@jbrowse/plugin-wiggle 2.1.4 → 2.1.6

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Files changed (46) hide show
  1. package/dist/BigWigAdapter/BigWigAdapter.js +6 -6
  2. package/dist/BigWigAdapter/BigWigAdapter.js.map +1 -1
  3. package/dist/CreateMultiWiggleExtension/index.js +48 -40
  4. package/dist/CreateMultiWiggleExtension/index.js.map +1 -1
  5. package/dist/LinearWiggleDisplay/models/model.d.ts +10 -6
  6. package/dist/LinearWiggleDisplay/models/model.js +1 -1
  7. package/dist/LinearWiggleDisplay/models/model.js.map +1 -1
  8. package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts +1 -1
  9. package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js +4 -5
  10. package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js.map +1 -1
  11. package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js +1 -1
  12. package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js.map +1 -1
  13. package/dist/MultiLinearWiggleDisplay/models/model.d.ts +7 -3
  14. package/dist/MultiLinearWiggleDisplay/models/model.js +1 -1
  15. package/dist/MultiLinearWiggleDisplay/models/model.js.map +1 -1
  16. package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.js +1 -1
  17. package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.js.map +1 -1
  18. package/dist/index.d.ts +30 -18
  19. package/esm/BigWigAdapter/BigWigAdapter.js +6 -6
  20. package/esm/BigWigAdapter/BigWigAdapter.js.map +1 -1
  21. package/esm/CreateMultiWiggleExtension/index.js +49 -41
  22. package/esm/CreateMultiWiggleExtension/index.js.map +1 -1
  23. package/esm/LinearWiggleDisplay/models/model.d.ts +10 -6
  24. package/esm/LinearWiggleDisplay/models/model.js +2 -2
  25. package/esm/LinearWiggleDisplay/models/model.js.map +1 -1
  26. package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts +1 -1
  27. package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js +4 -5
  28. package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js.map +1 -1
  29. package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js +1 -1
  30. package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js.map +1 -1
  31. package/esm/MultiLinearWiggleDisplay/models/model.d.ts +7 -3
  32. package/esm/MultiLinearWiggleDisplay/models/model.js +2 -2
  33. package/esm/MultiLinearWiggleDisplay/models/model.js.map +1 -1
  34. package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.js +1 -1
  35. package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.js.map +1 -1
  36. package/esm/index.d.ts +30 -18
  37. package/esm/index.js.map +1 -1
  38. package/package.json +3 -3
  39. package/src/BigWigAdapter/BigWigAdapter.ts +6 -12
  40. package/src/CreateMultiWiggleExtension/index.ts +57 -46
  41. package/src/LinearWiggleDisplay/models/model.tsx +5 -4
  42. package/src/MultiLinearWiggleDisplay/components/SetColorDialog.tsx +5 -9
  43. package/src/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.tsx +1 -1
  44. package/src/MultiLinearWiggleDisplay/models/model.tsx +2 -1
  45. package/src/MultiWiggleAddTrackWidget/AddTrackWorkflow.tsx +1 -1
  46. package/src/index.ts +1 -1
package/esm/MultiLinearWiggleDisplay/models/model.js.map CHANGED
@@ -1 +1 @@
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package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.js CHANGED
@@ -55,7 +55,7 @@ export default function MultiWiggleWidget({ model }) {
55
55
  bigWigs = JSON.parse(val);
56
56
  }
57
57
  catch (e) {
58
- bigWigs = val.split('\n');
58
+ bigWigs = val.split(/\n|\r\n|\r/);
59
59
  }
60
60
  const obj = typeof bigWigs[0] === 'string'
