├── FileSaver
    ├── FileSaver.js
    ├── LICENSE.md
    ├── README.md
    ├── bower.json
    ├── demo
    │   ├── demo.css
    │   ├── demo.js
    │   ├── demo.min.js
    │   └── index.xhtml
    └── package.json
├── LICENSE
├── README.md
├── canvg
    ├── MIT-LICENSE.txt
    ├── StackBlur.js
    ├── canvg.js
    └── rgbcolor.js
├── circularplot.js
├── d3
    ├── d3-tip.js
    └── d3.min.js
├── examples
    ├── circulardemo.html
    ├── circularsample.js
    ├── combodemo.html
    ├── data.js
    ├── data.simple.js
    ├── lineardemo.html
    ├── lineardemo.js
    └── tracks.css
├── linearbrush.js
├── linearplot.js
└── prototypes
    ├── islandplot.html
    ├── islandplot.js
    ├── lineartrack.js
    └── sample.js


/FileSaver/FileSaver.js:
--------------------------------------------------------------------------------
  1 | /* FileSaver.js
  2 |  * A saveAs() FileSaver implementation.
  3 |  * 2013-10-21
  4 |  *
  5 |  * By Eli Grey, http://eligrey.com
  6 |  * License: X11/MIT
  7 |  *   See LICENSE.md
  8 |  */
  9 | 
 10 | /*global self */
 11 | /*jslint bitwise: true, regexp: true, confusion: true, es5: true, vars: true, white: true,
 12 |   plusplus: true */
 13 | 
 14 | /*! @source http://purl.eligrey.com/github/FileSaver.js/blob/master/FileSaver.js */
 15 | 
 16 | var saveAs = saveAs
 17 |   || (typeof navigator !== 'undefined' && navigator.msSaveOrOpenBlob && navigator.msSaveOrOpenBlob.bind(navigator))
 18 |   || (function(view) {
 19 | 	"use strict";
 20 | 	var
 21 | 		  doc = view.document
 22 | 		  // only get URL when necessary in case BlobBuilder.js hasn't overridden it yet
 23 | 		, get_URL = function() {
 24 | 			return view.URL || view.webkitURL || view;
 25 | 		}
 26 | 		, URL = view.URL || view.webkitURL || view
 27 | 		, save_link = doc.createElementNS("http://www.w3.org/1999/xhtml", "a")
 28 | 		, can_use_save_link =  !view.externalHost && "download" in save_link
 29 | 		, click = function(node) {
 30 | 			var event = doc.createEvent("MouseEvents");
 31 | 			event.initMouseEvent(
 32 | 				"click", true, false, view, 0, 0, 0, 0, 0
 33 | 				, false, false, false, false, 0, null
 34 | 			);
 35 | 			node.dispatchEvent(event);
 36 | 		}
 37 | 		, webkit_req_fs = view.webkitRequestFileSystem
 38 | 		, req_fs = view.requestFileSystem || webkit_req_fs || view.mozRequestFileSystem
 39 | 		, throw_outside = function (ex) {
 40 | 			(view.setImmediate || view.setTimeout)(function() {
 41 | 				throw ex;
 42 | 			}, 0);
 43 | 		}
 44 | 		, force_saveable_type = "application/octet-stream"
 45 | 		, fs_min_size = 0
 46 | 		, deletion_queue = []
 47 | 		, process_deletion_queue = function() {
 48 | 			var i = deletion_queue.length;
 49 | 			while (i--) {
 50 | 				var file = deletion_queue[i];
 51 | 				if (typeof file === "string") { // file is an object URL
 52 | 					URL.revokeObjectURL(file);
 53 | 				} else { // file is a File
 54 | 					file.remove();
 55 | 				}
 56 | 			}
 57 | 			deletion_queue.length = 0; // clear queue
 58 | 		}
 59 | 		, dispatch = function(filesaver, event_types, event) {
 60 | 			event_types = [].concat(event_types);
 61 | 			var i = event_types.length;
 62 | 			while (i--) {
 63 | 				var listener = filesaver["on" + event_types[i]];
 64 | 				if (typeof listener === "function") {
 65 | 					try {
 66 | 						listener.call(filesaver, event || filesaver);
 67 | 					} catch (ex) {
 68 | 						throw_outside(ex);
 69 | 					}
 70 | 				}
 71 | 			}
 72 | 		}
 73 | 		, FileSaver = function(blob, name) {
 74 | 			// First try a.download, then web filesystem, then object URLs
 75 | 			var
 76 | 				  filesaver = this
 77 | 				, type = blob.type
 78 | 				, blob_changed = false
 79 | 				, object_url
 80 | 				, target_view
 81 | 				, get_object_url = function() {
 82 | 					var object_url = get_URL().createObjectURL(blob);
 83 | 					deletion_queue.push(object_url);
 84 | 					return object_url;
 85 | 				}
 86 | 				, dispatch_all = function() {
 87 | 					dispatch(filesaver, "writestart progress write writeend".split(" "));
 88 | 				}
 89 | 				// on any filesys errors revert to saving with object URLs
 90 | 				, fs_error = function() {
 91 | 					// don't create more object URLs than needed
 92 | 					if (blob_changed || !object_url) {
 93 | 						object_url = get_object_url(blob);
 94 | 					}
 95 | 					if (target_view) {
 96 | 						target_view.location.href = object_url;
 97 | 					} else {
 98 |                         window.open(object_url, "_blank");
 99 |                     }
100 | 					filesaver.readyState = filesaver.DONE;
101 | 					dispatch_all();
102 | 				}
103 | 				, abortable = function(func) {
104 | 					return function() {
105 | 						if (filesaver.readyState !== filesaver.DONE) {
106 | 							return func.apply(this, arguments);
107 | 						}
108 | 					};
109 | 				}
110 | 				, create_if_not_found = {create: true, exclusive: false}
111 | 				, slice
112 | 			;
113 | 			filesaver.readyState = filesaver.INIT;
114 | 			if (!name) {
115 | 				name = "download";
116 | 			}
117 | 			if (can_use_save_link) {
118 | 				object_url = get_object_url(blob);
119 | 				// FF for Android has a nasty garbage collection mechanism
120 | 				// that turns all objects that are not pure javascript into 'deadObject'
121 | 				// this means `doc` and `save_link` are unusable and need to be recreated
122 | 				// `view` is usable though:
123 | 				doc = view.document;
124 | 				save_link = doc.createElementNS("http://www.w3.org/1999/xhtml", "a");
125 | 				save_link.href = object_url;
126 | 				save_link.download = name;
127 | 				var event = doc.createEvent("MouseEvents");
128 | 				event.initMouseEvent(
129 | 					"click", true, false, view, 0, 0, 0, 0, 0
130 | 					, false, false, false, false, 0, null
131 | 				);
132 | 				save_link.dispatchEvent(event);
133 | 				filesaver.readyState = filesaver.DONE;
134 | 				dispatch_all();
135 | 				return;
136 | 			}
137 | 			// Object and web filesystem URLs have a problem saving in Google Chrome when
138 | 			// viewed in a tab, so I force save with application/octet-stream
139 | 			// http://code.google.com/p/chromium/issues/detail?id=91158
140 | 			if (view.chrome && type && type !== force_saveable_type) {
141 | 				slice = blob.slice || blob.webkitSlice;
142 | 				blob = slice.call(blob, 0, blob.size, force_saveable_type);
143 | 				blob_changed = true;
144 | 			}
145 | 			// Since I can't be sure that the guessed media type will trigger a download
146 | 			// in WebKit, I append .download to the filename.
147 | 			// https://bugs.webkit.org/show_bug.cgi?id=65440
148 | 			if (webkit_req_fs && name !== "download") {
149 | 				name += ".download";
150 | 			}
151 | 			if (type === force_saveable_type || webkit_req_fs) {
152 | 				target_view = view;
153 | 			}
154 | 			if (!req_fs) {
155 | 				fs_error();
156 | 				return;
157 | 			}
158 | 			fs_min_size += blob.size;
159 | 			req_fs(view.TEMPORARY, fs_min_size, abortable(function(fs) {
160 | 				fs.root.getDirectory("saved", create_if_not_found, abortable(function(dir) {
161 | 					var save = function() {
162 | 						dir.getFile(name, create_if_not_found, abortable(function(file) {
163 | 							file.createWriter(abortable(function(writer) {
164 | 								writer.onwriteend = function(event) {
165 | 									target_view.location.href = file.toURL();
166 | 									deletion_queue.push(file);
167 | 									filesaver.readyState = filesaver.DONE;
168 | 									dispatch(filesaver, "writeend", event);
169 | 								};
170 | 								writer.onerror = function() {
171 | 									var error = writer.error;
172 | 									if (error.code !== error.ABORT_ERR) {
173 | 										fs_error();
174 | 									}
175 | 								};
176 | 								"writestart progress write abort".split(" ").forEach(function(event) {
177 | 									writer["on" + event] = filesaver["on" + event];
178 | 								});
179 | 								writer.write(blob);
180 | 								filesaver.abort = function() {
181 | 									writer.abort();
182 | 									filesaver.readyState = filesaver.DONE;
183 | 								};
184 | 								filesaver.readyState = filesaver.WRITING;
185 | 							}), fs_error);
186 | 						}), fs_error);
187 | 					};
188 | 					dir.getFile(name, {create: false}, abortable(function(file) {
189 | 						// delete file if it already exists
190 | 						file.remove();
191 | 						save();
192 | 					}), abortable(function(ex) {
193 | 						if (ex.code === ex.NOT_FOUND_ERR) {
194 | 							save();
195 | 						} else {
196 | 							fs_error();
197 | 						}
198 | 					}));
199 | 				}), fs_error);
200 | 			}), fs_error);
201 | 		}
202 | 		, FS_proto = FileSaver.prototype
203 | 		, saveAs = function(blob, name) {
204 | 			return new FileSaver(blob, name);
205 | 		}
206 | 	;
207 | 	FS_proto.abort = function() {
208 | 		var filesaver = this;
209 | 		filesaver.readyState = filesaver.DONE;
210 | 		dispatch(filesaver, "abort");
211 | 	};
212 | 	FS_proto.readyState = FS_proto.INIT = 0;
213 | 	FS_proto.WRITING = 1;
214 | 	FS_proto.DONE = 2;
215 | 
216 | 	FS_proto.error =
217 | 	FS_proto.onwritestart =
218 | 	FS_proto.onprogress =
219 | 	FS_proto.onwrite =
220 | 	FS_proto.onabort =
221 | 	FS_proto.onerror =
222 | 	FS_proto.onwriteend =
223 | 		null;
224 | 
225 | 	view.addEventListener("unload", process_deletion_queue, false);
226 | 	return saveAs;
227 | }(this.self || this.window || this.content));
228 | // `self` is undefined in Firefox for Android content script context
229 | // while `this` is nsIContentFrameMessageManager
230 | // with an attribute `content` that corresponds to the window
231 | 
232 | if (typeof module !== 'undefined') module.exports = saveAs;
233 | 


--------------------------------------------------------------------------------
/FileSaver/LICENSE.md:
--------------------------------------------------------------------------------
 1 | This software is licensed under the MIT/X11 license.
 2 | 
 3 | MIT/X11 license
 4 | ---------------
 5 | 
 6 | Copyright © 2011 [Eli Grey][1].
 7 | 
 8 | Permission is hereby granted, free of charge, to any person
 9 | obtaining a copy of this software and associated documentation
10 | files (the "Software"), to deal in the Software without
11 | restriction, including without limitation the rights to use,
12 | copy, modify, merge, publish, distribute, sublicense, and/or sell
13 | copies of the Software, and to permit persons to whom the
14 | Software is furnished to do so, subject to the following
15 | conditions:
16 | 
17 | The above copyright notice and this permission notice shall be
18 | included in all copies or substantial portions of the Software.
19 | 
20 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
21 | EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
22 | OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
23 | NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
24 | HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
25 | WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
26 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
27 | OTHER DEALINGS IN THE SOFTWARE.
28 | 
29 | 
30 |   [1]: http://eligrey.com


--------------------------------------------------------------------------------
/FileSaver/README.md:
--------------------------------------------------------------------------------
 1 | FileSaver.js
 2 | ============
 3 | 
 4 | FileSaver.js implements the HTML5 W3C `saveAs()` [FileSaver][1] interface in browsers that do
 5 | not natively support it. There is a [FileSaver.js demo][2] that demonstrates saving
 6 | various media types.
 7 | 
 8 | FileSaver.js is the solution to saving files on the client-side, and is perfect for
 9 | webapps that need to generate files, or for saving sensitive information that shouldn't be
10 | sent to an external server.
11 | 
12 | Looking for `canvas.toBlob()` for saving canvases? Check out
13 | [canvas-toBlob.js](https://github.com/eligrey/canvas-toBlob.js) for a cross-browser implementation.
14 | 
15 | Supported Browsers
16 | ------------------
17 | 
18 | | Browser        | Constructs as | Filenames    | Max Blob Size | Dependencies |
19 | | -------------- | ------------- | ------------ | ------------- | ------------ |
20 | | Firefox 20+    | Blob          | Yes          | 800MiB        | None         |
21 | | Firefox ≤ 19   | data: URI     | No           | n/a           | [Blob.js](https://github.com/eligrey/Blob.js) |
22 | | Chrome         | Blob          | Yes          | 345MiB        | None         |
23 | | Chrome for Android | Blob      | Yes          | ?             | None         |
24 | | IE 10+         | Blob          | Yes          | 600MiB        | None         |
25 | | Opera Next     | Blob          | Yes          | ?             | None         |
26 | | Opera < 15     | data: URI     | No           | n/a           | [Blob.js](https://github.com/eligrey/Blob.js) |
27 | | Safari 6.1+    | Blob          | No           | ?             | None         |
28 | | Safari < 6     | data: URI     | No           | n/a           | [Blob.js](https://github.com/eligrey/Blob.js) |
29 | 
30 | Feature detection is possible:
31 | 
32 |     try { var isFileSaverSupported = !!new Blob(); } catch(e){}
33 | 
34 | Syntax
35 | ------
36 | 
37 |     FileSaver saveAs(in Blob data, in DOMString filename)
38 | 
39 | Examples
40 | --------
41 | 
42 | ### Saving text
43 | 
44 |     var blob = new Blob(["Hello, world!"], {type: "text/plain;charset=utf-8"});
45 |     saveAs(blob, "hello world.txt");
46 | 
47 | The standard W3C File API [`Blob`][3] interface is not available in all browsers.
48 | [Blob.js][4] is a cross-browser `Blob` implementation that solves this.
49 | 
50 | ### Saving a canvas
51 | 
52 |     var canvas = document.getElementById("my-canvas"), ctx = canvas.getContext("2d");
53 | 	// draw to canvas...
54 |     canvas.toBlob(function(blob) {
55 |         saveAs(blob, "pretty image.png");
56 |     });
57 | 
58 | Note: The standard HTML5 `canvas.toBlob()` method is not available in all browsers.
59 | [canvas-toBlob.js][5] is a cross-browser `canvas.toBlob()` that polyfills this.
60 | 
61 | ### Aborting a save
62 | 
63 |     var filesaver = saveAs(blob, "whatever");
64 |     cancel_button.addEventListener("click", function() {
65 |         if (filesaver.abort) {
66 |             filesaver.abort();
67 |         }
68 |     }, false);
69 | 
70 | This isn't that useful unless you're saving very large files (e.g. generated video).
71 | 
72 | ![Tracking image](https://in.getclicky.com/212712ns.gif)
73 | 
74 |   [1]: http://www.w3.org/TR/file-writer-api/#the-filesaver-interface
75 |   [2]: http://eligrey.com/demos/FileSaver.js/
76 |   [3]: https://developer.mozilla.org/en-US/docs/DOM/Blob
77 |   [4]: https://github.com/eligrey/Blob.js
78 |   [5]: https://github.com/eligrey/canvas-toBlob.js
79 | 


--------------------------------------------------------------------------------
/FileSaver/bower.json:
--------------------------------------------------------------------------------
1 | {
2 |     "name": "FileSaver",
3 |     "version": "1.0.0",
4 |     "main": "./FileSaver.js",
5 |     "dependencies": {
6 |     }
7 | }
8 | 


--------------------------------------------------------------------------------
/FileSaver/demo/demo.css:
--------------------------------------------------------------------------------
 1 | html {
 2 | 	background-color: #DDD;
 3 | }
 4 | body {
 5 | 	width: 900px;
 6 | 	margin: 0 auto;
 7 | 	font-family: Verdana, Helvetica, Arial, sans-serif;
 8 | 	box-shadow: 0 0 5px #000;
 9 | 	box-shadow: 0 0 10px 2px rgba(0, 0, 0, .5);
10 | 	padding: 7px 25px 70px;
11 | 	background-color: #FFF;
12 | }
13 | h1, h2, h3, h4, h5, h6 {
14 | 	font-family: Georgia, "Times New Roman", serif;
15 | }
16 | h2, form {
17 | 	text-align: center;
18 | }
19 | form {
20 | 	margin-top: 5px;
21 | }
22 | .input {
23 | 	width: 500px;
24 | 	height: 300px;
25 | 	margin: 0 auto;
26 | 	display: block;
27 | }
28 | section {
29 | 	margin-top: 40px;
30 | }
31 | dt {
32 | 	font-weight: bold;
33 | 	font-size: larger;
34 | }
35 | #canvas {
36 | 	cursor: crosshair;
37 | }
38 | #canvas, #html {
39 | 	border: 1px solid black;
40 | }
41 | .filename {
42 | 	text-align: right;
43 | }
44 | #html {
45 | 	box-sizing: border-box;
46 | 	ms-box-sizing: border-box;
47 | 	webkit-box-sizing: border-box;
48 | 	moz-box-sizing: border-box;
49 | 	overflow: auto;
50 | 	padding: 1em;
51 | }
52 | dt:target {
53 | 	background-color: Highlight;
54 | 	color: HighlightText;
55 | }
56 | 


--------------------------------------------------------------------------------
/FileSaver/demo/demo.js:
--------------------------------------------------------------------------------
  1 | /* FileSaver.js demo script
  2 |  * 2012-01-23
  3 |  * 
  4 |  * By Eli Grey, http://eligrey.com
  5 |  * License: X11/MIT
  6 |  *   See LICENSE.md
  7 |  */
  8 | 
  9 | /*! @source http://purl.eligrey.com/github/FileSaver.js/blob/master/demo/demo.js */
 10 | 
 11 | (function(view) {
 12 | "use strict";
 13 | // The canvas drawing portion of the demo is based off the demo at
 14 | // http://www.williammalone.com/articles/create-html5-canvas-javascript-drawing-app/
 15 | var
 16 | 	  document = view.document
 17 | 	, $ = function(id) {
 18 | 		return document.getElementById(id);
 19 | 	}
 20 | 	, session = view.sessionStorage
 21 | 	// only get URL when necessary in case Blob.js hasn't defined it yet
 22 | 	, get_blob = function() {
 23 | 		return view.Blob;
 24 | 	}
 25 | 
 26 | 	, canvas = $("canvas")
 27 | 	, canvas_options_form = $("canvas-options")
 28 | 	, canvas_filename = $("canvas-filename")
 29 | 	, canvas_clear_button = $("canvas-clear")
 30 | 	
 31 | 	, text = $("text")
 32 | 	, text_options_form = $("text-options")
 33 | 	, text_filename = $("text-filename")
 34 | 	
 35 | 	, html = $("html")
 36 | 	, html_options_form = $("html-options")
 37 | 	, html_filename = $("html-filename")
 38 | 	
 39 | 	, ctx = canvas.getContext("2d")
 40 | 	, drawing = false
 41 | 	, x_points = session.x_points || []
 42 | 	, y_points = session.y_points || []
 43 | 	, drag_points = session.drag_points || []
 44 | 	, add_point = function(x, y, dragging) {
 45 | 		x_points.push(x);
 46 | 		y_points.push(y);
 47 | 		drag_points.push(dragging);
 48 | 	}
 49 | 	, draw = function(){
 50 | 		canvas.width = canvas.width;
 51 | 		ctx.lineWidth = 6;
 52 | 		ctx.lineJoin = "round";
 53 | 		ctx.strokeStyle = "#000000";
 54 | 		var
 55 | 			  i = 0
 56 | 			, len = x_points.length
 57 | 		;
 58 | 		for(; i < len; i++) {
 59 | 			ctx.beginPath();
 60 | 			if (i && drag_points[i]) {
 61 | 				ctx.moveTo(x_points[i-1], y_points[i-1]);
 62 | 			} else {
 63 | 				ctx.moveTo(x_points[i]-1, y_points[i]);
 64 | 			}
 65 | 			ctx.lineTo(x_points[i], y_points[i]);
 66 | 			ctx.closePath();
 67 | 			ctx.stroke();
 68 | 		}
 69 | 	}
 70 | 	, stop_drawing = function() {
 71 | 		drawing = false;
 72 | 	}
 73 | 	
 74 | 	// Title guesser and document creator available at https://gist.github.com/1059648
 75 | 	, guess_title = function(doc) {
 76 | 		var
 77 | 			  h = "h6 h5 h4 h3 h2 h1".split(" ")
 78 | 			, i = h.length
 79 | 			, headers
 80 | 			, header_text
 81 | 		;
 82 | 		while (i--) {
 83 | 			headers = doc.getElementsByTagName(h[i]);
 84 | 			for (var j = 0, len = headers.length; j < len; j++) {
 85 | 				header_text = headers[j].textContent.trim();
 86 | 				if (header_text) {
 87 | 					return header_text;
 88 | 				}
 89 | 			}
 90 | 		}
 91 | 	}
 92 | 	, doc_impl = document.implementation
 93 | 	, create_html_doc = function(html) {
 94 | 		var
 95 | 			  dt = doc_impl.createDocumentType('html', null, null)
 96 | 			, doc = doc_impl.createDocument("http://www.w3.org/1999/xhtml", "html", dt)
 97 | 			, doc_el = doc.documentElement
 98 | 			, head = doc_el.appendChild(doc.createElement("head"))
 99 | 			, charset_meta = head.appendChild(doc.createElement("meta"))
100 | 			, title = head.appendChild(doc.createElement("title"))
101 | 			, body = doc_el.appendChild(doc.createElement("body"))
102 | 			, i = 0
103 | 			, len = html.childNodes.length
104 | 		;
105 | 		charset_meta.setAttribute("charset", html.ownerDocument.characterSet);
106 | 		for (; i < len; i++) {
107 | 			body.appendChild(doc.importNode(html.childNodes.item(i), true));
108 | 		}
109 | 		var title_text = guess_title(doc);
110 | 		if (title_text) {
111 | 			title.appendChild(doc.createTextNode(title_text));
112 | 		}
113 | 		return doc;
114 | 	}
115 | ;
116 | canvas.width = 500;
117 | canvas.height = 300;
118 | 
119 |   if (typeof x_points === "string") {
120 | 	x_points = JSON.parse(x_points);
121 | } if (typeof y_points === "string") {
122 | 	y_points = JSON.parse(y_points);
123 | } if (typeof drag_points === "string") {
124 | 	drag_points = JSON.parse(drag_points);
125 | } if (session.canvas_filename) {
126 | 	canvas_filename.value = session.canvas_filename;
127 | } if (session.text) {
128 | 	text.value = session.text;
129 | } if (session.text_filename) {
130 | 	text_filename.value = session.text_filename;
131 | } if (session.html) {
132 | 	html.innerHTML = session.html;
133 | } if (session.html_filename) {
134 | 	html_filename.value = session.html_filename;
135 | }
136 | 
137 | drawing = true;
138 | draw();
139 | drawing = false;
140 | 
141 | canvas_clear_button.addEventListener("click", function() {
142 | 	canvas.width = canvas.width;
143 | 	x_points.length =
144 | 	y_points.length =
145 | 	drag_points.length =
146 | 		0;
147 | }, false);
148 | canvas.addEventListener("mousedown", function(event) {
149 | 	event.preventDefault();
150 | 	drawing = true;
151 | 	add_point(event.pageX - canvas.offsetLeft, event.pageY - canvas.offsetTop, false);
152 | 	draw();
153 | }, false);
154 | canvas.addEventListener("mousemove", function(event) {
155 | 	if (drawing) {
156 | 		add_point(event.pageX - canvas.offsetLeft, event.pageY - canvas.offsetTop, true);
157 | 		draw();
158 | 	}
159 | }, false);
160 | canvas.addEventListener("mouseup", stop_drawing, false);
161 | canvas.addEventListener("mouseout", stop_drawing, false);
162 | 
163 | canvas_options_form.addEventListener("submit", function(event) {
164 | 	event.preventDefault();
165 | 	canvas.toBlob(function(blob) {
166 | 		saveAs(
167 | 			  blob
168 | 			, (canvas_filename.value || canvas_filename.placeholder) + ".png"
169 | 		);
170 | 	}, "image/png");
171 | }, false);
172 | 
173 | text_options_form.addEventListener("submit", function(event) {
174 | 	event.preventDefault();
175 | 	var BB = get_blob();
176 | 	saveAs(
177 | 		  new BB(
178 | 			  [text.value || text.placeholder]
179 | 			, {type: "text/plain;charset=" + document.characterSet}
180 | 		)
181 | 		, (text_filename.value || text_filename.placeholder) + ".txt"
182 | 	);
183 | }, false);
184 | 
185 | html_options_form.addEventListener("submit", function(event) {
186 | 	event.preventDefault();
187 | 	var
188 | 		  BB = get_blob()
189 | 		, xml_serializer = new XMLSerializer
190 | 		, doc = create_html_doc(html)
191 | 	;
192 | 	saveAs(
193 | 		  new BB(
194 | 			  [xml_serializer.serializeToString(doc)]
195 | 			, {type: "application/xhtml+xml;charset=" + document.characterSet}
196 | 		)
197 | 		, (html_filename.value || html_filename.placeholder) + ".xhtml"
198 | 	);
199 | }, false);
200 | 
201 | view.addEventListener("unload", function() {
202 | 	session.x_points = JSON.stringify(x_points);
203 | 	session.y_points = JSON.stringify(y_points);
204 | 	session.drag_points = JSON.stringify(drag_points);
205 | 	session.canvas_filename = canvas_filename.value;
206 | 	
207 | 	session.text = text.value;
208 | 	session.text_filename = text_filename.value;
209 | 	
210 | 	session.html = html.innerHTML;
211 | 	session.html_filename = html_filename.value;
212 | }, false);
213 | }(self));
214 | 


--------------------------------------------------------------------------------
/FileSaver/demo/demo.min.js:
--------------------------------------------------------------------------------
1 | /*! @source http://purl.eligrey.com/github/FileSaver.js/blob/master/demo/demo.js */
2 | (function(n){"use strict";var s=n.document,g=function(A){return s.getElementById(A)},b=n.sessionStorage,x=function(){return n.Blob},f=g("canvas"),r=g("canvas-options"),y=g("canvas-filename"),p=g("canvas-clear"),q=g("text"),t=g("text-options"),h=g("text-filename"),m=g("html"),e=g("html-options"),i=g("html-filename"),u=f.getContext("2d"),z=false,a=b.x_points||[],o=b.y_points||[],d=b.drag_points||[],j=function(A,C,B){a.push(A);o.push(C);d.push(B)},l=function(){f.width=f.width;u.lineWidth=6;u.lineJoin="round";u.strokeStyle="#000000";var B=0,A=a.length;for(;B<A;B++){u.beginPath();if(B&&d[B]){u.moveTo(a[B-1],o[B-1])}else{u.moveTo(a[B]-1,o[B])}u.lineTo(a[B],o[B]);u.closePath();u.stroke()}},c=function(){z=false},w=function(E){var D="h6 h5 h4 h3 h2 h1".split(" "),C=D.length,F,G;while(C--){F=E.getElementsByTagName(D[C]);for(var B=0,A=F.length;B<A;B++){G=F[B].textContent.trim();if(G){return G}}}},v=s.implementation,k=function(D){var B=v.createDocumentType("html",null,null),J=v.createDocument("http://www.w3.org/1999/xhtml","html",B),A=J.documentElement,H=A.appendChild(J.createElement("head")),K=H.appendChild(J.createElement("meta")),I=H.appendChild(J.createElement("title")),E=A.appendChild(J.createElement("body")),C=0,G=D.childNodes.length;K.setAttribute("charset",D.ownerDocument.characterSet);for(;C<G;C++){E.appendChild(J.importNode(D.childNodes.item(C),true))}var F=w(J);if(F){I.appendChild(J.createTextNode(F))}return J};f.width=500;f.height=300;if(typeof a==="string"){a=JSON.parse(a)}if(typeof o==="string"){o=JSON.parse(o)}if(typeof d==="string"){d=JSON.parse(d)}if(b.canvas_filename){y.value=b.canvas_filename}if(b.text){q.value=b.text}if(b.text_filename){h.value=b.text_filename}if(b.html){m.innerHTML=b.html}if(b.html_filename){i.value=b.html_filename}z=true;l();z=false;p.addEventListener("click",function(){f.width=f.width;a.length=o.length=d.length=0},false);f.addEventListener("mousedown",function(A){A.preventDefault();z=true;j(A.pageX-f.offsetLeft,A.pageY-f.offsetTop,false);l()},false);f.addEventListener("mousemove",function(A){if(z){j(A.pageX-f.offsetLeft,A.pageY-f.offsetTop,true);l()}},false);f.addEventListener("mouseup",c,false);f.addEventListener("mouseout",c,false);r.addEventListener("submit",function(A){A.preventDefault();f.toBlob(function(B){saveAs(B,(y.value||y.placeholder)+".png")},"image/png")},false);t.addEventListener("submit",function(A){A.preventDefault();var B=x();saveAs(new B([q.value||q.placeholder],{type:"text/plain;charset="+s.characterSet}),(h.value||h.placeholder)+".txt")},false);e.addEventListener("submit",function(B){B.preventDefault();var D=x(),A=new XMLSerializer,C=k(m);saveAs(new D([A.serializeToString(C)],{type:"application/xhtml+xml;charset="+s.characterSet}),(i.value||i.placeholder)+".xhtml")},false);n.addEventListener("unload",function(){b.x_points=JSON.stringify(a);b.y_points=JSON.stringify(o);b.drag_points=JSON.stringify(d);b.canvas_filename=y.value;b.text=q.value;b.text_filename=h.value;b.html=m.innerHTML;b.html_filename=i.value},false)}(self));


--------------------------------------------------------------------------------
/FileSaver/demo/index.xhtml:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html>
 2 | <html xmlns="http://www.w3.org/1999/xhtml" dir="ltr" lang="en-US-x-Hixie">
 3 | <head>
 4 | <meta charset="utf-8"/>
 5 | <title>FileSaver.js demo</title>
 6 | <link rel="stylesheet" type="text/css" href="demo.css"/>
 7 | </head>
 8 | <body>
 9 | <h1><a href="https://github.com/eligrey/FileSaver.js">FileSaver.js</a> demo</h1>
10 | <p>
11 | The following examples demonstrate how it is possible to generate and save any type of data right in the browser using the W3C <code>saveAs()</code> <a href="http://www.w3.org/TR/file-writer-api/#the-filesaver-interface">FileSaver</a> interface, without contacting any servers.
12 | </p>
13 | <section id="image-demo">
14 | 	<h2>Saving an image</h2>
15 | 	<canvas class="input" id="canvas" width="500" height="300"/>
16 | 	<form id="canvas-options">
17 | 		<label>Filename: <input type="text" class="filename" id="canvas-filename" placeholder="doodle"/>.png</label>
18 | 		<input type="submit" value="Save"/>
19 | 		<input type="button" id="canvas-clear" value="Clear"/>
20 | 	</form>
21 | </section>
22 | <section id="text-demo">
23 | 	<h2>Saving text</h2>
24 | 	<textarea class="input" id="text" placeholder="Once upon a time..."/>
25 | 	<form id="text-options">
26 | 		<label>Filename: <input type="text" class="filename" id="text-filename" placeholder="a plain document"/>.txt</label>
27 | 		<input type="submit" value="Save"/>
28 | 	</form>
29 | </section>
30 | <section id="html-demo">
31 | 	<h2>Saving rich text</h2>
32 | 	<div class="input" id="html" contenteditable="">
33 | 		<h3>Some example rich text</h3>
34 | 		<ul>
35 | 			<li><del>Plain</del> <ins>Boring</ins> text.</li>
36 | 			<li><em>Emphasized text!</em></li>
37 | 			<li><strong>Strong text!</strong></li>
38 | 			<li>
39 | 				<svg xmlns="http://www.w3.org/2000/svg" version="1.1" width="70" height="70">
40 | 					<circle cx="35" cy="35" r="35" fill="red"/>
41 | 					<text x="10" y="40">image</text>
42 | 				</svg>
43 | 			</li>
44 | 			<li><a href="https://github.com/eligrey/FileSaver.js">A link.</a></li>
45 | 		</ul>
46 | 	</div>
47 | 	<form id="html-options">
48 | 		<label>Filename: <input type="text" class="filename" id="html-filename" placeholder="a rich document"/>.xhtml</label>
49 | 		<input type="submit" value="Save"/>
50 | 	</form>
51 | </section>
52 | <script type="application/ecmascript" async="" src="https://raw.github.com/eligrey/Blob.js/master/Blob.min.js"/>
53 | <script type="application/ecmascript" async="" src="https://raw.github.com/eligrey/canvas-toBlob.js/master/canvas-toBlob.js"/>
54 | <script type="application/ecmascript" async="" src="https://raw.github.com/eligrey/FileSaver.js/master/FileSaver.js"/>
55 | <script type="application/ecmascript" async="" src="https://raw.github.com/eligrey/FileSaver.js/master/demo/demo.js"/>
56 | </body>
57 | </html>
58 | 


