@jbrowse/plugin-arc 2.11.2 → 2.12.1

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.
@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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  return (mod && mod.__esModule) ? mod : { "default": mod };
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  };
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  Object.defineProperty(exports, "__esModule", { value: true });
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+ exports.default = ArcRendererF;
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  const ArcRendering_1 = __importDefault(require("./ArcRendering"));
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  const configSchema_1 = __importDefault(require("./configSchema"));
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  const ArcRenderer_1 = __importDefault(require("./ArcRenderer"));
@@ -14,4 +15,3 @@ function ArcRendererF(pluginManager) {
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  pluginManager,
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  }));
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  }
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- exports.default = ArcRendererF;
@@ -1,6 +1,6 @@
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  "use strict";
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  Object.defineProperty(exports, "__esModule", { value: true });
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- exports.configSchemaFactory = void 0;
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+ exports.configSchemaFactory = configSchemaFactory;
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  const mobx_state_tree_1 = require("mobx-state-tree");
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  const configuration_1 = require("@jbrowse/core/configuration");
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  const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
@@ -21,4 +21,3 @@ function configSchemaFactory(pluginManager) {
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  explicitlyTyped: true,
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  });
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  }
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- exports.configSchemaFactory = configSchemaFactory;
@@ -1,5 +1,6 @@
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  "use strict";
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  Object.defineProperty(exports, "__esModule", { value: true });
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+ exports.default = LinearArcDisplayF;
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  const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
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  const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
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  const configSchema_1 = require("./configSchema");
@@ -18,4 +19,3 @@ function LinearArcDisplayF(pluginManager) {
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  });
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  });
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  }
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- exports.default = LinearArcDisplayF;
@@ -1,4 +1,3 @@
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- /// <reference types="react" />
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  import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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  /**
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  * #stateModel LinearArcDisplay
@@ -8,9 +7,7 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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  export declare 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>>; /**
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- * #property
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- */
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+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  } & {
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  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  } & {
@@ -35,7 +32,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  }, {
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  renderInProgress: AbortController | undefined;
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  filled: boolean;
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- reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
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+ reactElement: import("react").ReactElement | undefined;
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  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
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  layout: any;
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  status: string;
@@ -43,16 +40,13 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  message: string | undefined;
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  maxHeightReached: boolean;
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  ReactComponent: ({ model, }: {
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- /**
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- * #getter
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- */
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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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+ filled?: boolean;
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+ status?: string;
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+ reactElement?: import("react").ReactElement;
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  };
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  }) => import("react").JSX.Element | undefined;
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  renderProps: any;
@@ -63,7 +57,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  setLoading(abortController: AbortController): void;
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  setMessage(messageText: string): void;
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  setRendered(props: {
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- reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
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+ reactElement: import("react").ReactElement;
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  features: Map<string, import("@jbrowse/core/util").Feature>;
