch(e) {
			alert("Cannot access local image");
			throw new Error("unable to access local image data: " + e);
			return;
		}
	  }
	} catch(e) {
	  alert("Cannot access image");
	  throw new Error("unable to access image data: " + e);
	}
			
	var pixels = imageData.data;
			
	var x, y, i, p, yp, yi, yw, r_sum, g_sum, b_sum,
	r_out_sum, g_out_sum, b_out_sum,
	r_in_sum, g_in_sum, b_in_sum,
	pr, pg, pb, rbs;
			
	var div = radius + radius + 1;
	var w4 = width << 2;
	var widthMinus1  = width - 1;
	var heightMinus1 = height - 1;
	var radiusPlus1  = radius + 1;
	var sumFactor = radiusPlus1 * ( radiusPlus1 + 1 ) / 2;
	
	var stackStart = new BlurStack();
	var stack = stackStart;
	for ( i = 1; i < div; i++ )
	{
		stack = stack.next = new BlurStack();
		if ( i == radiusPlus1 ) var stackEnd = stack;
	}
	stack.next = stackStart;
	var stackIn = null;
	var stackOut = null;
	
	yw = yi = 0;
	
	var mul_sum = mul_table[radius];
	var shg_sum = shg_table[radius];
	
	for ( y = 0; y < height; y++ )
	{
		r_in_sum = g_in_sum = b_in_sum = r_sum = g_sum = b_sum = 0;
		
		r_out_sum = radiusPlus1 * ( pr = pixels[yi] );
		g_out_sum = radiusPlus1 * ( pg = pixels[yi+1] );
		b_out_sum = radiusPlus1 * ( pb = pixels[yi+2] );
		
		r_sum += sumFactor * pr;
		g_sum += sumFactor * pg;
		b_sum += sumFactor * pb;
		
		stack = stackStart;
		
		for( i = 0; i < radiusPlus1; i++ )
		{
			stack.r = pr;
			stack.g = pg;
			stack.b = pb;
			stack = stack.next;
		}
		
		for( i = 1; i < radiusPlus1; i++ )
		{
			p = yi + (( widthMinus1 < i ? widthMinus1 : i ) << 2 );
			r_sum += ( stack.r = ( pr = pixels[p])) * ( rbs = radiusPlus1 - i );
			g_sum += ( stack.g = ( pg = pixels[p+1])) * rbs;
			b_sum += ( stack.b = ( pb = pixels[p+2])) * rbs;
			
			r_in_sum += pr;
			g_in_sum += pg;
			b_in_sum += pb;
			
			stack = stack.next;
		}
		
		
		stackIn = stackStart;
		stackOut = stackEnd;
		for ( x = 0; x < width; x++ )
		{
			pixels[yi]   = (r_sum * mul_sum) >> shg_sum;
			pixels[yi+1] = (g_sum * mul_sum) >> shg_sum;
			pixels[yi+2] = (b_sum * mul_sum) >> shg_sum;
			
			r_sum -= r_out_sum;
			g_sum -= g_out_sum;
			b_sum -= b_out_sum;
			
			r_out_sum -= stackIn.r;
			g_out_sum -= stackIn.g;
			b_out_sum -= stackIn.b;
			
			p =  ( yw + ( ( p = x + radius + 1 ) < widthMinus1 ? p : widthMinus1 ) ) << 2;
			
			r_in_sum += ( stackIn.r = pixels[p]);
			g_in_sum += ( stackIn.g = pixels[p+1]);
			b_in_sum += ( stackIn.b = pixels[p+2]);
			
			r_sum += r_in_sum;
			g_sum += g_in_sum;
			b_sum += b_in_sum;
			
			stackIn = stackIn.next;
			
			r_out_sum += ( pr = stackOut.r );
			g_out_sum += ( pg = stackOut.g );
			b_out_sum += ( pb = stackOut.b );
			
			r_in_sum -= pr;
			g_in_sum -= pg;
			b_in_sum -= pb;
			
			stackOut = stackOut.next;

			yi += 4;
		}
		yw += width;
	}

	
	for ( x = 0; x < width; x++ )
	{
		g_in_sum = b_in_sum = r_in_sum = g_sum = b_sum = r_sum = 0;
		