--------------------------------------------------------------------------------
/FileSaver/package.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "name": "filesaver.js",
 3 |   "version": "2013.1.23",
 4 |   "description": "A saveAs() FileSaver implementation",
 5 |   "main": "FileSaver.js",
 6 |   "scripts": {
 7 |     "test": "echo \"Error: no test specified\" && exit 1"
 8 |   },
 9 |   "repository": {
10 |     "type": "git",
11 |     "url": "https://github.com/eligrey/FileSaver.js.git"
12 |   },
13 |   "keywords": [
14 |     "filesaver",
15 |     "saveas",
16 |     "blob"
17 |   ],
18 |   "author": "Eli Grey",
19 |   "license": "MIT/X11",
20 |   "bugs": {
21 |     "url": "https://github.com/eligrey/FileSaver.js/issues"
22 |   }
23 | }
24 | 


--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
  1 | GNU GENERAL PUBLIC LICENSE
  2 |                        Version 2, June 1991
  3 | 
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  5 |  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
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  8 | 
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308 |     51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
309 | 
310 | Also add information on how to contact you by electronic and paper mail.
311 | 
312 | If the program is interactive, make it output a short notice like this
313 | when it starts in an interactive mode:
314 | 
315 |     Gnomovision version 69, Copyright (C) year name of author
316 |     Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
317 |     This is free software, and you are welcome to redistribute it
318 |     under certain conditions; type `show c' for details.
319 | 
320 | The hypothetical commands `show w' and `show c' should show the appropriate
321 | parts of the General Public License.  Of course, the commands you use may
322 | be called something other than `show w' and `show c'; they could even be
323 | mouse-clicks or menu items--whatever suits your program.
324 | 
325 | You should also get your employer (if you work as a programmer) or your
326 | school, if any, to sign a "copyright disclaimer" for the program, if
327 | necessary.  Here is a sample; alter the names:
328 | 
329 |   Yoyodyne, Inc., hereby disclaims all copyright interest in the program
330 |   `Gnomovision' (which makes passes at compilers) written by James Hacker.
331 | 
332 |   {signature of Ty Coon}, 1 April 1989
333 |   Ty Coon, President of Vice
334 | 
335 | This General Public License does not permit incorporating your program into
336 | proprietary programs.  If your program is a subroutine library, you may
337 | consider it more useful to permit linking proprietary applications with the
338 | library.  If this is what you want to do, use the GNU Lesser General
339 | Public License instead of this License.
340 | 


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
  1 | islandplot
  2 | ==========
  3 | 
  4 | Islandplot is an SVG based genome viewer written in javascript using D3
  5 | 
  6 | There are three pieces to the package, a circular genome viewer, a linear
  7 | genome viewer and a linear brush element.  Simply include the js files for
  8 | the elements you need in your page and you're ready to go.  
  9 | 
 10 | Both view types take the same data format, a javascript data structure, with
 11 | a few extra tags for each type.  Tracks can not be added after creation of the initial plot objects (but they can be initialized as visible: false) and in the linear plot they can not be reordered
 12 | 
 13 | The circular viewer was written first, hence why you might find the configuration options
 14 | seem more aimed towards it as their default, most options have a linear_ prefixed
 15 | version for the linear viewer.
 16 | 
 17 | Examples
 18 | ========
 19 | 
 20 | Demo of the circular plot can be found at [this gist](http://bl.ocks.org/lairdm/6a770c94c6793eee660d).
 21 | 
 22 | Demo of the linear plot can be found at [this gist](http://bl.ocks.org/lairdm/c6c235dbfa6e6ee61565).
 23 | 
 24 | A demo of the circular and linear plots with their panning features linked together can be found at [this gist](http://bl.ocks.org/lairdm/3a38883488d71623901c).
 25 | 
 26 | Available track types
 27 | =====================
 28 | 
 29 | * block track (simply start and end basepairs for each element)
 30 | * stranded track (allowing visualizing of the forward or reverse strand)
 31 | * plot track (for visualizing things such as average GC content)
 32 | * glyph track (for visualizing specific features at a given point)
 33 | 
 34 | Data format
 35 | ===========
 36 | 
 37 | The data passed in must be an array of track objects (see included data.js for sample data).  Each track has the format of:
 38 | 
 39 | ```
 40 | { 
 41 |   trackName: "track1",
 42 |   trackType: "stranded",
 43 |   visible: true,
 44 |   inner_radius: 125,
 45 |   outer_radius: 175,
 46 |   items: [
 47 |           {id: 1, start:0, end:30000, name:"island0", strand: -1},
 48 |            ...
 49 |          ]
 50 | }
 51 | ```
 52 | 
 53 | trackName and trackType are mandatory.  visible defaults to true and is optional.  For all track types except the plot type, items is an array of objects, where each object is a track element with a start and end bp location.  For plot type tracks its simply an array of points for the track and the bp_per_element tag must be included, which is the number of bp between data points in the set.
 54 | 
 55 | Track colours and functionality can be customized via CSS, elements will have classes such as track1_pos for the forward (positive) strand elements of track1.  Use something like Chrome's element inspector to examine all the CSS classes that are added to visualization elements.
 56 | 
 57 | For glyph tracks the shapes allowed are standard SVG shapes.
 58 | 
 59 | Creating plots
 60 | ==============
 61 | 
 62 | Tracks also require a second object to be passed on when creating them, the layout of the track.  The minimum needed is the genomesize (in bp) and the div to create the object in.  Additional configuration options such as margin sizes can also be configured.
 63 | 
 64 | ```
 65 | var circularlayout = {genomesize: 6264404,
 66 |                       container: "#circularchart",
 67 |         };
 68 | 
 69 | var cTrack = new circularTrack(circularlayout, tracks);
 70 | ```
 71 | 
 72 | The two arguments are the layout and the track data.
 73 | 
 74 | Manipulating plots
 75 | ==================
 76 | 
 77 | You may also make JS calls to manipulate visualized tracks, the basic functionality is to show and hide a track, this is done via the name in the trackName element of the track.
 78 | 
 79 | ```
 80 | cTrack.showTrack("track1");
 81 | 
 82 | cTrack.hideTrack("track1");
 83 | ```
 84 | 
 85 | For glyph tracks the format is slightly different, you must specify which glyph type in the track is to be shown or hidden.
 86 | 
 87 | ```
 88 | cTrack.showGlyphTrackType("track5", "adb");
 89 | 
 90 | cTrack.hideGlyphTrackType("track5", "adb");
 91 | ```
 92 | 
 93 | There is also functionality to alter the radius of where a track is in a circular plot.  This is done by track id rather than name so a call to findTrackbyName must be done first:
 94 | 
 95 | ```
 96 | var id = cTrack.findTrackbyName('track1');
 97 | cTrack.moveTrack(id, newInnerRadius, newOuterRadius);
 98 | ```
 99 | 
100 | Attaching a brush
101 | =================
102 | 
103 | For zooming and resizing the linear track there's a brush element made to work with the track.  Once the linear track is made the brush can "attach" to it.
104 | 
105 | ```
106 | var linearTrack = new genomeTrack(linearlayout, tracks);
107 | var brush = new linearBrush(contextLayout,linearTrack);
108 | ```
109 | 
110 | There's also a polar brush element in the circular plot type that can be attached to a linear plot, so when the polar brush is moved on the ciruclar plot it will update the linear track.
111 | 
112 | ```
113 | var cTrack = new circularTrack(circularlayout, tracks);
114 | cTrack.attachBrush(linearTrack);
115 | ```
116 | 
117 | Both the linear and circular plots allow multiple callbacks if there is more than one element you need to alter when either the linear or circular brushes are altered.  Simply make multiple calls to attachBrush() in either plot type and the callbacks will each be called on update. 
118 | 
119 | ```
120 | cTrack.attachBrush(linearTrack);
121 | cTrack.attachBrush(someOtherObj);
122 | ```
123 | 
124 | Updating the view
125 | =================
126 | 
127 | The callback used when "attaching" a brush can either be a plot object or your own object, if creating your own callback listener it must implement two callback functions.  When an update occurs the plot will call callbackObj.update(newStartBP, newEndBP) and when the drag or zoom is finished it will call callbackObj.update_finished(newStartBP, newEndBP)
128 | 
129 | Stranded/Block Track configuration options
130 | ==========================================
131 | 
132 | ```
133 | var tracks = [
134 | 	      { trackName: "track1",
135 | 		trackType: "stranded", [or "track" for non-stranded]
136 | 		visible: true,
137 | 		inner_radius: 125,
138 | 		outer_radius: 175,
139 | 		mouseclick: 'islandPopup',
140 | 		mouseover_callback: 'islandPopup',
141 | 		mouseout_callback: 'islandPopupClear',
142 | 		linear_mouseclick: 'linearPopup',
143 | 		showLabels: true,
144 | 		showTooltip: true,
145 | 		items: [
146 |                          {id: 1, start:0, end:30000, name:"island0", strand: -1},
147 |                           ...
148 |                        ]
149 |                }
150 |               ]
151 | ```
152 | 
153 | inner_radius: The inner radius of arcs, in px, for the track.
154 | outer_radius: The outer radius of arcs, in px, for the track. For stranded tracks each strand is half the radius between inner and outer radius
155 | 
156 | mouseclick: Callback for mouse clicks on arcs in a circular plot. Either a function(d) or an object, if an object is given callbackObj.mouseclick(d) will be called where d is the element in the items array.
157 | 
158 | linear_mouseclock: Same as mouseclick but for a linear plot
159 | 
160 | mouseover: Callback for a mouse over event for a circular plot, same as mouseclick, if an obj callbackObj.mouseover(d) is called otherwise callback(d)
161 | 
162 | linear_mouseover: Same as mouseover but for a linear plot
163 | 
164 | mouseout: Callback for a mouseout event for a circular plot, same as mouseclick, if an obj callbackObj.mouseout(d) is called otherwise callback(d)
165 | 
166 | linear_mouseout: Same as mouseout but for a linear plot
167 | 
168 | showLabels: Show the name element in an item on a linear plot if the plot is zoomed sufficiently so the text will fit in the element
169 | 
170 | showTooltip: Show a hoverover tooltip on a linear plot of the name element in the item when the mouse is over the element.
171 | 
172 | Plot configuration options
173 | ==========================
174 | 
175 | ```
176 | 	      { trackName: "track4",
177 | 		trackType: "plot",
178 | 		visible: true,
179 | 		plot_min: 0.4891,
180 | 		plot_max: 0.7274,
181 | 		plot_mean: 0.66558768401076,
182 | 		bp_per_element: 10000,
183 | 	        plot_width: 50,
184 | 		plot_radius: 100,
185 | 	        linear_plot_width: 50,
186 | 		linear_plot_height: 100,
187 | 		items: [
188 |                         ...
189 |                        ]
190 |               }
191 | ```
192 | 
193 | plot_min: The minimum value in the set of element
194 | plot_max: The maximum value in the set of element
195 | plot_mean: The mean value of the set of elements, if omited a mean value line isn't shown
196 | 
197 | bp_per_element: The number of bp between each element in the items list, number of items * bp_per_element should equal the genome size
198 | 
199 | plot_witdh: Number of px between the inner and outer radius of the plot
200 | plot_radius: The radius of the plot, the plot will extend plot_width/2 in either direction
201 | 
202 | linear_plot_width: Number of px between the top and bottom of a the plot on a linear plot
203 | linear_plot_height: The number of pixels from the top of a linear plot for the centre of a plot, the plot will extend plot_width/2 in either direction
204 | 
205 | Glyph configuration options
206 | ===========================
207 | 
208 | ```
209 | 	      { trackName: "track5",
210 | 		trackType: 'glyph',
211 | 		glyphType: 'circle',
212 | 		radius: 75,
213 | 		pixel_spacing: 8,
214 | 		linear_pixel_spacing: 8,
215 | 	        glyph_buffer: 8,
216 | 	        linear_glyph_buffer: 8,
217 | 		glyphSize: 20,
218 | 		linear_glyphSize: 20,
219 | 		linear_height: 100,
220 | 		items: [
221 | 			{id: 1, bp: 100, type: 'vfdb'},
222 |                         ...
223 |                        ]
224 |               }
225 | ```
226 | 
227 | glyphType: The type of glyph, any valid SVG shape is allowed
228 | radius: The starting radius on a circular plot the glyphs will begin stacking
229 | 
230 | pixel_spacing: The minimum number of pixels between glyphs on a circular plot before glyphs are stacked
231 | glyph_buffer: If a glyph is stacked, how many px to put between them
232 | 
233 | linear_pixel_spacing: The minimum number of pixels between glyphs on a linear plot before glyphs are stacked
234 | linear_glyph_buffer: If a glyph is stacked on a linear plot, how many px to put between them
235 | 
236 | glyphSize: Size of a glyph on a circular plot
237 | linear_glyphSize: Size of a glyph on a linear plot
238 | 
239 | linear_height: Distance from the top, in px, that a glyph track will start displaying on a linear track
240 | linear_invert: true or false, if false glyphs will begin stacking down on a linear track. If true glyphs will stack upwards
241 | 
242 | 


--------------------------------------------------------------------------------
/canvg/MIT-LICENSE.txt:
--------------------------------------------------------------------------------
 1 | Copyright (c) 2010-2011 Gabe Lerner (gabelerner@gmail.com) - http://code.google.com/p/canvg/
 2 | 
 3 |  Permission is hereby granted, free of charge, to any person
 4 |  obtaining a copy of this software and associated documentation
 5 |  files (the "Software"), to deal in the Software without
 6 |  restriction, including without limitation the rights to use,
 7 |  copy, modify, merge, publish, distribute, sublicense, and/or sell
 8 |  copies of the Software, and to permit persons to whom the
 9 |  Software is furnished to do so, subject to the following
10 |  conditions:
11 | 
12 |  The above copyright notice and this permission notice shall be
13 |  included in all copies or substantial portions of the Software.
14 | 
15 |  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
16 |  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
17 |  OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
18 |  NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
19 |  HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
20 |  WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
21 |  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
22 |  OTHER DEALINGS IN THE SOFTWARE.


--------------------------------------------------------------------------------
/canvg/StackBlur.js:
--------------------------------------------------------------------------------
  1 | /*
  2 | 
  3 | StackBlur - a fast almost Gaussian Blur For Canvas
  4 | 
  5 | Version: 	0.5
  6 | Author:		Mario Klingemann
  7 | Contact: 	mario@quasimondo.com
  8 | Website:	http://www.quasimondo.com/StackBlurForCanvas
  9 | Twitter:	@quasimondo
 10 | 
 11 | In case you find this class useful - especially in commercial projects -
 12 | I am not totally unhappy for a small donation to my PayPal account
 13 | mario@quasimondo.de
 14 | 
 15 | Or support me on flattr: 
 16 | https://flattr.com/thing/72791/StackBlur-a-fast-almost-Gaussian-Blur-Effect-for-CanvasJavascript
 17 | 
 18 | Copyright (c) 2010 Mario Klingemann
 19 | 
 20 | Permission is hereby granted, free of charge, to any person
 21 | obtaining a copy of this software and associated documentation
 22 | files (the "Software"), to deal in the Software without
 23 | restriction, including without limitation the rights to use,
 24 | copy, modify, merge, publish, distribute, sublicense, and/or sell
 25 | copies of the Software, and to permit persons to whom the
 26 | Software is furnished to do so, subject to the following
 27 | conditions:
 28 | 
 29 | The above copyright notice and this permission notice shall be
 30 | included in all copies or substantial portions of the Software.
 31 | 
 32 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 33 | EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 34 | OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 35 | NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 36 | HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 37 | WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 38 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 39 | OTHER DEALINGS IN THE SOFTWARE.
 40 | */
 41 | 
 42 | var mul_table = [
 43 |         512,512,456,512,328,456,335,512,405,328,271,456,388,335,292,512,
 44 |         454,405,364,328,298,271,496,456,420,388,360,335,312,292,273,512,
 45 |         482,454,428,405,383,364,345,328,312,298,284,271,259,496,475,456,
 46 |         437,420,404,388,374,360,347,335,323,312,302,292,282,273,265,512,
 47 |         497,482,468,454,441,428,417,405,394,383,373,364,354,345,337,328,
 48 |         320,312,305,298,291,284,278,271,265,259,507,496,485,475,465,456,
 49 |         446,437,428,420,412,404,396,388,381,374,367,360,354,347,341,335,
 50 |         329,323,318,312,307,302,297,292,287,282,278,273,269,265,261,512,
 51 |         505,497,489,482,475,468,461,454,447,441,435,428,422,417,411,405,
 52 |         399,394,389,383,378,373,368,364,359,354,350,345,341,337,332,328,
 53 |         324,320,316,312,309,305,301,298,294,291,287,284,281,278,274,271,
 54 |         268,265,262,259,257,507,501,496,491,485,480,475,470,465,460,456,
 55 |         451,446,442,437,433,428,424,420,416,412,408,404,400,396,392,388,
 56 |         385,381,377,374,370,367,363,360,357,354,350,347,344,341,338,335,
 57 |         332,329,326,323,320,318,315,312,310,307,304,302,299,297,294,292,
 58 |         289,287,285,282,280,278,275,273,271,269,267,265,263,261,259];
 59 |         
 60 |    
 61 | var shg_table = [
 62 | 	     9, 11, 12, 13, 13, 14, 14, 15, 15, 15, 15, 16, 16, 16, 16, 17, 
 63 | 		17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 19, 
 64 | 		19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 20,
 65 | 		20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 21,
 66 | 		21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
 67 | 		21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 
 68 | 		22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22,
 69 | 		22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 
 70 | 		23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
 71 | 		23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
 72 | 		23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 
 73 | 		23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 
 74 | 		24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
 75 | 		24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
 76 | 		24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
 77 | 		24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24 ];
 78 | 
 79 | function stackBlurImage( imageID, canvasID, radius, blurAlphaChannel )
 80 | {
 81 | 			
 82 |  	var img = document.getElementById( imageID );
 83 | 	var w = img.naturalWidth;
 84 |     var h = img.naturalHeight;
 85 |        
 86 | 	var canvas = document.getElementById( canvasID );
 87 |       
 88 |     canvas.style.width  = w + "px";
 89 |     canvas.style.height = h + "px";
 90 |     canvas.width = w;
 91 |     canvas.height = h;
 92 |     
 93 |     var context = canvas.getContext("2d");
 94 |     context.clearRect( 0, 0, w, h );
 95 |     context.drawImage( img, 0, 0 );
 96 | 
 97 | 	if ( isNaN(radius) || radius < 1 ) return;
 98 | 	
 99 | 	if ( blurAlphaChannel )
100 | 		stackBlurCanvasRGBA( canvasID, 0, 0, w, h, radius );
101 | 	else 
102 | 		stackBlurCanvasRGB( canvasID, 0, 0, w, h, radius );
103 | }
104 | 
105 | 
106 | function stackBlurCanvasRGBA( id, top_x, top_y, width, height, radius )
107 | {
108 | 	if ( isNaN(radius) || radius < 1 ) return;
109 | 	radius |= 0;
110 | 	
111 | 	var canvas  = document.getElementById( id );
112 | 	var context = canvas.getContext("2d");
113 | 	var imageData;
114 | 	
115 | 	try {
116 | 	  try {
117 | 		imageData = context.getImageData( top_x, top_y, width, height );
118 | 	  } catch(e) {
119 | 	  
120 | 		// NOTE: this part is supposedly only needed if you want to work with local files
121 | 		// so it might be okay to remove the whole try/catch block and just use
122 | 		// imageData = context.getImageData( top_x, top_y, width, height );
123 | 		try {
124 | 			netscape.security.PrivilegeManager.enablePrivilege("UniversalBrowserRead");
125 | 			imageData = context.getImageData( top_x, top_y, width, height );
126 | 		} catch(e) {
127 | 			alert("Cannot access local image");
128 | 			throw new Error("unable to access local image data: " + e);
129 | 			return;
130 | 		}
131 | 	  }
132 | 	} catch(e) {
133 | 	  alert("Cannot access image");
134 | 	  throw new Error("unable to access image data: " + e);
135 | 	}
136 | 			
137 | 	var pixels = imageData.data;
138 | 			
139 | 	var x, y, i, p, yp, yi, yw, r_sum, g_sum, b_sum, a_sum, 
140 | 	r_out_sum, g_out_sum, b_out_sum, a_out_sum,
141 | 	r_in_sum, g_in_sum, b_in_sum, a_in_sum, 
142 | 	pr, pg, pb, pa, rbs;
143 | 			
144 | 	var div = radius + radius + 1;
145 | 	var w4 = width << 2;
146 | 	var widthMinus1  = width - 1;
147 | 	var heightMinus1 = height - 1;
148 | 	var radiusPlus1  = radius + 1;
149 | 	var sumFactor = radiusPlus1 * ( radiusPlus1 + 1 ) / 2;
150 | 	
151 | 	var stackStart = new BlurStack();
152 | 	var stack = stackStart;
153 | 	for ( i = 1; i < div; i++ )
154 | 	{
155 | 		stack = stack.next = new BlurStack();
156 | 		if ( i == radiusPlus1 ) var stackEnd = stack;
157 | 	}
158 | 	stack.next = stackStart;
159 | 	var stackIn = null;
160 | 	var stackOut = null;
161 | 	
162 | 	yw = yi = 0;
163 | 	
164 | 	var mul_sum = mul_table[radius];
165 | 	var shg_sum = shg_table[radius];
166 | 	
167 | 	for ( y = 0; y < height; y++ )
168 | 	{
169 | 		r_in_sum = g_in_sum = b_in_sum = a_in_sum = r_sum = g_sum = b_sum = a_sum = 0;
170 | 		
171 | 		r_out_sum = radiusPlus1 * ( pr = pixels[yi] );
172 | 		g_out_sum = radiusPlus1 * ( pg = pixels[yi+1] );
173 | 		b_out_sum = radiusPlus1 * ( pb = pixels[yi+2] );
174 | 		a_out_sum = radiusPlus1 * ( pa = pixels[yi+3] );
175 | 		
176 | 		r_sum += sumFactor * pr;
177 | 		g_sum += sumFactor * pg;
178 | 		b_sum += sumFactor * pb;
179 | 		a_sum += sumFactor * pa;
180 | 		
181 | 		stack = stackStart;
182 | 		
183 | 		for( i = 0; i < radiusPlus1; i++ )
184 | 		{
185 | 			stack.r = pr;
186 | 			stack.g = pg;
187 | 			stack.b = pb;
188 | 			stack.a = pa;
189 | 			stack = stack.next;
190 | 		}
191 | 		
192 | 		for( i = 1; i < radiusPlus1; i++ )
193 | 		{
194 | 			p = yi + (( widthMinus1 < i ? widthMinus1 : i ) << 2 );
195 | 			r_sum += ( stack.r = ( pr = pixels[p])) * ( rbs = radiusPlus1 - i );
196 | 			g_sum += ( stack.g = ( pg = pixels[p+1])) * rbs;
197 | 			b_sum += ( stack.b = ( pb = pixels[p+2])) * rbs;
198 | 			a_sum += ( stack.a = ( pa = pixels[p+3])) * rbs;
199 | 			
200 | 			r_in_sum += pr;
201 | 			g_in_sum += pg;
202 | 			b_in_sum += pb;
203 | 			a_in_sum += pa;
204 | 			
205 | 			stack = stack.next;
206 | 		}
207 | 		
208 | 		
209 | 		stackIn = stackStart;
210 | 		stackOut = stackEnd;
211 | 		for ( x = 0; x < width; x++ )
212 | 		{
213 | 			pixels[yi+3] = pa = (a_sum * mul_sum) >> shg_sum;
214 | 			if ( pa != 0 )
215 | 			{
216 | 				pa = 255 / pa;
217 | 				pixels[yi]   = ((r_sum * mul_sum) >> shg_sum) * pa;
218 | 				pixels[yi+1] = ((g_sum * mul_sum) >> shg_sum) * pa;
219 | 				pixels[yi+2] = ((b_sum * mul_sum) >> shg_sum) * pa;
220 | 			} else {
221 | 				pixels[yi] = pixels[yi+1] = pixels[yi+2] = 0;
222 | 			}
223 | 			
224 | 			r_sum -= r_out_sum;
225 | 			g_sum -= g_out_sum;
226 | 			b_sum -= b_out_sum;
227 | 			a_sum -= a_out_sum;
228 | 			
229 | 			r_out_sum -= stackIn.r;
230 | 			g_out_sum -= stackIn.g;
231 | 			b_out_sum -= stackIn.b;
232 | 			a_out_sum -= stackIn.a;
233 | 			
234 | 			p =  ( yw + ( ( p = x + radius + 1 ) < widthMinus1 ? p : widthMinus1 ) ) << 2;
235 | 			
236 | 			r_in_sum += ( stackIn.r = pixels[p]);
237 | 			g_in_sum += ( stackIn.g = pixels[p+1]);
238 | 			b_in_sum += ( stackIn.b = pixels[p+2]);
239 | 			a_in_sum += ( stackIn.a = pixels[p+3]);
240 | 			
241 | 			r_sum += r_in_sum;
242 | 			g_sum += g_in_sum;
243 | 			b_sum += b_in_sum;
244 | 			a_sum += a_in_sum;
245 | 			
246 | 			stackIn = stackIn.next;
247 | 			
248 | 			r_out_sum += ( pr = stackOut.r );
249 | 			g_out_sum += ( pg = stackOut.g );
250 | 			b_out_sum += ( pb = stackOut.b );
251 | 			a_out_sum += ( pa = stackOut.a );
252 | 			
253 | 			r_in_sum -= pr;
254 | 			g_in_sum -= pg;
255 | 			b_in_sum -= pb;
256 | 			a_in_sum -= pa;
257 | 			
258 | 			stackOut = stackOut.next;
259 | 
260 | 			yi += 4;
261 | 		}
262 | 		yw += width;
263 | 	}
264 | 
265 | 	
266 | 	for ( x = 0; x < width; x++ )
267 | 	{
268 | 		g_in_sum = b_in_sum = a_in_sum = r_in_sum = g_sum = b_sum = a_sum = r_sum = 0;
269 | 		
270 | 		yi = x << 2;
271 | 		r_out_sum = radiusPlus1 * ( pr = pixels[yi]);
272 | 		g_out_sum = radiusPlus1 * ( pg = pixels[yi+1]);
273 | 		b_out_sum = radiusPlus1 * ( pb = pixels[yi+2]);
274 | 		a_out_sum = radiusPlus1 * ( pa = pixels[yi+3]);
275 | 		
276 | 		r_sum += sumFactor * pr;
277 | 		g_sum += sumFactor * pg;
278 | 		b_sum += sumFactor * pb;
279 | 		a_sum += sumFactor * pa;
280 | 		
281 | 		stack = stackStart;
282 | 		
283 | 		for( i = 0; i < radiusPlus1; i++ )
284 | 		{
285 | 			stack.r = pr;
286 | 			stack.g = pg;
287 | 			stack.b = pb;
288 | 			stack.a = pa;
289 | 			stack = stack.next;
290 | 		}
291 | 		
292 | 		yp = width;
293 | 		
294 | 		for( i = 1; i <= radius; i++ )
295 | 		{
296 | 			yi = ( yp + x ) << 2;
297 | 			
298 | 			r_sum += ( stack.r = ( pr = pixels[yi])) * ( rbs = radiusPlus1 - i );
299 | 			g_sum += ( stack.g = ( pg = pixels[yi+1])) * rbs;
300 | 			b_sum += ( stack.b = ( pb = pixels[yi+2])) * rbs;
301 | 			a_sum += ( stack.a = ( pa = pixels[yi+3])) * rbs;
302 | 		   
303 | 			r_in_sum += pr;
304 | 			g_in_sum += pg;
305 | 			b_in_sum += pb;
306 | 			a_in_sum += pa;
307 | 			
308 | 			stack = stack.next;
309 | 		
310 | 			if( i < heightMinus1 )
311 | 			{
312 | 				yp += width;
313 | 			}
314 | 		}
315 | 		
316 | 		yi = x;
317 | 		stackIn = stackStart;
318 | 		stackOut = stackEnd;
319 | 		for ( y = 0; y < height; y++ )
320 | 		{
321 | 			p = yi << 2;
322 | 			pixels[p+3] = pa = (a_sum * mul_sum) >> shg_sum;
323 | 			if ( pa > 0 )
324 | 			{
325 | 				pa = 255 / pa;
326 | 				pixels[p]   = ((r_sum * mul_sum) >> shg_sum ) * pa;
327 | 				pixels[p+1] = ((g_sum * mul_sum) >> shg_sum ) * pa;
328 | 				pixels[p+2] = ((b_sum * mul_sum) >> shg_sum ) * pa;
329 | 			} else {
330 | 				pixels[p] = pixels[p+1] = pixels[p+2] = 0;
331 | 			}
332 | 			
333 | 			r_sum -= r_out_sum;
334 | 			g_sum -= g_out_sum;
335 | 			b_sum -= b_out_sum;
336 | 			a_sum -= a_out_sum;
337 | 		   
338 | 			r_out_sum -= stackIn.r;
339 | 			g_out_sum -= stackIn.g;
340 | 			b_out_sum -= stackIn.b;
341 | 			a_out_sum -= stackIn.a;
342 | 			
343 | 			p = ( x + (( ( p = y + radiusPlus1) < heightMinus1 ? p : heightMinus1 ) * width )) << 2;
344 | 			
345 | 			r_sum += ( r_in_sum += ( stackIn.r = pixels[p]));
346 | 			g_sum += ( g_in_sum += ( stackIn.g = pixels[p+1]));
347 | 			b_sum += ( b_in_sum += ( stackIn.b = pixels[p+2]));
348 | 			a_sum += ( a_in_sum += ( stackIn.a = pixels[p+3]));
349 | 		   
350 | 			stackIn = stackIn.next;
351 | 			
352 | 			r_out_sum += ( pr = stackOut.r );
353 | 			g_out_sum += ( pg = stackOut.g );
354 | 			b_out_sum += ( pb = stackOut.b );
355 | 			a_out_sum += ( pa = stackOut.a );
356 | 			
357 | 			r_in_sum -= pr;
358 | 			g_in_sum -= pg;
359 | 			b_in_sum -= pb;
360 | 			a_in_sum -= pa;
361 | 			
362 | 			stackOut = stackOut.next;
363 | 			
364 | 			yi += width;
365 | 		}
366 | 	}
367 | 	
368 | 	context.putImageData( imageData, top_x, top_y );
369 | 	
370 | }
371 | 
372 | 
373 | function stackBlurCanvasRGB( id, top_x, top_y, width, height, radius )
374 | {
375 | 	if ( isNaN(radius) || radius < 1 ) return;
376 | 	radius |= 0;
377 | 	
378 | 	var canvas  = document.getElementById( id );
379 | 	var context = canvas.getContext("2d");
380 | 	var imageData;
381 | 	
382 | 	try {
383 | 	  try {
384 | 		imageData = context.getImageData( top_x, top_y, width, height );
385 | 	  } catch(e) {
386 | 	  
387 | 		// NOTE: this part is supposedly only needed if you want to work with local files
388 | 		// so it might be okay to remove the whole try/catch block and just use
389 | 		// imageData = context.getImageData( top_x, top_y, width, height );
390 | 		try {
391 | 			netscape.security.PrivilegeManager.enablePrivilege("UniversalBrowserRead");
392 | 			imageData = context.getImageData( top_x, top_y, width, height );
393 | 		} catch(e) {
394 | 			alert("Cannot access local image");
395 | 			throw new Error("unable to access local image data: " + e);
396 | 			return;
397 | 		}
398 | 	  }
399 | 	} catch(e) {
400 | 	  alert("Cannot access image");
401 | 	  throw new Error("unable to access image data: " + e);
402 | 	}
403 | 			
404 | 	var pixels = imageData.data;
405 | 			
406 | 	var x, y, i, p, yp, yi, yw, r_sum, g_sum, b_sum,
407 | 	r_out_sum, g_out_sum, b_out_sum,
408 | 	r_in_sum, g_in_sum, b_in_sum,
409 | 	pr, pg, pb, rbs;
410 | 			
411 | 	var div = radius + radius + 1;
412 | 	var w4 = width << 2;
413 | 	var widthMinus1  = width - 1;
414 | 	var heightMinus1 = height - 1;
415 | 	var radiusPlus1  = radius + 1;
416 | 	var sumFactor = radiusPlus1 * ( radiusPlus1 + 1 ) / 2;
417 | 	
418 | 	var stackStart = new BlurStack();
419 | 	var stack = stackStart;
420 | 	for ( i = 1; i < div; i++ )
421 | 	{
422 | 		stack = stack.next = new BlurStack();
423 | 		if ( i == radiusPlus1 ) var stackEnd = stack;
424 | 	}
425 | 	stack.next = stackStart;
426 | 	var stackIn = null;
427 | 	var stackOut = null;
428 | 	
429 | 	yw = yi = 0;
430 | 	
431 | 	var mul_sum = mul_table[radius];
432 | 	var shg_sum = shg_table[radius];
433 | 	
434 | 	for ( y = 0; y < height; y++ )
435 | 	{
436 | 		r_in_sum = g_in_sum = b_in_sum = r_sum = g_sum = b_sum = 0;
437 | 		
438 | 		r_out_sum = radiusPlus1 * ( pr = pixels[yi] );
439 | 		g_out_sum = radiusPlus1 * ( pg = pixels[yi+1] );
440 | 		b_out_sum = radiusPlus1 * ( pb = pixels[yi+2] );
441 | 		
442 | 		r_sum += sumFactor * pr;
443 | 		g_sum += sumFactor * pg;
444 | 		b_sum += sumFactor * pb;
445 | 		
446 | 		stack = stackStart;
447 | 		
448 | 		for( i = 0; i < radiusPlus1; i++ )
449 | 		{
450 | 			stack.r = pr;
451 | 			stack.g = pg;
452 | 			stack.b = pb;
453 | 			stack = stack.next;
454 | 		}
455 | 		
456 | 		for( i = 1; i < radiusPlus1; i++ )
457 | 		{
458 | 			p = yi + (( widthMinus1 < i ? widthMinus1 : i ) << 2 );
459 | 			r_sum += ( stack.r = ( pr = pixels[p])) * ( rbs = radiusPlus1 - i );
460 | 			g_sum += ( stack.g = ( pg = pixels[p+1])) * rbs;
461 | 			b_sum += ( stack.b = ( pb = pixels[p+2])) * rbs;
462 | 			
463 | 			r_in_sum += pr;
464 | 			g_in_sum += pg;
465 | 			b_in_sum += pb;
466 | 			
467 | 			stack = stack.next;
468 | 		}
469 | 		
470 | 		
471 | 		stackIn = stackStart;
472 | 		stackOut = stackEnd;
473 | 		for ( x = 0; x < width; x++ )
474 | 		{
475 | 			pixels[yi]   = (r_sum * mul_sum) >> shg_sum;
476 | 			pixels[yi+1] = (g_sum * mul_sum) >> shg_sum;
477 | 			pixels[yi+2] = (b_sum * mul_sum) >> shg_sum;
478 | 			
479 | 			r_sum -= r_out_sum;
480 | 			g_sum -= g_out_sum;
481 | 			b_sum -= b_out_sum;
482 | 			
483 | 			r_out_sum -= stackIn.r;
484 | 			g_out_sum -= stackIn.g;
485 | 			b_out_sum -= stackIn.b;
486 | 			
487 | 			p =  ( yw + ( ( p = x + radius + 1 ) < widthMinus1 ? p : widthMinus1 ) ) << 2;
488 | 			
489 | 			r_in_sum += ( stackIn.r = pixels[p]);
490 | 			g_in_sum += ( stackIn.g = pixels[p+1]);
491 | 			b_in_sum += ( stackIn.b = pixels[p+2]);
492 | 			
493 | 			r_sum += r_in_sum;
494 | 			g_sum += g_in_sum;
495 | 			b_sum += b_in_sum;
496 | 			
497 | 			stackIn = stackIn.next;
498 | 			
499 | 			r_out_sum += ( pr = stackOut.r );
500 | 			g_out_sum += ( pg = stackOut.g );
501 | 			b_out_sum += ( pb = stackOut.b );
502 | 			
503 | 			r_in_sum -= pr;
504 | 			g_in_sum -= pg;
505 | 			b_in_sum -= pb;
506 | 			
507 | 			stackOut = stackOut.next;
508 | 
509 | 			yi += 4;
510 | 		}
511 | 		yw += width;
512 | 	}
513 | 
514 | 	
515 | 	for ( x = 0; x < width; x++ )
516 | 	{
517 | 		g_in_sum = b_in_sum = r_in_sum = g_sum = b_sum = r_sum = 0;
518 | 		
519 | 		yi = x << 2;
520 | 		r_out_sum = radiusPlus1 * ( pr = pixels[yi]);
521 | 		g_out_sum = radiusPlus1 * ( pg = pixels[yi+1]);
522 | 		b_out_sum = radiusPlus1 * ( pb = pixels[yi+2]);
523 | 		
524 | 		r_sum += sumFactor * pr;
525 | 		g_sum += sumFactor * pg;
526 | 		b_sum += sumFactor * pb;
527 | 		
528 | 		stack = stackStart;
529 | 		
530 | 		for( i = 0; i < radiusPlus1; i++ )
531 | 		{
532 | 			stack.r = pr;
533 | 			stack.g = pg;
534 | 			stack.b = pb;
535 | 			stack = stack.next;
536 | 		}
537 | 		
538 | 		yp = width;
539 | 		
540 | 		for( i = 1; i <= radius; i++ )
541 | 		{
542 | 			yi = ( yp + x ) << 2;
543 | 			
544 | 			r_sum += ( stack.r = ( pr = pixels[yi])) * ( rbs = radiusPlus1 - i );
545 | 			g_sum += ( stack.g = ( pg = pixels[yi+1])) * rbs;
546 | 			b_sum += ( stack.b = ( pb = pixels[yi+2])) * rbs;
547 | 			
548 | 			r_in_sum += pr;
549 | 			g_in_sum += pg;
550 | 			b_in_sum += pb;
551 | 			
552 | 			stack = stack.next;
553 | 		
554 | 			if( i < heightMinus1 )
555 | 			{
556 | 				yp += width;
557 | 			}
558 | 		}
559 | 		
560 | 		yi = x;
561 | 		stackIn = stackStart;
562 | 		stackOut = stackEnd;
563 | 		for ( y = 0; y < height; y++ )
564 | 		{
565 | 			p = yi << 2;
566 | 			pixels[p]   = (r_sum * mul_sum) >> shg_sum;
567 | 			pixels[p+1] = (g_sum * mul_sum) >> shg_sum;
568 | 			pixels[p+2] = (b_sum * mul_sum) >> shg_sum;
569 | 			
570 | 			r_sum -= r_out_sum;
571 | 			g_sum -= g_out_sum;
572 | 			b_sum -= b_out_sum;
573 | 			
574 | 			r_out_sum -= stackIn.r;
575 | 			g_out_sum -= stackIn.g;
576 | 			b_out_sum -= stackIn.b;
577 | 			
578 | 			p = ( x + (( ( p = y + radiusPlus1) < heightMinus1 ? p : heightMinus1 ) * width )) << 2;
579 | 			
580 | 			r_sum += ( r_in_sum += ( stackIn.r = pixels[p]));
581 | 			g_sum += ( g_in_sum += ( stackIn.g = pixels[p+1]));
582 | 			b_sum += ( b_in_sum += ( stackIn.b = pixels[p+2]));
583 | 			
584 | 			stackIn = stackIn.next;
585 | 			
586 | 			r_out_sum += ( pr = stackOut.r );
587 | 			g_out_sum += ( pg = stackOut.g );
588 | 			b_out_sum += ( pb = stackOut.b );
589 | 			
590 | 			r_in_sum -= pr;
591 | 			g_in_sum -= pg;
592 | 			b_in_sum -= pb;
593 | 			
594 | 			stackOut = stackOut.next;
595 | 			
596 | 			yi += width;
597 | 		}
598 | 	}
599 | 	
600 | 	context.putImageData( imageData, top_x, top_y );
601 | 	
602 | }
603 | 
604 | function BlurStack()
605 | {
606 | 	this.r = 0;
607 | 	this.g = 0;
608 | 	this.b = 0;
609 | 	this.a = 0;
610 | 	this.next = null;
611 | }


