@jbrowse/plugin-variants 2.16.1 → 2.18.0

package/esm/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/esm/MultiLinearVariantMatrixDisplay/model.js

@@ -0,0 +1,189 @@
+import { lazy } from 'react';
+import { ConfigurationReference } from '@jbrowse/core/configuration';
+import { set1 } from '@jbrowse/core/ui/colors';
+import { getSession } from '@jbrowse/core/util';
+import { stopStopToken } from '@jbrowse/core/util/stopToken';
+import { linearBareDisplayStateModelFactory } from '@jbrowse/plugin-linear-genome-view';
+import deepEqual from 'fast-deep-equal';
+import { isAlive, types } from 'mobx-state-tree';
+import { randomColor } from '../util';
+const SetColorDialog = lazy(() => import('../shared/SetColorDialog'));
+const MAFFilterDialog = lazy(() => import('../shared/MAFFilterDialog'));
+const ClusterDialog = lazy(() => import('../shared/ClusterDialog'));
+export default function stateModelFactory(configSchema) {
+    return types
+        .compose('LinearVariantMatrixDisplay', linearBareDisplayStateModelFactory(configSchema), types.model({
+        type: types.literal('LinearVariantMatrixDisplay'),
+        layout: types.optional(types.frozen(), []),
+        configuration: ConfigurationReference(configSchema),
+        mafFilter: types.optional(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) {
+                stopStopToken(self.sourcesLoadingStopToken);
+            }
+            self.sourcesLoadingStopToken = str;
+        },
+        setSources(sources) {
+            if (!deepEqual(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 || set1[i] || 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: () => {
+                            getSession(self).queueDialog(handleClose => [
+                                MAFFilterDialog,
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
+                            ]);
+                        },
+                    },
+                    {
+                        label: 'Cluster by genotype',
+                        onClick: () => {
+                            getSession(self).queueDialog(handleClose => [
+                                ClusterDialog,
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
+                            ]);
+                        },
+                    },
+                    {
+                        label: 'Edit colors/arrangement...',
+                        onClick: () => {
+                            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 import('../getMultiVariantSourcesAutorun');
+                        const { getMultiVariantFeaturesAutorun } = await import('../getMultiVariantFeaturesAutorun');
+                        getMultiVariantSourcesAutorun(self);
+                        getMultiVariantFeaturesAutorun(self);
+                    }
+                    catch (e) {
+                        if (isAlive(self)) {
+                            console.error(e);
+                            getSession(self).notifyError(`${e}`, e);
+                        }
+                    }
+                })();
+            },
+            async renderSvg(opts) {
+                const { renderSvg } = await import('./renderSvg');
+                return renderSvg(self, opts, superRenderSvg);
+            },
+        };
+    });
+}

package/esm/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>;

package/esm/MultiLinearVariantMatrixDisplay/renderSvg.js

@@ -0,0 +1,15 @@
+import React from 'react';
+import { getContainingView } from '@jbrowse/core/util';
+import { when } from 'mobx';
+import LegendBar from '../shared/LegendBar';
+import LinesConnectingMatrixToGenomicPosition from './components/LinesConnectingMatrixToGenomicPosition';
+export async function renderSvg(model, opts, superRenderSvg) {
+    await when(() => !!model.regionCannotBeRenderedText);
+    const { offsetPx } = getContainingView(model);
+    return (React.createElement(React.Fragment, null,
+        React.createElement("g", { transform: `translate(${Math.max(-offsetPx, 0)})` },
+            React.createElement(LinesConnectingMatrixToGenomicPosition, { exportSVG: true, model: model }),
+            React.createElement("g", { transform: `translate(0,${model.lineZoneHeight})` },
+                React.createElement("g", null, await superRenderSvg(opts)),
+                React.createElement(LegendBar, { model: model, orientation: "left", exportSVG: true })))));
+}

package/esm/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.d.ts

@@ -0,0 +1,62 @@
+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 { 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;
+        height: number;
+        width: number;
+        canvasRecordedData: any;
+        layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
+        reactElement?: import("react").ReactElement;
+        html?: string;
+    } | {
+        features: Map<any, any>;
+        simplifiedFeatures: any;
+        height: number;
+        width: number;
+        reactElement: React.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?: import("react").ReactElement;
+        html?: string;
+    }>;
+}
+export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';

package/esm/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.js

@@ -0,0 +1,100 @@
+import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { SimpleFeature, renderToAbstractCanvas } from '@jbrowse/core/util';
+import { getCol } from '../util';
+const fudgeFactor = 0.6;
+const f2 = fudgeFactor / 2;
+export default class LinearVariantMatrixRenderer extends BoxRendererType {
+    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 = 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 renderToAbstractCanvas(width, height, renderProps, ctx => {
+            return this.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 SimpleFeature({
+                id: s.id(),
+                data: {
+                    start: s.get('start'),
+                    end: s.get('end'),
+                    refName: s.get('refName'),
+                },
+            })),
+            height,
+            width,
+        };
+    }
+}

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

@@ -0,0 +1,6 @@
+import React from 'react';
+declare const LinearVariantMatrixRendering: (props: {
+    width: number;
+    height: number;
+}) => React.JSX.Element;
+export default LinearVariantMatrixRendering;

package/esm/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.js

@@ -0,0 +1,7 @@
+import React from 'react';
+import { PrerenderedCanvas } from '@jbrowse/core/ui';
+import { observer } from 'mobx-react';
+const LinearVariantMatrixRendering = observer(function (props) {
+    return React.createElement(PrerenderedCanvas, { ...props });
+});
+export default LinearVariantMatrixRendering;

package/esm/MultiLinearVariantMatrixRenderer/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const LinearVariantMatrixRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default LinearVariantMatrixRenderer;

package/esm/MultiLinearVariantMatrixRenderer/configSchema.js

@@ -0,0 +1,4 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+function x() { }
+const LinearVariantMatrixRenderer = ConfigurationSchema('LinearVariantMatrixRenderer', {}, { explicitlyTyped: true });
+export default LinearVariantMatrixRenderer;

package/esm/MultiLinearVariantMatrixRenderer/index.d.ts

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