		yi = x << 2;
		r_out_sum = radiusPlus1 * ( pr = pixels[yi]);
		g_out_sum = radiusPlus1 * ( pg = pixels[yi+1]);
		b_out_sum = radiusPlus1 * ( pb = pixels[yi+2]);
		
		r_sum += sumFactor * pr;
		g_sum += sumFactor * pg;
		b_sum += sumFactor * pb;
		
		stack = stackStart;
		
		for( i = 0; i < radiusPlus1; i++ )
		{
			stack.r = pr;
			stack.g = pg;
			stack.b = pb;
			stack = stack.next;
		}
		
		yp = width;
		
		for( i = 1; i <= radius; i++ )
		{
			yi = ( yp + x ) << 2;
			
			r_sum += ( stack.r = ( pr = pixels[yi])) * ( rbs = radiusPlus1 - i );
			g_sum += ( stack.g = ( pg = pixels[yi+1])) * rbs;
			b_sum += ( stack.b = ( pb = pixels[yi+2])) * rbs;
			
			r_in_sum += pr;
			g_in_sum += pg;
			b_in_sum += pb;
			
			stack = stack.next;
		
			if( i < heightMinus1 )
			{
				yp += width;
			}
		}
		
		yi = x;
		stackIn = stackStart;
		stackOut = stackEnd;
		for ( y = 0; y < height; y++ )
		{
			p = yi << 2;
			pixels[p]   = (r_sum * mul_sum) >> shg_sum;
			pixels[p+1] = (g_sum * mul_sum) >> shg_sum;
			pixels[p+2] = (b_sum * mul_sum) >> shg_sum;
			
			r_sum -= r_out_sum;
			g_sum -= g_out_sum;
			b_sum -= b_out_sum;
			
			r_out_sum -= stackIn.r;
			g_out_sum -= stackIn.g;
			b_out_sum -= stackIn.b;
			
			p = ( x + (( ( p = y + radiusPlus1) < heightMinus1 ? p : heightMinus1 ) * width )) << 2;
			
			r_sum += ( r_in_sum += ( stackIn.r = pixels[p]));
			g_sum += ( g_in_sum += ( stackIn.g = pixels[p+1]));
			b_sum += ( b_in_sum += ( stackIn.b = pixels[p+2]));
			
			stackIn = stackIn.next;
			
			r_out_sum += ( pr = stackOut.r );
			g_out_sum += ( pg = stackOut.g );
			b_out_sum += ( pb = stackOut.b );
			
			r_in_sum -= pr;
			g_in_sum -= pg;
			b_in_sum -= pb;
			
			stackOut = stackOut.next;
			
			yi += width;
		}
	}
	
	context.putImageData( imageData, top_x, top_y );
	
}

function BlurStack()
{
	this.r = 0;
	this.g = 0;
	this.b = 0;
	this.a = 0;
	this.next = null;
}

data.simple.js

var tracks = [
	      { trackName: "track1",
		trackType: "stranded",
		visible: true,
		inner_radius: 130,
		outer_radius: 185,
		trackFeatures: "complex",
		featureThreshold: 7000000,
		mouseclick: 'islandPopup',
		mouseover_callback: 'islandPopup',
		mouseout_callback: 'islandPopupClear',
		linear_mouseclick: 'linearPopup',
		showLabels: true,
		showTooltip: true,
		linear_mouseclick: 'linearClick',
		items: [
                         {id: 1, start:0, end:30000, name:"island0", strand: -1},
                         {id: 2, start:60000,end:100000, name:"island1", strand: -1},
                         {id: 3, start:800000,end:1000000, name:"island with a very long name", strand: 1},
                         {id: 7, start:1000000,end:1200000, name:"intergenic", strand: 0},
                         {id: 4, start:1200000,end:1500000, name:"island3", strand: 1},
                         {id: 5, start:1500000,end:1700000, name:"island4",strand: -1, extraclass: "cellwall"},
                         {id: 6, start:2000000,end:2100000, name:"the tasty gene", strand: -1, extraclass: "innermembrane"},
                         {id: 5, start:4500000,end:4700000, name:"an interesting region",strand: -1, extraclass: "cellwall"},
                         {id: 6, start:5000000,end:5100000, name:"causes bad things", strand: 1, extraclass: "innermembrane"},
                         {id: 7, start:5100000,end:5300000, name:"cures bad hair days", strand: -1, extraclass: "extracelluar"},
                         {id: 8, start:100000,end:115000, name:"cheeky gene", strand: 1, extraclass: "outermembrane"},
                         {id: 9, start:3000000,end:3100000, name:"meow meow", strand: 1, extraclass: "innermembrane"},
                         {id: 10, start:120000,end:136000, name:"turtle power", strand: -1, extraclass: "extrashelluar"},
                         {id: 11, start:3200000,end:3300000, name:"out of ideas", strand: -1, extraclass: "lostinspace"},

