@jbrowse/plugin-variants 4.0.4 → 4.1.3

package/esm/LDDisplay/stateModel2.d.ts

@@ -0,0 +1,365 @@
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Instance } from '@jbrowse/mobx-state-tree';
+export default function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+} & {
+    heightPreConfig: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+} & {
+    configuration: AnyConfigurationSchemaType;
+    minorAlleleFrequencyFilterSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    lengthCutoffFilterSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    lineZoneHeightSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    ldMetricSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    colorSchemeSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    showLegendSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    showLDTriangleSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    showRecombinationSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    recombinationZoneHeightSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    fitToHeightSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    hweFilterThresholdSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    callRateFilterSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    showVerticalGuidesSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    showLabelsSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    tickHeightSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    useGenomicPositionsSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    signedLDSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    jexlFiltersSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
+} & {
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"LDTrackDisplay">;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+    statusMessage: string | undefined;
+} & {
+    readonly RenderingComponent: React.FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: () => void;
+        blockState?: Record<string, any>;
+    }>;
+    readonly DisplayBlurb: React.FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }> | null;
+    readonly adapterConfig: any;
+    readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
+    readonly parentDisplay: any;
+    readonly effectiveRpcDriverName: any;
+} & {
+    renderProps(): any;
+    renderingProps(): {
+        displayModel: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & {
+            readonly RenderingComponent: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: () => void;
+                blockState?: Record<string, any>;
+            }>;
+            readonly DisplayBlurb: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
+            readonly parentDisplay: any;
+            readonly effectiveRpcDriverName: any;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & {
+            readonly RenderingComponent: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: () => void;
+                blockState?: Record<string, any>;
+            }>;
+            readonly DisplayBlurb: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
+            readonly parentDisplay: any;
+            readonly effectiveRpcDriverName: any;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    };
+    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;
+} & {
+    setStatusMessage(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;
+} & {
+    loading: boolean;
+    lastDrawnOffsetPx: number | undefined;
+    lastDrawnBpPerPx: number | undefined;
+    ref: HTMLCanvasElement | null;
+    renderingImageData: ImageBitmap | undefined;
+    renderingStopToken: import("@jbrowse/core/util").StopToken | undefined;
+    statusMessage: string | undefined;
+    canvasDrawn: boolean;
+} & {
+    readonly drawn: boolean;
+    readonly fullyDrawn: boolean;
+} & {
+    setLastDrawnOffsetPx(n: number): void;
+    setLastDrawnBpPerPx(n: number): void;
+    setLoading(f: boolean): void;
+    setRef(ref: HTMLCanvasElement | null): void;
+    setRenderingImageData(imageData: ImageBitmap | undefined): void;
+    setRenderingStopToken(token?: import("@jbrowse/core/util").StopToken): void;
+    setStatusMessage(msg?: string): void;
+    setCanvasDrawn(drawn: boolean): void;
+} & {
+    beforeDestroy(): void;
+} & {
+    flatbush: ArrayBufferLike | undefined;
+    flatbushItems: import("../LDRenderer/types.ts").LDFlatbushItem[];
+    snps: import("../VariantRPC/getLDMatrix.ts").LDMatrixResult["snps"];
+    maxScore: number;
+    yScalar: number;
+    cellWidth: number;
+    error: Error | undefined;
+    filterStats: import("../VariantRPC/getLDMatrix.ts").FilterStats | undefined;
+    recombination: {
+        values: number[];
+        positions: number[];