--------------------------------------------------------------------------------
/canvg/rgbcolor.js:
--------------------------------------------------------------------------------
  1 | /**
  2 |  * A class to parse color values
  3 |  * @author Stoyan Stefanov <sstoo@gmail.com>
  4 |  * @link   http://www.phpied.com/rgb-color-parser-in-javascript/
  5 |  * @license Use it if you like it
  6 |  */
  7 | function RGBColor(color_string)
  8 | {
  9 |     this.ok = false;
 10 | 
 11 |     // strip any leading #
 12 |     if (color_string.charAt(0) == '#') { // remove # if any
 13 |         color_string = color_string.substr(1,6);
 14 |     }
 15 | 
 16 |     color_string = color_string.replace(/ /g,'');
 17 |     color_string = color_string.toLowerCase();
 18 | 
 19 |     // before getting into regexps, try simple matches
 20 |     // and overwrite the input
 21 |     var simple_colors = {
 22 |         aliceblue: 'f0f8ff',
 23 |         antiquewhite: 'faebd7',
 24 |         aqua: '00ffff',
 25 |         aquamarine: '7fffd4',
 26 |         azure: 'f0ffff',
 27 |         beige: 'f5f5dc',
 28 |         bisque: 'ffe4c4',
 29 |         black: '000000',
 30 |         blanchedalmond: 'ffebcd',
 31 |         blue: '0000ff',
 32 |         blueviolet: '8a2be2',
 33 |         brown: 'a52a2a',
 34 |         burlywood: 'deb887',
 35 |         cadetblue: '5f9ea0',
 36 |         chartreuse: '7fff00',
 37 |         chocolate: 'd2691e',
 38 |         coral: 'ff7f50',
 39 |         cornflowerblue: '6495ed',
 40 |         cornsilk: 'fff8dc',
 41 |         crimson: 'dc143c',
 42 |         cyan: '00ffff',
 43 |         darkblue: '00008b',
 44 |         darkcyan: '008b8b',
 45 |         darkgoldenrod: 'b8860b',
 46 |         darkgray: 'a9a9a9',
 47 |         darkgreen: '006400',
 48 |         darkkhaki: 'bdb76b',
 49 |         darkmagenta: '8b008b',
 50 |         darkolivegreen: '556b2f',
 51 |         darkorange: 'ff8c00',
 52 |         darkorchid: '9932cc',
 53 |         darkred: '8b0000',
 54 |         darksalmon: 'e9967a',
 55 |         darkseagreen: '8fbc8f',
 56 |         darkslateblue: '483d8b',
 57 |         darkslategray: '2f4f4f',
 58 |         darkturquoise: '00ced1',
 59 |         darkviolet: '9400d3',
 60 |         deeppink: 'ff1493',
 61 |         deepskyblue: '00bfff',
 62 |         dimgray: '696969',
 63 |         dodgerblue: '1e90ff',
 64 |         feldspar: 'd19275',
 65 |         firebrick: 'b22222',
 66 |         floralwhite: 'fffaf0',
 67 |         forestgreen: '228b22',
 68 |         fuchsia: 'ff00ff',
 69 |         gainsboro: 'dcdcdc',
 70 |         ghostwhite: 'f8f8ff',
 71 |         gold: 'ffd700',
 72 |         goldenrod: 'daa520',
 73 |         gray: '808080',
 74 |         green: '008000',
 75 |         greenyellow: 'adff2f',
 76 |         honeydew: 'f0fff0',
 77 |         hotpink: 'ff69b4',
 78 |         indianred : 'cd5c5c',
 79 |         indigo : '4b0082',
 80 |         ivory: 'fffff0',
 81 |         khaki: 'f0e68c',
 82 |         lavender: 'e6e6fa',
 83 |         lavenderblush: 'fff0f5',
 84 |         lawngreen: '7cfc00',
 85 |         lemonchiffon: 'fffacd',
 86 |         lightblue: 'add8e6',
 87 |         lightcoral: 'f08080',
 88 |         lightcyan: 'e0ffff',
 89 |         lightgoldenrodyellow: 'fafad2',
 90 |         lightgrey: 'd3d3d3',
 91 |         lightgreen: '90ee90',
 92 |         lightpink: 'ffb6c1',
 93 |         lightsalmon: 'ffa07a',
 94 |         lightseagreen: '20b2aa',
 95 |         lightskyblue: '87cefa',
 96 |         lightslateblue: '8470ff',
 97 |         lightslategray: '778899',
 98 |         lightsteelblue: 'b0c4de',
 99 |         lightyellow: 'ffffe0',
100 |         lime: '00ff00',
101 |         limegreen: '32cd32',
102 |         linen: 'faf0e6',
103 |         magenta: 'ff00ff',
104 |         maroon: '800000',
105 |         mediumaquamarine: '66cdaa',
106 |         mediumblue: '0000cd',
107 |         mediumorchid: 'ba55d3',
108 |         mediumpurple: '9370d8',
109 |         mediumseagreen: '3cb371',
110 |         mediumslateblue: '7b68ee',
111 |         mediumspringgreen: '00fa9a',
112 |         mediumturquoise: '48d1cc',
113 |         mediumvioletred: 'c71585',
114 |         midnightblue: '191970',
115 |         mintcream: 'f5fffa',
116 |         mistyrose: 'ffe4e1',
117 |         moccasin: 'ffe4b5',
118 |         navajowhite: 'ffdead',
119 |         navy: '000080',
120 |         oldlace: 'fdf5e6',
121 |         olive: '808000',
122 |         olivedrab: '6b8e23',
123 |         orange: 'ffa500',
124 |         orangered: 'ff4500',
125 |         orchid: 'da70d6',
126 |         palegoldenrod: 'eee8aa',
127 |         palegreen: '98fb98',
128 |         paleturquoise: 'afeeee',
129 |         palevioletred: 'd87093',
130 |         papayawhip: 'ffefd5',
131 |         peachpuff: 'ffdab9',
132 |         peru: 'cd853f',
133 |         pink: 'ffc0cb',
134 |         plum: 'dda0dd',
135 |         powderblue: 'b0e0e6',
136 |         purple: '800080',
137 |         red: 'ff0000',
138 |         rosybrown: 'bc8f8f',
139 |         royalblue: '4169e1',
140 |         saddlebrown: '8b4513',
141 |         salmon: 'fa8072',
142 |         sandybrown: 'f4a460',
143 |         seagreen: '2e8b57',
144 |         seashell: 'fff5ee',
145 |         sienna: 'a0522d',
146 |         silver: 'c0c0c0',
147 |         skyblue: '87ceeb',
148 |         slateblue: '6a5acd',
149 |         slategray: '708090',
150 |         snow: 'fffafa',
151 |         springgreen: '00ff7f',
152 |         steelblue: '4682b4',
153 |         tan: 'd2b48c',
154 |         teal: '008080',
155 |         thistle: 'd8bfd8',
156 |         tomato: 'ff6347',
157 |         turquoise: '40e0d0',
158 |         violet: 'ee82ee',
159 |         violetred: 'd02090',
160 |         wheat: 'f5deb3',
161 |         white: 'ffffff',
162 |         whitesmoke: 'f5f5f5',
163 |         yellow: 'ffff00',
164 |         yellowgreen: '9acd32'
165 |     };
166 |     for (var key in simple_colors) {
167 |         if (color_string == key) {
168 |             color_string = simple_colors[key];
169 |         }
170 |     }
171 |     // emd of simple type-in colors
172 | 
173 |     // array of color definition objects
174 |     var color_defs = [
175 |         {
176 |             re: /^rgb\((\d{1,3}),\s*(\d{1,3}),\s*(\d{1,3})\)$/,
177 |             example: ['rgb(123, 234, 45)', 'rgb(255,234,245)'],
178 |             process: function (bits){
179 |                 return [
180 |                     parseInt(bits[1]),
181 |                     parseInt(bits[2]),
182 |                     parseInt(bits[3])
183 |                 ];
184 |             }
185 |         },
186 |         {
187 |             re: /^(\w{2})(\w{2})(\w{2})$/,
188 |             example: ['#00ff00', '336699'],
189 |             process: function (bits){
190 |                 return [
191 |                     parseInt(bits[1], 16),
192 |                     parseInt(bits[2], 16),
193 |                     parseInt(bits[3], 16)
194 |                 ];
195 |             }
196 |         },
197 |         {
198 |             re: /^(\w{1})(\w{1})(\w{1})$/,
199 |             example: ['#fb0', 'f0f'],
200 |             process: function (bits){
201 |                 return [
202 |                     parseInt(bits[1] + bits[1], 16),
203 |                     parseInt(bits[2] + bits[2], 16),
204 |                     parseInt(bits[3] + bits[3], 16)
205 |                 ];
206 |             }
207 |         }
208 |     ];
209 | 
210 |     // search through the definitions to find a match
211 |     for (var i = 0; i < color_defs.length; i++) {
212 |         var re = color_defs[i].re;
213 |         var processor = color_defs[i].process;
214 |         var bits = re.exec(color_string);
215 |         if (bits) {
216 |             channels = processor(bits);
217 |             this.r = channels[0];
218 |             this.g = channels[1];
219 |             this.b = channels[2];
220 |             this.ok = true;
221 |         }
222 | 
223 |     }
224 | 
225 |     // validate/cleanup values
226 |     this.r = (this.r < 0 || isNaN(this.r)) ? 0 : ((this.r > 255) ? 255 : this.r);
227 |     this.g = (this.g < 0 || isNaN(this.g)) ? 0 : ((this.g > 255) ? 255 : this.g);
228 |     this.b = (this.b < 0 || isNaN(this.b)) ? 0 : ((this.b > 255) ? 255 : this.b);
229 | 
230 |     // some getters
231 |     this.toRGB = function () {
232 |         return 'rgb(' + this.r + ', ' + this.g + ', ' + this.b + ')';
233 |     }
234 |     this.toHex = function () {
235 |         var r = this.r.toString(16);
236 |         var g = this.g.toString(16);
237 |         var b = this.b.toString(16);
238 |         if (r.length == 1) r = '0' + r;
239 |         if (g.length == 1) g = '0' + g;
240 |         if (b.length == 1) b = '0' + b;
241 |         return '#' + r + g + b;
242 |     }
243 | 
244 |     // help
245 |     this.getHelpXML = function () {
246 | 
247 |         var examples = new Array();
248 |         // add regexps
249 |         for (var i = 0; i < color_defs.length; i++) {
250 |             var example = color_defs[i].example;
251 |             for (var j = 0; j < example.length; j++) {
252 |                 examples[examples.length] = example[j];
253 |             }
254 |         }
255 |         // add type-in colors
256 |         for (var sc in simple_colors) {
257 |             examples[examples.length] = sc;
258 |         }
259 | 
260 |         var xml = document.createElement('ul');
261 |         xml.setAttribute('id', 'rgbcolor-examples');
262 |         for (var i = 0; i < examples.length; i++) {
263 |             try {
264 |                 var list_item = document.createElement('li');
265 |                 var list_color = new RGBColor(examples[i]);
266 |                 var example_div = document.createElement('div');
267 |                 example_div.style.cssText =
268 |                         'margin: 3px; '
269 |                         + 'border: 1px solid black; '
270 |                         + 'background:' + list_color.toHex() + '; '
271 |                         + 'color:' + list_color.toHex()
272 |                 ;
273 |                 example_div.appendChild(document.createTextNode('test'));
274 |                 var list_item_value = document.createTextNode(
275 |                     ' ' + examples[i] + ' -> ' + list_color.toRGB() + ' -> ' + list_color.toHex()
276 |                 );
277 |                 list_item.appendChild(example_div);
278 |                 list_item.appendChild(list_item_value);
279 |                 xml.appendChild(list_item);
280 | 
281 |             } catch(e){}
282 |         }
283 |         return xml;
284 | 
285 |     }
286 | 
287 | }
288 | 
289 | 


--------------------------------------------------------------------------------
/d3/d3-tip.js:
--------------------------------------------------------------------------------
  1 | // d3.tip
  2 | // Copyright (c) 2013 Justin Palmer
  3 | //
  4 | // Tooltips for d3.js SVG visualizations
  5 | 
  6 | (function (root, factory) {
  7 |   if (typeof define === 'function' && define.amd) {
  8 |     // AMD. Register as an anonymous module with d3 as a dependency.
  9 |     define(['d3'], factory)
 10 |   } else {
 11 |     // Browser global.
 12 |     root.d3.tip = factory(root.d3)
 13 |   }
 14 | }(this, function (d3) {
 15 | 
 16 |   // Public - contructs a new tooltip
 17 |   //
 18 |   // Returns a tip
 19 |   return function() {
 20 |     var direction = d3_tip_direction,
 21 |         offset    = d3_tip_offset,
 22 |         html      = d3_tip_html,
 23 |         node      = initNode(),
 24 |         svg       = null,
 25 |         point     = null,
 26 |         target    = null
 27 |   
 28 |     function tip(vis) {
 29 |       svg = getSVGNode(vis)
 30 |       point = svg.createSVGPoint()
 31 |       document.body.appendChild(node)
 32 |     }
 33 |   
 34 |     // Public - show the tooltip on the screen
 35 |     //
 36 |     // Returns a tip
 37 |     tip.show = function() {
 38 |       var args = Array.prototype.slice.call(arguments)
 39 |       if(args[args.length - 1] instanceof SVGElement) target = args.pop()
 40 |   
 41 |       var content = html.apply(this, args),
 42 |           poffset = offset.apply(this, args),
 43 |           dir     = direction.apply(this, args),
 44 |           nodel   = d3.select(node),
 45 |           i       = directions.length,
 46 |           coords
 47 |   
 48 |       nodel.html(content)
 49 |         .style({ opacity: 1, 'pointer-events': 'all' })
 50 |   
 51 |       while(i--) nodel.classed(directions[i], false)
 52 |       coords = direction_callbacks.get(dir).apply(this)
 53 |       nodel.classed(dir, true).style({
 54 |         top: (coords.top +  poffset[0]) + 'px',
 55 |         left: (coords.left + poffset[1]) + 'px'
 56 |       })
 57 |   
 58 |       return tip
 59 |     }
 60 |   
 61 |     // Public - hide the tooltip
 62 |     //
 63 |     // Returns a tip
 64 |     tip.hide = function() {
 65 |       nodel = d3.select(node)
 66 |       nodel.style({ opacity: 0, 'pointer-events': 'none' })
 67 |       return tip
 68 |     }
 69 |   
 70 |     // Public: Proxy attr calls to the d3 tip container.  Sets or gets attribute value.
 71 |     //
 72 |     // n - name of the attribute
 73 |     // v - value of the attribute
 74 |     //
 75 |     // Returns tip or attribute value
 76 |     tip.attr = function(n, v) {
 77 |       if (arguments.length < 2 && typeof n === 'string') {
 78 |         return d3.select(node).attr(n)
 79 |       } else {
 80 |         var args =  Array.prototype.slice.call(arguments)
 81 |         d3.selection.prototype.attr.apply(d3.select(node), args)
 82 |       }
 83 |   
 84 |       return tip
 85 |     }
 86 |   
 87 |     // Public: Proxy style calls to the d3 tip container.  Sets or gets a style value.
 88 |     //
 89 |     // n - name of the property
 90 |     // v - value of the property
 91 |     //
 92 |     // Returns tip or style property value
 93 |     tip.style = function(n, v) {
 94 |       if (arguments.length < 2 && typeof n === 'string') {
 95 |         return d3.select(node).style(n)
 96 |       } else {
 97 |         var args =  Array.prototype.slice.call(arguments)
 98 |         d3.selection.prototype.style.apply(d3.select(node), args)
 99 |       }
100 |   
101 |       return tip
102 |     }
103 |   
104 |     // Public: Set or get the direction of the tooltip
105 |     //
106 |     // v - One of n(north), s(south), e(east), or w(west), nw(northwest),
107 |     //     sw(southwest), ne(northeast) or se(southeast)
108 |     //
109 |     // Returns tip or direction
110 |     tip.direction = function(v) {
111 |       if (!arguments.length) return direction
112 |       direction = v == null ? v : d3.functor(v)
113 |   
114 |       return tip
115 |     }
116 |   
117 |     // Public: Sets or gets the offset of the tip
118 |     //
119 |     // v - Array of [x, y] offset
120 |     //
121 |     // Returns offset or
122 |     tip.offset = function(v) {
123 |       if (!arguments.length) return offset
124 |       offset = v == null ? v : d3.functor(v)
125 |   
126 |       return tip
127 |     }
128 |   
129 |     // Public: sets or gets the html value of the tooltip
130 |     //
131 |     // v - String value of the tip
132 |     //
133 |     // Returns html value or tip
134 |     tip.html = function(v) {
135 |       if (!arguments.length) return html
136 |       html = v == null ? v : d3.functor(v)
137 |   
138 |       return tip
139 |     }
140 |   
141 |     function d3_tip_direction() { return 'n' }
142 |     function d3_tip_offset() { return [0, 0] }
143 |     function d3_tip_html() { return ' ' }
144 |   
145 |     var direction_callbacks = d3.map({
146 |       n:  direction_n,
147 |       s:  direction_s,
148 |       e:  direction_e,
149 |       w:  direction_w,
150 |       nw: direction_nw,
151 |       ne: direction_ne,
152 |       sw: direction_sw,
153 |       se: direction_se
154 |     }),
155 |   
156 |     directions = direction_callbacks.keys()
157 |   
158 |     function direction_n() {
159 |       var bbox = getScreenBBox()
160 |       return {
161 |         top:  bbox.n.y - node.offsetHeight,
162 |         left: bbox.n.x - node.offsetWidth / 2
163 |       }
164 |     }
165 |   
166 |     function direction_s() {
167 |       var bbox = getScreenBBox()
168 |       return {
169 |         top:  bbox.s.y,
170 |         left: bbox.s.x - node.offsetWidth / 2
171 |       }
172 |     }
173 |   
174 |     function direction_e() {
175 |       var bbox = getScreenBBox()
176 |       return {
177 |         top:  bbox.e.y - node.offsetHeight / 2,
178 |         left: bbox.e.x
179 |       }
180 |     }
181 |   
182 |     function direction_w() {
183 |       var bbox = getScreenBBox()
184 |       return {
185 |         top:  bbox.w.y - node.offsetHeight / 2,
186 |         left: bbox.w.x - node.offsetWidth
187 |       }
188 |     }
189 |   
190 |     function direction_nw() {
191 |       var bbox = getScreenBBox()
192 |       return {
193 |         top:  bbox.nw.y - node.offsetHeight,
194 |         left: bbox.nw.x - node.offsetWidth
195 |       }
196 |     }
197 |   
198 |     function direction_ne() {
199 |       var bbox = getScreenBBox()
200 |       return {
201 |         top:  bbox.ne.y - node.offsetHeight,
202 |         left: bbox.ne.x
203 |       }
204 |     }
205 |   
206 |     function direction_sw() {
207 |       var bbox = getScreenBBox()
208 |       return {
209 |         top:  bbox.sw.y,
210 |         left: bbox.sw.x - node.offsetWidth
211 |       }
212 |     }
213 |   
214 |     function direction_se() {
215 |       var bbox = getScreenBBox()
216 |       return {
217 |         top:  bbox.se.y,
218 |         left: bbox.e.x
219 |       }
220 |     }
221 |   
222 |     function initNode() {
223 |       var node = d3.select(document.createElement('div'))
224 |       node.style({
225 |         position: 'absolute',
226 |         top: 0,
227 |         opacity: 0,
228 |         'pointer-events': 'none',
229 |         'box-sizing': 'border-box'
230 |       })
231 |   
232 |       return node.node()
233 |     }
234 |   
235 |     function getSVGNode(el) {
236 |       el = el.node()
237 |       if(el.tagName.toLowerCase() == 'svg')
238 |         return el
239 |   
240 |       return el.ownerSVGElement
241 |     }
242 |   
243 |     // Private - gets the screen coordinates of a shape
244 |     //
245 |     // Given a shape on the screen, will return an SVGPoint for the directions
246 |     // n(north), s(south), e(east), w(west), ne(northeast), se(southeast), nw(northwest),
247 |     // sw(southwest).
248 |     //
249 |     //    +-+-+
250 |     //    |   |
251 |     //    +   +
252 |     //    |   |
253 |     //    +-+-+
254 |     //
255 |     // Returns an Object {n, s, e, w, nw, sw, ne, se}
256 |     function getScreenBBox() {
257 |       var targetel   = target || d3.event.target,
258 |           bbox       = {},
259 |           matrix     = targetel.getScreenCTM(),
260 |           tbbox      = targetel.getBBox(),
261 |           width      = tbbox.width,
262 |           height     = tbbox.height,
263 |           x          = tbbox.x,
264 |           y          = tbbox.y,
265 |           scrollEl   = document.documentElement? document.documentElement : document.body,
266 |           scrollTop  = scrollEl.scrollTop,
267 |           scrollLeft = scrollEl.scrollLeft
268 |   
269 |   
270 |       point.x = x + scrollLeft
271 |       point.y = y + scrollTop
272 |       bbox.nw = point.matrixTransform(matrix)
273 |       point.x += width
274 |       bbox.ne = point.matrixTransform(matrix)
275 |       point.y += height
276 |       bbox.se = point.matrixTransform(matrix)
277 |       point.x -= width
278 |       bbox.sw = point.matrixTransform(matrix)
279 |       point.y -= height / 2
280 |       bbox.w  = point.matrixTransform(matrix)
281 |       point.x += width
282 |       bbox.e = point.matrixTransform(matrix)
283 |       point.x -= width / 2
284 |       point.y -= height / 2
285 |       bbox.n = point.matrixTransform(matrix)
286 |       point.y += height
287 |       bbox.s = point.matrixTransform(matrix)
288 |   
289 |       return bbox
290 |     }
291 |   
292 |     return tip
293 |   };
294 | 
295 | }));