			]
	      },
	      { trackName: "track2",
		visible: true,
		trackType: "stranded",
		inner_radius: 215,
		outer_radius: 265,
		centre_line_stroke: "grey",
		showLabels: true,

		items: [
{id: 1, start:483, end:2027, name:"PA0001", strand:1},
{id: 2, start:2056, end:3159, name:"PA0002", strand:1},
{id: 3, start:3169, end:4278, name:"PA0003", strand:1},
{id: 4, start:4275, end:6695, name:"PA0004", strand:1},
{id: 5, start:7018, end:7791, name:"PA0005", strand:-1},
{id: 6, start:7803, end:8339, name:"PA0006", strand:-1},
{id: 7, start:8671, end:10377, name:"PA0007", strand:1},
{id: 8, start:10434, end:12488, name:"PA0008", strand:-1},
{id: 9, start:12488, end:13435, name:"PA0009", strand:-1},
{id: 10, start:13540, end:14091, name:"PA0010", strand:1},
{id: 11, start:14235, end:15122, name:"PA0011", strand:1},
{id: 12, start:15207, end:15473, name:"PA0012", strand:1},
{id: 13, start:15620, end:16273, name:"PA0013", strand:1},
{id: 14, start:16335, end:16607, name:"PA0014", strand:-1},
{id: 15, start:16900, end:17217, name:"PA0015", strand:-1},
{id: 16, start:17366, end:18739, name:"PA0016", strand:-1},
{id: 17, start:18767, end:20071, name:"PA0017", strand:-1},
{id: 18, start:20068, end:21012, name:"PA0018", strand:-1},
{id: 19, start:21067, end:21573, name:"PA0019", strand:-1},
{id: 20, start:21712, end:22737, name:"PA0020", strand:1},
{id: 21, start:22872, end:23960, name:"PA0021", strand:1},
{id: 22, start:24001, end:24558, name:"PA0022", strand:1},
{id: 23, start:24568, end:25545, name:"PA0023", strand:-1},
{id: 24, start:25736, end:26653, name:"PA0024", strand:1},
{id: 25, start:26711, end:27535, name:"PA0025", strand:1},
{id: 26, start:27646, end:28632, name:"PA0026", strand:1},
{id: 27, start:28613, end:29899, name:"PA0027", strand:1},
{id: 28, start:29896, end:30498, name:"PA0028", strand:1},
{id: 29, start:30502, end:32055, name:"PA0029", strand:-1},
{id: 30, start:32060, end:32983, name:"PA0030", strand:-1},
{id: 31, start:33000, end:34511, name:"PA0031", strand:-1},
{id: 32, start:34624, end:35538, name:"PA0032", strand:1},
{id: 33, start:35905, end:36270, name:"PA0033", strand:-1},
{id: 34, start:36278, end:36901, name:"PA0034", strand:-1},
{id: 35, start:37087, end:37893, name:"PA0035", strand:-1},
{id: 36, start:37890, end:39098, name:"PA0036", strand:-1},
{id: 37, start:39202, end:40089, name:"PA0037", strand:1},
{id: 38, start:40190, end:40405, name:"PA0038", strand:1},
{id: 39, start:40589, end:40816, name:"PA0039", strand:1},
{id: 40, start:41113, end:42801, name:"PA0040", strand:1},
{id: 41, start:42914, end:53521, name:"PA0041", strand:1},
{id: 42, start:56546, end:56941, name:"PA0042", strand:1},
{id: 43, start:57212, end:58594, name:"PA0043", strand:-1},
{id: 44, start:58786, end:60159, name:"PA0044", strand:1},
{id: 45, start:60656, end:61342, name:"PA0045", strand:1},
{id: 46, start:61373, end:61726, name:"PA0046", strand:1},
{id: 47, start:61879, end:62388, name:"PA0047", strand:1},
{id: 48, start:62403, end:62786, name:"PA0048", strand:-1},
{id: 49, start:63068, end:64729, name:"PA0049", strand:-1},
{id: 50, start:65339, end:65479, name:"PA0050", strand:1},
{id: 51, start:66303, end:68135, name:"PA0051", strand:1},
{id: 52, start:68188, end:68616, name:"PA0052", strand:-1},
{id: 53, start:69272, end:69526, name:"PA0053", strand:1},
{id: 54, start:69543, end:70091, name:"PA0054", strand:-1},
