bio 0.7.1 → 1.0.0

Sign up to get free protection for your applications and to get access to all the features.
Files changed (142) hide show
  1. data/bin/bioruby +71 -27
  2. data/bin/br_biofetch.rb +5 -17
  3. data/bin/br_bioflat.rb +14 -26
  4. data/bin/br_biogetseq.rb +6 -18
  5. data/bin/br_pmfetch.rb +6 -16
  6. data/doc/Changes-0.7.rd +35 -0
  7. data/doc/KEGG_API.rd +287 -172
  8. data/doc/KEGG_API.rd.ja +273 -160
  9. data/doc/Tutorial.rd +18 -9
  10. data/doc/Tutorial.rd.ja +656 -138
  11. data/lib/bio.rb +6 -24
  12. data/lib/bio/alignment.rb +5 -5
  13. data/lib/bio/appl/blast.rb +132 -98
  14. data/lib/bio/appl/blast/format0.rb +9 -19
  15. data/lib/bio/appl/blast/wublast.rb +5 -18
  16. data/lib/bio/appl/emboss.rb +40 -47
  17. data/lib/bio/appl/hmmer.rb +116 -82
  18. data/lib/bio/appl/hmmer/report.rb +509 -364
  19. data/lib/bio/appl/spidey/report.rb +7 -18
  20. data/lib/bio/data/na.rb +3 -21
  21. data/lib/bio/db.rb +3 -21
  22. data/lib/bio/db/aaindex.rb +147 -52
  23. data/lib/bio/db/embl/common.rb +27 -6
  24. data/lib/bio/db/embl/embl.rb +18 -10
  25. data/lib/bio/db/embl/sptr.rb +87 -67
  26. data/lib/bio/db/embl/swissprot.rb +32 -3
  27. data/lib/bio/db/embl/trembl.rb +32 -3
  28. data/lib/bio/db/embl/uniprot.rb +32 -3
  29. data/lib/bio/db/fasta.rb +327 -289
  30. data/lib/bio/db/medline.rb +25 -4
  31. data/lib/bio/db/nbrf.rb +12 -20
  32. data/lib/bio/db/pdb.rb +4 -1
  33. data/lib/bio/db/pdb/chemicalcomponent.rb +240 -0
  34. data/lib/bio/db/pdb/pdb.rb +13 -8
  35. data/lib/bio/db/rebase.rb +93 -97
  36. data/lib/bio/feature.rb +2 -31
  37. data/lib/bio/io/ddbjxml.rb +167 -139
  38. data/lib/bio/io/fastacmd.rb +89 -56
  39. data/lib/bio/io/flatfile.rb +994 -278
  40. data/lib/bio/io/flatfile/index.rb +257 -194
  41. data/lib/bio/io/flatfile/indexer.rb +37 -29
  42. data/lib/bio/reference.rb +147 -64
  43. data/lib/bio/sequence.rb +57 -417
  44. data/lib/bio/sequence/aa.rb +64 -0
  45. data/lib/bio/sequence/common.rb +175 -0
  46. data/lib/bio/sequence/compat.rb +68 -0
  47. data/lib/bio/sequence/format.rb +134 -0
  48. data/lib/bio/sequence/generic.rb +24 -0
  49. data/lib/bio/sequence/na.rb +189 -0
  50. data/lib/bio/shell.rb +9 -23
  51. data/lib/bio/shell/core.rb +130 -125
  52. data/lib/bio/shell/demo.rb +143 -0
  53. data/lib/bio/shell/{session.rb → interface.rb} +42 -40
  54. data/lib/bio/shell/object.rb +52 -0
  55. data/lib/bio/shell/plugin/codon.rb +4 -22
  56. data/lib/bio/shell/plugin/emboss.rb +23 -0
  57. data/lib/bio/shell/plugin/entry.rb +34 -25
  58. data/lib/bio/shell/plugin/flatfile.rb +5 -23
  59. data/lib/bio/shell/plugin/keggapi.rb +11 -24
  60. data/lib/bio/shell/plugin/midi.rb +5 -23
  61. data/lib/bio/shell/plugin/obda.rb +4 -22
  62. data/lib/bio/shell/plugin/seq.rb +6 -24
  63. data/lib/bio/shell/rails/Rakefile +10 -0
  64. data/lib/bio/shell/rails/app/controllers/application.rb +4 -0
  65. data/lib/bio/shell/rails/app/controllers/shell_controller.rb +94 -0
