@jbrowse/plugin-variants 2.4.1 → 2.4.2

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Files changed (10) hide show
  1. package/dist/LinearVariantDisplay/model.d.ts +23 -26
  2. package/dist/LinearVariantDisplay/model.js.map +1 -1
  3. package/dist/VariantFeatureWidget/index.d.ts +1 -1
  4. package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts +1 -1
  5. package/esm/LinearVariantDisplay/model.d.ts +23 -26
  6. package/esm/LinearVariantDisplay/model.js.map +1 -1
  7. package/esm/VariantFeatureWidget/index.d.ts +1 -1
  8. package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts +1 -1
  9. package/package.json +2 -2
  10. package/src/LinearVariantDisplay/model.ts +10 -4
package/dist/LinearVariantDisplay/model.d.ts CHANGED
@@ -1,12 +1,13 @@
1
1
  /// <reference types="react" />
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- import { Feature } from '@jbrowse/core/util/simpleFeature';
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- import { LinearVariantDisplayConfigModel } from './configSchema';
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+ import { Feature } from '@jbrowse/core/util';
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+ import { Instance } from 'mobx-state-tree';
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+ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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  /**
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  * #stateModel LinearVariantDisplay
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  * extends `LinearBasicDisplay`
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  * very similar to basic display, but provides custom widget on feature click
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  */
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- export default function stateModelFactory(configSchema: LinearVariantDisplayConfigModel): import("mobx-state-tree").IModelType<{
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+ export default function stateModelFactory(configSchema: AnyConfigurationSchemaType): 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>>;
@@ -63,7 +64,9 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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  } & {
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  type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
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  trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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- trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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+ trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
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+ * #action
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+ */
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  trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
@@ -134,8 +137,8 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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  message: string;
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  featureIdUnderMouse: string | undefined;
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  contextMenuFeature: Feature | undefined;
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- estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
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- estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
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+ estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
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+ estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
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  } & {
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  readonly height: number;
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  readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -148,7 +151,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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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): any;
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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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  searchFeatureByID(id: string): [number, number, number, number] | undefined;
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  readonly currentBytesRequested: number;
@@ -158,19 +161,16 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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  readonly maxAllowableBytes: number;
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  } & {
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  setMessage(message: string): void;
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+ } & {
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  afterAttach(): void;
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- estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
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- headers?: Record<string, string> | undefined;
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- signal?: AbortSignal | undefined;
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- filters?: string[] | undefined;
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- }): Promise<{}>;
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- setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
