wuepgg3-track 1.0.2

package/dist/components/GenomeView/TrackComponents/geneAnnotationTrackComponents/GeneAnnotationScaffold.d.ts

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+import React from "react";
+import OpenInterval from "../../../../models/OpenInterval";
+import Gene from "../../../../models/Gene";
+import { GeneDisplayOptions } from "./GeneAnnotation";
+interface GeneAnnotationScaffoldProps {
+    gene: Gene;
+    xSpan: OpenInterval;
+    viewWindow?: OpenInterval;
+    y?: number;
+    isMinimal?: boolean;
+    options?: {
+        color?: string;
+        backgroundColor?: string;
+        italicizeText?: boolean;
+        hideMinimalItems?: boolean;
+    };
+    children: React.ReactNode;
+    onClick(event: React.MouseEvent, gene: Gene): void;
+}
+declare const GeneAnnotationScaffold: React.FC<GeneAnnotationScaffoldProps>;
+export default GeneAnnotationScaffold;
+export declare function getDrawColors(gene: Gene, options?: GeneDisplayOptions): {
+    color: any;
+    backgroundColor: string;
+    italicizeText: boolean;
+};

package/dist/components/GenomeView/TrackComponents/geneAnnotationTrackComponents/GeneDetail.d.ts

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+import React from "react";
+import Gene from "../../../../models/Gene";
+/**
+ * Box that contains gene details when a gene annotation is clicked.
+ *
+ * @author Silas Hsu
+ */
+interface GeneDetailProps {
+    gene: Gene;
+    collectionName: string;
+    queryEndpoint?: Record<string, any>;
+}
+/**
+ * Box that contains gene details when a gene annotation is clicked.
+ *
+ * @author Silas Hsu
+ */
+declare const GeneDetail: React.FC<GeneDetailProps>;
+export default GeneDetail;

package/dist/components/GenomeView/TrackComponents/geneAnnotationTrackComponents/TranslatableG.d.ts

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+import { SVGProps } from "react";
+interface TranslatableGProps extends SVGProps<SVGGElement> {
+    x?: number;
+    y?: number;
+    innerRef?(element: SVGGElement): void;
+}
+/**
+ * Ever wish <g> elements accepted `x` and `y` attributes?  This one does!
+ *
+ * @param {TranslatableGProps} props - props as specified by React
+ * @return {JSX.Element} - <g> element
+ * @author Silas Hsu
+ */
+export declare function TranslatableG(props: TranslatableGProps): import("react/jsx-runtime").JSX.Element;
+export {};

package/dist/components/GenomeView/TrackComponents/imageTrackComponents/OmeroHtmlVisualizer.d.ts

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+import React from "react";
+import OpenInterval from "../../../../models/OpenInterval";
+import TrackModel from "../../../../models/TrackModel";
+interface ObjectAsTableProps {
+    title?: string;
+    content: any;
+}
+interface OmeroHtmlVisualizerProps {
+    options?: any;
+    data: {
+        images: {
+            imageId: string;
+        }[];
+    }[];
+    viewWindow: OpenInterval;
+    trackModel: TrackModel;
+    imageAspectRatio: number;
+    layout?: any;
+    layoutModel: any;
+    thumbnailHeight: any;
+    height: any;
+    onSetImageInfo: any;
+    onSetLayout?: (layout: any) => void;
+    onShowTooltip?: (tooltip: React.ReactNode) => void;
+    onHideTooltip?: () => void;
+    isThereG3dTrack: boolean;
+}
+export declare function ObjectAsTable(props: ObjectAsTableProps): import("react/jsx-runtime").JSX.Element;
+declare class OmeroHtmlVisualizer extends React.PureComponent<OmeroHtmlVisualizerProps> {
+    static propTypes: {
+        options: any;
+        data: any;
+        viewWindow: any;
+        trackModel: any;
+        imageAspectRatio: any;
+    };
+    newPanelWithImage: (imageId: string, imageUrl: string, imageUrlSuffix: string, detailUrl: string) => void;
+    renderTooltip: (event: React.MouseEvent, imgHash: Record<string, any>, imgId: string, imageUrl: string, imageUrlSuffix: string, detailUrl: string) => void;
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export default OmeroHtmlVisualizer;

package/dist/components/GenomeView/TrackComponents/imageTrackComponents/OmeroSvgVisualizer.d.ts

