@jbrowse/core 2.1.3 → 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/NCDN.js ADDED
@@ -0,0 +1,1118 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.default = {
4
+ source: 'BestRefSeq',
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+ type: 'gene',
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+ start: 36023399,
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+ end: 36032380,
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+ strand: 1,
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+ phase: 0,
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+ refName: 'NC_000001.10',
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+ id: 'gene634',
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+ dbxref: ['GeneID:23154', 'HGNC:HGNC:17597', 'MIM:608458'],
13
+ name: 'NCDN',
14
+ description: 'neurochondrin',
15
+ gbkey: 'Gene',
16
+ gene: 'NCDN',
17
+ gene_biotype: 'protein_coding',
18
+ subfeatures: [
19
+ {
20
+ source: 'BestRefSeq',
21
+ type: 'mRNA',
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+ start: 36023399,
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+ end: 36032380,
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+ strand: 1,
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+ phase: 0,
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+ refName: 'NC_000001.10',
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+ id: 'mRNA1331',
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+ parent: 'gene634',
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+ dbxref: [
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+ 'GeneID:23154',
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+ 'Genbank:NM_014284.3',
32
+ 'HGNC:HGNC:17597',
33
+ 'MIM:608458',
34
+ ],
35
+ name: 'NM_014284.3',
36
+ gbkey: 'mRNA',
37
+ gene: 'NCDN',
38
+ product: 'neurochondrin, transcript variant 3',
39
+ tag: 'RefSeq Select',
40
+ transcript_id: 'NM_014284.3',
41
+ subfeatures: [
42
+ {
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+ source: 'BestRefSeq',
44
+ type: 'exon',
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+ start: 36023399,
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+ end: 36023824,
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+ strand: 1,
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+ phase: 0,
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+ refName: 'NC_000001.10',
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+ parent: 'mRNA1331',
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+ dbxref: [
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+ 'GeneID:23154',
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+ 'Genbank:NM_014284.3',
54
+ 'HGNC:HGNC:17597',
55
+ 'MIM:608458',
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+ ],
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+ gbkey: 'mRNA',
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+ gene: 'NCDN',
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+ product: 'neurochondrin, transcript variant 3',
60
+ tag: 'RefSeq Select',
61
+ transcript_id: 'NM_014284.3',
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+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-0',
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+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
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+ },
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+ {
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+ source: 'BestRefSeq',
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+ type: 'CDS',
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+ start: 36023791,
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+ end: 36023824,
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+ strand: 1,
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+ phase: 0,
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+ refName: 'NC_000001.10',
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+ id: 'CDS1286',
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+ parent: 'mRNA1331',
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+ dbxref: [
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+ 'CCDS:CCDS392.1',
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+ 'GeneID:23154',
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+ 'Genbank:NP_055099.1',
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+ 'HGNC:HGNC:17597',
80
+ 'MIM:608458',
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+ ],
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+ name: 'NP_055099.1',