  66. data/lib/bio/shell/rails/app/helpers/application_helper.rb +3 -0
  67. data/lib/bio/shell/rails/app/models/shell_connection.rb +30 -0
  68. data/lib/bio/shell/rails/app/views/layouts/shell.rhtml +37 -0
  69. data/lib/bio/shell/rails/app/views/shell/history.rhtml +5 -0
  70. data/lib/bio/shell/rails/app/views/shell/index.rhtml +2 -0
  71. data/lib/bio/shell/rails/app/views/shell/show.rhtml +13 -0
  72. data/lib/bio/shell/rails/config/boot.rb +19 -0
  73. data/lib/bio/shell/rails/config/database.yml +85 -0
  74. data/lib/bio/shell/rails/config/environment.rb +53 -0
  75. data/lib/bio/shell/rails/config/environments/development.rb +19 -0
  76. data/lib/bio/shell/rails/config/environments/production.rb +19 -0
  77. data/lib/bio/shell/rails/config/environments/test.rb +19 -0
  78. data/lib/bio/shell/rails/config/routes.rb +19 -0
  79. data/lib/bio/shell/rails/doc/README_FOR_APP +2 -0
  80. data/lib/bio/shell/rails/public/404.html +8 -0
  81. data/lib/bio/shell/rails/public/500.html +8 -0
  82. data/lib/bio/shell/rails/public/dispatch.cgi +10 -0
  83. data/lib/bio/shell/rails/public/dispatch.fcgi +24 -0
  84. data/lib/bio/shell/rails/public/dispatch.rb +10 -0
  85. data/lib/bio/shell/rails/public/favicon.ico +0 -0
  86. data/lib/bio/shell/rails/public/images/icon.png +0 -0
  87. data/lib/bio/shell/rails/public/images/rails.png +0 -0
  88. data/lib/bio/shell/rails/public/index.html +277 -0
  89. data/lib/bio/shell/rails/public/javascripts/controls.js +750 -0
  90. data/lib/bio/shell/rails/public/javascripts/dragdrop.js +584 -0
  91. data/lib/bio/shell/rails/public/javascripts/effects.js +854 -0
  92. data/lib/bio/shell/rails/public/javascripts/prototype.js +1785 -0
  93. data/lib/bio/shell/rails/public/robots.txt +1 -0
  94. data/lib/bio/shell/rails/public/stylesheets/main.css +187 -0
  95. data/lib/bio/shell/rails/script/about +3 -0
  96. data/lib/bio/shell/rails/script/breakpointer +3 -0
  97. data/lib/bio/shell/rails/script/console +3 -0
  98. data/lib/bio/shell/rails/script/destroy +3 -0
  99. data/lib/bio/shell/rails/script/generate +3 -0
  100. data/lib/bio/shell/rails/script/performance/benchmarker +3 -0
  101. data/lib/bio/shell/rails/script/performance/profiler +3 -0
  102. data/lib/bio/shell/rails/script/plugin +3 -0
  103. data/lib/bio/shell/rails/script/process/reaper +3 -0
  104. data/lib/bio/shell/rails/script/process/spawner +3 -0
  105. data/lib/bio/shell/rails/script/process/spinner +3 -0
  106. data/lib/bio/shell/rails/script/runner +3 -0
  107. data/lib/bio/shell/rails/script/server +42 -0
  108. data/lib/bio/shell/rails/test/test_helper.rb +28 -0
  109. data/lib/bio/shell/web.rb +90 -0
  110. data/lib/bio/util/contingency_table.rb +231 -225
  111. data/sample/any2fasta.rb +59 -0
  112. data/test/data/HMMER/hmmpfam.out +64 -0
  113. data/test/data/HMMER/hmmsearch.out +88 -0
  114. data/test/data/aaindex/DAYM780301 +30 -0
  115. data/test/data/aaindex/PRAM900102 +20 -0
