@jbrowse/plugin-variants 2.17.0 → 3.0.0

package/dist/MultiLinearVariantDisplay/model.d.ts

@@ -0,0 +1,351 @@
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
+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>>;
+} & {
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
+        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>;
+    }, {
+        stopToken: string | undefined;
+        filled: boolean;
+        reactElement: React.ReactElement | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: React.ReactNode;
+                filled?: boolean;
+                status?: string;
+                reactElement?: React.ReactElement;
+            };
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(newStopToken: string): void;
+        setMessage(messageText: string): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    configuration: 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">>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearBareDisplay">;
+    configuration: AnyConfigurationSchemaType;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearVariantMatrixDisplay">;
+    layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("../types").Source[], import("../types").Source[], import("../types").Source[]>, [undefined]>;
+    configuration: AnyConfigurationSchemaType;
+    minorAlleleFrequencyFilter: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    showSidebarLabelsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    renderingMode: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    autoHeight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"MultiLinearVariantDisplay">;
+    rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    minorAlleleFrequencyFilter: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    autoHeight: 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;
+} & {
+    featureIdUnderMouse: undefined | string;
+    contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
+} & {
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
+    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
+} & {
+    readonly renderDelay: number;
+    readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
+    readonly selectedFeatureId: string | 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): string | undefined;
+    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
+    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+} & {
+    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
+    deleteBlock(key: string): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    navToFeature(feature: import("@jbrowse/core/util").Feature): void;
+    clearFeatureSelection(): void;
+    setFeatureIdUnderMouse(feature?: string): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
+} & {
+    reload(): Promise<void>;
+} & {
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    renderProps(): any;
+} & {
+    renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
+    afterAttach(): void;
+} & {
+    readonly rendererConfig: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+    readonly rendererTypeName: any;
+} & {
+    renderProps(): any;
+} & {
+    sourcesLoadingStopToken: string | undefined;
+    featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
+    sourcesVolatile: import("../types").Source[] | undefined;
+    featuresVolatile: import("@jbrowse/core/util").Feature[] | undefined;
+    hasPhased: boolean;
+    sampleInfo: undefined | Record<string, import("../types").SampleInfo>;
+    hoveredGenotype: string | undefined;
+} & {
+    setRowHeight(arg: number): void;
+    setHoveredGenotype(arg: string): void;
+    setFeatures(f: import("@jbrowse/core/util").Feature[]): void;
+    setLayout(layout: import("../types").Source[]): void;
+    clearLayout(): void;
+    setSourcesLoading(str: string): void;
+    setSources(sources: import("../types").Source[]): void;
+    setMafFilter(arg: number): void;
+    setShowSidebarLabels(arg: boolean): void;
+    setPhasedMode(arg: string): void;
+    setAutoHeight(arg: boolean): void;
+    setHasPhased(arg: boolean): void;
+    setSampleInfo(arg: Record<string, import("../types").SampleInfo>): void;
+} & {
+    readonly preSources: import("../types").Source[] | undefined;
+    readonly sources: {
+        label: string;
+        id: string;
+        baseUri?: string;
+        name: string;
+        color?: string;
+        group?: string;
+        HP?: number;
+    }[] | undefined;
+} & {
+    readonly rowHeight: number;
+    adapterProps(): 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;
+        };
+        type: string;
+        checked: boolean;
+        onClick: () => void;
+        subMenu?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        subMenu: ({
+            label: string;
+            disabled: boolean;
+            onClick: () => void;
+            type?: undefined;
+            checked?: undefined;
+        } | {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+            disabled?: undefined;
+        })[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        subMenu: ({
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+            disabled?: undefined;
+        } | {
+            label: string;
+            disabled: boolean;
+            checked: boolean;
+            type: string;
+            onClick: () => void;
+        })[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: 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;
+    })[];
+} & {
+    readonly canDisplayLabels: boolean;
+    readonly totalHeight: number;
+} & {
+    renderProps(): any;
+} & {
+    readonly rendererTypeName: string;
+} & {
+    afterAttach(): void;
+    renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export type MultiLinearVariantDisplayStateModel = ReturnType<typeof stateModelFactory>;
+export type MultiLinearVariantDisplayModel = Instance<MultiLinearVariantDisplayStateModel>;
+export default stateModelFactory;

