@jbrowse/plugin-alignments 3.7.0 → 4.0.1

package/dist/LinearReadCloudDisplay/configSchema.js

@@ -1,30 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const util_1 = require("../shared/util");
-function configSchemaF(pluginManager) {
-    return (0, configuration_1.ConfigurationSchema)('LinearReadCloudDisplay', {
-        maxFeatureScreenDensity: {
-            type: 'number',
-            description: 'maximum features per pixel that is displayed in the view',
-            defaultValue: 5,
-        },
-        featureHeight: {
-            type: 'number',
-            defaultValue: 7,
-        },
-        colorBy: {
-            type: 'frozen',
-            defaultValue: { type: 'insertSizeAndOrientation' },
-        },
-        filterBy: {
-            type: 'frozen',
-            defaultValue: util_1.defaultFilterFlags,
-        },
-    }, {
-        baseConfiguration: (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager),
-        explicitlyTyped: true,
-    });
-}
-exports.default = configSchemaF;

package/dist/LinearReadCloudDisplay/drawFeatsAbstract.d.ts

@@ -1,2 +0,0 @@
-import type { LinearReadCloudDisplayModel } from './model';
-export declare function drawFeats(self: LinearReadCloudDisplayModel, ctx: CanvasRenderingContext2D): void;

package/dist/LinearReadCloudDisplay/drawFeatsAbstract.js

@@ -1,13 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.drawFeats = drawFeats;
-const drawFeatsCloud_1 = require("./drawFeatsCloud");
-const drawFeatsStack_1 = require("./drawFeatsStack");
-function drawFeats(self, ctx) {
-    if (self.drawCloud) {
-        (0, drawFeatsCloud_1.drawFeats)(self, ctx);
-    }
-    else {
-        (0, drawFeatsStack_1.drawFeats)(self, ctx);
-    }
-}

package/dist/LinearReadCloudDisplay/drawFeatsCloud.d.ts

@@ -1,2 +0,0 @@
-import type { LinearReadCloudDisplayModel } from './model';
-export declare function drawFeats(self: LinearReadCloudDisplayModel, ctx: CanvasRenderingContext2D): void;

package/dist/LinearReadCloudDisplay/drawFeatsCloud.js

@@ -1,24 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.drawFeats = drawFeats;
-const util_1 = require("@jbrowse/core/util");
-const drawFeatsCommon_1 = require("./drawFeatsCommon");
-function calculateCloudYOffsets(computedChains, self, _view, _featureHeight) {
-    const distances = computedChains.map(c => c.distance).filter(d => d > 0);
-    if (distances.length === 0) {
-        return { chainYOffsets: new Map() };
-    }
-    const logOffset = 10;
-    const maxD = Math.log((0, util_1.max)(distances) + logOffset);
-    const minD = Math.log((0, util_1.min)(distances) + logOffset);
-    const scaler = (self.height - 20) / (maxD - minD || 1);
-    const chainYOffsets = new Map();
-    for (const { id, distance } of computedChains) {
-        const top = distance > 0 ? (Math.log(distance + logOffset) - minD) * scaler : 0;
-        chainYOffsets.set(id, top);
-    }
-    return { chainYOffsets };
-}
-function drawFeats(self, ctx) {
-    (0, drawFeatsCommon_1.drawFeatsCommon)(self, ctx, calculateCloudYOffsets);
-}