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  layout: any;
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  maxHeightReached: boolean;
@@ -82,15 +76,10 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  fetchSizeLimit: {
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  type: string;
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  defaultValue: number;
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- /**
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- * #getter
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- */
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  description: string;
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  };
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  height: {
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- type: string; /**
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- * #getter
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- */
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+ type: string;
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  defaultValue: number;
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  description: string;
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  };
@@ -129,7 +118,9 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  id: string;
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  type: string;
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  rpcDriverName: string | undefined;
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- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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+ } & import("mobx-state-tree/dist/internal" /**
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+ * #getter
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+ */).NonEmptyObject & {
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  rendererTypeName: string;
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  error: unknown;
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  message: string | undefined;
@@ -142,8 +133,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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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>>;
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- onHorizontalScroll?: Function | undefined;
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- blockState?: Record<string, any> | undefined;
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+ onHorizontalScroll?: Function;
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+ blockState?: Record<string, any>;
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  }>;
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  readonly DisplayBlurb: import("react").FC<{
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  model: {
@@ -155,7 +146,9 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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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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+ id: import("mobx-state-tree" /**
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+ * #method
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+ */).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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  }, {
@@ -168,12 +161,12 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  readonly parentTrack: any;
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  renderProps(): any;
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  readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
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- readonly DisplayMessageComponent: import("react").FC<any> | undefined;
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+ readonly DisplayMessageComponent: undefined | import("react").FC<any>;
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  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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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): void;
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  setError(error?: unknown): void;
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  setRpcDriverName(rpcDriverName: string): void;
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  reload(): void;
@@ -186,8 +179,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  setHeight(displayHeight: number): number;
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  resizeHeight(distance: number): number;
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  } & {
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- featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
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- featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
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+ featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
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+ featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
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  currStatsBpPerPx: number;
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  } & {
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  readonly currentBytesRequested: number;
@@ -199,10 +192,10 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  afterAttach(): void;
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  } & {
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  setCurrStatsBpPerPx(n: number): void;
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- setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
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+ setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
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  getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
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  setFeatureDensityStatsP(arg: any): void;
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- setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
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+ setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
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  clearFeatureDensityStats(): void;
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  } & {
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  readonly regionTooLarge: boolean;