61
61
  ? { bigWigs }
package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.js.map CHANGED
@@ -1 +1 @@
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package/esm/index.d.ts CHANGED
@@ -173,7 +173,7 @@ export default class WigglePlugin extends Plugin {
173
173
  readonly adapterConfig: any;
174
174
  readonly parentTrack: any;
175
175
  renderProps(): any;
176
- readonly rendererType: any;
176
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
177
177
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
178
178
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
179
179
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -240,7 +240,7 @@ export default class WigglePlugin extends Plugin {
240
240
  afterAttach(): void;
241
241
  } & {
242
242
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util/types").Region): "" | "Force load to see features";
243
- regionCannotBeRendered(_region: import("@jbrowse/core/util/types").Region): JSX.Element | undefined;
243
+ regionCannotBeRendered(_region: import("@jbrowse/core/util/types").Region): JSX.Element | null;
244
244
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
245
245
  contextMenuItems(): {
246
246
  label: string;
@@ -267,9 +267,9 @@ export default class WigglePlugin extends Plugin {
267
267
  scoreMin: number;
268
268
  scoreMax: number;
269
269
  }): void;
270
- setColor(color: string): void;
271
- setPosColor(color: string): void;
272
- setNegColor(color: string): void;
270
+ setColor(color?: string | undefined): void;
271
+ setPosColor(color?: string | undefined): void;
272
+ setNegColor(color?: string | undefined): void;
273
273
  setLoading(aborter: AbortController): void;
274
274
  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
275
275
  setResolution(res: number): void;
@@ -293,7 +293,11 @@ export default class WigglePlugin extends Plugin {
293
293
  readonly maxScore: any;
294
294
  readonly minScore: any;
295
295
  } & {
296
- readonly rendererConfig: any;
296
+ readonly rendererConfig: {
297
+ [x: string]: any;
298
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
299
+ setSubschema(slotName: string, data: unknown): any;
300
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
297
301
  } & {
298
302
  readonly filled: any;
299
303
  readonly summaryScoreModeSetting: any;
@@ -466,7 +470,7 @@ export default class WigglePlugin extends Plugin {
466
470
  readonly adapterConfig: any;
467
471
  readonly parentTrack: any;
468
472
  renderProps(): any;
469
- readonly rendererType: any;
473
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
470
474
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
471
475
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
472
476
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -533,7 +537,7 @@ export default class WigglePlugin extends Plugin {
533
537
  afterAttach(): void;
534
538
  } & {
535
539
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util/types").Region): "" | "Force load to see features";
536
- regionCannotBeRendered(_region: import("@jbrowse/core/util/types").Region): JSX.Element | undefined;
540
+ regionCannotBeRendered(_region: import("@jbrowse/core/util/types").Region): JSX.Element | null;
537
541
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
538
542
  contextMenuItems(): {
539
543
  label: string;
@@ -560,9 +564,9 @@ export default class WigglePlugin extends Plugin {
560
564
  scoreMin: number;
561
565
  scoreMax: number;
562
566
  }): void;
563
- setColor(color: string): void;
564
- setPosColor(color: string): void;
565
- setNegColor(color: string): void;