+    } | undefined;
+} & {
+    setFlatbushData(flatbush: ArrayBufferLike | undefined, items: import("../LDRenderer/types.ts").LDFlatbushItem[], snps: import("../VariantRPC/getLDMatrix.ts").LDMatrixResult["snps"], maxScore: number, yScalar: number, cellWidth: number): void;
+    setLineZoneHeight(n: number): void;
+    setError(error: unknown): void;
+    reload(): void;
+    setMafFilter(arg: number): void;
+    setLengthCutoffFilter(arg: number): void;
+    setLDMetric(metric: string): void;
+    setColorScheme(scheme: string | undefined): void;
+    setShowLegend(show: boolean): void;
+    setShowLDTriangle(show: boolean): void;
+    setShowRecombination(show: boolean): void;
+    setRecombinationZoneHeight(n: number): void;
+    setFitToHeight(value: boolean): void;
+    setHweFilter(threshold: number): void;
+    setCallRateFilter(threshold: number): void;
+    setFilterStats(stats: import("../VariantRPC/getLDMatrix.ts").FilterStats | undefined): void;
+    setRecombination(data: {
+        values: number[];
+        positions: number[];
+    } | undefined): void;
+    setShowVerticalGuides(show: boolean): void;
+    setShowLabels(show: boolean): void;
+    setTickHeight(height: number): void;
+    setUseGenomicPositions(value: boolean): void;
+    setSignedLD(value: boolean): void;
+    setJexlFilters(filters: string[] | undefined): void;
+} & {
+    readonly blockType: string;
+    readonly prefersOffset: boolean;
+    readonly rendererTypeName: string;
+    readonly rendererConfig: any;
+    readonly regionTooLarge: boolean;
+    readonly minorAlleleFrequencyFilter: any;
+    readonly lengthCutoffFilter: any;
+    readonly lineZoneHeight: any;
+    readonly ldMetric: any;
+    readonly colorScheme: any;
+    readonly showLegend: any;
+    readonly showLDTriangle: any;
+    readonly showRecombination: any;
+    readonly recombinationZoneHeight: any;
+    readonly fitToHeight: any;
+    readonly hweFilterThreshold: any;
+    readonly callRateFilter: any;
+    readonly showVerticalGuides: any;
+    readonly showLabels: any;
+    readonly tickHeight: any;
+    readonly useGenomicPositions: any;
+    readonly signedLD: any;
+    readonly jexlFilters: any;
+    readonly isPrecomputedLD: boolean;
+    regionCannotBeRendered(): null;
+} & {
+    readonly ldCanvasHeight: number;
+} & {
+    filterMenuItems(): {
+        label: string;
+        onClick: () => void;
+    }[];
+    renderProps(): 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;
+        subMenu: ({
+            label: string;
+            type: string;
+            checked: any;
+            onClick: () => void;
+            helpText?: undefined;
+        } | {
+            label: string;
+            helpText: string;
+            type: string;
+            checked: any;
+            onClick: () => void;
+        })[];
+    } | {
+        label: string;
+        type: string;
+        subMenu: {
+            label: string;
+            onClick: () => void;
+        }[];
+    })[];
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<React.ReactNode>;
+} & {
+    afterAttach(): void;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+} & {
+    heightPreConfig: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+} & {
+    configuration: AnyConfigurationSchemaType;
+    minorAlleleFrequencyFilterSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    lengthCutoffFilterSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    lineZoneHeightSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    ldMetricSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    colorSchemeSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    showLegendSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    showLDTriangleSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    showRecombinationSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    recombinationZoneHeightSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    fitToHeightSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    hweFilterThresholdSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    callRateFilterSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    showVerticalGuidesSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    showLabelsSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    tickHeightSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    useGenomicPositionsSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    signedLDSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    jexlFiltersSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
+}>>;
+export type LDTrackDisplayStateModel = ReturnType<typeof stateModelFactory>;
+export type LDTrackDisplayModel = Instance<LDTrackDisplayStateModel>;

