@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/esm/LinearPileupDisplay/model.d.ts

@@ -0,0 +1,332 @@
+/// <reference types="react" />
+import { Instance } from 'mobx-state-tree';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { Feature } from '@jbrowse/core/util';
+import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
+import { LinearPileupDisplayConfigModel } from './configSchema';
+declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel) => 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>>;
+} & {
+    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        region: import("mobx-state-tree").IModelType<{
+            refName: import("mobx-state-tree").ISimpleType<string>;
+            start: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        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>;
+    }, {
+        renderInProgress: AbortController | undefined;
+        filled: boolean;
+        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        features: Map<string, Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: any;
+        }) => any;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(abortController: AbortController): void;
+        setMessage(messageText: string): void;
+        setRendered(props: {
+            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            features: Map<string, Feature>;
+            layout: any;
+            maxHeightReached: boolean;
+            renderProps: any;
+        } | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    showSoftClipping: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    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>>;
+    mismatchAlpha: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    sortedBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+        type: import("mobx-state-tree").ISimpleType<string>;
+        pos: import("mobx-state-tree").ISimpleType<number>;
+        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        refName: import("mobx-state-tree").ISimpleType<string>;
+        assemblyName: import("mobx-state-tree").ISimpleType<string>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+        type: import("mobx-state-tree").ISimpleType<string>;
+        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        extra: import("mobx-state-tree").IType<any, any, any>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            tag: import("mobx-state-tree").ISimpleType<string>;
+            value: import("mobx-state-tree").ISimpleType<string>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+} & {
+    readonly RenderingComponent: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+        } & 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;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+        } & 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;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }> | null;
+    readonly adapterConfig: any;
+    readonly parentTrack: any;
+    renderProps(): any;
+    readonly rendererType: any;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): undefined;
+} & {
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    currBpPerPx: number;
+    message: string;
+    featureIdUnderMouse: string | undefined;
+    contextMenuFeature: Feature | undefined;
+    scrollTop: number;
+    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+} & {
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
+} & {
+    readonly renderDelay: number;
+    readonly TooltipComponent: import("react").FC<any>;
+    readonly selectedFeatureId: string | undefined;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+} & {
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
+    readonly featureUnderMouse: Feature | undefined;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
+    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly estimatedStatsReady: boolean;
+    readonly maxAllowableBytes: number;
+} & {
+    setMessage(message: string): void;
+    afterAttach(): void;
+    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
+        headers?: Record<string, string> | undefined;
+        signal?: AbortSignal | undefined;
+        filters?: string[] | undefined;
+    }): Promise<{}>;
+    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
+    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    clearRegionStats(): void;
+    setHeight(displayHeight: number): number;
+    resizeHeight(distance: number): number;
+    setScrollTop(scrollTop: number): void;
+    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
+    setCurrBpPerPx(n: number): void;
+    deleteBlock(key: string): void;
+    selectFeature(feature: Feature): void;
+    clearFeatureSelection(): void;
+    setFeatureIdUnderMouse(feature: string | undefined): void;
+    reload(): void;
+    setContextMenuFeature(feature?: Feature | undefined): void;
+} & {
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    reload(): Promise<void>;
+    afterAttach(): void;
+} & {
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    contextMenuItems(): {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+    }[];
+    renderProps(): any;
+} & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
+        overrideHeight: number;
+    }): Promise<JSX.Element>;
+} & {
+    colorTagMap: import("mobx").ObservableMap<string, string>;
+    modificationTagMap: import("mobx").ObservableMap<string, string>;
+    featureUnderMouseVolatile: Feature | undefined;
+    ready: boolean;
+} & {
+    setReady(flag: boolean): void;
+    setMaxHeight(n: number): void;
+    setFeatureHeight(n: number): void;
+    setNoSpacing(flag: boolean): void;
+    setColorScheme(colorScheme: {
+        type: string;
+        tag?: string;
+    }): void;
+    updateModificationColorMap(uniqueModifications: string[]): void;
+    updateColorTagMap(uniqueTag: string[]): void;
+    setFeatureUnderMouse(feat?: Feature): void;
+} & {
+    afterAttach(): void;
+    selectFeature(feature: Feature): void;
+    clearSelected(): void;
+    copyFeatureToClipboard(feature: Feature): void;
+    toggleSoftClipping(): void;
+    toggleMismatchAlpha(): void;
+    setConfig(configuration: AnyConfigurationModel): void;
+    setSortedBy(type: string, tag?: string): void;
+    setFilterBy(filter: {
+        flagInclude: number;
+        flagExclude: number;
+        readName?: string;
+        tagFilter?: {
+            tag: string;
+            value: string;
+        };
+    }): void;
+} & {
+    reload(): void;
+} & {
+    readonly maxHeight: any;
+    readonly rendererConfig: any;
+    readonly featureHeightSetting: any;
+    readonly mismatchAlphaSetting: any;
+    readonly featureUnderMouse: Feature | undefined;
+} & {
+    readonly rendererTypeName: string;
+    contextMenuItems(): {
+        label: string;
+        icon: typeof ContentCopyIcon;
+        onClick: () => void;
+    }[];
+    readonly DisplayBlurb: (props: import("./components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => JSX.Element | null;
+    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;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        type: string;
+        checked: boolean;
+        onClick: () => void;
+        disabled?: undefined;
+        subMenu?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        disabled: boolean;
+        subMenu: {
+            label: string;
+            onClick: () => void;
+        }[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        subMenu: {
+            label: string;
+            onClick: () => void;
+        }[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
+        disabled?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+        type?: undefined;
+        checked?: undefined;
+        disabled?: undefined;
+        subMenu?: undefined;
+    } | {
+        label: string;
+        type: string;
+        checked: any;
+        onClick: () => void;
+        icon?: undefined;
+        disabled?: undefined;
+        subMenu?: undefined;
+    })[];
+}, import("mobx-state-tree")._NotCustomized, {
+    type: string;
+    height: number;
+    id: string;
+    rpcDriverName: string | undefined;
+    userBpPerPxLimit: number | undefined;
+    userByteSizeLimit: number | undefined;
+} & import("mobx-state-tree")._NotCustomized>;
+export declare type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
+export declare type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>;
+export default stateModelFactory;