@jbrowse/plugin-wiggle 2.5.0 → 2.6.1

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 (151) hide show
  1. package/dist/BigWigAdapter/BigWigAdapter.js +2 -1
  2. package/dist/BigWigAdapter/BigWigAdapter.js.map +1 -1
  3. package/dist/CreateMultiWiggleExtension/ConfirmDialog.d.ts +2 -1
  4. package/dist/LinearWiggleDisplay/components/SetColorDialog.d.ts +2 -1
  5. package/dist/LinearWiggleDisplay/components/Tooltip.d.ts +1 -1
  6. package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +2 -1
  7. package/dist/LinearWiggleDisplay/index.js +27 -4
  8. package/dist/LinearWiggleDisplay/index.js.map +1 -1
  9. package/dist/LinearWiggleDisplay/models/configSchema.d.ts +18 -35
  10. package/dist/LinearWiggleDisplay/models/configSchema.js +6 -67
  11. package/dist/LinearWiggleDisplay/models/configSchema.js.map +1 -1
  12. package/dist/LinearWiggleDisplay/models/model.d.ts +147 -342
  13. package/dist/LinearWiggleDisplay/models/model.js +17 -432
  14. package/dist/LinearWiggleDisplay/models/model.js.map +1 -1
  15. package/dist/LinearWiggleDisplay/models/renderSvg.d.ts +4 -0
  16. package/dist/LinearWiggleDisplay/models/renderSvg.js +21 -0
  17. package/dist/LinearWiggleDisplay/models/renderSvg.js.map +1 -0
  18. package/dist/MultiDensityRenderer/MultiDensityRenderer.js +1 -1
  19. package/dist/MultiDensityRenderer/MultiDensityRenderer.js.map +1 -1
  20. package/dist/MultiLineRenderer/MultiLineRenderer.js +1 -1
  21. package/dist/MultiLineRenderer/MultiLineRenderer.js.map +1 -1
  22. package/dist/MultiLinearWiggleDisplay/components/DraggableDialog.d.ts +2 -1
  23. package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts +2 -1
  24. package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js +2 -2
  25. package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js.map +1 -1
  26. package/dist/MultiLinearWiggleDisplay/components/Tooltip.d.ts +1 -1
  27. package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +3 -2
  28. package/dist/MultiLinearWiggleDisplay/index.js +25 -2
  29. package/dist/MultiLinearWiggleDisplay/index.js.map +1 -1
  30. package/dist/MultiLinearWiggleDisplay/models/configSchema.d.ts +24 -44
  31. package/dist/MultiLinearWiggleDisplay/models/configSchema.js +6 -66
  32. package/dist/MultiLinearWiggleDisplay/models/configSchema.js.map +1 -1
  33. package/dist/MultiLinearWiggleDisplay/models/model.d.ts +263 -175
  34. package/dist/MultiLinearWiggleDisplay/models/model.js +335 -508
  35. package/dist/MultiLinearWiggleDisplay/models/model.js.map +1 -1
  36. package/dist/MultiLinearWiggleDisplay/models/renderSvg.d.ts +4 -0
  37. package/dist/MultiLinearWiggleDisplay/models/renderSvg.js +20 -0
  38. package/dist/MultiLinearWiggleDisplay/models/renderSvg.js.map +1 -0
  39. package/dist/MultiRowLineRenderer/MultiRowLineRenderer.js +1 -1
  40. package/dist/MultiRowLineRenderer/MultiRowLineRenderer.js.map +1 -1
  41. package/dist/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js +1 -1
  42. package/dist/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js.map +1 -1
  43. package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.d.ts +2 -1
  44. package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.js +1 -1
  45. package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.js.map +1 -1
  46. package/dist/MultiWiggleRendering.d.ts +2 -1
  47. package/dist/MultiXYPlotRenderer/MultiXYPlotRenderer.js +3 -2
  48. package/dist/MultiXYPlotRenderer/MultiXYPlotRenderer.js.map +1 -1
  49. package/dist/Tooltip.d.ts +1 -1
  50. package/dist/WiggleBaseRenderer.d.ts +1 -1
  51. package/dist/WiggleRendering.d.ts +2 -1
  52. package/dist/index.d.ts +222 -198
  53. package/dist/shared/SetMinMaxDialog.d.ts +2 -1
  54. package/dist/shared/YScaleBar.d.ts +4 -2
  55. package/dist/shared/YScaleBar.js +1 -1
  56. package/dist/shared/YScaleBar.js.map +1 -1
  57. package/dist/shared/configShared.d.ts +85 -0
  58. package/dist/shared/configShared.js +84 -0
  59. package/dist/shared/configShared.js.map +1 -0
  60. package/dist/shared/modelShared.d.ts +576 -0
  61. package/dist/shared/modelShared.js +480 -0
