grnsight 3.0.0 → 5.1.0

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Files changed (489) hide show
  1. package/.eslintignore +1 -0
  2. package/.travis.yml +1 -1
  3. package/GRNsight - Beta.html +194 -0
  4. package/Gemfile.lock +259 -0
  5. package/README.md +1 -1
  6. package/_gh_pages/about.html +360 -45
  7. package/_gh_pages/assets/css/footer.css +3 -0
  8. package/_gh_pages/assets/css/main.css +28 -14
  9. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_estimation_output_binary-no-targetless-genes_sif.png +0 -0
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  25. package/{documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure1_zoom145_900pix-wide.png → _gh_pages/assets/images/demo-3_network-sheet.png} +0 -0
  26. package/{documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure2_zoom145_900pix-wide.png → _gh_pages/assets/images/demo-4_network-optimized-weights-sheet.png} +0 -0
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  88. package/_gh_pages/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_manuscript_2016_text-only_revised-Dondi.docx +0 -0
  89. package/_gh_pages/encryption/server.cert +21 -0
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  109. package/coverage/coverage.json +1 -1
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  145. package/server/app.js +6 -2
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  476. package/test-files/demo-files/21-genes_50-edges_Dahlquist-data_estimation_output.xlsx +0 -0
  477. package/test-files/demo-files/21-genes_50-edges_Dahlquist-data_input.xlsx +0 -0
  478. package/test-files/graph-tests/different-sized-networks/10-genes-max-edges.xlsx +0 -0
  479. package/test-files/graph-tests/different-sized-networks/12-genes-max-edges.xlsx +0 -0
  480. package/test-files/graph-tests/different-sized-networks/35-genes-max-edges.xlsx +0 -0
  481. package/test-files/graph-tests/different-sized-networks/40-genes-0-edges.xlsx +0 -0
  482. package/test-files/graph-tests/different-sized-networks/40-genes-max-edges.xlsx +0 -0
  483. package/test-files/graph-tests/different-sized-networks/42-genes-max-edges.xlsx +0 -0
  484. package/test-files/graph-tests/different-sized-networks/50-genes-max-edges.xlsx +0 -0
  485. package/test-files/graph-tests/different-sized-networks/75-genes-150-edges.xlsx +0 -0
  486. package/web-client/public/js/container.js +0 -121
  487. package/web-client/public/js/node-coloring.js +0 -306
  488. package/web-client/public/js/sliders.js +0 -197
  489. package/web-client/views/upload.jade +0 -458
@@ -0,0 +1,617 @@
1
+ import { updaters } from "./graph";
2
+ import { updateApp, identifySpeciesMenu } from "./update-app";
3
+ import { saveSvgAsPng } from "save-svg-as-png";
4
+ import * as jsPDF from "jspdf";
5
+ import canvg from "canvg";
6
+
7
+ import {
8
+ HOST_SITE,
9
+ FORCE_GRAPH,
10
+ GRID_LAYOUT,
11
+ SET_NORMALIZATION_SIDEBAR,
12
+ SET_NORMALIZATION_SIDEBAR_VALUE,
13
