@jbrowse/core 2.1.4 → 2.1.5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (32) hide show
  1. package/BaseFeatureWidget/BaseFeatureDetail.d.ts +2 -2
  2. package/BaseFeatureWidget/BaseFeatureDetail.js +2 -2
  3. package/BaseFeatureWidget/SequenceFeatureDetails.d.ts +6 -3
  4. package/BaseFeatureWidget/SequenceFeatureDetails.js +74 -34
  5. package/BaseFeatureWidget/SequenceFeatureSettingsDialog.d.ts +9 -0
  6. package/BaseFeatureWidget/SequenceFeatureSettingsDialog.js +71 -0
  7. package/BaseFeatureWidget/test_data/DLGAP3.d.ts +80 -0
  8. package/BaseFeatureWidget/test_data/DLGAP3.js +585 -0
  9. package/BaseFeatureWidget/test_data/NCDN.d.ts +141 -0
  10. package/BaseFeatureWidget/test_data/NCDN.js +1118 -0
  11. package/BaseFeatureWidget/types.d.ts +2 -2
  12. package/BaseFeatureWidget/util.d.ts +2 -2
  13. package/PluginManager.d.ts +3 -3
  14. package/PluginManager.js +7 -5
  15. package/assemblyManager/assemblyManager.js +2 -1
  16. package/package.json +2 -2
  17. package/pluggableElementTypes/ViewType.d.ts +2 -0
  18. package/pluggableElementTypes/ViewType.js +1 -0
  19. package/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +7 -5
  20. package/pluggableElementTypes/models/BaseConnectionModelFactory.js +3 -2
  21. package/tsconfig.build.tsbuildinfo +1 -1
  22. package/ui/App.d.ts +1 -1
  23. package/ui/App.js +49 -42
  24. package/ui/DrawerWidget.js +4 -1
  25. package/ui/theme.d.ts +18 -171
  26. package/ui/theme.js +17 -20
  27. package/util/calculateStaticBlocks.js +3 -8
  28. package/util/index.d.ts +1 -1
  29. package/util/index.js +29 -10
  30. package/util/simpleFeature.d.ts +1 -2
  31. package/util/types/index.d.ts +1 -1
  32. package/util/types/index.js +3 -1
package/BaseFeatureWidget/test_data/DLGAP3.js ADDED
@@ -0,0 +1,585 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.default = {
4
+ source: 'BestRefSeq',
5
+ type: 'gene',
6
+ start: 35331036,
7
+ end: 35395251,
8
+ strand: -1,
9
+ phase: 0,
10
+ refName: 'NC_000001.10',
11
+ id: 'gene625',
12
+ dbxref: ['GeneID:58512', 'HGNC:HGNC:30368', 'MIM:611413'],
13
+ name: 'DLGAP3',
14
+ description: 'DLG associated protein 3',
15
+ gbkey: 'Gene',
16
+ gene: 'DLGAP3',
17
+ gene_biotype: 'protein_coding',
18
+ gene_synonym: ['DAP3', 'SAPAP3'],
19
+ subfeatures: [
20
+ {
21
+ source: 'BestRefSeq',
22
+ type: 'mRNA',
23
+ start: 35331036,
24
+ end: 35395251,
25
+ strand: -1,
26
+ phase: 0,
27
+ refName: 'NC_000001.10',
28
+ id: 'mRNA1315',
29
+ parent: 'gene625',
30
+ dbxref: [
31
+ 'GeneID:58512',
32
+ 'Genbank:NM_001080418.3',
33
+ 'HGNC:HGNC:30368',
34
+ 'MIM:611413',
35
+ ],
36
+ name: 'NM_001080418.3',
37
+ gbkey: 'mRNA',
38
+ gene: 'DLGAP3',
39
+ product: 'DLG associated protein 3',
40
+ tag: 'RefSeq Select',
41
+ transcript_id: 'NM_001080418.3',
42
+ subfeatures: [
43
+ {
44
+ source: 'BestRefSeq',
45
+ type: 'exon',
46
+ start: 35331036,
47
+ end: 35331902,
48
+ strand: -1,
49
+ phase: 0,
50
+ refName: 'NC_000001.10',
51
+ parent: 'mRNA1315',
52
+ dbxref: [
53
+ 'GeneID:58512',
54
+ 'Genbank:NM_001080418.3',
55
+ 'HGNC:HGNC:30368',
56
+ 'MIM:611413',
57
+ ],
58
+ gbkey: 'mRNA',
59
+ gene: 'DLGAP3',
60
+ product: 'DLG associated protein 3',
61
+ tag: 'RefSeq Select',
62
+ transcript_id: 'NM_001080418.3',
63
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-0',