  62. package/dist/shared/modelShared.js.map +1 -0
  63. package/dist/util.d.ts +0 -3
  64. package/dist/util.js +1 -11
  65. package/dist/util.js.map +1 -1
  66. package/esm/BigWigAdapter/BigWigAdapter.js +2 -1
  67. package/esm/BigWigAdapter/BigWigAdapter.js.map +1 -1
  68. package/esm/CreateMultiWiggleExtension/ConfirmDialog.d.ts +2 -1
  69. package/esm/LinearWiggleDisplay/components/SetColorDialog.d.ts +2 -1
  70. package/esm/LinearWiggleDisplay/components/Tooltip.d.ts +1 -1
  71. package/esm/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +2 -1
  72. package/esm/LinearWiggleDisplay/index.js +2 -2
  73. package/esm/LinearWiggleDisplay/index.js.map +1 -1
  74. package/esm/LinearWiggleDisplay/models/configSchema.d.ts +18 -35
  75. package/esm/LinearWiggleDisplay/models/configSchema.js +3 -67
  76. package/esm/LinearWiggleDisplay/models/configSchema.js.map +1 -1
  77. package/esm/LinearWiggleDisplay/models/model.d.ts +147 -342
  78. package/esm/LinearWiggleDisplay/models/model.js +20 -435
  79. package/esm/LinearWiggleDisplay/models/model.js.map +1 -1
  80. package/esm/LinearWiggleDisplay/models/renderSvg.d.ts +4 -0
  81. package/esm/LinearWiggleDisplay/models/renderSvg.js +14 -0
  82. package/esm/LinearWiggleDisplay/models/renderSvg.js.map +1 -0
  83. package/esm/MultiDensityRenderer/MultiDensityRenderer.js +1 -1
  84. package/esm/MultiDensityRenderer/MultiDensityRenderer.js.map +1 -1
  85. package/esm/MultiLineRenderer/MultiLineRenderer.js +1 -1
  86. package/esm/MultiLineRenderer/MultiLineRenderer.js.map +1 -1
  87. package/esm/MultiLinearWiggleDisplay/components/DraggableDialog.d.ts +2 -1
  88. package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts +2 -1
  89. package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js +1 -1
  90. package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js.map +1 -1
  91. package/esm/MultiLinearWiggleDisplay/components/Tooltip.d.ts +1 -1
  92. package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +3 -2
  93. package/esm/MultiLinearWiggleDisplay/index.js +2 -2
  94. package/esm/MultiLinearWiggleDisplay/index.js.map +1 -1
  95. package/esm/MultiLinearWiggleDisplay/models/configSchema.d.ts +24 -44
  96. package/esm/MultiLinearWiggleDisplay/models/configSchema.js +3 -66
  97. package/esm/MultiLinearWiggleDisplay/models/configSchema.js.map +1 -1
  98. package/esm/MultiLinearWiggleDisplay/models/model.d.ts +263 -175
  99. package/esm/MultiLinearWiggleDisplay/models/model.js +337 -512
  100. package/esm/MultiLinearWiggleDisplay/models/model.js.map +1 -1
  101. package/esm/MultiLinearWiggleDisplay/models/renderSvg.d.ts +4 -0
  102. package/esm/MultiLinearWiggleDisplay/models/renderSvg.js +13 -0
  103. package/esm/MultiLinearWiggleDisplay/models/renderSvg.js.map +1 -0
  104. package/esm/MultiRowLineRenderer/MultiRowLineRenderer.js +1 -1
  105. package/esm/MultiRowLineRenderer/MultiRowLineRenderer.js.map +1 -1
  106. package/esm/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js +1 -1
  107. package/esm/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js.map +1 -1
  108. package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.d.ts +2 -1
  109. package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.js +1 -1
  110. package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.js.map +1 -1
  111. package/esm/MultiWiggleRendering.d.ts +2 -1
  112. package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.js +2 -1
  113. package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.js.map +1 -1
  114. package/esm/Tooltip.d.ts +1 -1
  115. package/esm/WiggleBaseRenderer.d.ts +1 -1
  116. package/esm/WiggleRendering.d.ts +2 -1
  117. package/esm/index.d.ts +222 -198
  118. package/esm/shared/SetMinMaxDialog.d.ts +2 -1
  119. package/esm/shared/YScaleBar.d.ts +4 -2
  120. package/esm/shared/YScaleBar.js +1 -1
  121. package/esm/shared/YScaleBar.js.map +1 -1
  122. package/esm/shared/configShared.d.ts +85 -0
  123. package/esm/shared/configShared.js +81 -0
  124. package/esm/shared/configShared.js.map +1 -0
  125. package/esm/shared/modelShared.d.ts +576 -0