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+ note: 'isoform 1 is encoded by transcript variant 3',
84
+ gbkey: 'CDS',
85
+ gene: 'NCDN',
86
+ product: 'neurochondrin isoform 1',
87
+ protein_id: 'NP_055099.1',
88
+ tag: 'RefSeq Select',
89
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-1',
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+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
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+ },
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+ {
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+ source: 'BestRefSeq',
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+ type: 'CDS',
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+ start: 36024707,
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+ end: 36024848,
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+ strand: 1,
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+ phase: 0,
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+ refName: 'NC_000001.10',
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+ id: 'CDS1286',
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+ parent: 'mRNA1331',
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+ dbxref: [
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+ 'CCDS:CCDS392.1',
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+ 'GeneID:23154',
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+ 'Genbank:NP_055099.1',
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+ 'HGNC:HGNC:17597',
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+ 'MIM:608458',
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+ ],
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+ name: 'NP_055099.1',
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+ note: 'isoform 1 is encoded by transcript variant 3',
111
+ gbkey: 'CDS',
112
+ gene: 'NCDN',
113
+ product: 'neurochondrin isoform 1',
114
+ protein_id: 'NP_055099.1',
115
+ tag: 'RefSeq Select',
116
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-2',
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+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
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+ },
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+ {
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+ source: 'BestRefSeq',
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+ type: 'CDS',
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+ start: 36025926,
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+ end: 36026895,
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+ strand: 1,
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+ phase: 0,
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+ refName: 'NC_000001.10',
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+ id: 'CDS1286',
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+ parent: 'mRNA1331',
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+ dbxref: [
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+ 'CCDS:CCDS392.1',
131
+ 'GeneID:23154',
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+ 'Genbank:NP_055099.1',
133
+ 'HGNC:HGNC:17597',
134
+ 'MIM:608458',
135
+ ],
136
+ name: 'NP_055099.1',
137
+ note: 'isoform 1 is encoded by transcript variant 3',
138
+ gbkey: 'CDS',
139
+ gene: 'NCDN',
140
+ product: 'neurochondrin isoform 1',
141
+ protein_id: 'NP_055099.1',
142
+ tag: 'RefSeq Select',
143
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-3',
144
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
145
+ },
146
+ {
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+ source: 'BestRefSeq',
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+ type: 'CDS',
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+ start: 36027992,
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+ end: 36028234,
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+ strand: 1,
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+ phase: 0,
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+ refName: 'NC_000001.10',
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+ id: 'CDS1286',
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+ parent: 'mRNA1331',
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+ dbxref: [
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+ 'CCDS:CCDS392.1',
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+ 'GeneID:23154',
159
+ 'Genbank:NP_055099.1',
160
+ 'HGNC:HGNC:17597',
161
+ 'MIM:608458',
162
+ ],
163
+ name: 'NP_055099.1',
164