--------------------------------------------------------------------------------
/examples/circulardemo.html:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html>
 2 | <html>
 3 |   <head>
 4 |     <meta http-equiv="Content-Type" content="text/html;charset=utf-8"/>
 5 |     <title>GenomeD3Plot Circularplot Example</title>
 6 |     <script src="../d3/d3.min.js"></script>
 7 |     <script src="../d3/d3-tip.js"></script>
 8 |     <style>
 9 |       body {
10 |         overflow: hidden;
11 |         margin: 0;
12 |         font-size: 14px;
13 |         font-family: "Helvetica Neue", Helvetica;
14 |       }
15 | 
16 |       #circularchart {
17 |         position: absolute;
18 |         top: 0px;
19 |         left: 125px;
20 |       }
21 |     </style>
22 |     <link href="tracks.css" rel="stylesheet">
23 |   </head>
24 |   <body>
25 |     <div id="plotbody">
26 |       <!-- The container that will hold the SVG of the plot -->
27 |       <div id="circularchart"></div>
28 |     </div>
29 |     
30 |     <!-- Libraries needed for save feature -->
31 |     <script type="text/javascript" src="../canvg/rgbcolor.js"></script>
32 |     <script type="text/javascript" src="../canvg/canvg.js"></script>
33 |     <script type="text/javascript" src="../FileSaver/FileSaver.js"></script>
34 | 
35 |     <!-- Sample data to be rendered -->
36 |     <script type="text/javascript" src="data.simple.js"></script>
37 | 
38 |     <!-- Circular plot library -->
39 |     <script type="text/javascript" src="../circularplot.js"></script>
40 | 
41 |     <!-- Initialization code to initialize the plot, this is what you would write
42 |          and place in your application. -->
43 |     <script type="text/javascript" src="circularsample.js"></script>
44 |  
45 | 
46 |     <!-- Controls on the demo -->
47 |     <div id="demo-controls">
48 |       <div class="control-item"><input type="checkbox" name="showGC" onchange="updateGC(this); return false" checked>Show GC plot</div>
49 | 
50 |       <div class="control-item"><input type="checkbox" name="showStrand" onchange="updateStrand(this); return false" checked>Show stranded track</div>
51 | 
52 |       <div class="control-item"><input type="checkbox" name="showvfdb" onchange="updateAdb(this); return false" checked>Show ADB glyph type</div>
53 | 
54 |       <div class="control-item"><input type="checkbox" name="showgaps" onchange="updateGaps(this); return false" checked>Show contig gap region type</div>
55 | 
56 |       <div class="control-item"><button name="saveImage" onclick="saveImage(); return false">Save Image</button></div>
57 | 
58 |       <div class="control-item"><input type="button" onClick="resizePlot(); return false;" value="Resize plot diameter"></button></div>
59 | 
60 |     </div>
61 | 
62 |  </body>
63 | </html>
64 | 


--------------------------------------------------------------------------------
/examples/circularsample.js:
--------------------------------------------------------------------------------
  1 | // Sample routines to initialize the plot for rendering
  2 | // and add some basic functionality.
  3 | 
  4 | // Initialize the defaults for the chart such as
  5 | // the genome size, the div container to put the
  6 | // SVG object in, what function to call during a
  7 | // double click and the initial chart size.
  8 | var genomesize = 6264404;
  9 | var circularlayout = {genomesize: genomesize,
 10 | 		      container: "#circularchart",
 11 | 		      dblclick: "doubleClick",
 12 |                       w: 550, h: 550
 13 |         };
 14 | 
 15 | // The actual initialization call which takes two
 16 | // parameters, the layout (above) for the plot and
 17 | // the dataset to visualize (from data.js, a json
 18 | // data structure)
 19 | var cTrack = new circularTrack(circularlayout, tracks);
 20 | 
 21 | // If we're showing both a circular and linear chart,
 22 | // and have a linear brush, attach it (see combo plot demo)
 23 | if('undefined' !== typeof linearTrack) {
 24 |     console.log("Attaching linear track");
 25 |     cTrack.attachBrush(linearTrack);
 26 |     cTrack.showBrush();
 27 | }
 28 | 
 29 | if('undefined' !== typeof brush) {
 30 |     console.log("Attaching linear track brush");
 31 |     cTrack.attachBrush(brush);
 32 | }
 33 | 
 34 | // Now some callbacks to make the interactive functionality work.
 35 | 
 36 | // Attached to the onchange callback for the GC Plot checkbox,
 37 | // call the plot to add/remove the GC Plot as needed
 38 | function updateGC(cb) {
 39 |     if(cb.checked) {
 40 | 	cTrack.showTrack("gcplot");
 41 |     } else {
 42 | 	cTrack.hideTrack("gcplot");
 43 |     }
 44 | }
 45 | 
 46 | // Attached to strand track checkbox, call the plot to
 47 | // add/remove the inner stranded track
 48 | function updateStrand(cb) {
 49 |     if(cb.checked) {
 50 | 	cTrack.showTrack("track1");
 51 |     } else {
 52 | 	cTrack.hideTrack("track1");
 53 |     }
 54 | }
 55 | 
 56 | // Attached to the contig gap checkbox, call the plot to
 57 | // add/remove the contig gap squiggles
 58 | function updateGaps(cb) {
 59 |     if(cb.checked) {
 60 | 	cTrack.showTrack("gapTrack");
 61 |     } else {
 62 | 	cTrack.hideTrack("gapTrack");
 63 |     }
 64 | }
 65 | 
 66 | // Attached to the ADB glyph checkbox, call the plot to
 67 | // add/remove only the ADB type of glyph
 68 | function updateAdb(cb) {
 69 |     if(cb.checked) {
 70 | 	cTrack.showGlyphTrackType("track5", "adb");
 71 |     } else {
 72 | 	cTrack.hideGlyphTrackType("track5", "adb");
 73 |     }
 74 | }
 75 | 
 76 | // Attached to the resize plot button, call the plot to
 77 | // resize the plot to 650px diameter
 78 | function resizePlot() {
 79 |     cTrack.resize(650);
 80 | }
 81 | 
 82 | function saveImage() {
 83 |     cTrack.savePlot(4.0, "islandviewer.png", "tracks.css", 'png');
 84 | }
 85 | 
 86 | // Demo of the hover over timer, we had to
 87 | // do it this way to get around IE <9 not supporting
 88 | // parameters to the function called by setTimeout()
 89 | //
 90 | // If you have over an island, the console log will 
 91 | // display the callback parameters when the timer expires
 92 | //
 93 | // The callback for hover (along with click) are defined in
 94 | // the data definition for each track in the dataset (data.js)
 95 | var timer;
 96 | var d_callback;
 97 | function islandPopup(d) {
 98 |     d_callback = d;
 99 |     timer = setTimeout(function() {console.log(d_callback);}, 1000);
100 | }
101 | 
102 | function islandPopupClear(d) {
103 |     clearTimeout(timer);
104 | }
105 | 
106 | // Callback defined at the top of this file, for
107 | // double clicks on the plot
108 | function doubleClick(plotid, bp) {
109 |     // If we have an attached linear plot, we're going
110 |     // to refocus the zoomed area, otherwise we'll just
111 |     // alert the user that a double click happened
112 |     if('undefined' !== typeof linearTrack) {
113 |         var halfBP = (cTrack.brushEndBP - cTrack.brushStartBP) /2;
114 | 
115 | 	var newStart = Math.max(0, (bp - halfBP));
116 | 	var newEnd = Math.min(genomesize, (bp + halfBP));
117 | 
118 |         console.log("Moving zoom area to: " + newStart + ", " + newEnd);
119 |         cTrack.moveBrushbyBP(newStart,
120 |                              newEnd);
121 |         linearTrack.update(newStart, newEnd);
122 |     } else {
123 |       alert("Double click! From " + plotid + " at " + bp + " bp" )
124 |       console.log("double click!");
125 |       console.log(plotid);
126 |       console.log(bp);
127 | 
128 |     }
129 | }
130 | 
131 | 


--------------------------------------------------------------------------------
/examples/combodemo.html:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html>
 2 | <html>
 3 |   <head>
 4 |     <meta http-equiv="Content-Type" content="text/html;charset=utf-8"/>
 5 |     <title>GenomeD3Plot Combo Plots Example</title>
 6 |     <script src="../d3/d3.min.js"></script>
 7 |     <script src="../d3/d3-tip.js"></script>
 8 |     <style>
 9 |     body {
10 |       overflow: hidden;
11 |       margin: 0;
12 |       font-size: 14px;
13 |       font-family: "Helvetica Neue", Helvetica;
14 |     }
15 |  
16 |     #linearchart {
17 |       position: absolute;
18 |       top: 650px;
19 |       left: 10px;
20 |     }
21 | 
22 |     #brush {
23 |       position: absolute;
24 |       top: 900px;
25 |       left: 250px;
26 |     }
27 | 
28 |     #circularchart {
29 |       position: absolute;
30 |       top: 0px;
31 |       left: 125px;
32 |     }
33 |        </style>
34 |     <link rel="stylesheet" type="text/css" href="tracks.css">
35 |   </head>
36 |   <body>
37 |     <div id="body">
38 |       <!-- The containers that will hold the SVG of the plots -->
39 |       <div id="circularchart"></div>
40 |       <div id="linearchart"></div>      
41 |       <div id="brush"></div>
42 |     </div>
43 |     
44 |     <!-- Sample data to be rendered -->
45 |     <script type="text/javascript" src="data.simple.js"></script>
46 | 
47 |     <!-- Circular plot library -->
48 |     <script type="text/javascript" src="../circularplot.js"></script>
49 | 
50 |     <!-- Linear plot library -->
51 |     <script type="text/javascript" src="../linearplot.js"></script>
52 | 
53 |     <!-- Linear brush library -->
54 |     <script type="text/javascript" src="../linearbrush.js"></script>
55 | 
56 |     <!-- Initialization code to initialize the plots, this is what you would write
57 |          and place in your application. Note, pulled from the linear and circular
58 |          plot demo Gists -->
59 |     <script type="text/javascript" src="lineardemo.js"></script>
60 |     <script type="text/javascript" src="circularsample.js"></script>
61 | 
62 |     <!-- Controls on the demo -->
63 |     <div id="demo-controls">
64 |       <div class="control-item"><input type="checkbox" name="showGC" onchange="updateGC(this); return false" checked>Show GC plot</div>
65 | 
66 |       <div class="control-item"><input type="checkbox" name="showStrand" onchange="updateStrand(this); return false" checked>Show stranded track</div>
67 | 
68 |       <div class="control-item"><input type="checkbox" name="showvfdb" onchange="updateAdb(this); return false" checked>Show ADB glyph type</div>
69 | 
70 |       <div class="control-item"><input type="checkbox" name="showgaps" onchange="updateGaps(this); return false" checked>Show contig gap region type</div>
71 |     </div>
72 | 
73 |   </body>
74 | </html>
75 | 


--------------------------------------------------------------------------------
/examples/lineardemo.html:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html>
 2 | <html>
 3 |   <head>
 4 |     <meta http-equiv="Content-Type" content="text/html;charset=utf-8"/>
 5 |   <title>GenomeD3Plot Linear Plot Example</title>
 6 |     <script src="../d3/d3.min.js"></script>
 7 |     <script src="../d3/d3-tip.js"></script>
 8 |     <style>
 9 |       body {
10 |         overflow: hidden;
11 |         margin: 0;
12 |         font-size: 14px;
13 |         font-family: "Helvetica Neue", Helvetica;
14 |       }
15 |  
16 |       #linearchart {
17 |         position: absolute;
18 |         top: 10px;
19 |         left: 10px;
20 |       }
21 | 
22 |       #brush {
23 |         position: absolute;
24 |         top: 260px;
25 |         left: 200px;
26 |       }
27 | 
28 |       #resizeButton {
29 |         position: absolute;
30 |         top: 300px;
31 |         left: 100px;
32 |       }
33 |     </style>
34 |     <link rel="stylesheet" type="text/css" href="tracks.css">
35 |   </head>
36 |   <body>
37 |     <div id="body">
38 |       <div id="linearchart"></div>      
39 |       <div id="brush"></div>
40 |     </div>
41 | 
42 |     <input type="button" id="resizeButton" onClick="resizeLinearPlot(); return false;" value="Resize plot">
43 |     
44 |     <script type="text/javascript" src="data.js"></script>
45 |     <script type="text/javascript" src="../linearplot.js"></script>
46 |     <script type="text/javascript" src="../linearbrush.js"></script>
47 |     <script type="text/javascript" src="lineardemo.js"></script>
48 |  
49 |   </body>
50 | </html>
51 | 


--------------------------------------------------------------------------------
/examples/lineardemo.js:
--------------------------------------------------------------------------------
 1 | /* Initialize the layout for the linear plot, the base
 2 |    parameters such as the genome size, the height of the
 3 |    plot in px, the width of the plot, the div container to
 4 |    put the SVG element, and an initial zoom level */
 5 | var linearlayout = { genomesize: 6264404,
 6 |                      height: 250,
 7 |                      width: 900,
 8 |                      container: "#linearchart",
 9 |                      initStart: 0,
10 |                      initEnd: 200000,
11 | 		    };
12 | 
13 | /* Initialize the layout for the linear brush, including
14 |    what container to put the brush in to */
15 | var contextLayout = { genomesize: 6264404,
16 |                       container: "#brush" };
17 | 
18 | /* Initialize the plot with the layout and the tracks data,
19 |    then initialize the brush telling it the plot it needs
20 |    to update */
21 | var linearTrack = new genomeTrack(linearlayout, tracks);
22 | var brush = new linearBrush(contextLayout,linearTrack);
23 | 
24 | /* Tell the linear plot about the brush so when the linear
25 |    track is updated (via a drag event, etc) it will update
26 |    the brush */
27 | linearTrack.addBrushCallback(brush);
28 | 
29 | /* If we have a circular plot, tell the linear plot
30 |    to let it know about updates, this is needed for
31 |    the combo demo */
32 | window.onload = function() {
33 |   if('undefined' !== typeof cTrack) {
34 |     console.log("Hooking up circular plot callback");
35 |     linearTrack.addBrushCallback(cTrack);
36 |   }
37 | }
38 | 
39 | /* Callback to demo resizing the linear plot */
40 | function resizeLinearPlot() {
41 |     linearTrack.resize(1000);
42 | }
43 | 
44 | /* Catch a click callback on the linear plot and show what
45 |    information we're given about the track item */
46 | function linearPopup(trackName, d) {
47 |     console.log(d);
48 |     alert("Received click event from track " + trackName + ", item: " + JSON.stringify(d));
49 | }
50 | 
51 | /* Callback to demo click functionality on the linear plot,
52 |    the click callback is defined in the data json object for
53 |    each track */
54 | function linearClick(trackName, d) {
55 |     console.log(d);
56 |     window.open("https://github.com/lairdm/islandplot", '_blank');
57 | }
58 | 


--------------------------------------------------------------------------------
/examples/tracks.css:
--------------------------------------------------------------------------------
  1 | /* Classes for the demo's controls */
  2 | #demo-controls {
  3 |   padding: 10px;
  4 | }
  5 | 
  6 | .control-item {
  7 |   padding: 5px;
  8 | }
  9 | 
 10 | /* Render the chart as cleanly as possible */
 11 | #circularchart {
 12 |     shape-rendering: geometricPrecision;
 13 | }
 14 | 
 15 | /* Text on the demo */
 16 | .mini text {
 17 |     font: 9px sans-serif;	
 18 | }
 19 | 
 20 | .main text {
 21 |     font: 12px sans-serif;	
 22 | }
 23 | 
 24 | /* Definitions for the plot resize dragger, and
 25 |    resizing shadow */
 26 | .dragbar-line {
 27 |     stroke-width: 1;	
 28 |     stroke: lightgrey;
 29 |     pointer-events: inherit;
 30 | }
 31 | 
 32 | .dragbar-shadow {
 33 |     stroke-width: 1;	
 34 |     stroke: lightgrey;
 35 |     fill: transparent;
 36 | }
 37 | 
 38 | /* Style for the plot move arrow if active */
 39 | .move-cross {
 40 |     stroke-width: 1;
 41 |     stroke: lightgrey;
 42 |     fill: lightgrey;
 43 |     cursor:move;
 44 | }
 45 | 
 46 | .move-shadow {
 47 |     cursor:move !important;
 48 | }
 49 | 
 50 | /* For resizing the linear chart */
 51 | #linearchart {
 52 |     cursor: -webkit-grab; cursor: -moz-grab;
 53 | }
 54 | 
 55 | #linearchart:active {
 56 |     cursor: -webkit-grabbing; cursor: -moz-grabbing;
 57 | }
 58 | 
 59 | .mainTrack {
 60 |     cursor: pointer; 
 61 |     cursor: hand;
 62 | }
 63 | 
 64 | /* Definitions for first stranded track, colour, stroke */
 65 | .track1_pos {
 66 |     fill: darksalmon;
 67 |     stroke: #d1876d;
 68 |     stroke-opacity: 0.8;
 69 |     stroke-width: 1;	
 70 | }
 71 | 
 72 | .track1_neg {
 73 |     fill: #FFCC00;
 74 |     fill-opacity: .7;
 75 |     /*stroke-width: 1;
 76 |     stroke: #4c602a;*/
 77 | }
 78 | 
 79 | /* In a linear track if an intergenic
 80 |    region is defined, give it a colour */
 81 | .track1_none {
 82 |     fill: #cccccc;
 83 |     fill-opacity: .7;
 84 |     stroke-width: 1;
 85 | }
 86 | 
 87 | /* And we want to show the user as they hover
 88 |    over a track, change the colour */
 89 | .track1_pos:hover {
 90 |     fill: red;
 91 |     stroke-width: 1;
 92 |     stroke: 1;
 93 | }
 94 | 
 95 | .track1_neg:hover {
 96 |     fill: red;
 97 |     fill-opacity: .9;
 98 |     stroke-width: 1;
 99 |     stroke: red;
100 | }
101 | 
102 | /* In a linear track, if there are regulatory
103 |    elements such as transcription factors and
104 |    terminators, give them a colour for the stroke */
105 | .track1_arrow_pos, .track1_arrow_neg, .track3_arrow {
106 |     stroke-width: 1;
107 |     stroke: black;
108 | }
109 | 
110 | /* Labels on the linear track */
111 | .track1_text {
112 |     fill: white;
113 |     font-weight: bold;
114 |     font: 12px arial;
115 | }
116 | 
117 | /* Track 2 is also a stranded track, give it
118 |    a different set of colours */
119 | .track2_pos {
120 |     fill: #000099;
121 |     fill-opacity: .7;
122 | }
123 | 
124 | /* When a linear track is zoomed to the point 
125 |    it's text is visible an extra class is added
126 |    to the element we can hook in to */
127 | .track2_pos_zoomed {
128 |     stroke-width: 1px;
129 |     stroke: #647381;
130 | }
131 | 
132 | .track2_neg {
133 |     fill: #006600;
134 |     fill-opacity: .7;
135 | }
136 | 
137 | .track2_neg_zoomed {
138 |     stroke-width: 1px;
139 |     stroke: #007300;
140 |     stroke-opacity: 0.7;
141 | }
142 | 
143 | .track2_text {
144 |     fill: white;
145 |     font-weight: bold;
146 |     font: 12px arial;
147 | }
148 | 
149 | /* Track 3 is a non-stranded track, so no _pos
150 |    and _neg modifiers on the classes */
151 | .track3 {
152 |     fill: #3399FF;
153 |     fill-opacity: .7;
154 | }
155 | 
156 | .track3:hover {
157 |     fill: blue;
158 |     fill-opacity: .9;
159 | }
160 | 
161 | .track3_text {
162 |     fill: white;
163 |     font-weight: bold;
164 |     font: 12px arial;
165 | }
166 | 
167 | /* The GC Plot type track, give the stroke a colour */
168 | .gcplot {
169 |     stroke: black;
170 | }
171 | 
172 | /* Track 5 is the glyphs, classes of a concatenation 
173 |    of the track name and the type of glyph in the track */
174 | .track5_vfdb {
175 |     fill: #663300;
176 | }
177 | 
178 | .track5_adb {
179 |     fill: #FF9933;
180 | }
181 | 
182 | /* Give a colour to the glyph track's stroke */
183 | .linearplot.gapTrack {
184 |     stroke: grey;
185 |     fill: lightgrey;
186 |     opacity: 0.5;
187 | }
188 | 
189 | .gapTrack {
190 |     stroke: grey;
191 | }
192 | 
193 | /* Set the stroke width of the axis lines */
194 | .trackAxis .domain {
195 |     stroke-width: 1;
196 | }
197 | 
198 | /* In a linear track, we need to set the
199 |    colours for the drag brush */
200 | .brush .background {
201 |     stroke: black;
202 |     stroke-width: 2;
203 |     fill: slategray;
204 |     fill-opacity: .3;
205 | }
206 | 
207 | .brush .extent {
208 |     stroke: gray;
209 |     fill: dodgerblue;
210 |     fill-opacity: .365;
211 | }
212 | 
213 | /* In a circular plot if there's a
214 |    drag brush for zoomed region, define the
215 |    colours and style */
216 | .polarbrush {
217 |     fill: lightgrey;
218 |     opacity: 0.5;
219 | }
220 | 
221 | /* In the circular plot, the circular end points
222 |    for the drag brush */
223 | .brushEnd {
224 |     fill: "red";
225 | }
226 | 
227 | .brushStart {
228 |     fill: "green";
229 | }
230 | 
231 | /* If we need to set an element to hidden, give
232 |    ourselves a class */
233 | .linear_hidden {
234 | 	visibility: hidden;
235 | }
236 | 
237 | /* For regulatory elements in a linear plot,
238 |    define the colours and stroke for the lollipop
239 |    head (terminator site) */
240 | .lollipophead {
241 |   stroke:#000000;
242 |   stroke-opacity: 1;
243 |   fill: none;
244 | }
245 | 
246 | .lollipopstemstart {
247 |   fill:none;
248 |   stroke:#000000;
249 |   stroke-width: 1px;
250 |   stroke-linecap:butt;
251 |   stroke-linejoin:miter;
252 |   stroke-dasharray: 5,5;
253 | }
254 | 
255 | .lollipopstemend {
256 |   fill:none;
257 |   stroke:#000000;
258 |   stroke-width: 1px;
259 |   stroke-linecap:butt;
260 |   stroke-linejoin:miter;
261 | }
262 | 
263 | /* For our tooltips, how should we display them? */
264 | .d3-tip {
265 |   line-height: 1;
266 |   font: 12px arial;
267 |   font-weight: bold;
268 |   padding: 12px;
269 |   background: rgba(0, 0, 0, 0.8);
270 |   color: #fff;
271 |   border-radius: 2px;
272 | }
273 | 
274 | /* Creates a small triangle extender for the tooltip */
275 | .d3-tip:after {
276 |   box-sizing: border-box;
277 |   display: inline;
278 |   font-size: 10px;
279 |   width: 100%;
280 |   line-height: 1;
281 |   color: rgba(0, 0, 0, 0.8);
282 |   content: "\25BC";
283 |   position: absolute;
284 |   text-align: center;
285 | }
286 | 
287 | /* Style northward tooltips differently */
288 | .d3-tip.n:after {
289 |   margin: -1px 0 0 0;
290 |   top: 100%;
291 |   left: 0;
292 | }
293 | 


--------------------------------------------------------------------------------
/linearbrush.js:
--------------------------------------------------------------------------------
  1 | var contextMargin = {top: 10, right: 40, bottom: 25, left: 60},
  2 | contextWidth = 440 - contextMargin.left - contextMargin.right,
  3 | contextHeight = 100 - contextMargin.top - contextMargin.bottom;
  4 | 
  5 | function linearBrush(layout, callbackObj) {
  6 |     this.layout;
  7 |     this.callbackObj = callbackObj;
  8 | 
  9 |     if('undefined' !== typeof layout.offset) {
 10 | 	this.start_offset = layout.offset;
 11 |     } else {
 12 | 	this.start_offset = 0;
 13 |     }
 14 | 
 15 |     this.brushContainer = d3.select(layout.container)
 16 | 	.append("svg")
 17 | 	.attr("width", contextWidth + contextMargin.left + contextMargin.right)
 18 | 	.attr("height", contextHeight + contextMargin.top + contextMargin.bottom)
 19 | 	.attr("class", "contextTracks");
 20 | 
 21 |     this.x1 = d3.scale.linear()
 22 | 	.range([0,contextWidth])
 23 |        	.domain([this.start_offset, layout.genomesize + this.start_offset]);
 24 | 
 25 |     this.mini = this.brushContainer.append("g")
 26 | 	.attr("transform", "translate(" + contextMargin.left + "," + contextMargin.top + ")")
 27 | 	.attr("width", contextWidth)
 28 | 	.attr("height", contextHeight)
 29 | 	.attr("class", "miniBrush");
 30 | 
 31 |     this.brush = d3.svg.brush()
 32 | 	.x(this.x1)
 33 | 	.on("brush", this.brushUpdate.bind(this));
 34 | 
 35 |     //    this.brush = brush;
 36 | 
 37 |     this.brushContainer = this.mini.append("g")
 38 | 	.attr("class", "track brush")
 39 | 	.call(this.brush.bind(this))
 40 | 	.selectAll("rect")
 41 | 	.attr("y", 1)
 42 | 	.attr("height", contextHeight - 1);
 43 |  
 44 |     this.axisContainer = this.mini.append("g")
 45 | 	.attr('class', 'brushAxis')
 46 | 	.attr("transform", "translate(" + 0 + "," + contextHeight + ")");
 47 | 
 48 |     this.xAxis = d3.svg.axis().scale(this.x1).orient("bottom")
 49 | 	.tickFormat(d3.format("s"));
 50 | 
 51 |     this.axisContainer.append("g")
 52 |     .attr("class", "context axis bottom")
 53 |     .attr("transform", "translate(0," + 0 + ")")
 54 |     .call(this.xAxis);
 55 | 
 56 | }
 57 | 
 58 | linearBrush.prototype.brushUpdate = function(b) {
 59 |     var minExtent = this.brush.extent()[0];
 60 |     var maxExtent = this.brush.extent()[1];
 61 | 
 62 |     if( Object.prototype.toString.call( this.callbackObj ) === '[object Array]' ) {
 63 |         for(var obj in this.callbackObj) {
 64 |             if(this.callbackObj.hasOwnProperty(obj)) {
 65 |                 this.callbackObj[obj].update(minExtent, maxExtent);
 66 |             }
 67 |         }
 68 |     } else {
 69 |         this.callbackObj.update(minExtent, maxExtent);
 70 |     }
 71 | 
 72 | }
 73 | 
 74 | linearBrush.prototype.update = function(startBP, endBP) {
 75 | 
 76 | 	this.brush.extent([startBP, endBP]);
 77 | 	
 78 | 	d3.selectAll('.brush').call(this.brush);
 79 | 
 80 | }
 81 | 
 82 | linearBrush.prototype.update_finished = function(startBP, endBP) {
 83 | 
 84 | }
 85 | 
 86 | linearBrush.prototype.addBrushCallback = function(obj) {
 87 | 
 88 |     // We allow multiple brushes to be associated with a linear plot, if we have
 89 |     // a brush already, add this new one on.  Otherwise just remember it.
 90 | 
 91 |     if('undefined' !== typeof this.callbackObj) {
 92 | 
 93 | 	if( Object.prototype.toString.call( obj ) === '[object Array]' ) { 
 94 | 	    this.callbackObj.push(obj);
 95 | 	} else {
 96 | 	    var tmpobj = this.callbackObj;
 97 | 	    this.callbackObj = [tmpobj, obj];
 98 | 	}
 99 |     } else {
100 | 	this.callbackObj = obj;
101 |     }
102 | 
103 | }
104 | 