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- setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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- clearRegionStats(): void;
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+ estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
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+ setRegionsStatsP(arg: any): void;
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+ setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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+ clearRegionsStats(): void;
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  setHeight(displayHeight: number): number;
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  resizeHeight(distance: number): number;
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  setScrollTop(scrollTop: number): void;
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- updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
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+ updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
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  setCurrBpPerPx(n: number): void;
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  deleteBlock(key: string): void;
@@ -184,18 +184,13 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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  readonly regionTooLargeReason: string;
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  } & {
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  reload(): Promise<void>;
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+ } & {
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  afterAttach(): void;
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  } & {
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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): JSX.Element | null;
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  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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- contextMenuItems(): {
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- label: string;
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- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
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- muiName: string;
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- };
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- onClick: () => void;
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- }[];
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+ contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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  renderProps(): any;
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  } & {
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  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
@@ -213,19 +208,19 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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  [x: string]: any;
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  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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  setSubschema(slotName: string, data: unknown): any;
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- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
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+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
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  } & {
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  toggleShowLabels(): void;
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  toggleShowDescriptions(): void;
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  setDisplayMode(val: string): void;
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- setMaxHeight(val: number): void;
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+ setMaxHeight(val?: number | undefined): void;
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  } & {
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  renderProps(): {
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  config: {
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  [x: string]: any;
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  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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  setSubschema(slotName: string, data: unknown): any;
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- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
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+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
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  };
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  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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  } & {
@@ -234,3 +229,5 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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  */
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  selectFeature(feature: Feature): Promise<void>;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
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+ export type LinearVariantDisplayStateModel = ReturnType<typeof stateModelFactory>;
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+ export type LinearVariantDisplayModel = Instance<LinearVariantDisplayStateModel>;