  126. package/esm/shared/modelShared.js +454 -0
  127. package/esm/shared/modelShared.js.map +1 -0
  128. package/esm/util.d.ts +0 -3
  129. package/esm/util.js +0 -9
  130. package/esm/util.js.map +1 -1
  131. package/package.json +3 -3
  132. package/src/BigWigAdapter/BigWigAdapter.ts +2 -4
  133. package/src/LinearWiggleDisplay/index.ts +2 -2
  134. package/src/LinearWiggleDisplay/models/configSchema.ts +4 -73
  135. package/src/LinearWiggleDisplay/models/model.tsx +22 -503
  136. package/src/LinearWiggleDisplay/models/renderSvg.tsx +29 -0
  137. package/src/MultiDensityRenderer/MultiDensityRenderer.ts +1 -2
  138. package/src/MultiLineRenderer/MultiLineRenderer.ts +1 -2
  139. package/src/MultiLinearWiggleDisplay/components/SetColorDialog.tsx +1 -1
  140. package/src/MultiLinearWiggleDisplay/index.ts +2 -2
  141. package/src/MultiLinearWiggleDisplay/models/configSchema.ts +4 -72
  142. package/src/MultiLinearWiggleDisplay/models/model.tsx +132 -371
  143. package/src/MultiLinearWiggleDisplay/models/renderSvg.tsx +26 -0
  144. package/src/MultiRowLineRenderer/MultiRowLineRenderer.ts +1 -2
  145. package/src/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.ts +1 -2
  146. package/src/MultiWiggleAddTrackWidget/AddTrackWorkflow.tsx +1 -1
  147. package/src/MultiXYPlotRenderer/MultiXYPlotRenderer.ts +2 -2
  148. package/src/shared/YScaleBar.tsx +4 -2
  149. package/src/shared/configShared.ts +90 -0
  150. package/src/shared/modelShared.ts +510 -0
  151. package/src/util.ts +1 -10
@@ -1,14 +1,13 @@
1
- import React, { lazy } from 'react';
2
- import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
3
- import { getEnv, getSession, getContainingView, isSelectionContainer, } from '@jbrowse/core/util';
4
- import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
5
- import { when } from 'mobx';
1
+ import { lazy } from 'react';
2
+ import { getConf, } from '@jbrowse/core/configuration';
3
+ import { getSession } from '@jbrowse/core/util';
6
4
  import { types } from 'mobx-state-tree';
7
5
  import { axisPropsFromTickScale } from 'react-d3-axis-mod';
8
- import { getNiceDomain, getScale, quantitativeStatsAutorun, YSCALEBAR_LABEL_OFFSET, } from '../../util';
6
+ // locals
7
+ import { getScale, quantitativeStatsAutorun, YSCALEBAR_LABEL_OFFSET, } from '../../util';
9
8
  import Tooltip from '../components/Tooltip';
10
- import YScaleBar from '../../shared/YScaleBar';
11
- const SetMinMaxDlg = lazy(() => import('../../shared/SetMinMaxDialog'));
9
+ import SharedWiggleMixin from '../../shared/modelShared';
10
+ // lazies
12
11
  const SetColorDlg = lazy(() => import('../components/SetColorDialog'));
13
12
  // using a map because it preserves order
14
13
  const rendererTypes = new Map([
@@ -18,212 +17,15 @@ const rendererTypes = new Map([
18
17
  ]);
19
18
  /**
20
19
  * #stateModel LinearWiggleDisplay
21
- * Extends `BaseLinearDisplay`
20
+ * extends `SharedWiggleMixin`
22
21
  */
23
22
  function stateModelFactory(pluginManager, configSchema) {
24
23
  return types
25
- .compose('LinearWiggleDisplay', BaseLinearDisplay, types.model({
24
+ .compose('LinearWiggleDisplay', SharedWiggleMixin(configSchema), types.model({
26
25
  /**
27
26
  * #property
28
27
  */
29
28
  type: types.literal('LinearWiggleDisplay'),
30
- /**
31
- * #property
32
- */
33
- configuration: ConfigurationReference(configSchema),
34
- /**
35
- * #property
36
- */
37
- selectedRendering: types.optional(types.string, ''),
38
- /**
39
- * #property
40
- */
41
- resolution: types.optional(types.number, 1),
42
- /**
43
- * #property
44
- */
45
- fill: types.maybe(types.boolean),
46
- /**
47
- * #property
48
- */
49
- minSize: types.maybe(types.number),
50
- /**
51
- * #property
52
- */
53
- color: types.maybe(types.string),
54
- /**
55
- * #property
56
- */
57
- posColor: types.maybe(types.string),
58
- /**
59
- * #property
60
- */
61
- negColor: types.maybe(types.string),
62
- /**
63
- * #property
64
- */
65
- summaryScoreMode: types.maybe(types.string),
66
- /**
67
- * #property
68
- */
69
- rendererTypeNameState: types.maybe(types.string),
70
- /**
71
- * #property
72
- */