567
+ setColor(color?: string | undefined): void;
568
+ setPosColor(color?: string | undefined): void;
569
+ setNegColor(color?: string | undefined): void;
566
570
  setLoading(aborter: AbortController): void;
567
571
  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
568
572
  setResolution(res: number): void;
@@ -586,7 +590,11 @@ export default class WigglePlugin extends Plugin {
586
590
  readonly maxScore: any;
587
591
  readonly minScore: any;
588
592
  } & {
589
- readonly rendererConfig: any;
593
+ readonly rendererConfig: {
594
+ [x: string]: any;
595
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
596
+ setSubschema(slotName: string, data: unknown): any;
597
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
590
598
  } & {
591
599
  readonly filled: any;
592
600
  readonly summaryScoreModeSetting: any;
@@ -783,7 +791,7 @@ export default class WigglePlugin extends Plugin {
783
791
  readonly adapterConfig: any;
784
792
  readonly parentTrack: any;
785
793
  renderProps(): any;
786
- readonly rendererType: any;
794
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
787
795
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
788
796
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
789
797
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -850,7 +858,7 @@ export default class WigglePlugin extends Plugin {
850
858
  afterAttach(): void;
851
859
  } & {
852
860
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util/types").Region): "" | "Force load to see features";
853
- regionCannotBeRendered(_region: import("@jbrowse/core/util/types").Region): JSX.Element | undefined;
861
+ regionCannotBeRendered(_region: import("@jbrowse/core/util/types").Region): JSX.Element | null;
854
862
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
855
863
  contextMenuItems(): {
856
864
  label: string;
@@ -877,9 +885,9 @@ export default class WigglePlugin extends Plugin {
877
885
  scoreMin: number;
878
886
  scoreMax: number;
879
887
  }): void;
880
- setColor(color: string): void;
881
- setPosColor(color: string): void;
882
- setNegColor(color: string): void;
888
+ setColor(color?: string | undefined): void;
889
+ setPosColor(color?: string | undefined): void;
890
+ setNegColor(color?: string | undefined): void;
883
891
  setLoading(aborter: AbortController): void;
884
892
  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
885
893
  setResolution(res: number): void;
@@ -903,7 +911,11 @@ export default class WigglePlugin extends Plugin {
903
911
  readonly maxScore: any;
904
912
  readonly minScore: any;
905
913
  } & {
906
- readonly rendererConfig: any;
914
+ readonly rendererConfig: {
915
+ [x: string]: any;
916
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
917
+ setSubschema(slotName: string, data: unknown): any;
918
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
907
919
  } & {
908
920
  readonly filled: any;
909
921
  readonly summaryScoreModeSetting: any;
package/esm/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,EAEL,WAAW,GAEZ,MAAM,2BAA2B,CAAA;AAElC,SAAS;AACT,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,mBAAmB,MAAM,sBAAsB,CAAA;AACtD,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,eAAe,MAAM,kBAAkB,CAAA;AAC9C,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,yBAAyB,MAAM,4BAA4B,CAAA;AAClE,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAC1D,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAC1D,OAAO,2BAA2B,MAAM,8BAA8B,CAAA;AACtE,OAAO,0BAA0B,MAAM,6BAA6B,CAAA;AAEpE,OAAO,KAAK,KAAK,MAAM,QAAQ,CAAA;AAE/B,OAAO,EACL,oBAAoB,EACpB