@jbrowse/plugin-variants 2.16.1 → 2.18.0

package/dist/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.js

@@ -0,0 +1,81 @@
+"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 (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const ui_1 = require("@jbrowse/core/ui");
+const BaseTooltip_1 = __importDefault(require("@jbrowse/core/ui/BaseTooltip"));
+const util_1 = require("@jbrowse/core/util");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const LinesConnectingMatrixToGenomicPosition_1 = __importDefault(require("./LinesConnectingMatrixToGenomicPosition"));
+const LegendBar_1 = __importDefault(require("../../shared/LegendBar"));
+const useStyles = (0, mui_1.makeStyles)()({
+    cursor: {
+        pointerEvents: 'none',
+        zIndex: 1000,
+        position: 'relative',
+    },
+});
+const MultiLinearVariantMatrixDisplayComponent = (0, mobx_react_1.observer)(function (props) {
+    const { classes } = useStyles();
+    const { model } = props;
+    const { height, sources, rowHeight } = model;
+    const ref = (0, react_1.useRef)(null);
+    const [mouseY, setMouseY] = (0, react_1.useState)();
+    const [mouseX, setMouseX] = (0, react_1.useState)();
+    const { width } = (0, util_1.getContainingView)(model);
+    return (react_1.default.createElement("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);
+        } },
+        react_1.default.createElement("div", { style: { position: 'relative' } },
+            react_1.default.createElement(LinesConnectingMatrixToGenomicPosition_1.default, { model: model }),
+            react_1.default.createElement("div", { style: { position: 'absolute', top: 20 } },
+                react_1.default.createElement(LegendBar_1.default, { model: model }),
+                react_1.default.createElement(plugin_linear_genome_view_1.BaseLinearDisplayComponent, { ...props }))),
+        mouseY &&
+            mouseY > 20 &&
+            (sources === null || sources === void 0 ? void 0 : sources[Math.floor((mouseY - 20) / rowHeight)]) ? (react_1.default.createElement(react_1.default.Fragment, null,
+            react_1.default.createElement("svg", { className: classes.cursor, width: width, height: height },
+                react_1.default.createElement("line", { x1: 0, x2: width, y1: mouseY, y2: mouseY, stroke: "black" }),
+                react_1.default.createElement("line", { x1: mouseX, x2: mouseX, y1: 0, y2: height, stroke: "black" })),
+            react_1.default.createElement(BaseTooltip_1.default, null,
+                react_1.default.createElement(ui_1.SanitizedHTML, { html: Object.entries(sources[Math.floor((mouseY - 20) / rowHeight)] || {})
+                        .filter(([key]) => key !== 'color')
+                        .map(([key, value]) => `${key}:${value}`)
+                        .join('\n') })))) : 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;