+ SET_NORMALIZATION_MENU,
14
+ RESET_NORMALIZATION_SIDEBAR,
15
+ RESET_NORMALIZATION_MENU,
16
+ GREY_EDGES_DASHED_MENU,
17
+ GREY_EDGES_DASHED_SIDEBAR,
18
+ GREY_EDGE_THRESHOLD_MENU,
19
+ GREY_EDGE_THRESHOLD_SLIDER_SIDEBAR,
20
+ WEIGHTS_SHOW_MOUSE_OVER_CLASS,
21
+ WEIGHTS_SHOW_ALWAYS_CLASS,
22
+ WEIGHTS_HIDE_CLASS,
23
+ SHOW_WEIGHTS_MOUSEOVER,
24
+ SHOW_ALL_WEIGHTS,
25
+ HIDE_ALL_WEIGHTS,
26
+ COLOR_EDGES,
27
+ LINK_DIST_SLIDER_SIDEBAR,
28
+ LINK_DIST_MENU,
29
+ CHARGE_SLIDER_SIDEBAR,
30
+ CHARGE_MENU,
31
+ CHARGE_DEFAULT_VALUE,
32
+ LINK_DIST_DEFAULT_VALUE,
33
+ LOCK_SLIDERS_CLASS,
34
+ RESET_SLIDERS_CLASS,
35
+ UNDO_SLIDERS_RESET_CLASS,
36
+ FORCE_GRAPH_BUTTON,
37
+ FORCE_GRAPH_MENU,
38
+ GRID_LAYOUT_BUTTON,
39
+ GRID_LAYOUT_MENU,
40
+ NODE_COLORING_TOGGLE_CLASS,
41
+ AVG_REPLICATE_VALS_TOP_MENU,
42
+ AVG_REPLICATE_VALS_TOP_SIDEBAR,
43
+ AVG_REPLICATE_VALS_BOTTOM_MENU,
44
+ AVG_REPLICATE_VALS_BOTTOM_SIDEBAR,
45
+ LOG_FOLD_CHANGE_MAX_VALUE_SIDEBAR_BUTTON,
46
+ LOG_FOLD_CHANGE_MAX_VALUE_MENU,
47
+ LOG_FOLD_CHANGE_MAX_VALUE_SIDEBAR_INPUT,
48
+ TOP_DATASET_SELECTION_SIDEBAR,
49
+ BOTTOM_DATASET_SELECTION_SIDEBAR,
50
+ TOP_DATASET_SELECTION_MENU,
51
+ BOTTOM_DATASET_SELECTION_MENU,
52
+ ZOOM_DISPLAY_MAXIMUM_SELECTOR,
53
+ ZOOM_DISPLAY_MAXIMUM_VALUE,
54
+ ZOOM_DISPLAY_MINIMUM_SELECTOR,
55
+ ZOOM_DISPLAY_MINIMUM_VALUE,
56
+ EXPORT_TO_PNG,
57
+ EXPORT_TO_SVG,
58
+ EXPORT_TO_PDF,
59
+ SPECIES_DISPLAY,
60
+ SPECIES_BUTTON_CRESS,
61
+ SPECIES_BUTTON_FLY,
62
+ SPECIES_BUTTON_HUMAN,
63
+ SPECIES_BUTTON_MOUSE,
64
+ SPECIES_BUTTON_NEMATODE,
65
+ SPECIES_BUTTON_YEAST,
66
+ VIEWPORT_FIT,
67
+ VIEWPORT_INIT,
68
+ VIEWPORT_OPTION_CLASS,
69
+ VIEWPORT_OPTION_CLASS_SIDEBAR
70
+ } from "./constants";
71
+
72
+ import { setupLoadAndImportHandlers } from "./setup-load-and-import-handlers";
73
+
74
+ export const setupHandlers = grnState => {
75
+ setupLoadAndImportHandlers(grnState);
76
+
77
+ var valueValidator = (min, max, value) => {
78
+ return Math.min(max, Math.max(min, value));
79
+ };
80
+
81
+ const determineFileType = filename => {
82
+ if (filename.includes(".xlsx")) {
83
+ return ".xlsx";
84
+ } else if (filename.includes(".sif")) {
85
+ return ".sif";
86
+ } else if (filename.includes(".graphml")) {
87
+ return ".graphml";
88
+ }
89
+ };
90
+
91
+ // thank you for the help https://github.com/nytimes/svg-crowbar/blob/gh-pages/svg-crowbar-2.js
92
+ const setInlineStyles = (svg) => {
93
+ var emptySvg = window.document.createElementNS("http://www.w3.org/2000/svg", "svg");
94
+ window.document.body.appendChild(emptySvg);
95
+ var emptySvgDeclarationComputed = getComputedStyle(emptySvg);
96
+
97
+ const traverse = svg => {
98
+ var tree = [];
99
+ tree.push(svg);
100
+ // implement DFS
101
+ const visit = (node) => {
102
+ if (node && node.hasChildNodes()) {
103
+ var child = node.firstChild;
104
+ while (child) {
105
+ if (child.nodeType === 1 && child.nodeName !== "SCRIPT") {
106
+ tree.push(child);
107
