@jbrowse/plugin-alignments 2.1.4 → 2.1.6

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Files changed (38) hide show
  1. package/dist/AlignmentsFeatureDetail/index.d.ts +7 -0
  2. package/dist/CramAdapter/CramTestAdapters.js +1 -1
  3. package/dist/CramAdapter/CramTestAdapters.js.map +1 -1
  4. package/dist/LinearAlignmentsDisplay/models/model.d.ts +1 -1
  5. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +2 -2
  6. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -1
  7. package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts +1 -5
  8. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
  9. package/dist/LinearPileupDisplay/model.d.ts +8 -4
  10. package/dist/LinearPileupDisplay/model.js +7 -8
  11. package/dist/LinearPileupDisplay/model.js.map +1 -1
  12. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +15 -7
  13. package/dist/LinearSNPCoverageDisplay/models/model.js +10 -16
  14. package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
  15. package/dist/SNPCoverageRenderer/configSchema.js.map +1 -1
  16. package/esm/AlignmentsFeatureDetail/index.d.ts +7 -0
  17. package/esm/CramAdapter/CramTestAdapters.js +1 -1
  18. package/esm/CramAdapter/CramTestAdapters.js.map +1 -1
  19. package/esm/LinearAlignmentsDisplay/models/model.d.ts +1 -1
  20. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +1 -1
  21. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -1
  22. package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts +1 -5
  23. package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
  24. package/esm/LinearPileupDisplay/model.d.ts +8 -4
  25. package/esm/LinearPileupDisplay/model.js +8 -9
  26. package/esm/LinearPileupDisplay/model.js.map +1 -1
  27. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +15 -7
  28. package/esm/LinearSNPCoverageDisplay/models/model.js +10 -16
  29. package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -1
  30. package/esm/SNPCoverageRenderer/configSchema.js.map +1 -1
  31. package/package.json +2 -2
  32. package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +51 -12
  33. package/src/CramAdapter/CramTestAdapters.ts +1 -1
  34. package/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx +1 -1
  35. package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx +1 -5
  36. package/src/LinearPileupDisplay/model.ts +11 -12
  37. package/src/LinearSNPCoverageDisplay/models/model.ts +18 -20
  38. /package/src/SNPCoverageRenderer/{configSchema.js → configSchema.ts} +0 -0
package/esm/LinearPileupDisplay/model.js CHANGED
@@ -1,10 +1,10 @@
1
1
  import { lazy } from 'react';
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  import { autorun, observable } from 'mobx';
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- import { cast, types, addDisposer, getEnv } from 'mobx-state-tree';
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+ import { cast, types, addDisposer } from 'mobx-state-tree';
4
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  import copy from 'copy-to-clipboard';
5
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  import { ConfigurationReference, readConfObject, getConf, } from '@jbrowse/core/configuration';
6
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  import { getRpcSessionId } from '@jbrowse/core/util/tracks';
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- import { getSession, isSessionModelWithWidgets, getContainingView, SimpleFeature, } from '@jbrowse/core/util';
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+ import { getEnv, getSession, isSessionModelWithWidgets, getContainingView, SimpleFeature, } from '@jbrowse/core/util';
8
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  import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
9
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  // icons
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  import VisibilityIcon from '@mui/icons-material/Visibility';
@@ -125,18 +125,16 @@ const stateModelFactory = (configSchema) => types
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  const { rpcManager } = getSession(self);
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  const view = getContainingView(self);
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  const { sortedBy, colorBy, parentTrack, adapterConfig, rendererType, } = self;
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- const { staticBlocks, bpPerPx } = view;
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- if (!self.estimatedStatsReady) {
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- return;
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- }
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- if (self.regionTooLarge) {