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 +1,274 @@
+import type { Source } from '../util';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
+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, 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.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<Source[], Source[], Source[]>, [undefined]>;
+    configuration: AnyConfigurationSchemaType;
+    mafFilter: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    showSidebarLabelsSetting: 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.Element | null;
+} & {
+    featureIdUnderMouse: undefined | string;
+    contextMenuFeature: undefined | Feature;
+} & {
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    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, Feature>;
+    readonly featureUnderMouse: 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: Feature): void;
+    navToFeature(feature: Feature): void;
+    clearFeatureSelection(): void;
+    setFeatureIdUnderMouse(feature?: string): void;
+    setContextMenuFeature(feature?: 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.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: Feature | undefined;
+    sourcesVolatile: Source[] | undefined;
+    featuresVolatile: Feature[] | undefined;
+    lineZoneHeight: number;
+} & {
+    setFeatures(f: Feature[]): void;
+    setLayout(layout: Source[]): void;
+    clearLayout(): void;
+    setSourcesLoading(str: string): void;
+    setSources(sources: Source[]): void;
+    setMafFilter(arg: number): void;
+    setShowSidebarLabels(arg: boolean): void;
+} & {
+    readonly preSources: Source[] | undefined;
+    readonly sources: {
+        color: string;
+        baseUri?: string;
+        name: string;
+        group?: string;
+    }[] | undefined;
+} & {
+    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;
+        type: string;
+        checked: boolean;
+        onClick: () => void;
+    })[];
+} & {
+    readonly blockType: string;
+    readonly totalHeight: number;
+    readonly rowHeight: number;
+} & {
+    renderProps(): any;
+    readonly canDisplayLabels: boolean;
+} & {
+    afterAttach(): void;
+    renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react").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 +1,218 @@
+"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 (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __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 react_1 = require("react");
+const configuration_1 = require("@jbrowse/core/configuration");
+const colors_1 = require("@jbrowse/core/ui/colors");
+const util_1 = require("@jbrowse/core/util");
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
+const mobx_state_tree_1 = require("mobx-state-tree");
+const util_2 = require("../util");
+const SetColorDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/SetColorDialog'))));
+const MAFFilterDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/MAFFilterDialog'))));
+const ClusterDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/ClusterDialog'))));
+function stateModelFactory(configSchema) {
+    return mobx_state_tree_1.types
+        .compose('LinearVariantMatrixDisplay', (0, plugin_linear_genome_view_1.linearBareDisplayStateModelFactory)(configSchema), mobx_state_tree_1.types.model({
+        type: mobx_state_tree_1.types.literal('LinearVariantMatrixDisplay'),
+        layout: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), []),
+        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
+        mafFilter: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0.1),
+        showSidebarLabelsSetting: true,
+    }))
+        .volatile(() => ({
+        sourcesLoadingStopToken: undefined,
+        featureUnderMouseVolatile: undefined,
+        sourcesVolatile: undefined,
+        featuresVolatile: undefined,
+        lineZoneHeight: 20,
+    }))
+        .actions(self => ({
+        setFeatures(f) {
+            self.featuresVolatile = f;
+        },
+        setLayout(layout) {
+            self.layout = layout;
+        },
+        clearLayout() {
+            self.layout = [];
+        },
+        setSourcesLoading(str) {
+            if (self.sourcesLoadingStopToken) {
+                (0, stopToken_1.stopStopToken)(self.sourcesLoadingStopToken);
+            }
+            self.sourcesLoadingStopToken = str;
+        },
+        setSources(sources) {
+            if (!(0, fast_deep_equal_1.default)(sources, self.sourcesVolatile)) {
+                self.sourcesVolatile = sources;
+            }
+        },
+        setMafFilter(arg) {
+            self.mafFilter = arg;
+        },
+        setShowSidebarLabels(arg) {
+            self.showSidebarLabelsSetting = arg;
+        },
+    }))
+        .views(self => ({
+        get preSources() {
+            return self.layout.length ? self.layout : self.sourcesVolatile;
+        },
+        get sources() {
+            var _a, _b;
+            const sources = Object.fromEntries(((_a = self.sourcesVolatile) === null || _a === void 0 ? void 0 : _a.map(s => [s.name, s])) || []);
+            return (_b = this.preSources) === null || _b === void 0 ? void 0 : _b.map(s => ({
+                ...sources[s.name],
+                ...s,
+            })).map((s, i) => ({
+                ...s,
+                color: s.color || colors_1.set1[i] || (0, util_2.randomColor)(s.name),
+            }));
+        },
+    }))
+        .views(self => {
+        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
+        return {
+            adapterProps() {
+                const superProps = superRenderProps();
+                return {
+                    ...superProps,
+                    rpcDriverName: self.rpcDriverName,
+                    displayModel: self,
+                    config: self.rendererConfig,
+                };
+            },
+            trackMenuItems() {
+                return [
+                    ...superTrackMenuItems(),
+                    {
+                        label: 'Show sidebar labels',
+                        type: 'checkbox',
+                        checked: self.showSidebarLabelsSetting,
+                        onClick: () => {
+                            self.setShowSidebarLabels(!self.showSidebarLabelsSetting);
+                        },
+                    },
+                    {
+                        label: 'Minimum allele frequency',
+                        onClick: () => {
+                            (0, util_1.getSession)(self).queueDialog(handleClose => [
+                                MAFFilterDialog,
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
+                            ]);
+                        },
+                    },
+                    {
+                        label: 'Cluster by genotype',
+                        onClick: () => {
+                            (0, util_1.getSession)(self).queueDialog(handleClose => [
+                                ClusterDialog,
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
+                            ]);
+                        },
+                    },
+                    {
+                        label: 'Edit colors/arrangement...',
+                        onClick: () => {
+                            (0, util_1.getSession)(self).queueDialog(handleClose => [
+                                SetColorDialog,
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
+                            ]);
+                        },
+                    },
+                ];
+            },
+        };
+    })
+        .views(self => ({
+        get blockType() {
+            return 'dynamicBlocks';
+        },
+        get totalHeight() {
+            return self.height - self.lineZoneHeight;
+        },
+        get rowHeight() {
+            var _a;
+            return this.totalHeight / (((_a = self.sources) === null || _a === void 0 ? void 0 : _a.length) || 1);
+        },
+    }))
+        .views(self => ({
+        renderProps() {
+            const superProps = self.adapterProps();
+            return {
+                ...superProps,
+                notReady: superProps.notReady || !self.sources || !self.featuresVolatile,
+                mafFilter: self.mafFilter,
+                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 +1,4 @@
+import React from 'react';
+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<React.JSX.Element>;