73
- scale: types.maybe(types.string),
74
- /**
75
- * #property
76
- */
77
- autoscale: types.maybe(types.string),
78
- /**
79
- * #property
80
- */
81
- displayCrossHatches: types.maybe(types.boolean),
82
- /**
83
- * #property
84
- */
85
- constraints: types.optional(types.model({
86
- max: types.maybe(types.number),
87
- min: types.maybe(types.number),
88
- }), {}),
89
- }))
90
- .volatile(() => ({
91
- message: undefined,
92
- stats: undefined,
93
- statsFetchInProgress: undefined,
94
- }))
95
- .actions(self => ({
96
- /**
97
- * #action
98
- */
99
- updateQuantitativeStats(stats) {
100
- const { scoreMin, scoreMax } = stats;
101
- const EPSILON = 0.000001;
102
- if (!self.stats) {
103
- self.stats = { scoreMin, scoreMax };
104
- }
105
- else if (Math.abs(self.stats.scoreMax - scoreMax) > EPSILON ||
106
- Math.abs(self.stats.scoreMin - scoreMin) > EPSILON) {
107
- self.stats = { scoreMin, scoreMax };
108
- }
109
- },
110
- /**
111
- * #action
112
- */
113
- setColor(color) {
114
- self.color = color;
115
- },
116
- /**
117
- * #action
118
- */
119
- setPosColor(color) {
120
- self.posColor = color;
121
- },
122
- /**
123
- * #action
124
- */
125
- setNegColor(color) {
126
- self.negColor = color;
127
- },
128
- /**
129
- * #action
130
- */
131
- setLoading(aborter) {
132
- const { statsFetchInProgress: statsFetch } = self;
133
- if (statsFetch !== undefined && !statsFetch.signal.aborted) {
134
- statsFetch.abort();
135
- }
136
- self.statsFetchInProgress = aborter;
137
- },
138
- /**
139
- * #action
140
- * this overrides the BaseLinearDisplayModel to avoid popping up a
141
- * feature detail display, but still sets the feature selection on the
142
- * model so listeners can detect a click
143
- */
144
- selectFeature(feature) {
145
- const session = getSession(self);
146
- if (isSelectionContainer(session)) {
147
- session.setSelection(feature);
148
- }
149
- },
150
- /**
151
- * #action
152
- */
153
- setResolution(res) {
154
- self.resolution = res;
155
- },
156
- /**
157
- * #action
158
- */
159
- setFill(fill) {
160
- if (fill === 0) {
161
- self.fill = true;
162
- self.minSize = 0;
163
- }
164
- else if (fill === 1) {
165
- self.fill = false;
166
- self.minSize = 1;
167
- }
168
- else if (fill === 2) {
169
- self.fill = false;
170
- self.minSize = 2;
171
- }
172
- },
173
- /**
174
- * #action
175
- */
176
- toggleLogScale() {
177
- self.scale = self.scale === 'log' ? 'linear' : 'log';
178
- },
179
- /**
180
- * #action
181
- */
182
- setScaleType(scale) {
183
- self.scale = scale;
184
- },
185
- /**
186
- * #action
187
- */
188
- setSummaryScoreMode(val) {
189
- self.summaryScoreMode = val;
190
- },
191
- /**
192
- * #action
193
- */
194
- setAutoscale(val) {
195
- self.autoscale = val;
196
- },
197
- /**
198
- * #action
199
- */
200
- setMaxScore(val) {
201
- self.constraints.max = val;
202
- },
203
- /**
204
- * #action
205
- */
206
- setRendererType(val) {
207
- self.rendererTypeNameState = val;
208
- },
209
- /**
210
- * #action
211
- */
212
- setMinScore(val) {
213
- self.constraints.min = val;
214
- },
215
- /**
216
- * #action
217
- */
218
- toggleCrossHatches() {
219
- self.displayCrossHatches = !self.displayCrossHatches;
220
- },
221
- /**
222
- * #action
223
- */
224
- setCrossHatches(cross) {
225
- self.displayCrossHatches = cross;
226
- },
227
29
  }))
228
30
  .views(self => ({
229
31
  /**
@@ -232,157 +34,18 @@ function stateModelFactory(pluginManager, configSchema) {
232
34
  get TooltipComponent() {
233
35
  return Tooltip;
234
36
  },
235
- /**
236
- * #getter
237
- */
238
- get adapterTypeName() {
239
- return self.adapterConfig.type;
240
- },
241
- /**
242
- * #getter
243
- */
244
- get rendererTypeNameSimple() {
245
- return self.rendererTypeNameState || getConf(self, 'defaultRendering');
246
- },
247
37
  /**
248
38
  * #getter
249
39
  */
250
40
  get rendererTypeName() {
251
- const name = this.rendererTypeNameSimple;
41
+ const name = self.rendererTypeNameSimple;
252
42
  const rendererType = rendererTypes.get(name);
253
43
  if (!rendererType) {
254
44
  throw new Error(`unknown renderer ${name}`);
