@jbrowse/plugin-arc 3.6.5 → 4.0.0

package/dist/LinearPairedArcDisplay/components/util.d.ts

@@ -1,17 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-export declare function makeFeaturePair(feature: Feature, alt?: string): {
-    k1: {
-        refName: string;
-        start: number;
-        end: number;
-        strand: any;
-        mateDirection: number;
-    };
-    k2: {
-        refName: string;
-        start: number;
-        end: number;
-        mateDirection?: number;
-    };
-};
-export declare function makeSummary(feature: Feature, alt?: string): string;

package/dist/LinearPairedArcDisplay/components/util.js

@@ -1,66 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.makeFeaturePair = makeFeaturePair;
-exports.makeSummary = makeSummary;
-const vcf_1 = require("@gmod/vcf");
-const util_1 = require("@jbrowse/core/util");
-function makeFeaturePair(feature, alt) {
-    var _a, _b, _c, _d;
-    const bnd = alt ? (0, vcf_1.parseBreakend)(alt) : undefined;
-    const start = feature.get('start');
-    let end = feature.get('end');
-    const strand = feature.get('strand');
-    const mate = feature.get('mate');
-    const refName = feature.get('refName');
-    let mateRefName;
-    let mateEnd = 0;
-    let mateStart = 0;
-    let joinDirection = 0;
-    let mateDirection = 0;
-    const symbolicAlleles = ['<TRA', '<DEL', '<INV', '<INS', '<DUP', '<CNV'];
-    if (symbolicAlleles.some(a => alt === null || alt === void 0 ? void 0 : alt.startsWith(a))) {
-        const info = feature.get('INFO');
-        const e = (_b = (_a = info === null || info === void 0 ? void 0 : info.END) === null || _a === void 0 ? void 0 : _a[0]) !== null && _b !== void 0 ? _b : end;
-        mateRefName = (_d = (_c = info === null || info === void 0 ? void 0 : info.CHR2) === null || _c === void 0 ? void 0 : _c[0]) !== null && _d !== void 0 ? _d : refName;
-        mateEnd = e;
-        mateStart = e - 1;
-        end = start + 1;
-    }
-    else if (bnd === null || bnd === void 0 ? void 0 : bnd.MatePosition) {
-        const matePosition = bnd.MatePosition.split(':');
-        mateDirection = bnd.MateDirection === 'left' ? 1 : -1;
-        joinDirection = bnd.Join === 'left' ? -1 : 1;
-        mateEnd = +matePosition[1];
-        mateStart = +matePosition[1] - 1;
-        mateRefName = matePosition[0];
-    }
-    return {
-        k1: {
-            refName,
-            start,
-            end,
-            strand,
-            mateDirection,
-        },
-        k2: mate !== null && mate !== void 0 ? mate : {
-            refName: mateRefName || 'unknown',
-            end: mateEnd,
-            start: mateStart,
-            mateDirection: joinDirection,
-        },
-    };
-}
-function makeSummary(feature, alt) {
-    var _a;
-    const { k1, k2 } = makeFeaturePair(feature, alt);
-    return [
-        feature.get('name'),
-        feature.get('id'),
-        (0, util_1.assembleLocString)(k1),
-        (0, util_1.assembleLocString)(k2),
-        (_a = feature.get('INFO')) === null || _a === void 0 ? void 0 : _a.SVTYPE,
-        alt,
-    ]
-        .filter(f => !!f)
-        .join('<br/>');
-}

package/dist/LinearPairedArcDisplay/configSchema.d.ts

@@ -1,35 +0,0 @@
-export declare function configSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    color: {
-        type: string;
-        description: string;
-        defaultValue: string;
-        contextVariable: string[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    maxFeatureScreenDensity: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    fetchSizeLimit: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    height: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    mouseover: {
-        type: string;
-        description: string;
-        defaultValue: string;
-        contextVariable: string[];
-    };
-    jexlFilters: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/dist/LinearPairedArcDisplay/configSchema.js