+ note: 'isoform 1 is encoded by transcript variant 3',
165
+ gbkey: 'CDS',
166
+ gene: 'NCDN',
167
+ product: 'neurochondrin isoform 1',
168
+ protein_id: 'NP_055099.1',
169
+ tag: 'RefSeq Select',
170
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-4',
171
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
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+ },
173
+ {
174
+ source: 'BestRefSeq',
175
+ type: 'CDS',
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+ start: 36028802,
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+ end: 36029027,
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+ strand: 1,
179
+ phase: 1,
180
+ refName: 'NC_000001.10',
181
+ id: 'CDS1286',
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+ parent: 'mRNA1331',
183
+ dbxref: [
184
+ 'CCDS:CCDS392.1',
185
+ 'GeneID:23154',
186
+ 'Genbank:NP_055099.1',
187
+ 'HGNC:HGNC:17597',
188
+ 'MIM:608458',
189
+ ],
190
+ name: 'NP_055099.1',
191
+ note: 'isoform 1 is encoded by transcript variant 3',
192
+ gbkey: 'CDS',
193
+ gene: 'NCDN',
194
+ product: 'neurochondrin isoform 1',
195
+ protein_id: 'NP_055099.1',
196
+ tag: 'RefSeq Select',
197
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-5',
198
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
199
+ },
200
+ {
201
+ source: 'BestRefSeq',
202
+ type: 'CDS',
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+ start: 36029367,
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+ end: 36029510,
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+ strand: 1,
206
+ phase: 1,
207
+ refName: 'NC_000001.10',
208
+ id: 'CDS1286',
209
+ parent: 'mRNA1331',
210
+ dbxref: [
211
+ 'CCDS:CCDS392.1',
212
+ 'GeneID:23154',
213
+ 'Genbank:NP_055099.1',
214
+ 'HGNC:HGNC:17597',
215
+ 'MIM:608458',
216
+ ],
217
+ name: 'NP_055099.1',
218
+ note: 'isoform 1 is encoded by transcript variant 3',
219
+ gbkey: 'CDS',
220
+ gene: 'NCDN',
221
+ product: 'neurochondrin isoform 1',
222
+ protein_id: 'NP_055099.1',
223
+ tag: 'RefSeq Select',
224
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-6',
225
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
226
+ },
227
+ {
228
+ source: 'BestRefSeq',
229
+ type: 'CDS',
230
+ start: 36030827,
231
+ end: 36031264,
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+ strand: 1,
233
+ phase: 2,
234
+ refName: 'NC_000001.10',
235
+ id: 'CDS1286',
236
+ parent: 'mRNA1331',
237
+ dbxref: [
238
+ 'CCDS:CCDS392.1',
239
+ 'GeneID:23154',
240
+ 'Genbank:NP_055099.1',
241
+ 'HGNC:HGNC:17597',
242
+ 'MIM:608458',
243
+ ],
244
+ name: 'NP_055099.1',
245
+ note: 'isoform 1 is encoded by transcript variant 3',
246
+ gbkey: 'CDS',
247
+ gene: 'NCDN',
248
+ product: 'neurochondrin isoform 1',
249
+ protein_id: 'NP_055099.1',
250
+ tag: 'RefSeq Select',
251
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-7',
252
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
253
+ },
254
+ {
255
+ source: 'BestRefSeq',
256
+ type: 'exon',
257
+ start: 36024707,
258
+ end: 36024848,
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+ strand: 1,
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+ phase: 0,
261
+ refName: 'NC_000001.10',
262
+ parent: 'mRNA1331',
263
+ dbxref: [
264
+ 'GeneID:23154',
265
+ 'Genbank:NM_014284.3',
266
+ 'HGNC:HGNC:17597',
267
+ 'MIM:608458',
268
+ ],
269
+ gbkey: 'mRNA',
270
+ gene: 'NCDN',
271
+ product: 'neurochondrin, transcript variant 3',
272
+ tag: 'RefSeq Select',
273
+ transcript_id: 'NM_014284.3',
274
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-8',
275
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
276
+ },
277
+ {
278
+ source: 'BestRefSeq',
279
+ type: 'exon',
280
+ start: 36025926,
281
+ end: 36026895,
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+ strand: 1,
283
+ phase: 0,
284
+ refName: 'NC_000001.10',
285
+ parent: 'mRNA1331',
286
+ dbxref: [
287
+ 'GeneID:23154',
288
+ 'Genbank:NM_014284.3',
289
+ 'HGNC:HGNC:17597',
290
+ 'MIM:608458',
291
+ ],
292
+ gbkey: 'mRNA',
293
+ gene: 'NCDN',
294
+ product: 'neurochondrin, transcript variant 3',
295
+ tag: 'RefSeq Select',
296
+ transcript_id: 'NM_014284.3',
297
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-9',
298
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
299
+ },
300
+ {
301
+ source: 'BestRefSeq',
302
+ type: 'exon',
303
+ start: 36027992,
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+ end: 36028234,
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+ strand: 1,
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+ phase: 0,
307
+ refName: 'NC_000001.10',
