@jbrowse/plugin-alignments 2.10.1 → 2.10.3

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 (85) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +2 -2
  2. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +10 -113
  3. package/dist/AlignmentsFeatureDetail/BreakendOptionDialog.d.ts +12 -0
  4. package/dist/AlignmentsFeatureDetail/BreakendOptionDialog.js +89 -0
  5. package/dist/AlignmentsFeatureDetail/Formatter.d.ts +4 -0
  6. package/dist/AlignmentsFeatureDetail/Formatter.js +47 -0
  7. package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.d.ts +9 -0
  8. package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js +92 -0
  9. package/dist/AlignmentsFeatureDetail/PairLink.d.ts +6 -0
  10. package/dist/AlignmentsFeatureDetail/PairLink.js +16 -0
  11. package/dist/AlignmentsFeatureDetail/SuppAlignments.d.ts +8 -0
  12. package/dist/AlignmentsFeatureDetail/SuppAlignments.js +26 -0
  13. package/dist/AlignmentsFeatureDetail/SuppAlignmentsLocStrings.d.ts +6 -0
  14. package/dist/AlignmentsFeatureDetail/{AlignmentsFeatureSuppAligns.js → SuppAlignmentsLocStrings.js} +8 -7
  15. package/dist/AlignmentsFeatureDetail/configSchema.d.ts +1 -0
  16. package/dist/AlignmentsFeatureDetail/configSchema.js +5 -0
  17. package/dist/AlignmentsFeatureDetail/getSAFeatures.d.ts +23 -0
  18. package/dist/AlignmentsFeatureDetail/getSAFeatures.js +41 -0
  19. package/dist/AlignmentsFeatureDetail/index.d.ts +1 -50
  20. package/dist/AlignmentsFeatureDetail/index.js +6 -17
  21. package/dist/AlignmentsFeatureDetail/launchBreakpointSplitView.d.ts +22 -0
  22. package/dist/AlignmentsFeatureDetail/launchBreakpointSplitView.js +50 -0
  23. package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts +51 -0
  24. package/dist/AlignmentsFeatureDetail/stateModelFactory.js +12 -0
  25. package/dist/AlignmentsFeatureDetail/tagInfo.d.ts +63 -0
  26. package/dist/AlignmentsFeatureDetail/tagInfo.js +66 -0
  27. package/dist/BamAdapter/BamAdapter.js +10 -9
  28. package/dist/CramAdapter/CramAdapter.js +17 -19
  29. package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +38 -24
  30. package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +8 -8
  31. package/dist/LinearPileupDisplay/model.d.ts +24 -26
  32. package/dist/LinearPileupDisplay/model.js +4 -4
  33. package/dist/LinearReadArcsDisplay/model.d.ts +8 -8
  34. package/dist/LinearReadArcsDisplay/model.js +2 -2
  35. package/dist/LinearReadCloudDisplay/model.d.ts +13 -7
  36. package/dist/LinearReadCloudDisplay/model.js +2 -2
  37. package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +5 -2
  38. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +11 -2
  39. package/dist/shared/BaseDisplayComponent.js +3 -1
  40. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +2 -2
  41. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +12 -92
  42. package/esm/AlignmentsFeatureDetail/BreakendOptionDialog.d.ts +12 -0
  43. package/esm/AlignmentsFeatureDetail/BreakendOptionDialog.js +64 -0
  44. package/esm/AlignmentsFeatureDetail/Formatter.d.ts +4 -0
  45. package/esm/AlignmentsFeatureDetail/Formatter.js +18 -0
  46. package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.d.ts +9 -0
  47. package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js +66 -0
  48. package/esm/AlignmentsFeatureDetail/PairLink.d.ts +6 -0
  49. package/esm/AlignmentsFeatureDetail/PairLink.js +10 -0
  50. package/esm/AlignmentsFeatureDetail/SuppAlignments.d.ts +8 -0
  51. package/esm/AlignmentsFeatureDetail/SuppAlignments.js +20 -0
  52. package/esm/AlignmentsFeatureDetail/SuppAlignmentsLocStrings.d.ts +6 -0
  53. package/esm/AlignmentsFeatureDetail/{AlignmentsFeatureSuppAligns.js → SuppAlignmentsLocStrings.js} +7 -6
  54. package/esm/AlignmentsFeatureDetail/configSchema.d.ts +1 -0
  55. package/esm/AlignmentsFeatureDetail/configSchema.js +2 -0
  56. package/esm/AlignmentsFeatureDetail/getSAFeatures.d.ts +23 -0
  57. package/esm/AlignmentsFeatureDetail/getSAFeatures.js +37 -0
  58. package/esm/AlignmentsFeatureDetail/index.d.ts +1 -50
  59. package/esm/AlignmentsFeatureDetail/index.js +4 -13
  60. package/esm/AlignmentsFeatureDetail/launchBreakpointSplitView.d.ts +22 -0
  61. package/esm/AlignmentsFeatureDetail/launchBreakpointSplitView.js +46 -0
  62. package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts +51 -0
  63. package/esm/AlignmentsFeatureDetail/stateModelFactory.js +8 -0
  64. package/esm/AlignmentsFeatureDetail/tagInfo.d.ts +63 -0
  65. package/esm/AlignmentsFeatureDetail/tagInfo.js +63 -0
  66. package/esm/BamAdapter/BamAdapter.js +10 -9
  67. package/esm/CramAdapter/CramAdapter.js +18 -20
  68. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +38 -24
  69. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +8 -8
  70. package/esm/LinearPileupDisplay/model.d.ts +24 -26
  71. package/esm/LinearPileupDisplay/model.js +4 -4
  72. package/esm/LinearReadArcsDisplay/model.d.ts +8 -8
  73. package/esm/LinearReadArcsDisplay/model.js +2 -2
  74. package/esm/LinearReadCloudDisplay/model.d.ts +13 -7
  75. package/esm/LinearReadCloudDisplay/model.js +2 -2
  76. package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +5 -2
  77. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +11 -2
  78. package/esm/shared/BaseDisplayComponent.js +3 -1
  79. package/package.json +2 -2
  80. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts +0 -6
  81. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts +0 -6
  82. /package/dist/AlignmentsFeatureDetail/{AlignmentsFeatureFlags.d.ts → Flags.d.ts} +0 -0
  83. /package/dist/AlignmentsFeatureDetail/{AlignmentsFeatureFlags.js → Flags.js} +0 -0
  84. /package/esm/AlignmentsFeatureDetail/{AlignmentsFeatureFlags.d.ts → Flags.d.ts} +0 -0
  85. /package/esm/AlignmentsFeatureDetail/{AlignmentsFeatureFlags.js → Flags.js} +0 -0
@@ -46,28 +46,32 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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  message: string | undefined;
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  maxHeightReached: boolean;
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  ReactComponent: ({ model, }: {
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- model: any;
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- }) => any;
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+ model: {
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+ error?: unknown;
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+ reload: () => void;
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+ message: import("react").ReactNode;