package/dist/MultiLinearVariantDisplay/model.js

@@ -0,0 +1,83 @@
+"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.stateModelFactory = stateModelFactory;
+const util_1 = require("@jbrowse/core/util");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const MultiVariantBaseModel_1 = __importDefault(require("../shared/MultiVariantBaseModel"));
+function stateModelFactory(configSchema) {
+    return mobx_state_tree_1.types
+        .compose('MultiLinearVariantDisplay', (0, MultiVariantBaseModel_1.default)(configSchema), mobx_state_tree_1.types.model({
+        type: mobx_state_tree_1.types.literal('MultiLinearVariantDisplay'),
+        rowHeightSetting: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 11),
+        minorAlleleFrequencyFilter: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
+        autoHeight: false,
+    }))
+        .views(() => ({
+        get rendererTypeName() {
+            return 'MultiVariantRenderer';
+        },
+    }))
+        .actions(self => {
+        const { renderSvg: superRenderSvg } = self;
+        return {
+            afterAttach() {
+                ;
+                (async () => {
+                    try {
+                        const { getMultiVariantSourcesAutorun } = await Promise.resolve().then(() => __importStar(require('../getMultiVariantSourcesAutorun')));
+                        const { getMultiVariantFeaturesAutorun } = await Promise.resolve().then(() => __importStar(require('../getMultiVariantFeaturesAutorun')));
+                        getMultiVariantSourcesAutorun(self);
+                        getMultiVariantFeaturesAutorun(self);
+                    }
+                    catch (e) {
+                        if ((0, mobx_state_tree_1.isAlive)(self)) {
+                            console.error(e);
+                            (0, util_1.getSession)(self).notifyError(`${e}`, e);
+                        }
+                    }
+                })();
+            },
+            async renderSvg(opts) {
+                const { renderSvg } = await Promise.resolve().then(() => __importStar(require('./renderSvg')));
+                return renderSvg(self, opts, superRenderSvg);
+            },
+        };
+    });
+}
+exports.default = stateModelFactory;

package/dist/MultiLinearVariantDisplay/renderSvg.d.ts

@@ -0,0 +1,3 @@
+import type { MultiLinearVariantDisplayModel } from './model';
+import type { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
+export declare function renderSvg(self: MultiLinearVariantDisplayModel, opts: ExportSvgDisplayOptions, superRenderSvg: (opts: ExportSvgDisplayOptions) => Promise<React.ReactNode>): Promise<import("react/jsx-runtime").JSX.Element>;

package/dist/MultiLinearVariantDisplay/renderSvg.js

@@ -0,0 +1,15 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderSvg = renderSvg;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const util_1 = require("@jbrowse/core/util");
+const mobx_1 = require("mobx");
+const LegendBar_1 = __importDefault(require("../shared/LegendBar"));
+async function renderSvg(self, opts, superRenderSvg) {
+    await (0, mobx_1.when)(() => !!self.regionCannotBeRenderedText);
+    const { offsetPx } = (0, util_1.getContainingView)(self);
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("g", { children: await superRenderSvg(opts) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(${Math.max(-offsetPx, 0)})`, children: (0, jsx_runtime_1.jsx)(LegendBar_1.default, { model: self, orientation: "left", exportSVG: true }) })] }));
+}

package/dist/MultiLinearVariantMatrixDisplay/components/Crosshair.d.ts

@@ -0,0 +1,7 @@
+import type { MultiLinearVariantMatrixDisplayModel } from '../model';
+declare const Crosshair: ({ mouseX, mouseY, model, }: {
+    mouseX: number;
+    mouseY: number;
+    model: MultiLinearVariantMatrixDisplayModel;
+}) => import("react/jsx-runtime").JSX.Element | null;
+export default Crosshair;

