@jbrowse/plugin-wiggle 1.7.11 → 2.0.0

package/dist/util.js

@@ -1,18 +1,23 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.getNiceDomain = getNiceDomain;
-exports.getOrigin = getOrigin;
-exports.getScale = getScale;
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _d3Scale = require("d3-scale");
-
+var __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
+    }
+    return ar;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getNiceDomain = exports.getOrigin = exports.getScale = void 0;
+var d3_scale_1 = require("d3-scale");
 /**
  * produces a d3-scale from arguments. applies a "nice domain" adjustment
  *
@@ -24,75 +29,60 @@ var _d3Scale = require("d3-scale");
  *   - pivotValue (number)
  *   - inverted (boolean)
  */
-function getScale(_ref) {
-  var _ref$domain = _ref.domain,
-      domain = _ref$domain === void 0 ? [] : _ref$domain,
-      _ref$range = _ref.range,
-      range = _ref$range === void 0 ? [] : _ref$range,
-      scaleType = _ref.scaleType,
-      pivotValue = _ref.pivotValue,
-      inverted = _ref.inverted;
-  var scale;
-
-  var _domain = (0, _slicedToArray2.default)(domain, 2),
-      min = _domain[0],
-      max = _domain[1];
-
-  if (min === undefined || max === undefined) {
-    throw new Error('invalid domain');
-  }
-
-  if (scaleType === 'linear') {
-    scale = (0, _d3Scale.scaleLinear)();
-  } else if (scaleType === 'log') {
-    scale = (0, _d3Scale.scaleLog)();
-    scale.base(2);
-  } else if (scaleType === 'quantize') {
-    scale = (0, _d3Scale.scaleQuantize)();
-  } else {
-    throw new Error('undefined scaleType');
-  }
-
-  scale.domain(pivotValue !== undefined ? [min, pivotValue, max] : [min, max]);
-  scale.nice();
-
-  var _range = (0, _slicedToArray2.default)(range, 2),
-      rangeMin = _range[0],
-      rangeMax = _range[1];
-
-  if (rangeMin === undefined || rangeMax === undefined) {
-    throw new Error('invalid range');
-  }
-
-  scale.range(inverted ? range.slice().reverse() : range);
-  return scale;
+function getScale(_a) {
+    var _b = _a.domain, domain = _b === void 0 ? [] : _b, _c = _a.range, range = _c === void 0 ? [] : _c, scaleType = _a.scaleType, pivotValue = _a.pivotValue, inverted = _a.inverted;
+    var scale;
+    var _d = __read(domain, 2), min = _d[0], max = _d[1];
+    if (min === undefined || max === undefined) {
+        throw new Error('invalid domain');
+    }
+    if (scaleType === 'linear') {
+        scale = (0, d3_scale_1.scaleLinear)();
+    }
+    else if (scaleType === 'log') {
+        scale = (0, d3_scale_1.scaleLog)();
+        scale.base(2);
+    }
+    else if (scaleType === 'quantize') {
+        scale = (0, d3_scale_1.scaleQuantize)();
+    }
+    else {
+        throw new Error('undefined scaleType');
+    }
+    scale.domain(pivotValue !== undefined ? [min, pivotValue, max] : [min, max]);
+    scale.nice();
+    var _e = __read(range, 2), rangeMin = _e[0], rangeMax = _e[1];
+    if (rangeMin === undefined || rangeMax === undefined) {
+        throw new Error('invalid range');
+    }
+    scale.range(inverted ? range.slice().reverse() : range);
+    return scale;
 }
+exports.getScale = getScale;
 /**
  * gets the origin for drawing the graph. for linear this is 0, for log this is arbitrarily set to log(1)==0
  *
  * @param scaleType -
  */
-
-
-function getOrigin(scaleType) {
-  // if (pivot) {
-  //   if (pivot === 'mean') {
-  //     return stats.scoreMean || 0
-  //   }
-  //   if (pivot === 'zero') {
-  //     return 0
-  //   }
-  //   return parseFloat()
-  // }
-  // if (scaleType === 'z_score') {
-  //   return stats.scoreMean || 0
-  // }
-  if (scaleType === 'log') {
-    return 1;
-  }
-
-  return 0;
+function getOrigin(scaleType /* , pivot, stats */) {
+    // if (pivot) {
+    //   if (pivot === 'mean') {
+    //     return stats.scoreMean || 0
+    //   }
+    //   if (pivot === 'zero') {
+    //     return 0
+    //   }