,yBAAyB,EACzB,qBAAqB,GACtB,MAAM,wBAAwB,CAAA;AAE/B,OAAO,EACL,cAAc,IAAI,iCAAiC,EACnD,YAAY,IAAI,+BAA+B,EAC/C,OAAO,GACR,MAAM,uBAAuB,CAAA;AAE9B,OAAO,EACL,cAAc,IAAI,4BAA4B,EAC9C,YAAY,IAAI,0BAA0B,EAC1C,cAAc,GACf,MAAM,kBAAkB,CAAA;AAEzB,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,MAAM;IAAhD;;QACE,SAAI,GAAG,cAAc,CAAA;QA2DrB,YAAO,GAAG;YACR,iCAAiC;YACjC,4BAA4B;YAC5B,cAAc;YACd,kBAAkB;YAElB,0BAA0B;YAC1B,KAAK;YACL,+BAA+B;SAChC,CAAA;IACH,CAAC;IAnEC,OAAO,CAAC,EAAiB;QACvB,mBAAmB,CAAC,EAAE,CAAC,CAAA;QACvB,cAAc,CAAC,EAAE,CAAC,CAAA;QAClB,kBAAkB,CAAC,EAAE,CAAC,CAAA;QACtB,uBAAuB,CAAC,EAAE,CAAC,CAAA;QAC3B,oBAAoB,CAAC,EAAE,CAAC,CAAA;QACxB,yBAAyB,CAAC,EAAE,CAAC,CAAA;QAC7B,iBAAiB,CAAC,EAAE,CAAC,CAAA;QACrB,eAAe,CAAC,EAAE,CAAC,CAAA;QACnB,gBAAgB,CAAC,EAAE,CAAC,CAAA;QACpB,oBAAoB,CAAC,EAAE,CAAC,CAAA;QACxB,uBAAuB,CAAC,EAAE,CAAC,CAAA;QAC3B,qBAAqB,CAAC,EAAE,CAAC,CAAA;QACzB,kBAAkB,CAAC,EAAE,CAAC,CAAA;QACtB,qBAAqB,CAAC,EAAE,CAAC,CAAA;QACzB,0BAA0B,CAAC,EAAE,CAAC,CAAA;QAC9B,2BAA2B,CAAC,EAAE,CAAC,CAAA;QAE/B,EAAE,CAAC,mBAAmB,CACpB,8BAA8B,EAC9B,CAAC,EAAkB,EAAE,EAAE;YACrB,OAAO,CAAC,IAAkB,EAAE,KAAoB,EAAE,IAAa,EAAE,EAAE;gBACjE,MAAM,UAAU,GAAG,iBAAiB,CAAA;gBACpC,MAAM,WAAW,GAAG,eAAe,CAAA;gBACnC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,cAAc,EAAE,IAAI;iBACrB,CAAA;gBAED,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,IAAI,KAAK,WAAW,EAAE;oBAC/B,OAAO,GAAG,CAAA;iBACX;gBAED,OAAO,EAAE,CAAC,IAAI,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;YAC9B,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QACD,EAAE,CAAC,mBAAmB,CACpB,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;YACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;gBAC7B,IAAI,WAAW,KAAK,eAAe,EAAE;oBACnC,OAAO,mBAAmB,CAAA;iBAC3B;gBACD,OAAO,gBAAgB,CAAC,WAAW,CAAC,CAAA;YACtC,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,oBAAoB,CAAC,EAAE,CAAC,CAAC,CAAA;QACnD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,yBAAyB,CAAC,EAAE,CAAC,CAAC,CAAA;QACxD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,qBAAqB,CAAC,EAAE,CAAC,CAAC,CAAA;IACtD,CAAC;CAYF;AAED,cAAc,QAAQ,CAAA;AAEtB,OAAO,EACL,iCAAiC,EACjC,OAAO,EACP,eAAe,EACf,kBAAkB,EAClB,+BAA+B,GAChC,CAAA"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,EAGL,WAAW,GACZ,MAAM,2BAA2B,CAAA;AAElC,SAAS;AACT,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,mBAAmB,MAAM,sBAAsB,CAAA;AACtD,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,eAAe,MAAM,kBAAkB,CAAA;AAC9C,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,yBAAyB,MAAM,4BAA4B,CAAA;AAClE,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAC1D,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAC1D,OAAO,2BAA2B,MAAM,8BAA8B,CAAA;AACtE,OAAO,0BAA0B,MAAM,6BAA6B,CAAA;AAEpE,OAAO,KAAK,KAAK,MAAM,QAAQ,CAAA;AAE/B,OAAO,EACL,oBAAoB,EACpB,yBAAyB,EACzB,qBAAqB,GACtB,MAAM,wBAAwB,CAAA;AAE/B,OAAO,EACL,cAAc,IAAI,iCAAiC,EACnD,YAAY,IAAI,+BAA+B,EAC/C,OAAO,GACR,MAAM,uBAAuB,CAAA;AAE9B,OAAO,EACL,cAAc,IAAI,4BAA4B,EAC9C,YAAY,IAAI,0BAA0B,EAC1C,cAAc,GACf,MAAM,kBAAkB,CAAA;AAEzB,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,MAAM;IAAhD;;QACE,SAAI,GAAG,cAAc,CAAA;QA2DrB,YAAO,GAAG;YACR,iCAAiC;YACjC,4BAA4B;YAC5B,cAAc;YACd,kBAAkB;YAElB,0BAA0B;YAC1B,KAAK;YACL,+BAA+B;SAChC,CAAA;IACH,CAAC;IAnEC,OAAO,CAAC,EAAiB;QACvB,mBAAmB,CAAC,EAAE,CAAC,CAAA;QACvB,cAAc,CAAC,EAAE,CAAC,CAAA;QAClB,kBAAkB,CAAC,EAAE,CAAC,CAAA;QACtB,uBAAuB,CAAC,EAAE,CAAC,CAAA;QAC3B,oBAAoB,CAAC,EAAE,CAAC,CAAA;QACxB,yBAAyB,CAAC,EAAE,CAAC,CAAA;QAC7B,iBAAiB,CAAC,EAAE,CAAC,CAAA;QACrB,eAAe,CAAC,EAAE,CAAC,CAAA;QACnB,gBAAgB,CAAC,EAAE,CAAC,CAAA;QACpB,oBAAoB,CAAC,EAAE,CAAC,CAAA;QACxB,uBAAuB,CAAC,EAAE,CAAC,CAAA;QAC3B,qBAAqB,CAAC,EAAE,CAAC,