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+ if (!view.initialized ||
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+ !self.estimatedStatsReady ||
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+ self.regionTooLarge) {
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  return;
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  }
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+ const { staticBlocks, bpPerPx } = view;
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  // continually generate the vc pairing, set and rerender if any
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  // new values seen
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  if (colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) {
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- const uniqueTagSet = await getUniqueTagValues(self, colorBy, staticBlocks);
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- self.updateColorTagMap(uniqueTagSet);
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+ self.updateColorTagMap(await getUniqueTagValues(self, colorBy, staticBlocks));
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  }
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  if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
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  const adapter = getConf(parentTrack, ['adapter']);
@@ -145,6 +143,7 @@ const stateModelFactory = (configSchema) => types
145
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  if (sortedBy) {
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  const { pos, refName, assemblyName } = sortedBy;
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  // render just the sorted region first
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+ // @ts-ignore
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  await self.rendererType.renderInClient(rpcManager, {
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  assemblyName,
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  regions: [
package/esm/LinearPileupDisplay/model.js.map CHANGED
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1
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package/esm/LinearSNPCoverageDisplay/models/model.d.ts CHANGED
@@ -135,7 +135,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
135
135
  readonly adapterConfig: any;
136
136
  readonly parentTrack: any;
137
137
  renderProps(): any;
138
- readonly rendererType: any;
138
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
139
139
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
140
140
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
141
141
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -202,7 +202,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
202
202
  afterAttach(): void;
203
203
  } & {
204
204
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
205
- regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
205
+ regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
206
206
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
207
207
  contextMenuItems(): {
208
208
  label: string;
@@ -229,9 +229,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
229
229
  scoreMin: number;
230
230
  scoreMax: number;
231
231
  }): void;
232
- setColor(color: string): void;
233
- setPosColor(color: string): void;
234
- setNegColor(color: string): void;
232
+ setColor(color?: string | undefined): void;
233
+ setPosColor(color?: string | undefined): void;
234
+ setNegColor(color?: string | undefined): void;
235
235
  setLoading(aborter: AbortController): void;
236
236
  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
237
237
  setResolution(res: number): void;
@@ -255,7 +255,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
255
255
  readonly maxScore: any;
256
256
  readonly minScore: any;
257
257
  } & {
258
- readonly rendererConfig: any;
258
+ readonly rendererConfig: {
259
+ [x: string]: any;
260
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
261
+ setSubschema(slotName: string, data: unknown): any;
262
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
259
263
  } & {
260
264
  readonly filled: any;
261
265
  readonly summaryScoreModeSetting: any;
@@ -331,7 +335,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
331
335
  }): void;
332
336
  updateModificationColorMap(uniqueModifications: string[]): void;
333
337
  } & {
334
- readonly rendererConfig: any;
338
+ readonly rendererConfig: {
339
+ [x: string]: any;
340
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
341
+ setSubschema(slotName: string, data: unknown): any;
342
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
335
343
  readonly drawArcsSetting: any;
336
344
  readonly drawInterbaseCountsSetting: any;
