@jbrowse/plugin-sequence 2.5.0 → 2.6.1

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.
Files changed (10) hide show
  1. package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts +2 -1
  2. package/dist/LinearReferenceSequenceDisplay/model.d.ts +60 -53
  3. package/dist/TwoBitAdapter/TwoBitAdapter.js +2 -1
  4. package/dist/TwoBitAdapter/TwoBitAdapter.js.map +1 -1
  5. package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts +2 -1
  6. package/esm/LinearReferenceSequenceDisplay/model.d.ts +60 -53
  7. package/esm/TwoBitAdapter/TwoBitAdapter.js +2 -1
  8. package/esm/TwoBitAdapter/TwoBitAdapter.js.map +1 -1
  9. package/package.json +2 -2
  10. package/src/TwoBitAdapter/TwoBitAdapter.ts +2 -4
package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts CHANGED
@@ -1,3 +1,4 @@
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+ import React from 'react';
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  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
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  import { Feature, Region } from '@jbrowse/core/util';
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  declare function Sequence(props: {
@@ -12,6 +13,6 @@ declare function Sequence(props: {
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  showForward?: boolean;
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  showReverse?: boolean;
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  showTranslation?: boolean;
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- }): JSX.Element;
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+ }): React.JSX.Element;
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  declare const _default: typeof Sequence;
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  export default _default;
package/dist/LinearReferenceSequenceDisplay/model.d.ts CHANGED
@@ -9,10 +9,11 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  type: import("mobx-state-tree").ISimpleType<string>;
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  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  } & {
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- /**
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- * #getter
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- */
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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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+ } & {
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  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
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  key: import("mobx-state-tree").ISimpleType<string>;
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  region: import("mobx-state-tree").IModelType<{
@@ -62,8 +63,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  reload(): void;
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  beforeDestroy(): void;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  maxFeatureScreenDensity: {
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  type: string;
@@ -76,9 +75,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  description: string;
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  };
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  height: {
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- /**
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- * #property
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- */
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  type: string;
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  defaultValue: number;
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  description: string;
@@ -99,6 +95,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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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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  } & {
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  readonly RenderingComponent: import("react").FC<{
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  model: {
@@ -106,8 +103,11 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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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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- rendererTypeName: string;
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+ rendererTypeName: string; /**
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+ * #property
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+ */
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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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  type: import("mobx-state-tree").ISimpleType<string>;
@@ -115,18 +115,22 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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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>>;
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  onHorizontalScroll?: Function | undefined;
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  blockState?: Record<string, any> | undefined;
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  }>;
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  readonly DisplayBlurb: import("react").FC<{
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  model: {
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- id: string;
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+ id: string; /**
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+ * #action
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+ */
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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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  rendererTypeName: string;
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  error: unknown;
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+ message: string | undefined;
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  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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  type: import("mobx-state-tree").ISimpleType<string>;
@@ -134,8 +138,12 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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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>>;