{id: 55, start:70130, end:70636, name:"PA0055", strand:-1},
{id: 56, start:70702, end:71622, name:"PA0056", strand:-1},
{id: 57, start:71730, end:72617, name:"PA0057", strand:1},
{id: 58, start:72680, end:73384, name:"PA0058", strand:1},
{id: 59, start:73468, end:73923, name:"PA0059", strand:1},
{id: 60, start:74034, end:74267, name:"PA0060", strand:1},
{id: 61, start:74279, end:74716, name:"PA0061", strand:-1},
{id: 62, start:74773, end:75189, name:"PA0062", strand:-1},
{id: 63, start:75281, end:76408, name:"PA0063", strand:1},
{id: 64, start:76416, end:77399, name:"PA0064", strand:-1},
{id: 65, start:77432, end:78097, name:"PA0065", strand:-1},
{id: 66, start:78090, end:78632, name:"PA0066", strand:-1},
{id: 67, start:78710, end:80755, name:"PA0067", strand:1},
{id: 68, start:80752, end:81027, name:"PA0068", strand:1},
{id: 69, start:81116, end:82174, name:"PA0069", strand:1},
{id: 70, start:82404, end:83318, name:"PA0070", strand:-1},
{id: 71, start:83380, end:85092, name:"PA0071", strand:-1},
{id: 72, start:85085, end:86284, name:"PA0072", strand:-1},
{id: 73, start:86284, end:87003, name:"PA0073", strand:-1},
{id: 74, start:87000, end:90098, name:"PA0074", strand:-1},
{id: 75, start:90106, end:90834, name:"PA0075", strand:-1},
{id: 76, start:90844, end:91524, name:"PA0076", strand:-1},
{id: 77, start:91521, end:94826, name:"PA0077", strand:-1},
{id: 78, start:95048, end:96397, name:"PA0078", strand:-1},
{id: 79, start:96404, end:97738, name:"PA0079", strand:-1},
{id: 80, start:97754, end:98218, name:"PA0080", strand:-1},
{id: 81, start:98263, end:99756, name:"PA0081", strand:-1},
{id: 82, start:100124, end:101158, name:"PA0082", strand:1},
{id: 83, start:101247, end:101765, name:"PA0083", strand:1},
{id: 84, start:101778, end:103274, name:"PA0084", strand:1},
{id: 85, start:103350, end:103838, name:"PA0085", strand:1},
{id: 86, start:104006, end:104851, name:"PA0086", strand:1},
{id: 87, start:104853, end:105362, name:"PA0087", strand:1},
{id: 88, start:105359, end:107218, name:"PA0088", strand:1},
{id: 89, start:107182, end:108228, name:"PA0089", strand:1},
{id: 90, start:108221, end:110929, name:"PA0090", strand:1},
{id: 91, start:110976, end:112907, name:"PA0091", strand:1},
{id: 92, start:113022, end:113306, name:"PA0092", strand:-1},
{id: 93, start:113303, end:114595, name:"PA0093", strand:-1},
{id: 94, start:114611, end:115045, name:"PA0094", strand:-1},
{id: 95, start:115299, end:117524, name:"PA0095", strand:1},
{id: 96, start:117552, end:118001, name:"PA0096", strand:1},
{id: 97, start:117931, end:119130, name:"PA0097", strand:1},
{id: 98, start:119127, end:120164, name:"PA0098", strand:1},
{id: 99, start:120164, end:121324, name:"PA0099", strand:1},
{id: 100, start:121346, end:122266, name:"PA0100", strand:1},
{id: 101, start:122248, end:123495, name:"PA0101", strand:1},
{id: 102, start:123871, end:124599, name:"PA0102", strand:1},
{id: 103, start:124810, end:126381, name:"PA0103", strand:1},
{id: 104, start:126518, end:127114, name:"PA0104", strand:1},
{id: 105, start:127378, end:128502, name:"PA0105", strand:1},
{id: 106, start:128512, end:130104, name:"PA0106", strand:1},
{id: 107, start:130115, end:130669, name:"PA0107", strand:1},
{id: 108, start:130680, end:131567, name:"PA0108", strand:1},
{id: 109, start:131583, end:131792, name:"PA0109", strand:-1},