337
345
  readonly drawIndicatorsSetting: any;
package/esm/LinearSNPCoverageDisplay/models/model.js CHANGED
@@ -110,16 +110,16 @@ const stateModelFactory = (pluginManager, configSchema) => types
110
110
  addDisposer(self, autorun(async () => {
111
111
  try {
112
112
  const { colorBy } = self;
113
- const { staticBlocks } = getContainingView(self);
114
- if (!self.estimatedStatsReady) {
115
- return;
116
- }
117
- if (self.regionTooLarge) {
113
+ const view = getContainingView(self);
114
+ if (!view.initialized ||
115
+ !self.estimatedStatsReady ||
116
+ self.regionTooLarge) {
118
117
  return;
119
118
  }
119
+ const { staticBlocks } = view;
120
120
  if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
121
- const vals = await getUniqueModificationValues(self, getConf(self.parentTrack, 'adapter'), colorBy, staticBlocks);
122
- self.updateModificationColorMap(vals);
121
+ const adapter = getConf(self.parentTrack, 'adapter');
122
+ self.updateModificationColorMap(await getUniqueModificationValues(self, adapter, colorBy, staticBlocks));
123
123
  }
124
124
  }
125
125
  catch (error) {
@@ -158,25 +158,19 @@ const stateModelFactory = (pluginManager, configSchema) => types
158
158
  label: 'Draw insertion/clipping indicators',
159
159
  type: 'checkbox',
160
160
  checked: self.drawIndicatorsSetting,
161
- onClick: () => {
162
- self.toggleDrawIndicators();
163
- },
161
+ onClick: () => self.toggleDrawIndicators(),
164
162
  },
165
163
  {
166
164
  label: 'Draw insertion/clipping counts',
167
165
  type: 'checkbox',
168
166
  checked: self.drawInterbaseCountsSetting,
169
- onClick: () => {
170
- self.toggleDrawInterbaseCounts();
171
- },
167
+ onClick: () => self.toggleDrawInterbaseCounts(),
172
168
  },
173
169
  {
174
170
  label: 'Draw arcs',
175
171
  type: 'checkbox',
176
172
  checked: self.drawArcsSetting,
177
- onClick: () => {
178
- self.toggleDrawArcs();
179
- },
173
+ onClick: () => self.toggleDrawArcs(),
180
174
  },
181
175
  ];
182
176
  },
package/esm/LinearSNPCoverageDisplay/models/model.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/SNPCoverageRenderer/configSchema.js.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,qBAAqB,EACrB;IACE,SAAS,EAAE;QACT,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,kCAAkC;QAC/C,YAAY,EAAE,KAAK;KACpB;IACD,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,+DAA+D;QACjE,YAAY,EAAE,GAAG;KAClB;IACD,QAAQ,EAAE;QACR,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,6CAA6C;QAC1D,YAAY,EAAE,IAAI;KACnB;IACD,mBAAmB,EAAE;QACnB,IAAI,EAAE,SAAS;QACf,WAAW,EACT,iJAAiJ;QACnJ,YAAY,EAAE,IAAI;KACnB;IACD,cAAc,EAAE;QACd,IAAI,EAAE,SAAS;QACf,WAAW,EACT,8DAA8D;QAChE,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-alignments",
3
- "version": "2.1.4",
3
+ "version": "2.1.6",
4
4
  "description": "JBrowse 2 alignments adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -64,5 +64,5 @@
64
64
  "distModule": "esm/index.js",
65
65
  "srcModule": "src/index.ts",
66
66
  "module": "esm/index.js",
67
- "gitHead": "8f53e016dd83b01a1beea0fc61c33964f5b6c809"
67
+ "gitHead": "df810d2a4f057adcd8f5345d54972508fba007a7"
68
68
  }
package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap CHANGED
@@ -280,6 +280,45 @@ exports[`open up a widget 1`] = `
280
280
  </div>
281
281
  </div>
282
282
  </div>
283
+ <div
284
+ class="tss-1upvn7b-container2"
285
+ >
286
+ <button
287
+ class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium css-sghohy-MuiButtonBase-root-MuiButton-root"
288
+ tabindex="0"
289
+ type="button"
290
+ >
291
+ Show feature sequence
292
+ <span
293
+ class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
294
+ />
295
+ </button>
296
+ <div
297
+ class="MuiFormControl-root tss-1x17dzq-formControl css-1nrlq1o-MuiFormControl-root"
298
+ >
299
+ <button
300
+ class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeMedium css-78trlr-MuiButtonBase-root-MuiIconButton-root"
301
+ tabindex="0"
302
+ type="button"
303
+ >
304
+ <svg
305
+ aria-hidden="true"
306
+ class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
307
+ data-testid="HelpIcon"
308
+ focusable="false"
309
+ viewBox="0 0 24 24"
310
+ >
311
+ <path
312
+ d="M12 2C6.48 2 2 6.48 2 12s4.48 10 10 10 10-4.48 10-10S17.52 2 12 2zm1 17h-2v-2h2v2zm2.07-7.75-.9.92C13.45 12.9 13 13.5 13 15h-2v-.5c0-1.1.45-2.1 1.17-2.83l1.24-1.26c.37-.36.59-.86.59-1.41 0-1.1-.9-2-2-2s-2 .9-2 2H8c0-2.21 1.79-4 4-4s4 1.79 4 4c0 .88-.36 1.68-.93 2.25z"
313
+ />
314
+ </svg>
315
+ <span
316
+ class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
317
+ />
318
+ </button>
319
+ </div>
320
+ <br />
321
+ </div>
283
322
  </div>
284
323
  </div>
285
324
  </div>
@@ -345,7 +384,7 @@ exports[`open up a widget 1`] = `
345
384
  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