  116. data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
  117. data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
  118. data/test/data/blast/{eco:b0002.faa → b0002.faa} +0 -0
  119. data/test/data/blast/{eco:b0002.faa.m0 → b0002.faa.m0} +2 -2
  120. data/test/data/blast/{eco:b0002.faa.m7 → b0002.faa.m7} +1 -1
  121. data/test/data/blast/{eco:b0002.faa.m8 → b0002.faa.m8} +0 -0
  122. data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
  123. data/test/unit/bio/appl/blast/test_report.rb +15 -12
  124. data/test/unit/bio/appl/blast/test_xmlparser.rb +4 -4
  125. data/test/unit/bio/appl/hmmer/test_report.rb +355 -0
  126. data/test/unit/bio/appl/test_blast.rb +5 -5
  127. data/test/unit/bio/data/test_na.rb +9 -18
  128. data/test/unit/bio/db/pdb/test_pdb.rb +169 -0
  129. data/test/unit/bio/db/test_aaindex.rb +197 -0
  130. data/test/unit/bio/io/test_fastacmd.rb +55 -0
  131. data/test/unit/bio/sequence/test_aa.rb +102 -0
  132. data/test/unit/bio/sequence/test_common.rb +178 -0
  133. data/test/unit/bio/sequence/test_compat.rb +82 -0
  134. data/test/unit/bio/sequence/test_na.rb +242 -0
  135. data/test/unit/bio/shell/plugin/test_seq.rb +29 -19
  136. data/test/unit/bio/test_alignment.rb +15 -7
  137. data/test/unit/bio/test_reference.rb +198 -0
  138. data/test/unit/bio/test_sequence.rb +4 -49
  139. data/test/unit/bio/test_shell.rb +2 -2
  140. metadata +118 -15
  141. data/lib/bio/io/brdb.rb +0 -103
  142. data/lib/bioruby.rb +0 -34
@@ -0,0 +1,584 @@
1
+ // Copyright (c) 2005 Thomas Fuchs (http://script.aculo.us, http://mir.aculo.us)
2
+ //
3
+ // See scriptaculous.js for full license.
4
+
5
+ /*--------------------------------------------------------------------------*/
6
+
7
+ var Droppables = {
8
+ drops: [],
9
+
10
+ remove: function(element) {
11
+ this.drops = this.drops.reject(function(d) { return d.element==$(element) });
12
+ },
13
+
14
+ add: function(element) {
15
+ element = $(element);
16
+ var options = Object.extend({
17
+ greedy: true,
18
+ hoverclass: null
19
+ }, arguments[1] || {});
20
+
21
+ // cache containers
22
+ if(options.containment) {
23
+ options._containers = [];
24
+ var containment = options.containment;
25
+ if((typeof containment == 'object') &&
26
+ (containment.constructor == Array)) {
27
+ containment.each( function(c) { options._containers.push($(c)) });
28
+ } else {
29
+ options._containers.push($(containment));
30
+ }
31
+ }
32
+
33
+ if(options.accept) options.accept = [options.accept].flatten();
34
+
35
+ Element.makePositioned(element); // fix IE
36
+ options.element = element;
37
+
38
+ this.drops.push(options);
39
+ },
40
+
41
+ isContained: function(element, drop) {
42
+ var parentNode = element.parentNode;
43
+ return drop._containers.detect(function(c) { return parentNode == c });
44
+ },
45
+
46
+ isAffected: function(point, element, drop) {
47
+ return (
48
+ (drop.element!=element) &&
49
+ ((!drop._containers) ||
50
+ this.isContained(element, drop)) &&
