@jbrowse/plugin-alignments 2.2.2 → 2.3.0

package/dist/LinearReadCloudDisplay/components/ReactComponent.d.ts

@@ -0,0 +1,6 @@
+/// <reference types="react" />
+import { LinearReadCloudDisplayModel } from '../model';
+declare const _default: ({ model, }: {
+    model: LinearReadCloudDisplayModel;
+}) => JSX.Element;
+export default _default;

package/dist/LinearReadCloudDisplay/components/ReactComponent.js

@@ -0,0 +1,49 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const util_1 = require("@jbrowse/core/util");
+const ui_1 = require("@jbrowse/core/ui");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    loading: {
+        paddingLeft: '0.6em',
+        backgroundColor: theme.palette.action.disabledBackground,
+        backgroundImage: 'repeating-linear-gradient(45deg, transparent, transparent 5px, rgba(255,255,255,.5) 5px, rgba(255,255,255,.5) 10px)',
+        height: '100%',
+        width: '100%',
+        pointerEvents: 'none',
+        textAlign: 'center',
+    },
+}));
+const Cloud = (0, mobx_react_1.observer)(function ({ model, }) {
+    const view = (0, util_1.getContainingView)(model);
+    return (react_1.default.createElement("canvas", { "data-testid": `ReadCloud-display-${model.drawn}`, ref: ref => {
+            if ((0, mobx_state_tree_1.isAlive)(model)) {
+                model.setRef(ref);
+            }
+        }, style: {
+            position: 'absolute',
+            left: -view.offsetPx + model.lastDrawnOffsetPx,
+            width: view.dynamicBlocks.totalWidthPx,
+            height: model.height,
+        }, width: view.dynamicBlocks.totalWidthPx * 2, height: model.height * 2 }));
+});
+exports.default = (0, mobx_react_1.observer)(function ({ model, }) {
+    const view = (0, util_1.getContainingView)(model);
+    const { classes } = useStyles();
+    const err = model.error;
+    return err ? (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${err}`, severity: "error", buttonText: 'Reload', action: model.reload })) : model.loading ? (react_1.default.createElement("div", { className: classes.loading, style: {
+            width: view.dynamicBlocks.totalWidthPx,
+            height: 20,
+            position: 'absolute',
+            left: Math.max(0, -view.offsetPx),
+        } },
+        react_1.default.createElement(ui_1.LoadingEllipses, { message: model.message }))) : (react_1.default.createElement(Cloud, { model: model }));
+});
+//# sourceMappingURL=ReactComponent.js.map

package/dist/LinearReadCloudDisplay/components/ReactComponent.js.map

@@ -0,0 +1 @@
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package/dist/LinearReadCloudDisplay/configSchema.d.ts

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+import PluginManager from '@jbrowse/core/PluginManager';
+/**
+ * #config LinearReadCloudDisplay
+ */
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchemaF;

package/dist/LinearReadCloudDisplay/configSchema.js

@@ -0,0 +1,51 @@
+"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 mobx_state_tree_1 = require("mobx-state-tree");
+/**
+ * #config LinearReadCloudDisplay
+ */
+function configSchemaF(pluginManager) {
+    return (0, configuration_1.ConfigurationSchema)('LinearReadCloudDisplay', {
+        /**
+         * #slot
+         */
+        maxFeatureScreenDensity: {
+            type: 'number',
+            description: 'maximum features per pixel that is displayed in the view',
+            defaultValue: 5,
+        },
+        /**
+         * #slot
+         */
+        featureHeight: {
+            type: 'number',
+            defaultValue: 7,
+        },
+        /**
+         * #slot
+         */
+        colorScheme: {
+            type: 'stringEnum',
+            model: mobx_state_tree_1.types.enumeration('colorScheme', [
+                'strand',
+                'normal',
+                'insertSize',
+                'insertSizeAndOrientation',
+                'mappingQuality',
+                'tag',
+            ]),
+            description: 'color scheme to use',
+            defaultValue: 'normal',
+        },
+    }, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager),
+        explicitlyTyped: true,
+    });
+}
+exports.default = configSchemaF;
+//# sourceMappingURL=configSchema.js.map

package/dist/LinearReadCloudDisplay/configSchema.js.map

@@ -0,0 +1 @@
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package/dist/LinearReadCloudDisplay/drawFeats.d.ts