--------------------------------------------------------------------------------
/linearplot.js:
--------------------------------------------------------------------------------
   1 | var linearTrackDefaults = {
   2 |     width: 940,
   3 |     height: 500,
   4 |     left_margin: 15,
   5 |     right_margin: 15,
   6 |     bottom_margin: 5,
   7 |     axis_height: 50,
   8 |     name: "defaultlinear",
   9 |     dragresize: true
  10 | };
  11 | 
  12 | function genomeTrack(layout,tracks) {
  13 | 
  14 |     this.tracks = tracks;
  15 |     this.layout = layout;
  16 |     this.numTracks = this.countTracks();
  17 | 
  18 |     if('undefined' !== typeof layout) {
  19 | 	// Copy over any defaults not passed in
  20 | 	// by the user
  21 | 	for(var i in linearTrackDefaults) {
  22 | 	    if('undefined' == typeof layout[i]) {
  23 | 		this.layout[i] = linearTrackDefaults[i];
  24 | 	    }
  25 | 	}
  26 |     }
  27 | 
  28 |     if('undefined' == typeof layout.plotid) {
  29 | 	this.layout.plotid = layout.container.slice(1);
  30 |     }
  31 | 
  32 |     this.layout.containerid = layout.container.slice(1);
  33 | 
  34 |     this.layout.width_without_margins =
  35 | 	this.layout.width - this.layout.left_margin -
  36 | 	this.layout.right_margin;
  37 | 
  38 |     this.layout.height_without_axis = this.layout.height -
  39 | 	this.layout.axis_height;
  40 | 
  41 | 
  42 |     if('undefined' !== typeof layout.offset) {
  43 | 	this.start_offset = layout.offset;
  44 |     } else {
  45 | 	this.start_offset = 0;
  46 |     }
  47 | 
  48 |     this.itemRects = [];
  49 | 
  50 |     // Start with showing the entire genome unless otherwise stated
  51 |     this.visStart = 'undefined' !== typeof layout.initStart ? layout.initStart : this.start_offset;
  52 |     this.visEnd = 'undefined' !== typeof layout.initEnd ? layout.initEnd : layout.genomesize + this.start_offset;
  53 | 
  54 |     this.x = d3.scale.linear()
  55 | //	.domain([0, layout.genomesize])
  56 | 	.domain([this.visStart, this.visEnd])
  57 | 	.range([0,this.layout.width_without_margins]);
  58 |     this.x1 = d3.scale.linear()
  59 | 	.range([0,this.layout.width_without_margins])
  60 | //       	.domain([0, layout.genomesize]);
  61 |        	.domain([this.visStart, this.visEnd]);
  62 |     this.y1 = d3.scale.linear()
  63 | 	.domain([0,this.numTracks])
  64 | 	.range([0,(this.layout.height_without_axis-this.layout.bottom_margin)]);
  65 |     // We need x1 and y1 in the initialization's scope too
  66 |     // to deal with passing it in to make the lollipops
  67 | 
  68 |     this.zoom = d3.behavior.zoom()
  69 | 	.x(this.x1)
  70 | 	.on("zoomstart", function () {d3.event.sourceEvent.preventDefault()} )
  71 | 	.on("zoom", this.rescale.bind(this))
  72 | 	.on("zoomend", this.callBrushFinished.bind(this) );
  73 | 
  74 |     if('undefined' == typeof layout.plotid) {
  75 | 	this.layout.plotid = layout.container.slice(1);
  76 |     }
  77 | 
  78 |     d3.select(layout.container).select("svg").remove();
  79 | 
  80 |     this.chart = d3.select(layout.container)
  81 | 	.append("svg")
  82 | 	.attr("id", function() { return layout.container.slice(1) + "_svg"; })
  83 | 	.attr("width", this.layout.width)
  84 | 	.attr("height", this.layout.height)
  85 | 	.attr("class", "mainTracks")
  86 | 	.call(this.zoom);
  87 | 
  88 |     this.defs = this.chart.append("defs");
  89 |     this.clipPath = this.defs.append("clipPath")
  90 | 	.attr("id", "trackClip_" + this.layout.containerid)
  91 | 	.append("rect")
  92 | 	.attr("width", this.layout.width_without_margins)
  93 | 	//	.attr("width", this.layout.width_without_margins + this.layout.right_margin)
  94 | 	.attr("height", this.layout.height)
  95 | 	.attr("transform", "translate(0,0)");
  96 |     //	.attr("transform", "translate(" + this.layout.left_margin + ",0)");
  97 |     
  98 |     this.drawFeatures();
  99 | 
 100 |     this.main = this.chart.append("g")
 101 |        	.attr("transform", "translate(" + this.layout.left_margin + ",0)")
 102 | 	.attr("width", this.layout.width_without_margins)
 103 | 	.attr("height", this.layout.height)
 104 | 	.attr("class", "mainTrack");
 105 | 
 106 |     // Resize dragger
 107 |     if(this.layout.dragresize == true) {
 108 | 	var dragright = d3.behavior.drag()
 109 | 	    .on("dragstart", function() {  d3.event.sourceEvent.stopPropagation(); })
 110 | 	    .on("drag", this.dragresize.bind(this));
 111 | 
 112 | 	this.dragbar_y_mid = this.layout.height/2;
 113 | 	this.dragbar = this.chart.append("g")
 114 | 	    .attr("transform", "translate(" + (this.layout.width-this.layout.right_margin) + "," + (this.dragbar_y_mid-10) + ")")
 115 | 	    .attr("width", 25)
 116 | 	    .attr("height", 20)
 117 | 	    .attr("fill", "lightblue")
 118 | 	    .attr("fill-opacity", .2)
 119 | 	    .attr("cursor", "ew-resize")
 120 | 	    .attr("id", "dragbar_" + this.layout.containerid)
 121 | 	    .call(dragright);
 122 | 
 123 | 	this.dragbar.append("rect")
 124 | 	    .attr("width", 25)
 125 | 	    .attr("height", 20)
 126 | 	    .attr("fill-opacity", 0);
 127 | 
 128 | 	this.dragbar.append("line")
 129 | 	    .attr("x1", 6)
 130 | 	    .attr("x2", 6)
 131 | 	    .attr("y1", 0)
 132 | 	    .attr("y2", 20)
 133 | 	    .attr("class", "dragbar-line");
 134 | 	this.dragbar.append("line")
 135 | 	    .attr("x1", 9)
 136 | 	    .attr("x2", 9)
 137 | 	    .attr("y1", 0)
 138 | 	    .attr("y2", 20)
 139 | 	    .attr("class", "dragbar-line");
 140 | 	this.dragbar.append("line")
 141 | 	    .attr("x1", 12)
 142 | 	    .attr("x2", 12)
 143 | 	    .attr("y1", 0)
 144 | 	    .attr("y2", 20)
 145 | 	    .attr("class", "dragbar-line");
 146 |     }
 147 | 	
 148 | 
 149 |     this.genomesize = layout.genomesize;
 150 | 
 151 |     this.tip = d3.tip()
 152 | 	.attr('class', 'd3-tip')
 153 | 	.offset([-10, 0])
 154 | 	.html(function(d) {
 155 | 		return "<strong>Name:</strong> <span style='color:red'>" + d.name + "</span>";
 156 | 	    });
 157 |     
 158 |     this.chart.call(this.tip);
 159 | 
 160 |     this.axisContainer = this.chart.append("g")
 161 | 	.attr('class', 'trackAxis')
 162 | 	.attr('width', this.layout.width_without_margins)
 163 | 	.attr("transform", "translate(" + (this.layout.left_margin + 5) + "," + this.layout.height_without_axis + ")");
 164 | 
 165 |     this.xAxis = d3.svg.axis().scale(this.x1).orient("bottom")
 166 | 	.innerTickSize(-this.layout.height)
 167 | 	.outerTickSize(0)
 168 | 	.tickFormat(d3.format("s"));
 169 | 
 170 |     this.axisContainer.append("g")
 171 | 	.attr("class", "xaxislinear")
 172 | 	.attr('width', this.layout.width_without_margins)
 173 | 
 174 | 	.attr("transform", "translate(0," + 10 + ")")
 175 | 	.call(this.xAxis);
 176 | 
 177 | 
 178 |     for(var i=0; i < this.tracks.length; i++) {
 179 | 	// We're going to see what type of tracks we have
 180 | 	// and dispatch them appropriately
 181 | 
 182 | 	 if("undefined" !== typeof this.tracks[i].skipLinear
 183 | 	    &&  this.tracks[i].skipLinear == true) {
 184 | 	     continue;
 185 | 	 }
 186 | 
 187 | 	 if("undefined" == typeof this.tracks[i].trackFeatures) {
 188 | 	     this.tracks[i].trackFeatures = "simple";
 189 | 	 } else if(this.tracks[i].trackFeatures == "complex") {
 190 | 	     // We need to pre-calculate the stacking order for
 191 | 	     // all arrow type features
 192 | 
 193 | 	     // 0.77 * 0.9
 194 | 	     if(this.tracks[i].trackType == "stranded") {
 195 | 		 this.tracks[i].baseheight = (this.y1(1) * 0.693);
 196 | 	     } else {
 197 | 		 this.tracks[i].baseheight = (this.y1(1) * 0.616);
 198 | 	     }
 199 | 	     var inframe = [];
 200 | 	     this.tracks[i].maxStackOrder = 1;
 201 | 	     for(var j = 0; j < this.tracks[i].items.length; j++) {
 202 | 		 // If it's the arrow type we're looking for
 203 | 		 if("undefined" !== typeof this.tracks[i].items[j].feature && this.tracks[i].items[j].feature == "arrow") {
 204 | 		     item = this.tracks[i].items[j];
 205 | 		     // Is there anything else still in frame we need to check?
 206 | 
 207 | 		     this.tracks[i].items[j].stackOrder = 1;
 208 | 		     // Next one we encoutner will be 2
 209 | 		     var curr_stackorder = 2;
 210 | 		     // Go backwards through the possible inframe elements
 211 | 		     // and increase their stack order if needed
 212 | 		     for(var k = inframe.length - 1; k >= 0; k--) {
 213 | 			 curr_k = inframe[k];
 214 | 			 if(this.tracks[i].items[curr_k].end >= item.start) {
 215 | 			     // If the current item in the possible stack
 216 | 			     // items is overlapping...
 217 | 			     if(this.tracks[i].items[curr_k].stackOrder <= curr_stackorder) {
 218 | 				 // If the examined item is below or
 219 | 				 // equal to the current stack order
 220 | 				 this.tracks[i].items[curr_k].stackOrder = curr_stackorder;
 221 | 				 curr_stackorder++;
 222 | 			     }
 223 | 			     // This takes care of ignoring items that
 224 | 			     // are already well above the current stack order
 225 | 			     
 226 | 			 } else {
 227 | 			     // Or if it no longer overlaps, remove it
 228 | 			     inframe.splice(k, 1);
 229 | 			 }
 230 | 		     }
 231 | 
 232 | 		     // Push ourselves on the inframe so the next
 233 | 		     // guy can check us out
 234 | 		     inframe.push(j);
 235 | 		     this.tracks[i].maxStackOrder = Math.max(this.tracks[i].maxStackOrder, curr_stackorder);
 236 | 		     // Save the maximum stackorder we've seen
 237 | 		 }
 238 | 	     }
 239 | 	     this.tracks[i].increment = this.y1(0.23) / this.tracks[i].maxStackOrder;
 240 | 	 }
 241 | 
 242 | 	 if("undefined" == typeof this.tracks[i].featureThreshold) {
 243 | 	     this.tracks[i].featureThreshold = this.genomesize;
 244 | 	 }
 245 | 
 246 | 	switch(this.tracks[i].trackType) {
 247 | 	case "gap":
 248 | 	    this.itemRects[i] = this.main.append("g")
 249 | 		.attr("class", this.tracks[i].trackName)
 250 | 		.attr("width", this.layout.width_without_margins)
 251 | 		.attr("clip-path", "url(#trackClip_" + this.layout.containerid + ")");
 252 | 	    this.displayGapTrack(this.tracks[i], i);
 253 | 	    break;
 254 | 	case "stranded":
 255 | 	    this.itemRects[i] = this.main.append("g")
 256 | 		.attr("class", this.tracks[i].trackName)
 257 | 		.attr("width", this.layout.width_without_margins)
 258 | 		.attr("clip-path", "url(#trackClip_" + this.layout.containerid + ")");
 259 | 	    if('undefined' !== typeof this.tracks[i].linear_skipInit && this.tracks[i].linear_skipInit) {
 260 | 		break;
 261 | 	    }
 262 | 	    this.displayStranded(this.tracks[i], i);
 263 | 	    break;
 264 | 	case "track":
 265 | 	    this.itemRects[i] = this.main.append("g")
 266 | 		.attr("class", this.tracks[i].trackName)
 267 | 		.attr("width", this.layout.width_without_margins)
 268 | 		.attr("clip-path", "url(#trackClip_" + this.layout.containerid + ")");
 269 | 	    if('undefined' !== typeof this.tracks[i].linear_skipInit && this.tracks[i].linear_skipInit) {
 270 | 		break;
 271 | 	    }
 272 | 	    this.displayTrack(this.tracks[i], i);
 273 | 	    break;
 274 | 	case "glyph":
 275 | 	    if(typeof this.tracks[i].linear_invert !== 'undefined' && this.tracks[i].linear_invert == true) {
 276 | 		this.tracks[i].invert = -1;
 277 | 	    } else {
 278 | 		this.tracks[i].invert = 1;
 279 | 	    }
 280 | 	    if(typeof this.tracks[i].linear_padding !== 'undefined') {
 281 | 		this.tracks[i].padding = this.tracks[i].linear_padding;
 282 | 	    } else {
 283 | 		this.tracks[i].padding = 0;
 284 | 	    }
 285 | 	    this.itemRects[i] = this.main.append("g")
 286 | 		.attr("class", this.tracks[i].trackName)
 287 | 		.attr("width", this.layout.width_without_margins)
 288 | 		.attr("clip-path", "url(#trackClip_" + this.layout.containerid + ")");
 289 | 	    this.displayGlyphTrack(this.tracks[i], i);
 290 | 	    break;
 291 | 	case "plot":
 292 | 	    this.tracks[i].g = this.itemRects[i] = this.main.append("g")
 293 | 		.attr("class", this.tracks[i].trackName)
 294 | 		.attr("width", this.layout.width_without_margins)
 295 | 		.attr("clip-path", "url(#trackClip_" + this.layout.containerid + ")");
 296 | 	    this.tracks[i].g.append("path")
 297 | 		.attr("class", this.tracks[i].trackName)
 298 | 		.attr("id", this.tracks[i].trackName)
 299 | 		.attr("stroke-width", 1)
 300 | 		.attr("fill", "none");
 301 | 
 302 | 	    this.displayPlotTrack(this.tracks[i], i);
 303 | 	    break;
 304 | 	default:
 305 | 	    // Do nothing for an unknown track type
 306 | 	}
 307 |     }
 308 | 
 309 |     //    this.main.append("g").attr("transform", "matrix(0.7, 0, 0, 0.7, 0, 0)").append("use").attr("xlink:href", "#lollipop");
 310 |     //    this.main.append("g").attr("transform", "translate(100,137)").on("click", function() { console.log("click!");}).append("use").attr("xlink:href", "#lollipop_strand_pos");
 311 | 
 312 | }
 313 | 
 314 | // We can't display all track types, or some don't
 315 | // add to the stacking (ie. graph type)
 316 | 
 317 | genomeTrack.prototype.countTracks = function() {
 318 |     var track_count = 0;
 319 | 
 320 |      for(var i=0; i < this.tracks.length; i++) {
 321 | 
 322 | 	 if("undefined" !== this.tracks[i].skipLinear
 323 | 	    &&  this.tracks[i].skipLinear == true) {
 324 | 	     continue;
 325 | 	 }
 326 | 
 327 | 	switch(this.tracks[i].trackType) {
 328 | 	case "stranded":
 329 | 	    // a linear track counts as two
 330 | 	    track_count++;
 331 | 	    this.tracks[i].stackNum = track_count;
 332 | 	    track_count++;
 333 | 	    break;
 334 | 	case "track":
 335 | 	    this.tracks[i].stackNum = track_count;
 336 | 	    track_count++;
 337 | 	    break;
 338 | 	default:
 339 | 	    // Do nothing for an unknown track type
 340 | 	}
 341 |     }
 342 |    
 343 |     return track_count;
 344 | }
 345 | 
 346 | genomeTrack.prototype.displayStranded = function(track, i) {
 347 |     var visStart = this.visStart,
 348 |     visEnd = this.visEnd,
 349 |     visRange = visEnd - visStart,
 350 |     x1 = this.x1,
 351 |     y1 = this.y1;
 352 |     var cfg = this.layout;
 353 | 
 354 |     // Because of how the tooltip library binds to the SVG object we have to turn it
 355 |     // on or off here rather than in the .on() call, we'll redirect the calls to
 356 |     // a dummy do-nothing object if we're not showing tips in this context.
 357 |     var tip = {show: function() {}, hide: function() {} };
 358 |     if(('undefined' !== typeof track.showTooltip) && track.showTooltip) {
 359 | 	tip = this.tip;
 360 |     }
 361 | 
 362 |     var stackNum = this.tracks[i].stackNum;
 363 |     //    console.log(visStart, visEnd);
 364 |     var visItems = track.items.filter(function(d) {
 365 | 	    if(typeof d.feature !== 'undefined' && d.feature !== 'gene') {
 366 | 		if(track.featureThreshold < visRange) {
 367 | 		    return false;
 368 | 		}
 369 | 	    }
 370 | 	    return d.start < visEnd && d.end > visStart;
 371 | 	});
 372 | 
 373 |     //    console.log(track.items);
 374 | 
 375 |     var rects = this.itemRects[i].selectAll("g")
 376 |     .data(visItems, function(d) { return d.id; })
 377 | 	.attr("transform", function(d,i) { 
 378 | 	    return "translate(" + x1(d.start) + ',' +  d.yshift + ")"; });
 379 | 
 380 |     // Process the changed/moved rects
 381 |     rects.selectAll("rect")
 382 |     .each(function (d) { d.width = x1(d.end + 1) - x1(d.start); })
 383 |     .attr("width", function(d) {return d.width;})
 384 |     // Yes we really don't need to set the class here again
 385 |     // except to deal with the _zoom class when zooming
 386 |     // in and out
 387 |     .attr("class", function(d) {
 388 | 	return track.trackName + '_' + d.suffix + ' ' + ((d.width > 5) ? (track.trackName + '_' + d.suffix + '_zoomed') : '' ) + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '');});
 389 | 
 390 |     // Process the text for changed/moved rects
 391 |     rects.selectAll("text")
 392 |     .attr("dx", "2px")
 393 |     .attr("dy", "0.94em")
 394 |     .each(function (d) {
 395 | 	    var bb = this.getBBox();
 396 | 	    var slice_length = x1(d.end) - x1(d.start) - 2; // -2 to offset the dx above
 397 | 	    d.visible = (slice_length > bb.width);
 398 | 	})
 399 |     .attr("class", function(d) {
 400 | 	return track.trackName + '_text ' + track.trackName + '_' + d.suffix + '_text ' + (d.visible ? '' : "linear_hidden " ) + ('undefined' !== typeof d.extraclass ? d.extraclass : ''); });
 401 | 
 402 |     this.itemRects[i].selectAll(".arrow")
 403 |     .each(function(d) {
 404 | 	    d.width = x1(d.end + 1) - x1(d.start);
 405 | 
 406 | 	    if(d.strand == -1) {
 407 | 		headxtranslate = 0;
 408 | 		arrowline = "m " + d.width + ",0 " + "l 0," + (track.baseheight + d.height) + " -" + d.width + ",0";
 409 | 	    } else {
 410 | 		headxtranslate = d.width;
 411 | 		arrowline = "m 0," + track.baseheight + "l 0,-" + (track.baseheight + d.height) + " " + d.width + ",0";
 412 | 	    }
 413 | 
 414 | 	    d3.select(this).select("path")
 415 | 		.attr("d", function(d) { 
 416 | 			return arrowline;
 417 | 		    });
 418 | 
 419 | 	    d3.select(this).select("use")
 420 | 		.attr("transform", function(d) {
 421 | 			return "translate(" + headxtranslate + "," + d.headytranslate + ")";
 422 | 		    });
 423 | 
 424 | 	});
 425 | 
 426 |     var entering_rects = rects.enter().append("g")
 427 |     .attr("transform", function(d,i) {
 428 | 	    if(d.strand == -1) {
 429 | 		ystack = stackNum;
 430 | 		d.suffix = 'neg';
 431 | 	    } else if(d.strand == "1") {
 432 | 		ystack = stackNum -1;
 433 | 		d.suffix = 'pos';
 434 | 	    } else {
 435 | 		ystack = stackNum - 0.3;
 436 | 		d.suffix = 'none';
 437 | 	    }
 438 | 	    var shift_gene = 0;
 439 | 	    if(typeof d.feature !== 'undefined' && d.feature == "terminator") {
 440 | 		ystack = ystack - 0.5;
 441 | 	    } else if (track.trackFeatures == 'complex' && d.strand == "1") {
 442 | 		    var shift_gene = y1(1) * .2;
 443 | 
 444 | 	    }
 445 | 	    d.yshift = y1(ystack) + 10 + shift_gene;
 446 | 	    return "translate(" + x1(d.start) + ',' +  d.yshift + ")"; })
 447 |     //	    return "translate(" + x1(d.start) + ',' +  (y1(ystack) + 10 + shift_gene) + ")"; })
 448 |     .attr("id", function(d,i) { return track.trackName + '_' + d.id; })
 449 |     .attr("class", function(d) {
 450 | 	    return track.trackName + '_' + d.suffix + '_group ' + (typeof d.feature === 'undefined' ? 'gene' : d.feature); })//;
 451 | 	   
 452 |     //        entering_rects
 453 |     .each(function(d) {
 454 | 	    d.width = x1(d.end) - x1(d.start);
 455 | 
 456 | 	    if (typeof d.feature === 'undefined' || d.feature == "gene") {
 457 | 		d3.select(this)
 458 | 		.append("rect")
 459 | 		.attr("class", function(d) {
 460 | 
 461 | 			return track.trackName + '_' + d.suffix + ' ' + ((d.width > 5) ? (track.trackName + '_' + d.suffix + '_zoomed') : '') + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '');})
 462 | 		.attr("width", function(d) {return d.width;})
 463 | 		.attr("height", function(d) {
 464 | 			if(track.trackFeatures == 'complex') { 
 465 | 			    var scale_factor = 0.77;
 466 | 			} else {
 467 | 			    var scale_factor = 1;
 468 | 			}
 469 | 			return (d.strand == 0 ? .4 : .9) * scale_factor * y1(1);
 470 | 		    })
 471 |     .on("click", function(d,i) {
 472 | 	    if (d3.event.defaultPrevented) return; // click suppressed
 473 | 	    if('undefined' !== typeof track.linear_mouseclick) {
 474 | 		var fn = window[track.linear_mouseclick];
 475 | 		if('object' ==  typeof fn) {
 476 | 		    return fn.onclick(track.trackName, d, cfg.plotid);
 477 | 		} else if('function' == typeof fn) {
 478 | 		    return fn(track.trackName, d, cfg.plotid);
 479 | 		}
 480 | 	    } else {
 481 | 		null;
 482 | 	    }
 483 | 	})
 484 |     .on('mouseover', function(d) { 
 485 | 	    tip.show(d);
 486 | 	    if('undefined' !== typeof track.linear_mouseover) {
 487 | 		var fn = window[track.linear_mouseover];
 488 | 		if('object' ==  typeof fn) {
 489 | 		    return fn.mouseover(track.trackName, d, cfg.plotid);
 490 | 		} else if('function' == typeof fn) {
 491 | 		    return fn(track.trackName, d, cfg.plotid);
 492 | 		}
 493 | 	    }	
 494 | 	})
 495 |     .on('mouseout', function(d) { 
 496 | 	    tip.hide(d);
 497 | 	    if('undefined' !== typeof track.linear_mouseout) {
 498 | 		var fn = window[track.linear_mouseout];
 499 | 		if('object' ==  typeof fn) {
 500 | 		    return fn.mouseout(track.trackName, d, cfg.plotid);
 501 | 		} else if('function' == typeof fn) {
 502 | 		    return fn(track.trackName, d, cfg.plotid);
 503 | 		}
 504 | 	    }	
 505 | 	});
 506 | 
 507 | 	    } else if(d.feature == "terminator") {
 508 | 		if(d.strand == 1) {
 509 | 		    lollipop = "#lollipop_strand_pos";
 510 | 		} else {
 511 | 		    lollipop = "#lollipop_strand_neg";
 512 | 		}
 513 | 		d3.select(this).append("use").attr("xlink:href", lollipop);
 514 | 
 515 | 	    } else if(d.feature == "arrow") {
 516 | 
 517 | 		if(d.strand == -1) {
 518 | 		    d.height = y1(0.23) - (d.stackOrder * track.increment);
 519 | 		    arrowhead = "#leftarrow";
 520 | 		    headxtranslate = 0;
 521 | 		    d.headytranslate = track.baseheight + d.height;
 522 | 		    //		    console.log(track.increment);
 523 | 		    //		    console.log(d.headytranslate);
 524 | 		    arrowline = "m " + d.width + ",0 " + "l 0," + (track.baseheight + d.height) + " -" + d.width + ",0";
 525 | 		    //		    console.log(arrowline);
 526 | 		} else {
 527 | 		    d.height = d.stackOrder * track.increment;
 528 | 		    arrowhead = "#rightarrow";
 529 | 		    headxtranslate = d.width;
 530 | 		    d.headytranslate = d.height * -1;
 531 | 		    arrowline = "m 0," + track.baseheight + "l 0,-" + (track.baseheight + d.height) + " " + d.width + ",0";
 532 | 
 533 | 		}
 534 | 		arrowclass = track.trackName + '_arrow_' + d.suffix + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '');
 535 | 		arrowbase = d3.select(this)
 536 | 		
 537 | 		arrowbase.append("path")
 538 | 		.attr("class", arrowclass)
 539 | 		.attr("d", function(d) { 
 540 | 			// 0.77 * 0.9
 541 | 			
 542 | 			return arrowline;
 543 | 		    })
 544 | 		.attr("fill-opacity", 0)
 545 | 		arrowbase.append("use").attr("xlink:href", arrowhead)
 546 | 		.attr("transform", function(d) {
 547 | 			return "translate(" + headxtranslate + "," + d.headytranslate + ")";
 548 | 		    })
 549 | 		.attr("class", arrowclass);
 550 | 
 551 | 
 552 | 	    } //else
 553 | 	});
 554 | 
 555 |     if(('undefined' !== typeof track.showLabels) && typeof track.showLabels) {
 556 | 	entering_rects.each(function(d) {
 557 | 		if(typeof d.feature == 'undefined' || d.feature == 'gene') {
 558 | 		    d3.select(this).append("text")
 559 | 			.text(function(d) {return d.name;})
 560 | 			.attr("dx", "2px")
 561 | 			.attr("dy", "1em")
 562 | 			.each(function (d) {
 563 | 				var bb = this.getBBox();
 564 | 				var slice_length = x1(d.end - d.start);
 565 | 				d.visible = (slice_length > bb.width);
 566 | 			    })
 567 | 			.attr("class", function(d) {
 568 | 				return track.trackName + '_text ' +  track.trackName + '_' + d.suffix + '_text ' + (d.visible ? null : "linear_hidden"  ); });
 569 | 		}
 570 | 	    });
 571 |     }
 572 | 
 573 |     rects.exit().remove();
 574 | }
 575 | 
 576 | genomeTrack.prototype.displayTrack = function(track, i) {
 577 |     var visStart = this.visStart,
 578 |     visEnd = this.visEnd,
 579 |     visRange = visEnd - visStart,
 580 |     x1 = this.x1,
 581 |     y1 = this.y1;
 582 |     var cfg = this.layout;
 583 | 
 584 |     // Because of how the tooltip library binds to the SVG object we have to turn it
 585 |     // on or off here rather than in the .on() call, we'll redirect the calls to
 586 |     // a dummy do-nothing object if we're not showing tips in this context.
 587 |     var tip = {show: function() {}, hide: function() {} };
 588 |     if(('undefined' !== typeof track.showTooltip) && track.showTooltip) {
 589 | 	tip = this.tip;
 590 |     }
 591 | 
 592 |     var stackNum = this.tracks[i].stackNum;
 593 |     //    console.log(visStart, visEnd, visRange);
 594 |     var visItems = track.items.filter(function(d) {
 595 | 	    if(typeof d.feature !== 'undefined' && d.feature !== 'gene') {
 596 | 		if(track.featureThreshold < visRange) {
 597 | 		    return false;
 598 | 		}
 599 | 	    }
 600 | 	    return d.start < visEnd && d.end > visStart;}
 601 | 	);
 602 | 
 603 |     //    console.log(track.items);
 604 | 
 605 |     var rects = this.itemRects[i].selectAll("g")
 606 |     .data(visItems, function(d) { return d.id; })
 607 |     .attr("transform", function(d,i) { 
 608 | 	    return "translate(" + x1(d.start) + ',' + d.yshift  + ")"; 
 609 | 	});
 610 | 
 611 | 
 612 |     this.itemRects[i].selectAll("rect")
 613 |     .each(function (d) { d.width = x1(d.end) - x1(d.start); })
 614 |     .attr("width", function(d) {return d.width; })
 615 |     // Yes we really don't need to set the class here again
 616 |     // except to deal with the _zoom class when zooming
 617 |     // in and out
 618 |     .attr("class", function(d) {return track.trackName + ' ' + ((d.width > 5) ? (track.trackName + '_zoomed') : '' ) + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '');});
 619 | 
 620 |     rects.selectAll("text")
 621 |     .attr("dx", "2px")
 622 |     .attr("dy", "1em")
 623 |     .each(function (d) {
 624 | 	    var bb = this.getBBox();
 625 | 	    var slice_length = x1(d.end) - x1(d.start) - 2; // -2 to offset the dx above
 626 | 	    d.visible = (slice_length > bb.width);
 627 | 	})
 628 |     .attr("class", function(d) {return track.trackName + '_text ' + (d.visible ? null : "linear_hidden" ); });
 629 | 
 630 |     this.itemRects[i].selectAll(".arrow")
 631 |     .each(function(d) {
 632 | 	    //	console.log(d);
 633 | 	    d.width = x1(d.end + 1) - x1(d.start);
 634 | 
 635 | 	    d3.select(this).select("path")
 636 | 		.attr("d", function(d) { 
 637 | 			return "m 0," + track.baseheight + "l 0,-" + (track.baseheight + d.height) + " " + d.width + ",0";
 638 | 		    });
 639 | 
 640 | 	    d3.select(this).select("use")
 641 | 		.attr("transform", function(d) {
 642 | 			return "translate(" + d.width + ",-" + d.headytranslate + ")";
 643 | 		    });
 644 | 
 645 | 	});
 646 | 
 647 |     var entering_rects = rects.enter().append("g")
 648 |     .attr("transform", function(d,i) { 
 649 | 	    ystack = stackNum;
 650 | 	    shift_gene = 0;
 651 | 	    if(typeof d.feature !== 'undefined' && d.feature == "terminator") {
 652 | 		ystack = ystack - 0.6;
 653 | 	    } else if (track.trackFeatures == 'complex') {
 654 | 		    var shift_gene = y1(1) * .175;
 655 | 
 656 | 	    }
 657 | 
 658 | 	    d.yshift = y1(ystack) + 10 + shift_gene;
 659 | 	    return "translate(" + x1(d.start) + ',' + d.yshift  + ")"; 
 660 | 	})
 661 |     .attr("id", function(d,i) { return track.trackName + '_' + d.id; })
 662 |     .attr("class", function(d) {return track.trackName + '_group ' + (typeof d.feature === 'undefined' ? 'gene' : d.feature); })//;
 663 | 
 664 |     //    entering_rects
 665 |     .each(function (d) { 
 666 | 	    d.width = x1(d.end) - x1(d.start); 
 667 | 
 668 | 	    if (typeof d.feature === 'undefined' || d.feature == "gene") {
 669 | 
 670 | 		d3.select(this).append("rect")
 671 | 
 672 | 		    .attr("class", function(d) {return track.trackName + ' ' + ((d.width > 5) ? (track.trackName + '_zoomed') : '' ) + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '');})
 673 | 		    .attr("width", function(d) {return d.width; })
 674 | 		    .attr("height", function(d) {
 675 | 			    if(track.trackFeatures == 'complex') {
 676 | 				var scale_factor = 0.77;
 677 | 			    } else {
 678 | 				var scale_factor = 1;
 679 | 			    }
 680 | 
 681 | 			    return .8 * scale_factor * y1(1);
 682 | 			})
 683 | 		    .on("click", function(d,i) {
 684 | 			    if (d3.event.defaultPrevented) return; // click suppressed
 685 | 			    if('undefined' !== typeof track.linear_mouseclick) {
 686 | 				var fn = window[track.linear_mouseclick];
 687 | 				if('object' ==  typeof fn) {
 688 | 				    return fn.onclick(track.trackName, d, cfg.plotid);
 689 | 				} else if('function' == typeof fn) {
 690 | 				    return fn(track.trackName, d, cfg.plotid);
 691 | 				}
 692 | 			    } else {
 693 | 				null;
 694 | 			    }
 695 | 			})
 696 | 		    .on('mouseover', function(d) { 
 697 | 			    tip.show(d);
 698 | 			    if('undefined' !== typeof track.linear_mouseover) {
 699 | 				var fn = window[track.linear_mouseover];
 700 | 				if('object' ==  typeof fn) {
 701 | 				    return fn.mouseover(track.trackName, d, cfg.plotid);
 702 | 				} else if('function' == typeof fn) {
 703 | 				    return fn(track.trackName, d, cfg.plotid);
 704 | 				}
 705 | 			    }	
 706 | 			})
 707 | 		    .on('mouseout', function(d) { 
 708 | 			    tip.hide(d);
 709 | 			    if('undefined' !== typeof track.linear_mouseout) {
 710 | 				var fn = window[track.linear_mouseout];
 711 | 				if('object' ==  typeof fn) {
 712 | 				    return fn.mouseout(track.trackName, d, cfg.plotid);
 713 | 				} else if('function' == typeof fn) {
 714 | 				    return fn(track.trackName, d, cfg.plotid);
 715 | 				}
 716 | 			    }	
 717 | 			})
 718 | 		    
 719 | 		    if('undefined' !== typeof track.showLabels) {
 720 | 			//		entering_rects
 721 | 			d3.select(this).append("text")
 722 | 			    .text(function(d) {return d.name;})
 723 | 			    .attr("dx", "2px")
 724 | 			    .attr("dy", "1em")
 725 | 			    .each(function (d) {
 726 | 				    var bb = this.getBBox();
 727 | 				    var slice_length = x1(d.end) - x1(d.start) -2 ; // -2 to offset the dx above
 728 | 				    d.visible = (slice_length > bb.width);
 729 | 				})
 730 | 			    .attr("class", function(d) {return track.trackName + '_text ' + (d.visible ? null : "linear_hidden" ); });
 731 | 		    }
 732 | 	    } else if(d.feature == "terminator") {
 733 | 		d3.select(this).append("use").attr("xlink:href", "#lollipop");
 734 | 	    } else if(d.feature == "arrow") {
 735 | 
 736 | 		d.height = d.stackOrder * track.increment;
 737 | 		d.headytranslate = d.height;
 738 | 
 739 | 		arrowclass = track.trackName + '_arrow' + ' ' + ('undefined' !== typeof d.extraclass ? d.extraclass : '');
 740 | 		arrowbase = d3.select(this)
 741 | 		
 742 | 		arrowbase.append("path")
 743 | 		.attr("class", arrowclass)
 744 | 		.attr("d", function(d) { 
 745 | 			// 0.77 * 0.9
 746 | 			return "m 0," + track.baseheight + "l 0,-" + (track.baseheight + d.height) + " " + d.width + ",0";
 747 | 			
 748 | 		    })
 749 | 		.attr("fill-opacity", 0)
 750 | 		arrowbase.append("use").attr("xlink:href", "#rightarrow")
 751 | 		.attr("transform", function(d) {
 752 | 			return "translate(" + d.width + ",-" + d.headytranslate + ")";
 753 | 		    })
 754 | 		.attr("class", arrowclass);
 755 | 
 756 | 
 757 | 	    } //else
 758 | 	});
 759 | 
 760 | 
 761 |     rects.exit().remove();
 762 | }
 763 | 
 764 | genomeTrack.prototype.displayPlotTrack = function(track, i) {
 765 |     var visStart = this.visStart,
 766 |     visEnd = this.visEnd,
 767 |     x1 = this.x1,
 768 |     y1 = this.y1;
 769 | 
 770 |     if((typeof track.visible == 'undefined') || (track.visible == false)) {
 771 |     	return;
 772 |     }
 773 | 
 774 |     if((typeof track.linear_plot_width == 'undefined') || (typeof track.linear_plot_height == 'undefined')) {
 775 | //    if((typeof track.linear_plot_width == 'undefined')) {
 776 | 	return;
 777 |     }
 778 | 
 779 |     var startItem = parseInt(visStart / track.bp_per_element);
 780 |     var endItem = Math.min(parseInt(visEnd / track.bp_per_element), track.items.length);
 781 |     var offset = ((startItem+1) * track.bp_per_element) - visStart;
 782 | 
 783 |     var items = track.items.filter(function(d, i) { return i >= startItem && i <= endItem } );
 784 | 
 785 |     track.plotScale = d3.scale.linear()
 786 | 	.domain([track.plot_min, track.plot_max])
 787 | 	.range([track.linear_plot_height+(track.linear_plot_width/2), track.linear_plot_height-(track.linear_plot_width/2)]);
 788 | 
 789 |     var lineFunction = d3.svg.line()
 790 | 	.x(function(d, i) { return x1((i*track.bp_per_element)); } )
 791 | 	.y(function(d, i) { return track.plotScale(d); } )
 792 | 	.interpolate("linear");
 793 | 
 794 |      var plot = this.itemRects[i].selectAll("path")
 795 | 	.attr("d", lineFunction(track.items))
 796 | 
 797 | //    plot.exit().remove();
 798 | 
 799 | }
 800 | 
 801 | genomeTrack.prototype.displayGapTrack = function(track, i) {
 802 |     var visStart = this.visStart,
 803 |     visEnd = this.visEnd,
 804 |     x1 = this.x1,
 805 |     y1 = this.y1;
 806 |     var cfg = this.layout;
 807 |     var self = this;
 808 | 
 809 |     // Because of how the tooltip library binds to the SVG object we have to turn it
 810 |     // on or off here rather than in the .on() call, we'll redirect the calls to
 811 |     // a dummy do-nothing object if we're not showing tips in this context.
 812 |     var tip = {show: function() {}, hide: function() {} };
 813 |     if(('undefined' !== typeof track.showTooltip) && track.showTooltip) {
 814 | 	tip = this.tip;
 815 |     }
 816 | 
 817 |     if((typeof track.visible !== 'undefined') && (track.visible == false)) {
 818 |     	return;
 819 |     }
 820 | 
 821 | //    var gap_range = d3.range(0, this.layout.height, 5);
 822 |     var gap_range = d3.range(0, y1(this.numTracks)+(this.numTracks*3), 5);
 823 | 
 824 |     var items = track.items.filter(function(d) {return (d.start <= visEnd && d.start >= visStart) || (d.end <= visEnd && d.end >= visStart);});
 825 | 
 826 |     var gaps = this.itemRects[i].selectAll("path")
 827 |     .data(items, function(d) { return d.id; })
 828 |     .attr("transform", function(d,i) { 
 829 | 	    return "translate(" + x1(d.start) + ', 0)'; 
 830 | 	})
 831 |     .each(function (d) { d.width = x1(d.end) - x1(d.start); })
 832 |     .attr('d', function(d) { return self.jaggedPathGenerator(d.width, gap_range); } );
 833 | 
 834 |     var entering_gaps = gaps.enter().append("path")
 835 |     .each(function (d) { d.width = x1(d.end) - x1(d.start); })
 836 |     .attr('d', function(d) { return self.jaggedPathGenerator(d.width, gap_range); } )
 837 |     .attr("transform", function(d,i) { 
 838 | 	    return "translate(" + x1(d.start) + ', 0)'; 
 839 | 	})
 840 |     .attr("id", function(d,i) { return track.trackName + '_' + d.id; })
 841 |     .attr("class", function(d) {return track.trackName + ' linearplot ' + (typeof d.feature === 'undefined' ? 'gene' : d.feature); })//;
 842 |     .on("click", function(d,i) {
 843 | 	    if (d3.event.defaultPrevented) return; // click suppressed
 844 | 	    if('undefined' !== typeof track.linear_mouseclick) {
 845 | 		var fn = window[track.linear_mouseclick];
 846 | 		if('object' ==  typeof fn) {
 847 | 		    return fn.onclick(track.trackName, d, cfg.plotid);
 848 | 		} else if('function' == typeof fn) {
 849 | 		    return fn(track.trackName, d, cfg.plotid);
 850 | 		}
 851 | 	    } else {
 852 | 		null;
 853 | 	    }
 854 | 	})
 855 |     .on('mouseover', function(d) { 
 856 | 	    tip.show(d);
 857 | 	    if('undefined' !== typeof track.linear_mouseover) {
 858 | 		var fn = window[track.linear_mouseover];
 859 | 		if('object' ==  typeof fn) {
 860 | 		    return fn.mouseover(track.trackName, d, cfg.plotid);
 861 | 		} else if('function' == typeof fn) {
 862 | 		    return fn(track.trackName, d, cfg.plotid);
 863 | 		}
 864 | 	    }	
 865 | 	})
 866 |     .on('mouseout', function(d) { 
 867 | 	    tip.hide(d);
 868 | 	    if('undefined' !== typeof track.linear_mouseout) {
 869 | 		var fn = window[track.linear_mouseout];
 870 | 		if('object' ==  typeof fn) {
 871 | 		    return fn.mouseout(track.trackName, d, cfg.plotid);
 872 | 		} else if('function' == typeof fn) {
 873 | 		    return fn(track.trackName, d, cfg.plotid);
 874 | 		}
 875 | 	    }	
 876 | 	});
 877 | 
 878 |     gaps.exit().remove();
 879 | 
 880 | }
 881 | 
 882 | genomeTrack.prototype.jaggedPathGenerator = function(width, data) {
 883 | 
 884 |     var down = [];
 885 |     //    var up = [];
 886 |     for(var i = 0; i < data.length; i++) {
 887 | 	var offset = ((i % 2 === 0) ? 3 : -3);
 888 | 	down.push({ x: offset, y: data[i] });
 889 | 	down.unshift({ x: offset+width, y: data[i] });
 890 |     }
 891 |     down.push(down[0]);
 892 | 
 893 |     var generator = d3.svg.line()
 894 |     .x(function(d,i) { return d.x; })
 895 |     .y(function(d,i) { return d.y; })
 896 |     .interpolate("linear");
 897 | 
 898 |     return generator(down);
 899 |     //    return generator(down.concat(up));
 900 | }
 901 | 
 902 | genomeTrack.prototype.displayGlyphTrack = function(track, i) {
 903 |     var visStart = this.visStart,
 904 |     visEnd = this.visEnd,
 905 |     x1 = this.x1,
 906 |     y1 = this.y1;
 907 |     var cfg = this.layout;
 908 | 
 909 |     if((typeof track.visible !== 'undefined') && (track.visible == false)) {
 910 |     	return;
 911 |     }
 912 | 
 913 |     // Because of how the tooltip library binds to the SVG object we have to turn it
 914 |     // on or off here rather than in the .on() call, we'll redirect the calls to
 915 |     // a dummy do-nothing object if we're not showing tips in this context.
 916 |     var tip = {show: function() {}, hide: function() {} };
 917 |     if(('undefined' !== typeof track.showTooltip) && track.showTooltip) {
 918 | 	tip = this.tip;
 919 |     }
 920 | 
 921 |     var items = track.items.filter(function(d) {return d.bp <= visEnd && d.bp >= visStart;});
 922 | 
 923 |     // When we move we need to recalculate the stacking order
 924 |     var stackCount = 0;
 925 |     for(var j = 0; j < items.length; j++) {
 926 | 	if(items[j].bp < visStart || items[j].bp > visEnd) {
 927 | 	    continue;
 928 | 	}
 929 | 	if(j < 1) {
 930 | 	    items[j].stackCount = 0;
 931 | 	    continue;
 932 | 	}
 933 | 
 934 | 	var dist = x1(items[j].bp) - x1(items[j-1].bp);
 935 | 
 936 | 	if(dist < track.linear_pixel_spacing) {
 937 | 	    items[j].stackCount = items[j-1].stackCount + 1;
 938 | 	    continue;
 939 | 	}
 940 | 
 941 | 	items[j].stackCount = 0;
 942 |     }
 943 | 
 944 |     // Because SVG coordinates are from the top-left, the "height" is pixels DOWN from
 945 |     // the top of the image to start stacking the glyphs
 946 | 
 947 |     var glyphs = this.itemRects[i].selectAll("path")
 948 |     .data(items, function(d) { return d.id; })
 949 |     .attr("transform", function(d,i) { return "translate(" + (x1(d.bp) + track.padding) + ',' + (track.linear_height - (track.linear_glyph_buffer * d.stackCount * track.invert))  + ")"; });
 950 |    
 951 |     var entering_glyphs = glyphs.enter()
 952 |     .append('path')
 953 |     .attr('id', function(d,i) { return track.trackName + "_glyph" + d.id; })
 954 |     .attr('class', function(d) {return track.trackName + '_' + d.type + " linear_" + track.trackName + '_' + d.type; })
 955 |     .attr("d", d3.svg.symbol().type(track.glyphType).size(track.linear_glyphSize))
 956 |     .attr("transform", function(d,i) {  return "translate(" + (x1(d.bp) + track.padding) + ',' + (track.linear_height - (track.linear_glyph_buffer * d.stackCount * track.invert))  + ")"; })
 957 |     .on("click", function(d,i) {
 958 | 	    if('undefined' !== typeof track.linear_mouseclick) {
 959 | 		var fn = window[track.linear_mouseclick];
 960 | 		if('object' ==  typeof fn) {
 961 | 		    return fn.onclick(track.trackName, d, cfg.plotid);
 962 | 		} else if('function' == typeof fn) {
 963 | 		    return fn(track.trackName, d, cfg.plotid);
 964 | 		}
 965 | 	    } else {
 966 | 		null;
 967 | 	    }
 968 | 	})
 969 |     .on('mouseover', function(d) { 
 970 | 	tip.show(d);
 971 | 	    if('undefined' !== typeof track.linear_mouseover) {
 972 | 		var fn = window[track.linear_mouseover];
 973 | 		if('object' ==  typeof fn) {
 974 | 		    return fn.mouseover(track.trackName, d, cfg.plotid);
 975 | 		} else if('function' == typeof fn) {
 976 | 		    return fn(track.trackName, d, cfg.plotid);
 977 | 		}
 978 | 	    }	
 979 | 	})
 980 |     .on('mouseout', function(d) { 
 981 | 	tip.hide(d);
 982 | 	    if('undefined' !== typeof track.linear_mouseout) {
 983 | 		var fn = window[track.linear_mouseout];
 984 | 		if('object' ==  typeof fn) {
 985 | 		    return fn.mouseout(track.trackName, d, cfg.plotid);
 986 | 		} else if('function' == typeof fn) {
 987 | 		    return fn(track.trackName, d, cfg.plotid);
 988 | 		}
 989 | 	    }	
 990 | 	});
 991 | 
 992 |     glyphs.exit()
 993 |     .remove();
 994 |     
 995 | }
 996 | 
 997 | genomeTrack.prototype.displayAxis = function() {
 998 |     this.axisContainer.select(".xaxislinear").call(this.xAxis);
 999 | }
1000 | 
1001 |     genomeTrack.prototype.update = function(startbp, endbp, params) {
1002 |     //    console.log(startbp, endbp);
1003 | 
1004 |     this.visStart = startbp;
1005 |     this.visEnd = endbp;
1006 | 
1007 |     this.zoom.x(this.x1.domain([startbp,endbp]));
1008 | 
1009 |     this.redraw();
1010 | }
1011 | 
1012 | genomeTrack.prototype.update_finished = function(startbp, endbp, params) {
1013 |     //    console.log("Thank you, got: " + startbp, endbp);
1014 | 
1015 | }
1016 | 
1017 | genomeTrack.prototype.resize = function(newWidth) {
1018 |     this.layout.width = newWidth;
1019 | 
1020 |     this.dragbar
1021 |     .attr("transform", "translate(" + (newWidth -
1022 | 				       this.layout.right_margin) + "," + (this.dragbar_y_mid-15) + ")")
1023 | 
1024 |     this.layout.width_without_margins =
1025 | 	this.layout.width - this.layout.left_margin -
1026 | 	this.layout.right_margin;
1027 | 
1028 |     this.x
1029 | 	.range([0,this.layout.width_without_margins]);
1030 |     this.x1
1031 | 	.range([0,this.layout.width_without_margins]);
1032 | 
1033 |     this.chart
1034 | 	.attr("width", this.layout.width)
1035 | 
1036 |     this.clipPath
1037 | 	.attr("width", this.layout.width_without_margins)
1038 |     
1039 |     this.main
1040 | 	.attr("width", this.layout.width_without_margins)
1041 | 
1042 |     this.redraw();
1043 | 
1044 | }
1045 | 
1046 | genomeTrack.prototype.dragresize = function(d) {
1047 |     var newWidth = d3.event.x;
1048 | 
1049 |     //    console.log(this.layout.containerid);
1050 |     this.resize(newWidth);
1051 |     //    d3.event.preventDefault();
1052 | 
1053 | }
1054 | 
1055 | genomeTrack.prototype.redraw = function() {
1056 | 
1057 |     for(var i = 0; i < this.tracks.length; i++) {
1058 | 
1059 | 	 if("undefined" !== this.tracks[i].skipLinear
1060 | 	    &&  this.tracks[i].skipLinear == true) {
1061 | 	     continue;
1062 | 	 }
1063 | 
1064 | 	switch(this.tracks[i].trackType) {
1065 | 	case 'gap':
1066 | 	    this.displayGapTrack(this.tracks[i], i);
1067 |             break;
1068 | 	case "stranded":
1069 | 	    this.displayStranded(this.tracks[i], i);
1070 | 	    break;
1071 | 	case "track":
1072 | 	    this.displayTrack(this.tracks[i], i);
1073 | 	    break;
1074 | 	case "glyph":
1075 | 	    this.displayGlyphTrack(this.tracks[i], i);
1076 | 	    break;
1077 | 	case "plot":
1078 | 	    this.displayPlotTrack(this.tracks[i], i);
1079 | 	    break;
1080 | 	default:
1081 | 	    // Do nothing for an unknown track type
1082 | 	}
1083 |     }
1084 |     
1085 |     this.axisContainer.select(".xaxislinear").call(this.xAxis);
1086 | 
1087 | }
1088 | 
1089 | genomeTrack.prototype.rescale = function() {
1090 |     var cfg = this.layout;
1091 | 
1092 |     var reset_s = 0;
1093 |     if ((this.x1.domain()[1] - this.x1.domain()[0]) >= (this.genomesize - this.start_offset)) {
1094 | 	this.zoom.x(this.x1.domain([this.start_offset, this.genomesize + this.start_offset]));
1095 | 	reset_s = 1;
1096 |     }
1097 | 
1098 |     if (reset_s == 1) { // Both axes are full resolution. Reset.
1099 | 	this.zoom.scale(1);
1100 | 	this.zoom.translate([0,0]);
1101 |     }
1102 |     else {
1103 | 	if (this.x1.domain()[0] < this.start_offset) {
1104 | 	    this.x1.domain([this.start_offset, this.x1.domain()[1] - this.x1.domain()[0] + this.start_offset]);
1105 | 	}
1106 | 	if (this.x1.domain()[1] > this.genomesize + this.start_offset) {
1107 | 	    var xdom0 = this.x1.domain()[0] - this.x1.domain()[1] + this.genomesize + this.start_offset;
1108 | 	    this.x1.domain([xdom0, this.genomesize + this.start_offset]);
1109 | 	}
1110 |     }
1111 | 
1112 |     var cur_domain = this.x1.domain();
1113 |     this.visStart = cur_domain[0];
1114 |     this.visEnd = cur_domain[1];
1115 | 
1116 |     if('undefined' !== typeof this.callbackObj) {
1117 | 	if( Object.prototype.toString.call( this.callbackObj ) === '[object Array]' ) { 
1118 | 	    for(var obj in this.callbackObj) {
1119 | 		if(this.callbackObj.hasOwnProperty(obj)) {
1120 | 		    this.callbackObj[obj].update(this.x1.domain()[0], this.x1.domain()[1], { plotid: cfg.plotid } );
1121 | 		}
1122 | 	    }
1123 | 	} else {
1124 | 	    this.callbackObj.update(this.x1.domain()[0], this.x1.domain()[1], { plotid: cfg.plotid } );
1125 | 	}
1126 |     }
1127 | 
1128 |     this.redraw();
1129 | 
1130 | }
1131 | 
1132 | genomeTrack.prototype.addBrushCallback = function(obj) {
1133 | 
1134 |     // We allow multiple brushes to be associated with a linear plot, if we have
1135 |     // a brush already, add this new one on.  Otherwise just remember it.
1136 | 
1137 |     if('undefined' !== typeof this.callbackObj) {
1138 | 
1139 | 	if( Object.prototype.toString.call( obj ) === '[object Array]' ) { 
1140 | 	    this.callbackObj.push(obj);
1141 | 	} else {
1142 | 	    var tmpobj = this.callbackObj;
1143 | 	    this.callbackObj = [tmpobj, obj];
1144 | 	}
1145 |     } else {
1146 | 	this.callbackObj = obj;
1147 |     }
1148 | 
1149 |     // And make sure our new brush is updated to reflect
1150 |     // the current visible area
1151 |     obj.update(this.visStart, this.visEnd);
1152 | }
1153 | 
1154 | genomeTrack.prototype.callBrushFinished = function() {
1155 |     var cfg = this.layout;
1156 | 
1157 |     if('undefined' !== typeof this.callbackObj) {
1158 | 	if( Object.prototype.toString.call( this.callbackObj ) === '[object Array]' ) { 
1159 | 	    for(var obj in this.callbackObj) {
1160 | 		if(this.callbackObj.hasOwnProperty(obj)) {
1161 | 		    this.callbackObj[obj].update_finished(this.x1.domain()[0], this.x1.domain()[1], { plotid: cfg.plotid } );
1162 | 		}
1163 | 	    }
1164 | 	} else {
1165 | 	    this.callbackObj.update_finished(this.x1.domain()[0], this.x1.domain()[1], { plotid: cfg.plotid } );
1166 | 	}
1167 |     }
1168 | 
1169 | }
1170 | 
1171 | ////////////////////////////////////////////////
1172 | //
1173 | // Export functionality
1174 | //
1175 | ////////////////////////////////////////////////
1176 | 
1177 | // Allowed export formats are 'png' and 'svg'
1178 | // The extension will be added, just summply the base
1179 | // filename.
1180 | 
1181 | // Saving to raster format is dependent on FileSaver.js
1182 | // and canvg.js (which include rgbcolor.js & StackBlur.js),
1183 | // they must be loaded before circularplot.js
1184 | 
1185 | genomeTrack.prototype.savePlot = function(scaling, filename, stylesheetfile, format) {
1186 |         // First lets get the stylesheet
1187 |     var sheetlength = stylesheetfile.length;
1188 |     var style = document.createElementNS("http://www.w3.org/1999/xhtml", "style");
1189 | 	style.textContent += "<![CDATA[\n";
1190 |     for (var i=0;i<document.styleSheets.length; i++) {
1191 | 	str = document.styleSheets[i].href;
1192 | 	if(null == str) continue;
1193 | 
1194 | 	if (str.substr(str.length-sheetlength)==stylesheetfile){
1195 |             var rules;
1196 |             if(document.styleSheets[i].cssRules) {
1197 |                 rules = document.styleSheets[i].cssRules;
1198 |             } else if (document.styleSheets[i].rules) {
1199 |                 rules = document.styleSheets[i].rules;
1200 |             }
1201 |             if(rules) {
1202 |                 for (var j=0; j<rules.length;j++){
1203 |                     style.textContent += (rules[j].cssText + "\n");
1204 |                 }
1205 |             }
1206 |             break;
1207 |     	}
1208 |     }
1209 |     style.textContent += "]]>";
1210 | 
1211 |     // Now we clone the SVG element, resize and scale it up
1212 |     var container = this.layout.container.slice(1);
1213 |     var containertag = document.getElementById(container);
1214 |     var clonedSVG = containertag.cloneNode(true);
1215 |     var svg = clonedSVG.getElementsByTagName("svg")[0];
1216 | 
1217 |     // Remove any hidden elements such as text that's not being shown
1218 |     var tags = svg.getElementsByClassName("linear_hidden")
1219 |     for(var i=tags.length-1; i>=0; i--) {
1220 | //	if(tags[i].getAttributeNS(null, "name") === name) {
1221 | 	    tags[i].parentNode.removeChild(tags[i]);
1222 | //        }
1223 |     }
1224 | 
1225 |     // We need to resize the svg with the new canvas size
1226 |     svg.removeAttribute('width');
1227 |     svg.removeAttribute('height');
1228 |     svg.setAttribute('width', this.layout.width*scaling);
1229 |     svg.setAttribute('height', this.layout.height*scaling);
1230 | 
1231 |     // Update first g tag with the scaling
1232 |     g = svg.getElementsByTagName("g")[0];
1233 |     transform = g.getAttribute("transform");
1234 | //    g.setAttribute("transform", transform + " scale(" + scaling + ")");
1235 | 
1236 |     // Append the stylehsheet to the cloned svg element
1237 |     // so when we export it the style are inline and 
1238 |     // get rendered
1239 |     svg.getElementsByTagName("defs")[0].appendChild(style);
1240 | 
1241 |     // Fetch the actual SVG tag and convert it to a canvas
1242 |     // element
1243 |     var content = clonedSVG.innerHTML.trim();
1244 | 
1245 |     if(format == 'svg') {
1246 | 	var a = document.createElement('a');
1247 | 	a.href = "data:application/octet-stream;base64;attachment," + btoa(content);
1248 | 	a.download = filename + ".svg";
1249 | 	a.click();
1250 | 
1251 |     } else if(format == 'png') {
1252 | 	var canvas = document.createElement('canvas');
1253 | 	canvg(canvas, content);
1254 | 
1255 | 	// Convert the canvas to a data url (this could
1256 | 	// be displayed inline by inserting it in to an 
1257 | 	// <img> tag in the src attribute, ie
1258 | 	// <img src="'+imgData+'">
1259 | 	var theImage = canvas.toDataURL('image/png');
1260 | 
1261 | 	// Convert to a blob
1262 | 	var blob = this.dataURLtoBlob(theImage);
1263 | 
1264 | 	// Prompt to save
1265 | 	saveAs(blob, filename);
1266 |     }
1267 | }
1268 | 
1269 | genomeTrack.prototype.dataURLtoBlob = function(dataURL) {
1270 |   // Decode the dataURL    
1271 |   var binary = atob(dataURL.split(',')[1]);
1272 |   // Create 8-bit unsigned array
1273 |   var array = [];
1274 |   for(var i = 0; i < binary.length; i++) {
1275 |       array.push(binary.charCodeAt(i));
1276 |   }
1277 |   // Return our Blob object
1278 |   return new Blob([new Uint8Array(array)], {type: 'image/png'});
1279 | }
1280 | 
1281 | genomeTrack.prototype.drawFeatures = function() {
1282 |     var x1 = this.x1;
1283 |     var y1 = this.y1;
1284 | 
1285 |     // Quick debugging variable to show click rects
1286 |     var opacity = 0;
1287 | 
1288 |     // Lollipop for terminator glyph (stranded, positive)
1289 |     var lollipop_strand_pos = this.defs.append("g").attr("id", "lollipop_strand_pos");
1290 |     lollipop_strand_pos.append("path")
1291 | 	.attr("class", "lollipophead")
1292 | 	.attr("d", function() {
1293 | 		arc = "m 0,";
1294 | 		arc += y1(1) * 0.69;
1295 | 		arc += " a ";
1296 | 		arc += y1(1) * 0.13;
1297 | 		arc += ",";
1298 | 		arc += y1(1) * 0.13;
1299 | 		arc += " 0 1 1 ";
1300 | 		arc += y1(1) * 0.09;
1301 | 		arc += ",0";
1302 | 		//		console.log(arc);
1303 | 		return arc;
1304 | 		//		"m 0,60 a 12,12 0 1 1 8,0"
1305 | 	    });
1306 |     lollipop_strand_pos.append("path")
1307 | 	.attr("class", "lollipopstemend")
1308 | 	.attr("d", function() {
1309 | 		line = "m " + (y1(1) * 0.09) + ",";
1310 | 		line += y1(1) * 0.69;
1311 | 		line += " l 0,";
1312 | 		line += y1(1) * 0.70;
1313 | 		//		console.log("line " + line);
1314 | 		return line;
1315 | 		//		"m 8,60 l 0,65"
1316 | 		    });
1317 |     lollipop_strand_pos.append("path")
1318 | 	.attr("class", "lollipopstemstart")
1319 | 	.attr("d", function() {
1320 | 		line = "m 0,";
1321 | 		line += y1(1) * 0.69;
1322 | 		line += " l 0,";
1323 | 		line += y1(1) * 0.70;
1324 | 		//		console.log(line);
1325 | 		return line;
1326 | 		//		"m 0,60 l 0,65"
1327 | 	    });
1328 |     lollipop_strand_pos.append("rect")
1329 | 	.attr("transform", function () {
1330 | 		return "translate(-" + (y1(1) * 0.1) + "," + (y1(1) * 0.43) + ")";
1331 | 	    })
1332 | 	.attr("width", function() { 
1333 | 		return y1(1) * 0.3;
1334 | 	    })
1335 | 	.attr("height", function() { 
1336 | 		return y1(1) * 0.26;
1337 | 	    })
1338 | 	.attr("fill-opacity", opacity);
1339 |     lollipop_strand_pos.append("rect")
1340 |         .attr("transform", function() {
1341 | 		return "translate(0, " + (y1(1) * 0.68) + ")";
1342 | 		//		"translate(0,60)"
1343 | 		    })
1344 | 	.attr("width", 8)
1345 | 	.attr("height", function() {
1346 | 		return  y1(1) * 0.72;
1347 | 	    })
1348 | 	.attr("fill-opacity", opacity);
1349 | 
1350 |     // Lollipop for terminator glyph (stranded, negative)
1351 |     var lollipop_strand_neg = this.defs.append("g").attr("id", "lollipop_strand_neg");
1352 |     lollipop_strand_neg.append("path")
1353 | 	.attr("class", "lollipophead")
1354 | 	.attr("d", function() {
1355 | 		arc = "m 0,";
1356 | 		arc += y1(1) * 1.20;
1357 | 		arc += " a ";
1358 | 		arc += y1(1) * 0.13;
1359 | 		arc += ",";
1360 | 		arc += y1(1) * 0.13;
1361 | 		arc += " 0 1 0 ";
1362 | 		arc += y1(1) * 0.09;
1363 | 		arc += ",0";
1364 | 		//		console.log(arc);
1365 | 		return arc;
1366 | 		//		"m 0,60 a 12,12 0 1 1 8,0"
1367 | 	    });
1368 |     lollipop_strand_neg.append("path")
1369 | 	.attr("class", "lollipopstemstart")
1370 | 	.attr("d", function() {
1371 | 		line = "m " + (y1(1) * 0.09) + ",";
1372 | 		line += y1(1) * 1.20;
1373 | 		line += " l 0,";
1374 | 		line += y1(1) * 0.71 * -1;
1375 | 		//		console.log(line);
1376 | 		return line;
1377 | 		//		"m 8,60 l 0,65"
1378 | 		    });
1379 |     lollipop_strand_neg.append("path")
1380 | 	.attr("class", "lollipopstemend")
1381 | 	.attr("d", function() {
1382 | 		line = "m 0,";
1383 | 		line += y1(1) * 1.20;
1384 | 		line += " l 0,";
1385 | 		line += y1(1) * 0.71 * -1;
1386 | 		//		console.log(line);
1387 | 		return line;
1388 | 		//		"m 0,60 l 0,65"
1389 | 	    });
1390 |     lollipop_strand_neg.append("rect")
1391 | 	.attr("transform", function () {
1392 | 		return "translate(-" + (y1(1) * 0.1) + "," + (y1(1) * 1.20) + ")";
1393 | 	    })
1394 | 	.attr("width", function() { 
1395 | 		return y1(1) * 0.3;
1396 | 	    })
1397 | 	.attr("height", function() { 
1398 | 		return y1(1) * 0.26;
1399 | 	    })
1400 | 	.attr("fill-opacity", opacity);
1401 |     lollipop_strand_neg.append("rect")
1402 | 	.attr("transform", function() {
1403 | 		return "translate(0, " + (y1(1) * 0.50) + ")";
1404 | 		//		"translate(0,60)"
1405 | 		    })
1406 | 	.attr("width", 8)
1407 | 	.attr("height", function() {
1408 | 		return  y1(1) * 0.71;
1409 | 	    })
1410 | 	.attr("fill-opacity", opacity);
1411 | 
1412 |     // Lollipop for terminator glyph (unstranded)
1413 |     var lollipop = this.defs.append("g").attr("id", "lollipop");
1414 |     lollipop.append("path")
1415 |         .attr("class", "lollipophead")
1416 | 	.attr("d", function() {
1417 | 		arc = "m 0,";
1418 | 		arc += y1(1) * 0.77;
1419 | 		arc += " a ";
1420 | 		arc += y1(1) * 0.13;
1421 | 		arc += ",";
1422 | 		arc += y1(1) * 0.13;
1423 | 		arc += " 0 1 1 ";
1424 | 		arc += y1(1) * 0.09;
1425 | 		arc += ",0";
1426 | 		//		console.log(arc);
1427 | 		return arc;
1428 | 		//		"m 0,60 a 12,12 0 1 1 8,0"
1429 | 	    });
1430 |     lollipop.append("path")
1431 | 	.attr("class", "lollipopstemend")
1432 | 	.attr("d", function() {
1433 | 		line = "m " + (y1(1) * 0.09) + ",";
1434 | 		line += y1(1) * 0.77;
1435 | 		line += " l 0,";
1436 | 		line += y1(1) * 0.62;
1437 | 		//		console.log(line);
1438 | 		return line;
1439 | 		//		"m 8,60 l 0,65"
1440 | 		    });
1441 |     lollipop.append("path")
1442 | 	.attr("class", "lollipopstemstart")
1443 | 	.attr("d", function() {
1444 | 		line = "m 0,";
1445 | 		line += y1(1) * 0.77;
1446 | 		line += " l 0,";
1447 | 		line += y1(1) * 0.62;
1448 | 		//		console.log(line);
1449 | 		return line;
1450 | 		//		"m 0,60 l 0,65"
1451 | 	    });
1452 |     lollipop.append("rect")
1453 | 	.attr("transform", function () {
1454 | 		return "translate(-" + (y1(1) * 0.1) + "," + (y1(1) * 0.51) + ")";
1455 | 	    })
1456 | 	.attr("width", function() { 
1457 | 		return y1(1) * 0.3;
1458 | 	    })
1459 | 	.attr("height", function() { 
1460 | 		return y1(1) * 0.26;
1461 | 	    })
1462 | 	.attr("fill-opacity", opacity);
1463 |     lollipop.append("rect")
1464 |         .attr("transform", function() {
1465 | 		return "translate(0, " + (y1(1) * 0.76) + ")";
1466 | 		//		"translate(0,60)"
1467 | 		    })
1468 | 	.attr("width", 8)
1469 | 	.attr("height", function() {
1470 | 		return  y1(1) * 0.64;
1471 | 	    })
1472 | 	.attr("fill-opacity", opacity);
1473 | 
1474 |     // Right arrow
1475 |     var rightarrow = this.defs.append("g").attr("id", "rightarrow");
1476 |     rightarrow.append("path")
1477 |         .attr("class", "rightarrow")
1478 |         .attr("d", function() {
1479 | 		return "m 0,0 l -4,4 m 0,-8 l 4,4";
1480 | 	    });
1481 | 
1482 |     // Left arrow
1483 |     var leftarrow = this.defs.append("g").attr("id", "leftarrow");
1484 |     leftarrow.append("path")
1485 |         .attr("class", "rightarrow")
1486 |         .attr("d", function() {
1487 | 		return "m 0,0 l 4,4 m 0,-8 l -4,4";
1488 | 		//		return "m 0," + y1(1) + " l 4,4 m 0,-8 l -4,4";
1489 | 	    });
1490 | 
1491 | }
1492 | 


