@jbrowse/plugin-variants 2.17.0 → 3.0.0

package/dist/MultiLinearVariantMatrixDisplay/index.js

@@ -0,0 +1,24 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LinearVariantMatrixDisplayF;
+const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+const VariantDisplayComponent_1 = __importDefault(require("./components/VariantDisplayComponent"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+const model_1 = __importDefault(require("./model"));
+function LinearVariantMatrixDisplayF(pluginManager) {
+    pluginManager.addDisplayType(() => {
+        const configSchema = (0, configSchema_1.default)(pluginManager);
+        return new DisplayType_1.default({
+            name: 'LinearVariantMatrixDisplay',
+            displayName: 'Multi-variant display (matrix)',
+            configSchema,
+            stateModel: (0, model_1.default)(configSchema),
+            trackType: 'VariantTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: VariantDisplayComponent_1.default,
+        });
+    });
+}

package/dist/MultiLinearVariantMatrixDisplay/model.d.ts

@@ -0,0 +1,356 @@
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
+import type { Instance } from 'mobx-state-tree';
+export default 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<"LinearVariantMatrixDisplay">;
+    rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+}, {
+    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;
+} & {
+    lineZoneHeight: number;
+} & {
+    readonly nrow: number;
+    readonly blockType: string;
+    readonly totalHeight: number;
+    readonly rowHeight: number;
+} & {
+    renderProps(): any;
+    readonly canDisplayLabels: boolean;
+} & {
+    afterAttach(): void;
+    renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export type MultiLinearVariantMatrixDisplayStateModel = ReturnType<typeof stateModelFactory>;
+export type MultiLinearVariantMatrixDisplayModel = Instance<MultiLinearVariantMatrixDisplayStateModel>;

package/dist/MultiLinearVariantMatrixDisplay/model.js

@@ -0,0 +1,113 @@
+"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 = 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('LinearVariantMatrixDisplay', (0, MultiVariantBaseModel_1.default)(configSchema), mobx_state_tree_1.types.model({
+        type: mobx_state_tree_1.types.literal('LinearVariantMatrixDisplay'),
+        rowHeightSetting: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1),
+    }))
+        .volatile(() => ({
+        lineZoneHeight: 20,
+    }))
+        .views(self => ({
+        get nrow() {
+            var _a;
+            return ((_a = self.sources) === null || _a === void 0 ? void 0 : _a.length) || 1;
+        },
+        get blockType() {
+            return 'dynamicBlocks';
+        },
+        get totalHeight() {
+            return self.autoHeight
+                ? self.height - self.lineZoneHeight
+                : this.nrow * self.rowHeightSetting;
+        },
+        get rowHeight() {
+            return self.autoHeight
+                ? self.totalHeight / this.nrow
+                : self.rowHeightSetting;
+        },
+    }))
+        .views(self => ({
+        renderProps() {
+            const superProps = self.adapterProps();
+            return {
+                ...superProps,
+                notReady: superProps.notReady || !self.sources || !self.featuresVolatile,
+                renderingMode: self.renderingMode,
+                minorAlleleFrequencyFilter: self.minorAlleleFrequencyFilter,
+                height: self.totalHeight,
+                sources: self.sources,
+            };
+        },
+        get canDisplayLabels() {
+            return self.rowHeight > 8 && self.showSidebarLabelsSetting;
+        },
+    }))
+        .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);
+            },
+        };
+    });
+}

package/dist/MultiLinearVariantMatrixDisplay/renderSvg.d.ts

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

package/dist/MultiLinearVariantMatrixDisplay/renderSvg.js

@@ -0,0 +1,17 @@
+"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"));
+const LinesConnectingMatrixToGenomicPosition_1 = __importDefault(require("./components/LinesConnectingMatrixToGenomicPosition"));
+async function renderSvg(model, opts, superRenderSvg) {
+    await (0, mobx_1.when)(() => !!model.regionCannotBeRenderedText);
+    const { offsetPx } = (0, util_1.getContainingView)(model);
+    const { lineZoneHeight } = model;
+    return ((0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsxs)("g", { transform: `translate(${Math.max(-offsetPx, 0)})`, children: [(0, jsx_runtime_1.jsx)(LinesConnectingMatrixToGenomicPosition_1.default, { exportSVG: true, model: model }), (0, jsx_runtime_1.jsxs)("g", { transform: `translate(0,${lineZoneHeight})`, children: [(0, jsx_runtime_1.jsx)("g", { children: await superRenderSvg(opts) }), (0, jsx_runtime_1.jsx)(LegendBar_1.default, { model: model, orientation: "left", exportSVG: true })] })] }) }));
+}

package/dist/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.d.ts

@@ -0,0 +1,34 @@
+import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import type { RenderArgsDeserialized } from './types';
+import type { Feature } from '@jbrowse/core/util';
+export default class LinearVariantMatrixRenderer extends BoxRendererType {
+    supportsSVG: boolean;
+    render(renderProps: RenderArgsDeserialized): Promise<{
+        features: Map<any, any>;
+        simplifiedFeatures: any;
+        height: number;
+        width: number;
+        canvasRecordedData: any;
+        layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
+        reactElement?: React.ReactElement;
+        html?: string;
+    } | {
+        features: Map<any, any>;
+        simplifiedFeatures: any;
+        height: number;
+        width: number;
+        reactElement: import("react/jsx-runtime").JSX.Element;
+        layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
+        html?: string;
+    } | {
+        features: Map<any, any>;
+        simplifiedFeatures: any;
+        height: number;
+        width: number;
+        imageData: any;
+        layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
+        reactElement?: React.ReactElement;
+        html?: string;
+    }>;
+}
+export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';

package/dist/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.js

@@ -0,0 +1,87 @@
+"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 BoxRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType"));
+const util_1 = require("@jbrowse/core/util");
+class LinearVariantMatrixRenderer extends BoxRendererType_1.default {
+    constructor() {
+        super(...arguments);
+        this.supportsSVG = true;
+    }
+    async render(renderProps) {
+        const features = await this.getFeatures(renderProps);
+        const { height, sources, regions, bpPerPx } = renderProps;
+        const region = regions[0];
+        const { end, start } = region;
+        const width = (end - start) / bpPerPx;
+        const { makeImageData } = await Promise.resolve().then(() => __importStar(require('./makeImageData')));
+        const { mafs, ...res } = await (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => makeImageData({
+            ctx,
+            canvasWidth: width,
+            canvasHeight: height,
+            renderArgs: {
+                ...renderProps,
+                features,
+                sources,
+            },
+        }));
+        const results = await super.render({
+            ...renderProps,
+            ...res,
+            features,
+            height,
+            width,
+        });
+        return {
+            ...results,
+            ...res,
+            features: new Map(),
+            simplifiedFeatures: mafs.map((s) => new util_1.SimpleFeature({
+                id: s.id(),
+                data: {
+                    start: s.get('start'),
+                    end: s.get('end'),
+                    refName: s.get('refName'),
+                },
+            })),
+            height,
+            width,
+        };
+    }
+}
+exports.default = LinearVariantMatrixRenderer;

package/dist/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.d.ts

@@ -0,0 +1,7 @@
+declare const LinearVariantMatrixRendering: (props: {
+    width: number;
+    height: number;
+    displayModel: any;
+    arr: string[];
+}) => import("react/jsx-runtime").JSX.Element;
+export default LinearVariantMatrixRendering;