@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.
- package/dist/ArcRenderer/index.js +1 -1
- package/dist/LinearArcDisplay/configSchema.js +1 -2
- package/dist/LinearArcDisplay/index.js +1 -1
- package/dist/LinearArcDisplay/model.d.ts +40 -51
- package/dist/LinearArcDisplay/model.js +1 -2
- package/dist/LinearPairedArcDisplay/afterAttach.js +1 -2
- package/dist/LinearPairedArcDisplay/components/util.d.ts +1 -1
- package/dist/LinearPairedArcDisplay/components/util.js +2 -3
- package/dist/LinearPairedArcDisplay/configSchema.js +1 -2
- package/dist/LinearPairedArcDisplay/fetchChains.js +1 -2
- package/dist/LinearPairedArcDisplay/index.js +1 -1
- package/dist/LinearPairedArcDisplay/model.d.ts +20 -16
- package/dist/LinearPairedArcDisplay/model.js +1 -2
- package/dist/LinearPairedArcDisplay/renderSvg.js +1 -2
- package/dist/LinearPairedArcDisplay/util.d.ts +1 -1
- package/dist/LinearPairedArcDisplay/util.js +8 -8
- package/esm/LinearArcDisplay/model.d.ts +40 -51
- package/esm/LinearPairedArcDisplay/components/util.d.ts +1 -1
- package/esm/LinearPairedArcDisplay/model.d.ts +20 -16
- package/esm/LinearPairedArcDisplay/util.d.ts +1 -1
- package/package.json +2 -2
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@@ -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"));
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@@ -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;
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.configSchemaFactory =
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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");
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explicitlyTyped: true,
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});
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}
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exports.configSchemaFactory = configSchemaFactory;
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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");
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});
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});
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}
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exports.default = LinearArcDisplayF;
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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
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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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} & {
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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
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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;
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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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model: {
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reload: () => void;
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message: import("react").ReactNode;
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filled?: boolean
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status?: string
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reactElement?: import("react").ReactElement
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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;
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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
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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;
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fetchSizeLimit: {
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type: string;
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defaultValue: number;
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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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description: string;
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};
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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"
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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;
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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
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blockState?: Record<string, any
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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: {
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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"
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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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}, {
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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
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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
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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;
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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
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featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
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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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} & {
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afterAttach(): void;
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setCurrStatsBpPerPx(n: number): void;
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setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
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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
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setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
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regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
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} & {
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} & {
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readonly TooltipComponent: import("react").FC<any>;
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readonly selectedFeatureId: string | undefined;
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} & {
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navToFeature(feature: import("@jbrowse/core/util").Feature): 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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setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
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} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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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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exports.
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.filter(f => !!f)
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.fetchChains =
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|
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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|
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree"
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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(
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+
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|
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|
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"mobx-state-tree").ISimpleType<string>>;
|
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|
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}, import("mobx-state-tree"
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|
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}, import("mobx-state-tree" /**
|
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|
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* #action
|
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|
+
*/)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
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|
|
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}>;
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|
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model: {
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|
@@ -85,12 +91,12 @@ 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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|
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readonly DisplayMessageComponent: React.FC<any
|
|
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|
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readonly DisplayMessageComponent: undefined | 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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|
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setMessage(arg?: string
|
|
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|
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|
|
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|
setError(error?: unknown): void;
|
|
95
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|
setRpcDriverName(rpcDriverName: string): void;
|
|
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|
reload(): void;
|
|
@@ -103,10 +109,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
103
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|
setHeight(displayHeight: number): number;
|
|
104
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|
resizeHeight(distance: number): number;
|
|
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|
} & {
|
|
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|
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featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
|
|
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|
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featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
|
|
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|
-
* #property
|
|
109
|
-
*/
|
|
112
|
+
featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
|
|
113
|
+
featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
|
|
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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
|
|
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
|
|
128
|
+
setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
|
|
125
129
|
clearFeatureDensityStats(): void;
|
|
126
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|
} & {
|
|
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 =
|
|
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 =
|
|
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):
|
|
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.
|
|
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
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};
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} & import("mobx-state-tree/dist/internal" /**
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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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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readonly DisplayMessageComponent: import("react").FC<any
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setMessage(arg?: string
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@@ -186,8 +179,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
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currStatsBpPerPx: number;
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} & {
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@@ -199,10 +192,10 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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afterAttach(): void;
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} & {
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setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
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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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setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
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clearFeatureDensityStats(): void;
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} & {
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readonly regionTooLarge: boolean;
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@@ -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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|
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} & {
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featureIdUnderMouse:
|
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contextMenuFeature: import("@jbrowse/core/util").Feature
|
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|
+
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} & {
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readonly blockType: "dynamicBlocks" | "staticBlocks";
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|
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@@ -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
|
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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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|
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setFeatureIdUnderMouse(feature?: string
|
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setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature
|
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|
+
setFeatureIdUnderMouse(feature?: string): void;
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|
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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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|
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setSubschema(slotName: string, data: unknown):
|
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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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267
|
+
} & 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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|
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@@ -299,9 +298,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
299
298
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} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
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300
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
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|
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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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307
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|
} & {
|
|
@@ -326,7 +323,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
326
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|
}, {
|
|
327
324
|
renderInProgress: AbortController | undefined;
|
|
328
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|
filled: boolean;
|
|
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|
-
reactElement: import("react").ReactElement
|
|
326
|
+
reactElement: import("react").ReactElement | undefined;
|
|
330
327
|
features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
|
|
331
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|
layout: any;
|
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|
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
|
|
345
|
-
status?: string
|
|
346
|
-
reactElement?: import("react").ReactElement
|
|
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
|
|
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
|
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* #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
|
|
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"
|
|
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(
|
|
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"
|
|
62
|
-
|
|
63
|
-
|
|
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
|
|
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
|
|
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
|
|
107
|
-
featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
|
|
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
|
|
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
|
|
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):
|
|
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.
|
|
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": "
|
|
56
|
+
"gitHead": "20f16ae5a56ae5e4806aaa373131e540b0b5b0fd"
|
|
57
57
|
}
|