@@ -1,18 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.configSchemaFactory = configSchemaFactory;
-const configuration_1 = require("@jbrowse/core/configuration");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-function configSchemaFactory() {
-    return (0, configuration_1.ConfigurationSchema)('LinearPairedArcDisplay', {
-        color: {
-            type: 'color',
-            description: 'the color of the arcs',
-            defaultValue: 'jexl:defaultPairedArcColor(feature,alt)',
-            contextVariable: ['feature', 'alt'],
-        },
-    }, {
-        baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
-        explicitlyTyped: true,
-    });
-}

package/dist/LinearPairedArcDisplay/fetchChains.d.ts

@@ -1,27 +0,0 @@
-import type { LinearArcDisplayModel } from './model';
-export interface ReducedFeature {
-    name: string;
-    strand: number;
-    refName: string;
-    start: number;
-    end: number;
-    id: string;
-    flags: number;
-    tlen: number;
-    pair_orientation: string;
-    next_ref?: string;
-    next_pos?: number;
-    clipPos: number;
-    SA?: string;
-}
-export interface ChainStats {
-    max: number;
-    min: number;
-    upper: number;
-    lower: number;
-}
-export interface ChainData {
-    chains: ReducedFeature[][];
-    stats?: ChainStats;
-}
-export declare function fetchChains(self: LinearArcDisplayModel): Promise<void>;

package/dist/LinearPairedArcDisplay/fetchChains.js

@@ -1,21 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.fetchChains = fetchChains;
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-async function fetchChains(self) {
-    const sessionId = (0, tracks_1.getRpcSessionId)(self);
-    const { rpcManager } = (0, util_1.getSession)(self);
-    const view = (0, util_1.getContainingView)(self);
-    if (!view.initialized || self.error || !self.statsReadyAndRegionNotTooLarge) {
-        return;
-    }
-    self.setLoading(true);
-    const ret = (await rpcManager.call(sessionId, 'CoreGetFeatures', {
-        sessionId,
-        regions: view.staticBlocks.contentBlocks,
-        adapterConfig: self.adapterConfig,
-    }));
-    self.setFeatures((0, util_1.dedupe)(ret, r => r.id()));
-    self.setLoading(false);
-}

package/dist/LinearPairedArcDisplay/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function LinearPairedArcDisplayF(pluginManager: PluginManager): void;

package/dist/LinearPairedArcDisplay/index.js

@@ -1,54 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = LinearPairedArcDisplayF;
-const react_1 = require("react");
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const configSchema_1 = require("./configSchema");
-const model_1 = require("./model");
-function LinearPairedArcDisplayF(pluginManager) {
-    pluginManager.addDisplayType(() => {
-        const configSchema = (0, configSchema_1.configSchemaFactory)();
-        return new pluggableElementTypes_1.DisplayType({
-            name: 'LinearPairedArcDisplay',
-            displayName: 'Arc display',
-            configSchema,
-            stateModel: (0, model_1.stateModelFactory)(configSchema),
-            trackType: 'VariantTrack',
-            viewType: 'LinearGenomeView',
-            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ReactComponent')))),
-        });
-    });
-}

package/dist/LinearPairedArcDisplay/model.d.ts

@@ -1,129 +0,0 @@
-import type React from 'react';
-import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import type { Feature } from '@jbrowse/core/util';
-import type { Instance } from 'mobx-state-tree';
-export declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<string>;
-    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-} & {
-    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-} & {
-    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"LinearPairedArcDisplay">;
-    configuration: AnyConfigurationSchemaType;
-    displayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-}, {
-    rendererTypeName: string;
-    error: unknown;
-    message: string | undefined;
-} & {
-    readonly RenderingComponent: React.FC<{
-        model: {
-            id: string;
-            type: string;
-            rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }, {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: () => void;
-        blockState?: Record<string, any>;
-    }>;
-    readonly DisplayBlurb: React.FC<{
-        model: {
-            id: string;
-            type: string;
-            rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }, {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }> | null;
-    readonly adapterConfig: any;
-    readonly parentTrack: any;
-    renderProps(): any;
-    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: undefined | React.FC<any>;
-    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-    regionCannotBeRendered(): null;
-} & {
-    setMessage(arg?: string): void;
-    setError(error?: unknown): void;
-    setRpcDriverName(rpcDriverName: string): void;
-    reload(): void;
-} & {
-    scrollTop: number;
-} & {
-    readonly height: number;
-} & {
-    setScrollTop(scrollTop: number): void;
-    setHeight(displayHeight: number): number;
-    resizeHeight(distance: number): number;
-} & {
-    featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
-    featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
-    currStatsBpPerPx: number;
-} & {
-    readonly currentBytesRequested: number;
-    readonly currentFeatureScreenDensity: number;
-    readonly maxFeatureScreenDensity: any;
-    readonly featureDensityStatsReady: boolean;
-    readonly maxAllowableBytes: number;
-} & {
-    afterAttach(): void;
-} & {
-    setCurrStatsBpPerPx(n: number): void;
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
-    getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
-    setFeatureDensityStatsP(arg: any): void;
-    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
-    clearFeatureDensityStats(): void;
-} & {
-    readonly regionTooLarge: boolean;
-    readonly regionTooLargeReason: string;
-} & {
-    readonly statsReadyAndRegionNotTooLarge: boolean;
-    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
-} & {
-    lastDrawnOffsetPx: number;
-    features: Feature[] | undefined;
-    loading: boolean;
-    drawn: boolean;
-} & {
-    readonly displayModeSetting: any;
-} & {
-    selectFeature(feature: Feature): void;
-    setLoading(flag: boolean): void;
-    setFeatures(f: Feature[]): void;
-    setDisplayMode(flag: string): void;
-} & {
-    afterAttach(): void;
-    renderSvg(opts: {
-        rasterizeLayers?: boolean;
-    }): Promise<React.ReactNode>;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export type LinearArcDisplayStateModel = ReturnType<typeof stateModelFactory>;
-export type LinearArcDisplayModel = Instance<LinearArcDisplayStateModel>;