+ visit(child);
108
+ }
109
+ child = child.nextSibling;
110
+ }
111
+ }
112
+ };
113
+ visit(svg);
114
+ return tree;
115
+ };
116
+
117
+ const explicitlySetStyle = element => {
118
+ const cSSStyleDeclarationComputed = window.getComputedStyle(element);
119
+ let i;
120
+ let len;
121
+ let key;
122
+ let value;
123
+ let computedStyleStr = "";
124
+
125
+ for (i = 0, len = cSSStyleDeclarationComputed.length; i < len; i++) {
126
+ key = cSSStyleDeclarationComputed[i];
127
+ value = cSSStyleDeclarationComputed.getPropertyValue(key);
128
+ if (value !== emptySvgDeclarationComputed.getPropertyValue(key)) {
129
+ // Don't set computed style of width and height. Makes SVG elmements disappear.
130
+ if ((key !== "height") && (key !== "width")) {
131
+ computedStyleStr += key + ":" + value + ";";
132
+ }
133
+
134
+ }
135
+ }
136
+ element.setAttribute("style", computedStyleStr);
137
+ };
138
+
139
+ // hardcode computed css styles inside svg
140
+ var allElements = traverse(svg);
141
+ var i = allElements.length;
142
+ while (i--) {
143
+ explicitlySetStyle(allElements[i]);
144
+ }
145
+ };
146
+
147
+ const sourceAttributeSetter = (svg) => {
148
+ svg.setAttribute("version", "1.1");
149
+
150
+ svg.removeAttribute("xmlns");
151
+ svg.removeAttribute("xlink");
152
+
153
+ if (!svg.hasAttributeNS("http://www.w3.org/2000/xmlns/", "xmlns")) {
154
+ svg.setAttributeNS("http://www.w3.org/2000/xmlns/", "xmlns", "http://www.w3.org/2000/svg");
155
+ }
156
+
157
+ if (!svg.hasAttributeNS("http://www.w3.org/2000/xmlns/", "xmlns:xlink")) {
158
+ svg.setAttributeNS("http://www.w3.org/2000/xmlns/", "xmlns:xlink", "http://www.w3.org/1999/xlink");
159
+ }
160
+ };
161
+
162
+ const exportSVG = (svgElement, name) => {
163
+ let source = svgElement;
164
+
165
+ sourceAttributeSetter(source);
166
+ setInlineStyles(source);
167
+
168
+ var doctype = "<?xml version=\"1.0\" standalone=\"no\"?><!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\" \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">"; // eslint-disable-line
169
+ var sourceString = (new XMLSerializer()).serializeToString(source);
170
+ const finalSvgString = [doctype + sourceString];
171
+
172
+ var svgUrl = window.URL.createObjectURL(new Blob(finalSvgString, { "type" : "image\/svg+xml" }));
173
+
174
+ $("#exportAsSvg").attr("href", svgUrl);
175
+ $("#exportAsSvg").attr("download", name);
176
+ };
177
+
178
+ const exportPDF = (svgElement, name) => {
179
+ if (svgElement) {
180
+ svgElement = svgElement.replace(/\r?\n|\r/g, "").trim();
181
+ }
182
+
183
+ let canvas = document.createElement("canvas");
184
+ canvg(canvas, svgElement);
185
+ const imgData = canvas.toDataURL("image/png");
186
+
187
+ const pdf = new jsPDF("l", "mm", "letter");
188
+ const width = pdf.internal.pageSize.getWidth();
189
+ const height = pdf.internal.pageSize.getHeight();
190
+
191
+ pdf.addImage(imgData, "PNG", 0, 0, width, height);
192
+ pdf.save(name);
193
+ };
194
+