package/dist/LinearReadCloudDisplay/drawFeatsCommon.d.ts

@@ -1,23 +0,0 @@
-import type { LinearReadCloudDisplayModel } from './model';
-import type { ChainData, ReducedFeature } from '../shared/fetchChains';
-import type { FlatbushEntry } from '../shared/flatbushType';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-type LGV = LinearGenomeViewModel;
-export interface ComputedChain {
-    distance: number;
-    minX: number;
-    maxX: number;
-    chain: ReducedFeature[];
-    id: string;
-}
-export declare function filterChains(chains: ReducedFeature[][], drawSingletons: boolean, drawProperPairs: boolean, type: string, chainData: ChainData): ReducedFeature[][];
-export declare function computeChainBounds(chains: ReducedFeature[][], view: LGV, asm: Assembly): ComputedChain[];
-export declare function sortComputedChains(computedChains: ComputedChain[]): void;
-export declare function buildFlatbushIndex(featuresForFlatbush: FlatbushEntry[], self: LinearReadCloudDisplayModel): void;
-export declare function addChainMouseoverRects(computedChains: ComputedChain[], chainYOffsets: Map<string, number>, featureHeight: number, view: LGV, featuresForFlatbush: FlatbushEntry[]): void;
-export declare function drawFeatsCommon(self: LinearReadCloudDisplayModel, ctx: CanvasRenderingContext2D, calculateYOffsets: (computedChains: ComputedChain[], self: LinearReadCloudDisplayModel, view: LGV, featureHeight: number) => {
-    chainYOffsets: Map<string, number>;
-    layoutHeight?: number;
-}): void;
-export {};

