@jbrowse/plugin-linear-genome-view 1.4.1 → 1.5.2

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 (43) hide show
  1. package/dist/BaseLinearDisplay/components/Block.d.ts +7 -10
  2. package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +16 -9
  3. package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.d.ts +2 -2
  4. package/dist/LinearBareDisplay/model.d.ts +8 -8
  5. package/dist/LinearBasicDisplay/model.d.ts +11 -8
  6. package/dist/LinearGenomeView/components/HelpDialog.d.ts +5 -0
  7. package/dist/LinearGenomeView/components/LinearGenomeView.d.ts +3 -5
  8. package/dist/LinearGenomeView/components/LinearGenomeViewSvg.d.ts +4 -0
  9. package/dist/LinearGenomeView/components/OverviewRubberBand.d.ts +2 -3
  10. package/dist/LinearGenomeView/components/OverviewScaleBar.d.ts +116 -2
  11. package/dist/LinearGenomeView/components/RefNameAutocomplete.d.ts +3 -11
  12. package/dist/LinearGenomeView/components/ScaleBar.d.ts +36 -2
  13. package/dist/LinearGenomeView/components/util.d.ts +2 -0
  14. package/dist/LinearGenomeView/index.d.ts +22 -4
  15. package/dist/index.d.ts +26 -26
  16. package/dist/plugin-linear-genome-view.cjs.development.js +3178 -2884
  17. package/dist/plugin-linear-genome-view.cjs.development.js.map +1 -1
  18. package/dist/plugin-linear-genome-view.cjs.production.min.js +1 -1
  19. package/dist/plugin-linear-genome-view.cjs.production.min.js.map +1 -1
  20. package/dist/plugin-linear-genome-view.esm.js +3191 -2898
  21. package/dist/plugin-linear-genome-view.esm.js.map +1 -1
  22. package/package.json +2 -2
  23. package/src/BaseLinearDisplay/components/BaseLinearDisplay.tsx +3 -0
  24. package/src/BaseLinearDisplay/components/Block.tsx +20 -33
  25. package/src/BaseLinearDisplay/models/BaseLinearDisplayModel.tsx +3 -7
  26. package/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts +15 -13
  27. package/src/LinearBasicDisplay/model.ts +25 -3
  28. package/src/LinearGenomeView/components/ExportSvgDialog.tsx +6 -6
  29. package/src/LinearGenomeView/components/Header.tsx +56 -78
  30. package/src/LinearGenomeView/components/HelpDialog.tsx +81 -0
  31. package/src/LinearGenomeView/components/ImportForm.tsx +139 -158
  32. package/src/LinearGenomeView/components/LinearGenomeView.test.js +6 -6
  33. package/src/LinearGenomeView/components/LinearGenomeView.tsx +30 -245
  34. package/src/LinearGenomeView/components/LinearGenomeViewSvg.tsx +317 -0
  35. package/src/LinearGenomeView/components/OverviewRubberBand.tsx +74 -34
  36. package/src/LinearGenomeView/components/OverviewScaleBar.tsx +326 -177
  37. package/src/LinearGenomeView/components/RefNameAutocomplete.tsx +152 -157
  38. package/src/LinearGenomeView/components/SearchResultsDialog.tsx +12 -34
  39. package/src/LinearGenomeView/components/SequenceDialog.tsx +10 -9
  40. package/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.js.snap +127 -254
  41. package/src/LinearGenomeView/components/util.ts +10 -0
  42. package/src/LinearGenomeView/index.tsx +69 -27
  43. package/src/index.ts +3 -1
package/dist/LinearGenomeView/index.d.ts CHANGED
@@ -4,8 +4,8 @@ import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
4
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  import { BlockSet, BaseBlock } from '@jbrowse/core/util/blockTypes';
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  import { Instance } from 'mobx-state-tree';
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  import PluginManager from '@jbrowse/core/PluginManager';
7
- import { renderToSvg } from './components/LinearGenomeView';
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- export { default as ReactComponent } from './components/LinearGenomeView';
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+ import { renderToSvg } from './components/LinearGenomeViewSvg';
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+ import RefNameAutocomplete from './components/RefNameAutocomplete';
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  export interface BpOffset {
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  refName?: string;
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  index: number;
@@ -55,6 +55,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<"hierarchical">, [undefined]>;
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  trackLabels: import("mobx-state-tree").IType<string | undefined, string, string>;
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  showCenterLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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+ showCytobandsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  }, {
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  width: number;
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  } & {
@@ -154,6 +155,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  assemblyName: string;
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  } | undefined;
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  } & {
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+ setShowCytobands(flag: boolean): void;
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  setWidth(newWidth: number): void;
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  setError(error: Error | undefined): void;
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  toggleHeader(): void;
@@ -174,7 +176,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  setTrackLabels(setting: 'overlapping' | 'offset' | 'hidden'): void;
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  toggleCenterLine(): void;
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  setDisplayedRegions(regions: Region[]): void;
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- activateTrackSelector(): void;
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+ activateTrackSelector(): import("@jbrowse/core/util").Widget;
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  navToLocString(locString: string, optAssemblyName?: string | undefined): void;
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  /**
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  * Navigate to a location based on its refName and optionally start, end,
@@ -210,10 +212,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  getSelectedRegions(leftOffset: BpOffset | undefined, rightOffset: BpOffset | undefined): {
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  start: number;
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  end: number;
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+ regionNumber?: number | undefined;
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+ reversed?: boolean | undefined;
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  refName: string;
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  assemblyName: string;
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  key: string;
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  offsetPx: number;
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+ widthPx: number;
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+ variant?: string | undefined;
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+ isLeftEndOfDisplayedRegion?: boolean | undefined;
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  }[];
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  afterDisplayedRegionsSet(cb: Function): void;
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  /**
@@ -242,6 +249,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  slide: (viewWidths: number) => void;
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  } & {
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  zoom: (targetBpPerPx: number) => void;
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+ } & {
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+ readonly canShowCytobands: boolean;
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+ readonly showCytobands: boolean;
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+ readonly anyCytobandsExist: boolean;
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+ readonly cytobandOffset: number;
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  } & {
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  menuItems(): MenuItem[];
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  readonly staticBlocks: BlockSet;
@@ -249,10 +261,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  readonly roundedDynamicBlocks: {
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  start: number;