255
45
  }
256
46
  return rendererType;
257
47
  },
258
- /**
259
- * #getter
260
- * subclasses can define these, as snpcoverage track does
261
- */
262
- get filters() {
263
- return undefined;
264
- },
265
- /**
266
- * #getter
267
- */
268
- get scaleType() {
269
- return self.scale || getConf(self, 'scaleType');
270
- },
271
- /**
272
- * #getter
273
- */
274
- get maxScore() {
275
- var _a;
276
- return (_a = self.constraints.max) !== null && _a !== void 0 ? _a : getConf(self, 'maxScore');
277
- },
278
- /**
279
- * #getter
280
- */
281
- get minScore() {
282
- var _a;
283
- return (_a = self.constraints.min) !== null && _a !== void 0 ? _a : getConf(self, 'minScore');
284
- },
285
48
  }))
286
- .views(self => ({
287
- /**
288
- * #getter
289
- */
290
- get rendererConfig() {
291
- const { color, displayCrossHatches, fill, minSize, negColor, posColor, summaryScoreMode, scaleType, rendererTypeName, } = self;
292
- const configBlob = getConf(self, ['renderers', rendererTypeName]) || {};
293
- return self.rendererType.configSchema.create({
294
- ...configBlob,
295
- ...(scaleType ? { scaleType } : {}),
296
- ...(fill !== undefined ? { filled: fill } : {}),
297
- ...(displayCrossHatches !== undefined
298
- ? { displayCrossHatches }
299
- : {}),
300
- ...(summaryScoreMode !== undefined ? { summaryScoreMode } : {}),
301
- ...(color !== undefined ? { color } : {}),
302
- ...(negColor !== undefined ? { negColor } : {}),
303
- ...(posColor !== undefined ? { posColor } : {}),
304
- ...(minSize !== undefined ? { minSize } : {}),
305
- }, getEnv(self));
306
- },
307
- }))
308
- .views(self => {
309
- let oldDomain = [0, 0];
310
- return {
311
- /**
312
- * #getter
313
- */
314
- get filled() {
315
- return readConfObject(self.rendererConfig, 'filled');
316
- },
317
- /**
318
- * #getter
319
- */
320
- get summaryScoreModeSetting() {
321
- return readConfObject(self.rendererConfig, 'summaryScoreMode');
322
- },
323
- /**
324
- * #getter
325
- */
326
- get domain() {
327
- const { stats, scaleType, minScore, maxScore } = self;
328
- if (!stats) {
329
- return undefined;
330
- }
331
- const ret = getNiceDomain({
332
- domain: [stats.scoreMin, stats.scoreMax],
333
- bounds: [minScore, maxScore],
334
- scaleType,
335
- });
336
- // avoid weird scalebar if log value and empty region displayed
337
- if (scaleType === 'log' && ret[1] === Number.MIN_VALUE) {
338
- return [0, Number.MIN_VALUE];
339
- }
340
- // avoid returning a new object if it matches the old value
341
- if (JSON.stringify(oldDomain) !== JSON.stringify(ret)) {
342
- oldDomain = ret;
343
- }
344
- return oldDomain;
345
- },
346
- /**
347
- * #getter
348
- */
349
- get needsScalebar() {
350
- return (self.rendererTypeName === 'XYPlotRenderer' ||
351
- self.rendererTypeName === 'LinePlotRenderer');
352
- },
353
- /**
354
- * #getter
355
- */
356
- get scaleOpts() {
357
- return {
358
- domain: this.domain,
359
- stats: self.stats,
360
- autoscaleType: this.autoscaleType,
361
- scaleType: self.scaleType,
362
- inverted: getConf(self, 'inverted'),
363
- };
364
- },
365
- /**
366
- * #getter
367
- */
368
- get canHaveFill() {
369
- return self.rendererTypeName === 'XYPlotRenderer';
370
- },
371
- /**
372
- * #getter
373
- */
374
- get autoscaleType() {
375
- var _a;
376
- return (_a = self.autoscale) !== null && _a !== void 0 ? _a : getConf(self, 'autoscale');
377
- },
378
- /**
379
- * #getter
380
- */
381
- get displayCrossHatchesSetting() {
382
- return readConfObject(self.rendererConfig, 'displayCrossHatches');
383
- },
384
- };
385
- })
386
49
  .views(self => ({
387
50
  /**
388
51
  * #getter
@@ -406,13 +69,6 @@ function stateModelFactory(pluginManager, configSchema) {
406
69
  ? { ...ticks, values: domain }
407
70
  : ticks;
408
71
  },
409
- /**
410
- * #getter
411
- */
412
- get adapterCapabilities() {
413
- const type = self.adapterTypeName;
414
- return pluginManager.getAdapterType(type).adapterCapabilities;
415
- },
416
72
  }))
417
73
  .views(self => {
418
74
  const { renderProps: superRenderProps } = self;
@@ -440,14 +96,9 @@ function stateModelFactory(pluginManager, configSchema) {