195
+ // Grid and Force Graph Layout
196
+ $(`${FORCE_GRAPH_MENU}, ${FORCE_GRAPH_BUTTON}`).click(() => {
197
+ updaters.setNodesToForceGraph();
198
+ grnState.graphLayout = FORCE_GRAPH;
199
+ updateApp(grnState);
200
+ });
201
+
202
+ $(`${GRID_LAYOUT_MENU}, ${GRID_LAYOUT_BUTTON}`).click(() => {
203
+ updaters.setNodesToGrid();
204
+ grnState.graphLayout = GRID_LAYOUT;
205
+ updateApp(grnState);
206
+ });
207
+
208
+ // Image Export
209
+ $(EXPORT_TO_PNG).click(() => {
210
+ var svgContainer = document.getElementById("exportContainer");
211
+ var editedName = grnState.name.replace(determineFileType(grnState.name), "") + ".png";
212
+ saveSvgAsPng(svgContainer, editedName);
213
+ });
214
+
215
+ $(EXPORT_TO_SVG).click(() => {
216
+ var svgContainer = document.getElementById("exportContainer");
217
+ var editedName = grnState.name.replace(determineFileType(grnState.name), "") + ".svg";
218
+ exportSVG(svgContainer, editedName );
219
+ });
220
+
221
+ $(EXPORT_TO_PDF).click(() => {
222
+ var svgContainer = document.getElementById("exportContainer").innerHTML;
223
+ var editedName = grnState.name.replace(determineFileType(grnState.name), "") + ".pdf";
224
+ exportPDF(svgContainer, editedName);
225
+ });
226
+
227
+ // Node Coloring
228
+ $(NODE_COLORING_TOGGLE_CLASS).click(() => {
229
+ grnState.nodeColoring.nodeColoringEnabled = !grnState.nodeColoring.nodeColoringEnabled;
230
+ updateApp(grnState);
231
+ });
232
+
233
+ $(TOP_DATASET_SELECTION_SIDEBAR).change(() => {
234
+ var selection = $(TOP_DATASET_SELECTION_SIDEBAR).find(":selected").attr("value");
235
+ grnState.nodeColoring.topDataset = selection;
236
+ if (grnState.nodeColoring.bottomDataSameAsTop) {
237
+ grnState.nodeColoring.bottomDataset = selection;
238
+ }
239
+ updateApp(grnState);
240
+ });
241
+
242
+ $(TOP_DATASET_SELECTION_MENU).click(() => {
243
+ var selection = $(this).attr("value");
244
+ grnState.nodeColoring.topDataset = selection;
245
+ if (grnState.nodeColoring.bottomDataSameAsTop) {
246
+ grnState.nodeColoring.bottomDataset = selection;
247
+ }
248
+ updateApp(grnState);
249
+ });
250
+
251
+ $(AVG_REPLICATE_VALS_TOP_SIDEBAR).change(() => {
252
+ grnState.nodeColoring.averageTopDataset = !grnState.nodeColoring.averageTopDataset;
253
+ updateApp(grnState);
254
+ });
255
+
256
+ $(AVG_REPLICATE_VALS_TOP_MENU).click(() => {
257
+ grnState.nodeColoring.averageTopDataset = !grnState.nodeColoring.averageTopDataset;
258
+ updateApp(grnState);
259
+ });
260
+
261
+ $(BOTTOM_DATASET_SELECTION_SIDEBAR).change(() => {
262
+ var selection = $(BOTTOM_DATASET_SELECTION_SIDEBAR).find(":selected").attr("value");
263
+ grnState.nodeColoring.bottomDataset = selection;
264
+ if (grnState.nodeColoring.bottomDataset === "Same as Top Dataset") {
265
+ grnState.nodeColoring.bottomDataset = grnState.nodeColoring.topDataset;
266
+ grnState.nodeColoring.bottomDataSameAsTop = true;
267
+ } else {
268
+ grnState.nodeColoring.bottomDataSameAsTop = false;