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  }> | null;
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+ /**
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+ * #method
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+ */
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  readonly adapterConfig: any;
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  readonly parentTrack: any;
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  renderProps(): any;
@@ -143,21 +151,51 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
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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(): undefined;
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+ regionCannotBeRendered(): null;
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  } & {
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+ setMessage(arg?: string | undefined): void;
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  setError(error?: unknown): void;
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  setRpcDriverName(rpcDriverName: string): void;
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  reload(): void;
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  } & {
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- currBpPerPx: number;
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  scrollTop: number;
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- message: string;
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- featureIdUnderMouse: string | undefined;
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- contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
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+ } & {
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+ readonly height: number;
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+ } & {
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+ setScrollTop(scrollTop: number): void; /**
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+ * #property
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+ */
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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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+ currStatsBpPerPx: number;
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+ } & {
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+ readonly currentBytesRequested: number;
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+ readonly currentFeatureScreenDensity: number;
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+ readonly maxFeatureScreenDensity: any;
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+ readonly featureDensityStatsReady: boolean;
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+ readonly maxAllowableBytes: number;
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+ } & {
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+ afterAttach(): void;
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+ } & {
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+ setCurrStatsBpPerPx(n: number): void;
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+ setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
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+ getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
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+ setFeatureDensityStatsP(arg: any): void;
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+ setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
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+ clearFeatureDensityStats(): void;
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+ } & {
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+ readonly regionTooLarge: boolean;
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+ readonly regionTooLargeReason: string;
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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): 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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  } & {
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- readonly height: number;
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  readonly blockType: "dynamicBlocks" | "staticBlocks";
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  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
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  } & {
@@ -171,49 +209,22 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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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;
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- readonly currentFeatureScreenDensity: number;
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- readonly maxFeatureScreenDensity: any;
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- readonly featureDensityStatsReady: boolean;
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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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- 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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- clearFeatureDensityStats(): 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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- setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | 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;
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  selectFeature(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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- reload(): void;
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  setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
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- } & {
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- readonly regionTooLarge: boolean;
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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(): 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 & {
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- overrideHeight: number;
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- theme: import("@mui/material").ThemeOptions;