51
+ ((!drop.accept) ||
52
+ (Element.classNames(element).detect(
53
+ function(v) { return drop.accept.include(v) } ) )) &&
54
+ Position.within(drop.element, point[0], point[1]) );
55
+ },
56
+
57
+ deactivate: function(drop) {
58
+ if(drop.hoverclass)
59
+ Element.removeClassName(drop.element, drop.hoverclass);
60
+ this.last_active = null;
61
+ },
62
+
63
+ activate: function(drop) {
64
+ if(drop.hoverclass)
65
+ Element.addClassName(drop.element, drop.hoverclass);
66
+ this.last_active = drop;
67
+ },
68
+
69
+ show: function(point, element) {
70
+ if(!this.drops.length) return;
71
+
72
+ if(this.last_active) this.deactivate(this.last_active);
73
+ this.drops.each( function(drop) {
74
+ if(Droppables.isAffected(point, element, drop)) {
75
+ if(drop.onHover)
76
+ drop.onHover(element, drop.element, Position.overlap(drop.overlap, drop.element));
77
+ if(drop.greedy) {
78
+ Droppables.activate(drop);
79
+ throw $break;
80
+ }
81
+ }
82
+ });
83
+ },
84
+
85
+ fire: function(event, element) {
86
+ if(!this.last_active) return;
87
+ Position.prepare();
88
+
89
+ if (this.isAffected([Event.pointerX(event), Event.pointerY(event)], element, this.last_active))
90
+ if (this.last_active.onDrop)
91
+ this.last_active.onDrop(element, this.last_active.element, event);
92
+ },
93
+
94
+ reset: function() {
95
+ if(this.last_active)
96
+ this.deactivate(this.last_active);
97
+ }
98
+ }
99
+
100
+ var Draggables = {
101
+ drags: [],
102
+ observers: [],
103
+
104
+ register: function(draggable) {
105
+ if(this.drags.length == 0) {
106
+ this.eventMouseUp = this.endDrag.bindAsEventListener(this);
107
+ this.eventMouseMove = this.updateDrag.bindAsEventListener(this);
108
+ this.eventKeypress = this.keyPress.bindAsEventListener(this);
109
+
110
+ Event.observe(document, "mouseup", this.eventMouseUp);
111
+ Event.observe(document, "mousemove", this.eventMouseMove);
112
+ Event.observe(document, "keypress", this.eventKeypress);
113
+ }
114
+ this.drags.push(draggable);
115
+ },
116
+
117
+ unregister: function(draggable) {
118
+ this.drags = this.drags.reject(function(d) { return d==draggable });
119
+ if(this.drags.length == 0) {
120
+ Event.stopObserving(document, "mouseup", this.eventMouseUp);
121
+ Event.stopObserving(document, "mousemove", this.eventMouseMove);
122
+ Event.stopObserving(document, "keypress", this.eventKeypress);
123
+ }
124
+ },
125
+
126
+ activate: function(draggable) {
127
+ window.focus(); // allows keypress events if window isn't currently focused, fails for Safari
128
+ this.activeDraggable = draggable;
129
+ },
130
+
131
+ deactivate: function(draggbale) {
132
+ this.activeDraggable = null;
133
+ },
134
+
135
+ updateDrag: function(event) {
136
+ if(!this.activeDraggable) return;
137
+ var pointer = [Event.pointerX(event), Event.pointerY(event)];
138
+ // Mozilla-based browsers fire successive mousemove events with
139
+ // the same coordinates, prevent needless redrawing (moz bug?)