@@ -0,0 +1,10 @@
+import { ChainData } from '../shared/fetchChains';
+export default function drawFeats(self: {
+    setLastDrawnOffsetPx: (n: number) => void;
+    setError: (e: unknown) => void;
+    colorBy?: {
+        type: string;
+    };
+    height: number;
+    chainData?: ChainData;
+}, ctx: CanvasRenderingContext2D): Promise<void>;

package/dist/LinearReadCloudDisplay/drawFeats.js

@@ -0,0 +1,159 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+// locals
+const color_1 = require("../shared/color");
+// avoid drawing negative width features for SVG exports
+function fillRectCtx(x, y, width, height, ctx, color) {
+    if (width < 0) {
+        x += width;
+        width = -width;
+    }
+    if (height < 0) {
+        y += height;
+        height = -height;
+    }
+    if (color) {
+        ctx.fillStyle = color;
+    }
+    ctx.fillRect(x, y, width, height);
+}
+async function drawFeats(self, ctx) {
+    var _a;
+    const { chainData } = self;
+    if (!chainData) {
+        return;
+    }
+    const featureHeight = (0, configuration_1.getConf)(self, 'featureHeight');
+    const displayHeight = self.height;
+    const view = (0, util_1.getContainingView)(self);
+    self.setLastDrawnOffsetPx(view.offsetPx);
+    const { chains, stats } = chainData;
+    const coords = [];
+    for (let i = 0; i < chains.length; i++) {
+        const chain = chains[i];
+        // if we're looking at a paired read (flag 1) then assume it is just two
+        // reads (some small cases may defy this assumption such as secondary
+        // alignments but this may be uncommon)
+        if (chain[0].flags & 1 && chain.length > 1) {
+            const v0 = chain[0];
+            const v1 = chain[1];
+            const r1s = view.bpToPx({
+                refName: v0.refName,
+                coord: v0.start,
+            });
+            const r1e = view.bpToPx({
+                refName: v0.refName,
+                coord: v0.end,
+            });
+            const r2s = view.bpToPx({
+                refName: v1.refName,
+                coord: v1.start,
+            });
+            const r2e = view.bpToPx({
+                refName: v1.refName,
+                coord: v1.end,
+            });
+            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: r1s.offsetPx,
+                    r1e: r1e.offsetPx,
+                    r2s: r2s.offsetPx,
+                    r2e: r2e.offsetPx,
+                    v0,
+                    v1,
+                    distance,
+                });
+            }
+        }
+        else {
+            // if we're not looking at pairs, then it could be a multiply-split-long
+            // read, so traverse chain
+            for (let i = 1; i < chain.length; i++) {
+                const v0 = chain[i - 1];
+                const v1 = chain[i];
+                const r1s = view.bpToPx({
+                    refName: v0.refName,
+                    coord: v0.start,
+                });
+                const r1e = view.bpToPx({
+                    refName: v0.refName,
+                    coord: v0.end,
+                });
+                const r2s = view.bpToPx({
+                    refName: v1.refName,
+                    coord: v1.start,
+                });
+                const r2e = view.bpToPx({
+                    refName: v1.refName,
+                    coord: v1.end,
+                });
+                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: r1s.offsetPx,
+                        r1e: r1e.offsetPx,
+                        r2s: r2s.offsetPx,
+                        r2e: r2e.offsetPx,
+                        v0,
+                        v1,
+                        distance,
+                    });
+                }
+            }
+        }
+    }
+    let max = 0;
+    for (let i = 0; i < coords.length; i++) {
+        const { distance } = coords[i];
+        max = Math.max(max, distance);
+    }
+    const halfHeight = featureHeight / 2 - 0.5;
+    const scaler = (displayHeight - 20) / Math.log(max);
+    for (let i = 0; i < coords.length; i++) {
+        const { r1s, r1e, r2s, r2e, v0, v1, distance } = coords[i];
+        const type = ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) || 'insertSizeAndOrientation';
+        const top = Math.log(distance) * scaler;
+        ctx.fillStyle = 'black';
+        const w = r2s - r1e;
+        fillRectCtx(r1e - view.offsetPx, top + halfHeight, w, 1, ctx);
+        if (type === 'insertSizeAndOrientation') {
+            ctx.fillStyle = (0, color_1.getInsertSizeAndOrientationColor)(v0, v1, stats);
+        }
+        else if (type === 'orientation') {
+            ctx.fillStyle = (0, color_1.getOrientationColor)(v0);
+        }
+        else if (type === 'insertSize') {
+            ctx.fillStyle = (0, color_1.getInsertSizeColor)(v0, v1, stats) || 'grey';
+        }
+        else if (type === 'gradient') {
+            const s = Math.min(v0.start, v1.start);
+            const e = Math.max(v0.end, v1.end);
+            ctx.fillStyle = `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,50%)`;
+        }
+        const w1 = Math.max(r1e - r1s, 2);
+        const w2 = Math.max(r2e - r2s, 2);
+        fillRectCtx(r1s - view.offsetPx, top, w1, featureHeight, ctx);
+        fillRectCtx(r2s - view.offsetPx, top, w2, featureHeight, ctx);
+    }
+}
+exports.default = drawFeats;
+//# sourceMappingURL=drawFeats.js.map