269
+ }
270
+ updateApp(grnState);
271
+ });
272
+
273
+ $(BOTTOM_DATASET_SELECTION_MENU).click(() => {
274
+ var selection = $(this).attr("value");
275
+ grnState.nodeColoring.bottomDataset = selection;
276
+ if (selection === "Same as Top Dataset") {
277
+ grnState.nodeColoring.bottomDataset = grnState.nodeColoring.topDataset;
278
+ grnState.nodeColoring.bottomDataSameAsTop = true;
279
+ } else {
280
+ grnState.nodeColoring.bottomDataSameAsTop = false;
281
+ grnState.nodeColoring.bottomDataset = selection;
282
+ }
283
+ updateApp(grnState);
284
+ });
285
+
286
+ $(AVG_REPLICATE_VALS_BOTTOM_SIDEBAR).change(() => {
287
+ grnState.nodeColoring.averageBottomDataset = !grnState.nodeColoring.averageBottomDataset;
288
+ updateApp(grnState);
289
+ });
290
+
291
+ $(AVG_REPLICATE_VALS_BOTTOM_MENU).click(() => {
292
+ grnState.nodeColoring.averageBottomDataset = !grnState.nodeColoring.averageBottomDataset;
293
+ updateApp(grnState);
294
+ });
295
+
296
+ var logFoldChangeMaxValueValidator = value => {
297
+ return valueValidator(0.01, 100, value);
298
+ };
299
+
300
+ $(LOG_FOLD_CHANGE_MAX_VALUE_SIDEBAR_BUTTON).click(() => {
301
+ var value = logFoldChangeMaxValueValidator($(LOG_FOLD_CHANGE_MAX_VALUE_SIDEBAR_INPUT).val());
302
+ grnState.nodeColoring.logFoldChangeMaxValue = value;
303
+ updateApp(grnState);
304
+ });
305
+
306
+ $(LOG_FOLD_CHANGE_MAX_VALUE_MENU).change(() => {
307
+ var value = logFoldChangeMaxValueValidator($(LOG_FOLD_CHANGE_MAX_VALUE_MENU).val());
308
+ grnState.nodeColoring.logFoldChangeMaxValue = value;
309
+ updateApp(grnState);
310
+ });
311
+
312
+ // Sliders Code
313
+ var linkDistValidator = value => {
314
+ return valueValidator(1, 1000, value);
315
+ };
316
+
317
+ var chargeValidator = value => {
318
+ return valueValidator(-2000, 0, value);
319
+ };
320
+
321
+ $(LINK_DIST_SLIDER_SIDEBAR).change(() => {
322
+ var value = linkDistValidator($(LINK_DIST_SLIDER_SIDEBAR).val());
323
+ grnState.linkDistanceSlider.currentVal = value;
324
+ updateApp(grnState);
325
+ });
326
+
327
+ $(LINK_DIST_MENU).change(() => {
328
+ var value = linkDistValidator($(LINK_DIST_MENU).val());
329
+ grnState.linkDistanceSlider.currentVal = value;
330
+ updateApp(grnState);
331
+ });
332
+
333
+ $(CHARGE_SLIDER_SIDEBAR).change(() => {
334
+ var value = chargeValidator($(CHARGE_SLIDER_SIDEBAR).val());
335
+ grnState.chargeSlider.currentVal = value;
336
+ updateApp(grnState);
337
+ });
338
+
339
+ $(CHARGE_MENU).change(() => {
340
+ var value = chargeValidator($(CHARGE_MENU).val());
341
+ grnState.chargeSlider.currentVal = value;
342
+ updateApp(grnState);
343
+ });
344
+
345
+ $(LOCK_SLIDERS_CLASS).click(() => {
346
+ grnState.slidersLocked = !grnState.slidersLocked;
347
+ if (grnState.slidersLocked) {
348
+ grnState.showUndoReset = false;
349
+ }
350
+ updateApp(grnState);
351
+ });
352
+
353
+ $(VIEWPORT_OPTION_CLASS_SIDEBAR).click(function () {
354
+ grnState.viewportSize = $(this).val();