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- }): Promise<JSX.Element>;
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+ renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
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+ afterAttach(): void;
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  } & {
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  /**
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  * #method
@@ -259,10 +270,11 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  type: import("mobx-state-tree").ISimpleType<string>;
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  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  } & {
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- /**
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- * #getter
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- */
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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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+ } & {
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  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
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  key: import("mobx-state-tree").ISimpleType<string>;
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  region: import("mobx-state-tree").IModelType<{
@@ -312,8 +324,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  reload(): void;
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  beforeDestroy(): void;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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  configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  maxFeatureScreenDensity: {
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  type: string;
@@ -326,9 +336,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  description: string;
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  };
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  height: {
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- /**
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- * #property
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- */
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  type: string;
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  defaultValue: number;
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  description: string;
package/dist/TwoBitAdapter/TwoBitAdapter.js CHANGED
@@ -27,9 +27,10 @@ class TwoBitAdapter extends BaseAdapter_1.BaseSequenceAdapter {
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  }
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  constructor(config, getSubAdapter, pluginManager) {
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  super(config, getSubAdapter, pluginManager);
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+ const pm = this.pluginManager;
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  this.chromSizesData = this.initChromSizes();
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  this.twobit = new twobit_1.TwoBitFile({
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- filehandle: (0, io_1.openLocation)((0, configuration_1.readConfObject)(config, 'twoBitLocation'), this.pluginManager),
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+ filehandle: (0, io_1.openLocation)(this.getConf('twoBitLocation'), pm),
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  });
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  }
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  async getRefNames() {
package/dist/TwoBitAdapter/TwoBitAdapter.js.map CHANGED
@@ -1 +1 @@
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1
+ {"version":3,"file":"TwoBitAdapter.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/TwoBitAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAA6E;AAE7E,8CAAoD;AACpD,kDAA0D;AAC1D,qFAAyE;AACzE,yCAAyC;AACzC,+DAA4D;AAK5D,MAAqB,aAAc,SAAQ,iCAAmB;IAOpD,KAAK,CAAC,cAAc;QAC1B,MAAM,IAAI,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QAC9D,2EAA2E;QAC3E,yEAAyE;QACzE,SAAS;QACT,IAAI,IAAI,CAAC,GAAG,KAAK,8BAA8B,IAAI,IAAI,CAAC,GAAG,KAAK,EAAE,EAAE;YAClE,MAAM,IAAI,GAAG,IAAA,iBAAY,EAAC,IAAI,EAAE,IAAI,CAAC,aAAa,CAAC,CAAA;YACnD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CACA,KAAK,CAAC,YAAY,EACnB,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,EAAE,EAC5B,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,CAAC,IAAI,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBACvC,OAAO,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC,CAAA;YACxB,CAAC,CAAC,CACL,CAAA;SACF;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAC3C,IAAI,CAAC,MAAM,GAAG,IAAI,mBAAU,CAAC;YAC3B,UAAU,EAAE,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,gBAAgB,CAAC,EAAE,EAAE,CAAC;SAC7D,CAAC,CAAA;IACJ,CAAC;IAEM,KAAK,CAAC,WAAW;QACtB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAA;SACnC;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;IACvC,CAAC;IAEM,KAAK,CAAC,UAAU;QACrB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;gBACjD,OAAO;gBACP,KAAK,EAAE,CAAC;gBACR,GAAG,EAAE,cAAc,CAAC,OAAO,CAAC;aAC7B,CAAC,CAAC,CAAA;SACJ;QACD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;QACrD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAED;;;;OAIG;IACI,WAAW,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAoB;QAC1D,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;YACpE,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AA9FD,gCA8FC"}
package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts CHANGED
@@ -1,3 +1,4 @@
1
+ import React from 'react';
1
2
  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
2
3
  import { Feature, Region } from '@jbrowse/core/util';
3
4
  declare function Sequence(props: {
@@ -12,6 +13,6 @@ declare function Sequence(props: {
12
13
  showForward?: boolean;
13
14
  showReverse?: boolean;
14
15
  showTranslation?: boolean;
15
- }): JSX.Element;
16
+ }): React.JSX.Element;
16
17
  declare const _default: typeof Sequence;
17
18
  export default _default;
package/esm/LinearReferenceSequenceDisplay/model.d.ts CHANGED
@@ -9,10 +9,11 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
9
9
  type: import("mobx-state-tree").ISimpleType<string>;
10
10
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
11
11