140
+ if(this._lastPointer && (this._lastPointer.inspect() == pointer.inspect())) return;
141
+ this._lastPointer = pointer;
142
+ this.activeDraggable.updateDrag(event, pointer);
143
+ },
144
+
145
+ endDrag: function(event) {
146
+ if(!this.activeDraggable) return;
147
+ this._lastPointer = null;
148
+ this.activeDraggable.endDrag(event);
149
+ },
150
+
151
+ keyPress: function(event) {
152
+ if(this.activeDraggable)
153
+ this.activeDraggable.keyPress(event);
154
+ },
155
+
156
+ addObserver: function(observer) {
157
+ this.observers.push(observer);
158
+ this._cacheObserverCallbacks();
159
+ },
160
+
161
+ removeObserver: function(element) { // element instead of observer fixes mem leaks
162
+ this.observers = this.observers.reject( function(o) { return o.element==element });
163
+ this._cacheObserverCallbacks();
164
+ },
165
+
166
+ notify: function(eventName, draggable, event) { // 'onStart', 'onEnd', 'onDrag'
167
+ if(this[eventName+'Count'] > 0)
168
+ this.observers.each( function(o) {
169
+ if(o[eventName]) o[eventName](eventName, draggable, event);
170
+ });
171
+ },
172
+
173
+ _cacheObserverCallbacks: function() {
174
+ ['onStart','onEnd','onDrag'].each( function(eventName) {
175
+ Draggables[eventName+'Count'] = Draggables.observers.select(
176
+ function(o) { return o[eventName]; }
177
+ ).length;
178
+ });
179
+ }
180
+ }
181
+
182
+ /*--------------------------------------------------------------------------*/
183
+
184
+ var Draggable = Class.create();
185
+ Draggable.prototype = {
186
+ initialize: function(element) {
187
+ var options = Object.extend({
188
+ handle: false,
189
+ starteffect: function(element) {
190
+ new Effect.Opacity(element, {duration:0.2, from:1.0, to:0.7});
191
+ },
192
+ reverteffect: function(element, top_offset, left_offset) {
193
+ var dur = Math.sqrt(Math.abs(top_offset^2)+Math.abs(left_offset^2))*0.02;
194
+ element._revert = new Effect.MoveBy(element, -top_offset, -left_offset, {duration:dur});
195
+ },
196
+ endeffect: function(element) {
197
+ new Effect.Opacity(element, {duration:0.2, from:0.7, to:1.0});
198
+ },
199
+ zindex: 1000,
200
+ revert: false,
201
+ snap: false // false, or xy or [x,y] or function(x,y){ return [x,y] }
202
+ }, arguments[1] || {});
203
+
204
+ this.element = $(element);
205
+
206
+ if(options.handle && (typeof options.handle == 'string'))
207
+ this.handle = Element.childrenWithClassName(this.element, options.handle)[0];
208
+ if(!this.handle) this.handle = $(options.handle);
209
+ if(!this.handle) this.handle = this.element;
210
+
211
+ Element.makePositioned(this.element); // fix IE
212
+
213
+ this.delta = this.currentDelta();
214
+ this.options = options;
215
+ this.dragging = false;
216
+
217
+ this.eventMouseDown = this.initDrag.bindAsEventListener(this);
218
+ Event.observe(this.handle, "mousedown", this.eventMouseDown);
219
+
220
+ Draggables.register(this);
221
+ },
222
+
223
+ destroy: function() {
224
+ Event.stopObserving(this.handle, "mousedown", this.eventMouseDown);
225
+ Draggables.unregister(this);
226
+ },
227
+
228
+ currentDelta: function() {
229
+ return([
230
+ parseInt(this.element.style.left || '0'),
231
+ parseInt(this.element.style.top || '0')]);
232
+ },
233
+
234
+ initDrag: function(event) {
235
+ if(Event.isLeftClick(event)) {
236
+ // abort on form elements, fixes a Firefox issue
237
+ var src = Event.element(event);
238
+ if(src.tagName && (
239
+ src.tagName=='INPUT' ||
240
+ src.tagName=='SELECT' ||
241
+ src.tagName=='BUTTON' ||
242
+ src.tagName=='TEXTAREA')) return;
243
+
244
+ if(this.element._revert) {
245
+ this.element._revert.cancel();
246
+ this.element._revert = null;