{id: 110, start:131808, end:132602, name:"PA0110", strand:1},
{id: 111, start:132577, end:133155, name:"PA0111", strand:1},
{id: 112, start:133220, end:134293, name:"PA0112", strand:1},
{id: 113, start:134319, end:135233, name:"PA0113", strand:1},
{id: 114, start:135259, end:135894, name:"PA0114", strand:1},
{id: 115, start:135934, end:136386, name:"PA0115", strand:-1},
{id: 116, start:136518, end:136991, name:"PA0116", strand:1},
{id: 117, start:137248, end:137976, name:"PA0117", strand:1},
{id: 118, start:138001, end:138588, name:"PA0118", strand:1},
{id: 119, start:138818, end:140167, name:"PA0119", strand:1},
{id: 120, start:140216, end:140902, name:"PA0120", strand:1},
{id: 121, start:141003, end:141737, name:"PA0121", strand:1},
{id: 122, start:141917, end:142327, name:"PA0122", strand:1},
{id: 123, start:142359, end:143267, name:"PA0123", strand:-1},
{id: 124, start:143567, end:143848, name:"PA0124", strand:-1},
{id: 125, start:143845, end:144072, name:"PA0125", strand:-1},
{id: 126, start:144248, end:144868, name:"PA0126", strand:-1},
{id: 127, start:144969, end:145469, name:"PA0127", strand:1},
{id: 128, start:145542, end:145883, name:"PA0128", strand:1},
{id: 129, start:145965, end:147392, name:"PA0129", strand:-1},
{id: 130, start:147561, end:149054, name:"PA0130", strand:-1},
{id: 131, start:149138, end:149425, name:"PA0131", strand:-1},
{id: 132, start:149425, end:150771, name:"PA0132", strand:-1},
{id: 133, start:150906, end:151823, name:"PA0133", strand:1},
{id: 134, start:151936, end:153306, name:"PA0134", strand:-1},
{id: 135, start:153696, end:153836, name:"PA0135", strand:1},
{id: 136, start:154417, end:155988, name:"PA0136", strand:1},
{id: 137, start:155988, end:157085, name:"PA0137", strand:1},
{id: 138, start:157108, end:158034, name:"PA0138", strand:1},
{id: 139, start:158199, end:158762, name:"PA0139", strand:1},
{id: 140, start:158907, end:160472, name:"PA0140", strand:1},
{id: 141, start:160552, end:161448, name:"PA0141", strand:-1},
{id: 142, start:161906, end:163255, name:"PA0142", strand:1},
{id: 143, start:163363, end:164415, name:"PA0143", strand:1},
{id: 144, start:164443, end:165069, name:"PA0144", strand:-1},
{id: 145, start:165219, end:165737, name:"PA0145", strand:-1},
{id: 146, start:165976, end:167073, name:"PA0146", strand:1},
{id: 147, start:167146, end:168108, name:"PA0147", strand:1},
{id: 148, start:168213, end:169163, name:"PA0148", strand:1},
{id: 149, start:169361, end:169906, name:"PA0149", strand:1},
{id: 150, start:169903, end:170898, name:"PA0150", strand:1},
{id: 151, start:171047, end:173434, name:"PA0151", strand:1},
{id: 152, start:173811, end:174638, name:"PA0152", strand:1},
{id: 153, start:174773, end:175492, name:"PA0153", strand:1},
{id: 154, start:175503, end:176108, name:"PA0154", strand:1},
{id: 155, start:176315, end:177154, name:"PA0155", strand:1},
{id: 156, start:177307, end:178458, name:"PA0156", strand:1},
{id: 157, start:178455, end:179525, name:"PA0157", strand:1},
{id: 158, start:179522, end:182569, name:"PA0158", strand:1},
{id: 159, start:182768, end:183706, name:"PA0159", strand:1},
{id: 160, start:183822, end:184007, name:"PA0160", strand:1},
{id: 161, start:184287, end:184439, name:"PA0161", strand:1},
{id: 162, start:184594, end:185928, name:"PA0162", strand:1},
{id: 163, start:185957, end:186754, name:"PA0163", strand:-1},