346
385
  >
347
386
  <span
348
- class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
387
+ class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
349
388
  >
350
389
  <input
351
390
  class="PrivateSwitchBase-input css-1m9pwf3"
@@ -379,7 +418,7 @@ exports[`open up a widget 1`] = `
379
418
  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
380
419
  >
381
420
  <span
382
- class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
421
+ class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
383
422
  >
384
423
  <input
385
424
  class="PrivateSwitchBase-input css-1m9pwf3"
@@ -413,7 +452,7 @@ exports[`open up a widget 1`] = `
413
452
  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
414
453
  >
415
454
  <span
416
- class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
455
+ class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
417
456
  >
418
457
  <input
419
458
  class="PrivateSwitchBase-input css-1m9pwf3"
@@ -447,7 +486,7 @@ exports[`open up a widget 1`] = `
447
486
  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
448
487
  >
449
488
  <span
450
- class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
489
+ class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
451
490
  >
452
491
  <input
453
492
  class="PrivateSwitchBase-input css-1m9pwf3"
@@ -481,7 +520,7 @@ exports[`open up a widget 1`] = `
481
520
  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
482
521
  >
483
522
  <span
484
- class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
523
+ class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
485
524
  >
486
525
  <input
487
526
  class="PrivateSwitchBase-input css-1m9pwf3"
@@ -515,7 +554,7 @@ exports[`open up a widget 1`] = `
515
554
  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
516
555
  >
517
556
  <span
518
- class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
557
+ class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
519
558
  >
520
559
  <input
521
560
  class="PrivateSwitchBase-input css-1m9pwf3"
@@ -549,7 +588,7 @@ exports[`open up a widget 1`] = `
549
588
  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
550
589
  >
551
590
  <span
552
- class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
591
+ class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
553
592
  >
554
593
  <input
555
594
  class="PrivateSwitchBase-input css-1m9pwf3"
@@ -583,7 +622,7 @@ exports[`open up a widget 1`] = `
583
622
  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
584
623
  >
585
624
  <span
586
- class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
625
+ class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
587
626
  >
588
627
  <input
589
628
  class="PrivateSwitchBase-input css-1m9pwf3"
@@ -617,7 +656,7 @@ exports[`open up a widget 1`] = `
617
656
  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
618
657
  >
619
658
  <span
620
- class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
659
+ class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
621
660
  >
622
661
  <input
623
662
  class="PrivateSwitchBase-input css-1m9pwf3"
@@ -651,7 +690,7 @@ exports[`open up a widget 1`] = `
651
690
  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
652
691
  >
653
692
  <span
654
- class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
693
+ class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
655
694
  >
656
695
  <input
657
696
  class="PrivateSwitchBase-input css-1m9pwf3"
@@ -685,7 +724,7 @@ exports[`open up a widget 1`] = `
685
724
  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
686
725
  >
687
726
  <span
688
- class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
727
+ class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
689
728
  >
690
729
  <input
691
730
  class="PrivateSwitchBase-input css-1m9pwf3"
@@ -719,7 +758,7 @@ exports[`open up a widget 1`] = `
719
758
  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
720
759
  >
721
760
  <span
722
- class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
761
+ class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
723
762
  >
724
763
  <input
725
764
  class="PrivateSwitchBase-input css-1m9pwf3"
package/src/CramAdapter/CramTestAdapters.ts CHANGED
@@ -10,7 +10,7 @@ export function parseSmallFasta(text: string) {
10
10
  .split('>')
11
11
  .filter(t => /\S/.test(t))
12
12
  .map(entryText => {
13
- const [defLine, ...seqLines] = entryText.split('\n')
13
+ const [defLine, ...seqLines] = entryText.split(/\n|\r\n|\r/)
14
14
  const [id, ...descriptionLines] = defLine.split(' ')
15
15
  const description = descriptionLines.join(' ')
16
16
  const sequence = seqLines.join('').replace(/\s/g, '')
package/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx CHANGED
