1 // MISC
  2 
  3 /**
  4  * @namespace
  5  */
  6 
  7 var Util = {};
  8 
  9 Util.is_ie = navigator.appVersion.indexOf('MSIE') >= 0;
 10 Util.is_ie6 = navigator.appVersion.indexOf('MSIE 6') >= 0;
 11 Util.addCommas = function(nStr)
 12 {
 13 	nStr += '';
 14 	var x = nStr.split('.');
 15 	var x1 = x[0];
 16 	var x2 = x.length > 1 ? '.' + x[1] : '';
 17 	var rgx = /(\d+)(\d{3})/;
 18 	while (rgx.test(x1)) {
 19 		x1 = x1.replace(rgx, '$1' + ',' + '$2');
 20 	}
 21 	return x1 + x2;
 22 };
 23 
 24 Util.wheel = function(event){
 25     var delta = 0;
 26     if (!event) event = window.event;
 27     if (event.wheelDelta) {
 28         delta = event.wheelDelta/120;
 29         if (window.opera) delta = -delta;
 30     } else if (event.detail) { delta = -event.detail/3;	}
 31     return Math.round(delta); //Safari Round
 32 };
 33 
 34 Util.isRightButton = function(e) {
 35     if (!e) var e = window.event;
 36     if (e.which) return e.which == 3;
 37     else if (e.button) return e.button == 2;
 38 };
 39 
 40 Util.getViewportWidth = function() {
 41   var width = 0;
 42   if( document.documentElement && document.documentElement.clientWidth ) {
 43     width = document.documentElement.clientWidth;
 44   }
 45   else if( document.body && document.body.clientWidth ) {
 46     width = document.body.clientWidth;
 47   }
 48   else if( window.innerWidth ) {
 49     width = window.innerWidth - 18;
 50   }
 51   return width;
 52 };
 53 
 54 Util.getViewportHeight = function() {
 55   var height = 0;
 56   if( document.documentElement && document.documentElement.clientHeight ) {
 57     height = document.documentElement.clientHeight;
 58   }
 59   else if( document.body && document.body.clientHeight ) {
 60     height = document.body.clientHeight;
 61   }
 62   else if( window.innerHeight ) {
 63     height = window.innerHeight - 18;
 64   }
 65   return height;
 66 };
 67 
 68 Util.findNearest = function(numArray, num) {
 69     var minIndex = 0;
 70     var min = Math.abs(num - numArray[0]);
 71     for (var i = 0; i < numArray.length; i++) {
 72         if (Math.abs(num - numArray[i]) < min) {
 73             minIndex = i;
 74             min = Math.abs(num - numArray[i]);
 75         }
 76     }
 77     return minIndex;
 78 };
 79 
 80 /**
 81  * replace variables in a template string with values
 82  * @param template String with variable names in curly brackets
 83  *                 e.g., "http://foo/{bar}?arg={baz}
 84  * @param fillWith object with attribute-value mappings
 85  *                 e.g., {'bar': 'someurl', 'baz': 'valueforbaz'}
 86  * @returns the template string with variables in fillWith replaced
 87  *                 e.g., 'htp://foo/someurl?arg=valueforbaz'
 88  */
 89 Util.fillTemplate = function(template, fillWith) {
 90     return template.replace(/\{([^}]+)\}/g,
 91                             function(match, group) {
 92                                 if (fillWith[group] !== undefined)
 93                                     return fillWith[group];
 94                                 else
 95                                     return "{" + group + "}";
 96                             });
 97 };
 98 
 99 /**
100  * function to load a specified resource only once
101  * @param {Object}   dojoXhrArgs object containing arguments for dojo.xhrGet,
102  *                               like <code>url</code> and <code>handleAs</code>
103  * @param {Object}   stateObj object that stores the state of the load
104  * @param {Function} successCallback function to call on a successful load
105  * @param {Function} errorCallback function to call on an unsuccessful load