@@ -211,8 +204,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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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;
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  } & {
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- featureIdUnderMouse: string | undefined;
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- contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
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+ featureIdUnderMouse: undefined | string;
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+ contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
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  } & {
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  readonly blockType: "dynamicBlocks" | "staticBlocks";
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  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -220,7 +213,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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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 DisplayMessageComponent: import("react").FC<any> | undefined;
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+ readonly DisplayMessageComponent: undefined | import("react").FC<any>;
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  } & {
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  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
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  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -233,8 +226,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
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  navToFeature(feature: import("@jbrowse/core/util").Feature): void;
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  clearFeatureSelection(): void;
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- setFeatureIdUnderMouse(feature?: string | undefined): void;
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- setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
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+ setFeatureIdUnderMouse(feature?: string): void;
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+ setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
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  } & {
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  reload(): Promise<void>;
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  } & {
@@ -269,7 +262,13 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  readonly rendererConfig: {
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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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+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
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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: Record<string, unknown>): Record<string, unknown> | ({
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+ [x: string]: any;
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+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
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+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
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  } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
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  } & {
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  /**
@@ -299,9 +298,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
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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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- * #property
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- */
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+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  } & {
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  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  } & {
@@ -326,7 +323,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  }, {
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  renderInProgress: AbortController | undefined;
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  filled: boolean;
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- reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
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+ reactElement: import("react").ReactElement | undefined;
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  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
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  layout: any;
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  status: string;
@@ -334,16 +331,13 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  message: string | undefined;
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  maxHeightReached: boolean;
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  ReactComponent: ({ model, }: {
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- /**
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- * #getter
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- */
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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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+ filled?: boolean;
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+ status?: string;
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+ reactElement?: import("react").ReactElement;
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  };
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  }) => import("react").JSX.Element | undefined;
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  renderProps: any;
@@ -354,7 +348,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  setLoading(abortController: AbortController): void;
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  setMessage(messageText: string): void;
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  setRendered(props: {
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- reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
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+ reactElement: import("react").ReactElement;
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  features: Map<string, import("@jbrowse/core/util").Feature>;
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  layout: any;
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  maxHeightReached: boolean;