package/dist/MultiLinearVariantMatrixDisplay/components/Crosshair.js

@@ -0,0 +1,28 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const jsx_runtime_1 = require("react/jsx-runtime");
+const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const MultiVariantTooltip_1 = __importDefault(require("../../shared/MultiVariantTooltip"));
+const useStyles = (0, mui_1.makeStyles)()({
+    cursor: {
+        pointerEvents: 'none',
+        zIndex: 1000,
+        position: 'relative',
+    },
+});
+const Crosshair = (0, mobx_react_1.observer)(function ({ mouseX, mouseY, model, }) {
+    const { classes } = useStyles();
+    const { hoveredGenotype, lineZoneHeight, totalHeight, rowHeight, sources } = model;
+    const { width } = (0, util_1.getContainingView)(model);
+    const source = sources === null || sources === void 0 ? void 0 : sources[Math.floor((mouseY - lineZoneHeight) / rowHeight)];
+    const yoff = mouseY - lineZoneHeight;
+    return source ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("svg", { className: classes.cursor, width: width, height: totalHeight, style: {
+                    top: lineZoneHeight,
+                }, children: [(0, jsx_runtime_1.jsx)("line", { x1: 0, x2: width, y1: yoff, y2: yoff, stroke: "black" }), (0, jsx_runtime_1.jsx)("line", { x1: mouseX, x2: mouseX, y1: 0, y2: totalHeight, stroke: "black" })] }), (0, jsx_runtime_1.jsx)(MultiVariantTooltip_1.default, { source: { ...source, hoveredGenotype } })] })) : null;
+});
+exports.default = Crosshair;

package/dist/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.d.ts

@@ -0,0 +1,6 @@
+import type { MultiLinearVariantMatrixDisplayModel } from '../model';
+declare const LinesConnectingMatrixToGenomicPosition: ({ model, exportSVG, }: {
+    model: MultiLinearVariantMatrixDisplayModel;
+    exportSVG?: boolean;
+}) => import("react/jsx-runtime").JSX.Element | null;
+export default LinesConnectingMatrixToGenomicPosition;

package/dist/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.js

@@ -0,0 +1,39 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const jsx_runtime_1 = require("react/jsx-runtime");
+const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
+const Wrapper = (0, mobx_react_1.observer)(function ({ children, model, exportSVG, }) {
+    const { height } = model;
+    const { width, offsetPx } = (0, util_1.getContainingView)(model);
+    const left = Math.max(0, -offsetPx);
+    return exportSVG ? ((0, jsx_runtime_1.jsx)("g", { transform: `translate(${left})`, children: children })) : ((0, jsx_runtime_1.jsx)("svg", { style: {
+            position: 'absolute',
+            top: 0,
+            left,
+            pointerEvents: 'none',
+            height,
+            width,
+        }, children: children }));
+});
+const LinesConnectingMatrixToGenomicPosition = (0, mobx_react_1.observer)(function ({ model, exportSVG, }) {
+    var _a;
+    const { assemblyManager } = (0, util_1.getSession)(model);
+    const view = (0, util_1.getContainingView)(model);
+    const { lineZoneHeight, featuresVolatile } = model;
+    const { offsetPx, assemblyNames, dynamicBlocks } = view;
+    const assembly = assemblyManager.get(assemblyNames[0]);
+    const b0 = ((_a = dynamicBlocks.contentBlocks[0]) === null || _a === void 0 ? void 0 : _a.widthPx) || 0;
+    const w = b0 / ((featuresVolatile === null || featuresVolatile === void 0 ? void 0 : featuresVolatile.length) || 1);
+    const l = Math.max(offsetPx, 0);
+    return assembly && featuresVolatile ? ((0, jsx_runtime_1.jsx)(Wrapper, { exportSVG: exportSVG, model: model, children: featuresVolatile.map((f, i) => {
+            var _a;
+            const ref = f.get('refName');
+            const c = (((_a = view.bpToPx({
+                refName: assembly.getCanonicalRefName(ref) || ref,
+                coord: f.get('start'),
+            })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - l;
+            return ((0, jsx_runtime_1.jsx)("line", { stroke: "#0004", x1: i * w + w / 2, x2: c, y1: lineZoneHeight, y2: 0 }, f.id()));
+        }) })) : null;
+});
+exports.default = LinesConnectingMatrixToGenomicPosition;