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+import React from "react";
+export declare const MAX_NUMBER_THUMBNAILS = 384;
+export declare const THUMBNAIL_PADDING = 2;
+export declare const CORS_PROXY = "https://epigenome.wustl.edu/cors";
+interface ImageProperties {
+    viewWindow: any;
+    width: number;
+    height: number;
+    thumbnailHeight: number;
+    imageAspectRatio: number;
+    data: any;
+    trackModel: any;
+}
+interface ComponentState {
+    imageData: any[];
+    isLoading: boolean;
+}
+export declare class OmeroSvgVisualizer extends React.PureComponent<ImageProperties, ComponentState> {
+    static propTypes: {
+        options: any;
+        data: any;
+        viewWindow: any;
+        width: any;
+        trackModel: any;
+        imageAspectRatio: any;
+    };
+    constructor(props: any);
+    componentDidMount(): Promise<void>;
+    componentDidUpdate(prevProps: any, prevState: any, snapshot: any): Promise<void>;
+    fetchAllImage: () => Promise<void>;
+    fetchImageData: (imgId: any) => Promise<any>;
+    getBase64: (url: string) => Promise<string>;
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export {};

package/dist/components/GenomeView/TrackComponents/imageTrackComponents/OmeroTrackComponents.d.ts

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+import React from "react";
+export declare const MAX_NUMBER_THUMBNAILS = 384;
+export declare const THUMBNAIL_PADDING = 2;
+export declare const DEFAULT_OPTIONS: {
+    imageHeight: number[];
+    backgroundColor: string;
+    fetchViewWindowOnly: boolean;
+    imageAspectRatio: number;
+    displayMode: string;
+    height: number;
+};
+interface OmeroTrackProps {
+    data: {
+        images: any[];
+    }[];
+    options: typeof DEFAULT_OPTIONS;
+    viewWindow: {
+        start: number;
+        end: number;
+    };
+    trackModel: any;
+    forceSvg: boolean;
+    width: number;
+    layoutModel: any;
+    isThereG3dTrack: boolean;
+    onSetImageInfo: any;
+    heightObj: any;
+}
+declare class OmeroTrackComponents extends React.PureComponent<OmeroTrackProps> {
+    constructor(props: OmeroTrackProps);
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export default OmeroTrackComponents;

package/dist/components/GenomeView/TrackManager.d.ts

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+import DisplayedRegionModel from "../../models/DisplayedRegionModel";
+import TrackModel from "../../models/TrackModel";
+import React from "react";
+import { GenomeConfig } from "../../models/genomes/GenomeConfig";
+import { ITrackModel } from "../../types";
+export declare const convertTrackModelToITrackModel: (track: TrackModel) => ITrackModel;
+export declare function objToInstanceAlign(alignment: {
+    [key: string]: any;
+}): DisplayedRegionModel;
+export declare function bpNavToGenNav(bpNaletr: Array<any>, genome: GenomeConfig): any[];
+interface TrackManagerProps {
+    windowWidth: number;
+    legendWidth: number;
+    userViewRegion?: any;
+    genomeConfig: any;
+    highlights: Array<any>;
+    tracks: Array<TrackModel>;
+    onNewRegion: (startbase: number, endbase: number) => void | undefined;
+    onNewHighlight: (highlightState: Array<any>) => void;
+    onTrackSelected: (trackSelected: TrackModel[]) => void;
+    onTrackDeleted: (currenTracks: TrackModel[]) => void;
+    onNewRegionSelect: (startbase: number, endbase: number, highlightSearch: boolean) => void;
+    tool: any;
+    viewRegion?: any;
+    showGenomeNav: boolean;
+    setScreenshotData: any;
+    isScreenShotOpen: boolean;
+    selectedRegionSet: any;
+}
+declare const _default: React.NamedExoticComponent<TrackManagerProps>;
+export default _default;