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+ filled?: boolean | undefined;
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+ status?: string | undefined;
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+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
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+ };
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+ }) => import("react").JSX.Element | undefined;
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  renderProps: any;
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  } & {
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  doReload(): void;
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  afterAttach(): void;
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  setStatus(message: string): void;
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  setLoading(abortController: AbortController): void;
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- setMessage(messageText: string): void;
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+ setMessage(messageText: string): void; /**
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+ * #action
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+ */
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  setRendered(props: {
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  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
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- /**
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- * #action
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- */
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  features: Map<string, Feature>;
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  layout: any;
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  maxHeightReached: boolean;
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  renderProps: any;
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  } | undefined): void;
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- setError(error: unknown): void; /**
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- * #action
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- */
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+ setError(error: unknown): void;
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  reload(): void;
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  beforeDestroy(): void;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -173,11 +177,11 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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  rendererTypeName: string;
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  error: unknown;
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- message: string | undefined;
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- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
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+ message: string | undefined; /**
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  * #property
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  */
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+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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  type: import("mobx-state-tree").ISimpleType<string>;
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  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  }, {
@@ -220,7 +224,9 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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  } & {
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  afterAttach(): void;
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  } & {
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- setCurrStatsBpPerPx(n: number): void;
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+ setCurrStatsBpPerPx(n: number): void; /**
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+ * #property
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+ */
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  setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
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  getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
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  setFeatureDensityStatsP(arg: any): void;
@@ -241,13 +247,17 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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  } & {
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  readonly renderDelay: number;
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  readonly TooltipComponent: import("react").FC<any>;
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- readonly selectedFeatureId: string | undefined;
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+ readonly selectedFeatureId: string | undefined; /**
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+ * #action
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+ */
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  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
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  } & {
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  readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
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  readonly featureUnderMouse: Feature | undefined;
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  getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
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- getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
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+ getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined; /**
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+ * #action
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+ */
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  searchFeatureByID(id: string): [number, number, number, number] | undefined;
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  } & {
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  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
@@ -450,28 +460,32 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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  message: string | undefined;
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  maxHeightReached: boolean;
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  ReactComponent: ({ model, }: {
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- model: any;
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- }) => any;