package/dist/LinearVariantDisplay/model.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":";;AAAA,+DAA6E;AAC7E,sDAA2D;AAC3D,6CAK2B;AAG3B,kFAAmF;AACnF,qDAAuC;AAGvC;;;;GAIG;AACH,SAAwB,iBAAiB,CACvC,YAA6C;IAE7C,OAAO,uBAAK;SACT,OAAO,CACN,sBAAsB,EACtB,IAAA,0DAA8B,EAAC,YAAY,CAAC,EAC5C,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,KAAK,CAAC,aAAa,CAAC,OAAgB;YAClC,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAI,IAAA,gCAAyB,EAAC,OAAO,CAAC,EAAE;gBACtC,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAC9B,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,IAAI,CAAC,CAAA;gBACvC,MAAM,KAAK,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,CAAA;gBACtC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;gBACpC,MAAM,aAAa,GAAG,IAAA,uBAAO,EAAC,KAAK,EAAE,SAAS,CAAC,CAAA;gBAC/C,MAAM,YAAY,GAAG,MAAM,UAAU,CAAC,IAAI,CACxC,SAAS,EACT,iBAAiB,EACjB;oBACE,aAAa;iBACd,CACF,CAAA;gBACD,OAAO,CAAC,UAAU,CAChB,OAAO,CAAC,SAAS,CAAC,sBAAsB,EAAE,gBAAgB,EAAE;oBAC1D,WAAW,EAAE,OAAO,CAAC,MAAM,EAAE;oBAC7B,IAAI;oBACJ,KAAK;oBACL,YAAY;iBACb,CAAC,CACH,CAAA;aACF;YAED,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;QAC/B,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AAlDD,oCAkDC"}
1
+ {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":";;AAAA,+DAA6E;AAC7E,sDAA2D;AAC3D,6CAM2B;AAE3B,kFAAmF;AACnF,qDAAiD;AAGjD;;;;GAIG;AACH,SAAwB,iBAAiB,CACvC,YAAwC;IAExC,OAAO,uBAAK;SACT,OAAO,CACN,sBAAsB,EACtB,IAAA,0DAA8B,EAAC,YAAY,CAAC,EAC5C,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SAEA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,KAAK,CAAC,aAAa,CAAC,OAAgB;YAClC,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAI,IAAA,gCAAyB,EAAC,OAAO,CAAC,EAAE;gBACtC,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAC9B,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,IAAI,CAAC,CAAA;gBACvC,MAAM,KAAK,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,CAAA;gBACtC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;gBACpC,MAAM,aAAa,GAAG,IAAA,uBAAO,EAAC,KAAK,EAAE,SAAS,CAAC,CAAA;gBAC/C,MAAM,YAAY,GAAG,MAAM,UAAU,CAAC,IAAI,CACxC,SAAS,EACT,iBAAiB,EACjB;oBACE,aAAa;iBACd,CACF,CAAA;gBACD,OAAO,CAAC,UAAU,CAChB,OAAO,CAAC,SAAS,CAAC,sBAAsB,EAAE,gBAAgB,EAAE;oBAC1D,WAAW,EAAE,OAAO,CAAC,MAAM,EAAE;oBAC7B,IAAI;oBACJ,KAAK;oBACL,YAAY;iBACb,CAAC,CACH,CAAA;aACF;YAED,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;QAC/B,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AAnDD,oCAmDC"}
package/dist/VariantFeatureWidget/index.d.ts CHANGED
@@ -33,8 +33,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
36
- id: string;
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  type: "BaseFeatureWidget";
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+ id: string;
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  track: import("mobx-state-tree").ReferenceIdentifier | undefined;
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  view: import("mobx-state-tree").ReferenceIdentifier | undefined;
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  trackId: string | undefined;
package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts CHANGED
@@ -10,7 +10,7 @@ export default class extends BaseFeatureDataAdapter {
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  vcf: TabixIndexedFile;
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  parser: VcfParser;
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  }>;
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- getRefNames(opts?: BaseOptions): Promise<any>;
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+ getRefNames(opts?: BaseOptions): Promise<string[]>;
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  getHeader(): Promise<string>;
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  getMetadata(): Promise<any>;
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  getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
package/esm/LinearVariantDisplay/model.d.ts CHANGED
@@ -1,12 +1,13 @@
1
1
  /// <reference types="react" />
2
- import { Feature } from '@jbrowse/core/util/simpleFeature';
3
- import { LinearVariantDisplayConfigModel } from './configSchema';
2
+ import { Feature } from '@jbrowse/core/util';
3
+ import { Instance } from 'mobx-state-tree';
4
+ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
4
5
  /**
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  * #stateModel LinearVariantDisplay
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  * extends `LinearBasicDisplay`
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  * very similar to basic display, but provides custom widget on feature click
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  */
9
- export default function stateModelFactory(configSchema: LinearVariantDisplayConfigModel): import("mobx-state-tree").IModelType<{
10
+ export default function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
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  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
11
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  type: import("mobx-state-tree").ISimpleType<string>;
12
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  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -63,7 +64,9 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
63
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  } & {
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  type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
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  trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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- trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