package/dist/components/GenomeView/genomeNavigator/Chromosomes.d.ts

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+import React from "react";
+import DisplayedRegionModel from "../../../models/DisplayedRegionModel";
+import { FeaturePlacer } from "../../../models/getXSpan/FeaturePlacer";
+import TwoBitSource from "../../../getRemoteData/TwoBitSource";
+/**
+ * Draws rectangles that represent features in a navigation context, and labels for the features.  Called "Chromosomes"
+ * because at first, NavigationContexts only held chromosomes as features.
+ *
+ * @author Silas Hsu and Daofeng Li
+ */
+interface ChromosomesProps {
+    genomeConfig: any;
+    viewRegion: DisplayedRegionModel;
+    width: number;
+    labelOffset?: number;
+    x?: number;
+    y?: number;
+    drawHeights?: number[];
+    zeroLine?: number;
+    height?: number;
+    hideCytoband?: boolean;
+    minXwidthPerBase?: number;
+    hideChromName?: any;
+}
+interface ChromosomesState {
+    sequenceData: Array<any>;
+}
+declare class Chromosomes extends React.PureComponent<ChromosomesProps, ChromosomesState> {
+    static propTypes: {
+        genomeConfig: any;
+        viewRegion: any;
+        width: any;
+        labelOffset: any;
+        x: any;
+        y: any;
+        drawHeights: any;
+        zeroLine: any;
+        height: any;
+        hideCytoband: any;
+        minXwidthPerBase: any;
+    };
+    static defaultProps: {
+        minXwidthPerBase: number;
+        hideCytoband: boolean;
+    };
+    twoBitSource: TwoBitSource | null;
+    fastaSeq: any;
+    featurePlacer: FeaturePlacer;
+    constructor(props: any);
+    componentDidMount(): void;
+    /**
+     * Fetches sequence data for the view region stored in `props`, if zoomed in enough.
+     *
+     * @param {Object} props - props as specified by React
+     */
+    fetchSequence: (props: any) => Promise<void>;
+    /**
+     * If zoomed in enough, fetches sequence.
+     *
+     * @param {Object} nextProps - props as specified by React
+     */
+    componentDidUpdate(prevProps: any, prevState: any): void;
+    /**
+     *
+     * @param {*} cytoband
+     * @param {ChromosomeInterval} cytobandLocus
+     * @param {LinearDrawingModel} drawModel
+     */
+    renderOneCytoband(cytoband: any, cytobandLocus: any, drawModel: any): any[];
+    /**
+     * Gets the cytoband elements to draw within a genomic interval.
+     *
+     * @param {ChromosomeInterval} locus - genetic locus for which to draw cytobands
+     * @param {LinearDrawingModel} drawModel - draw model to use
+     * @return {JSX.Element[]} cytoband elements
+     */
+    renderCytobandsInLocus(locus: any, drawModel: any): any[];
+    /**
+     * Tries to find a label size that fits within `maxWidth`.  Returns `undefined` if it cannot find one.
+     *
+     * @param {string} label - the label contents
+     * @param {number} maxWidth - max requested width of the label
+     * @return {number | undefined} an appropriate width for the label, or undefined if there is none
+     */
+    getSizeForFeatureLabel(label: any, maxWidth: any): number | undefined;
+    renderSequences(): import("react/jsx-runtime").JSX.Element[];
+    /**
+     * Redraws all the feature boxes
+     *
+     * @override
+     */
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export default Chromosomes;