package/esm/LDDisplay/stateModel2.js

@@ -0,0 +1,10 @@
+import { types } from '@jbrowse/mobx-state-tree';
+import sharedModelFactory from "./shared.js";
+function x() { }
+export default function stateModelFactory(configSchema) {
+    return sharedModelFactory(configSchema)
+        .named('LDTrackDisplay')
+        .props({
+        type: types.literal('LDTrackDisplay'),
+    });
+}

package/esm/LDRenderer/LDRenderer.d.ts

@@ -0,0 +1,30 @@
+import ServerSideRendererType from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
+import type { LDMatrixResult, LDMetric } from '../VariantRPC/getLDMatrix.ts';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { RenderArgsDeserialized as ServerSideRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
+import type { Region } from '@jbrowse/core/util/types';
+export interface RenderArgsDeserialized extends ServerSideRenderArgsDeserialized {
+    regions: Region[];
+    bpPerPx: number;
+    highResolutionScaling: number;
+    adapterConfig: AnyConfigurationModel;
+    displayHeight?: number;
+    ldMetric?: LDMetric;
+    minorAlleleFrequencyFilter?: number;
+    lengthCutoffFilter?: number;
+    hweFilterThreshold?: number;
+    callRateFilter?: number;
+    jexlFilters?: string[];
+    colorScheme?: string;
+    fitToHeight?: boolean;
+    useGenomicPositions?: boolean;
+    signedLD?: boolean;
+}
+export interface RenderArgsDeserializedWithLDData extends RenderArgsDeserialized {
+    ldData: LDMatrixResult;
+}
+export default class LDRenderer extends ServerSideRendererType {
+    supportsSVG: boolean;
+    render(renderProps: RenderArgsDeserialized): Promise<import("librpc-web-mod").RpcResult>;
+    getLDData(args: RenderArgsDeserialized): Promise<LDMatrixResult | null>;
+}

package/esm/LDRenderer/LDRenderer.js

@@ -0,0 +1,109 @@
+import ServerSideRendererType from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
+import { rpcResult } from '@jbrowse/core/util/librpc';
+import { collectTransferables } from '@jbrowse/core/util/offscreenCanvasPonyfill';
+import { renderToAbstractCanvas } from '@jbrowse/core/util/offscreenCanvasUtils';
+import { getLDMatrix } from "../VariantRPC/getLDMatrix.js";
+import { getLDMatrixFromPlink } from "../VariantRPC/getLDMatrixFromPlink.js";
+export default class LDRenderer extends ServerSideRendererType {
+    supportsSVG = true;
+    async render(renderProps) {
+        const { displayHeight, regions, bpPerPx, ldMetric = 'r2', fitToHeight = false, useGenomicPositions = false, signedLD = false, } = renderProps;
+        let totalWidthBp = 0;
+        for (const region of regions) {
+            totalWidthBp += region.end - region.start;
+        }
+        const width = totalWidthBp / bpPerPx;
+        const hyp = width / 2;
+        const height = fitToHeight ? (displayHeight ?? hyp) : hyp;
+        const matrixHeight = height;
+        const ldData = await this.getLDData(renderProps);
+        if (!ldData || ldData.snps.length === 0) {
+            const res = await renderToAbstractCanvas(width, height, renderProps, ctx => {
+                ctx.fillStyle = '#666';
+                ctx.font = '12px sans-serif';
+                ctx.textAlign = 'center';
+                ctx.fillText('No variants in view (try adjusting MAF filter or zooming in)', width / 2, height / 2);
+                return undefined;
+            });
+            return rpcResult({
+                ...res,
+                height,
+                width,
+                ldData: null,
+                filterStats: ldData?.filterStats,
+            }, collectTransferables(res));
+        }
+        const yScalar = fitToHeight ? matrixHeight / hyp : 1;
+        const { makeImageData } = await import("./makeImageData.js");
+        const res = await renderToAbstractCanvas(width, height, renderProps, ctx => {
+            return makeImageData(ctx, {
+                ldData,
+                regions,
+                bpPerPx,
+                stopTokenCheck: renderProps.stopTokenCheck,
+                yScalar,
+                useGenomicPositions,
+                signedLD,
+            });
+        });
+        const serialized = {
+            ...res,
+            height,
+            width,
+            yScalar,
+            ldMetric,
+            signedLD,
+            ldData: {
+                snps: ldData.snps,
+                metric: ldData.metric,
+                numValues: ldData.ldValues.length,
+            },
+            filterStats: ldData.filterStats,
+            recombination: {
+                values: Array.from(ldData.recombination.values),
+                positions: ldData.recombination.positions,
+            },
+        };
+        return rpcResult(serialized, collectTransferables(serialized));
+    }
+    async getLDData(args) {
+        const { regions, sessionId, adapterConfig, bpPerPx, ldMetric = 'r2', minorAlleleFrequencyFilter = 0.01, lengthCutoffFilter = Number.MAX_SAFE_INTEGER, hweFilterThreshold = 0.001, callRateFilter = 0, jexlFilters = [], signedLD = false, stopTokenCheck, } = args;
+        try {
+            const adapterType = adapterConfig.type;
+            if (adapterType === 'PlinkLDAdapter' ||
+                adapterType === 'PlinkLDTabixAdapter' ||
+                adapterType === 'LdmatAdapter') {
+                return await getLDMatrixFromPlink({
+                    pluginManager: this.pluginManager,
+                    args: {
+                        regions,
+                        sessionId,
+                        adapterConfig,
+                        ldMetric,
+                    },
+                });
+            }
+            return await getLDMatrix({
+                pluginManager: this.pluginManager,
+                args: {
+                    regions,
+                    sessionId,
+                    adapterConfig,
+                    bpPerPx,
+                    ldMetric,
+                    minorAlleleFrequencyFilter,
+                    lengthCutoffFilter,
+                    hweFilterThreshold,
+                    callRateFilter,
+                    jexlFilters,
+                    signedLD,
+                    stopTokenCheck,
+                },
+            });
+        }
+        catch (e) {
+            console.error('Error computing LD matrix:', e);
+            throw e;
+        }
+    }
+}