CAAA;QACzB,kBAAkB,CAAC,EAAE,CAAC,CAAA;QACtB,qBAAqB,CAAC,EAAE,CAAC,CAAA;QACzB,0BAA0B,CAAC,EAAE,CAAC,CAAA;QAC9B,2BAA2B,CAAC,EAAE,CAAC,CAAA;QAE/B,EAAE,CAAC,mBAAmB,CACpB,8BAA8B,EAC9B,CAAC,EAAkB,EAAE,EAAE;YACrB,OAAO,CAAC,IAAkB,EAAE,KAAoB,EAAE,IAAa,EAAE,EAAE;gBACjE,MAAM,UAAU,GAAG,iBAAiB,CAAA;gBACpC,MAAM,WAAW,GAAG,eAAe,CAAA;gBACnC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,cAAc,EAAE,IAAI;iBACrB,CAAA;gBAED,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,IAAI,KAAK,WAAW,EAAE;oBAC/B,OAAO,GAAG,CAAA;iBACX;gBAED,OAAO,EAAE,CAAC,IAAI,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;YAC9B,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QACD,EAAE,CAAC,mBAAmB,CACpB,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;YACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;gBAC7B,IAAI,WAAW,KAAK,eAAe,EAAE;oBACnC,OAAO,mBAAmB,CAAA;iBAC3B;gBACD,OAAO,gBAAgB,CAAC,WAAW,CAAC,CAAA;YACtC,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,oBAAoB,CAAC,EAAE,CAAC,CAAC,CAAA;QACnD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,yBAAyB,CAAC,EAAE,CAAC,CAAC,CAAA;QACxD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,qBAAqB,CAAC,EAAE,CAAC,CAAC,CAAA;IACtD,CAAC;CAYF;AAED,cAAc,QAAQ,CAAA;AAEtB,OAAO,EACL,iCAAiC,EACjC,OAAO,EACP,eAAe,EACf,kBAAkB,EAClB,+BAA+B,GAChC,CAAA"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-wiggle",
3
- "version": "2.1.4",
3
+ "version": "2.1.6",
4
4
  "description": "JBrowse 2 wiggle adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -37,7 +37,7 @@
37
37
  "clean": "rimraf dist esm *.tsbuildinfo"
38
38
  },
39
39
  "dependencies": {
40
- "@gmod/bbi": "^2.0.2",
40
+ "@gmod/bbi": "^2.0.3",
41
41
  "@mui/icons-material": "^5.0.2",
42
42
  "@popperjs/core": "^2.11.0",
43
43
  "clone": "^2.1.2",
@@ -70,5 +70,5 @@
70
70
  "distModule": "esm/index.js",
71
71
  "srcModule": "src/index.ts",
72
72
  "module": "esm/index.js",
73
- "gitHead": "8f53e016dd83b01a1beea0fc61c33964f5b6c809"
73
+ "gitHead": "df810d2a4f057adcd8f5345d54972508fba007a7"
74
74
  }
package/src/BigWigAdapter/BigWigAdapter.ts CHANGED
@@ -50,24 +50,18 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
50
50
  }
51
51
 
52
52
  public async getRefNames(opts?: BaseOptions) {
53
- const {
54
- header: { refsByName },
55
- } = await this.setup(opts)
56
- return Object.keys(refsByName)
53
+ const { header } = await this.setup(opts)
54
+ return Object.keys(header.refsByName)
57
55
  }
58
56
 
59
57
  public async refIdToName(refId: number) {
60
- const {
61
- header: { refsByNumber },
62
- } = await this.setup()
63
- return refsByNumber[refId]?.name
58
+ const { header } = await this.setup()
59
+ return header.refsByNumber[refId]?.name
64
60
  }
65
61
 
66
62
  public async getGlobalStats(opts?: BaseOptions) {
67
- const {
68
- header: { totalSummary },
69
- } = await this.setup(opts)
70
- return rectifyStats(totalSummary as UnrectifiedFeatureStats)
63
+ const { header } = await this.setup(opts)
64
+ return rectifyStats(header.totalSummary as UnrectifiedFeatureStats)
71
65
  }
72
66
 
73
67
  public getFeatures(region: Region, opts: WiggleOptions = {}) {
package/src/CreateMultiWiggleExtension/index.ts CHANGED
@@ -1,57 +1,68 @@
1
1
  import { lazy } from 'react'
2
2
  import PluginManager from '@jbrowse/core/PluginManager'
3
3
  import { readConfObject } from '@jbrowse/core/configuration'
4
- import { getSession } from '@jbrowse/core/util'
4
+ import { getSession, isSessionWithAddTracks } from '@jbrowse/core/util'
5
5
  import { HierarchicalTrackSelectorModel } from '@jbrowse/plugin-data-management'
6
6
 
7
7