247
+ }
248
+
249
+ var pointer = [Event.pointerX(event), Event.pointerY(event)];
250
+ var pos = Position.cumulativeOffset(this.element);
251
+ this.offset = [0,1].map( function(i) { return (pointer[i] - pos[i]) });
252
+
253
+ Draggables.activate(this);
254
+ Event.stop(event);
255
+ }
256
+ },
257
+
258
+ startDrag: function(event) {
259
+ this.dragging = true;
260
+
261
+ if(this.options.zindex) {
262
+ this.originalZ = parseInt(Element.getStyle(this.element,'z-index') || 0);
263
+ this.element.style.zIndex = this.options.zindex;
264
+ }
265
+
266
+ if(this.options.ghosting) {
267
+ this._clone = this.element.cloneNode(true);
268
+ Position.absolutize(this.element);
269
+ this.element.parentNode.insertBefore(this._clone, this.element);
270
+ }
271
+
272
+ Draggables.notify('onStart', this, event);
273
+ if(this.options.starteffect) this.options.starteffect(this.element);
274
+ },
275
+
276
+ updateDrag: function(event, pointer) {
277
+ if(!this.dragging) this.startDrag(event);
278
+ Position.prepare();
279
+ Droppables.show(pointer, this.element);
280
+ Draggables.notify('onDrag', this, event);
281
+ this.draw(pointer);
282
+ if(this.options.change) this.options.change(this);
283
+
284
+ // fix AppleWebKit rendering
285
+ if(navigator.appVersion.indexOf('AppleWebKit')>0) window.scrollBy(0,0);
286
+ Event.stop(event);
287
+ },
288
+
289
+ finishDrag: function(event, success) {
290
+ this.dragging = false;
291
+
292
+ if(this.options.ghosting) {
293
+ Position.relativize(this.element);
294
+ Element.remove(this._clone);
295
+ this._clone = null;
296
+ }
297
+
298
+ if(success) Droppables.fire(event, this.element);
299
+ Draggables.notify('onEnd', this, event);
300
+
301
+ var revert = this.options.revert;
302
+ if(revert && typeof revert == 'function') revert = revert(this.element);
303
+
304
+ var d = this.currentDelta();
305
+ if(revert && this.options.reverteffect) {
306
+ this.options.reverteffect(this.element,
307
+ d[1]-this.delta[1], d[0]-this.delta[0]);
308
+ } else {
309
+ this.delta = d;
310
+ }
311
+
312
+ if(this.options.zindex)
313
+ this.element.style.zIndex = this.originalZ;
314
+
315
+ if(this.options.endeffect)
316
+ this.options.endeffect(this.element);
317
+
318
+ Draggables.deactivate(this);
319
+ Droppables.reset();
320
+ },
321
+
322
+ keyPress: function(event) {
323
+ if(!event.keyCode==Event.KEY_ESC) return;
324
+ this.finishDrag(event, false);
325
+ Event.stop(event);
326
+ },
327
+
328
+ endDrag: function(event) {
329
+ if(!this.dragging) return;
330
+ this.finishDrag(event, true);
331
+ Event.stop(event);
332
+ },
333
+
334
+ draw: function(point) {
335
+ var pos = Position.cumulativeOffset(this.element);
336
+ var d = this.currentDelta();
337
+ pos[0] -= d[0]; pos[1] -= d[1];
338
+
339
+ var p = [0,1].map(function(i){ return (point[i]-pos[i]-this.offset[i]) }.bind(this));
340
+
341
+ if(this.options.snap) {
342
+ if(typeof this.options.snap == 'function') {
343
+ p = this.options.snap(p[0],p[1]);
344
+ } else {
345
+ if(this.options.snap instanceof Array) {
346
+ p = p.map( function(v, i) {
347
+ return Math.round(v/this.options.snap[i])*this.options.snap[i] }.bind(this))
348
+ } else {
349
+ p = p.map( function(v) {
350
+ return Math.round(v/this.options.snap)*this.options.snap }.bind(this))
351
+ }
352
+ }}
353
+
354
+ var style = this.element.style;
355
+ if((!this.options.constraint) || (this.options.constraint=='horizontal'))
356
+ style.left = p[0] + "px";
357
+ if((!this.options.constraint) || (this.options.constraint=='vertical'))
358
+ style.top = p[1] + "px";
359
+ if(style.visibility=="hidden") style.visibility = ""; // fix gecko rendering
