@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/dist/LinearReadCloudDisplay/drawLongReadChains.d.ts

@@ -1,11 +0,0 @@
-import type { LinearReadCloudDisplayModel } from './model';
-import type { ChainData } from '../shared/fetchChains';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function drawLongReadChains({ ctx, self, chainData, view, asm, }: {
-    ctx: CanvasRenderingContext2D;
-    self: LinearReadCloudDisplayModel;
-    chainData: ChainData;
-    view: LinearGenomeViewModel;
-    asm: Assembly;
-}): void;

package/dist/LinearReadCloudDisplay/drawLongReadChains.js

@@ -1,64 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.drawLongReadChains = drawLongReadChains;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const util_2 = require("./util");
-const color_1 = require("../shared/color");
-function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
-    var _a, _b, _c, _d, _e;
-    const computedChains = [];
-    const { chains } = chainData;
-    const { height } = self;
-    const featureHeight = (0, configuration_1.getConf)(self, 'featureHeight');
-    for (const chain of chains) {
-        let minX = Number.MAX_VALUE;
-        let maxX = Number.MIN_VALUE;
-        for (const elt of chain) {
-            const refName = asm.getCanonicalRefName(elt.refName) || elt.refName;
-            const rs = (_a = view.bpToPx({ refName, coord: elt.start })) === null || _a === void 0 ? void 0 : _a.offsetPx;
-            const re = (_b = view.bpToPx({ refName, coord: elt.end })) === null || _b === void 0 ? void 0 : _b.offsetPx;
-            if (rs !== undefined && re !== undefined) {
-                minX = Math.min(minX, rs);
-                maxX = Math.max(maxX, re);
-            }
-        }
-        computedChains.push({
-            distance: Math.abs(maxX - minX),
-            minX,
-            chain,
-        });
-    }
-    const distances = computedChains.map(d => d.distance);
-    const maxD = Math.log((0, util_1.max)(distances));
-    const minD = Math.max(Math.log((0, util_1.min)(distances)) - 1, 0);
-    const scaler = (height - 20) / (maxD - minD);
-    const halfHeight = featureHeight / 2 - 0.5;
-    for (const { minX, distance, chain } of computedChains) {
-        const w = distance;
-        const top = (Math.log(w) - minD) * scaler;
-        (0, util_2.fillRectCtx)(minX - view.offsetPx, top + halfHeight, w, 1, ctx, 'black');
-        const c1 = chain[0];
-        let primaryStrand;
-        if (!(c1.flags & 2048)) {
-            primaryStrand = c1.strand;
-        }
-        else {
-            const res = (_c = c1.SA) === null || _c === void 0 ? void 0 : _c.split(';')[0].split(',')[2];
-            primaryStrand = res === '-' ? -1 : 1;
-        }
-        for (const v0 of chain) {
-            const ra = asm.getCanonicalRefName(v0.refName) || v0.refName;
-            const rs = (_d = view.bpToPx({ refName: ra, coord: v0.start })) === null || _d === void 0 ? void 0 : _d.offsetPx;
-            const re = (_e = view.bpToPx({ refName: ra, coord: v0.end })) === null || _e === void 0 ? void 0 : _e.offsetPx;
-            if (rs !== undefined && re !== undefined) {
-                const w = Math.max(re - rs, 2);
-                const l = rs - view.offsetPx;
-                const effectiveStrand = v0.strand * primaryStrand;
-                const c = effectiveStrand === -1 ? 'color_rev_strand' : 'color_fwd_strand';
-                (0, util_2.strokeRectCtx)(l, top, w, featureHeight, ctx, color_1.strokeColor[c]);
-                (0, util_2.fillRectCtx)(l, top, w, featureHeight, ctx, color_1.fillColor[c]);
-            }
-        }
-    }
-}

package/dist/LinearReadCloudDisplay/drawPairChains.d.ts

@@ -1,17 +0,0 @@
-import type { LinearReadCloudDisplayModel } from './model';
-import type { ChainData, ChainStats, ReducedFeature } from '../shared/fetchChains';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function drawPairChains({ ctx, self, chainData, view, asm, }: {
-    ctx: CanvasRenderingContext2D;
-    self: LinearReadCloudDisplayModel;
-    chainData: ChainData;
-    view: LinearGenomeViewModel;
-    asm: Assembly;
-}): void;
-export declare function getPairedColor({ type, v0, v1, stats, }: {
-    type: string;
-    v0: ReducedFeature;
-    v1: ReducedFeature;
-    stats?: ChainStats;
-}): readonly [string, string] | undefined;