+    //   return parseFloat()
+    // }
+    // if (scaleType === 'z_score') {
+    //   return stats.scoreMean || 0
+    // }
+    if (scaleType === 'log') {
+        return 1;
+    }
+    return 0;
 }
+exports.getOrigin = getOrigin;
 /**
  * produces a "nice" domain that actually rounds down to 0 for the min
  * or 0 to the max depending on if all values are positive or negative
@@ -104,75 +94,54 @@ function getOrigin(scaleType) {
  *   - stddev
  *   - scaleType (linear or log)
  */
-
-
-function getNiceDomain(_ref2) {
-  var scaleType = _ref2.scaleType,
-      domain = _ref2.domain,
-      bounds = _ref2.bounds;
-
-  var _bounds = (0, _slicedToArray2.default)(bounds, 2),
-      minScore = _bounds[0],
-      maxScore = _bounds[1];
-
-  var _domain2 = (0, _slicedToArray2.default)(domain, 2),
-      min = _domain2[0],
-      max = _domain2[1];
-
-  if (scaleType === 'linear') {
-    if (max < 0) {
-      max = 0;
-    }
-
-    if (min > 0) {
-      min = 0;
+function getNiceDomain(_a) {
+    var scaleType = _a.scaleType, domain = _a.domain, bounds = _a.bounds;
+    var _b = __read(bounds, 2), minScore = _b[0], maxScore = _b[1];
+    var _c = __read(domain, 2), min = _c[0], max = _c[1];
+    if (scaleType === 'linear') {
+        if (max < 0) {
+            max = 0;
+        }
+        if (min > 0) {
+            min = 0;
+        }
     }
-  }
-
-  if (scaleType === 'log') {
-    // if the min is 0, assume that it's just something
-    // with no read coverage and that we should ignore it in calculations
-    // if it's greater than 1 pin to 1 for the full range also
-    // otherwise, we may see bigwigs with fractional values
-    if (min === 0 || min > 1) {
-      min = 1;
+    if (scaleType === 'log') {
+        // if the min is 0, assume that it's just something
+        // with no read coverage and that we should ignore it in calculations
+        // if it's greater than 1 pin to 1 for the full range also
+        // otherwise, we may see bigwigs with fractional values
+        if (min === 0 || min > 1) {
+            min = 1;
+        }
     }
-  }
-
-  if (min === undefined || max === undefined) {
-    throw new Error('invalid domain supplied to stats function');
-  }
-
-  if (minScore !== undefined && minScore !== Number.MIN_VALUE) {
-    min = minScore;
-  }
-
-  if (maxScore !== undefined && maxScore !== Number.MAX_VALUE) {
-    max = maxScore;
-  }
-
-  var getScaleType = function getScaleType(type) {
-    if (type === 'linear') {
-      return (0, _d3Scale.scaleLinear)();
+    if (min === undefined || max === undefined) {
+        throw new Error('invalid domain supplied to stats function');
     }
-
-    if (type === 'log') {
-      var _scale = (0, _d3Scale.scaleLog)();
-
-      _scale.base(2);
-
-      return _scale;
+    if (minScore !== undefined && minScore !== Number.MIN_VALUE) {
+        min = minScore;
     }
-
-    if (type === 'quantize') {
-      return (0, _d3Scale.scaleQuantize)();
+    if (maxScore !== undefined && maxScore !== Number.MAX_VALUE) {
+        max = maxScore;
     }
-
-    throw new Error("undefined scaleType ".concat(type));
-  };
-
-  var scale = getScaleType(scaleType);
-  scale.domain([min, max]);
-  scale.nice();
-  return scale.domain();
-}
+    var getScaleType = function (type) {
+        if (type === 'linear') {
+            return (0, d3_scale_1.scaleLinear)();
+        }
+        if (type === 'log') {
+            var scale_1 = (0, d3_scale_1.scaleLog)();
+            scale_1.base(2);
+            return scale_1;
+        }
+        if (type === 'quantize') {
+            return (0, d3_scale_1.scaleQuantize)();
+        }
+        throw new Error("undefined scaleType ".concat(type));
+    };
+    var scale = getScaleType(scaleType);
+    scale.domain([min, max]);
+    scale.nice();
+    return scale.domain();
+}
+exports.getNiceDomain = getNiceDomain;
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