  } & {
12
- /**
13
- * #getter
14
- */
15
12
  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
13
+ } & {
14
+ userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
15
+ userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
16
+ } & {
16
17
  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
17
18
  key: import("mobx-state-tree").ISimpleType<string>;
18
19
  region: import("mobx-state-tree").IModelType<{
@@ -62,8 +63,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
62
63
  reload(): void;
63
64
  beforeDestroy(): void;
64
65
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
65
- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
66
- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
67
66
  configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
68
67
  maxFeatureScreenDensity: {
69
68
  type: string;
@@ -76,9 +75,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
76
75
  description: string;
77
76
  };
78
77
  height: {
79
- /**
80
- * #property
81
- */
82
78
  type: string;
83
79
  defaultValue: number;
84
80
  description: string;
@@ -99,6 +95,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
99
95
  }, {
100
96
  rendererTypeName: string;
101
97
  error: unknown;
98
+ message: string | undefined;
102
99
  } & {
103
100
  readonly RenderingComponent: import("react").FC<{
104
101
  model: {
@@ -106,8 +103,11 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
106
103
  type: string;
107
104
  rpcDriverName: string | undefined;
108
105
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
109
- rendererTypeName: string;
106
+ rendererTypeName: string; /**
107
+ * #property
108
+ */
110
109
  error: unknown;
110
+ message: string | undefined;
111
111
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
112
112
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
113
113
  type: import("mobx-state-tree").ISimpleType<string>;
@@ -115,18 +115,22 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
115
115
  }, {
116
116
  rendererTypeName: string;
117
117
  error: unknown;
118
+ message: string | undefined;
118
119
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
119
120
  onHorizontalScroll?: Function | undefined;
120
121
  blockState?: Record<string, any> | undefined;
121
122
  }>;
122
123
  readonly DisplayBlurb: import("react").FC<{
123
124
  model: {
124
- id: string;
125
+ id: string; /**
126
+ * #action
127
+ */
125
128
  type: string;
126
129
  rpcDriverName: string | undefined;
127
130
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
128
131
  rendererTypeName: string;
129
132
  error: unknown;
133
+ message: string | undefined;
130
134
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
131
135
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
132
136
  type: import("mobx-state-tree").ISimpleType<string>;
@@ -134,8 +138,12 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
134
138
  }, {
135
139
  rendererTypeName: string;
136
140
  error: unknown;
141
+ message: string | undefined;
137
142
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
138
143
  }> | null;
144
+ /**
145
+ * #method
146
+ */
139
147
  readonly adapterConfig: any;
140
148
  readonly parentTrack: any;
141
149
  renderProps(): any;
@@ -143,21 +151,51 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
143
151
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
144
152
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
145
153
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
146
- regionCannotBeRendered(): undefined;
154
+ regionCannotBeRendered(): null;
147
155
  } & {
156
+ setMessage(arg?: string | undefined): void;
148
157
  setError(error?: unknown): void;
149
158
  setRpcDriverName(rpcDriverName: string): void;
150
159
  reload(): void;
151
160
  } & {
152
- currBpPerPx: number;
153
161
  scrollTop: number;
154
- message: string;
155
- featureIdUnderMouse: string | undefined;
156
- contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
162
+ } & {
163
+ readonly height: number;
164
+ } & {
165
+ setScrollTop(scrollTop: number): void; /**
166
+ * #property
167
+ */
168
+ setHeight(displayHeight: number): number;
169
+ resizeHeight(distance: number): number;
170
+ } & {
157
171
  featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
158
172
  featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
173
+ currStatsBpPerPx: number;
174
+ } & {
175
+ readonly currentBytesRequested: number;
176
+ readonly currentFeatureScreenDensity: number;
177
+ readonly maxFeatureScreenDensity: any;
178
+ readonly featureDensityStatsReady: boolean;
179
+ readonly maxAllowableBytes: number;
180
+ } & {
181
+ afterAttach(): void;
182
+ } & {
183
+ setCurrStatsBpPerPx(n: number): void;
184
+ setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
185
+ getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
186
+ setFeatureDensityStatsP(arg: any): void;
187
+ setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
188
+ clearFeatureDensityStats(): void;
189
+ } & {
190
+ readonly regionTooLarge: boolean;
191
+ readonly regionTooLargeReason: string;
192
+ } & {
193
+ regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
194
+ regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
195
+ } & {
196
+ featureIdUnderMouse: string | undefined;
197
+ contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
159
198
  } & {
160
- readonly height: number;
161
199
  readonly blockType: "dynamicBlocks" | "staticBlocks";
162
200
  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
163
201
  } & {
@@ -171,49 +209,22 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
171
209
  getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
172
210
  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
173
211
  searchFeatureByID(id: string): [number, number, number, number] | undefined;
174
- readonly currentBytesRequested: number;
175
- readonly currentFeatureScreenDensity: number;
176
- readonly maxFeatureScreenDensity: any;
177
- readonly featureDensityStatsReady: boolean;
178
- readonly maxAllowableBytes: number;
179
212
  } & {
180
- setMessage(message: string): void;
181
- } & {
182
- afterAttach(): void;
183
- getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
184
- setFeatureDensityStatsP(arg: any): void;
185
- setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