package/dist/components/GenomeView/genomeNavigator/DragAcrossDiv.d.ts

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+import React from "react";
+import { MouseButton } from "../../../models/util";
+export interface CoordinateDiff {
+    dx: number;
+    dy: number;
+}
+interface DragAcrossDivProps {
+    mouseButton: MouseButton | undefined;
+    style?: object;
+    children: React.ReactNode;
+    /**
+     * Callback for when dragging starts.
+     *
+     * @param {React.MouseEvent} event - the event that triggered this callback
+     */
+    onDragStart?(event: React.MouseEvent): void;
+    /**
+     * Callback for each little bit of movement during a drag.
+     *
+     * @param {React.MouseEvent} event - the event that triggered this callback
+     * @param {CoordinateDiff} coordinateDiff - how far the mouse has moved since the drag started
+     */
+    onDrag?(event: React.MouseEvent, coordinateDiff: CoordinateDiff): void;
+    /**
+     * Callback for when the user lets go of the mouse and stops dragging.
+     *
+     * @param {React.MouseEvent} event - the event that triggered this callback
+     * @param {CoordinateDiff} coordinateDiff - how far the mouse has moved since the drag started
+     */
+    onDragEnd?(event: React.MouseEvent, coordinateDiff: CoordinateDiff): void;
+}
+declare function doNothing(): void;
+/**
+ * A <div> that listens for drag-across events, where a user drags the cursor inside the div.  The drag callbacks will
+ * fire even for short clicks; be sure to take this possibility into account when working with this component!
+ *
+ * @author Silas Hsu
+ */
+export declare class DragAcrossDiv extends React.Component<DragAcrossDivProps> {
+    static defaultProps: {
+        onDragStart: typeof doNothing;
+        onDrag: typeof doNothing;
+        onDragEnd: typeof doNothing;
+    };
+    private originEvent;
+    constructor(props: DragAcrossDivProps);
+    /**
+     * Callback for mousedown events on the <div>.
+     *
+     * @param {React.MouseEvent} event - mouse event that triggered this callback
+     */
+    mousedown(event: React.MouseEvent): void;
+    /**
+     * Callback for mousemove events on the <div>.
+     *
+     * @param {React.MouseEvent} event - mouse event that triggered this callback
+     */
+    mousemove(event: React.MouseEvent): void;
+    /**
+     * Callback for mouseup events on the <div>.
+     *
+     * @param {React.MouseEvent} event - mouse event that triggered this callback
+     */
+    mouseup(event: React.MouseEvent): void;
+    /**
+     * @return {JSX.Element} a div that listens to drag events
+     * @override
+     */
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export {};

package/dist/components/GenomeView/genomeNavigator/GeneSearchBox.d.ts

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+import { FC } from "react";
+import NavigationContext from "../../../models/NavigationContext";
+import Genome from "../../../models/Genome";
+interface GeneSearchBoxProps {
+    navContext: NavigationContext;
+    onRegionSelected: (newStart: number, newEnd: number, toolTitle: number | string, highlightSearch: boolean) => void;
+    handleCloseModal: () => void;
+    onNewHighlight?: (newStart: number, newEnd: number, geneName: string) => void;
+    doHighlight: boolean;
+    color: string;
+    background: string;
+    genomeConfig: Genome;
+}
+declare const GeneSearchBox: FC<GeneSearchBoxProps>;
+export default GeneSearchBox;

package/dist/components/GenomeView/genomeNavigator/GeneSearchBox3D.d.ts

@@ -0,0 +1,22 @@
+import React from "react";
+/**
+ * gene search box for 3d module.
+ *
+ * @author Daofeng Li
+ */
+interface GeneSearchBox3DProps {
+    color?: any;
+    background?: any;
+    setGeneCallback?: any;
+}
+declare class GeneSearchBox3D extends React.PureComponent<GeneSearchBox3DProps> {
+    static propTypes: {
+        setGeneCallback: any;
+    };
+    /**
+     * @param {Gene} gene
+     */
+    setGene: (gene: any) => void;
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export default GeneSearchBox3D;

package/dist/components/GenomeView/genomeNavigator/GeneSearchBoxBase.d.ts

@@ -0,0 +1,18 @@
+import React from "react";
+import Gene from "../../../models/Gene";
+export declare const AWS_API = "https://lambda.epigenomegateway.org/v3";
+interface GeneSearchBoxBaseProps {
+    genomeConfig: any;
+    onGeneSelected: (gene: Gene) => void;
+    voiceInput?: boolean;
+    simpleMode?: boolean;
+    color: string;
+    background: string;
+    transcript?: string;
+    resetTranscript?: () => void;
+    startListening?: () => void;
+    stopListening?: () => void;
+    browserSupportsSpeechRecognition?: boolean;
+}
+declare const GeneSearchBoxBase: React.FC<GeneSearchBoxBaseProps>;
+export default GeneSearchBoxBase;

