@jbrowse/plugin-variants 2.18.0 → 3.0.1

package/dist/MultiLinearVariantMatrixDisplay/model.d.ts

@@ -1,6 +1,4 @@
-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<{
@@ -23,7 +21,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
-        features: Map<string, Feature> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
         error: unknown;
@@ -38,7 +36,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -84,10 +82,16 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     configuration: AnyConfigurationSchemaType;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearVariantMatrixDisplay">;
-    layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>;
+    layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("../types").Source[], import("../types").Source[], import("../types").Source[]>, [undefined]>;
     configuration: AnyConfigurationSchemaType;
-    mafFilter: 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]>;
     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;
@@ -179,32 +183,32 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     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;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
-    contextMenuFeature: undefined | Feature;
+    contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    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, Feature>;
-    readonly featureUnderMouse: Feature | 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: Feature): void;
-    navToFeature(feature: Feature): 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?: Feature): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -212,7 +216,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     readonly rendererConfig: {
@@ -231,35 +235,113 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderProps(): any;
 } & {
     sourcesLoadingStopToken: string | undefined;
-    featureUnderMouseVolatile: Feature | undefined;
-    sourcesVolatile: Source[] | undefined;
-    featuresVolatile: Feature[] | undefined;
-    lineZoneHeight: number;
-} & {
-    setFeatures(f: Feature[]): void;
-    setLayout(layout: Source[]): void;
+    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: Source[]): 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: Source[] | undefined;
+    readonly preSources: import("../types").Source[] | undefined;
     readonly sources: {
-        color: string;
+        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;
@@ -268,7 +350,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly canDisplayLabels: boolean;
 } & {
     afterAttach(): void;
-    renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    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

@@ -15,163 +15,57 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __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 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'))));
+const MultiVariantBaseModel_1 = __importDefault(require("../shared/MultiVariantBaseModel"));
 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({
+        .compose('LinearVariantMatrixDisplay', (0, MultiVariantBaseModel_1.default)(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,
+        rowHeightSetting: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1),
     }))
         .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),
-            }));
+        get nrow() {
+            var _a;
+            return ((_a = self.sources) === null || _a === void 0 ? void 0 : _a.length) || 1;
         },
-    }))
-        .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;
+            return self.autoHeight
+                ? self.height - self.lineZoneHeight
+                : this.nrow * self.rowHeightSetting;
         },
         get rowHeight() {
-            var _a;
-            return this.totalHeight / (((_a = self.sources) === null || _a === void 0 ? void 0 : _a.length) || 1);
+            return self.autoHeight
+                ? self.totalHeight / this.nrow
+                : self.rowHeightSetting;
         },
     }))
         .views(self => ({
@@ -180,7 +74,8 @@ function stateModelFactory(configSchema) {
             return {
                 ...superProps,
                 notReady: superProps.notReady || !self.sources || !self.featuresVolatile,
-                mafFilter: self.mafFilter,
+                renderingMode: self.renderingMode,
+                minorAlleleFrequencyFilter: self.minorAlleleFrequencyFilter,
                 height: self.totalHeight,
                 sources: self.sources,
             };

package/dist/MultiLinearVariantMatrixDisplay/renderSvg.d.ts

@@ -1,4 +1,3 @@
-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>;
+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

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderSvg = renderSvg;
-const react_1 = __importDefault(require("react"));
+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"));
@@ -12,10 +12,6 @@ const LinesConnectingMatrixToGenomicPosition_1 = __importDefault(require("./comp
 async function renderSvg(model, opts, superRenderSvg) {
     await (0, mobx_1.when)(() => !!model.regionCannotBeRenderedText);
     const { offsetPx } = (0, util_1.getContainingView)(model);
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement("g", { transform: `translate(${Math.max(-offsetPx, 0)})` },
-            react_1.default.createElement(LinesConnectingMatrixToGenomicPosition_1.default, { exportSVG: true, model: model }),
-            react_1.default.createElement("g", { transform: `translate(0,${model.lineZoneHeight})` },
-                react_1.default.createElement("g", null, await superRenderSvg(opts)),
-                react_1.default.createElement(LegendBar_1.default, { model: model, orientation: "left", exportSVG: true })))));
+    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