355
+ updateApp(grnState);
356
+ });
357
+
358
+ $(VIEWPORT_OPTION_CLASS).click(function () {
359
+ grnState.viewportSize = $(this).attr("value");
360
+ updateApp(grnState);
361
+ });
362
+
363
+ $(RESET_SLIDERS_CLASS).click(() => {
364
+ grnState.chargeSlider.backup = grnState.chargeSlider.currentVal;
365
+ grnState.linkDistanceSlider.backup = grnState.linkDistanceSlider.currentVal;
366
+ grnState.chargeSlider.currentVal = CHARGE_DEFAULT_VALUE;
367
+ grnState.linkDistanceSlider.currentVal = LINK_DIST_DEFAULT_VALUE;
368
+ grnState.showUndoReset = true;
369
+ updateApp(grnState);
370
+ });
371
+
372
+ $(UNDO_SLIDERS_RESET_CLASS).click(() => {
373
+ grnState.chargeSlider.currentVal = grnState.chargeSlider.backup;
374
+ grnState.linkDistanceSlider.currentVal = grnState.linkDistanceSlider.backup;
375
+ grnState.showUndoReset = false;
376
+ updateApp(grnState);
377
+ });
378
+
379
+ // Weights Visualization
380
+ $(WEIGHTS_SHOW_ALWAYS_CLASS).click(() => {
381
+ grnState.edgeWeightDisplayOption = SHOW_ALL_WEIGHTS;
382
+ updateApp(grnState);
383
+ });
384
+
385
+ $(WEIGHTS_HIDE_CLASS).click(() => {
386
+ grnState.edgeWeightDisplayOption = HIDE_ALL_WEIGHTS;
387
+ updateApp(grnState);
388
+ });
389
+
390
+ // Normalization Options
391
+ $(SET_NORMALIZATION_SIDEBAR).click(() => {
392
+ grnState.normalizationMax = $(SET_NORMALIZATION_SIDEBAR_VALUE).val();
393
+ updateApp(grnState);
394
+ });
395
+
396
+ $(SET_NORMALIZATION_MENU).change(() => {
397
+ grnState.normalizationMax = $(SET_NORMALIZATION_MENU).val();
398
+ updateApp(grnState);
399
+ });
400
+
401
+ $(RESET_NORMALIZATION_SIDEBAR).click(() => {
402
+ grnState.normalizationMax = grnState.resetNormalizationMax;
403
+ updateApp(grnState);
404
+ });
405
+
406
+ $(RESET_NORMALIZATION_MENU).click(() => {
407
+ grnState.normalizationMax = grnState.resetNormalizationMax;
408
+ updateApp(grnState);
409
+ });
410
+
411
+ // Grey Edges
412
+ $(GREY_EDGES_DASHED_SIDEBAR).change(() => {
413
+ grnState.dashedLine = $(GREY_EDGES_DASHED_SIDEBAR).prop("checked");
414
+ updateApp(grnState);
415
+ });
416
+
417
+ $(GREY_EDGES_DASHED_MENU).click(() => {
418
+ grnState.dashedLine = !$(GREY_EDGES_DASHED_MENU).prop("checked");
419
+ updateApp(grnState);
420
+ });
421
+
422
+ $(GREY_EDGE_THRESHOLD_MENU).change(() => {
423
+ grnState.grayEdgeThreshold = Math.round($(GREY_EDGE_THRESHOLD_MENU).val());
424
+ updateApp(grnState);
425
+ });
426
+
427
+ $(GREY_EDGE_THRESHOLD_SLIDER_SIDEBAR).change(() => {
428
+ grnState.grayEdgeThreshold = Math.round($(GREY_EDGE_THRESHOLD_SLIDER_SIDEBAR).val() * 100);
429
+ updateApp(grnState);
430
+ });
431
+
432
+ $(WEIGHTS_SHOW_MOUSE_OVER_CLASS).click(() => {
433
+ grnState.edgeWeightDisplayOption = SHOW_WEIGHTS_MOUSEOVER;
434
+ updateApp(grnState);
435
+ });
436
+
437
+ $(COLOR_EDGES).click(() => {
438
+ grnState.colorOptimal = !grnState.colorOptimal;
439
+ updateApp(grnState);
440
+ });
441
+
442
+ // Species Selection
443