package/esm/LDRenderer/components/LDRendering.d.ts

@@ -0,0 +1,2 @@
+declare const LDRendering: () => null;
+export default LDRendering;

package/esm/LDRenderer/components/LDRendering.js

@@ -0,0 +1,4 @@
+const LDRendering = function LDRendering() {
+    return null;
+};
+export default LDRendering;

package/esm/LDRenderer/configSchema.d.ts

@@ -0,0 +1,8 @@
+declare const LDRenderer: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    maxHeight: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default LDRenderer;

package/esm/LDRenderer/configSchema.js

@@ -0,0 +1,10 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+function x() { }
+const LDRenderer = ConfigurationSchema('LDRenderer', {
+    maxHeight: {
+        type: 'integer',
+        description: 'the maximum height to be used in LD rendering',
+        defaultValue: 600,
+    },
+}, { explicitlyTyped: true });
+export default LDRenderer;

package/esm/LDRenderer/index.d.ts

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

package/esm/LDRenderer/index.js

@@ -0,0 +1,11 @@
+import { lazy } from 'react';
+import LDRenderer from "./LDRenderer.js";
+import configSchema from "./configSchema.js";
+export default function LDRendererF(pluginManager) {
+    pluginManager.addRendererType(() => new LDRenderer({
+        name: 'LDRenderer',
+        ReactComponent: lazy(() => import("./components/LDRendering.js")),
+        configSchema,
+        pluginManager,
+    }));
+}

package/esm/LDRenderer/makeImageData.d.ts

@@ -0,0 +1,20 @@
+import type { LDFlatbushItem } from './types.ts';
+import type { LDMatrixResult } from '../VariantRPC/getLDMatrix.ts';
+import type { LastStopTokenCheck, Region } from '@jbrowse/core/util';
+export interface MakeImageDataResult {
+    flatbush: ArrayBufferLike;
+    items: LDFlatbushItem[];
+    maxScore: number;
+    w: number;
+}
+export interface MakeImageDataProps {
+    ldData: LDMatrixResult;
+    regions: Region[];
+    bpPerPx: number;
+    stopTokenCheck?: LastStopTokenCheck;
+    yScalar: number;
+    colorScheme?: string;
+    useGenomicPositions?: boolean;
+    signedLD?: boolean;
+}
+export declare function makeImageData(ctx: CanvasRenderingContext2D, props: MakeImageDataProps): MakeImageDataResult | undefined;