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+ parent: 'mRNA1331',
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+ dbxref: [
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+ 'GeneID:23154',
311
+ 'Genbank:NM_014284.3',
312
+ 'HGNC:HGNC:17597',
313
+ 'MIM:608458',
314
+ ],
315
+ gbkey: 'mRNA',
316
+ gene: 'NCDN',
317
+ product: 'neurochondrin, transcript variant 3',
318
+ tag: 'RefSeq Select',
319
+ transcript_id: 'NM_014284.3',
320
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-10',
321
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
322
+ },
323
+ {
324
+ source: 'BestRefSeq',
325
+ type: 'exon',
326
+ start: 36028802,
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+ end: 36029027,
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+ strand: 1,
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+ phase: 0,
330
+ refName: 'NC_000001.10',
331
+ parent: 'mRNA1331',
332
+ dbxref: [
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+ 'GeneID:23154',
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+ 'Genbank:NM_014284.3',
335
+ 'HGNC:HGNC:17597',
336
+ 'MIM:608458',
337
+ ],
338
+ gbkey: 'mRNA',
339
+ gene: 'NCDN',
340
+ product: 'neurochondrin, transcript variant 3',
341
+ tag: 'RefSeq Select',
342
+ transcript_id: 'NM_014284.3',
343
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-11',
344
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
345
+ },
346
+ {
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+ source: 'BestRefSeq',
348
+ type: 'exon',
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+ start: 36029367,
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+ end: 36029510,
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+ strand: 1,
352
+ phase: 0,
353
+ refName: 'NC_000001.10',
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+ parent: 'mRNA1331',
355
+ dbxref: [
356
+ 'GeneID:23154',
357
+ 'Genbank:NM_014284.3',
358
+ 'HGNC:HGNC:17597',
359
+ 'MIM:608458',
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+ ],
361
+ gbkey: 'mRNA',
362
+ gene: 'NCDN',
363
+ product: 'neurochondrin, transcript variant 3',
364
+ tag: 'RefSeq Select',
365
+ transcript_id: 'NM_014284.3',
366
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-12',
367
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
368
+ },
369
+ {
370
+ source: 'BestRefSeq',
371
+ type: 'exon',
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+ start: 36030827,
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+ end: 36032380,
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+ strand: 1,
375
+ phase: 0,
376
+ refName: 'NC_000001.10',
377
+ parent: 'mRNA1331',
378
+ dbxref: [
379
+ 'GeneID:23154',
380
+ 'Genbank:NM_014284.3',
381
+ 'HGNC:HGNC:17597',
382
+ 'MIM:608458',
383
+ ],
384
+ gbkey: 'mRNA',
385
+ gene: 'NCDN',
386
+ product: 'neurochondrin, transcript variant 3',
387
+ tag: 'RefSeq Select',
388
+ transcript_id: 'NM_014284.3',
389
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0-13',
390
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
391
+ },
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+ ],
393
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-0',
394
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638',
395
+ },
396
+ {
397
+ source: 'BestRefSeq',
398
+ type: 'mRNA',
399
+ start: 36023399,
400
+ end: 36032380,
401
+ strand: 1,
402
+ phase: 0,
403
+ refName: 'NC_000001.10',
404
+ id: 'mRNA1333',
405
+ parent: 'gene634',
406
+ dbxref: [
407
+ 'GeneID:23154',
408
+ 'Genbank:NM_001014841.2',
409
+ 'HGNC:HGNC:17597',
410
+ 'MIM:608458',
411
+ ],
412
+ name: 'NM_001014841.2',
413
+ gbkey: 'mRNA',
414
+ gene: 'NCDN',
415
+ product: 'neurochondrin, transcript variant 2',
416
+ transcript_id: 'NM_001014841.2',
417
+ subfeatures: [
418
+ {
419
+ source: 'BestRefSeq',
420
+ type: 'exon',
421
+ start: 36023399,
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+ end: 36023484,
423
+ strand: 1,
424
+ phase: 0,
425
+ refName: 'NC_000001.10',
426
+ parent: 'mRNA1333',
427
+ dbxref: [
428
+ 'GeneID:23154',
429
+ 'Genbank:NM_001014841.2',
430
+ 'HGNC:HGNC:17597',
431
+ 'MIM:608458',
432
+ ],
433
+ gbkey: 'mRNA',
434
+ gene: 'NCDN',
435
+ product: 'neurochondrin, transcript variant 2',
436
+ transcript_id: 'NM_001014841.2',
437
+ uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-1-0',
438
+ parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-164287638-1',
439
+ },
440
+ {
441
+ source: 'BestRefSeq',
442
+ type: 'exon',
443
+ start: 36024707,
444
+ end: 36024848,
445
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