440
96
  /**
441
97
  * #getter
442
98
  */
443
- get hasResolution() {
444
- return self.adapterCapabilities.includes('hasResolution');
445
- },
446
- /**
447
- * #getter
448
- */
449
- get hasGlobalStats() {
450
- return self.adapterCapabilities.includes('hasGlobalStats');
99
+ get needsScalebar() {
100
+ const { rendererTypeName: type } = self;
101
+ return type === 'XYPlotRenderer' || type === 'LinePlotRenderer';
451
102
  },
452
103
  /**
453
104
  * #getter
@@ -475,32 +126,10 @@ function stateModelFactory(pluginManager, configSchema) {
475
126
  trackMenuItems() {
476
127
  return [
477
128
  ...superTrackMenuItems(),
478
- ...(self.hasResolution
479
- ? [
480
- {
481
- label: 'Resolution',
482
- subMenu: [
483
- {
484
- label: 'Finer resolution',
485
- onClick: () => self.setResolution(self.resolution * 5),
486
- },
487
- {
488
- label: 'Coarser resolution',
489
- onClick: () => self.setResolution(self.resolution / 5),
490
- },
491
- ],
492
- },
493
- {
494
- label: 'Summary score mode',
495
- subMenu: ['min', 'max', 'avg', 'whiskers'].map(elt => ({
496
- label: elt,
497
- type: 'radio',
498
- checked: self.summaryScoreModeSetting === elt,
499
- onClick: () => self.setSummaryScoreMode(elt),
500
- })),
501
- },
502
- ]
503
- : []),
129
+ {
130
+ label: 'Score',
131
+ subMenu: self.scoreTrackMenuItems(),
132
+ },
504
133
  ...(self.canHaveFill
505
134
  ? [
506
135
  {
@@ -514,10 +143,6 @@ function stateModelFactory(pluginManager, configSchema) {
514
143
  },
515
144
  ]
516
145
  : []),
517
- {
518
- label: self.scaleType === 'log' ? 'Set linear scale' : 'Set log scale',
519
- onClick: () => self.toggleLogScale(),
520
- },
521
146
  ...(self.needsScalebar
522
147
  ? [
523
148
  {
@@ -541,33 +166,6 @@ function stateModelFactory(pluginManager, configSchema) {
541
166
  },
542
167
  ]
543
168
  : []),
544
- {
545
- label: 'Autoscale type',
546
- subMenu: [
547
- ['local', 'Local'],
548
- ...(self.hasGlobalStats
549
- ? [
550
- ['global', 'Global'],
551
- ['globalsd', 'Global ± 3σ'],
552
- ]
553
- : []),
554
- ['localsd', 'Local ± 3σ'],
555
- ].map(([val, label]) => ({
556
- label,
557
- type: 'radio',
558
- checked: self.autoscaleType === val,
559
- onClick: () => self.setAutoscale(val),
560
- })),
561
- },
562
- {
563
- label: 'Set min/max score',
564
- onClick: () => {
565
- getSession(self).queueDialog(handleClose => [
566
- SetMinMaxDlg,
567
- { model: self, handleClose },
568
- ]);
569
- },
570
- },
571
169
  {
572
170
  label: 'Set color',
573
171
  onClick: () => {
@@ -582,16 +180,8 @@ function stateModelFactory(pluginManager, configSchema) {
582
180
  };
583
181
  })
584
182
  .actions(self => {
585
- const { reload: superReload, renderSvg: superRenderSvg } = self;
183
+ const { renderSvg: superRenderSvg } = self;
586
184
  return {
587
- /**
588
- * #action
589
- * re-runs stats and refresh whole display on reload
590
- */
591
- async reload() {
592
- self.setError();
593
- superReload();
594
- },
595
185
  afterAttach() {
596
186
  quantitativeStatsAutorun(self);
597
187
  },
@@ -599,13 +189,8 @@ function stateModelFactory(pluginManager, configSchema) {
599
189
  * #action
600
190
  */
601
191
  async renderSvg(opts) {
602
- await when(() => !!self.stats && !!self.regionCannotBeRenderedText);
603
- const { needsScalebar, stats } = self;
604
- const { offsetPx } = getContainingView(self);
605
- return (React.createElement(React.Fragment, null,
606
- React.createElement("g", { id: "snpcov" }, await superRenderSvg(opts)),
607
- needsScalebar && stats ? (React.createElement("g", { transform: `translate(${Math.max(-offsetPx, 0)})` },
608
- React.createElement(YScaleBar, { model: self, orientation: "left" }))) : null));
192
+ const { renderSvg } = await import('./renderSvg');
193
+ return renderSvg(self, opts, superRenderSvg);
609
194
  },
610
195
  };
611
196
  });
@@ -1 +1 @@
1
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@@ -0,0 +1,4 @@
1
+ import React from 'react';
2
+ import { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
3
+ import { WiggleDisplayModel } from './model';
4