106  */
107 Util.maybeLoad = function ( dojoXhrArgs, stateObj, successCallback, errorCallback) {
108     if (stateObj.state) {
109         if ("loaded" == stateObj.state) {
110             successCallback(stateObj.data);
111         } else if ("error" == stateObj.state) {
112             errorCallback();
113         } else if ("loading" == stateObj.state) {
114             stateObj.successCallbacks.push(successCallback);
115             if (errorCallback) stateObj.errorCallbacks.push(errorCallback);
116         }
117     } else {
118         stateObj.state = "loading";
119         stateObj.successCallbacks = [successCallback];
120         stateObj.errorCallbacks = [errorCallback];
121 
122         var args = dojo.clone( dojoXhrArgs );
123         args.load = function(o) {
124             stateObj.state = "loaded";
125             stateObj.data = o;
126             var cbs = stateObj.successCallbacks;
127             for (var c = 0; c < cbs.length; c++) cbs[c](o);
128         };
129         args.error = function(error) {
130             console.error(''+error);
131             stateObj.state = "error";
132             var cbs = stateObj.errorCallbacks;
133             for (var c = 0; c < cbs.length; c++) cbs[c]();
134         };
135 
136         dojo.xhrGet( args );
137     }
138 };
139 
140 /**
141  * updates a with values from b, recursively
142  */
143 Util.deepUpdate = function(a, b) {
144     for (var prop in b) {
145         if ((prop in a)
146             && ("object" == typeof b[prop])
147             && ("object" == typeof a[prop]) ) {
148             Util.deepUpdate(a[prop], b[prop]);
149         } else if( typeof a[prop] == 'undefined' || typeof b[prop] != undefined ){
150             a[prop] = b[prop];
151         }
152     }
153     return a;
154 };
155 
156 // from http://bugs.dojotoolkit.org/ticket/5794
157 Util.resolveUrl = function(baseUrl, relativeUrl) {
158     // summary:
159     // This takes a base url and a relative url and resolves the target url.
160     // For example:
161     // resolveUrl("http://www.domain.com/path1/path2","../path3") ->"http://www.domain.com/path1/path3"
162     //
163     if (relativeUrl.match(/\w+:\/\//))
164 	return relativeUrl;
165     if (relativeUrl.charAt(0)=='/') {
166 	baseUrl = baseUrl.match(/.*\/\/[^\/]*/);
167 	return (baseUrl ? baseUrl[0] : '') + relativeUrl;
168     }
169     //TODO: handle protocol relative urls:  ://www.domain.com
170     baseUrl = baseUrl.substring(0,baseUrl.length - baseUrl.match(/[^\/]*$/)[0].length);// clean off the trailing path
171     if (relativeUrl == '.')
172 	return baseUrl;
173     while (relativeUrl.substring(0,3) == '../') {
174 	baseUrl = baseUrl.substring(0,baseUrl.length - baseUrl.match(/[^\/]*\/$/)[0].length);
175 	relativeUrl = relativeUrl.substring(3);
176     }
177     return baseUrl + relativeUrl;
178 };
179 
180 Util.parseLocString = function( locstring ) {
181     locstring = dojo.trim( locstring );
182 
183     //                                (chromosome)    (    start      )   (  sep     )     (    end   )
184     var matches = locstring.match(/^(((\S*)\s*:)?\s*(-?[\d,.']+)\s*(\.\.|-|\s+))?\s*(-?[\d,.']+)$/i);
185     //matches potentially contains location components:
186     //matches[3] = chromosome (optional)
187     //matches[4] = start base (optional)
188     //matches[6] = end base (or center base, if it's the only one)
189 
190     if( !matches )
191         return null;
192 
193     // parses a number from a locstring that's a coordinate, and
194     // converts it from 1-based to interbase coordinates
195     var parseCoord = function( coord ) {
196         coord = (coord+'').replace(/\D/g,'');