--------------------------------------------------------------------------------
/prototypes/islandplot.html:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html>
 2 | <html>
 3 |   <head>
 4 |     <meta http-equiv="Content-Type" content="text/html;charset=utf-8"/>
 5 |   <title>IslandPlot Example</title>
 6 |     <script src="http://d3js.org/d3.v3.min.js"></script>
 7 |     <style>
 8 |     body {
 9 |       overflow: hidden;
10 |         margin: 0;
11 | 	  font-size: 14px;
12 | 	    font-family: "Helvetica Neue", Helvetica;
13 | 	    }
14 |  
15 |  #chart {
16 |    position: absolute;
17 |      top: 50px;
18 |        left: 100px;
19 |        }
20 |        </style>
21 |   </head>
22 |   <body>
23 |     <div id="body">
24 |       <div id="chart"></div>
25 |     </div>
26 |     
27 |     <script type="text/javascript" src="islandplot.js"></script>
28 |     <script type="text/javascript" src="sample.js"></script>
29 |  
30 | 
31 | &nbsp;<br />
32 | &nbsp;&nbsp;&nbsp;&nbsp;  <input type="checkbox" name="showGC" onchange="updateGC(this); return false" checked>Show GC plot<br />
33 | &nbsp;<br />
34 | &nbsp;&nbsp;&nbsp;&nbsp;  <input type="checkbox" name="showStrand" onchange="updateStrand(this); return false" checked>Show stranded track<br />
35 | &nbsp;<br />
36 | &nbsp;&nbsp;&nbsp;&nbsp;  <input type="checkbox" name="showadb" onchange="updateAdb(this); return false" checked>Show second glyph type
37 |   </body>
38 | </html>
39 | 