+ export declare function renderSvg(self: WiggleDisplayModel, opts: ExportSvgDisplayOptions, superRenderSvg: (opts: ExportSvgDisplayOptions) => Promise<React.ReactNode>): Promise<React.JSX.Element>;
@@ -0,0 +1,14 @@
1
+ import React from 'react';
2
+ import { getContainingView } from '@jbrowse/core/util';
3
+ import { when } from 'mobx';
4
+ import YScaleBar from '../../shared/YScaleBar';
5
+ export async function renderSvg(self, opts, superRenderSvg) {
6
+ await when(() => !!self.stats && !!self.regionCannotBeRenderedText);
7
+ const { needsScalebar, stats } = self;
8
+ const { offsetPx } = getContainingView(self);
9
+ return (React.createElement(React.Fragment, null,
10
+ React.createElement("g", { id: "snpcov" }, await superRenderSvg(opts)),
11
+ needsScalebar && stats ? (React.createElement("g", { transform: `translate(${Math.max(-offsetPx, 0)})` },
12
+ React.createElement(YScaleBar, { model: self, orientation: "left" }))) : null));
13
+ }
14
+ //# sourceMappingURL=renderSvg.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"renderSvg.js","sourceRoot":"","sources":["../../../src/LinearWiggleDisplay/models/renderSvg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AAC3B,OAAO,SAAS,MAAM,wBAAwB,CAAA;AAO9C,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,IAAwB,EACxB,IAA6B,EAC7B,cAA2E;IAE3E,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,CAAC,IAAI,CAAC,0BAA0B,CAAC,CAAA;IACnE,MAAM,EAAE,aAAa,EAAE,KAAK,EAAE,GAAG,IAAI,CAAA;IACrC,MAAM,EAAE,QAAQ,EAAE,GAAG,iBAAiB,CAAC,IAAI,CAA0B,CAAA;IACrE,OAAO,CACL;QACE,2BAAG,EAAE,EAAC,QAAQ,IAAE,MAAM,cAAc,CAAC,IAAI,CAAC,CAAK;QAC9C,aAAa,IAAI,KAAK,CAAC,CAAC,CAAC,CACxB,2BAAG,SAAS,EAAE,aAAa,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,GAAG;YAClD,oBAAC,SAAS,IAAC,KAAK,EAAE,IAAI,EAAE,WAAW,EAAC,MAAM,GAAG,CAC3C,CACL,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC"}
@@ -1,4 +1,4 @@
1
- import { groupBy } from '../util';
1
+ import { groupBy } from '@jbrowse/core/util';
2
2
  import WiggleBaseRenderer from '../WiggleBaseRenderer';
3
3
  import { drawDensity } from '../drawxy';
4
4
  export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
@@ -1 +1 @@
1
- {"version":3,"file":"MultiDensityRenderer.js","sourceRoot":"","sources":["../../src/MultiDensityRenderer/MultiDensityRenderer.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,OAAO,EAAE,MAAM,SAAS,CAAA;AACjC,OAAO,kBAEN,MAAM,uBAAuB,CAAA;AAC9B,OAAO,EAAE,WAAW,EAAE,MAAM,WAAW,CAAA;AAEvC,MAAM,CAAC,OAAO,OAAO,mBAAoB,SAAQ,kBAAkB;IACjE,mBAAmB;IACnB,KAAK,CAAC,IAAI,CAAC,GAA6B,EAAE,KAAgB;QACxD,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;QACrD,MAAM,CAAC,MAAM,CAAC,GAAG,OAAO,CAAA;QACxB,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAA;QACpE,MAAM,MAAM,GAAG,KAAK,CAAC,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,MAAM,CAAA;QACxD,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;QACnD,IAAI,KAAK,GAAG,EAAe,CAAA;QAC3B,GAAG,CAAC,IAAI,EAAE,CAAA;QACV,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;YACvB,MAAM,QAAQ,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;YACpC,IAAI,CAAC,QAAQ,EAAE;gBACb,OAAM;aACP;YACD,MAAM,EAAE,eAAe,EAAE,GAAG,WAAW,CAAC,GAAG,EAAE;gBAC3C,GAAG,KAAK;gBACR,QAAQ;gBACR,MAAM;aACP,CAAC,CAAA;YACF,GAAG,CAAC,WAAW,GAAG,uBAAuB,CAAA;YACzC,GAAG,CAAC,SAAS,EAAE,CAAA;YACf,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,MAAM,CAAC,CAAA;YACrB,GAAG,CAAC,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;YACzB,GAAG,CAAC,MAAM,EAAE,CAAA;YACZ,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,MAAM,CAAC,CAAA;YACxB,KAAK,GAAG,CAAC,GAAG,KAAK,EAAE,GAAG,eAAe,CAAC,CAAA;QACxC,CAAC,CAAC,CAAA;QACF,GAAG,CAAC,OAAO,EAAE,CAAA;QACb,OAAO,EAAE,eAAe,EAAE,KAAK,EAAE,CAAA;IACnC,CAAC;CACF"}
1