@@ -373,15 +367,10 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  fetchSizeLimit: {
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  type: string;
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  defaultValue: number;
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- /**
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- * #getter
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- */
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  description: string;
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  };
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  height: {
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- type: string; /**
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- * #getter
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- */
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+ type: string;
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  defaultValue: number;
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  description: string;
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  };
@@ -1,6 +1,6 @@
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  "use strict";
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  Object.defineProperty(exports, "__esModule", { value: true });
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- exports.stateModelFactory = void 0;
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+ exports.stateModelFactory = stateModelFactory;
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  const configuration_1 = require("@jbrowse/core/configuration");
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  const mobx_state_tree_1 = require("mobx-state-tree");
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  const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
@@ -123,4 +123,3 @@ function stateModelFactory(configSchema) {
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  };
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  });
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  }
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- exports.stateModelFactory = stateModelFactory;
@@ -1,6 +1,6 @@
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  "use strict";
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  Object.defineProperty(exports, "__esModule", { value: true });
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- exports.doAfterAttach = void 0;
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+ exports.doAfterAttach = doAfterAttach;
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  const util_1 = require("./util");
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  const fetchChains_1 = require("./fetchChains");
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  function doAfterAttach(self) {
@@ -8,4 +8,3 @@ function doAfterAttach(self) {
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  await (0, fetchChains_1.fetchChains)(self);
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  }, { delay: 1000 });
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  }
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- exports.doAfterAttach = doAfterAttach;
@@ -11,7 +11,7 @@ export declare function makeFeaturePair(feature: Feature, alt?: string): {
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  refName: string;
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  start: number;
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  end: number;
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- mateDirection?: number | undefined;
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+ mateDirection?: number;
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  };
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  };
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  export declare function makeSummary(feature: Feature, alt?: string): string;
@@ -1,6 +1,7 @@
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  "use strict";
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  Object.defineProperty(exports, "__esModule", { value: true });
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- exports.makeSummary = exports.makeFeaturePair = void 0;
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+ exports.makeFeaturePair = makeFeaturePair;
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+ exports.makeSummary = makeSummary;
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  const vcf_1 = require("@gmod/vcf");
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  const util_1 = require("@jbrowse/core/util");
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  function makeFeaturePair(feature, alt) {
@@ -55,7 +56,6 @@ function makeFeaturePair(feature, alt) {
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  },
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  };
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  }
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- exports.makeFeaturePair = makeFeaturePair;
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  function makeSummary(feature, alt) {
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  var _a;
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  const { k1, k2 } = makeFeaturePair(feature, alt);
@@ -70,4 +70,3 @@ function makeSummary(feature, alt) {
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  .filter(f => !!f)
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  .join(' - ');
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  }
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- exports.makeSummary = makeSummary;
@@ -1,6 +1,6 @@
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  "use strict";
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  Object.defineProperty(exports, "__esModule", { value: true });
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- exports.configSchemaFactory = void 0;
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+ exports.configSchemaFactory = configSchemaFactory;
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  const configuration_1 = require("@jbrowse/core/configuration");
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  const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
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  /**
@@ -25,4 +25,3 @@ function configSchemaFactory() {
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  explicitlyTyped: true,
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  });
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  }