{id: 164, start:186832, end:188448, name:"PA0164", strand:1},
{id: 165, start:189120, end:189956, name:"PA0165", strand:1},
{id: 166, start:190198, end:191604, name:"PA0166", strand:1},
{id: 167, start:191697, end:192362, name:"PA0167", strand:1},
{id: 168, start:192368, end:192958, name:"PA0168", strand:1},
{id: 169, start:192965, end:193672, name:"PA0169", strand:-1},
{id: 170, start:193799, end:194179, name:"PA0170", strand:-1},
{id: 171, start:194206, end:194748, name:"PA0171", strand:-1},
{id: 172, start:194757, end:196748, name:"PA0172", strand:-1},
{id: 173, start:197011, end:198060, name:"PA0173", strand:-1},
{id: 174, start:198080, end:198682, name:"PA0174", strand:-1},
{id: 175, start:198688, end:199530, name:"PA0175", strand:-1},
{id: 176, start:199600, end:201639, name:"PA0176", strand:-1},
{id: 177, start:201675, end:202160, name:"PA0177", strand:-1},
{id: 178, start:202147, end:204066, name:"PA0178", strand:-1},
{id: 179, start:204094, end:204459, name:"PA0179", strand:-1},
{id: 180, start:204657, end:205829, name:"PA0180", strand:-1},
{id: 181, start:206022, end:206954, name:"PA0181", strand:-1},
{id: 182, start:207071, end:207823, name:"PA0182", strand:1},
{id: 183, start:207923, end:209533, name:"PA0183", strand:-1},
{id: 184, start:209621, end:210460, name:"PA0184", strand:-1},
{id: 185, start:210457, end:212073, name:"PA0185", strand:-1},
{id: 186, start:212340, end:213401, name:"PA0186", strand:1},
{id: 187, start:213819, end:214634, name:"PA0187", strand:1},
{id: 188, start:214631, end:215512, name:"PA0188", strand:1},
{id: 189, start:215550, end:216908, name:"PA0189", strand:-1},
{id: 190, start:217156, end:217881, name:"PA0190", strand:1},
{id: 191, start:217905, end:218822, name:"PA0191", strand:-1},
{id: 192, start:219172, end:221544, name:"PA0192", strand:1},
{id: 193, start:221585, end:222487, name:"PA0193", strand:1},
{id: 194, start:222555, end:223454, name:"PA0194", strand:1},
{id: 195, start:224101, end:225219, name:"PA0195", strand:1},
{id: 196, start:225295, end:225603, name:"PA0195.1", strand:1},
{id: 197, start:225603, end:227039, name:"PA0196", strand:1},
{id: 198, start:227382, end:228194, name:"PA0197", strand:1},
{id: 199, start:228223, end:228942, name:"PA0198", strand:1},
{id: 200, start:228944, end:229345, name:"PA0199", strand:1},
{id: 201, start:229526, end:229738, name:"PA0200", strand:-1},
{id: 202, start:229954, end:230535, name:"PA0201", strand:1},
{id: 203, start:230543, end:232000, name:"PA0202", strand:-1},
{id: 204, start:232066, end:233100, name:"PA0203", strand:-1},
{id: 205, start:233123, end:233932, name:"PA0204", strand:-1},
{id: 206, start:233929, end:234849, name:"PA0205", strand:-1},
{id: 207, start:234875, end:235987, name:"PA0206", strand:-1},
{id: 208, start:236218, end:237111, name:"PA0207", strand:1},
{id: 209, start:237232, end:238896, name:"PA0208", strand:1},
{id: 210, start:238896, end:239777, name:"PA0209", strand:1},
{id: 211, start:239779, end:240078, name:"PA0210", strand:1},
{id: 212, start:240071, end:240934, name:"PA0211", strand:1},
{id: 213, start:240931, end:241737, name:"PA0212", strand:1},
{id: 214, start:241753, end:242445, name:"PA0213", strand:1},
{id: 215, start:242442, end:243374, name:"PA0214", strand:1},
{id: 216, start:243431, end:243835, name:"PA0215", strand:1},
{id: 217, start:243841, end:244605, name:"PA0216", strand:1},