package/dist/LinearPairedArcDisplay/model.js

@@ -1,105 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.stateModelFactory = stateModelFactory;
-const configuration_1 = require("@jbrowse/core/configuration");
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const util_1 = require("@jbrowse/core/util");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function stateModelFactory(configSchema) {
-    return mobx_state_tree_1.types
-        .compose('LinearPairedArcDisplay', pluggableElementTypes_1.BaseDisplay, (0, plugin_linear_genome_view_1.TrackHeightMixin)(), (0, plugin_linear_genome_view_1.FeatureDensityMixin)(), mobx_state_tree_1.types.model({
-        type: mobx_state_tree_1.types.literal('LinearPairedArcDisplay'),
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        displayMode: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-    }))
-        .volatile(() => ({
-        lastDrawnOffsetPx: 0,
-        features: undefined,
-        loading: false,
-        drawn: true,
-    }))
-        .views(self => ({
-        get displayModeSetting() {
-            var _a;
-            return (_a = self.displayMode) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, ['renderer', 'displayMode']);
-        },
-    }))
-        .actions(self => ({
-        selectFeature(feature) {
-            const session = (0, util_1.getSession)(self);
-            if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                const featureWidget = session.addWidget('VariantFeatureWidget', 'variantFeature', {
-                    view: (0, util_1.getContainingView)(self),
-                    track: (0, util_1.getContainingTrack)(self),
-                    featureData: feature.toJSON(),
-                });
-                session.showWidget(featureWidget);
-            }
-            if ((0, util_1.isSelectionContainer)(session)) {
-                session.setSelection(feature);
-            }
-        },
-        setLoading(flag) {
-            self.loading = flag;
-        },
-        setFeatures(f) {
-            self.features = f;
-        },
-        setDisplayMode(flag) {
-            self.displayMode = flag;
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            ;
-            (async () => {
-                try {
-                    const { doAfterAttach } = await Promise.resolve().then(() => __importStar(require('./afterAttach')));
-                    doAfterAttach(self);
-                }
-                catch (e) {
-                    console.error(e);
-                    self.setError(e);
-                }
-            })();
-        },
-        async renderSvg(opts) {
-            const { renderArcSvg } = await Promise.resolve().then(() => __importStar(require('./renderSvg')));
-            return renderArcSvg(self, opts);
-        },
-    }));
-}

package/dist/LinearPairedArcDisplay/renderSvg.d.ts

@@ -1,4 +0,0 @@
-import type { LinearArcDisplayModel } from './model';
-export declare function renderArcSvg(model: LinearArcDisplayModel, _opts: {
-    rasterizeLayers?: boolean;
-}): Promise<import("react/jsx-runtime").JSX.Element>;

package/dist/LinearPairedArcDisplay/renderSvg.js

@@ -1,17 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderArcSvg = renderArcSvg;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const Arcs_1 = __importDefault(require("./components/Arcs"));
-async function renderArcSvg(model, _opts) {
-    await (0, util_1.when)(() => !model.loading);
-    const view = (0, util_1.getContainingView)(model);
-    const width = view.dynamicBlocks.totalWidthPx;
-    const height = model.height;
-    const clipid = `arc-${model.id}`;
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("defs", { children: (0, jsx_runtime_1.jsx)("clipPath", { id: clipid, children: (0, jsx_runtime_1.jsx)("rect", { x: 0, y: 0, width: width, height: height }) }) }), (0, jsx_runtime_1.jsx)("g", { clipPath: `url(#${clipid})`, children: (0, jsx_runtime_1.jsx)(Arcs_1.default, { model: model, exportSVG: true }) })] }));
-}