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+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
65
+ },
66
+ {
67
+ source: 'BestRefSeq',
68
+ type: 'CDS',
69
+ start: 35331683,
70
+ end: 35331902,
71
+ strand: -1,
72
+ phase: 0,
73
+ refName: 'NC_000001.10',
74
+ id: 'CDS1270',
75
+ parent: 'mRNA1315',
76
+ dbxref: [
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+ 'CCDS:CCDS30670.1',
78
+ 'GeneID:58512',
79
+ 'Genbank:NP_001073887.1',
80
+ 'HGNC:HGNC:30368',
81
+ 'MIM:611413',
82
+ ],
83
+ name: 'NP_001073887.1',
84
+ gbkey: 'CDS',
85
+ gene: 'DLGAP3',
86
+ product: 'disks large-associated protein 3',
87
+ protein_id: 'NP_001073887.1',
88
+ tag: 'RefSeq Select',
89
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-1',
90
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
91
+ },
92
+ {
93
+ source: 'BestRefSeq',
94
+ type: 'CDS',
95
+ start: 35332648,
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+ end: 35332792,
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+ strand: -1,
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+ phase: 0,
99
+ refName: 'NC_000001.10',
100
+ id: 'CDS1270',
101
+ parent: 'mRNA1315',
102
+ dbxref: [
103
+ 'CCDS:CCDS30670.1',
104
+ 'GeneID:58512',
105
+ 'Genbank:NP_001073887.1',
106
+ 'HGNC:HGNC:30368',
107
+ 'MIM:611413',
108
+ ],
109
+ name: 'NP_001073887.1',
110
+ gbkey: 'CDS',
111
+ gene: 'DLGAP3',
112
+ product: 'disks large-associated protein 3',
113
+ protein_id: 'NP_001073887.1',
114
+ tag: 'RefSeq Select',
115
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-2',
116
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
117
+ },
118
+ {
119
+ source: 'BestRefSeq',
120
+ type: 'CDS',
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+ start: 35333136,
122
+ end: 35333228,
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+ strand: -1,
124
+ phase: 2,
125
+ refName: 'NC_000001.10',
126
+ id: 'CDS1270',
127
+ parent: 'mRNA1315',
128
+ dbxref: [
129
+ 'CCDS:CCDS30670.1',
130
+ 'GeneID:58512',
131
+ 'Genbank:NP_001073887.1',
132
+ 'HGNC:HGNC:30368',
133
+ 'MIM:611413',
134
+ ],
135
+ name: 'NP_001073887.1',
136
+ gbkey: 'CDS',
137
+ gene: 'DLGAP3',
138
+ product: 'disks large-associated protein 3',
139
+ protein_id: 'NP_001073887.1',
140
+ tag: 'RefSeq Select',
141
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-3',
142
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
143
+ },
144
+ {
145
+ source: 'BestRefSeq',
146
+ type: 'CDS',
147
+ start: 35334205,
148
+ end: 35334690,
149
+ strand: -1,
150
+ phase: 1,
151
+ refName: 'NC_000001.10',
152
+ id: 'CDS1270',
153
+ parent: 'mRNA1315',
154
+ dbxref: [
155
+ 'CCDS:CCDS30670.1',
156
+ 'GeneID:58512',
157
+ 'Genbank:NP_001073887.1',
158
+ 'HGNC:HGNC:30368',
159
+ 'MIM:611413',
160
+ ],
161
+ name: 'NP_001073887.1',
162
+ gbkey: 'CDS',
163
+ gene: 'DLGAP3',
164
+ product: 'disks large-associated protein 3',
165
+ protein_id: 'NP_001073887.1',
166
+ tag: 'RefSeq Select',
167
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-4',
168
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
169
+ },
170
+ {
171
+ source: 'BestRefSeq',
172
+ type: 'CDS',
173
+ start: 35350578,
174
+ end: 35350664,
175
+ strand: -1,
176
+ phase: 0,
177
+ refName: 'NC_000001.10',
178
+ id: 'CDS1270',
179
+ parent: 'mRNA1315',
180
+ dbxref: [
181
+ 'CCDS:CCDS30670.1',
182
+ 'GeneID:58512',
183
+ 'Genbank:NP_001073887.1',
184