package/dist/LinearReadCloudDisplay/drawFeats.js.map

@@ -0,0 +1 @@
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package/dist/LinearReadCloudDisplay/index.d.ts

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

package/dist/LinearReadCloudDisplay/index.js

@@ -0,0 +1,27 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+// locals
+const ReactComponent_1 = __importDefault(require("./components/ReactComponent"));
+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: ReactComponent_1.default,
+        });
+    });
+}
+exports.default = register;
+//# sourceMappingURL=index.js.map

package/dist/LinearReadCloudDisplay/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearReadCloudDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,kGAAyE;AAEzE,SAAS;AACT,iFAAwD;AACxD,kEAA0C;AAC1C,oDAAiC;AAEjC,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QACjD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,wBAAwB;YAC9B,WAAW,EAAE,oBAAoB;YACjC,YAAY;YACZ,UAAU,EAAE,IAAA,eAAW,EAAC,YAAY,CAAC;YACrC,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,UAAU,EAAE,EAAE,IAAI,EAAE,yBAAyB,EAAE,UAAU,EAAE,IAAI,EAAE;YACjE,cAAc,EAAd,wBAAc;SACf,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAdD,2BAcC"}

package/dist/LinearReadCloudDisplay/model.d.ts

@@ -0,0 +1,320 @@
+import React from 'react';
+import { Instance } from 'mobx-state-tree';
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import { ChainData } from '../shared/fetchChains';
+import { ExportSvgOptions } from '@jbrowse/plugin-linear-genome-view/src/LinearGenomeView';
+interface Filter {
+    flagInclude: number;
+    flagExclude: number;
+    readName?: string;
+    tagFilter?: {
+        tag: string;
+        value: string;
+    };
+}
+/**
+ * #stateModel LinearReadCloudDisplay
+ * extends `BaseLinearDisplay`
+ */
+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>>;
+} & {
+    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        region: import("mobx-state-tree").IModelType<{
+            refName: import("mobx-state-tree").ISimpleType<string>;
+            /**
+             * #property
+             */
+            start: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        renderInProgress: AbortController | undefined;
+        filled: boolean;
+        reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+        layout: any;
+        /**
+         * #action
+         */
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: any;
+        }) => any;
+        /**
+         * #action
+         */
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(abortController: AbortController): void;
+        setMessage(messageText: string): void;
+        setRendered(props: {
+            reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
+            features: Map<string, import("@jbrowse/core/util").Feature>; /**
+             * #getter
+             */
+            layout: any;
+            maxHeightReached: boolean;
+            renderProps: any;
+        } | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    /**
+     * #property
+     */
+    type: import("mobx-state-tree").ISimpleType<"LinearReadCloudDisplay">;
+    /**
+     * #property
+     */
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    /**
+     * #property
+     */
+    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            tag: import("mobx-state-tree").ISimpleType<string>;
+            value: import("mobx-state-tree").ISimpleType<string>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    /**
+     * #property
+     */
+    colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+        type: import("mobx-state-tree").ISimpleType<string>;
+        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        extra: import("mobx-state-tree").IType<any, any, any>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+} & {
+    readonly RenderingComponent: React.FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+        } & 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;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: React.FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+        } & 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;