+ $(SPECIES_DISPLAY).change(() => {
444
+ var selection = $(SPECIES_DISPLAY).find(":selected").attr("value");
445
+ grnState.genePageData.identified = false;
446
+ identifySpeciesMenu(selection);
447
+ updateApp(grnState);
448
+ });
449
+
450
+ $(SPECIES_BUTTON_YEAST).click(function () {
451
+ var selection = $(SPECIES_BUTTON_YEAST).attr("id");
452
+ grnState.genePageData.identified = false;
453
+ identifySpeciesMenu(selection);
454
+ updateApp(grnState);
455
+ });
456
+
457
+ $(SPECIES_BUTTON_MOUSE).click(function () {
458
+ var selection = $(SPECIES_BUTTON_MOUSE).attr("id");
459
+ grnState.genePageData.identified = false;
460
+ identifySpeciesMenu(selection);
461
+ updateApp(grnState);
462
+ });
463
+
464
+ $(SPECIES_BUTTON_HUMAN).click(function () {
465
+ var selection = $(SPECIES_BUTTON_HUMAN).attr("id");
466
+ grnState.genePageData.identified = false;
467
+ identifySpeciesMenu(selection);
468
+ updateApp(grnState);
469
+ });
470
+
471
+ $(SPECIES_BUTTON_NEMATODE).click(function () {
472
+ var selection = $(SPECIES_BUTTON_NEMATODE).attr("id");
473
+ grnState.genePageData.identified = false;
474
+ identifySpeciesMenu(selection);
475
+ updateApp(grnState);
476
+ });
477
+
478
+ $(SPECIES_BUTTON_CRESS).click(function () {
479
+ var selection = $(SPECIES_BUTTON_CRESS).attr("id");
480
+ grnState.genePageData.identified = false;
481
+ identifySpeciesMenu(selection);
482
+ updateApp(grnState);
483
+ });
484
+
485
+ $(SPECIES_BUTTON_FLY).click(function () {
486
+ var selection = $(SPECIES_BUTTON_FLY).attr("id");
487
+ grnState.genePageData.identified = false;
488
+ identifySpeciesMenu(selection);
489
+ updateApp(grnState);
490
+ });
491
+
492
+ // Allow text-selection for input elements embedded within menu items.
493
+ //
494
+ // Partial thank you:
495
+ // https://stackoverflow.com/questions/6848140/how-do-i-prevent-drag-on-a-child-but-allow-drag-on-the-parent
496
+ //
497
+ // We use function syntax so that internal `this` can be used.
498
+ $(".dropdown input.keepopen").parent().attr({
499
+ draggable: false
500
+ });
501
+
502
+ // Prevent Bootstrap dropdown from closing on clicks in menu input boxes
503
+ // https://stackoverflow.com/a/27759926
504
+ $(".dropdown").on({
505
+ "click": function (event) {
506
+ if ($(event.target).hasClass("keepopen")) {
507
+ $(this).data("closable", $(event.target).closest(".dropdown-toggle").length !== 0);
508
+ }
509
+ },
510
+
511
+ "mouseup": function (event) {
512
+ if ($(event.target).find(".keepopen").length > 0) {
513
+ $(this).data("closable", $(event.target).closest(".dropdown-toggle").length !== 0);
514
+ }
515
+ },
516
+
517
+ "hide.bs.dropdown": function () {
518
+ var hide = $(this).data("closable");
519
+ $(this).data("closable", true);
520
+ return hide;
521
+ }
522
+ });
523
+
524
+ $(ZOOM_DISPLAY_MAXIMUM_SELECTOR).text(ZOOM_DISPLAY_MAXIMUM_VALUE);
525
+ $(ZOOM_DISPLAY_MINIMUM_SELECTOR).text(ZOOM_DISPLAY_MINIMUM_VALUE);
526
+
527
+ // Viewport handling.