360
+ }
361
+ }
362
+
363
+ /*--------------------------------------------------------------------------*/
364
+
365
+ var SortableObserver = Class.create();
366
+ SortableObserver.prototype = {
367
+ initialize: function(element, observer) {
368
+ this.element = $(element);
369
+ this.observer = observer;
370
+ this.lastValue = Sortable.serialize(this.element);
371
+ },
372
+
373
+ onStart: function() {
374
+ this.lastValue = Sortable.serialize(this.element);
375
+ },
376
+
377
+ onEnd: function() {
378
+ Sortable.unmark();
379
+ if(this.lastValue != Sortable.serialize(this.element))
380
+ this.observer(this.element)
381
+ }
382
+ }
383
+
384
+ var Sortable = {
385
+ sortables: new Array(),
386
+
387
+ options: function(element){
388
+ element = $(element);
389
+ return this.sortables.detect(function(s) { return s.element == element });
390
+ },
391
+
392
+ destroy: function(element){
393
+ element = $(element);
394
+ this.sortables.findAll(function(s) { return s.element == element }).each(function(s){
395
+ Draggables.removeObserver(s.element);
396
+ s.droppables.each(function(d){ Droppables.remove(d) });
397
+ s.draggables.invoke('destroy');
398
+ });
399
+ this.sortables = this.sortables.reject(function(s) { return s.element == element });
400
+ },
401
+
402
+ create: function(element) {
403
+ element = $(element);
404
+ var options = Object.extend({
405
+ element: element,
406
+ tag: 'li', // assumes li children, override with tag: 'tagname'
407
+ dropOnEmpty: false,
408
+ tree: false, // fixme: unimplemented
409
+ overlap: 'vertical', // one of 'vertical', 'horizontal'
410
+ constraint: 'vertical', // one of 'vertical', 'horizontal', false
411
+ containment: element, // also takes array of elements (or id's); or false
412
+ handle: false, // or a CSS class
413
+ only: false,
414
+ hoverclass: null,
415
+ ghosting: false,
416
+ format: null,
417
+ onChange: Prototype.emptyFunction,
418
+ onUpdate: Prototype.emptyFunction
419
+ }, arguments[1] || {});
420
+
421
+ // clear any old sortable with same element
422
+ this.destroy(element);
423
+
424
+ // build options for the draggables
425
+ var options_for_draggable = {
426
+ revert: true,
427
+ ghosting: options.ghosting,
428
+ constraint: options.constraint,
429
+ handle: options.handle };
430
+
431
+ if(options.starteffect)
432
+ options_for_draggable.starteffect = options.starteffect;
433
+
434
+ if(options.reverteffect)
435
+ options_for_draggable.reverteffect = options.reverteffect;
436
+ else
437
+ if(options.ghosting) options_for_draggable.reverteffect = function(element) {
438
+ element.style.top = 0;
439
+ element.style.left = 0;
440
+ };
441
+
442
+ if(options.endeffect)
443
+ options_for_draggable.endeffect = options.endeffect;
444
+
445
+ if(options.zindex)
446
+ options_for_draggable.zindex = options.zindex;
447
+
448
+ // build options for the droppables
449
+ var options_for_droppable = {
450
+ overlap: options.overlap,
451
+ containment: options.containment,
452
+ hoverclass: options.hoverclass,
453
+ onHover: Sortable.onHover,
454
+ greedy: !options.dropOnEmpty
455
+ }
456
+
457
+ // fix for gecko engine
458
+ Element.cleanWhitespace(element);
459
+
460
+ options.draggables = [];
461
+ options.droppables = [];
462
+
463
+ // make it so
464
+
465
+ // drop on empty handling
466
+ if(options.dropOnEmpty) {
467
+ Droppables.add(element,
468
+ {containment: options.containment, onHover: Sortable.onEmptyHover, greedy: false});
469
+ options.droppables.push(element);
470
+ }
471
+
472
+ (this.findElements(element, options) || []).each( function(e) {
473
+ // handles are per-draggable
474
+ var handle = options.handle ?