{id: 218, start:244690, end:245619, name:"PA0217", strand:-1},
{id: 219, start:245948, end:246868, name:"PA0218", strand:-1},
{id: 220, start:247219, end:248709, name:"PA0219", strand:1},
{id: 221, start:248767, end:250200, name:"PA0220", strand:1},
{id: 222, start:250231, end:251613, name:"PA0221", strand:1},
{id: 223, start:251777, end:252835, name:"PA0222", strand:1},
{id: 224, start:252913, end:253794, name:"PA0223", strand:-1},
{id: 225, start:253854, end:254636, name:"PA0224", strand:-1},
{id: 226, start:254791, end:255330, name:"PA0225", strand:1},
{id: 227, start:255481, end:256332, name:"PA0226", strand:1},
{id: 228, start:256329, end:257111, name:"PA0227", strand:1},
{id: 229, start:257108, end:258313, name:"PA0228", strand:1},
{id: 230, start:258463, end:259761, name:"PA0229", strand:1},
{id: 231, start:259784, end:261163, name:"PA0230", strand:1},
{id: 232, start:261179, end:261970, name:"PA0231", strand:1},
{id: 233, start:261981, end:262382, name:"PA0232", strand:1},
{id: 234, start:262557, end:263498, name:"PA0233", strand:1},
{id: 235, start:263689, end:264522, name:"PA0234", strand:1},
{id: 236, start:264964, end:266310, name:"PA0235", strand:-1},
{id: 237, start:266616, end:267395, name:"PA0236", strand:1},
{id: 238, start:267638, end:268681, name:"PA0237", strand:1},
{id: 239, start:268704, end:269519, name:"PA0238", strand:1},
{id: 240, start:269669, end:270547, name:"PA0239", strand:1},
{id: 241, start:270573, end:271838, name:"PA0240", strand:-1},
{id: 242, start:271904, end:273229, name:"PA0241", strand:-1},
{id: 243, start:273775, end:275679, name:"PA0242", strand:1},
{id: 244, start:275772, end:276440, name:"PA0243", strand:1},
{id: 245, start:276480, end:277334, name:"PA0244", strand:-1},
{id: 246, start:277331, end:277777, name:"PA0245", strand:-1},
{id: 247, start:277894, end:279399, name:"PA0246", strand:-1},
{id: 248, start:279574, end:280758, name:"PA0247", strand:-1},
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{id: 3004, start:3359269, end:3360654, name:"PA3001", strand:-1},
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{id: 3006, start:3364332, end:3364961, name:"PA3003", strand:1},
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{id: 3009, start:3366970, end:3367671, name:"PA3006", strand:-1},
{id: 3010, start:3367903, end:3368517, name:"PA3007", strand:1},
{id: 3011, start:3368529, end:3369014, name:"PA3008", strand:1},
{id: 3012, start:3369036, end:3369269, name:"PA3009", strand:-1},
{id: 3013, start:3369475, end:3369993, name:"PA3010", strand:-1},
{id: 3014, start:3370100, end:3372706, name:"PA3011", strand:-1},
{id: 3015, start:3372797, end:3373171, name:"PA3012", strand:-1},
{id: 3016, start:3373254, end:3374429, name:"PA3013", strand:-1},
{id: 3017, start:3374460, end:3376607, name:"PA3014", strand:-1},
{id: 3018, start:3377035, end:3377853, name:"PA3015", strand:1},
{id: 3019, start:3377870, end:3378304, name:"PA3016", strand:-1},
{id: 3020, start:3378512, end:3378949, name:"PA3017", strand:1},
{id: 3021, start:3378979, end:3379665, name:"PA3018", strand:-1},
{id: 3022, start:3379815, end:3381737, name:"PA3019", strand:-1},
{id: 3023, start:3381963, end:3383891, name:"PA3020", strand:1},
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{id: 3026, start:3385287, end:3386195, name:"PA

linearbrush.js

linearplot.js

rgbcolor.js