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- exports.configSchemaFactory = configSchemaFactory;
@@ -1,6 +1,6 @@
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  "use strict";
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  Object.defineProperty(exports, "__esModule", { value: true });
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- exports.fetchChains = void 0;
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+ exports.fetchChains = fetchChains;
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  const util_1 = require("@jbrowse/core/util");
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  async function fetchChains(self) {
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  // @ts-expect-error
@@ -19,4 +19,3 @@ async function fetchChains(self) {
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  self.setFeatures(ret);
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  self.setLoading(false);
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  }
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- exports.fetchChains = fetchChains;
@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
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  return result;
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  };
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  Object.defineProperty(exports, "__esModule", { value: true });
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+ exports.default = LinearPairedArcDisplayF;
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  const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
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  const configSchema_1 = require("./configSchema");
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  const model_1 = require("./model");
@@ -41,4 +42,3 @@ function LinearPairedArcDisplayF(pluginManager) {
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  });
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  });
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  }
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- exports.default = LinearPairedArcDisplayF;
@@ -20,9 +20,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  } & {
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  userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>; /**
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- * #property
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- */
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+ userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  } & {
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  /**
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  * #property
@@ -51,16 +49,24 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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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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+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree" /**
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+ * #property
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+ */).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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+ rpcDriverName: import("mobx-state-tree").IMaybe<import(
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+ /**
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+ * #getter
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+ */
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+ "mobx-state-tree").ISimpleType<string>>;
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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>>;
62
- onHorizontalScroll?: Function | undefined;
63
- blockState?: Record<string, any> | undefined;
65
+ }, import("mobx-state-tree" /**
66
+ * #action
67
+ */)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
68
+ onHorizontalScroll?: Function;
69
+ blockState?: Record<string, any>;
64
70
  }>;
65
71
  readonly DisplayBlurb: React.FC<{
66
72
  model: {
@@ -85,12 +91,12 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
85
91
  readonly parentTrack: any;
86
92
  renderProps(): any;
87
93
  readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
88
- readonly DisplayMessageComponent: React.FC<any> | undefined;
94
+ readonly DisplayMessageComponent: undefined | React.FC<any>;
89
95
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
90
96
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
91
97
  regionCannotBeRendered(): null;
92
98
  } & {
93
- setMessage(arg?: string | undefined): void;
99
+ setMessage(arg?: string): void;
94
100
  setError(error?: unknown): void;
95
101
  setRpcDriverName(rpcDriverName: string): void;
96
102
  reload(): void;
@@ -103,10 +109,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
103
109
  setHeight(displayHeight: number): number;
104
110
  resizeHeight(distance: number): number;
105
111
  } & {
106
- featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
107
- featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined; /**
108
- * #property
109
- */
112
+ featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
113
+ featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
110
114
  currStatsBpPerPx: number;
111
115
  } & {
112
116
  readonly currentBytesRequested: number;
@@ -118,10 +122,10 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
118
122
  afterAttach(): void;
119
123
  } & {
120
124
  setCurrStatsBpPerPx(n: number): void;
121
- setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
125
+ setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
122
126
  getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
123
127
  setFeatureDensityStatsP(arg: any): void;
124
- setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
128
+ setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
125
129
  clearFeatureDensityStats(): void;
126
130
  } & {
127
131
  readonly regionTooLarge: boolean;
@@ -23,7 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
23
23
  return result;
24
24
  };
25
25
  Object.defineProperty(exports, "__esModule", { value: true });
26
- exports.stateModelFactory = void 0;
26
+ exports.stateModelFactory = stateModelFactory;
27
27
  const configuration_1 = require("@jbrowse/core/configuration");
28
28
  const mobx_state_tree_1 = require("mobx-state-tree");
29
29
  const util_1 = require("@jbrowse/core/util");
@@ -132,4 +132,3 @@ function stateModelFactory(configSchema) {
132
132
  },
133