475
+ Element.childrenWithClassName(e, options.handle)[0] : e;
476
+ options.draggables.push(
477
+ new Draggable(e, Object.extend(options_for_draggable, { handle: handle })));
478
+ Droppables.add(e, options_for_droppable);
479
+ options.droppables.push(e);
480
+ });
481
+
482
+ // keep reference
483
+ this.sortables.push(options);
484
+
485
+ // for onupdate
486
+ Draggables.addObserver(new SortableObserver(element, options.onUpdate));
487
+
488
+ },
489
+
490
+ // return all suitable-for-sortable elements in a guaranteed order
491
+ findElements: function(element, options) {
492
+ if(!element.hasChildNodes()) return null;
493
+ var elements = [];
494
+ $A(element.childNodes).each( function(e) {
495
+ if(e.tagName && e.tagName.toUpperCase()==options.tag.toUpperCase() &&
496
+ (!options.only || (Element.hasClassName(e, options.only))))
497
+ elements.push(e);
498
+ if(options.tree) {
499
+ var grandchildren = this.findElements(e, options);
500
+ if(grandchildren) elements.push(grandchildren);
501
+ }
502
+ });
503
+
504
+ return (elements.length>0 ? elements.flatten() : null);
505
+ },
506
+
507
+ onHover: function(element, dropon, overlap) {
508
+ if(overlap>0.5) {
509
+ Sortable.mark(dropon, 'before');
510
+ if(dropon.previousSibling != element) {
511
+ var oldParentNode = element.parentNode;
512
+ element.style.visibility = "hidden"; // fix gecko rendering
513
+ dropon.parentNode.insertBefore(element, dropon);
514
+ if(dropon.parentNode!=oldParentNode)
515
+ Sortable.options(oldParentNode).onChange(element);
516
+ Sortable.options(dropon.parentNode).onChange(element);
517
+ }
518
+ } else {
519
+ Sortable.mark(dropon, 'after');
520
+ var nextElement = dropon.nextSibling || null;
521
+ if(nextElement != element) {
522
+ var oldParentNode = element.parentNode;
523
+ element.style.visibility = "hidden"; // fix gecko rendering
524
+ dropon.parentNode.insertBefore(element, nextElement);
525
+ if(dropon.parentNode!=oldParentNode)
526
+ Sortable.options(oldParentNode).onChange(element);
527
+ Sortable.options(dropon.parentNode).onChange(element);
528
+ }
529
+ }
530
+ },
531
+
532
+ onEmptyHover: function(element, dropon) {
533
+ if(element.parentNode!=dropon) {
534
+ var oldParentNode = element.parentNode;
535
+ dropon.appendChild(element);
536
+ Sortable.options(oldParentNode).onChange(element);
537
+ Sortable.options(dropon).onChange(element);
538
+ }
539
+ },
540
+
541
+ unmark: function() {
542
+ if(Sortable._marker) Element.hide(Sortable._marker);
543
+ },
544
+
545
+ mark: function(dropon, position) {
546
+ // mark on ghosting only
547
+ var sortable = Sortable.options(dropon.parentNode);
548
+ if(sortable && !sortable.ghosting) return;
549
+
550
+ if(!Sortable._marker) {
551
+ Sortable._marker = $('dropmarker') || document.createElement('DIV');
552
+ Element.hide(Sortable._marker);
553
+ Element.addClassName(Sortable._marker, 'dropmarker');
554
+ Sortable._marker.style.position = 'absolute';
555
+ document.getElementsByTagName("body").item(0).appendChild(Sortable._marker);
556
+ }
557
+ var offsets = Position.cumulativeOffset(dropon);
558
+ Sortable._marker.style.left = offsets[0] + 'px';
559
+ Sortable._marker.style.top = offsets[1] + 'px';
560
+
561
+ if(position=='after')
562
+ if(sortable.overlap == 'horizontal')
563
+ Sortable._marker.style.left = (offsets[0]+dropon.clientWidth) + 'px';
564
+ else
565
+ Sortable._marker.style.top = (offsets[1]+dropon.clientHeight) + 'px';
566
+
567
+ Element.show(Sortable._marker);
568
+ },
569
+
570
+ serialize: function(element) {
571
+ element = $(element);
572
+ var sortableOptions = this.options(element);
573
+ var options = Object.extend({
574
+ tag: sortableOptions.tag,
575
+ only: sortableOptions.only,
576
+ name: element.id,
577
+ format: sortableOptions.format || /^[^_]*_(.*)$/
578
+ }, arguments[1] || {});
579
+ return $(this.findElements(element, options) || []).map( function(item) {
580
+ return (encodeURIComponent(options.name) + "[]=" +
581
+ encodeURIComponent(item.id.match(options.format) ? item.id.match(options.format)[1] : ''));
582
+ }).join("&");
583
+ }
584
+ }