package/dist/components/GenomeView/genomeNavigator/GenomeNavigator.d.ts

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+import React from "react";
+export declare const MIN_VIEW_REGION_SIZE = 5;
+import DisplayedRegionModel from "../../../models/DisplayedRegionModel";
+/**
+ * A navigator that allows users to scroll around the genome and select what region for tracks to display.
+ *
+ * @author Silas Hsu
+ */
+interface GenomeNavigatorProps {
+    selectedRegion: DisplayedRegionModel;
+    windowWidth: number;
+    /**
+     * Called when the user selects a new region to display.  Has the signature
+     *     (newStart: number, newEnd: number): void
+     *         `newStart`: the nav context coordinate of the start of the selected interval
+     *         `newEnd`: the nav context coordinate of the end of the selected interval
+     */
+    onRegionSelected: any;
+    genomeConfig: any;
+}
+interface GenomeNavigatorState {
+    viewRegion?: any;
+}
+declare class GenomeNavigator extends React.Component<GenomeNavigatorProps, GenomeNavigatorState> {
+    static defaultProps: {
+        onRegionSelected: () => undefined;
+    };
+    /**
+     * Binds functions, and also forks that view region that was passed via props.
+     */
+    constructor(props: GenomeNavigatorProps);
+    /**
+     * Sets the default region for MainPane to cover whole chromosomes/features that are in `selectedRegion`
+     *
+     * @param {DisplayedRegionModel} selectedRegion - the currently selected region
+     * @return {DisplayedRegionModel} the default view region for the genome navigator
+     */
+    _setInitialView(selectedRegion: {
+        getNavigationContext: () => any;
+        getFeatureSegments: () => any[];
+    }): DisplayedRegionModel;
+    /**
+     * Resets the view region if a new one is received.
+     *
+     * @param {any} nextProps - new props that this component will receive
+     * @override
+     */
+    UNSAFE_componentWillReceiveProps(nextProps: any): void;
+    /**
+     * Copies this.state.viewRegion, mutates it by calling `methodName` with `args`, and then calls this.setState().
+     *
+     * @param {string} methodName - the method to call on the model
+     * @param {any[]} args - arguments to provide to the method
+     */
+    _setModelState(methodName: string, args: any[]): void;
+    /**
+     * Wrapper for calling zoom() on the view model.
+     *
+     * @param {number} amount - amount to zoom
+     * @param {number} [focusPoint] - focal point of the zoom
+     * @see DisplayedRegionModel#zoom
+     */
+    zoom(amount: any, focusPoint: any): void;
+    /**
+     * Wrapper for calling setRegion() on the view model
+     *
+     * @param {number} newStart - start nav context coordinate
+     * @param {number} newEnd - end nav context coordinate
+     * @see DisplayedRegionModel#setRegion
+     */
+    setNewView(newStart: any, newEnd: any): void;
+    /**
+     * Zooms the view to the right level when the zoom slider is dragged.
+     *
+     * @param {React.SyntheticEvent} event - the event that react fired when the zoom slider was changed
+     */
+    zoomSliderDragged(event: {
+        target: {
+            value: number;
+        };
+    }): void;
+    /**
+     * @inheritdoc
+     */
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export default GenomeNavigator;

package/dist/components/GenomeView/genomeNavigator/IsoformSelection.d.ts

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+import React from "react";
+interface IsoformSelectionProps {
+    genomeConfig: any;
+    geneName: string;
+    onGeneSelected: any;
+    simpleMode: boolean;
+    color: string;
+    background: string;
+}
+declare const IsoformSelection: React.FC<IsoformSelectionProps>;
+export default IsoformSelection;