package/dist/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.d.ts

@@ -0,0 +1,5 @@
+import type { MultiLinearVariantMatrixDisplayModel } from '../model';
+declare const MultiLinearVariantMatrixDisplayComponent: (props: {
+    model: MultiLinearVariantMatrixDisplayModel;
+}) => import("react/jsx-runtime").JSX.Element;
+export default MultiLinearVariantMatrixDisplayComponent;

package/dist/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.js

@@ -0,0 +1,31 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const mobx_react_1 = require("mobx-react");
+const Crosshair_1 = __importDefault(require("./Crosshair"));
+const LinesConnectingMatrixToGenomicPosition_1 = __importDefault(require("./LinesConnectingMatrixToGenomicPosition"));
+const LegendBar_1 = __importDefault(require("../../shared/LegendBar"));
+const MultiLinearVariantMatrixDisplayComponent = (0, mobx_react_1.observer)(function (props) {
+    const { model } = props;
+    const { lineZoneHeight } = model;
+    const ref = (0, react_1.useRef)(null);
+    const [mouseY, setMouseY] = (0, react_1.useState)();
+    const [mouseX, setMouseX] = (0, react_1.useState)();
+    return ((0, jsx_runtime_1.jsxs)("div", { ref: ref, onMouseMove: event => {
+            var _a;
+            const rect = (_a = ref.current) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect();
+            const top = (rect === null || rect === void 0 ? void 0 : rect.top) || 0;
+            const left = (rect === null || rect === void 0 ? void 0 : rect.left) || 0;
+            setMouseY(event.clientY - top);
+            setMouseX(event.clientX - left);
+        }, onMouseLeave: () => {
+            setMouseY(undefined);
+            setMouseX(undefined);
+        }, children: [(0, jsx_runtime_1.jsxs)("div", { style: { position: 'relative' }, children: [(0, jsx_runtime_1.jsx)(LinesConnectingMatrixToGenomicPosition_1.default, { model: model }), (0, jsx_runtime_1.jsxs)("div", { style: { position: 'absolute', top: lineZoneHeight }, children: [(0, jsx_runtime_1.jsx)(LegendBar_1.default, { model: model }), (0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.BaseLinearDisplayComponent, { ...props })] })] }), mouseX && mouseY && mouseY > lineZoneHeight ? ((0, jsx_runtime_1.jsx)(Crosshair_1.default, { mouseX: mouseX, mouseY: mouseY, model: model })) : null] }));
+});
+exports.default = MultiLinearVariantMatrixDisplayComponent;

package/dist/MultiLinearVariantMatrixDisplay/configSchema.d.ts

@@ -0,0 +1,37 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    renderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    height: {
+        type: string;
+        defaultValue: number;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    renderer: import("mobx-state-tree").IAnyModelType;
+}, 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>>, undefined>>;

package/dist/MultiLinearVariantMatrixDisplay/configSchema.js

@@ -0,0 +1,22 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = configSchemaF;
+const configuration_1 = require("@jbrowse/core/configuration");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const configSchema_1 = __importDefault(require("../MultiLinearVariantMatrixRenderer/configSchema"));
+function x() { }
+function configSchemaF(pluginManager) {
+    return (0, configuration_1.ConfigurationSchema)('LinearVariantMatrixDisplay', {
+        renderer: configSchema_1.default,
+        height: {
+            type: 'number',
+            defaultValue: 250,
+        },
+    }, {
+        baseConfiguration: (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager),
+        explicitlyTyped: true,
+    });
+}

package/dist/MultiLinearVariantMatrixDisplay/index.d.ts

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