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  end: number;
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+ regionNumber?: number | undefined;
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+ reversed?: boolean | undefined;
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  refName: string;
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  assemblyName: string;
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  key: string;
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  offsetPx: number;
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+ widthPx: number;
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+ variant?: string | undefined;
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+ isLeftEndOfDisplayedRegion?: boolean | undefined;
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  }[];
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  readonly visibleLocStrings: string;
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  readonly coarseVisibleLocStrings: string;
@@ -265,6 +282,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  } & {
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  rubberBandMenuItems(): MenuItem[];
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
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- export { renderToSvg };
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+ export { renderToSvg, RefNameAutocomplete };
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  export declare type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
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  export declare type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
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+ export { default as ReactComponent } from './components/LinearGenomeView';
package/dist/index.d.ts CHANGED
@@ -3,7 +3,7 @@ import Plugin from '@jbrowse/core/Plugin';
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  import PluginManager from '@jbrowse/core/PluginManager';
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  import { BaseLinearDisplay, BaseLinearDisplayComponent, baseLinearDisplayConfigSchema, BlockModel } from './BaseLinearDisplay';
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  import { configSchemaFactory as linearBareDisplayConfigSchemaFactory } from './LinearBareDisplay';
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- import { LinearGenomeViewModel, LinearGenomeViewStateModel, renderToSvg } from './LinearGenomeView';
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+ import { LinearGenomeViewModel, LinearGenomeViewStateModel, renderToSvg, RefNameAutocomplete } from './LinearGenomeView';
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  import { configSchema as linearBasicDisplayConfigSchemaFactory, modelFactory as linearBasicDisplayModelFactory } from './LinearBasicDisplay';
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  export default class LinearGenomeViewPlugin extends Plugin {
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  name: string;
@@ -37,7 +37,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
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  features: Map<string, import("@jbrowse/core/util/simpleFeature").Feature> | undefined;
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  layout: any;
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  status: string;
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- error: Error | undefined;
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+ error: unknown;
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  message: string | undefined;
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  maxHeightReached: boolean;
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  ReactComponent: ({ model, }: {
@@ -57,14 +57,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
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  maxHeightReached: boolean;
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  renderProps: any;
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  } | undefined): void;
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- setError(error: Error): void;
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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>>;
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  userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  }> & {
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  rendererTypeName: string;
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- error: Error | undefined;
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+ error: unknown;
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  } & {
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  readonly RenderingComponent: import("react").FC<{
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  model: import("mobx-state-tree").ModelInstanceTypeProps<{
@@ -73,14 +73,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
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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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- error: Error | undefined;
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+ error: unknown;
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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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- error: Error | undefined;
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+ error: unknown;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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  onHorizontalScroll?: Function | undefined;
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  blockState?: Record<string, any> | undefined;
@@ -92,14 +92,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
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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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- error: Error | undefined;
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+ error: unknown;
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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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- error: Error | undefined;
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+ error: unknown;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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  }> | null;
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  readonly adapterConfig: any;
@@ -111,7 +111,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
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  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
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  regionCannotBeRendered(): undefined;
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  } & {
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- setError(error?: Error | undefined): void;
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+ setError(error?: unknown): void;
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  setRpcDriverName(rpcDriverName: string): void;
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  reload(): void;
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  } & {
@@ -190,7 +190,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
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  features: Map<string, import("@jbrowse/core/util/simpleFeature").Feature> | undefined;
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  layout: any;
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  status: string;
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- error: Error | undefined;
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+ error: unknown;
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  message: string | undefined;
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  maxHeightReached: boolean;
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  ReactComponent: ({ model, }: {
@@ -210,14 +210,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
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  maxHeightReached: boolean;
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  renderProps: any;
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  } | undefined): void;
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- setError(error: Error): void;
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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>>;