@@ -1,36 +1,8 @@
 import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import type { Source } from '../util';
-import type { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import type { RenderArgsDeserialized } from './types';
 import type { Feature } from '@jbrowse/core/util';
-export interface SortParams {
-    type: string;
-    pos: number;
-    refName: string;
-    assemblyName: string;
-    tag?: string;
-}
-export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
-    sources: {
-        name: string;
-    }[];
-    mafFilter: number;
-    highResolutionScaling: number;
-    height: number;
-}
-export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsDeserialized {
-    sources: Source[];
-    features: Map<string, Feature>;
-}
 export default class LinearVariantMatrixRenderer extends BoxRendererType {
     supportsSVG: boolean;
-    makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }: {
-        ctx: CanvasRenderingContext2D;
-        canvasWidth: number;
-        canvasHeight: number;
-        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
-    }): {
-        mafs: Feature[];
-    };
     render(renderProps: RenderArgsDeserialized): Promise<{
         features: Map<any, any>;
         simplifiedFeatures: any;
@@ -38,14 +10,14 @@ export default class LinearVariantMatrixRenderer extends BoxRendererType {
         width: number;
         canvasRecordedData: any;
         layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
-        reactElement?: import("react").ReactElement;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<any, any>;
         simplifiedFeatures: any;
         height: number;
         width: number;
-        reactElement: React.JSX.Element;
+        reactElement: import("react/jsx-runtime").JSX.Element;
         layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
         html?: string;
     } | {
@@ -55,7 +27,7 @@ export default class LinearVariantMatrixRenderer extends BoxRendererType {
         width: number;
         imageData: any;
         layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
-        reactElement?: import("react").ReactElement;
+        reactElement?: React.ReactElement;
         html?: string;
     }>;
 }

package/dist/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.js

@@ -1,84 +1,65 @@
 "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");
-const util_2 = require("../util");
-const fudgeFactor = 0.6;
-const f2 = fudgeFactor / 2;
 class LinearVariantMatrixRenderer extends BoxRendererType_1.default {
     constructor() {
         super(...arguments);
         this.supportsSVG = true;
     }
-    makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
-        const { mafFilter, sources, features } = renderArgs;
-        const feats = [...features.values()];
-        const h = canvasHeight / sources.length;
-        const mafs = [];
-        for (const feat of feats) {
-            let c = 0;
-            let c2 = 0;
-            const samp = feat.get('genotypes');
-            if (feat.get('end') - feat.get('start') <= 10) {
-                for (const { name } of sources) {
-                    const s = samp[name];
-                    if (s === '0|0' || s === './.') {
-                        c2++;
-                    }
-                    else if (s === '1|0' || s === '0|1') {
-                        c++;
-                    }
-                    else if (s === '1|1') {
-                        c++;
-                        c2++;
-                    }
-                    else {
-                        c++;
-                    }
-                }
-                if (c / sources.length > mafFilter &&
-                    c2 / sources.length < 1 - mafFilter) {
-                    mafs.push(feat);
-                }
-            }
-        }
-        const w = canvasWidth / mafs.length;
-        for (let i = 0; i < mafs.length; i++) {
-            const f = mafs[i];
-            if (f.get('end') - f.get('start') <= 10) {
-                const samp = f.get('genotypes');
-                const x = (i / mafs.length) * canvasWidth;
-                for (let j = 0; j < sources.length; j++) {
-                    const y = (j / sources.length) * canvasHeight;
-                    const { name } = sources[j];
-                    ctx.fillStyle = (0, util_2.getCol)(samp[name]);
-                    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
-                }
-            }
-        }
-        return { mafs };
-    }
     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 { mafs, ...res } = await (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => {
-            return this.makeImageData({
-                ctx,
-                canvasWidth: width,
-                canvasHeight: height,
-                renderArgs: {
-                    ...renderProps,
-                    features,
-                    sources,
-                },
-            });
-        });
+        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,

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

@@ -1,6 +1,7 @@
-import React from 'react';
 declare const LinearVariantMatrixRendering: (props: {
     width: number;
     height: number;
-}) => React.JSX.Element;
+    displayModel: any;
+    arr: string[];
+}) => import("react/jsx-runtime").JSX.Element;
 export default LinearVariantMatrixRendering;