+ 'HGNC:HGNC:30368',
185
+ 'MIM:611413',
186
+ ],
187
+ name: 'NP_001073887.1',
188
+ gbkey: 'CDS',
189
+ gene: 'DLGAP3',
190
+ product: 'disks large-associated protein 3',
191
+ protein_id: 'NP_001073887.1',
192
+ tag: 'RefSeq Select',
193
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-5',
194
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
195
+ },
196
+ {
197
+ source: 'BestRefSeq',
198
+ type: 'CDS',
199
+ start: 35351078,
200
+ end: 35351392,
201
+ strand: -1,
202
+ phase: 2,
203
+ refName: 'NC_000001.10',
204
+ id: 'CDS1270',
205
+ parent: 'mRNA1315',
206
+ dbxref: [
207
+ 'CCDS:CCDS30670.1',
208
+ 'GeneID:58512',
209
+ 'Genbank:NP_001073887.1',
210
+ 'HGNC:HGNC:30368',
211
+ 'MIM:611413',
212
+ ],
213
+ name: 'NP_001073887.1',
214
+ gbkey: 'CDS',
215
+ gene: 'DLGAP3',
216
+ product: 'disks large-associated protein 3',
217
+ protein_id: 'NP_001073887.1',
218
+ tag: 'RefSeq Select',
219
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-6',
220
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
221
+ },
222
+ {
223
+ source: 'BestRefSeq',
224
+ type: 'CDS',
225
+ start: 35351672,
226
+ end: 35351886,
227
+ strand: -1,
228
+ phase: 0,
229
+ refName: 'NC_000001.10',
230
+ id: 'CDS1270',
231
+ parent: 'mRNA1315',
232
+ dbxref: [
233
+ 'CCDS:CCDS30670.1',
234
+ 'GeneID:58512',
235
+ 'Genbank:NP_001073887.1',
236
+ 'HGNC:HGNC:30368',
237
+ 'MIM:611413',
238
+ ],
239
+ name: 'NP_001073887.1',
240
+ gbkey: 'CDS',
241
+ gene: 'DLGAP3',
242
+ product: 'disks large-associated protein 3',
243
+ protein_id: 'NP_001073887.1',
244
+ tag: 'RefSeq Select',
245
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-7',
246
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
247
+ },
248
+ {
249
+ source: 'BestRefSeq',
250
+ type: 'CDS',
251
+ start: 35365269,
252
+ end: 35365342,
253
+ strand: -1,
254
+ phase: 1,
255
+ refName: 'NC_000001.10',
256
+ id: 'CDS1270',
257
+ parent: 'mRNA1315',
258
+ dbxref: [
259
+ 'CCDS:CCDS30670.1',
260
+ 'GeneID:58512',
261
+ 'Genbank:NP_001073887.1',
262
+ 'HGNC:HGNC:30368',
263
+ 'MIM:611413',
264
+ ],
265
+ name: 'NP_001073887.1',
266
+ gbkey: 'CDS',
267
+ gene: 'DLGAP3',
268
+ product: 'disks large-associated protein 3',
269
+ protein_id: 'NP_001073887.1',
270
+ tag: 'RefSeq Select',
271
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-8',
272
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
273
+ },
274
+ {
275
+ source: 'BestRefSeq',
276
+ type: 'CDS',
277
+ start: 35365668,
278
+ end: 35365874,
279
+ strand: -1,
280
+ phase: 0,
281
+ refName: 'NC_000001.10',
282
+ id: 'CDS1270',
283
+ parent: 'mRNA1315',
284
+ dbxref: [
285
+ 'CCDS:CCDS30670.1',
286
+ 'GeneID:58512',
287
+ 'Genbank:NP_001073887.1',
288
+ 'HGNC:HGNC:30368',
289
+ 'MIM:611413',
290
+ ],
291
+ name: 'NP_001073887.1',
292
+ gbkey: 'CDS',
293
+ gene: 'DLGAP3',
294
+ product: 'disks large-associated protein 3',
295
+ protein_id: 'NP_001073887.1',
296
+ tag: 'RefSeq Select',
297
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-9',
298
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
299
+ },
300
+ {
301
+ source: 'BestRefSeq',
302
+ type: 'CDS',
303
+ start: 35369877,
304
+ end: 35370984,
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+ strand: -1,
306
+ phase: 0,
307
+ refName: 'NC_000001.10',
308
+ id: 'CDS1270',
309
+ parent: 'mRNA1315',
310
+ dbxref: [
311