package/dist/LinearReadCloudDisplay/drawPairChains.js

@@ -1,94 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.drawPairChains = drawPairChains;
-exports.getPairedColor = getPairedColor;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const util_2 = require("./util");
-const color_1 = require("../shared/color");
-function drawPairChains({ ctx, self, chainData, view, asm, }) {
-    var _a, _b, _c, _d, _e, _f, _g;
-    const coords = [];
-    const featureHeight = (0, configuration_1.getConf)(self, 'featureHeight');
-    const type = ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) || 'insertSizeAndOrientation';
-    const { chains, stats } = chainData;
-    for (const chain of chains) {
-        if (chain.length > 1) {
-            const v0 = chain[0];
-            const v1 = chain[1];
-            const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName;
-            const ra2 = asm.getCanonicalRefName(v1.refName) || v1.refName;
-            const r1s = (_b = view.bpToPx({ refName: ra1, coord: v0.start })) === null || _b === void 0 ? void 0 : _b.offsetPx;
-            const r1e = (_c = view.bpToPx({ refName: ra1, coord: v0.end })) === null || _c === void 0 ? void 0 : _c.offsetPx;
-            const r2s = (_d = view.bpToPx({ refName: ra2, coord: v1.start })) === null || _d === void 0 ? void 0 : _d.offsetPx;
-            const r2e = (_e = view.bpToPx({ refName: ra2, coord: v1.end })) === null || _e === void 0 ? void 0 : _e.offsetPx;
-            let distance = 0;
-            if (r1s !== undefined &&
-                r1e !== undefined &&
-                r2s !== undefined &&
-                r2e !== undefined) {
-                if (v0.refName === v1.refName) {
-                    const s = Math.min(v0.start, v1.start);
-                    const e = Math.max(v0.end, v1.end);
-                    distance = Math.abs(e - s);
-                }
-                coords.push({
-                    r1s,
-                    r1e,
-                    r2s,
-                    r2e,
-                    v0,
-                    v1,
-                    distance,
-                });
-            }
-        }
-        else if (self.drawSingletons) {
-            const v0 = chain[0];
-            const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName;
-            const r1s = (_f = view.bpToPx({ refName: ra1, coord: v0.start })) === null || _f === void 0 ? void 0 : _f.offsetPx;
-            const r1e = (_g = view.bpToPx({ refName: ra1, coord: v0.end })) === null || _g === void 0 ? void 0 : _g.offsetPx;
-            if (r1s !== undefined && r1e !== undefined) {
-                const w1 = Math.max(r1e - r1s, 2);
-                (0, util_2.fillRectCtx)(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#f00');
-                (0, util_2.strokeRectCtx)(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#a00');
-            }
-        }
-    }
-    const maxD = Math.log((0, util_1.max)(coords.map(c => c.distance)));
-    const minD = Math.max(Math.log((0, util_1.min)(coords.map(c => c.distance))) - 1, 0);
-    const scaler = (self.height - 20) / (maxD - minD);
-    for (const { r1e, r1s, r2e, r2s, distance, v0, v1 } of coords) {
-        const w1 = Math.max(r1e - r1s, 2);
-        const w2 = Math.max(r2e - r2s, 2);
-        const [fill, stroke] = getPairedColor({ type, v0, v1, stats }) || [];
-        const top = (Math.log(distance) - minD) * scaler;
-        const halfHeight = featureHeight / 2 - 0.5;
-        const w = r2s - r1e;
-        (0, util_2.fillRectCtx)(r1e - view.offsetPx, top + halfHeight, w, 1, ctx, 'black');
-        (0, util_2.strokeRectCtx)(r1s - view.offsetPx, top, w1, featureHeight, ctx, stroke);
-        (0, util_2.strokeRectCtx)(r2s - view.offsetPx, top, w2, featureHeight, ctx, stroke);
-        (0, util_2.fillRectCtx)(r1s - view.offsetPx, top, w1, featureHeight, ctx, fill);
-        (0, util_2.fillRectCtx)(r2s - view.offsetPx, top, w2, featureHeight, ctx, fill);
-    }
-}
-function getPairedColor({ type, v0, v1, stats, }) {
-    if (type === 'insertSizeAndOrientation') {
-        return (0, color_1.getPairedInsertSizeAndOrientationColor)(v0, v1, stats);
-    }
-    if (type === 'orientation') {
-        return (0, color_1.getPairedOrientationColor)(v0);
-    }
-    if (type === 'insertSize') {
-        return (0, color_1.getPairedInsertSizeColor)(v0, v1, stats);
-    }
-    if (type === 'gradient') {
-        const s = Math.min(v0.start, v1.start);
-        const e = Math.max(v0.end, v1.end);
-        return [
-            `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,50%)`,
-            `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,30%)`,
-        ];
-    }
-    return undefined;
-}