  const ConfirmDialog = lazy(() => import('./ConfirmDialog'))
8
8
 
9
9
  export default function (pm: PluginManager) {
10
- pm.addToExtensionPoint('TrackSelector-multiTrackMenuItems', () => {
11
- return [
12
- {
13
- label: 'Create multi-wiggle track',
14
- onClick: (model: HierarchicalTrackSelectorModel) => {
15
- const tracks = model.selection
16
- const trackIds = tracks.map(c => readConfObject(c, 'name'))
17
- function makeTrack(arg: { name: string }) {
18
- const subadapters = tracks
19
- .map(c => readConfObject(c, 'adapter'))
20
- .map((c, idx) => ({ ...c, source: trackIds[idx] }))
21
- const assemblyNames = [
22
- ...new Set(
23
- tracks.map(c => readConfObject(c, 'assemblyNames')).flat(),
24
- ),
25
- ]
26
- const now = +Date.now()
27
- const trackId = `multitrack-${now}-sessionTrack`
10
+ pm.addToExtensionPoint(
11
+ 'TrackSelector-multiTrackMenuItems',
12
+ (items: unknown[], props: Record<string, unknown>) => {
13
+ const { session } = props
14
+ return [
15
+ ...items,
16
+ ...(isSessionWithAddTracks(session)
17
+ ? [
18
+ {
19
+ label: 'Create multi-wiggle track',
20
+ onClick: (model: HierarchicalTrackSelectorModel) => {
21
+ const tracks = model.selection
22
+ const trackIds = tracks.map(c => readConfObject(c, 'name'))
23
+ function makeTrack(arg: { name: string }) {
24
+ const subadapters = tracks
25
+ .map(c => readConfObject(c, 'adapter'))
26
+ .map((c, idx) => ({ ...c, source: trackIds[idx] }))
27
+ const assemblyNames = [
28
+ ...new Set(
29
+ tracks
30
+ .map(c => readConfObject(c, 'assemblyNames'))
31
+ .flat(),
32
+ ),
33
+ ]
34
+ const now = +Date.now()
35
+ const trackId = `multitrack-${now}-sessionTrack`
28
36
 
29
- getSession(model).addTrackConf({
30
- type: 'MultiQuantitativeTrack',
31
- trackId,
32
- name: arg.name,
33
- assemblyNames,
34
- adapter: {
35
- type: 'MultiWiggleAdapter',
36
- subadapters,
37
- },
38
- })
39
- model.view.showTrack(trackId)
40
- }
41
- getSession(model).queueDialog(handleClose => [
42
- ConfirmDialog,
43
- {
44
- tracks,
45
- onClose: (arg: boolean, arg1: { name: string }) => {
46
- if (arg) {
47
- makeTrack(arg1)
48
- }
49
- handleClose()
37
+ getSession(model).addTrackConf({
38
+ type: 'MultiQuantitativeTrack',
39
+ trackId,
40
+ name: arg.name,
41
+ assemblyNames,
42
+ adapter: {
43
+ type: 'MultiWiggleAdapter',
44
+ subadapters,
45
+ },
46
+ })
47
+ model.view.showTrack(trackId)
48
+ }
49
+ getSession(model).queueDialog(handleClose => [
50
+ ConfirmDialog,
51
+ {
52
+ tracks,
53
+ onClose: (arg: boolean, arg1?: { name: string }) => {
54
+ if (arg && arg1) {
55
+ makeTrack(arg1)
56
+ }
57
+ handleClose()
58
+ },
59
+ },
60
+ ])
61
+ },
50
62
  },
51
- },
52
- ])
53
- },
54
- },
55
- ]
56
- })
63
+ ]
64
+ : []),
65
+ ]
66
+ },
67
+ )
57
68
  }
package/src/LinearWiggleDisplay/models/model.tsx CHANGED
@@ -6,6 +6,7 @@ import {
6
6
  readConfObject,
7
7
  } from '@jbrowse/core/configuration'
8
8
  import {
9
+ getEnv,
9
10
  getSession,
10
11
  getContainingView,
11
12
  isSelectionContainer,
@@ -15,7 +16,7 @@ import {
15
16
  LinearGenomeViewModel,
16
17
  } from '@jbrowse/plugin-linear-genome-view'
17
18
  import { when } from 'mobx'
18
- import { isAlive, types, getEnv, Instance } from 'mobx-state-tree'
19
+ import { isAlive, types, Instance } from 'mobx-state-tree'
19
20
  import PluginManager from '@jbrowse/core/PluginManager'
20
21
 
21
22
  import { Feature } from '@jbrowse/core/util/simpleFeature'
@@ -93,13 +94,13 @@ const stateModelFactory = (
93
94
  self.statsReady = true
94
95
  }
95
96
  },
96
- setColor(color: string) {
97
+ setColor(color?: string) {
97
98