@@ -1,6 +1,6 @@
1
1
  import React from 'react'
2
2
  import { observer } from 'mobx-react'
3
- import Typography from '@mui/material/Typography'
3
+ import { Typography } from '@mui/material'
4
4
 
5
5
  export interface LinearPileupDisplayBlurbProps {
6
6
  model: {
package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx CHANGED
@@ -26,14 +26,10 @@ const useStyles = makeStyles()(theme => ({
26
26
 
27
27
  function SetFeatureHeightDlg(props: {
28
28
  model: {
29
- minScore: number
30
- maxScore: number
31
- setMinScore: Function
32
- setMaxScore: Function
33
29
  setFeatureHeight: Function
34
30
  setNoSpacing: Function
35
31
  featureHeightSetting: number
36
- noSpacing: boolean
32
+ noSpacing?: boolean
37
33
  }
38
34
  handleClose: () => void
39
35
  }) {
package/src/LinearPileupDisplay/model.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import { lazy } from 'react'
2
2
  import { autorun, observable } from 'mobx'
3
- import { cast, types, addDisposer, getEnv, Instance } from 'mobx-state-tree'
3
+ import { cast, types, addDisposer, Instance } from 'mobx-state-tree'
4
4
  import copy from 'copy-to-clipboard'
5
5
  import {
6
6
  AnyConfigurationModel,
@@ -10,6 +10,7 @@ import {
10
10
  } from '@jbrowse/core/configuration'
11
11
  import { getRpcSessionId } from '@jbrowse/core/util/tracks'
12
12
  import {
13
+ getEnv,
13
14
  getSession,
14
15
  isSessionModelWithWidgets,
15
16
  getContainingView,
@@ -177,24 +178,22 @@ const stateModelFactory = (configSchema: LinearPileupDisplayConfigModel) =>
177
178
  adapterConfig,
178
179
  rendererType,
179
180
  } = self
180
- const { staticBlocks, bpPerPx } = view
181
181
 
182
- if (!self.estimatedStatsReady) {
183
- return
184
- }
185
- if (self.regionTooLarge) {
182
+ if (
183
+ !view.initialized ||
184
+ !self.estimatedStatsReady ||
185
+ self.regionTooLarge
186
+ ) {
186
187
  return
187
188
  }
188
189
 
190
+ const { staticBlocks, bpPerPx } = view
189
191
  // continually generate the vc pairing, set and rerender if any
190
192
  // new values seen
191
193
  if (colorBy?.tag) {
192
- const uniqueTagSet = await getUniqueTagValues(
193
- self,
194
- colorBy,
195
- staticBlocks,
194
+ self.updateColorTagMap(
195
+ await getUniqueTagValues(self, colorBy, staticBlocks),
196
196
  )
197
- self.updateColorTagMap(uniqueTagSet)
198
197
  }
199
198
 
200
199
  if (colorBy?.type === 'modifications') {
@@ -211,8 +210,8 @@ const stateModelFactory = (configSchema: LinearPileupDisplayConfigModel) =>
211
210
 
212
211
  if (sortedBy) {
213
212
  const { pos, refName, assemblyName } = sortedBy
214
-
215
213
  // render just the sorted region first
214
+ // @ts-ignore
216
215
  await self.rendererType.renderInClient(rpcManager, {
217
216
  assemblyName,
218
217
  regions: [
package/src/LinearSNPCoverageDisplay/models/model.ts CHANGED
@@ -160,22 +160,26 @@ const stateModelFactory = (
160
160
  async () => {
161
161
  try {
162
162
  const { colorBy } = self
163
- const { staticBlocks } = getContainingView(self) as LGV
163
+ const view = getContainingView(self) as LGV
164
164
 
165
- if (!self.estimatedStatsReady) {
166
- return
167
- }
168
- if (self.regionTooLarge) {
165
+ if (
166
+ !view.initialized ||
167
+ !self.estimatedStatsReady ||
168
+ self.regionTooLarge
169
+ ) {
169
170
  return
170
171
  }
172
+ const { staticBlocks } = view
171
173
  if (colorBy?.type === 'modifications') {
172
- const vals = await getUniqueModificationValues(
173
- self,
174
- getConf(self.parentTrack, 'adapter'),
175
- colorBy,
176
- staticBlocks,
174
+ const adapter = getConf(self.parentTrack, 'adapter')
175
+ self.updateModificationColorMap(
176
+ await getUniqueModificationValues(
177
+ self,
178
+ adapter,
179
+ colorBy,
180
+ staticBlocks,
181
+ ),
177
182
  )
178
- self.updateModificationColorMap(vals)
179
183
  }
180
184
  } catch (error) {
181
185
  console.error(error)
@@ -222,25 +226,19 @@ const stateModelFactory = (
222
226
  label: 'Draw insertion/clipping indicators',
223
227
  type: 'checkbox',
224
228
  checked: self.drawIndicatorsSetting,
225
- onClick: () => {
226
- self.toggleDrawIndicators()
227
- },
229
+ onClick: () => self.toggleDrawIndicators(),
228
230
  },
229
231
  {
230
232
  label: 'Draw insertion/clipping counts',
231
233
  type: 'checkbox',
232
234
  checked: self.drawInterbaseCountsSetting,
233
- onClick: () => {
234
- self.toggleDrawInterbaseCounts()
235
- },
235
+ onClick: () => self.toggleDrawInterbaseCounts(),
236
236
  },
237
237
  {
238
238
  label: 'Draw arcs',
239
239
  type: 'checkbox',
240
240
  checked: self.drawArcsSetting,
241
- onClick: () => {
242
- self.toggleDrawArcs()
243
- },
241
+ onClick: () => self.toggleDrawArcs(),
244
242
  },
245
243
  ]
246
244
  },