package/dist/LinearPairedArcDisplay/util.d.ts

@@ -1,27 +0,0 @@
-import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { AugmentedRegion, Feature } from '@jbrowse/core/util';
-import type { IAutorunOptions } from 'mobx';
-import type { IAnyStateTreeNode } from 'mobx-state-tree';
-export declare function getTag(feature: Feature, tag: string): any;
-export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
-export declare const orientationTypes: {
-    fr: Record<string, string>;
-    rf: Record<string, string>;
-    ff: Record<string, string>;
-};
-export declare const pairMap: {
-    readonly LR: "color_pair_lr";
-    readonly LL: "color_pair_ll";
-    readonly RR: "color_pair_rr";
-    readonly RL: "color_pair_rl";
-};
-export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
-export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
-export declare function shouldFetchReferenceSequence(type?: string): type is "methylation";
-export declare const modificationColors: Record<string, string>;
-type DisplayModel = IAnyStateTreeNode & {
-    setError: (arg: unknown) => void;
-};
-export declare function createAutorun(self: DisplayModel, cb: () => Promise<void>, opts?: IAutorunOptions): void;
-export declare function randomColor(): string;
-export {};

package/dist/LinearPairedArcDisplay/util.js

@@ -1,119 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.modificationColors = exports.pairMap = exports.orientationTypes = void 0;
-exports.getTag = getTag;
-exports.getTagAlt = getTagAlt;
-exports.getColorWGBS = getColorWGBS;
-exports.fetchSequence = fetchSequence;
-exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
-exports.createAutorun = createAutorun;
-exports.randomColor = randomColor;
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const rxjs_1 = require("rxjs");
-const operators_1 = require("rxjs/operators");
-function getTag(feature, tag) {
-    return feature.get('tags')[tag];
-}
-function getTagAlt(feature, tag, alt) {
-    var _a;
-    return (_a = getTag(feature, tag)) !== null && _a !== void 0 ? _a : getTag(feature, alt);
-}
-exports.orientationTypes = {
-    fr: {
-        F1R2: 'LR',
-        F2R1: 'LR',
-        F1F2: 'LL',
-        F2F1: 'LL',
-        R1R2: 'RR',
-        R2R1: 'RR',
-        R1F2: 'RL',
-        R2F1: 'RL',
-    },
-    rf: {
-        R1F2: 'LR',
-        R2F1: 'LR',
-        R1R2: 'LL',
-        R2R1: 'LL',
-        F1F2: 'RR',
-        F2F1: 'RR',
-        F1R2: 'RL',
-        F2R1: 'RL',
-    },
-    ff: {
-        F2F1: 'LR',
-        R1R2: 'LR',
-        F2R1: 'LL',
-        R1F2: 'LL',
-        R2F1: 'RR',
-        F1R2: 'RR',
-        R2R1: 'RL',
-        F1F2: 'RL',
-    },
-};
-exports.pairMap = {
-    LR: 'color_pair_lr',
-    LL: 'color_pair_ll',
-    RR: 'color_pair_rr',
-    RL: 'color_pair_rl',
-};
-function getColorWGBS(strand, base) {
-    if (strand === 1) {
-        if (base === 'C') {
-            return '#f00';
-        }
-        if (base === 'T') {
-            return '#00f';
-        }
-    }
-    else if (strand === -1) {
-        if (base === 'G') {
-            return '#f00';
-        }
-        if (base === 'A') {
-            return '#00f';
-        }
-    }
-    return '#888';
-}
-async function fetchSequence(region, adapter) {
-    var _a;
-    const { start, end, originalRefName, refName } = region;
-    const feats = await (0, rxjs_1.firstValueFrom)(adapter
-        .getFeatures({
-        ...region,
-        refName: originalRefName || refName,
-        end: end + 1,
-        start: Math.max(0, start - 1),
-    })
-        .pipe((0, operators_1.toArray)()));
-    return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
-}
-function shouldFetchReferenceSequence(type) {
-    return type === 'methylation';
-}
-exports.modificationColors = {
-    m: 'rgb(255,0,0)',
-    h: 'rgb(11, 132, 165)',
-    o: 'rgb(111, 78, 129)',
-    f: 'rgb(246, 200, 95)',
-    c: 'rgb(157, 216, 102)',
-    g: 'rgb(255, 160, 86)',
-    e: 'rgb(141, 221, 208)',
-    b: 'rgb(202, 71, 47)',
-};
-function createAutorun(self, cb, opts) {
-    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
-        try {
-            await cb();
-        }
-        catch (e) {
-            if ((0, mobx_state_tree_1.isAlive)(self)) {
-                self.setError(e);
-            }
-        }
-    }, opts));
-}
-function randomColor() {
-    return `hsl(${Math.random() * 200}, 50%, 50%)`;
-}

package/dist/index.d.ts

@@ -1,6 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin';
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default class ArcPlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-}