133
  }));
134
134
  }
135
- exports.stateModelFactory = stateModelFactory;
@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
3
3
  return (mod && mod.__esModule) ? mod : { "default": mod };
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.renderArcSvg = void 0;
6
+ exports.renderArcSvg = renderArcSvg;
7
7
  const react_1 = __importDefault(require("react"));
8
8
  const util_1 = require("@jbrowse/core/util");
9
9
  const Arcs_1 = __importDefault(require("./components/Arcs"));
@@ -20,4 +20,3 @@ async function renderArcSvg(model, _opts) {
20
20
  react_1.default.createElement("g", { clipPath: `url(#${clipid})` },
21
21
  react_1.default.createElement(Arcs_1.default, { model: model, exportSVG: true }))));
22
22
  }
23
- exports.renderArcSvg = renderArcSvg;
@@ -17,7 +17,7 @@ export declare const pairMap: {
17
17
  };
18
18
  export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
19
19
  export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
20
- export declare function shouldFetchReferenceSequence(type?: string): boolean;
20
+ export declare function shouldFetchReferenceSequence(type?: string): type is "methylation";
21
21
  export declare const modificationColors: Record<string, string | undefined>;
22
22
  type DisplayModel = IAnyStateTreeNode & {
23
23
  setError: (arg: unknown) => void;
@@ -1,6 +1,13 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.randomColor = exports.createAutorun = exports.modificationColors = exports.shouldFetchReferenceSequence = exports.fetchSequence = exports.getColorWGBS = exports.pairMap = exports.orientationTypes = exports.getTagAlt = exports.getTag = void 0;
3
+ exports.modificationColors = exports.pairMap = exports.orientationTypes = void 0;
4
+ exports.getTag = getTag;
5
+ exports.getTagAlt = getTagAlt;
6
+ exports.getColorWGBS = getColorWGBS;
7
+ exports.fetchSequence = fetchSequence;
8
+ exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
9
+ exports.createAutorun = createAutorun;
10
+ exports.randomColor = randomColor;
4
11
  const operators_1 = require("rxjs/operators");
5
12
  const rxjs_1 = require("rxjs");
6
13
  const mobx_state_tree_1 = require("mobx-state-tree");
@@ -11,14 +18,12 @@ function getTag(feature, tag) {
11
18
  const tags = feature.get('tags');
12
19
  return tags !== undefined ? tags[tag] : feature.get(tag);
13
20
  }
14
- exports.getTag = getTag;
15
21
  // use fallback alt tag, used in situations where upper case/lower case tags
16
22
  // exist e.g. Mm/MM for base modifications
17
23
  function getTagAlt(feature, tag, alt) {
18
24
  var _a;
19
25
  return (_a = getTag(feature, tag)) !== null && _a !== void 0 ? _a : getTag(feature, alt);
20
26
  }
21
- exports.getTagAlt = getTagAlt;
22
27
  // orientation definitions from igv.js, see also
23
28
  // https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
24
29
  exports.orientationTypes = {
@@ -78,7 +83,6 @@ function getColorWGBS(strand, base) {
78
83
  }
79
84
  return '#888';
80
85
  }
81
- exports.getColorWGBS = getColorWGBS;
82
86
  // fetches region sequence augmenting by +/- 1bp for CpG on either side of
83
87
  // requested region
84
88
  async function fetchSequence(region, adapter) {
@@ -94,12 +98,10 @@ async function fetchSequence(region, adapter) {
94
98
  .pipe((0, operators_1.toArray)()));
95
99
  return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
96
100
  }
97
- exports.fetchSequence = fetchSequence;
98
101
  // has to check underlying C-G (aka CpG) on the reference sequence
99
102
  function shouldFetchReferenceSequence(type) {
100
103
  return type === 'methylation';
101
104
  }
102
- exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
103
105
  // adapted from IGV
104
106
  // https://github.com/igvteam/igv/blob/e803e3af2d8c9ea049961dfd4628146bdde9a574/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java#L27
105
107
  exports.modificationColors = {
@@ -124,8 +126,6 @@ function createAutorun(self, cb, opts) {
124
126
  }
125
127
  }, opts));
126
128
  }
127
- exports.createAutorun = createAutorun;
128
129
  function randomColor() {
129
130
  return `hsl(${Math.random() * 200}, 50%, 50%)`;
130
131
  }
131
- exports.randomColor = randomColor;
@@ -1,4 +1,3 @@
1
- /// <reference types="react" />
2
1
  import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
3
2
  /**
4
3
  * #stateModel LinearArcDisplay
@@ -8,9 +7,7 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
8
7
  export declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
9
8
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
10
9
  type: import("mobx-state-tree").ISimpleType<string>;
11
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
12
- * #property
13
- */
10
+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
14
11
  } & {
15
12
  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
16
13
  } & {
@@ -35,7 +32,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
35
32
  }, {
36
33
  renderInProgress: AbortController | undefined;
37
34
  filled: boolean;
38
- reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
35
+ reactElement: import("react").ReactElement | undefined;
39
36
  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
40
37
  layout: any;
41
38
  status: string;
@@ -43,16 +40,13 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
43
40
  message: string | undefined;
44
41
  maxHeightReached: boolean;
45
42
  ReactComponent: ({ model, }: {
46
- /**
47
- * #getter
48
- */
49
43
  model: {
50
44
  error?: unknown;
51
45
  reload: () => void;
52
46
  message: import("react").ReactNode;
53
- filled?: boolean | undefined;
54
- status?: string | undefined;
55
- reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
47
+ filled?: boolean;
48
+ status?: string;
49
+ reactElement?: import("react").ReactElement;
56
50
  };
57
51
  }) => import("react").JSX.Element | undefined;
58
52
  renderProps: any;
@@ -63,7 +57,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
63
57
  setLoading(abortController: AbortController): void;
64
58
  setMessage(messageText: string): void;
65
59
  setRendered(props: {
66
- reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
60
+ reactElement: import("react").ReactElement;
67
61
  features: Map<string, import("@jbrowse/core/util").Feature>;
68
62
  layout: any;
69
63
  maxHeightReached: boolean;
@@ -82,15 +76,10 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
82
76
  fetchSizeLimit: {
83
77
  type: string;
84
78
  defaultValue: number;
85
- /**
86
- * #getter
87
- */
88
79
  description: string;
89
80
  };
90
81