package/dist/LinearReadCloudDisplay/index.d.ts

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

package/dist/LinearReadCloudDisplay/index.js

@@ -1,58 +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;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = register;
-const react_1 = require("react");
-const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-const model_1 = __importDefault(require("./model"));
-function register(pluginManager) {
-    pluginManager.addDisplayType(() => {
-        const configSchema = (0, configSchema_1.default)(pluginManager);
-        return new DisplayType_1.default({
-            name: 'LinearReadCloudDisplay',
-            displayName: 'Read cloud display',
-            configSchema,
-            stateModel: (0, model_1.default)(configSchema),
-            trackType: 'AlignmentsTrack',
-            viewType: 'LinearGenomeView',
-            subDisplay: { type: 'LinearAlignmentsDisplay', lowerPanel: true },
-            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ReactComponent')))),
-        });
-    });
-}

package/dist/LinearReadCloudDisplay/model.d.ts

@@ -1,175 +0,0 @@
-import type React from 'react';
-import type { ChainData } from '../shared/fetchChains';
-import type { ColorBy, FilterBy } from '../shared/types';
-import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import type { Instance } from 'mobx-state-tree';
-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<"LinearReadCloudDisplay">;
-    configuration: AnyConfigurationSchemaType;
-    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
-    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
-    drawSingletons: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-}, {
-    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;
-} & {
-    loading: boolean;
-    chainData: ChainData | undefined;
-    lastDrawnOffsetPx: number | undefined;
-    lastDrawnBpPerPx: number;
-    ref: HTMLCanvasElement | null;
-} & {
-    readonly colorBy: any;
-    readonly filterBy: any;
-} & {
-    setDrawSingletons(f: boolean): void;
-    setLastDrawnOffsetPx(n: number): void;
-    setLastDrawnBpPerPx(n: number): void;
-    setLoading(f: boolean): void;
-    reload(): void;
-    setRef(ref: HTMLCanvasElement | null): void;
-    setColorScheme(colorBy: {
-        type: string;
-    }): void;
-    setChainData(args: ChainData): void;
-    setFilterBy(filter: FilterBy): void;
-} & {
-    readonly drawn: boolean;
-} & {
-    renderProps(): any;
-    trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
-        label: string;
-        type: string;
-        checked: boolean;
-        onClick: () => void;
-        icon?: undefined;
-        subMenu?: undefined;
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-        type?: undefined;
-        checked?: undefined;
-        subMenu?: undefined;
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        subMenu: {
-            label: string;
-            onClick: () => void;
-        }[];
-        type?: undefined;
-        checked?: undefined;
-        onClick?: undefined;
-    })[];
-    renderSvg(opts: {
-        rasterizeLayers?: boolean;
-    }): Promise<React.ReactNode>;
-} & {
-    afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export type LinearReadCloudDisplayStateModel = ReturnType<typeof stateModelFactory>;
-export type LinearReadCloudDisplayModel = Instance<LinearReadCloudDisplayStateModel>;
-export default stateModelFactory;