+        }, 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: React.FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): undefined;
+} & {
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    currBpPerPx: number;
+    scrollTop: number;
+    message: string;
+    featureIdUnderMouse: string | undefined;
+    contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
+    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+} & {
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
+} & {
+    readonly renderDelay: number;
+    readonly TooltipComponent: React.FC<any>;
+    readonly selectedFeatureId: string | undefined;
+    readonly DisplayMessageComponent: React.FC<any> | undefined;
+} & {
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
+    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly estimatedStatsReady: boolean;
+    readonly maxAllowableBytes: number;
+} & {
+    setMessage(message: string): void;
+    afterAttach(): void;
+    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
+        headers?: Record<string, string> | undefined;
+        signal?: AbortSignal | undefined;
+        filters?: string[] | undefined;
+    }): Promise<{}>;
+    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
+    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    clearRegionStats(): void;
+    setHeight(displayHeight: number): number;
+    resizeHeight(distance: number): number;
+    setScrollTop(scrollTop: number): void;
+    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
+    setCurrBpPerPx(n: number): void;
+    deleteBlock(key: string): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    clearFeatureSelection(): void;
+    setFeatureIdUnderMouse(feature: string | undefined): void;
+    reload(): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
+} & {
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    reload(): Promise<void>;
+    afterAttach(): void;
+} & {
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    contextMenuItems(): {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+    }[];
+    renderProps(): any;
+} & {
+    renderSvg(opts: ExportSvgOptions & {
+        overrideHeight: number;
+    }): Promise<JSX.Element>;
+} & {
+    loading: boolean;
+    drawn: boolean;
+    chainData: ChainData | undefined;
+    ref: HTMLCanvasElement | null;
+    lastDrawnOffsetPx: number;
+} & {
+    /**
+     * #action
+     * internal, a reference to a HTMLCanvas because we use a autorun to draw the canvas
+     */
+    reload(): void;
+    /**
+     * #action
+     */
+    setRef(ref: HTMLCanvasElement | null): void;
+    setColorScheme(s: {
+        type: string;
+    }): void;
+    /**
+     * #action
+     */
+    setChainData(args: ChainData): void;
+    /**
+     * #action
+     */
+    setLoading(f: boolean): void;
+    /**
+     * #action
+     */
+    setDrawn(f: boolean): void;
+    /**
+     * #action
+     */
+    setFilterBy(filter: Filter): void;
+    /**
+     * #action
+     */
+    setLastDrawnOffsetPx(n: number): void;
+} & {
+    /**
+     * #getter
+     */
+    readonly ready: boolean;
+    readonly rendererTypeName: string;
+    renderProps(): any;
+    /**
+     * #method
+     */
+    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;
+        };
+        onClick: () => void;
+        subMenu?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        subMenu: {
+            label: string;
+            onClick: () => void;
+        }[];
+        onClick?: undefined;
+    })[];
+    /**
+     * #method
+     */
+    renderSvg(opts: ExportSvgOptions): Promise<JSX.Element | undefined>;
+} & {
+    afterAttach(): void;
+}, import("mobx-state-tree")._NotCustomized, {
+    type: string;
+    height: number;
+    id: string;
+    rpcDriverName: string | undefined;
+    userBpPerPxLimit: number | undefined;
+    userByteSizeLimit: number | undefined;
+} & import("mobx-state-tree")._NotCustomized>;
+export type LinearReadCloudDisplayStateModel = ReturnType<typeof stateModelFactory>;
+export type LinearReadCloudDisplayModel = Instance<LinearReadCloudDisplayStateModel>;
+export default stateModelFactory;