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+ model: {
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+ error?: unknown;
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+ reload: () => void;
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+ message: import("react").ReactNode;
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+ filled?: boolean | undefined;
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+ status?: string | undefined;
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+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
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+ };
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+ }) => import("react").JSX.Element | undefined;
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  renderProps: any;
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  } & {
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  doReload(): void;
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  afterAttach(): void;
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  setStatus(message: string): void;
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  setLoading(abortController: AbortController): void;
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- setMessage(messageText: string): void;
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+ setMessage(messageText: string): void; /**
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+ * #action
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+ */
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  setRendered(props: {
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  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
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- /**
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- * #action
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- */
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  features: Map<string, Feature>;
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  layout: any;
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  maxHeightReached: boolean;
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  renderProps: any;
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  } | undefined): void;
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- setError(error: unknown): void; /**
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- * #action
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- */
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+ setError(error: unknown): void;
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  reload(): void;
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  beforeDestroy(): void;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -17,10 +17,10 @@ import { getUniqueTagValues, FilterModel } from '../shared';
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  import { createAutorun } from '../util';
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  import { ColorByModel } from '../shared/color';
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  // async
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- const FilterByTagDlg = lazy(() => import('../shared/FilterByTag'));
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- const ColorByTagDlg = lazy(() => import('./components/ColorByTag'));
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- const SetFeatureHeightDlg = lazy(() => import('./components/SetFeatureHeight'));
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- const SetMaxHeightDlg = lazy(() => import('./components/SetMaxHeight'));
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+ const FilterByTagDialog = lazy(() => import('../shared/FilterByTag'));
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+ const ColorByTagDialog = lazy(() => import('./components/ColorByTag'));
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+ const SetFeatureHeightDialog = lazy(() => import('./components/SetFeatureHeight'));
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+ const SetMaxHeightDialog = lazy(() => import('./components/SetMaxHeight'));
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  // using a map because it preserves order
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  const rendererTypes = new Map([
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  ['pileup', 'PileupRenderer'],
@@ -392,7 +392,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
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  label: 'Color by tag...',
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  onClick: () => {
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  getSession(self).queueDialog(doneCallback => [
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- ColorByTagDlg,
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+ ColorByTagDialog,
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  { model: self, handleClose: doneCallback },
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  ]);
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  },
@@ -410,7 +410,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
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  icon: FilterListIcon,
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  onClick: () => {
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  getSession(self).queueDialog(doneCallback => [
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- FilterByTagDlg,
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+ FilterByTagDialog,
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  { model: self, handleClose: doneCallback },
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  ]);
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  },
@@ -436,7 +436,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
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  label: 'Manually set height',
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  onClick: () => {
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  getSession(self).queueDialog(doneCallback => [
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- SetFeatureHeightDlg,
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+ SetFeatureHeightDialog,
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  { model: self, handleClose: doneCallback },
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  ]);
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  },
@@ -447,7 +447,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
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  label: 'Set max height...',