package/dist/LinearReadCloudDisplay/model.js

@@ -1,198 +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;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = require("react");
-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 ClearAll_1 = __importDefault(require("@mui/icons-material/ClearAll"));
-const Palette_1 = __importDefault(require("@mui/icons-material/Palette"));
-const mobx_state_tree_1 = require("mobx-state-tree");
-const FilterByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/components/FilterByTagDialog'))));
-function stateModelFactory(configSchema) {
-    return mobx_state_tree_1.types
-        .compose('LinearReadCloudDisplay', 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('LinearReadCloudDisplay'),
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        filterBySetting: mobx_state_tree_1.types.frozen(),
-        colorBySetting: mobx_state_tree_1.types.frozen(),
-        drawSingletons: true,
-    }))
-        .volatile(() => ({
-        loading: false,
-        chainData: undefined,
-        lastDrawnOffsetPx: undefined,
-        lastDrawnBpPerPx: 0,
-        ref: null,
-    }))
-        .views(self => ({
-        get colorBy() {
-            var _a;
-            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'colorBy');
-        },
-        get filterBy() {
-            var _a;
-            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'filterBy');
-        },
-    }))
-        .actions(self => ({
-        setDrawSingletons(f) {
-            self.drawSingletons = f;
-        },
-        setLastDrawnOffsetPx(n) {
-            self.lastDrawnOffsetPx = n;
-        },
-        setLastDrawnBpPerPx(n) {
-            self.lastDrawnBpPerPx = n;
-        },
-        setLoading(f) {
-            self.loading = f;
-        },
-        reload() {
-            self.error = undefined;
-        },
-        setRef(ref) {
-            self.ref = ref;
-        },
-        setColorScheme(colorBy) {
-            self.colorBySetting = {
-                ...colorBy,
-            };
-        },
-        setChainData(args) {
-            self.chainData = args;
-        },
-        setFilterBy(filter) {
-            self.filterBySetting = {
-                ...filter,
-            };
-        },
-    }))
-        .views(self => ({
-        get drawn() {
-            return self.lastDrawnOffsetPx !== undefined;
-        },
-    }))
-        .views(self => {
-        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
-        return {
-            renderProps() {
-                return {
-                    ...superRenderProps(),
-                    notReady: !self.chainData,
-                };
-            },
-            trackMenuItems() {
-                return [
-                    ...superTrackMenuItems(),
-                    {
-                        label: 'Draw singletons',
-                        type: 'checkbox',
-                        checked: self.drawSingletons,
-                        onClick: () => {
-                            self.setDrawSingletons(!self.drawSingletons);
-                        },
-                    },
-                    {
-                        label: 'Filter by',
-                        icon: ClearAll_1.default,
-                        onClick: () => {
-                            (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                FilterByTagDialog,
-                                { model: self, handleClose },
-                            ]);
-                        },
-                    },
-                    {
-                        label: 'Color scheme',
-                        icon: Palette_1.default,
-                        subMenu: [
-                            {
-                                label: 'Insert size ± 3σ and orientation',
-                                onClick: () => {
-                                    self.setColorScheme({ type: 'insertSizeAndOrientation' });
-                                },
-                            },
-                            {
-                                label: 'Insert size ± 3σ',
-                                onClick: () => {
-                                    self.setColorScheme({ type: 'insertSize' });
-                                },
-                            },
-                            {
-                                label: 'Orientation',
-                                onClick: () => {
-                                    self.setColorScheme({ type: 'orientation' });
-                                },
-                            },
-                            {
-                                label: 'Insert size gradient',
-                                onClick: () => {
-                                    self.setColorScheme({ type: 'gradient' });
-                                },
-                            },
-                        ],
-                    },
-                ];
-            },
-            async renderSvg(opts) {
-                const { renderSvg } = await Promise.resolve().then(() => __importStar(require('../shared/renderSvgUtil')));
-                const { drawFeats } = await Promise.resolve().then(() => __importStar(require('./drawFeats')));
-                return renderSvg(self, opts, drawFeats);
-            },
-        };
-    })
-        .actions(self => ({
-        afterAttach() {
-            ;
-            (async () => {
-                try {
-                    const { doAfterAttach } = await Promise.resolve().then(() => __importStar(require('../shared/afterAttach')));
-                    const { drawFeats } = await Promise.resolve().then(() => __importStar(require('./drawFeats')));
-                    doAfterAttach(self, drawFeats);
-                }
-                catch (e) {
-                    console.error(e);
-                    self.setError(e);
-                }
-            })();
-        },
-    }));
-}
-exports.default = stateModelFactory;

package/dist/LinearReadCloudDisplay/util.js

@@ -1,32 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.fillRectCtx = fillRectCtx;
-exports.strokeRectCtx = strokeRectCtx;
-function fillRectCtx(x, y, width, height, ctx, fillColor) {
-    if (width < 0) {
-        x += width;
-        width = -width;
-    }
-    if (height < 0) {
-        y += height;
-        height = -height;
-    }
-    if (fillColor) {
-        ctx.fillStyle = fillColor;
-    }
-    ctx.fillRect(x, y, width, height);
-}
-function strokeRectCtx(x, y, width, height, ctx, strokeColor) {
-    if (width < 0) {
-        x += width;
-        width = -width;
-    }
-    if (height < 0) {
-        y += height;
-        height = -height;
-    }
-    if (strokeColor) {
-        ctx.strokeStyle = strokeColor;
-    }
-    ctx.strokeRect(x, y, width, height);
-}

package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts

@@ -1,12 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-type Coord = [number, number];
-declare const SNPCoverageTooltip: (props: {
-    model: {
-        featureUnderMouse?: Feature;
-    };
-    height: number;
-    offsetMouseCoord: Coord;
-    clientMouseCoord: Coord;
-    clientRect?: DOMRect;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default SNPCoverageTooltip;