--------------------------------------------------------------------------------
/prototypes/islandplot.js:
--------------------------------------------------------------------------------
  1 | var IslandPlot = {
  2 |     cfg: {
  3 |        radius: 5,
  4 |        w: 600,
  5 |        h: 600,
  6 |        factor: 1,
  7 |        factorLegend: .85,
  8 |        levels: 3,
  9 |        maxValue: 0,
 10 |        radians: 2 * Math.PI,
 11 |        opacityArea: 0.5,
 12 |        ToRight: 5,
 13 |        TranslateX: 80,
 14 |        TranslateY: 30,
 15 |        ExtraWidthX: 100,
 16 |        ExtraWidthY: 100,
 17 |        spacing: 100000,
 18 |        legend_spacing: 5,
 19 |        layout: "polar"
 20 |     },
 21 | 
 22 |     createCanvas: function(id, options) {
 23 |       if('undefined' !== typeof options){
 24 | 	    for(var i in options){
 25 | 		  if('undefined' !== typeof options[i]){
 26 | 		    IslandPlot.cfg[i] = options[i];
 27 | 		  }
 28 | 	    }
 29 | 	  }
 30 |       var cfg = IslandPlot.cfg;
 31 |         
 32 |       IslandPlot.cfg.radians_pre_bp = cfg.radians/cfg.genomesize;
 33 |       IslandPlot.cfg.radius = cfg.factor*Math.min(cfg.w/2, cfg.h/2);
 34 |       IslandPlot.cfg.tracks = [];
 35 |       IslandPlot.cfg.glyph_tracks = [];
 36 |       IslandPlot.cfg.plot_values = [];
 37 |       IslandPlot.cfg.plot_layout = [];
 38 | 	IslandPlot.cfg.xScale = d3.scale.linear()
 39 | 	    .range([0,cfg.radians])
 40 | 	    .domain([0, cfg.genomesize]);
 41 |       d3.select(id).select("svg").remove();
 42 | 	
 43 | 	  IslandPlot.g = d3.select(id)
 44 | 			.append("svg")
 45 | 			.attr("width", cfg.w+cfg.ExtraWidthX)
 46 | 			.attr("height", cfg.h+cfg.ExtraWidthY)
 47 | 			.append("g")
 48 | 			.attr("transform", "translate(" + cfg.TranslateX + "," + cfg.TranslateY + ")");
 49 | 			;
 50 | 
 51 |     },
 52 |     
 53 |     drawAxis: function() {
 54 |       var cfg = IslandPlot.cfg;
 55 |       var g = IslandPlot.g;
 56 |         
 57 |       var axis = g.selectAll(".axis")
 58 | 		.data(d3.range(0,cfg.genomesize, cfg.spacing))
 59 | 		.enter()
 60 | 		.append("g")
 61 | 		.attr("class", "axis");
 62 | 
 63 | 	  axis.append("line")
 64 | 		.attr("x1", function(d, i){return cfg.w/2 + (20*Math.cos((d*cfg.radians_pre_bp)-Math.PI/2));})
 65 | 		.attr("y1", function(d, i){return cfg.h/2 + (20*Math.sin((d*cfg.radians_pre_bp)-Math.PI/2));})
 66 | 		.attr("x2", function(d, i){return cfg.w/2 + (cfg.radius*Math.cos((d*cfg.radians_pre_bp)-Math.PI/2));})
 67 | 		.attr("y2", function(d, i){return cfg.h/2 + (cfg.radius*Math.sin((d*cfg.radians_pre_bp)-Math.PI/2));})
 68 | 		.attr("class", "line")
 69 | 		.style("stroke", "grey")
 70 | 		.style("stroke-width", "1px");
 71 | 
 72 |     var axis_label = g.selectAll(".axislabel")
 73 | 			.data(d3.range(0,cfg.genomesize, cfg.spacing*cfg.legend_spacing))
 74 | 			.enter()
 75 | 			.append("g")
 76 | 			.attr("class", "axislabel");
 77 |       
 78 | 	axis_label.append("text")
 79 | 		.attr("class", "legend")
 80 |         .text(function(d){ var prefix = d3.formatPrefix(d);
 81 |                                     return prefix.scale(d) + prefix.symbol;
 82 |                                  })
 83 |     
 84 | 		.style("font-family", "sans-serif")
 85 | 		.style("font-size", "11px")
 86 | 		.attr("text-anchor", "middle")
 87 | 		.attr("dy", "1.5em")
 88 | 		.attr("transform", function(d, i){return "translate(0, -10)"})
 89 |         .attr("x", function(d, i){return cfg.w/2 + ((cfg.radius+10)*Math.cos((d*cfg.radians_pre_bp)-Math.PI/2));})
 90 | 		.attr("y", function(d, i){return cfg.h/2 + ((cfg.radius+10)*Math.sin((d*cfg.radians_pre_bp)-Math.PI/2));});
 91 | 
 92 |     },
 93 |     
 94 |     // Default values for the plot, some sanity settings
 95 | 
 96 |     plot_layout: {
 97 |       fill: "none",
 98 |       stroke: "grey"
 99 |     },
100 |     
101 |     // Draw a plot function
102 | 
103 |     drawPlot: function(plot_layout, plot_values, animate) {
104 |       var cfg = IslandPlot.cfg;
105 |       var g = IslandPlot.g;
106 | 
107 |       for(var i in IslandPlot.default_plot_layout){
108 | 		if('undefined' == typeof plot_layout[i]){
109 | 		    plot_layout[i] = IslandPlot.default_plot_layout[i];
110 | 		  }
111 |       }    
112 | 
113 |       var from_range = [plot_layout.plot_min, plot_layout.plot_max];
114 |       var to_range = [plot_layout.plot_radius-(plot_layout.plot_width/2), plot_layout.plot_radius+(plot_layout.plot_width/2)];
115 |       
116 |       var lineFunction = d3.svg.line()
117 |       .x(function(d, i) { return cfg.w/2 + ((('undefined' == typeof animate) ? IslandPlot.mapRange(from_range, to_range, d) : 1 )*Math.cos((i*plot_layout.bp_per_element*cfg.radians_pre_bp)-(Math.PI/2))); })
118 |       .y(function(d, i) { return cfg.h/2 + ((('undefined' == typeof animate) ? IslandPlot.mapRange(from_range, to_range, d) : 1 )*Math.sin((i*plot_layout.bp_per_element*cfg.radians_pre_bp)-(Math.PI/2))); })
119 |         .interpolate("linear");
120 | 
121 |       g.append("path")
122 |         .attr("d", lineFunction(plot_values))
123 |         .attr("stroke", plot_layout.stroke)
124 |         .attr("class", plot_layout.name)
125 |         .attr("id", plot_layout.name)
126 |         .attr("stroke-width", 1)
127 |         .attr("fill", "none");
128 |       
129 |       // Now do the mean circle if we have one
130 |       if('undefined' !== typeof plot_layout.plot_mean) {
131 | 	  IslandPlot.drawCircle(plot_layout.name, IslandPlot.mapRange(from_range, to_range, plot_layout.plot_mean), plot_layout.mean_stroke, animate);
132 | 
133 |       }  
134 | 
135 |       // Save the plot_data for later if we need it
136 |       IslandPlot.cfg.plot_values[plot_layout.name] = plot_values;
137 |       IslandPlot.cfg.plot_layout[plot_layout.name] = plot_layout;
138 | 
139 |       if('undefined' !== typeof animate) {
140 | 	  IslandPlot.movePlot(plot_layout.name, plot_layout.plot_radius);
141 |       }
142 | 
143 |     },
144 | 
145 |     movePlot: function(name, radius) {
146 |       var cfg = IslandPlot.cfg;
147 |       var g = IslandPlot.g;
148 |       var plot_values = IslandPlot.cfg.plot_values[name];
149 |       var plot_layout = IslandPlot.cfg.plot_layout[name];
150 | 
151 |       IslandPlot.cfg.plot_layout[name].plot_radius = radius;
152 | 
153 |       var from_range = [plot_layout.plot_min, plot_layout.plot_max];
154 |       var to_range = [radius-(plot_layout.plot_width/2), radius+(plot_layout.plot_width/2)]; 
155 | 
156 |       var lineFunction = d3.svg.line()
157 |       .x(function(d, i, j) { return cfg.w/2 + (IslandPlot.mapRange(from_range, to_range, d)*Math.cos((i*plot_layout.bp_per_element*cfg.radians_pre_bp)-(Math.PI/2))); })
158 |         .y(function(d, i) { return cfg.h/2 + (IslandPlot.mapRange(from_range, to_range, d)*Math.sin((i*plot_layout.bp_per_element*cfg.radians_pre_bp)-(Math.PI/2))); })
159 |         .interpolate("linear");
160 | 
161 | 	var plot = g.selectAll("." + name)
162 | 
163 | 	plot.transition()
164 | 	    .duration(1000)
165 | 	    .attr("d", function(d,i) { return lineFunction(plot_values)})
166 |       	
167 |     },
168 | 
169 |     removePlot: function(name) {
170 |       var cfg = IslandPlot.cfg;
171 |       var g = IslandPlot.g;
172 |       var plot_values = IslandPlot.cfg.plot_values[name];
173 |       var plot_layout = IslandPlot.cfg.plot_layout[name];
174 | 
175 |       var from_range = [plot_layout.plot_min, plot_layout.plot_max];
176 |       var to_range = [1-(plot_layout.plot_width/2), 1+(plot_layout.plot_width/2)]; 
177 | 
178 |       var lineFunction = d3.svg.line()
179 |       .x(function(d, i) { return cfg.w/2 + (IslandPlot.mapRange(from_range, to_range, d)*Math.cos((i*plot_layout.bp_per_element*cfg.radians_pre_bp)-(Math.PI/2))); })
180 |         .y(function(d, i) { return cfg.h/2 + (IslandPlot.mapRange(from_range, to_range, d)*Math.sin((i*plot_layout.bp_per_element*cfg.radians_pre_bp)-(Math.PI/2))); })
181 |         .interpolate("linear");
182 | 
183 |       g.selectAll("." + name)
184 |       .transition()
185 |       .duration(1000)
186 |       .attr("d", lineFunction(plot_values))
187 |       .style("opacity", 0)
188 |       .remove();
189 | 
190 |       if('undefined' !== typeof plot_layout.plot_mean) {
191 | 	  IslandPlot.removeCircle(name);
192 |       }
193 |       
194 |       IslandPlot.cfg.plot_values[name] = undefined;
195 | 
196 |     },
197 | 
198 |     // The default layout for a track, some sanity values
199 | 
200 |     default_track_layout: {
201 |       fill: "black",
202 |       name: "mytrack",
203 |       inner_radius: 100,
204 |       outer_radius: 120,
205 |       centre_line_stroke: "grey"
206 |     },
207 |     
208 |     // Pass in a track_layout which may contain
209 |     // the following:
210 |     // track_layout: {
211 |     //    fill: "colour",
212 |     //    highlight: "colour",
213 |     //    name: "namestr"     [REQUIRED]
214 |     //    inner_radius: num   [REQUIRED]
215 |     //    outer_radius: num   [REQUIRED]
216 |     //    mouseover: callback(d, i)
217 |     //    mouseout: callback(d, i)
218 |     //    mouseclick: callback(d, i)
219 |     // }
220 | 
221 |     // track_coords is an array of objects
222 |     // track_coord = [
223 |     //    { 
224 |     //       start: num,  [REQUIRED] start point in bp
225 |     //       end: num,    [REQUIRED] end point in bp
226 |     //       fill: "colour",
227 |     //       highlight: "colour",
228 |     //       strand: [1,-1],
229 |     //       name: "string"
230 |     // ]
231 | 
232 |     // And a final argument to animate the addition of the elements
233 | 
234 |     drawTrack: function(track_layout, track_coords, animate) {
235 |       var cfg = IslandPlot.cfg;
236 |       var g = IslandPlot.g;
237 | 
238 |       // Fill in any mandatory defaults that weren't provided
239 |       for(var i in IslandPlot.default_track_layout){
240 | 		if('undefined' == typeof track_layout[i]){
241 | 		    track_layout[i] = IslandPlot.default_track_layout[i];
242 | 		  }
243 |       }
244 | 
245 |       // Save the track_layout for later if we need it
246 |       IslandPlot.cfg.tracks[track_layout.name] = track_layout;
247 |         
248 |       // The arc object which will be passed in to each
249 |       // set of data
250 |       var arc = d3.svg.arc()
251 |       .innerRadius(function(d){ return (('undefined' == typeof animate) ? 
252 | 					IslandPlot.calcInnerRadius(track_layout.inner_radius, track_layout.outer_radius, d.strand) 
253 | 					: 1);})
254 |       .outerRadius(function(d){ return (('undefined' == typeof animate) ? 
255 | 					IslandPlot.calcOuterRadius(track_layout.inner_radius, track_layout.outer_radius, d.strand)
256 | 					: 2);})
257 |       .startAngle(function(d){return IslandPlot.cfg.radians_pre_bp*d.start;})
258 |       .endAngle(function(d){return IslandPlot.cfg.radians_pre_bp*d.end;})
259 |       
260 |       // Draw the track, putting in elements such as hover colour change
261 |       // if one exists, click events, etc
262 |       g.selectAll(".tracks."+track_layout.name)
263 |       .data(track_coords)
264 |       .enter()
265 |       .append("path")
266 |       .attr("d", arc)
267 |       .attr("class", track_layout.name)
268 |       .style("fill", function(d) { return ('undefined' !== typeof d.fill) ? d.fill : track_layout.fill})
269 |       .attr("transform", "translate("+cfg.w/2+","+cfg.h/2+")")
270 |       .on("mouseover", function(d, i) {
271 | 	  if('undefined' !== typeof d.highlight) {
272 | 	    d3.select(this).style("fill", d.highlight);
273 |           } else if('undefined' !== typeof track_layout.highlight) {
274 |             d3.select(this).style("fill", track_layout.highlight);
275 |           }
276 |           if('undefined' !== typeof track_layout.mouseover) {
277 | 	      track_layout.mouseover(d, i);
278 | 	  } })
279 |        .on("mouseout", function(d, i) {
280 |           if('undefined' !== typeof d.fill) {
281 |             d3.select(this).style("fill", d.fill)
282 |           } else {
283 |       	    d3.select(this).style("fill", track_layout.fill)
284 |       	  }
285 |       	  if('undefined' !== typeof track_layout.mouseout) {
286 |       	      track_layout.mouseout(d, i);
287 |       	  } })
288 |       .on("click", function(d,i) {
289 | 	      if('undefined' !== typeof track_layout.mouseclick) {
290 | 		  track_layout.mouseclick(d,i);
291 | 	      }
292 | 	  });
293 | 
294 |       // If we're doing an animated addition, move the track out to its
295 |       // new spot
296 |       if('undefined' !== typeof animate) {
297 | 	  IslandPlot.moveTrack(track_layout.name, track_layout.inner_radius, track_layout.outer_radius);
298 |       }
299 | 
300 |       // And check if we've been asked to do a centre line
301 |       if('undefined' !== typeof track_layout.centre_line) {
302 | 	  IslandPlot.drawCircle(track_layout.name, (track_layout.inner_radius + track_layout.outer_radius)/2, track_layout.centre_line_stroke, animate);
303 |       }
304 | 
305 |     },
306 | 
307 |     // Helper function for drawing needed circles such
308 |     // as in stranded tracks
309 |     // Can be called standalone in setting up the look
310 |     // of your genome
311 |     drawCircle: function(name, radius, line_stroke, animate) {
312 | 	var g = IslandPlot.g;
313 | 	var cfg = IslandPlot.cfg;
314 | 
315 |         g.append("circle")
316 | 	.attr("r", (('undefined' == typeof animate) ? radius : 1 ))
317 |   	  .attr("class", name + "_circle")
318 |           .style("fill", "none")
319 |           .style("stroke", line_stroke)
320 |           .attr("cx", cfg.w/2)
321 |           .attr("cy", cfg.h/2);
322 | 
323 | 	// An animated entrance
324 | 	if('undefined' !== typeof animate) {
325 | 	    IslandPlot.moveCircle(name, radius);
326 | 	}
327 | 	
328 |     },
329 | 
330 |     // Change the radius of an inscribed circle
331 | 
332 |     moveCircle: function(name, radius) {
333 | 	var g = IslandPlot.g;
334 | 
335 | 	g.selectAll("." + name + "_circle")
336 | 	.transition()
337 | 	.duration(1000)
338 | 	.attr("r", radius);
339 |     },
340 | 
341 |     // Remove a drawn circle, in a pretty animated way
342 | 
343 |     removeCircle: function(name) {
344 | 	var g = IslandPlot.g;
345 | 
346 | 	g.selectAll("." + name + "_circle")
347 | 	.transition()
348 | 	.duration(1000)
349 | 	.attr("r", 1)
350 | 	.style("opacity", 0)
351 | 	.remove();
352 | 
353 |     },
354 | 
355 |     // If we're displaying a stranded track, calculate
356 |     // the inner radius depending on which strand the 
357 |     // gene is on.
358 | 
359 |     calcInnerRadius: function(inner, outer, strand) {
360 | 	if('undefined' == typeof strand) {
361 | 	    return inner;
362 | 	} else if(strand == -1) {
363 | 	    return inner;
364 | 	} else {
365 | 	    return (inner+outer)/2;
366 | 	}
367 |     },
368 | 
369 |     // If we're displaying a stranded track, calculate
370 |     // the outer radius depending on which strand the 
371 |     // gene is on.
372 | 
373 |     calcOuterRadius: function(inner, outer, strand) {
374 | 	if('undefined' == typeof strand) {
375 | 	    return outer;
376 | 	} else if(strand == -1) {
377 | 	    return (inner+outer)/2;
378 | 	} else {
379 | 	    return outer;
380 | 	}
381 |     },
382 | 
383 |     // Map ranges such as gc content which is a fractional number
384 |     // to the radius range we're going to be drawing in, I think
385 |     // the d3 range() function would have done this, but I'm still
386 |     // learning d3, this works efficiently for now.
387 | 
388 |     mapRange: function(from, to, s) {
389 |        return to[0] + (s - from[0]) * (to[1] - to[0]) / (from[1] - from[0]);
390 |     },
391 | 
392 |     moveTrack: function(name, innerRadius, outerRadius) {
393 | 	var track_layout = IslandPlot.cfg.tracks[name];
394 |         var g = IslandPlot.g;
395 | 
396 | 	var arcShrink = d3.svg.arc()
397 | 	.innerRadius(function(d){return IslandPlot.calcInnerRadius(innerRadius, outerRadius, d.strand);})
398 | 	.outerRadius(function(d){return IslandPlot.calcOuterRadius(innerRadius, outerRadius, d.strand);})
399 | 	.endAngle(function(d){return IslandPlot.cfg.radians_pre_bp*d.start;})
400 | 	.startAngle(function(d){return IslandPlot.cfg.radians_pre_bp*d.end;});
401 | 
402 | 	g.selectAll("." + name)
403 | 	.transition()
404 | 	.duration(1000)
405 |        	.attr("d", arcShrink)
406 | 
407 | 	// Just record the new radii in case we need them later
408 | 	IslandPlot.cfg.tracks[name].inner_radius = innerRadius;
409 | 	IslandPlot.cfg.tracks[name].outer_radius = outerRadius;
410 | 
411 |     },
412 | 
413 |     removeTrack: function(name) {
414 | 	var track_layout = IslandPlot.cfg.tracks[name];
415 |         var g = IslandPlot.g;
416 | 
417 | 	var arcShrink = d3.svg.arc()
418 | 	.innerRadius(1)
419 | 	.outerRadius(2)
420 | 	.endAngle(function(d){return IslandPlot.cfg.radians_pre_bp*d.start;})
421 | 	.startAngle(function(d){return IslandPlot.cfg.radians_pre_bp*d.end;});
422 | 
423 | 	g.selectAll("." + name)
424 | 	.transition()
425 | 	.duration(1000)
426 |        	.attr("d", arcShrink)
427 | 	.style("opacity", 0)
428 | 	.remove();
429 | 
430 | 	if('undefined' !== track_layout.centre_line) {
431 | 	    IslandPlot.removeCircle(name);
432 | 	}
433 | 
434 |     },
435 |  
436 |     default_glyph_track: {
437 | 	name: 'myglyphtrack',
438 | 	pixel_spacing: 8,
439 | 	glyph_buffer: 8
440 |     },
441 |    
442 |     drawGlyphTrack: function(track_info, track_data) {
443 | 	var cfg = IslandPlot.cfg;
444 |         var g = IslandPlot.g;
445 | 	var stack_count = 0;
446 | 
447 | 	// Fill in any mandatory defaults that weren't provided
448 | 	for(var i in IslandPlot.default_glyph_track){
449 | 	    if('undefined' == typeof track_info[i]){
450 | 		track_info[i] = IslandPlot.default_glyph_track[i];
451 | 	    }
452 | 	}
453 | 
454 | 	// Save the track_layout for later if we need it
455 | 	IslandPlot.cfg.glyph_tracks[track_info.name] = track_info;
456 | 
457 | 
458 | 	var x = function(d,i,proximity) { return cfg.w/2 + (((proximity == true ? (track_info.glyph_buffer * stack_count) : 0) + track_info.radius)*Math.cos((d.bp*cfg.radians_pre_bp)-Math.PI/2)); };
459 | 	var y = function(d,i,proximity) {return cfg.h/2 + (((proximity == true ? (track_info.glyph_buffer * stack_count) : 0) + track_info.radius)*Math.sin((d.bp*cfg.radians_pre_bp)-Math.PI/2)); };
460 | 
461 | 	var test_proximity = function(d,i) {
462 | 	    var xs = 0;
463 | 	    var ys = 0;
464 | 
465 | 	    if(i < 1) { return false; }
466 | 
467 | 	    xs = (cfg.h/2 + (track_info.radius*Math.sin((d.bp*cfg.radians_pre_bp)-Math.PI/2))) -
468 | 	    (cfg.h/2 + (track_info.radius*Math.sin((track_data[i-1].bp*cfg.radians_pre_bp)-Math.PI/2)));
469 | 	    ys = (cfg.h/2 + (track_info.radius*Math.cos((d.bp*cfg.radians_pre_bp)-Math.PI/2))) -
470 | 	    (cfg.h/2 + (track_info.radius*Math.cos((track_data[i-1].bp*cfg.radians_pre_bp)-Math.PI/2)));
471 | 	    xs = xs * xs;
472 | 	    ys = ys * ys;
473 | 	    var dist = Math.sqrt(xs + ys);
474 | 
475 | 	    if(dist < track_info.pixel_spacing) { stack_count++; return true; }
476 | 
477 | 	    stack_count = 0;
478 | 	    return false;
479 | 	}
480 | 
481 | 	var track = g.selectAll('.' + track_info.name)
482 | 	.data(track_data)
483 | 	.enter()
484 | 	.append('path')
485 | 	.attr('class', track_info.name)
486 | 	.attr("d", d3.svg.symbol().type(track_info.type))
487 | 	.attr("transform", function(d,i) { var proximity = test_proximity(d,i); 
488 | 					   return "translate(" + x(d,i, proximity) + ","
489 | 					   + y(d,i, proximity) + ")" })
490 | 	.style("fill", function(d) { return glyph_layout.colours[d.type] })
491 | 	
492 |     },
493 | 
494 |     updateGlyphTrack: function(name, track_data) {
495 | 	var cfg = IslandPlot.cfg;
496 |         var g = IslandPlot.g;
497 | 	var track_info = IslandPlot.cfg.glyph_tracks[name];
498 | 	var stack_count = 0;
499 | 
500 | 	var x = function(i,proximity) { return cfg.w/2 + (((proximity == true ? (track_info.pixel_spacing * stack_count) : 0) + track_info.radius)*Math.cos((track_data[i].bp*cfg.radians_pre_bp)-Math.PI/2)); };
501 | 	var y = function(i,proximity) {return cfg.h/2 + (((proximity == true ? (track_info.pixel_spacing * stack_count) : 0) + track_info.radius)*Math.sin((track_data[i].bp*cfg.radians_pre_bp)-Math.PI/2)); };
502 | 
503 | 	var test_proximity = function(i) {
504 | 	    var xs = 0;
505 | 	    var ys = 0;
506 | 
507 | 	    if(i < 1) { return false; }
508 | 
509 | 	    xs = (cfg.h/2 + (track_info.radius*Math.sin((track_data[i].bp*cfg.radians_pre_bp)-Math.PI/2))) -
510 | 	    (cfg.h/2 + (track_info.radius*Math.sin((track_data[i-1].bp*cfg.radians_pre_bp)-Math.PI/2)));
511 | 	    ys = (cfg.h/2 + (track_info.radius*Math.cos((track_data[i].bp*cfg.radians_pre_bp)-Math.PI/2))) -
512 | 	    (cfg.h/2 + (track_info.radius*Math.cos((track_data[i-1].bp*cfg.radians_pre_bp)-Math.PI/2)));
513 | 	    xs = xs * xs;
514 | 	    ys = ys * ys;
515 | 	    var dist = Math.sqrt(xs + ys);
516 | 
517 | 	    if(dist < track_info.pixel_spacing) { stack_count++; return true; }
518 | 
519 | 	    stack_count = 0;
520 | 	    return false;
521 | 	}
522 | 
523 | 	var track = g.selectAll('.' + name)
524 | 	.data(track_data);
525 | 
526 | 
527 | 	track.transition()
528 | 	.duration(1000)
529 | 	.attr("d", d3.svg.symbol().type(track_info.type))
530 | 	.attr("transform", function(d,i) { var proximity = test_proximity(i); 
531 | 					   return "translate(" + x(i, proximity) + ","
532 | 					   + y(i, proximity) + ")" })
533 | 	.style("fill", function(d) { return glyph_layout.colours[d.type] })
534 | 
535 | 	track.enter()
536 | 	.append('path')
537 | 	.attr('class', name)
538 | 	.attr("d", d3.svg.symbol().type(track_info.type))
539 | 	.attr("transform", "translate(" + cfg.h/2 + "," + cfg.w/2 + ")")
540 | 	.style("fill", function(d) { return glyph_layout.colours[d.type] })
541 | 	.transition()
542 | 	.duration(1000)
543 | 	.attr("transform", function(d,i) { var proximity = test_proximity(i); 
544 | 					   return "translate(" + x(i, proximity) + ","
545 | 					       + y(i, proximity) + ")"; })
546 | 
547 | 	track.exit()
548 | 	.transition()
549 | 	.duration(1000)
550 | 	.attr("transform", "translate(" + cfg.h/2 + "," + cfg.w/2 + ")")
551 | 	.style("opacity", 0)
552 | 	.remove()
553 | 
554 |     },
555 |     
556 |     attachBrush: function(callbackObj) {
557 | 	var cfg = IslandPlot.cfg;
558 | 	var g = IslandPlot.g;
559 | 
560 | 	IslandPlot.cfg.brushCallbackObj = callbackObj;
561 | 
562 | 	IslandPlot.cfg.brushStart = 0;
563 | 	IslandPlot.cfg.brushEnd = 0;
564 | 	IslandPlot.cfg.brushStartBP = 0;
565 | 	IslandPlot.cfg.brushEndBP = 0;
566 | 
567 | 	IslandPlot.cfg.BrushArc = d3.svg.arc()
568 | 	.innerRadius(20)
569 | 	.outerRadius(IslandPlot.cfg.radius-10)
570 | 	.endAngle(function(d){return IslandPlot.cfg.xScale(0);})
571 | 	.startAngle(function(d){return IslandPlot.cfg.xScale(0);});
572 | 
573 | 	g.append("path")
574 | 	    .attr("d", IslandPlot.cfg.BrushArc)
575 | 	    .attr("id", "polarbrush")
576 | 	    .style("fill", "lightgrey")
577 | 	    .style("opacity", 0.5)
578 | 	    .attr("transform", "translate("+cfg.w/2+","+cfg.h/2+")")
579 | 
580 | 	var dragStart = d3.behavior.drag()
581 | 	    .on("drag", function(d) {
582 | 		var mx = d3.mouse(this)[0];
583 | 		var my = d3.mouse(this)[1];
584 | 
585 | 		var curRadandBP = IslandPlot.calcRadBPfromXY((d3.mouse(this)[0] - (cfg.w/2)),
586 | 						-(d3.mouse(this)[1] - (cfg.h/2)));
587 | 
588 | 		d3.select("#brushStart")		
589 | 		    .attr("cx", function(d, i){return cfg.h/2 + (cfg.radius-10)*Math.cos((curRadandBP[0])-Math.PI/2);})
590 | 		    .attr("cy", function(d, i){return cfg.h/2 + (cfg.radius-10)*Math.sin((curRadandBP[0])-Math.PI/2); });
591 | 		
592 | 		IslandPlot.cfg.brushStart = curRadandBP[0];
593 | 		IslandPlot.cfg.brushStartBP = curRadandBP[1];
594 | 		IslandPlot.moveBrush(IslandPlot.cfg.brushStart, IslandPlot.cfg.brushEnd);
595 | 		if('undefined' !== typeof IslandPlot.cfg.brushCallbackObj) {
596 | 		    IslandPlot.cfg.brushCallbackObj.update(IslandPlot.cfg.brushEndBP, IslandPlot.cfg.brushStartBP);
597 | 		}
598 | 	    });
599 | 
600 | 	var dragEnd = d3.behavior.drag()
601 | 	    .on("drag", function(d) {
602 | 		var mx = d3.mouse(this)[0];
603 | 		var my = d3.mouse(this)[1];
604 | 
605 | 		var curRadandBP = IslandPlot.calcRadBPfromXY((d3.mouse(this)[0] - (cfg.w/2)),
606 | 						-(d3.mouse(this)[1] - (cfg.h/2)));
607 | 
608 | 		d3.select("#brushEnd")		
609 | 		    .attr("cx", function(d, i){return cfg.h/2 + (cfg.radius-10)*Math.cos((curRadandBP[0])-Math.PI/2);})
610 | 		    .attr("cy", function(d, i){return cfg.h/2 + (cfg.radius-10)*Math.sin((curRadandBP[0])-Math.PI/2); });
611 | 		
612 | 		IslandPlot.cfg.brushEnd = curRadandBP[0];
613 | 		IslandPlot.cfg.brushEndBP = curRadandBP[1];
614 | 		IslandPlot.moveBrush(IslandPlot.cfg.brushStart, IslandPlot.cfg.brushEnd);
615 | 		if('undefined' !== typeof IslandPlot.cfg.brushCallbackObj) {
616 | 		    IslandPlot.cfg.brushCallbackObj.update(IslandPlot.cfg.brushEndBP, IslandPlot.cfg.brushStartBP);
617 | 		}
618 | 	    });
619 | 
620 | 
621 | 	g.append("circle")
622 | 	    .attr({
623 | 		id: 'brushEnd',
624 | 		cx: (cfg.w/2 + ((cfg.radius-10)*Math.cos((cfg.xScale(0))-Math.PI/2))),
625 | 		cy: (cfg.h/2 + ((cfg.radius-10)*Math.sin((cfg.xScale(0))-Math.PI/2))),
626 | 		r: 5,
627 | 		fill: "red"
628 | 	    })
629 |             .call(dragEnd);
630 | 
631 | 	g.append("circle")
632 | 	    .attr({
633 | 		id: 'brushStart',
634 | 		cx: (cfg.w/2 + ((cfg.radius-10)*Math.cos((cfg.xScale(0))-Math.PI/2))),
635 | 		cy: (cfg.h/2 + ((cfg.radius-10)*Math.sin((cfg.xScale(0))-Math.PI/2))),
636 | 		r: 5,
637 | 		fill: "green"
638 | 	    })
639 |             .call(dragStart);
640 | 
641 | 	// Create the start and stop pointers
642 |     },
643 | 
644 |     moveBrush: function(startRad, endRad) {
645 | 	var cfg = IslandPlot.cfg;
646 | 	var g = IslandPlot.g;
647 | 
648 | 	console.log("moving brush to " + startRad, endRad);
649 | 
650 | 	IslandPlot.cfg.BrushArc
651 | 	    .startAngle(startRad)
652 | 	    .endAngle(endRad);
653 | 
654 | 	d3.select('#polarbrush')
655 | 	    .attr("d", IslandPlot.cfg.BrushArc);
656 |     },
657 | 
658 |     attachBrush2: function() {
659 | 	var cfg = IslandPlot.cfg;
660 | 	var g = IslandPlot.g;
661 | 
662 | 	IslandPlot.cfg.clickOn = false;
663 | 	IslandPlot.cfg.brushMove = false;
664 | 	IslandPlot.cfg.brushStart = 0;
665 | 	IslandPlot.cfg.brushEnd = 0;
666 | 
667 | 	IslandPlot.cfg.BrushArc = d3.svg.arc()
668 | 	.innerRadius(20)
669 | 	.outerRadius(IslandPlot.cfg.radius)
670 | 	.endAngle(function(d){return IslandPlot.cfg.xScale(0);})
671 | 	.startAngle(function(d){return IslandPlot.cfg.xScale(0);});
672 | 
673 | 	g.append("path")
674 | 	    .attr("d", IslandPlot.cfg.BrushArc)
675 | 	    .attr("class", ".polarbrush")
676 | 	    .style("fill", "lightgrey")
677 | 	    .attr("transform", "translate("+cfg.w/2+","+cfg.h/2+")")
678 | 
679 | 
680 | 	g.on('mousemove', function() {
681 | 	    if(IslandPlot.cfg.clickOn) {
682 | 		// We're drawing a new brush
683 | 		var curRadandBP = IslandPlot.calcRadBPfromXY((d3.mouse(this)[0] - (cfg.w/2)),
684 | 						-(d3.mouse(this)[1] - (cfg.h/2)));
685 | 
686 | 		IslandPlot.cfg.brushEnd = curRadandBP[0];
687 | 		IslandPlot.moveBrush(IslandPlot.cfg.brushStart, curRadandBP[0]);
688 | 		console.log("drawing... " + IslandPlot.cfg.brushStart, curRadandBP[0]);
689 | 	    }
690 | 
691 | 		var x = d3.mouse(this)[0] - (cfg.w/2);
692 | 		var y = -(d3.mouse(this)[1] - (cfg.h/2));
693 | 		rad = Math.PI/2 - Math.atan(y/x);// - Math.PI/2;
694 | 		if(x < 0) {
695 | 		    // II & III quadrant
696 | 		    rad = rad + Math.PI;
697 | 		}
698 | 		//		} else if(x < 0 && y < 0) {
699 | 		//		    rad = rad + Math.PI;
700 | 		//		}
701 | 		console.log(x, y, Math.floor(cfg.xScale.invert(rad)));
702 | 		    //		console.log(d3.mouse(this)[0], d3.mouse(this)[1]);
703 | 	    });
704 | 
705 | 	g.on('mousedown', function() {
706 | 	    IslandPlot.cfg.clickOn = true;
707 | 	    console.log("Click on!");
708 | 	    // Check if we're moving or redrawing a range
709 | 	    var curRadandBP = IslandPlot.calcRadBPfromXY((d3.mouse(this)[0] - (cfg.w/2)),
710 | 						-(d3.mouse(this)[1] - (cfg.h/2)));
711 | 	    if(curRadandBP[1] < IslandPlot.cfg.brushEnd && curRadandBP[1] > IslandPlot.cfg.brushStart) {
712 | 		// We're moving...
713 | 		IslandPlot.cfg.brushMove = true;
714 | 	    } else {
715 | 		IslandPlot.moveBrush(curRadandBP[0], curRadandBP[0]);
716 | 		IslandPlot.cfg.brushStart = curRadandBP[0];
717 | 	    }
718 | 	});
719 | 
720 | 	g.on('mouseup', function() {
721 | 	    IslandPlot.cfg.clickOn = false;
722 | 	    IslandPlot.cfg.brushMove = false;
723 | 	    var curRadandBP = IslandPlot.calcRadBPfromXY((d3.mouse(this)[0] - (cfg.w/2)),
724 | 						-(d3.mouse(this)[1] - (cfg.h/2)));
725 | 	    IslandPlot.cfg.brushEnd = curRadandBP[0];
726 | 	    IslandPlot.moveBrush(IslandPlot.cfg.brushStart, curRadandBP[0]);
727 | 	});
728 |     },
729 | 
730 |     calcRadBPfromXY: function(x,y) {
731 | 	var rad = Math.PI/2 - Math.atan(y/x);
732 | 	if(x < 0) {
733 | 	    // II & III quadrant
734 | 	    rad = rad + Math.PI;
735 | 	}
736 | 	return [rad,Math.floor(IslandPlot.cfg.xScale.invert(rad))];
737 |     }
738 | 
739 | };
740 | 
741 | 
742 | 