528
+ const setupContainer = function () {
529
+ const MEDIUM_PAGE_WIDTH = 1500;
530
+ const LARGE_PAGE_WIDTH = 2200;
531
+
532
+ const initializeViewportSize = (width) => {
533
+ if (width < MEDIUM_PAGE_WIDTH) {
534
+ grnState.viewportSize = "containerS";
535
+ } else if (width > MEDIUM_PAGE_WIDTH && width < LARGE_PAGE_WIDTH) {
536
+ grnState.viewportSize = "containerM";
537
+ } else {
538
+ grnState.viewportSize = "containerL";
539
+ }
540
+ };
541
+
542
+ // For viewport-fit, we create a transient `dimensions` property in `grnState`
543
+ // which `updateApp` will use to determine the latest size.
544
+ //
545
+ // For any other size, we blank out the transient `dimensions`.
546
+ if (window === window.top) {
547
+ initializeViewportSize($(window).width());
548
+ $(window).on("resize", () => {
549
+ if (grnState.viewportSize === VIEWPORT_FIT) {
550
+ grnState.dimensions = {
551
+ width: $(window).width(),
552
+ height: $(window).height(),
553
+ top: 0
554
+ };
555
+
556
+ updateApp(grnState);
557
+ } else {
558
+ delete grnState.dimensions;
559
+ }
560
+ });
561
+ } else {
562
+ window.addEventListener("message", event => {
563
+ if (event.origin.indexOf(HOST_SITE) !== 0) {
564
+ return;
565
+ }
566
+
567
+ // Also filter out all but dimensions messages.
568
+ const { data } = event;
569
+ if (typeof(data) !== "object" || (
570
+ data.width === undefined ||
571
+ data.height === undefined ||
572
+ data.top === undefined
573
+ )) {
574
+ return;
575
+ }
576
+
577
+ // Live changes only matter if we are doing Fit to Window or initializing.
578
+ if ([VIEWPORT_FIT, VIEWPORT_INIT].includes(grnState.viewportSize)) {
579
+ if (grnState.viewportSize === VIEWPORT_INIT) {
580
+ initializeViewportSize(data.width);
581
+ }
582
+
583
+ if (grnState.viewportSize === VIEWPORT_FIT) {
584
+ grnState.dimensions = data;
585
+ }
586
+
587
+ updateApp(grnState);
588
+ } else {
589
+ delete grnState.dimensions;
590
+ }
591
+ });
592
+ }
593
+
594
+ $("#restrict-graph-to-viewport").on("click", function () {
595
+ if ($(".viewport").prop("checked")) {
596
+ $("#restrict-graph-to-viewport span").removeClass("glyphicon-ok");
597
+ $(".viewport").prop("checked", false);
598
+ $(".viewport").trigger("change");
599
+ } else {
600
+ $("#restrict-graph-to-viewport span").addClass("glyphicon-ok");
601
+ $(".viewport").prop("checked", true).trigger("change");
602
+ }
603
+ });
604
+
605
+ $("#expressionDB").on("click", function () {
606
+ if (!$("#expressionDB span").hasClass("glyphicon-ok")) {
607
+ $("#expressionDB span").addClass("glyphicon-ok");
608
+ $("#expressionDB").trigger("change");
609
+ } else {
610
+ $("#expressionDB span").removeClass("glyphicon-ok");
611
+ $("#expressionDB").trigger("change");
612
+ }
613
+ });
614
+ };
615
+
616
+ setupContainer();
617
+ };