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  onClick: () => {
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  getSession(self).queueDialog(doneCallback => [
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- SetMaxHeightDlg,
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+ SetMaxHeightDialog,
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  { model: self, handleClose: doneCallback },
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  ]);
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  },
@@ -43,11 +43,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  message: string | undefined;
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  maxHeightReached: boolean;
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  ReactComponent: ({ model, }: {
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- model: any;
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- }) => any;
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- /**
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- * #property
50
- */
46
+ model: {
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+ error?: unknown;
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+ reload: () => void;
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+ message: import("react").ReactNode;
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+ filled?: boolean | undefined;
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+ status?: string | undefined;
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+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
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+ };
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+ }) => import("react").JSX.Element | undefined;
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  renderProps: any;
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  } & {
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  doReload(): void;
@@ -77,12 +81,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  defaultValue: number;
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  description: string;
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  };
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- /**
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- * #stateModel LinearPileupDisplay
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- * #category display
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- * extends
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- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
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- */
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  height: {
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  type: string;
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  defaultValue: number;
@@ -98,6 +96,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  } & {
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  configuration: AnyConfigurationSchemaType;
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  featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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+ /**
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+ * #action
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+ */
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  noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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  fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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  trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
@@ -162,15 +163,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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  rendererTypeName: string;
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  error: unknown;
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- message: string | undefined;
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+ message: string | undefined; /**
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+ * #action
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+ */
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  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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  type: import("mobx-state-tree").ISimpleType<string>;
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  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  }, {
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- rendererTypeName: string; /**
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- * #action
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- */
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+ rendererTypeName: string;
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  error: unknown;
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  message: string | undefined;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -184,7 +185,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
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  regionCannotBeRendered(): null;
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  } & {
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- setMessage(arg?: string | undefined): void;
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+ setMessage(arg?: string | undefined): void; /**
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+ * #getter
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+ */
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  setError(error?: unknown): void;
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  setRpcDriverName(rpcDriverName: string): void;
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  reload(): void;
@@ -201,9 +204,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
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  currStatsBpPerPx: number;
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  } & {
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- readonly currentBytesRequested: number; /**
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- * #property
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- */
207
+ readonly currentBytesRequested: number;
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  readonly currentFeatureScreenDensity: number;
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  readonly maxFeatureScreenDensity: any;
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  readonly featureDensityStatsReady: boolean;