--------------------------------------------------------------------------------
/prototypes/lineartrack.js:
--------------------------------------------------------------------------------
  1 | 
  2 | // Setup the defaults
  3 | var margin = {top: 10, right: 40, bottom: 150, left: 60},
  4 | width = 940 - margin.left - margin.right,
  5 | height = 500 - margin.top - margin.bottom,
  6 | contextHeight = 50;
  7 | contextWidth = width * .5;
  8 | 
  9 | var track_coords = [
 10 | 		    {start:0, end:30000, name:"island0", fill:"green", strand: -1},
 11 | 		    {start:60000,end:100000, name:"island1", fill:"green", strand: -1},
 12 | 		    {start:800000,end:1000000, name:"island2", strand: 1},
 13 | 		    {start:1200000,end:1500000, name:"island3", strand: 1},
 14 | 		    {start:1500000,end:1700000, name:"island4",fill:"green",strand: -1},
 15 | 		    {start:2000000,end:2100000, name:"island5", strand: 1}
 16 | 		    ]
 17 | 
 18 | 
 19 | 
 20 | var layout = {genomesize: 6200000};
 21 | 												
 22 | function genomeTrack(layout,svg) {
 23 | 
 24 |     this.svg = svg;
 25 | 
 26 |     // First let's make the axis
 27 |     var xAxisScale = d3.scale.linear()
 28 |     .range([0, width])
 29 |     .domain([0, layout.genomesize]);
 30 |     this.xScale = xAxisScale;
 31 | 
 32 |     var zoom = d3.behavior.zoom()
 33 | //    .scale(xAxisScale)
 34 | 	.x(xAxisScale)
 35 | 	.on("zoom", zoomed);
 36 |     this.zoom = zoom;
 37 | 
 38 |     var xAxisArea = d3.svg.area()
 39 |     .interpolate("basis")
 40 |     .x(function(d) {console.log(d); return d; })
 41 |     .y0(0)
 42 |     .y1(height);
 43 | 
 44 |     this.createAxis(layout);
 45 | 
 46 | //    svg.append("defs").append("clipPath")
 47 | //    .attr("id", "clip-xxis")
 48 | //    .append("rect")
 49 | //    .attr("width", width)
 50 | //    .attr("height", height);
 51 | 
 52 |     function zoomed() {
 53 | 	console.log(d3.event.translate);
 54 | 	console.log(d3.event.scale);
 55 | //	var t = d3.event.translate;
 56 | //	t[0] = Math.min(0, t[0]);
 57 | //	t[1] = Math.max(
 58 | 	axisContainer.select(".x.axis.bottom").call(xAxis);
 59 | 
 60 |     }
 61 | 
 62 | 
 63 | 
 64 | }
 65 | 
 66 | genomeTrack.prototype.createAxis = function(layout){
 67 |     
 68 |     var axisContainer = this.svg.append("g")
 69 |     .attr('class', 'axisContainter')
 70 |     .attr("transform", "translate(" + margin.left + "," + margin.top + ")")
 71 |     .call(this.zoom);
 72 |     this.axisContainer = axisContainer;
 73 |     
 74 |     this.xAxis = d3.svg.axis().scale(this.xScale).orient("bottom")
 75 |     .tickFormat(d3.format("s"));
 76 | 
 77 |     this.axisContainer.append("g")
 78 |     .attr("class", "x axis bottom")
 79 |     .attr("transform", "translate(0," + height + ")")
 80 |     .call(this.xAxis);
 81 | 
 82 | };
 83 | 
 84 | genomeTrack.prototype.updateAxis = function(b) {
 85 | 	this.xScale.domain(b);
 86 | 	console.log(b);
 87 | 	this.axisContainer.select(".x.axis.bottom").call(this.xAxis);
 88 | 
 89 | }
 90 | 
 91 | var svg = d3.select("#chart-container").append("svg")
 92 |     .attr("width", width + margin.left + margin.right)
 93 |     .attr("height", (height + margin.top + margin.bottom));
 94 | 
 95 | var axis = new genomeTrack(layout,svg);
 96 | var track = new Track({data: track_coords,
 97 | 		       id: 1,
 98 | 		       name: 'track_1',
 99 | 		       width: width,
100 | 		       height: height/2,
101 | 		       svg: svg,
102 | 		       margin: margin,
103 | 		       bp: layout.genomesize
104 | 		      });
105 | 
106 | /* Let's create the context brush that will 
107 |    let us zoom and pan the chart */
108 |     var contextXScale = d3.scale.linear()
109 | 	.range([0, contextWidth])
110 | 	.domain([0, layout.genomesize]);	
111 | 							
112 |     var contextAxis = d3.svg.axis()
113 | 	.scale(contextXScale).tickFormat(d3.format("s"))
114 | 	.tickSize(contextHeight)
115 | 	.tickPadding(0)
116 | 	.orient("bottom");
117 | 
118 |     var contextArea = d3.svg.area()
119 | 	.interpolate("monotone")
120 | 	.x(function(d) { return contextXScale(d); })
121 | 	.y0(contextHeight)
122 | 	.y1(0);
123 | 				
124 |     var brush = d3.svg.brush()
125 | 	.x(contextXScale)
126 | 	.on("brush", onBrush);
127 | 				
128 |     var context = svg.append("g")
129 | 	.attr("class","context")
130 | 	.attr("transform", "translate(" + (margin.left + width * .25) + "," + (height + margin.top+ 30) + ")");						
131 | 
132 |     context.append("g")
133 | 	.attr("class", "x axis top")
134 | 	.attr("transform", "translate(0,0)")
135 | 	.call(contextAxis)
136 | 																
137 |     context.append("g")
138 | 	.attr("class", "x brush")
139 | 	.call(brush)
140 | 	.selectAll("rect")
141 | 	.attr("y", 0)
142 | 	.attr("height", contextHeight);
143 | 							
144 |     context.append("text")
145 | 	.attr("class","instructions")
146 | 	.attr("transform", "translate(0," + (contextHeight + 20) + ")")
147 | 	.text('Click and drag above to zoom / pan the data');
148 | 												
149 | 							
150 | 
151 | 
152 |     function onBrush(){
153 | 	/* this will return a date range to pass into the chart object */
154 | 	var b = brush.empty() ? contextXScale.domain() : brush.extent();
155 | 	axis.updateAxis(b);
156 | 	track.update(b);
157 | //	xAxisScale.domain(b);
158 | //	console.log(b);
159 | //	var axisContainer = this.axisContainer;
160 | //	axisContainer.select(".x.axis.bottom").call(this.xAxis);
161 | //	for(var i = 0; i < countriesCount; i++){
162 | //	    charts[i].showOnly(b);
163 | //	}
164 |     }
165 | 


--------------------------------------------------------------------------------
/prototypes/sample.js:
--------------------------------------------------------------------------------
  1 | var w = 500,
  2 | 	h = 500;
  3 | 
  4 | var mycfg = {
  5 |   w: w,
  6 |   h: h,
  7 |   maxValue: 0.6,
  8 |   levels: 6,
  9 |   ExtraWidthX: 300,
 10 |   genomesize: 6264404
 11 | }
 12 | 
 13 | var gc_min = 0.4891;
 14 | var gc_max = 0.7274;
 15 | var gc_mean = 0.66558768401076;
 16 | var gc_radius = 100;
 17 | var gc_width = 50;
 18 | var bp_per_value = 10000;
 19 | var gc_values=[0.6271,0.6505,0.6809,0.6823,0.6971,0.608,0.6569,0.6855,0.6987,0.7005,0.6847,0.672,0.6525,0.6726,0.6595,0.6722,0.6874,0.6891,0.6571,0.69,0.6798,0.6787,0.6701,0.6893,0.6923,0.675,0.6876,0.6837,0.657,0.6285,0.6911,0.6765,0.6637,0.6409,0.6623,0.6571,0.6623,0.6836,0.6887,0.6778,0.6667,0.6816,0.6756,0.666,0.6741,0.6804,0.6876,0.6527,0.6679,0.6728,0.6707,0.6741,0.6834,0.6711,0.6654,0.6407,0.6792,0.6875,0.6758,0.6722,0.68,0.6599,0.6538,0.6489,0.6489,0.6538,0.653,0.6498,0.6478,0.639,0.6189,0.6574,0.5658,0.6861,0.6817,0.6776,0.6653,0.6869,0.5688,0.6159,0.6745,0.6826,0.674,0.6433,0.6687,0.6766,0.6766,0.686,0.6749,0.6484,0.6397,0.6765,0.6506,0.6759,0.6621,0.6607,0.6786,0.6596,0.6702,0.6345,0.6596,0.6633,0.635,0.6369,0.6262,0.6238,0.5394,0.5977,0.6546,0.6383,0.6877,0.6583,0.6614,0.6783,0.6763,0.6687,0.6415,0.6622,0.6385,0.6755,0.6786,0.6623,0.6795,0.6896,0.5812,0.6631,0.668,0.674,0.6691,0.6668,0.6702,0.6843,0.6835,0.7062,0.6774,0.6727,0.6982,0.7156,0.7131,0.6945,0.6612,0.6763,0.6644,0.6629,0.6856,0.6564,0.6875,0.6689,0.5174,0.6622,0.5647,0.6357,0.6966,0.6834,0.677,0.6617,0.6854,0.6694,0.659,0.6761,0.6824,0.6763,0.6812,0.6366,0.6322,0.663,0.6524,0.6552,0.6619,0.6461,0.6781,0.6635,0.6299,0.648,0.6815,0.6614,0.6887,0.6722,0.6853,0.6804,0.6312,0.6687,0.6689,0.6718,0.6804,0.6535,0.6749,0.6697,0.6575,0.6427,0.6504,0.634,0.6523,0.6651,0.6445,0.6127,0.6446,0.663,0.6632,0.6589,0.6604,0.6705,0.6873,0.6749,0.6867,0.6749,0.6576,0.6877,0.6852,0.6867,0.6831,0.6473,0.6322,0.679,0.6689,0.6855,0.6902,0.6882,0.685,0.6887,0.6794,0.667,0.6226,0.659,0.6923,0.688,0.695,0.6673,0.6794,0.6869,0.7054,0.6175,0.6943,0.6876,0.6752,0.6868,0.6589,0.6945,0.7036,0.6647,0.6687,0.6717,0.6733,0.6786,0.5441,0.6301,0.6943,0.6814,0.6881,0.6897,0.6819,0.6889,0.6844,0.706,0.693,0.6747,0.6859,0.6924,0.6893,0.6973,0.686,0.6859,0.6614,0.6824,0.6663,0.6333,0.6609,0.6639,0.677,0.6963,0.6677,0.7077,0.6648,0.7085,0.6899,0.6475,0.6029,0.6649,0.6824,0.7044,0.6782,0.6846,0.6818,0.684,0.6791,0.6833,0.6784,0.6781,0.6756,0.663,0.6285,0.6259,0.6455,0.6601,0.6669,0.6565,0.6336,0.6545,0.6517,0.6589,0.6751,0.6549,0.6609,0.6833,0.6658,0.6671,0.6661,0.687,0.6612,0.5835,0.64,0.6455,0.6481,0.656,0.6682,0.6206,0.6617,0.6588,0.6619,0.6886,0.6518,0.6827,0.6951,0.6765,0.6854,0.6919,0.7068,0.6939,0.6928,0.6639,0.6969,0.6415,0.6525,0.6624,0.6646,0.6417,0.6553,0.6382,0.684,0.6657,0.6451,0.6635,0.6739,0.6729,0.691,0.6639,0.6751,0.6832,0.6663,0.669,0.6629,0.658,0.6103,0.4891,0.54,0.6586,0.6784,0.6636,0.6719,0.6743,0.6786,0.6647,0.6544,0.666,0.6574,0.6512,0.6938,0.642,0.6264,0.6614,0.6785,0.6831,0.667,0.6974,0.6865,0.6645,0.6683,0.6611,0.6905,0.663,0.6827,0.695,0.7113,0.6775,0.672,0.6666,0.6897,0.6859,0.6689,0.661,0.6515,0.6654,0.6937,0.6495,0.6608,0.6709,0.6547,0.6633,0.6997,0.7091,0.6726,0.6702,0.688,0.6654,0.6678,0.6465,0.6651,0.6535,0.6417,0.6465,0.6804,0.668,0.6921,0.6685,0.672,0.6683,0.6604,0.6696,0.6501,0.6487,0.6798,0.6887,0.6601,0.6958,0.6848,0.6515,0.6513,0.6373,0.6599,0.6111,0.6705,0.6783,0.6289,0.6466,0.6792,0.6793,0.69,0.6703,0.6861,0.6741,0.66,0.6797,0.6562,0.6831,0.6875,0.6799,0.6619,0.6657,0.6746,0.6869,0.683,0.6666,0.6757,0.6845,0.6774,0.672,0.655,0.6804,0.6905,0.6849,0.6724,0.6826,0.6594,0.6823,0.6956,0.7,0.6754,0.6728,0.6851,0.68,0.6897,0.6785,0.7062,0.7274,0.6908,0.6096,0.5816,0.6208,0.584,0.604,0.7012,0.6747,0.6671,0.6511,0.6553,0.6829,0.6761,0.6931,0.6813,0.6719,0.6608,0.648,0.6591,0.6509,0.6624,0.6564,0.6237,0.65,0.6491,0.6371,0.6673,0.6718,0.6789,0.644,0.6745,0.6461,0.6323,0.6408,0.6467,0.659,0.6368,0.6457,0.6642,0.6622,0.6665,0.6745,0.6635,0.6591,0.6444,0.668,0.6628,0.6636,0.6729,0.6589,0.6463,0.6608,0.5708,0.6337,0.6646,0.666,0.6576,0.663,0.6352,0.6256,0.6479,0.6601,0.6879,0.6896,0.6741,0.693,0.6898,0.6845,0.6733,0.676,0.6692,0.6765,0.687,0.6611,0.6988,0.689,0.6786,0.652,0.6805,0.6603,0.6437,0.6768,0.6745,0.6731,0.683,0.6892,0.6965,0.6473,0.6686,0.6641,0.6686,0.667,0.6677,0.6417,0.6528,0.6662,0.6662,0.6584,0.6307,0.679,0.676,0.6842,0.6633,0.6627,0.677,0.6791,0.6633,0.6607,0.6492,0.671,0.6556,0.6738,0.6819,0.6823,0.6681,0.6545,0.6497,0.6554,0.6411,0.6652,0.6715,0.6633,0.6645,0.6629,0.6667,0.6657,0.6591,0.6739,0.6872,0.6448,0.5838,0.6587,0.6973,0.6726,0.6766,0.6637,0.6758,0.6794,0.6792,0.6606,0.6627,0.6832,0.6666,0.6583,0.6503,0.6679,0.6768,0.6609,0.6553,0.6706,0.6447,0.6162,0.630790190735695];
 20 | 
 21 | var gc_values2=[0.6271,0.6505,0.6809,0.6823,0.6971,0.608,0.6569,0.6855,0.6987,0.7005,0.6847,0.672,0.6525,0.6726,0.6595,0.6722,0.6874,0.6891,0.6571,0.69,0.6798,0.6787,0.6701,0.6893,0.6923,0.675,0.6876,0.6837,0.657,0.6285,0.6911,0.6765,0.6637,0.6409,0.6623,0.6571,0.6623,0.6836,0.6887,0.6778,0.6667,0.6816,0.6756,0.666,0.6741,0.6804,0.6876,0.6527,0.6679,0.6728,0.6707,0.6741,0.6834,0.6711,0.6654,0.6407,0.6792,0.6875,0.6758,0.6722,0.68,0.6599,0.6538,0.6489,0.6489,0.6538,0.653,0.6498,0.6478,0.639,0.6189,0.6574,0.5658,0.6861,0.6817,0.6776,0.6653,0.6869,0.5688,0.6159,0.6745,0.6826,0.674,0.6433,0.6687,0.6766,0.6766,0.686,0.6749,0.6484,0.6397,0.6765,0.6506,0.6759,0.6621,0.6607,0.6786,0.6596,0.6702,0.6345,0.6596,0.6633,0.635,0.6369,0.6262,0.6238,0.5394,0.5977,0.6546,0.6383,0.6877,0.6583,0.6614,0.6783,0.6763,0.6687,0.6415,0.6622,0.6385,0.6755,0.6786,0.6623,0.6795,0.6896,0.5812,0.6631,0.668,0.674,0.6691,0.6668,0.6702,0.6843,0.6835,0.7062,0.6774,0.6727,0.6982,0.7156,0.7131,0.6945,0.6612,0.6763,0.6644,0.6629,0.6856,0.6564,0.6875,0.6689,0.5174,0.6622,0.5647,0.6357,0.6966,0.6834,0.677,0.6617,0.6854,0.6694,0.659,0.6761,0.6824,0.6763,0.6812,0.6366,0.6322,0.663,0.6524,0.6552,0.6619,0.6461,0.6781,0.6635,0.6299,0.648,0.6815,0.6614,0.6887,0.6722,0.6853,0.6804,0.6312,0.6687,0.6689,0.6718,0.6804,0.6535,0.6749,0.6697,0.6575,0.6427,0.6504,0.634,0.6523,0.6651,0.6445,0.6127,0.6446,0.663,0.6632,0.6589,0.6604,0.6705,0.6873,0.6749,0.6867,0.6749,0.6576,0.6877,0.6852,0.6867,0.6831,0.6473,0.6322,0.679,0.6689,0.6855,0.6902,0.6882,0.685,0.6887,0.6794,0.667,0.6226,0.659,0.6923,0.688,0.695,0.6673,0.6794,0.6869,0.7054,0.6175,0.6943,0.6876,0.6752,0.6868,0.6589,0.6945,0.7036,0.6647,0.6687,0.6717,0.6733,0.6786,0.5441,0.6301,0.6943,0.6814,0.6881,0.6897,0.6819,0.6889,0.6844,0.706,0.693,0.6747,0.6859,0.6924,0.6893,0.6973,0.686,0.6859,0.6614,0.6824,0.6663,0.6333,0.6609,0.6639,0.677,0.6963,0.6677,0.7077,0.6648,0.7085,0.6899,0.6475,0.6029,0.6649,0.6824,0.7044,0.6782,0.6846,0.6818,0.684,0.6791,0.6833,0.6784,0.6781,0.6756,0.663,0.6285,0.6259,0.6455,0.6601,0.6669,0.6565,0.6336,0.6545,0.6517,0.6589,0.6751,0.6549,0.6609,0.6833,0.6658,0.6671,0.6661,0.687,0.6612,0.5835,0.64,0.6455,0.6481,0.656,0.6682,0.6206,0.6617,0.6588,0.6619,0.6886,0.6518,0.6827,0.6951,0.6765,0.6854,0.6919,0.7068,0.6939,0.6928,0.6639,0.6969,0.6415,0.6525,0.6624,0.6646,0.6417,0.6553,0.6382,0.684,0.6657,0.6451,0.6635,0.6739,0.6729,0.691,0.6639,0.6751,0.6832,0.6663,0.669,0.6629,0.658,0.6103,0.4891,0.54,0.6586,0.6784,0.6636,0.6719,0.6743,0.6786,0.6647,0.6544,0.666,0.6574,0.6512,0.6938,0.642,0.6264,0.6614,0.6785,0.6831,0.667,0.6974,0.6865,0.6645,0.6683,0.6611,0.6905,0.663,0.6827,0.695,0.7113,0.6775,0.672,0.6666,0.6897,0.6859,0.6689,0.661,0.6515,0.6654,0.6937,0.6495,0.6608,0.6709,0.6547,0.6633,0.6997,0.7091,0.6726,0.6702,0.688,0.6654,0.6678,0.6465,0.6651,0.6535,0.6417,0.6465,0.6804,0.668,0.6921,0.6685,0.672,0.6683,0.6604,0.6696,0.6501,0.6487,0.6798,0.6887,0.6601,0.6958,0.6848,0.6515,0.6513,0.6373,0.6599,0.6111,0.6705,0.6783,0.6289,0.6466,0.6792,0.6793,0.69,0.6703,0.6861,0.6741,0.66,0.6797,0.6562,0.6831,0.6875,0.6799,0.6619,0.6657,0.6746,0.6869,0.683,0.6666,0.6757,0.6845,0.6774,0.672,0.655,0.6804,0.6905,0.6849,0.6724,0.6826,0.6594,0.6823,0.6956,0.7,0.6754,0.6728,0.6851,0.68,0.6897,0.6785,0.7062,0.7274,0.6908,0.6096,0.5816,0.6208,0.584,0.604,0.7012,0.6747,0.6671,0.6511,0.6553,0.6829,0.6761,0.6931,0.6813,0.6719,0.6608,0.648,0.6591,0.6509,0.6624,0.6564,0.6237,0.65,0.6491,0.6371,0.6673,0.6718,0.6789,0.644,0.6745,0.6461,0.6323,0.6408,0.6467,0.659,0.6368,0.6457,0.6642,0.6622,0.6665,0.6745,0.6635,0.6591,0.6444,0.668,0.6628,0.6636,0.6729,0.6589,0.6463,0.6608,0.5708,0.6337,0.6646,0.666,0.6576,0.663,0.6352,0.6256,0.6479,0.6601,0.6879,0.6896,0.6741,0.693,0.6898,0.6845,0.6733,0.676,0.6692,0.6765,0.687,0.6611,0.6988,0.689,0.6786,0.652,0.6805,0.6603,0.6437,0.6768,0.6745,0.6731,0.683,0.6892,0.6965,0.6473,0.6686,0.6641,0.6686,0.667,0.6677,0.6417,0.6528,0.6662,0.6662,0.6584,0.6307,0.679,0.676,0.6842,0.6633,0.6627,0.677,0.6791,0.6633,0.6607,0.6492,0.671,0.6556,0.6738,0.6819,0.6823,0.6681,0.6545,0.6497,0.6554,0.6411,0.6652,0.6715,0.6633,0.6645,0.6629,0.6667,0.6657,0.6591,0.6739,0.6872,0.6448,0.5838,0.6587,0.6973,0.6726,0.6766,0.6637,0.6758,0.6794,0.6792,0.6606,0.6627,0.6832,0.6666,0.6583,0.6503,0.6679,0.6768,0.6609,0.6553,0.6706,0.6447,0.6162,0.630790190735695];
 22 | 
 23 | var track_layout = {
 24 |   fill: "blue",
 25 |   highlight: "red",
 26 |   name: "mytrack",
 27 |   inner_radius: 195,
 28 |   outer_radius: 225,
 29 |   mouseclick: mouse_callback,
 30 |   centre_line: true,
 31 |   centre_line_stroke: "black"
 32 | 
 33 | }
 34 | 
 35 | var track_layout2 = {
 36 |   fill: "blue",
 37 |   highlight: "red",
 38 |   name: "mytrack2",
 39 |   inner_radius: 130,
 40 |   outer_radius: 150
 41 | }
 42 | 
 43 | var track_coords2 = [
 44 | 		    {start:0, end:30000, name:"island0", fill:"yellow", highlight:"green"},
 45 | 		    {start:60000,end:100000, name:"island1"},
 46 | 		    {start:800000,end:1000000, name:"island2"},
 47 | 		    {start:1200000,end:1500000, name:"island3"},
 48 | 		    {start:1500000,end:1700000, name:"island4"},
 49 | 		    {start:2000000,end:2100000, name:"island5"}
 50 | 		    ]
 51 | 
 52 | var track_coords = [
 53 | 		    {start:0, end:30000, name:"island0", fill:"green", strand: -1},
 54 | 		    {start:60000,end:100000, name:"island1", fill:"green", strand: -1},
 55 | 		    {start:800000,end:1000000, name:"island2", strand: 1},
 56 | 		    {start:1200000,end:1500000, name:"island3", strand: 1},
 57 | 		    {start:1500000,end:1700000, name:"island4",fill:"green",strand: -1},
 58 | 		    {start:2000000,end:2100000, name:"island5", strand: 1}
 59 | 		    ]
 60 | 
 61 | function mouse_callback(d, i) {
 62 |   alert(d, i);   
 63 | }
 64 | 
 65 | var plot_layout = {
 66 |     plot_min: gc_min,
 67 |     plot_max: gc_max,
 68 |     plot_mean: gc_mean,
 69 |     plot_radius: gc_radius,
 70 |     plot_width: gc_width,
 71 |     bp_per_element: bp_per_value,
 72 |     stroke: "blue",
 73 |     mean_stroke: "grey",
 74 |     name: "gcvalues"
 75 | }
 76 | 
 77 | var plot_layout2 = {
 78 |     plot_min: gc_min,
 79 |     plot_max: gc_max,
 80 |     plot_radius: 160,
 81 |     plot_width: gc_width,
 82 |     bp_per_element: bp_per_value,
 83 |     stroke: "grey",
 84 |     name: "gcvalues2"
 85 | }
 86 | 
 87 | var glyph_layout = {
 88 |     name: 'myglyphtrack',
 89 |     type: 'circle',
 90 |     radius: 75,
 91 |     colours: {vfdb: 'green',
 92 |               adb: 'blue'}
 93 | }
 94 | 
 95 | var glyph_data = [
 96 | 		  {bp: 100, type: 'vfdb'},
 97 | 		  {bp: 50000, type: 'adb'},
 98 | 		  {bp: 51000, type: 'adb'},
 99 | 		  {bp: 52000, type: 'vfdb'},
100 | 		  {bp: 53000, type: 'adb'},
101 | 		  {bp: 54000, type: 'vfdb'},
102 | 		  {bp: 55000, type: 'adb'},
103 | 		  {bp: 56000, type: 'adb'}
104 | ]
105 | 
106 | var glyph_data2 = [
107 | 		  {bp: 100, type: 'vfdb'},
108 | 		  {bp: 52000, type: 'vfdb'},
109 | 		  {bp: 54000, type: 'vfdb'},
110 | ]
111 | 
112 | //console.log("Starting");
113 | IslandPlot.createCanvas("#chart", mycfg);
114 | IslandPlot.drawAxis();
115 | IslandPlot.drawPlot(plot_layout, gc_values, true);
116 | IslandPlot.drawPlot(plot_layout2, gc_values2);
117 | IslandPlot.drawTrack(track_layout, track_coords, true);
118 | IslandPlot.drawTrack(track_layout2, track_coords2);
119 | IslandPlot.drawCircle("outerlayer", 240, "grey");
120 | IslandPlot.drawGlyphTrack(glyph_layout, glyph_data);
121 | //glyph_data[1].bp = 1000000;
122 | //glyph_data[2] = {bp: 2000000, type: 'vfdb' };
123 | //IslandPlot.updateGlyphTrack("myglyphtrack", glyph_data);
124 | 
125 | //IslandPlot.removePlot("gcvalues");
126 | 
127 | IslandPlot.attachBrush(linearTrack);
128 | 
129 | function updateGC(cb) {
130 |     if(cb.checked) {
131 | 	IslandPlot.drawPlot(plot_layout, gc_values, true);
132 |     } else {
133 | 	IslandPlot.removePlot("gcvalues");
134 |     }
135 | }
136 | 
137 | function updateStrand(cb) {
138 |     if(cb.checked) {
139 | 	IslandPlot.drawTrack(track_layout, track_coords, true);
140 |     } else {
141 | 	IslandPlot.removeTrack("mytrack");
142 |     }
143 | }
144 | 
145 | function removelayer () {
146 |     IslandPlot.removeTrack("mytrack");
147 |     return false;
148 | }
149 | 
150 | function updateAdb(cb) {
151 |     if(cb.checked) {
152 | 	IslandPlot.updateGlyphTrack("myglyphtrack", glyph_data);
153 |     } else {
154 | 	IslandPlot.updateGlyphTrack("myglyphtrack", glyph_data2);
155 |     }
156 | }
157 | 


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