  height: {
91
- type: string; /**
92
- * #getter
93
- */
82
+ type: string;
94
83
  defaultValue: number;
95
84
  description: string;
96
85
  };
@@ -129,7 +118,9 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
129
118
  id: string;
130
119
  type: string;
131
120
  rpcDriverName: string | undefined;
132
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
121
+ } & import("mobx-state-tree/dist/internal" /**
122
+ * #getter
123
+ */).NonEmptyObject & {
133
124
  rendererTypeName: string;
134
125
  error: unknown;
135
126
  message: string | undefined;
@@ -142,8 +133,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
142
133
  error: unknown;
143
134
  message: string | undefined;
144
135
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
145
- onHorizontalScroll?: Function | undefined;
146
- blockState?: Record<string, any> | undefined;
136
+ onHorizontalScroll?: Function;
137
+ blockState?: Record<string, any>;
147
138
  }>;
148
139
  readonly DisplayBlurb: import("react").FC<{
149
140
  model: {
@@ -155,7 +146,9 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
155
146
  error: unknown;
156
147
  message: string | undefined;
157
148
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
158
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
149
+ id: import("mobx-state-tree" /**
150
+ * #method
151
+ */).IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
159
152
  type: import("mobx-state-tree").ISimpleType<string>;
160
153
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
161
154
  }, {
@@ -168,12 +161,12 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
168
161
  readonly parentTrack: any;
169
162
  renderProps(): any;
170
163
  readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
171
- readonly DisplayMessageComponent: import("react").FC<any> | undefined;
164
+ readonly DisplayMessageComponent: undefined | import("react").FC<any>;
172
165
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
173
166
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
174
167
  regionCannotBeRendered(): null;
175
168
  } & {
176
- setMessage(arg?: string | undefined): void;
169
+ setMessage(arg?: string): void;
177
170
  setError(error?: unknown): void;
178
171
  setRpcDriverName(rpcDriverName: string): void;
179
172
  reload(): void;
@@ -186,8 +179,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
186
179
  setHeight(displayHeight: number): number;
187
180
  resizeHeight(distance: number): number;
188
181
  } & {
189
- featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
190
- featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
182
+ featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
183
+ featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
191
184
  currStatsBpPerPx: number;
192
185
  } & {
193
186
  readonly currentBytesRequested: number;
@@ -199,10 +192,10 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
199
192
  afterAttach(): void;
200
193
  } & {
201
194
  setCurrStatsBpPerPx(n: number): void;
202
- setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
195
+ setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
203
196
  getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
204
197
  setFeatureDensityStatsP(arg: any): void;
205
- setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
198
+ setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
206
199
  clearFeatureDensityStats(): void;
207
200
  } & {
208
201
  readonly regionTooLarge: boolean;
@@ -211,8 +204,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
211
204
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
212
205
  regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
213
206
  } & {
214
- featureIdUnderMouse: string | undefined;
215
- contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
207
+ featureIdUnderMouse: undefined | string;
208
+ contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
216
209
  } & {
217
210
  readonly blockType: "dynamicBlocks" | "staticBlocks";
218
211
  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -220,7 +213,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
220
213
  readonly renderDelay: number;
221
214
  readonly TooltipComponent: import("react").FC<any>;
222
215
  readonly selectedFeatureId: string | undefined;
223
- readonly DisplayMessageComponent: import("react").FC<any> | undefined;
216
+ readonly DisplayMessageComponent: undefined | import("react").FC<any>;
224
217
  } & {
225
218
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
226
219
  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -233,8 +226,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
233
226
  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
234
227
  navToFeature(feature: import("@jbrowse/core/util").Feature): void;
235
228
  clearFeatureSelection(): void;
236
- setFeatureIdUnderMouse(feature?: string | undefined): void;
237
- setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
229
+ setFeatureIdUnderMouse(feature?: string): void;
230
+ setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
238
231
  } & {
239
232
  reload(): Promise<void>;
240
233
  } & {
@@ -269,7 +262,13 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
269
262
  readonly rendererConfig: {
270
263
  [x: string]: any;
271
264
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
272
- setSubschema(slotName: string, data: unknown): any;
265
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
266
+ [x: string]: any;
267
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
268
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
269
+ [x: string]: any;
270
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
271
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
273
272
  } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
274
273
  } & {
275
274
  /**
@@ -299,9 +298,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
299
298
  } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
300
299
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
301
300
  type: import("mobx-state-tree").ISimpleType<string>;
302
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
303
- * #property
304
- */
301
+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
305
302
  } & {
306
303
  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
307
304
  } & {
@@ -326,7 +323,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
326
323
  }, {
327
324
  renderInProgress: AbortController | undefined;
328
325
  filled: boolean;
329
- reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
326
+ reactElement: import("react").ReactElement | undefined;
330
327
  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
331
328
  layout: any;
332
329
  status: string;
@@ -334,16 +331,13 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
334
331
  message: string | undefined;
335
332
  maxHeightReached: boolean;
336
333
  ReactComponent: ({ model, }: {
337
- /**
338
- * #getter
339
- */
340
334
  model: {
341
335
  error?: unknown;
342
336
  reload: () => void;
343
337
  message: import("react").ReactNode;
344
- filled?: boolean | undefined;
345
- status?: string | undefined;
346
- reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
338
+ filled?: boolean;
339
+ status?: string;
340
+ reactElement?: import("react").ReactElement;
347
341
  };
348
342
  }) => import("react").JSX.Element | undefined;
349
343
  renderProps: any;
@@ -354,7 +348,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
354
348
  setLoading(abortController: AbortController): void;
355
349
  setMessage(messageText: string): void;
356
350
  setRendered(props: {
357
- reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
351
+ reactElement: import("react").ReactElement;
358
352
  features: Map<string, import("@jbrowse/core/util").Feature>;
359
353
  layout: any;
360
354
  maxHeightReached: boolean;
@@ -373,15 +367,10 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
373
367
  fetchSizeLimit: {
374
368
  type: string;
375
369
  defaultValue: number;
376
- /**
377
- * #getter
378
- */
379
370
  description: string;
380
371
  };
381
372
  height: {
382
- type: string; /**
383
- * #getter
384
- */
373
+ type: string;
385
374
  defaultValue: number;
386
375
  description: string;
387
376
  };
@@ -11,7 +11,7 @@ export declare function makeFeaturePair(feature: Feature, alt?: string): {
11
11
  refName: string;
12
12
  start: number;
13
13
  end: number;
14
- mateDirection?: number | undefined;
14
+ mateDirection?: number;
15
15
  };
16
16
  };
17
17
  export declare function makeSummary(feature: Feature, alt?: string): string;
@@ -20,9 +20,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
20
20
  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
21
21
  } & {
22
22
  userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
23
- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>; /**
24
- * #property
25
- */
23
+ userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
26
24
  } & {
27
25
  /**
28
26
  * #property
@@ -51,16 +49,24 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
51
49
  error: unknown;
52
50
  message: string | undefined;
53
51
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
54
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
52
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree" /**
53
+ * #property
54
+ */).ISimpleType<string>, [undefined]>;
55
55
  type: import("mobx-state-tree").ISimpleType<string>;
56
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
56
+ rpcDriverName: import("mobx-state-tree").IMaybe<import(
57
+ /**
58
+ * #getter
59
+ */
60
+ "mobx-state-tree").ISimpleType<string>>;
57
61
  }, {
58
62
  rendererTypeName: string;
59
63
  error: unknown;
60
64
  message: string | undefined;
61
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
62
- onHorizontalScroll?: Function | undefined;
63
- blockState?: Record<string, any> | undefined;
65
+ }, import("mobx-state-tree" /**
66
+ * #action
67
+ */)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
68
+ onHorizontalScroll?: Function;
69
+ blockState?: Record<string, any>;
64
70
  }>;
65
71
  readonly DisplayBlurb: React.FC<{
66
72
  model: {
@@ -85,12 +91,12 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
85
91
  readonly parentTrack: any;
86
92
  renderProps(): any;
87
93
  readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
88
- readonly DisplayMessageComponent: React.FC<any> | undefined;
94
+ readonly DisplayMessageComponent: undefined | React.FC<any>;
89
95
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
90
96
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
91
97
  regionCannotBeRendered(): null;
92
98
  } & {
93
- setMessage(arg?: string | undefined): void;
99
+ setMessage(arg?: string): void;
94
100
  setError(error?: unknown): void;
95
101
  setRpcDriverName(rpcDriverName: string): void;
96
102
  reload(): void;
@@ -103,10 +109,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
103
109
  setHeight(displayHeight: number): number;
104
110
  resizeHeight(distance: number): number;
105
111
  } & {
106
- featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
107
- featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined; /**
108
- * #property
109
- */
112
+ featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
113
+ featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
110
114
  currStatsBpPerPx: number;
111
115
  } & {
112
116
  readonly currentBytesRequested: number;
@@ -118,10 +122,10 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
118
122
  afterAttach(): void;
119
123
  } & {
120
124
  setCurrStatsBpPerPx(n: number): void;
121
- setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
125
+ setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
122
126
  getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
123
127
  setFeatureDensityStatsP(arg: any): void;
124
- setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
128
+ setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
125
129
  clearFeatureDensityStats(): void;
126
130
  } & {
127
131
  readonly regionTooLarge: boolean;
@@ -17,7 +17,7 @@ export declare const pairMap: {
17
17
  };
18
18
  export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
19
19
  export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
20
- export declare function shouldFetchReferenceSequence(type?: string): boolean;
20
+ export declare function shouldFetchReferenceSequence(type?: string): type is "methylation";
21
21
  export declare const modificationColors: Record<string, string | undefined>;
22
22
  type DisplayModel = IAnyStateTreeNode & {
23
23
  setError: (arg: unknown) => void;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-arc",
3
- "version": "2.11.2",
3
+ "version": "2.12.1",
4
4
  "description": "JBrowse 2 arc adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -53,5 +53,5 @@
53
53
  "publishConfig": {
54
54
  "access": "public"
55
55
  },
56
- "gitHead": "511048cb6965f0bf624c96de244e7fd47fce17d6"
56
+ "gitHead": "20f16ae5a56ae5e4806aaa373131e540b0b5b0fd"
57
57
  }