67
+ trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
68
+ * #action
69
+ */
67
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  trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
68
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  trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
@@ -134,8 +137,8 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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  message: string;
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  featureIdUnderMouse: string | undefined;
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  contextMenuFeature: Feature | undefined;
137
- estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
138
- estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
140
+ estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
141
+ estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
139
142
  } & {
140
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  readonly height: number;
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  readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -148,7 +151,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
148
151
  } & {
149
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  readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
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  readonly featureUnderMouse: Feature | undefined;
151
- getFeatureOverlapping(blockKey: string, x: number, y: number): any;
154
+ 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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  searchFeatureByID(id: string): [number, number, number, number] | undefined;
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  readonly currentBytesRequested: number;
@@ -158,19 +161,16 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
158
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  readonly maxAllowableBytes: number;
159
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  } & {
160
163
  setMessage(message: string): void;
164
+ } & {
161
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  afterAttach(): void;
162
- estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
163
- headers?: Record<string, string> | undefined;
164
- signal?: AbortSignal | undefined;
165
- filters?: string[] | undefined;
166
- }): Promise<{}>;
167
- setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
168
- setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
169
- clearRegionStats(): void;
166
+ estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
167
+ setRegionsStatsP(arg: any): void;
168
+ setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
169
+ clearRegionsStats(): void;
170
170
  setHeight(displayHeight: number): number;
171
171
  resizeHeight(distance: number): number;
172
172
  setScrollTop(scrollTop: number): void;
173
- updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
173
+ updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
175
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  setCurrBpPerPx(n: number): void;
176
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  deleteBlock(key: string): void;
@@ -184,18 +184,13 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
184
184
  readonly regionTooLargeReason: string;
185
185
  } & {
186
186
  reload(): Promise<void>;
187
+ } & {
187
188
  afterAttach(): void;
188
189
  } & {
189
190
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
190
191
  regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
191
192
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
192
- contextMenuItems(): {
193
- label: string;
194
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
195
- muiName: string;
196
- };
197
- onClick: () => void;
198
- }[];
193
+ contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
199
194
  renderProps(): any;
200
195
  } & {
201
196
  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
@@ -213,19 +208,19 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
213
208
  [x: string]: any;
214
209
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
215
210
  setSubschema(slotName: string, data: unknown): any;
216
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
211
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
217
212
  } & {
218
213
  toggleShowLabels(): void;
219
214
  toggleShowDescriptions(): void;
220
215
  setDisplayMode(val: string): void;
221
- setMaxHeight(val: number): void;
216
+ setMaxHeight(val?: number | undefined): void;
222
217
  } & {
223
218
  renderProps(): {
224
219
  config: {
225
220
  [x: string]: any;
226
221
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
227
222
  setSubschema(slotName: string, data: unknown): any;
228
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
223
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
229
224
  };
230
225
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
231
226
  } & {
@@ -234,3 +229,5 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
234
229
  */
235
230
  selectFeature(feature: Feature): Promise<void>;
236
231
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
232
+ export type LinearVariantDisplayStateModel = ReturnType<typeof stateModelFactory>;
233
+ export type LinearVariantDisplayModel = Instance<LinearVariantDisplayStateModel>;