197         var num = parseInt( coord, 10 );
198         return typeof num == 'number' && !isNaN(num) ? num : null;
199     };
200 
201     return {
202         start: parseCoord( matches[4] )-1,
203         end:   parseCoord( matches[6] ),
204         ref:   matches[3]
205     };
206 };
207 
208 Util.assembleLocString = function( loc_in ) {
209     var s = '',
210         types = { start: 'number', end: 'number', ref: 'string' },
211         location = {}
212        ;
213 
214     // filter the incoming loc_in to only pay attention to slots that we
215     // know how to handle
216     for( var slot in types ) {
217         if( types[slot] == typeof loc_in[slot]
218             && (types[slot] != 'number' || !isNaN(loc_in[slot])) //filter any NaNs
219           ) {
220             location[slot] = loc_in[slot];
221         }
222     }
223 
224     //finally assemble our string
225     if( 'ref' in location ) {
226         s += location.ref;
227         if( location.start || location.end )
228             s += ':';
229     }
230     if( 'start' in location ) {
231         s += (Math.round(location.start)+1).toFixed(0).toLocaleString();
232         if( 'end' in location )
233             s+= '..';
234     }
235     if( 'end' in location )
236         s += Math.round(location.end).toFixed(0).toLocaleString();
237 
238     return s;
239 };
240 
241 // given a possible reference sequence name and an object as { 'foo':
242 // <refseq foo>, ... }, try to match that reference sequence name
243 // against the actual name of one of the reference sequences.  returns
244 // the reference sequence record, or null
245 // if none matched.
246 Util.matchRefSeqName = function( name, refseqs ) {
247     for( var ref in refseqs ) {
248         if( ! refseqs.hasOwnProperty(ref) )
249             continue;
250 
251         var ucname = name.toUpperCase();
252         var ucref  = ref.toUpperCase();
253 
254 	if(    ucname == ucref
255             || "CHR" + ucname == ucref
256             || ucname == "CHR" + ucref
257           ) {
258             return refseqs[ref];
259         }
260     }
261     return null;
262 };
263 
264 /**
265  * Wrap a handler function to be called 1ms later in a window timeout.
266  * This will usually give a better stack trace for figuring out where
267  * errors are happening.
268  */
269 Util.debugHandler = function( context, func ) {
270     return function() {
271         var args = arguments;
272         window.setTimeout( function() {
273             var f = func;
274             if( typeof f == 'string' )
275                 f = context[f];
276             f.apply(context,args);
277         }, 1);
278     };
279 };
280 
281 Util.ucFirst = function(str) {
282     if( typeof str != 'string') return undefined;
283     return str.charAt(0).toUpperCase() + str.slice(1);
284 };
285 
286 /**
287  * Uniqify an array.
288  * @param stuff {Array} array of stuff
289  * @param normalizer {Function} optional function to be called on each
290  * element.  by default, just compares by stringification
291  */
292 Util.uniq = function( stuff, normalizer ) {
293     normalizer = normalizer || function(t) {
294         return ''+t;
295     };
296     var result = [],
297         seen   = {};
298     dojo.forEach( stuff, function(thing) {
299         var norm = normalizer(thing);
300         if( !seen[ normalizer(thing) ] )
301             result.push( thing );
302         seen[norm] = true;
303     });
304     return result;
305 };
306 
307 Util.crc32Table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
308 
309 /**
310  * Does a (deep) crc32 of any object.