  self.color = color
98
99
  },
99
- setPosColor(color: string) {
100
+ setPosColor(color?: string) {
100
101
  self.posColor = color
101
102
  },
102
- setNegColor(color: string) {
103
+ setNegColor(color?: string) {
103
104
  self.negColor = color
104
105
  },
105
106
 
package/src/MultiLinearWiggleDisplay/components/SetColorDialog.tsx CHANGED
@@ -61,7 +61,7 @@ export default function SetColorDialog({
61
61
  handleClose,
62
62
  }: {
63
63
  model: {
64
- sources: Source[]
64
+ sources?: Source[]
65
65
  setLayout: (s: Source[]) => void
66
66
  clearLayout: () => void
67
67
  }
@@ -70,11 +70,7 @@ export default function SetColorDialog({
70
70
  const { classes } = useStyles()
71
71
  const { sources } = model
72
72
  const [currLayout, setCurrLayout] = useState(clone(sources || []))
73
- const [showTipsTmp, setShowTips] = useLocalStorage(
74
- 'multiwiggle-showTips',
75
- 'true',
76
- )
77
- const showTips = showTipsTmp === 'true'
73
+ const [showTips, setShowTips] = useLocalStorage('multiwiggle-showTips', true)
78
74
  return (
79
75
  <Dialog
80
76
  PaperComponent={PaperComponent}
@@ -93,7 +89,7 @@ export default function SetColorDialog({
93
89
  <Button
94
90
  variant="contained"
95
91
  style={{ float: 'right' }}
96
- onClick={() => setShowTips(showTips ? 'false' : 'true')}
92
+ onClick={() => setShowTips(!showTips)}
97
93
  >
98
94
  {showTips ? 'Hide tips' : 'Show tips'}
99
95
  </Button>
@@ -136,7 +132,7 @@ export default function SetColorDialog({
136
132
  color="inherit"
137
133
  onClick={() => {
138
134
  model.clearLayout()
139
- setCurrLayout(model.sources)
135
+ setCurrLayout(model.sources || [])
140
136
  }}
141
137
  >
142
138
  Clear custom settings
@@ -146,7 +142,7 @@ export default function SetColorDialog({
146
142
  color="secondary"
147
143
  onClick={() => {
148
144
  handleClose()
149
- setCurrLayout([...model.sources])
145
+ setCurrLayout([...(model.sources || [])])
150
146
  }}
151
147
  >
152
148
  Cancel
package/src/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.tsx CHANGED
@@ -51,7 +51,7 @@ const Wrapper = observer(
51
51
  left: 0,
52
52
  pointerEvents: 'none',
53
53
  height,
54
- width: 1800,
54
+ width: getContainingView(model).width,
55
55
  }}
56
56
  >
57
57
  {children}
package/src/MultiLinearWiggleDisplay/models/model.tsx CHANGED
@@ -1,5 +1,5 @@
1
1
  import React, { lazy } from 'react'
2
- import { addDisposer, getEnv, isAlive, types, Instance } from 'mobx-state-tree'
2
+ import { addDisposer, isAlive, types, Instance } from 'mobx-state-tree'
3
3
  import { autorun, when } from 'mobx'
4
4
  import { axisPropsFromTickScale } from 'react-d3-axis-mod'
5
5
  import deepEqual from 'fast-deep-equal'
@@ -13,6 +13,7 @@ import {
13
13
  } from '@jbrowse/core/configuration'
14
14
  import {
15
15
  getSession,
16
+ getEnv,
16
17
  getContainingView,
17
18
  isSelectionContainer,
18
19
  Feature,
package/src/MultiWiggleAddTrackWidget/AddTrackWorkflow.tsx CHANGED
@@ -86,7 +86,7 @@ export default function MultiWiggleWidget({ model }: { model: AddTrackModel }) {
86
86
  try {
87
87
  bigWigs = JSON.parse(val)
88
88
  } catch (e) {
89
- bigWigs = val.split('\n')
89
+ bigWigs = val.split(/\n|\r\n|\r/)
90
90
  }
91
91
  const obj =
92
92
  typeof bigWigs[0] === 'string'
package/src/index.ts CHANGED
@@ -3,8 +3,8 @@ import PluginManager from '@jbrowse/core/PluginManager'
3
3
  import { FileLocation } from '@jbrowse/core/util/types'
4
4
  import {
5
5
  AdapterGuesser,
6
- getFileName,
7
6
  TrackTypeGuesser,
7
+ getFileName,
8
8
  } from '@jbrowse/core/util/tracks'
9
9
 
10
10
  // locals