package/dist/LinearReadCloudDisplay/drawFeatsCommon.js

@@ -1,198 +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.filterChains = filterChains;
-exports.computeChainBounds = computeChainBounds;
-exports.sortComputedChains = sortComputedChains;
-exports.buildFlatbushIndex = buildFlatbushIndex;
-exports.addChainMouseoverRects = addChainMouseoverRects;
-exports.drawFeatsCommon = drawFeatsCommon;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const flatbush_1 = __importDefault(require("@jbrowse/core/util/flatbush"));
-const color_1 = require("../shared/color");
-const drawLongReadChains_1 = require("../shared/drawLongReadChains");
-const drawPairChains_1 = require("../shared/drawPairChains");
-const util_2 = require("../shared/util");
-function filterChains(chains, drawSingletons, drawProperPairs, type, chainData) {
-    const filtered = [];
-    for (const chain_ of chains) {
-        const chain = chain_;
-        if (!drawSingletons && chain.length === 1) {
-            continue;
-        }
-        let isPairedEnd = false;
-        for (const element of chain) {
-            if (element.flags & 1) {
-                isPairedEnd = true;
-                break;
-            }
-        }
-        if (!drawProperPairs && isPairedEnd) {
-            const nonSupplementary = [];
-            for (const element of chain) {
-                if (!(element.flags & 2048)) {
-                    nonSupplementary.push(element);
-                }
-            }
-            if (nonSupplementary.length === 2) {
-                const v0 = nonSupplementary[0];
-                const v1 = nonSupplementary[1];
-                const pairType = (0, color_1.getPairedType)({
-                    type,
-                    f1: v0,
-                    f2: v1,
-                    stats: chainData.stats,
-                });
-                if (pairType === color_1.PairType.PROPER_PAIR) {
-                    continue;
-                }
-            }
-        }
-        filtered.push(chain);
-    }
-    return filtered;
-}
-function computeChainBounds(chains, view, asm) {
-    var _a, _b;
-    const computedChains = [];
-    for (const chain_ of chains) {
-        const chain = chain_;
-        let minX = Number.MAX_VALUE;
-        let maxX = Number.MIN_VALUE;
-        let chainId = '';
-        let tlenDistance = 0;
-        const chainLength = chain.length;
-        for (let j = 0; j < chainLength; j++) {
-            const elt = chain[j];
-            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);
-            }
-            if (!chainId) {
-                chainId = elt.id;
-            }
-            if (chainLength > 1 && tlenDistance === 0 && elt.tlen) {
-                tlenDistance = Math.abs(elt.tlen);
-            }
-        }
-        const distance = tlenDistance > 0 ? tlenDistance : Math.abs(maxX - minX);
-        computedChains.push({
-            distance,
-            minX,
-            maxX,
-            chain,
-            id: chainId,
-        });
-    }
-    return computedChains;
-}
-function sortComputedChains(computedChains) {
-    computedChains.sort((a, b) => {
-        const aIsSingleton = a.chain.length === 1 ? 1 : 0;
-        const bIsSingleton = b.chain.length === 1 ? 1 : 0;
-        if (bIsSingleton !== aIsSingleton) {
-            return bIsSingleton - aIsSingleton;
-        }
-        return a.distance - b.distance;
-    });
-}
-function buildFlatbushIndex(featuresForFlatbush, self) {
-    const finalFlatbush = new flatbush_1.default(Math.max(featuresForFlatbush.length, 1));
-    const length = featuresForFlatbush.length;
-    if (length) {
-        for (let i = 0; i < length; i++) {
-            const { x1, y1, x2, y2 } = featuresForFlatbush[i];
-            finalFlatbush.add(x1, y1, x2, y2);
-        }
-    }
-    else {
-        finalFlatbush.add(0, 0);
-    }
-    finalFlatbush.finish();
-    self.setFeatureLayout(finalFlatbush);
-    self.setFeaturesForFlatbush(featuresForFlatbush);
-}
-function addChainMouseoverRects(computedChains, chainYOffsets, featureHeight, view, featuresForFlatbush) {
-    for (const computedChain of computedChains) {
-        const { id, chain, minX, maxX } = computedChain;
-        const chainY = chainYOffsets.get(id);
-        if (chainY === undefined) {
-            continue;
-        }
-        const chainMinXPx = minX - view.offsetPx;
-        const chainMaxXPx = maxX - view.offsetPx;
-        if (chain.length > 0) {
-            featuresForFlatbush.push({
-                x1: chainMinXPx,
-                y1: chainY,
-                x2: chainMaxXPx,
-                y2: chainY + featureHeight,
-                data: chain[0],
-                chainId: id,
-                chainMinX: chainMinXPx,
-                chainMaxX: chainMaxXPx,
-                chain,
-            });
-        }
-    }
-}
-function drawFeatsCommon(self, ctx, calculateYOffsets) {
-    var _a, _b;
-    const { chainData } = self;
-    if (!chainData) {
-        return;
-    }
-    const { assemblyManager } = (0, util_1.getSession)(self);
-    const view = (0, util_1.getContainingView)(self);
-    const assemblyName = view.assemblyNames[0];
-    const asm = assemblyManager.get(assemblyName);
-    if (!asm) {
-        return;
-    }
-    const featureHeight = (_a = self.featureHeight) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'featureHeight');
-    const type = ((_b = self.colorBy) === null || _b === void 0 ? void 0 : _b.type) || 'insertSizeAndOrientation';
-    const drawSingletons = self.drawSingletons;
-    const drawProperPairs = self.drawProperPairs;
-    const { chains } = chainData;
-    const filteredChains = filterChains(chains, drawSingletons, drawProperPairs, type, chainData);
-    const computedChains = computeChainBounds(filteredChains, view, asm);
-    sortComputedChains(computedChains);
-    const { chainYOffsets, layoutHeight } = calculateYOffsets(computedChains, self, view, featureHeight);
-    const featuresForFlatbush = [];
-    const renderChevrons = (0, util_2.shouldRenderChevrons)(view.bpPerPx, featureHeight);
-    (0, drawPairChains_1.drawPairChains)({
-        ctx,
-        type,
-        chainData,
-        view,
-        asm,
-        chainYOffsets,
-        renderChevrons,
-        featureHeight,
-        featuresForFlatbush,
-        computedChains,
-    });
-    (0, drawLongReadChains_1.drawLongReadChains)({
-        ctx,
-        chainData,
-        view,
-        asm,
-        chainYOffsets,
-        renderChevrons,
-        featureHeight,
-        featuresForFlatbush,
-        computedChains,
-        flipStrandLongReadChains: self.flipStrandLongReadChains,
-    });
-    addChainMouseoverRects(computedChains, chainYOffsets, featureHeight, view, featuresForFlatbush);
-    buildFlatbushIndex(featuresForFlatbush, self);
-    if (layoutHeight !== undefined) {
-        self.setLayoutHeight(layoutHeight);
-    }
-}

package/dist/LinearReadCloudDisplay/drawFeatsStack.d.ts

@@ -1,2 +0,0 @@
-import type { LinearReadCloudDisplayModel } from './model';
-export declare function drawFeats(self: LinearReadCloudDisplayModel, ctx: CanvasRenderingContext2D): void;