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  userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  }, {
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  rendererTypeName: string;
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- error: Error | undefined;
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+ error: unknown;
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  } & {
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  readonly RenderingComponent: import("react").FC<{
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  model: import("mobx-state-tree").ModelInstanceTypeProps<{
@@ -226,14 +226,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
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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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- error: Error | undefined;
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+ error: unknown;
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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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- error: Error | undefined;
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+ error: unknown;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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  onHorizontalScroll?: Function | undefined;
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  blockState?: Record<string, any> | undefined;
@@ -245,14 +245,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
245
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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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- error: Error | undefined;
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+ error: unknown;
249
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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>>;
253
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  }, {
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  rendererTypeName: string;
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- error: Error | undefined;
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+ error: unknown;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
257
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  }> | null;
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  readonly adapterConfig: any;
@@ -264,7 +264,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
264
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  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
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  regionCannotBeRendered(): undefined;
266
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  } & {
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- setError(error?: Error | undefined): void;
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+ setError(error?: unknown): void;
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  setRpcDriverName(rpcDriverName: string): void;
269
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  reload(): void;
270
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  } & {
@@ -352,7 +352,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
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  features: Map<string, import("@jbrowse/core/util/simpleFeature").Feature> | undefined;
353
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  layout: any;
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  status: string;
355
- error: Error | undefined;
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+ error: unknown;
356
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  message: string | undefined;
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  maxHeightReached: boolean;
358
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  ReactComponent: ({ model, }: {
@@ -372,14 +372,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
372
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  maxHeightReached: boolean;
373
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  renderProps: any;
374
374
  } | undefined): void;
375
- setError(error: Error): void;
375
+ setError(error: unknown): void;
376
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  reload(): void;
377
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  beforeDestroy(): void;
378
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
379
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  userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
380
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  }, {
381
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  rendererTypeName: string;
382
- error: Error | undefined;
382
+ error: unknown;
383
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  } & {
384
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  readonly RenderingComponent: import("react").FC<{
385
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  model: import("mobx-state-tree").ModelInstanceTypeProps<{
@@ -388,14 +388,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
388
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  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
389
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  }> & {
390
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  rendererTypeName: string;
391
- error: Error | undefined;
391
+ error: unknown;
392
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  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
393
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  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
394
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  type: import("mobx-state-tree").ISimpleType<string>;
395
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  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
396
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  }, {
397
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  rendererTypeName: string;
398
- error: Error | undefined;
398
+ error: unknown;
399
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
400
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  onHorizontalScroll?: Function | undefined;
401
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  blockState?: Record<string, any> | undefined;
@@ -407,14 +407,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
407
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  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
408
408
  }> & {
409
409
  rendererTypeName: string;
410
- error: Error | undefined;
410
+ error: unknown;
411
411
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
412
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  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
413
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  type: import("mobx-state-tree").ISimpleType<string>;
414
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  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
415
415
  }, {
416
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  rendererTypeName: string;
417
- error: Error | undefined;
417
+ error: unknown;
418
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
419
419
  }> | null;
420
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  readonly adapterConfig: any;
@@ -426,7 +426,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
426
426
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
427
427
  regionCannotBeRendered(): undefined;
428
428
  } & {
429
- setError(error?: Error | undefined): void;
429
+ setError(error?: unknown): void;
430
430
  setRpcDriverName(rpcDriverName: string): void;
431
431
  reload(): void;
432
432
  } & {
@@ -489,6 +489,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
489
489
  install(pluginManager: PluginManager): void;
490
490
  configure(pluginManager: PluginManager): void;
491
491
  }
492
- export { BaseLinearDisplayComponent, BaseLinearDisplay, baseLinearDisplayConfigSchema, linearBareDisplayConfigSchemaFactory, linearBasicDisplayConfigSchemaFactory, linearBasicDisplayModelFactory, renderToSvg, };
492
+ export { BaseLinearDisplayComponent, BaseLinearDisplay, baseLinearDisplayConfigSchema, linearBareDisplayConfigSchemaFactory, linearBasicDisplayConfigSchemaFactory, linearBasicDisplayModelFactory, renderToSvg, RefNameAutocomplete, };
493
493
  export type { LinearGenomeViewModel, LinearGenomeViewStateModel, BlockModel };
494
494
  export type { BaseLinearDisplayModel } from './BaseLinearDisplay';