package/esm/LinearVariantDisplay/model.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,sBAAsB,EAAE,MAAM,6BAA6B,CAAA;AAC7E,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAC3D,OAAO,EACL,kBAAkB,EAClB,UAAU,EACV,iBAAiB,EACjB,yBAAyB,GAC1B,MAAM,oBAAoB,CAAA;AAG3B,OAAO,EAAE,8BAA8B,EAAE,MAAM,oCAAoC,CAAA;AACnF,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAGvC;;;;GAIG;AACH,MAAM,CAAC,OAAO,UAAU,iBAAiB,CACvC,YAA6C;IAE7C,OAAO,KAAK;SACT,OAAO,CACN,sBAAsB,EACtB,8BAA8B,CAAC,YAAY,CAAC,EAC5C,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,KAAK,CAAC,aAAa,CAAC,OAAgB;YAClC,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAChC,IAAI,yBAAyB,CAAC,OAAO,CAAC,EAAE;gBACtC,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAC9B,MAAM,SAAS,GAAG,eAAe,CAAC,IAAI,CAAC,CAAA;gBACvC,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;gBACtC,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAA;gBACpC,MAAM,aAAa,GAAG,OAAO,CAAC,KAAK,EAAE,SAAS,CAAC,CAAA;gBAC/C,MAAM,YAAY,GAAG,MAAM,UAAU,CAAC,IAAI,CACxC,SAAS,EACT,iBAAiB,EACjB;oBACE,aAAa;iBACd,CACF,CAAA;gBACD,OAAO,CAAC,UAAU,CAChB,OAAO,CAAC,SAAS,CAAC,sBAAsB,EAAE,gBAAgB,EAAE;oBAC1D,WAAW,EAAE,OAAO,CAAC,MAAM,EAAE;oBAC7B,IAAI;oBACJ,KAAK;oBACL,YAAY;iBACb,CAAC,CACH,CAAA;aACF;YAED,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;QAC/B,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
1
+ {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,sBAAsB,EAAE,MAAM,6BAA6B,CAAA;AAC7E,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAC3D,OAAO,EACL,kBAAkB,EAClB,UAAU,EACV,iBAAiB,EACjB,yBAAyB,GAE1B,MAAM,oBAAoB,CAAA;AAE3B,OAAO,EAAE,8BAA8B,EAAE,MAAM,oCAAoC,CAAA;AACnF,OAAO,EAAY,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAGjD;;;;GAIG;AACH,MAAM,CAAC,OAAO,UAAU,iBAAiB,CACvC,YAAwC;IAExC,OAAO,KAAK;SACT,OAAO,CACN,sBAAsB,EACtB,8BAA8B,CAAC,YAAY,CAAC,EAC5C,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;KACpD,CAAC,CACH;SAEA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,KAAK,CAAC,aAAa,CAAC,OAAgB;YAClC,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAChC,IAAI,yBAAyB,CAAC,OAAO,CAAC,EAAE;gBACtC,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAC9B,MAAM,SAAS,GAAG,eAAe,CAAC,IAAI,CAAC,CAAA;gBACvC,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;gBACtC,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAA;gBACpC,MAAM,aAAa,GAAG,OAAO,CAAC,KAAK,EAAE,SAAS,CAAC,CAAA;gBAC/C,MAAM,YAAY,GAAG,MAAM,UAAU,CAAC,IAAI,CACxC,SAAS,EACT,iBAAiB,EACjB;oBACE,aAAa;iBACd,CACF,CAAA;gBACD,OAAO,CAAC,UAAU,CAChB,OAAO,CAAC,SAAS,CAAC,sBAAsB,EAAE,gBAAgB,EAAE;oBAC1D,WAAW,EAAE,OAAO,CAAC,MAAM,EAAE;oBAC7B,IAAI;oBACJ,KAAK;oBACL,YAAY;iBACb,CAAC,CACH,CAAA;aACF;YAED,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;QAC/B,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
package/esm/VariantFeatureWidget/index.d.ts CHANGED
@@ -33,8 +33,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
33
33
  trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
34
34
  trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
35
35
  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
36
- id: string;
37
36
  type: "BaseFeatureWidget";
37
+ id: string;
38
38
  track: import("mobx-state-tree").ReferenceIdentifier | undefined;
39
39
  view: import("mobx-state-tree").ReferenceIdentifier | undefined;
40
40
  trackId: string | undefined;
package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts CHANGED
@@ -10,7 +10,7 @@ export default class extends BaseFeatureDataAdapter {
10
10
  vcf: TabixIndexedFile;
11
11
  parser: VcfParser;
12
12
  }>;
13
- getRefNames(opts?: BaseOptions): Promise<any>;
13
+ getRefNames(opts?: BaseOptions): Promise<string[]>;
14
14
  getHeader(): Promise<string>;
15
15
  getMetadata(): Promise<any>;
16
16
  getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-variants",
3
- "version": "2.4.1",
3
+ "version": "2.4.2",
4
4
  "description": "JBrowse 2 variant adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -64,5 +64,5 @@
64
64
  "distModule": "esm/index.js",
65
65
  "srcModule": "src/index.ts",
66
66
  "module": "esm/index.js",
67
- "gitHead": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
67
+ "gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
68
68
  }
package/src/LinearVariantDisplay/model.ts CHANGED
@@ -5,12 +5,12 @@ import {
5
5
  getSession,
6
6
  getContainingView,
7
7
  isSessionModelWithWidgets,
8
+ Feature,
8
9
  } from '@jbrowse/core/util'
9
10
 
10
- import { Feature } from '@jbrowse/core/util/simpleFeature'
11
11
  import { linearBasicDisplayModelFactory } from '@jbrowse/plugin-linear-genome-view'
12
- import { types } from 'mobx-state-tree'
13
- import { LinearVariantDisplayConfigModel } from './configSchema'
12
+ import { Instance, types } from 'mobx-state-tree'
13
+ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
14
14
 
15
15
  /**
16
16
  * #stateModel LinearVariantDisplay
@@ -18,7 +18,7 @@ import { LinearVariantDisplayConfigModel } from './configSchema'
18
18
  * very similar to basic display, but provides custom widget on feature click
19
19
  */
20
20
  export default function stateModelFactory(
21
- configSchema: LinearVariantDisplayConfigModel,
21
+ configSchema: AnyConfigurationSchemaType,
22
22
  ) {
23
23
  return types
24
24
  .compose(
@@ -35,6 +35,7 @@ export default function stateModelFactory(
35
35
  configuration: ConfigurationReference(configSchema),
36
36
  }),
37
37
  )
38
+
38
39
  .actions(self => ({
39
40
  /**
40
41
  * #action
@@ -68,3 +69,8 @@ export default function stateModelFactory(
68
69
  },
69
70
  }))
70
71
  }
72
+
73
+ export type LinearVariantDisplayStateModel = ReturnType<
74
+ typeof stateModelFactory
75
+ >
76
+ export type LinearVariantDisplayModel = Instance<LinearVariantDisplayStateModel>