@jbrowse/plugin-alignments 3.7.0 → 4.0.1

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -1,409 +0,0 @@
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import type { ColorBy, FilterBy } from '../shared/types';
-import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import type { Feature } from '@jbrowse/core/util';
-export declare function SharedLinearPileupDisplayMixin(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-runtime").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">>;
-} & {
-    configuration: AnyConfigurationSchemaType;
-    featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
-    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
-    jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
-    hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<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-runtime").JSX.Element | null;
-} & {
-    mouseoverExtraInformation: string | undefined;
-    featureIdUnderMouse: undefined | string;
-    contextMenuFeature: undefined | Feature;
-} & {
-    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;
-    copyInfoToClipboard(feature: Feature): void;
-} & {
-    readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
-    readonly featureUnderMouse: Feature | undefined;
-    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
-        label?: string;
-        description?: string;
-        refName: string;
-    }]>;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
-        label?: string;
-        description?: string;
-        refName: string;
-    }]) | undefined;
-    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
-        label?: string;
-        description?: string;
-        refName: string;
-    }]) | 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;
-    setMouseoverExtraInformation(extra?: string): void;
-} & {
-    reload(): Promise<void>;
-} & {
-    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    renderProps(): any;
-} & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
-    afterAttach(): void;
-} & {
-    colorTagMap: import("mobx").ObservableMap<string, string>;
-    featureUnderMouseVolatile: undefined | Feature;
-    tagsReady: boolean;
-} & {
-    readonly colorBy: any;
-    readonly filterBy: any;
-} & {
-    readonly autorunReady: boolean;
-    readonly hideSmallIndels: boolean | undefined;
-} & {
-    setTagsReady(flag: boolean): void;
-    setMaxHeight(n?: number): void;
-    setFeatureHeight(n?: number): void;
-    setNoSpacing(flag?: boolean): void;
-    setColorScheme(colorScheme: ColorBy): void;
-    updateColorTagMap(uniqueTag: string[]): void;
-    setFeatureUnderMouse(feat?: Feature): void;
-    selectFeature(feature: Feature): void;
-    setConfig(conf: AnyConfigurationModel): void;
-    setFilterBy(filter: FilterBy): void;
-    setJexlFilters(filters: string[]): void;
-    setHideSmallIndels(arg: boolean): void;
-} & {
-    copyFeatureToClipboard(feature: Feature): 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 maxHeight: any;
-    readonly featureHeightSetting: any;
-    readonly featureUnderMouse: Feature | undefined;
-    renderReady(): boolean;
-    readonly filters: SerializableFilterChain;
-} & {
-    readonly rendererTypeName: string;
-    contextMenuItems(): {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    }[];
-    readonly DisplayBlurb: ({ model, }: {
-        model: {
-            sortedBy?: import("../shared/types").SortedBy;
-        };
-    }) => import("react/jsx-runtime").JSX.Element | null;
-    renderPropsPre(): any;
-    colorSchemeSubMenuItems(): {
-        label: string;
-        onClick: () => void;
-    }[];
-    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;
-        priority: number;
-        type: string;
-        checked: boolean | undefined;
-        onClick: () => void;
-        icon?: undefined;
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-        priority?: undefined;
-        type?: undefined;
-        checked?: undefined;
-    })[];
-} & {
-    renderProps(): any;
-} & {
-    afterAttach(): void;
-}, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    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-runtime").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">>;
-} & {
-    configuration: AnyConfigurationSchemaType;
-    featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
-    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
-    jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
-    hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-}>>, {
-    id: string;
-    type: string;
-    configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
-    rpcDriverName: string | undefined;
-    heightPreConfig: number | undefined;
-    userBpPerPxLimit: number | undefined;
-    userByteSizeLimit: number | undefined;
-} & import("mobx-state-tree")._NotCustomized>;