@@ -224,18 +225,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
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  regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
226
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  } & {
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- featureIdUnderMouse: string | undefined; /**
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- * #action
229
- */
228
+ featureIdUnderMouse: string | undefined;
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  contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
231
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  } & {
232
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  readonly blockType: "dynamicBlocks" | "staticBlocks";
233
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  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
234
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  } & {
235
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  readonly renderDelay: number;
236
- /**
237
- * #action
238
- */
239
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  readonly TooltipComponent: import("react").FC<any>;
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  readonly selectedFeatureId: string | undefined;
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  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
@@ -263,7 +259,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  afterAttach(): void;
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  } & {
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  colorTagMap: import("mobx").ObservableMap<string, string>;
266
- featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
262
+ featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined; /**
263
+ * #action
264
+ */
267
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  tagsReady: boolean;
268
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  } & {
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  readonly autorunReady: boolean;
@@ -12,8 +12,8 @@ import SortIcon from '@mui/icons-material/Sort';
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  import { SharedLinearPileupDisplayMixin } from './SharedLinearPileupDisplayMixin';
13
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  import { observable } from 'mobx';
14
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  // async
15
- const SortByTagDlg = lazy(() => import('./components/SortByTag'));
16
- const ModificationsDlg = lazy(() => import('./components/ColorByModifications'));
15
+ const SortByTagDialog = lazy(() => import('./components/SortByTag'));
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+ const ModificationsDialog = lazy(() => import('./components/ColorByModifications'));
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  /**
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  * #stateModel LinearPileupDisplay
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  * #category display
@@ -237,7 +237,7 @@ function stateModelFactory(configSchema) {
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  label: 'Sort by tag...',
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  onClick: () => {
239
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  getSession(self).queueDialog(handleClose => [
240
- SortByTagDlg,
240
+ SortByTagDialog,
241
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  { model: self, handleClose },
242
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  ]);
243
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  },
@@ -259,7 +259,7 @@ function stateModelFactory(configSchema) {
259
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  label: 'Modifications or methylation',
260
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  onClick: () => {
261
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  getSession(self).queueDialog(doneCallback => [
262
- ModificationsDlg,
262
+ ModificationsDialog,
263
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  { model: self, handleClose: doneCallback },
264
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  ]);
265
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  },
@@ -61,7 +61,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
61
61
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
62
62
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
63
63
  type: import("mobx-state-tree").ISimpleType<string>;
64
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
64
+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
65
+ * #property
66
+ */
65
67
  }, {
66
68
  rendererTypeName: string;
67
69
  error: unknown;
@@ -80,7 +82,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
80
82
  error: unknown;
81
83
  message: string | undefined;
82
84
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
83
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
85
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
86
+ * #action
87
+ */
84
88
  type: import("mobx-state-tree").ISimpleType<string>;
85
89
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
86
90
  }, {
@@ -90,17 +94,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
90
94
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
91
95
  }> | null;
92
96
  readonly adapterConfig: any;
93
- readonly parentTrack: any; /**
94
- * #action
95
- */
97
+ readonly parentTrack: any;
96
98
  renderProps(): any;
97
99
  readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
98
100
  readonly DisplayMessageComponent: React.FC<any> | undefined;
99
101
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
100
102
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
101
- regionCannotBeRendered(): null; /**
102
- * #getter
103
- */
103
+ regionCannotBeRendered(): null;
104
104
  } & {
105
105
  setMessage(arg?: string | undefined): void;
106
106
  setError(error?: unknown): void; /**
@@ -10,7 +10,7 @@ import FilterListIcon from '@mui/icons-material/ClearAll';
10
10
  // locals
11
11
  import { FilterModel } from '../shared';
12
12
  // async
13
- const FilterByTagDlg = lazy(() => import('../shared/FilterByTag'));
13
+ const FilterByTagDialog = lazy(() => import('../shared/FilterByTag'));
14
14
  /**
15
15
  * #stateModel LinearReadArcsDisplay
16
16
  * the arc display is a non-block-based track, so draws to a single canvas and
@@ -192,7 +192,7 @@ function stateModelFactory(configSchema) {
192
192
  icon: FilterListIcon,
193
193
  onClick: () => {
194
194
  getSession(self).queueDialog(handleClose => [
195
- FilterByTagDlg,
195
+ FilterByTagDialog,
196