package/dist/LinearReadCloudDisplay/drawFeatsStack.js

@@ -1,36 +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.drawFeats = drawFeats;
-const GranularRectLayout_1 = __importDefault(require("@jbrowse/core/util/layouts/GranularRectLayout"));
-const drawFeatsCommon_1 = require("./drawFeatsCommon");
-function calculateStackYOffsets(computedChains, self, _view, featureHeight) {
-    var _a, _b;
-    const noSpacing = (_a = self.noSpacing) !== null && _a !== void 0 ? _a : false;
-    const maxHeight = (_b = self.trackMaxHeight) !== null && _b !== void 0 ? _b : 1200;
-    const layout = new GranularRectLayout_1.default({
-        pitchX: 1,
-        pitchY: 1,
-        maxHeight,
-    });
-    const layoutPadding = noSpacing ? 0 : 1;
-    for (const { id, minX, maxX, chain } of computedChains) {
-        layout.addRect(id, minX, maxX, featureHeight + layoutPadding, {
-            feat: chain[0],
-            fill: 'transparent',
-            stroke: 'transparent',
-            distance: maxX - minX,
-        });
-    }
-    const chainYOffsets = new Map();
-    for (const [id, rect] of layout.getRectangles()) {
-        const top = rect[1];
-        chainYOffsets.set(id, top);
-    }
-    return { chainYOffsets, layoutHeight: layout.getTotalHeight() };
-}
-function drawFeats(self, ctx) {
-    (0, drawFeatsCommon_1.drawFeatsCommon)(self, ctx, calculateStackYOffsets);
-}

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: 'Linked reads 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

@@ -1,195 +0,0 @@
-import type React from 'react';
-import type { ReducedFeature } from '../shared/fetchChains';
-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>>;
-} & {
-    filterBySetting: import("mobx-state-tree").IType<import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined>;
-    colorBySetting: import("mobx-state-tree").IType<import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined>;
-} & {
-    drawSingletons: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    drawProperPairs: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    flipStrandLongReadChains: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"LinearReadCloudDisplay">;
-    configuration: AnyConfigurationSchemaType;
-    drawCloud: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-}, {
-    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: import("../shared/fetchChains").ChainData | undefined;
-    lastDrawnOffsetPx: number | undefined;
-    lastDrawnBpPerPx: number;
-    ref: HTMLCanvasElement | null;
-} & {
-    setLastDrawnOffsetPx(n: number): void;
-    setLastDrawnBpPerPx(n: number): void;
-    setLoading(f: boolean): void;
-    setRef(ref: HTMLCanvasElement | null): void;
-    setColorScheme(colorBy: {
-        type: string;
-    }): void;
-    setChainData(args: import("../shared/fetchChains").ChainData): void;
-    setFilterBy(filter: import("../shared/types").FilterBy): void;
-} & {
-    readonly drawn: boolean;
-} & {
-    featureLayout: import("@jbrowse/core/util/flatbush").default | undefined;
-    mouseoverRef: HTMLCanvasElement | null;
-    featuresForFlatbush: import("../shared/flatbushType").FlatbushEntry[];
-} & {
-    setFeatureLayout(layout: import("@jbrowse/core/util/flatbush").default): void;
-    setMouseoverRef(ref: HTMLCanvasElement | null): void;
-    setFeaturesForFlatbush(features: import("../shared/flatbushType").FlatbushEntry[]): void;
-} & {
-    setDrawSingletons(f: boolean): void;
-    setDrawProperPairs(f: boolean): void;
-    setFlipStrandLongReadChains(f: boolean): void;
-    setFeatureHeight(n?: number): void;
-} & {
-    layoutHeight: number;
-} & {
-    readonly colorBy: any;
-    readonly filterBy: any;
-    readonly featureHeightSetting: any;
-} & {
-    reload(): void;
-    setNoSpacing(flag?: boolean): void;
-    setMaxHeight(n?: number): void;
-    setLayoutHeight(n: number): void;
-    selectFeature(chain: ReducedFeature[]): void;
-    setDrawCloud(b: boolean): void;
-} & {
-    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;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        subMenu: {
-            label: string;
-            onClick: () => void;
-        }[];
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    } | {
-        label: string;
-        type: string;
-        checked: boolean;
-        onClick: () => void;
-    })[];
-    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;