+ 'CCDS:CCDS30670.1',
312
+ 'GeneID:58512',
313
+ 'Genbank:NP_001073887.1',
314
+ 'HGNC:HGNC:30368',
315
+ 'MIM:611413',
316
+ ],
317
+ name: 'NP_001073887.1',
318
+ gbkey: 'CDS',
319
+ gene: 'DLGAP3',
320
+ product: 'disks large-associated protein 3',
321
+ protein_id: 'NP_001073887.1',
322
+ tag: 'RefSeq Select',
323
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-10',
324
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
325
+ },
326
+ {
327
+ source: 'BestRefSeq',
328
+ type: 'exon',
329
+ start: 35332648,
330
+ end: 35332792,
331
+ strand: -1,
332
+ phase: 0,
333
+ refName: 'NC_000001.10',
334
+ parent: 'mRNA1315',
335
+ dbxref: [
336
+ 'GeneID:58512',
337
+ 'Genbank:NM_001080418.3',
338
+ 'HGNC:HGNC:30368',
339
+ 'MIM:611413',
340
+ ],
341
+ gbkey: 'mRNA',
342
+ gene: 'DLGAP3',
343
+ product: 'DLG associated protein 3',
344
+ tag: 'RefSeq Select',
345
+ transcript_id: 'NM_001080418.3',
346
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-11',
347
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
348
+ },
349
+ {
350
+ source: 'BestRefSeq',
351
+ type: 'exon',
352
+ start: 35333136,
353
+ end: 35333228,
354
+ strand: -1,
355
+ phase: 0,
356
+ refName: 'NC_000001.10',
357
+ parent: 'mRNA1315',
358
+ dbxref: [
359
+ 'GeneID:58512',
360
+ 'Genbank:NM_001080418.3',
361
+ 'HGNC:HGNC:30368',
362
+ 'MIM:611413',
363
+ ],
364
+ gbkey: 'mRNA',
365
+ gene: 'DLGAP3',
366
+ product: 'DLG associated protein 3',
367
+ tag: 'RefSeq Select',
368
+ transcript_id: 'NM_001080418.3',
369
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-12',
370
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
371
+ },
372
+ {
373
+ source: 'BestRefSeq',
374
+ type: 'exon',
375
+ start: 35334205,
376
+ end: 35334690,
377
+ strand: -1,
378
+ phase: 0,
379
+ refName: 'NC_000001.10',
380
+ parent: 'mRNA1315',
381
+ dbxref: [
382
+ 'GeneID:58512',
383
+ 'Genbank:NM_001080418.3',
384
+ 'HGNC:HGNC:30368',
385
+ 'MIM:611413',
386
+ ],
387
+ gbkey: 'mRNA',
388
+ gene: 'DLGAP3',
389
+ product: 'DLG associated protein 3',
390
+ tag: 'RefSeq Select',
391
+ transcript_id: 'NM_001080418.3',
392
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-13',
393
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
394
+ },
395
+ {
396
+ source: 'BestRefSeq',
397
+ type: 'exon',
398
+ start: 35350578,
399
+ end: 35350664,
400
+ strand: -1,
401
+ phase: 0,
402
+ refName: 'NC_000001.10',
403
+ parent: 'mRNA1315',
404
+ dbxref: [
405
+ 'GeneID:58512',
406
+ 'Genbank:NM_001080418.3',
407
+ 'HGNC:HGNC:30368',
408
+ 'MIM:611413',
409
+ ],
410
+ gbkey: 'mRNA',
411
+ gene: 'DLGAP3',
412
+ product: 'DLG associated protein 3',
413
+ tag: 'RefSeq Select',
414
+ transcript_id: 'NM_001080418.3',
415
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-14',
416
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
417
+ },
418
+ {
419
+ source: 'BestRefSeq',
420
+ type: 'exon',
421
+ start: 35351078,
422
+ end: 35351392,
423
+ strand: -1,
424
+ phase: 0,
425
+ refName: 'NC_000001.10',
426
+ parent: 'mRNA1315',
427
+ dbxref: [
428
+ 'GeneID:58512',
429
+ 'Genbank:NM_001080418.3',
430
+ 'HGNC:HGNC:30368',
431
+ 'MIM:611413',
432
+ ],
433
+ gbkey: 'mRNA',
434
+ gene: 'DLGAP3',
435
+ product: 'DLG associated protein 3',
436
+ tag: 'RefSeq Select',
437
+ transcript_id: 'NM_001080418.3',
438
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