311  * @returns {Number}
312  */
313 Util.objectFingerprint = function( obj ) {
314     var crc = 0,
315           x = 0,
316           y = 0;
317 
318     var table = Util.crc32Table;
319     var crcstr = function( str ) {
320         for( var i = 0, iTop = str.length; i < iTop; i++ ) {
321             y = ( crc ^ str.charCodeAt( i ) ) & 0xFF;
322             x = "0x" + table.substr( y * 9, 8 );
323             crc = ( crc >>> 8 ) ^ x;
324         }
325     };
326 
327     if( typeof obj == 'object' ) {
328         for( var prop in obj ) {
329             crcstr( '' + Util.objectFingerprint( prop      ));
330             crcstr( '' + Util.objectFingerprint( obj[prop] ));
331         }
332     } else {
333         crcstr( ''+obj );
334     }
335     return crc;
336 };
337 
338 
339 
340 if (!Array.prototype.reduce)
341 {
342   Array.prototype.reduce = function(fun /*, initial*/)
343   {
344     var len = this.length;
345     if (typeof fun != "function")
346       throw new TypeError();
347 
348     // no value to return if no initial value and an empty array
349     if (len == 0 && arguments.length == 1)
350       throw new TypeError();
351 
352     var i = 0;
353     if (arguments.length >= 2)
354     {
355       var rv = arguments[1];
356     }
357     else
358     {
359       do
360       {
361         if (i in this)
362         {
363           rv = this[i++];
364           break;
365         }
366 
367         // if array contains no values, no initial value to return
368         if (++i >= len)
369           throw new TypeError();
370       }
371       while (true);
372     }
373 
374     for (; i < len; i++)
375     {
376       if (i in this)
377         rv = fun.call(null, rv, this[i], i, this);
378     }
379 
380     return rv;
381   };
382 }
383 
384 if (!Array.prototype.map)
385 {
386   Array.prototype.map = function(fun /*, thisp */)
387   {
388     "use strict";
389 
390     if (this === void 0 || this === null)
391       throw new TypeError();
392 
393     var t = Object(this);
394     var len = t.length >>> 0;
395     if (typeof fun !== "function")
396       throw new TypeError();
397 
398     var res = new Array(len);
399     var thisp = arguments[1];
400     for (var i = 0; i < len; i++)
401     {
402       if (i in t)
403         res[i] = fun.call(thisp, t[i], i, t);
404     }
405 
406     return res;
407   };
408 }
409 
410 if (!Array.prototype.indexOf)
411 {
412   Array.prototype.indexOf = function(searchElement /*, fromIndex */)
413   {
414     "use strict";
415 
416     if (this === void 0 || this === null)
417       throw new TypeError();
418 
419     var t = Object(this);
420     var len = t.length >>> 0;
421     if (len === 0)
422       return -1;
423 
424     var n = 0;
425     if (arguments.length > 0)
426     {
427       n = Number(arguments[1]);
428       if (n !== n) // shortcut for verifying if it's NaN
429         n = 0;
430       else if (n !== 0 && n !== (1 / 0) && n !== -(1 / 0))
431         n = (n > 0 || -1) * Math.floor(Math.abs(n));
432     }
433 
434     if (n >= len)
435       return -1;
436 
437     var k = n >= 0
438           ? n
439           : Math.max(len - Math.abs(n), 0);
440 
441     for (; k < len; k++)
442     {
443       if (k in t && t[k] === searchElement)
444         return k;
445     }
446     return -1;
447   };
448 }
449 
450 /**
451  * @class
452  */
453 function Finisher(fun) {
454     this.fun = fun;
455     this.count = 0;
456 }
457 
458 Finisher.prototype.inc = function() {
459     this.count++;
460 };
461 
462 Finisher.prototype.dec = function() {
463     this.count--;
464     this.finish();
465 };
466 
467 Finisher.prototype.finish = function() {
468     if (this.count <= 0) this.fun();
469 };
470 
471 
472 /*
473 
474 Copyright (c) 2007-2010 The Evolutionary Software Foundation
475 
476 Created by Mitchell Skinner <mitch_skinner@berkeley.edu>
477 
478 This package and its accompanying libraries are free software; you can
479 redistribute it and/or modify it under the terms of the LGPL (either
480 version 2.1, or at your option, any later version) or the Artistic
481 License 2.0.  Refer to LICENSE for the full license text.
482 
483 */
484