196
  { model: self, handleClose },
197
197
  ]);
198
198
  },
@@ -44,6 +44,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
44
44
  message: string | undefined;
45
45
  } & {
46
46
  readonly RenderingComponent: React.FC<{
47
+ /**
48
+ * #stateModel LinearReadCloudDisplay
49
+ * it is not a block based track, hence not BaseLinearDisplay
50
+ * extends
51
+ * - [BaseDisplay](../basedisplay)
52
+ * - [TrackHeightMixin](../trackheightmixin)
53
+ * - [FeatureDensityMixin](../featuredensitymixin)
54
+ */
47
55
  model: {
48
56
  id: string;
49
57
  type: string;
@@ -55,9 +63,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
55
63
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
56
64
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
57
65
  type: import("mobx-state-tree").ISimpleType<string>;
58
- /**
59
- * #property
60
- */
61
66
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
62
67
  }, {
63
68
  rendererTypeName: string;
@@ -78,7 +83,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
78
83
  message: string | undefined;
79
84
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
80
85
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
81
- type: import("mobx-state-tree").ISimpleType<string>;
86
+ type: import("mobx-state-tree").ISimpleType<string>; /**
87
+ * #action
88
+ * internal, a reference to a HTMLCanvas because we use a autorun to draw
89
+ * the canvas
90
+ */
82
91
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
83
92
  }, {
84
93
  rendererTypeName: string;
@@ -130,9 +139,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
130
139
  readonly regionTooLarge: boolean;
131
140
  readonly regionTooLargeReason: string;
132
141
  } & {
133
- /**
134
- * #method
135
- */
136
142
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
137
143
  regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
138
144
  } & {
@@ -10,7 +10,7 @@ import FilterListIcon from '@mui/icons-material/ClearAll';
10
10
  // locals
11
11
  import { FilterModel } from '../shared';
12
12
  // async
13
- const FilterByTagDlg = lazy(() => import('../shared/FilterByTag'));
13
+ const FilterByTagDialog = lazy(() => import('../shared/FilterByTag'));
14
14
  /**
15
15
  * #stateModel LinearReadCloudDisplay
16
16
  * it is not a block based track, hence not BaseLinearDisplay
@@ -142,7 +142,7 @@ function stateModelFactory(configSchema) {
142
142
  icon: FilterListIcon,
143
143
  onClick: () => {
144
144
  getSession(self).queueDialog(handleClose => [
145
- FilterByTagDlg,
145
+ FilterByTagDialog,
146
146
  { model: self, handleClose },
147
147
  ]);
148
148
  },
@@ -1,7 +1,7 @@
1
1
  import React from 'react';
2
2
  import { observer } from 'mobx-react';
3
+ import { toLocale } from '@jbrowse/core/util';
3
4
  import { Tooltip } from '@jbrowse/plugin-wiggle';
4
- const en = (n) => n.toLocaleString('en-US');
5
5
  const toP = (s = 0) => +(+s).toFixed(1);
6
6
  const pct = (n, total) => `${toP((n / (total || 1)) * 100)}%`;
7
7
  const TooltipContents = React.forwardRef(function TooltipContents2({ feature }, reactRef) {
@@ -9,7 +9,10 @@ const TooltipContents = React.forwardRef(function TooltipContents2({ feature },
9
9
  const end = feature.get('end');
10
10
  const name = feature.get('refName');
11
11
  const { refbase, all, total, ref, '-1': rn1, '1': r1, '0': r0, ...info } = feature.get('snpinfo');
12
- const loc = [name, start === end ? en(start) : `${en(start)}..${en(end)}`]
12
+ const loc = [
13
+ name,
14
+ start === end ? toLocale(start) : `${toLocale(start)}..${toLocale(end)}`,
15
+ ]
13
16
  .filter(f => !!f)
14
17
  .join(':');
15
18
  return (React.createElement("div", { ref: reactRef },
@@ -42,8 +42,17 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
42
42
  message: string | undefined;
43
43
  maxHeightReached: boolean;
44
44
  ReactComponent: ({ model, }: {
45
- model: any;
46
- }) => any;
45
+ model: {
46
+ error?: unknown;
47
+ reload: () => void;
48
+ message: import("react").ReactNode; /**
49
+ * #property
50
+ */
51
+ filled?: boolean | undefined;
52
+ status?: string | undefined;
53
+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
54
+ };
55
+ }) => import("react").JSX.Element | undefined;
47
56
  renderProps: any;
48
57
  } & {
49
58
  doReload(): void;
@@ -4,6 +4,7 @@ import { BlockMsg, } from '@jbrowse/plugin-linear-genome-view';
4
4
  import { makeStyles } from 'tss-react/mui';
5
5
  import { observer } from 'mobx-react';
6
6
  import { getContainingView } from '@jbrowse/core/util';
7
+ import { Button, Tooltip } from '@mui/material';
7
8
  const useStyles = makeStyles()(theme => ({
8
9
  loading: {
9
10
  backgroundColor: theme.palette.background.default,
@@ -19,7 +20,8 @@ const useStyles = makeStyles()(theme => ({
19
20
  }));
20
21
  const BaseDisplayComponent = observer(function ({ model, children, }) {
21
22
  const { error, regionTooLarge } = model;
22
- return error ? (React.createElement(BlockMsg, { message: `${error}`, severity: "error", buttonText: "Reload", action: model.reload })) : regionTooLarge ? (model.regionCannotBeRendered()) : (React.createElement(DataDisplay, { model: model }, children));
23
+ return error ? (React.createElement(BlockMsg, { message: `${error}`, severity: "error", action: React.createElement(Tooltip, { title: "Reload" },
24
+ React.createElement(Button, { "data-testid": "reload_button", onClick: () => model.reload() }, "Reload")) })) : regionTooLarge ? (model.regionCannotBeRendered()) : (React.createElement(DataDisplay, { model: model }, children));
23
25
  });
24
26
  const DataDisplay = observer(function ({ model, children, }) {
25
27
  const { drawn, loading } = model;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-alignments",
3
- "version": "2.10.1",
3
+ "version": "2.10.3",
4
4
  "description": "JBrowse 2 alignments adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -63,5 +63,5 @@
63
63
  "distModule": "esm/index.js",
64
64
  "srcModule": "src/index.ts",
65
65
  "module": "esm/index.js",
66
- "gitHead": "442b5f87efddfdf4ccf520b4d9dd01ddd370cb07"
66
+ "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
67
67
  }
@@ -1,6 +0,0 @@
1
- import React from 'react';
2
- import { IAnyStateTreeNode } from 'mobx-state-tree';
3
- export default function SupplementaryAlignments(props: {
4
- tag: string;
5
- model: IAnyStateTreeNode;
6
- }): React.JSX.Element;
@@ -1,6 +0,0 @@
1
- import React from 'react';
2
- import { IAnyStateTreeNode } from 'mobx-state-tree';
3
- export default function SupplementaryAlignments(props: {
4
- tag: string;
5
- model: IAnyStateTreeNode;
6
- }): React.JSX.Element;