+ {"version":3,"file":"MultiDensityRenderer.js","sourceRoot":"","sources":["../../src/MultiDensityRenderer/MultiDensityRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAW,MAAM,oBAAoB,CAAA;AACrD,OAAO,kBAEN,MAAM,uBAAuB,CAAA;AAC9B,OAAO,EAAE,WAAW,EAAE,MAAM,WAAW,CAAA;AAEvC,MAAM,CAAC,OAAO,OAAO,mBAAoB,SAAQ,kBAAkB;IACjE,mBAAmB;IACnB,KAAK,CAAC,IAAI,CAAC,GAA6B,EAAE,KAAgB;QACxD,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;QACrD,MAAM,CAAC,MAAM,CAAC,GAAG,OAAO,CAAA;QACxB,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAA;QACpE,MAAM,MAAM,GAAG,KAAK,CAAC,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,MAAM,CAAA;QACxD,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;QACnD,IAAI,KAAK,GAAG,EAAe,CAAA;QAC3B,GAAG,CAAC,IAAI,EAAE,CAAA;QACV,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;YACvB,MAAM,QAAQ,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;YACpC,IAAI,CAAC,QAAQ,EAAE;gBACb,OAAM;aACP;YACD,MAAM,EAAE,eAAe,EAAE,GAAG,WAAW,CAAC,GAAG,EAAE;gBAC3C,GAAG,KAAK;gBACR,QAAQ;gBACR,MAAM;aACP,CAAC,CAAA;YACF,GAAG,CAAC,WAAW,GAAG,uBAAuB,CAAA;YACzC,GAAG,CAAC,SAAS,EAAE,CAAA;YACf,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,MAAM,CAAC,CAAA;YACrB,GAAG,CAAC,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;YACzB,GAAG,CAAC,MAAM,EAAE,CAAA;YACZ,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,MAAM,CAAC,CAAA;YACxB,KAAK,GAAG,CAAC,GAAG,KAAK,EAAE,GAAG,eAAe,CAAC,CAAA;QACxC,CAAC,CAAC,CAAA;QACF,GAAG,CAAC,OAAO,EAAE,CAAA;QACb,OAAO,EAAE,eAAe,EAAE,KAAK,EAAE,CAAA;IACnC,CAAC;CACF"}
@@ -1,5 +1,5 @@
1
+ import { groupBy } from '@jbrowse/core/util';
1
2
  import { drawLine } from '../drawxy';
2
- import { groupBy } from '../util';
3
3
  import WiggleBaseRenderer from '../WiggleBaseRenderer';
4
4
  export default class MultiLineRenderer extends WiggleBaseRenderer {
5
5
  // @ts-expect-error
@@ -1 +1 @@
1
- {"version":3,"file":"MultiLineRenderer.js","sourceRoot":"","sources":["../../src/MultiLineRenderer/MultiLineRenderer.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,QAAQ,EAAE,MAAM,WAAW,CAAA;AACpC,OAAO,EAAE,OAAO,EAAE,MAAM,SAAS,CAAA;AAEjC,OAAO,kBAEN,MAAM,uBAAuB,CAAA;AAE9B,MAAM,CAAC,OAAO,OAAO,iBAAkB,SAAQ,kBAAkB;IAC/D,mBAAmB;IACnB,KAAK,CAAC,IAAI,CAAC,GAA6B,EAAE,KAAgB;QACxD,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;QACnC,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAA;QACpE,IAAI,KAAK,GAAG,EAAe,CAAA;QAC3B,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;YACvB,MAAM,QAAQ,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;YACpC,IAAI,CAAC,QAAQ,EAAE;gBACb,OAAM;aACP;YACD,MAAM,EAAE,eAAe,EAAE,GAAG,QAAQ,CAAC,GAAG,EAAE;gBACxC,GAAG,KAAK;gBACR,QAAQ;gBACR,aAAa,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,KAAK,IAAI,MAAM;aAC5C,CAAC,CAAA;YACF,KAAK,GAAG,CAAC,GAAG,KAAK,EAAE,GAAG,eAAe,CAAC,CAAA;QACxC,CAAC,CAAC,CAAA;QACF,OAAO,EAAE,eAAe,EAAE,KAAK,EAAE,CAAA;IACnC,CAAC;CACF"}
1
+ {"version":3,"file":"MultiLineRenderer.js","sourceRoot":"","sources":["../../src/MultiLineRenderer/MultiLineRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAW,MAAM,oBAAoB,CAAA;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,WAAW,CAAA;AAEpC,OAAO,kBAEN,MAAM,uBAAuB,CAAA;AAE9B,MAAM,CAAC,OAAO,OAAO,iBAAkB,SAAQ,kBAAkB;IAC/D,mBAAmB;IACnB,KAAK,CAAC,IAAI,CAAC,GAA6B,EAAE,KAAgB;QACxD,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;QACnC,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAA;QACpE,IAAI,KAAK,GAAG,EAAe,CAAA;QAC3B,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;YACvB,MAAM,QAAQ,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;YACpC,IAAI,CAAC,QAAQ,EAAE;gBACb,OAAM;aACP;YACD,MAAM,EAAE,eAAe,EAAE,GAAG,QAAQ,CAAC,GAAG,EAAE;gBACxC,GAAG,KAAK;gBACR,QAAQ;gBACR,aAAa,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,KAAK,IAAI,MAAM;aAC5C,CAAC,CAAA;YACF,KAAK,GAAG,CAAC,GAAG,KAAK,EAAE,GAAG,eAAe,CAAC,CAAA;QACxC,CAAC,CAAC,CAAA;QACF,OAAO,EAAE,eAAe,EAAE,KAAK,EAAE,CAAA;IACnC,CAAC;CACF"}
@@ -1,6 +1,7 @@
1
+ import React from 'react';
1
2
  import { DialogProps } from '@mui/material';
2
3
  declare function DraggableDialog(props: DialogProps & {
3
4
  title: string;
4
- }): JSX.Element;
5
+ }): React.JSX.Element;
5
6
  declare const _default: typeof DraggableDialog;
6
7
  export default _default;
@@ -1,3 +1,4 @@
1
+ import React from 'react';
1
2
  import { Source } from '../../util';
2
3
  export default function SetColorDialog({ model, handleClose, }: {
3
4
  model: {
@@ -6,4 +7,4 @@ export default function SetColorDialog({ model, handleClose, }: {
6
7
  clearLayout: () => void;
7
8
  };
8
9
  handleClose: () => void;
9
- }): JSX.Element;
10
+ }): React.JSX.Element;