package/dist/components/GenomeView/genomeNavigator/MainPane.d.ts

@@ -0,0 +1,68 @@
+import React from "react";
+import DisplayedRegionModel from "../../../models/DisplayedRegionModel";
+interface GenomeViewerProps {
+    containerWidth: number;
+    viewRegion: DisplayedRegionModel;
+    selectedRegion: DisplayedRegionModel;
+    onNewViewRequested: any;
+    onRegionSelected: any;
+    onZoom: any;
+    genomeConfig: any;
+}
+/**
+ * The main pane of the genome navigator.  Manages child components and listens for events that modify the view region.
+ *
+ * @author Silas Hsu
+ */
+declare class MainPane extends React.Component<GenomeViewerProps> {
+    static propTypes: {
+        containerWidth: any;
+        viewRegion: any;
+        /**
+         * The region that the tracks are displaying
+         */
+        selectedRegion: any;
+        /**
+         * Called when the user selects a new region to display.  Has the signature
+         *     (newStart: number, newEnd: number): void
+         *         `newStart`: the nav context coordinate of the start of the selected interval
+         *         `newEnd`: the nav context coordinate of the end of the selected interval
+         */
+        onRegionSelected: any;
+        /**
+         * Called when the user wants to view a new region.
+         *     (newStart: number, newEnd: number): void
+         *         `newStart`: the nav context coordinate of the start of the interval for the pane to display next
+         *         `newEnd`: the nav context coordinate of the end of the interval for the pane to display next
+         */
+        onNewViewRequested: any;
+        /**
+         * Called when the view should be zoomed.  Has the signature
+         *     (amount: number, focusPoint: number)
+         *         `amount`: amount to zoom
+         *          `focusPoint`: focal point of the zoom, which is where the mouse was as % of the width of the SVG.
+         */
+        onZoom: any;
+    };
+    static defaultProps: {
+        onRegionSelected: () => undefined;
+        onNewView: () => undefined;
+    };
+    constructor(props: any);
+    componentRef: any;
+    componentDidMount(): void;
+    componentWillUnmount(): void;
+    /**
+     * Zooms the view depending on the user's mousewheel action
+     *
+     * @param {React.SyntheticEvent} event - a wheel event fired from within this pane
+     */
+    mousewheel(event: any): void;
+    /**
+     * Places a <svg> and children that draw things.
+     *
+     * @override
+     */
+    render(): import("react/jsx-runtime").JSX.Element | null;
+}
+export default MainPane;

package/dist/components/GenomeView/genomeNavigator/Ruler.d.ts

@@ -0,0 +1,23 @@
+import React from "react";
+import DisplayedRegionModel from "../../../models/DisplayedRegionModel";
+/**
+ * Draws a ruler that displays feature coordinates.
+ *
+ * @author Silas Hsu
+ */
+interface RulerProps {
+    viewRegion: DisplayedRegionModel;
+    width: number;
+    x?: number;
+    y?: number;
+}
+declare class Ruler extends React.PureComponent<RulerProps> {
+    static propTypes: {
+        viewRegion: any;
+        width: any;
+        x: any;
+        y: any;
+    };
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export default Ruler;

package/dist/components/GenomeView/genomeNavigator/SelectableGenomeArea.d.ts

@@ -0,0 +1,34 @@
+import React from "react";
+export declare const MIN_VIEW_REGION_SIZE = 5;
+import OpenInterval from "../../../models/OpenInterval";
+import DisplayedRegionModel from "../../../models/DisplayedRegionModel";
+interface SelectableGenomeAreaProps {
+    selectableRegion: DisplayedRegionModel;
+    dragLimits: OpenInterval;
+    y?: number | string;
+    height?: number | string;
+    children?: React.ReactNode;
+    /**
+     * Callback for when a region is selected.
+     *
+     * @param {number} start - context coordinate of the start of the new region
+     * @param {number} end - context coordinate of the end of the new region
+     */
+    onRegionSelected?(start: number, end: number, selectedTool: number | string): void;
+    selectedTool?: any;
+}
+/**
+ * A SelectableArea, but also displays the selected length in base pairs, and puts a limit on the selected size.
+ *
+ * @author Silas Hsu
+ */
+export declare class SelectableGenomeArea extends React.PureComponent<SelectableGenomeAreaProps> {
+    constructor(props: SelectableGenomeAreaProps);
+    getSelectedBases(xSpan: OpenInterval): OpenInterval;
+    getIsBaseSpanValid(baseSpan: OpenInterval): boolean;
+    getIsAreaValid(xSpan: OpenInterval): boolean;
+    getBoxCaption(xSpan: OpenInterval): import("react/jsx-runtime").JSX.Element;
+    handleAreaSelect(xSpan: OpenInterval): void;
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export {};