186
- clearFeatureDensityStats(): void;
187
- setHeight(displayHeight: number): number;
188
- resizeHeight(distance: number): number;
189
- setScrollTop(scrollTop: number): void;
190
- setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
191
213
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
192
- setCurrBpPerPx(n: number): void;
193
214
  deleteBlock(key: string): void;
194
215
  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
195
216
  clearFeatureSelection(): void;
196
217
  setFeatureIdUnderMouse(feature?: string | undefined): void;
197
- reload(): void;
198
218
  setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
199
- } & {
200
- readonly regionTooLarge: boolean;
201
- readonly regionTooLargeReason: string;
202
219
  } & {
203
220
  reload(): Promise<void>;
204
221
  } & {
205
- afterAttach(): void;
206
- } & {
207
- regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
208
- regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
209
222
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
210
223
  contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
211
224
  renderProps(): any;
212
225
  } & {
213
- renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
214
- overrideHeight: number;
215
- theme: import("@mui/material").ThemeOptions;
216
- }): Promise<JSX.Element>;
226
+ renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
227
+ afterAttach(): void;
217
228
  } & {
218
229
  /**
219
230
  * #method
@@ -259,10 +270,11 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
259
270
  type: import("mobx-state-tree").ISimpleType<string>;
260
271
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
261
272
  } & {
262
- /**
263
- * #getter
264
- */
265
273
  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
274
+ } & {
275
+ userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
276
+ userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
277
+ } & {
266
278
  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
267
279
  key: import("mobx-state-tree").ISimpleType<string>;
268
280
  region: import("mobx-state-tree").IModelType<{
@@ -312,8 +324,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
312
324
  reload(): void;
313
325
  beforeDestroy(): void;
314
326
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
315
- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
316
- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
317
327
  configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
318
328
  maxFeatureScreenDensity: {
319
329
  type: string;
@@ -326,9 +336,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
326
336
  description: string;
327
337
  };
328
338
  height: {
329
- /**
330
- * #property
331
- */
332
339
  type: string;
333
340
  defaultValue: number;
334
341
  description: string;
package/esm/TwoBitAdapter/TwoBitAdapter.js CHANGED
@@ -22,9 +22,10 @@ export default class TwoBitAdapter extends BaseSequenceAdapter {
22
22
  }
23
23
  constructor(config, getSubAdapter, pluginManager) {
24
24
  super(config, getSubAdapter, pluginManager);
25
+ const pm = this.pluginManager;
25
26
  this.chromSizesData = this.initChromSizes();
26
27
  this.twobit = new TwoBitFile({
27
- filehandle: openLocation(readConfObject(config, 'twoBitLocation'), this.pluginManager),
28
+ filehandle: openLocation(this.getConf('twoBitLocation'), pm),
28
29
  });
29
30
  }
30
31
  async getRefNames() {
package/esm/TwoBitAdapter/TwoBitAdapter.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"TwoBitAdapter.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/TwoBitAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,yCAAyC,CAAA;AAE7E,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAA;AACzC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAK5D,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,mBAAmB;IAOpD,KAAK,CAAC,cAAc;QAC1B,MAAM,IAAI,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QAC9D,2EAA2E;QAC3E,yEAAyE;QACzE,SAAS;QACT,IAAI,IAAI,CAAC,GAAG,KAAK,8BAA8B,IAAI,IAAI,CAAC,GAAG,KAAK,EAAE,EAAE;YAClE,MAAM,IAAI,GAAG,YAAY,CAAC,IAAI,EAAE,IAAI,CAAC,aAAa,CAAC,CAAA;YACnD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CACA,KAAK,CAAC,YAAY,EACnB,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,EAAE,EAC5B,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,CAAC,IAAI,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBACvC,OAAO,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC,CAAA;YACxB,CAAC,CAAC,CACL,CAAA;SACF;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAC3C,IAAI,CAAC,MAAM,GAAG,IAAI,UAAU,CAAC;YAC3B,UAAU,EAAE,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,gBAAgB,CAAC,EAAE,EAAE,CAAC;SAC7D,CAAC,CAAA;IACJ,CAAC;IAEM,KAAK,CAAC,WAAW;QACtB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAA;SACnC;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;IACvC,CAAC;IAEM,KAAK,CAAC,UAAU;QACrB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;gBACjD,OAAO;gBACP,KAAK,EAAE,CAAC;gBACR,GAAG,EAAE,cAAc,CAAC,OAAO,CAAC;aAC7B,CAAC,CAAC,CAAA;SACJ;QACD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;QACrD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAED;;;;OAIG;IACI,WAAW,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAoB;QAC1D,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;YACpE,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-sequence",
3
- "version": "2.5.0",
3
+ "version": "2.6.1",
4
4
  "description": "JBrowse 2 sequence adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -58,5 +58,5 @@
58
58
  "distModule": "esm/index.js",
59
59
  "srcModule": "src/index.ts",
60
60
  "module": "esm/index.js",
61
- "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
61
+ "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
62
62
  }
package/src/TwoBitAdapter/TwoBitAdapter.ts CHANGED
@@ -43,12 +43,10 @@ export default class TwoBitAdapter extends BaseSequenceAdapter {
43
43
  pluginManager?: PluginManager,
44
44
  ) {
45
45
  super(config, getSubAdapter, pluginManager)
46
+ const pm = this.pluginManager
46
47
  this.chromSizesData = this.initChromSizes()
47
48
  this.twobit = new TwoBitFile({
48
- filehandle: openLocation(
49
- readConfObject(config, 'twoBitLocation'),
50
- this.pluginManager,
51
- ),
49
+ filehandle: openLocation(this.getConf('twoBitLocation'), pm),
52
50
  })
53
51
  }
54
52