@jbrowse/plugin-variants 4.0.4 → 4.1.3

package/esm/LDDisplay/shared.d.ts

@@ -0,0 +1,367 @@
+import type React from 'react';
+import type { LDFlatbushItem } from '../LDRenderer/types.ts';
+import type { FilterStats, LDMatrixResult } from '../VariantRPC/getLDMatrix.ts';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Instance } from '@jbrowse/mobx-state-tree';
+import type { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
+export default function sharedModelFactory(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>>>;
+}, {
+    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: LDFlatbushItem[];
+    snps: LDMatrixResult["snps"];
+    maxScore: number;
+    yScalar: number;
+    cellWidth: number;
+    error: Error | undefined;
+    filterStats: FilterStats | undefined;
+    recombination: {
+        values: number[];
+        positions: number[];
+    } | undefined;
+} & {
+    setFlatbushData(flatbush: ArrayBufferLike | undefined, items: LDFlatbushItem[], snps: 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: 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: 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 SharedLDStateModel = ReturnType<typeof sharedModelFactory>;
+export type SharedLDModel = Instance<SharedLDStateModel>;