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package/esm/BigWigAdapter/BigWigAdapter.d.ts

@@ -0,0 +1,24 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+interface WiggleOptions extends BaseOptions {
+    resolution?: number;
+}
+export default class BigWigAdapter extends BaseFeatureDataAdapter {
+    private bigwig;
+    static capabilities: string[];
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    private setup;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    refIdToName(refId: number): Promise<any>;
+    getGlobalStats(opts?: BaseOptions): Promise<import("@jbrowse/core/util/stats").FeatureStats>;
+    getFeatures(region: Region, opts?: WiggleOptions): import("rxjs").Observable<Feature>;
+    estimateRegionsStats(_regions: Region[]): Promise<{
+        featureDensity: number;
+    }>;
+    freeResources(): void;
+}
+export {};

package/esm/BigWigAdapter/BigWigAdapter.js

@@ -0,0 +1,62 @@
+import { BigWig } from '@gmod/bbi';
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { updateStatus } from '@jbrowse/core/util';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { map, mergeAll } from 'rxjs/operators';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { rectifyStats } from '@jbrowse/core/util/stats';
+export default class BigWigAdapter extends BaseFeatureDataAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        this.bigwig = new BigWig({
+            filehandle: openLocation(readConfObject(config, 'bigWigLocation'), this.pluginManager),
+        });
+    }
+    async setup(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        return updateStatus('Downloading bigwig header', statusCallback, () => this.bigwig.getHeader(opts));
+    }
+    async getRefNames(opts) {
+        const { refsByName } = await this.setup(opts);
+        return Object.keys(refsByName);
+    }
+    async refIdToName(refId) {
+        var _a;
+        const { refsByNumber } = await this.setup();
+        return (_a = refsByNumber[refId]) === null || _a === void 0 ? void 0 : _a.name;
+    }
+    async getGlobalStats(opts) {
+        const { totalSummary } = await this.setup(opts);
+        return rectifyStats(totalSummary);
+    }
+    getFeatures(region, opts = {}) {
+        const { refName, start, end } = region;
+        const { bpPerPx = 0, signal, resolution = 1, statusCallback = () => { }, } = opts;
+        return ObservableCreate(async (observer) => {
+            statusCallback('Downloading bigwig data');
+            const ob = await this.bigwig.getFeatureStream(refName, start, end, {
+                ...opts,
+                basesPerSpan: bpPerPx / resolution,
+            });
+            ob.pipe(mergeAll(), map(record => {
+                return new SimpleFeature({
+                    id: `${refName}:${record.start}-${record.end}`,
+                    data: { ...record, refName },
+                });
+            })).subscribe(observer);
+        }, signal);
+    }
+    // always render bigwig instead of calculating a feature density for it
+    async estimateRegionsStats(_regions) {
+        return { featureDensity: 0 };
+    }
+    freeResources() { }
+}
+BigWigAdapter.capabilities = [
+    'hasResolution',
+    'hasLocalStats',
+    'hasGlobalStats',
+];
+//# sourceMappingURL=BigWigAdapter.js.map

package/esm/BigWigAdapter/BigWigAdapter.js.map

@@ -0,0 +1 @@
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package/esm/BigWigAdapter/configSchema.js

@@ -0,0 +1,11 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('BigWigAdapter', {
+    bigWigLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.bw',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/BigWigAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigWigAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,gBAAgB;YACrB,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/esm/BigWigAdapter/index.d.ts

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema';

package/esm/BigWigAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/BigWigAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BigWigAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/DensityRenderer/index.d.ts

@@ -0,0 +1,6 @@
+import WiggleBaseRenderer, { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
+export { default as ReactComponent } from '../WiggleRendering';
+export default class DensityRenderer extends WiggleBaseRenderer {
+    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<void>;
+}
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/DensityRenderer/index.js

@@ -0,0 +1,39 @@
+import { readConfObject, ConfigurationSchema, } from '@jbrowse/core/configuration';
+import { featureSpanPx } from '@jbrowse/core/util';
+import { getScale } from '../util';
+import ConfigSchema from '../configSchema';
+import WiggleBaseRenderer from '../WiggleBaseRenderer';
+export { default as ReactComponent } from '../WiggleRendering';
+export default class DensityRenderer extends WiggleBaseRenderer {
+    async draw(ctx, props) {
+        const { features, regions, bpPerPx, scaleOpts, height, config } = props;
+        const [region] = regions;
+        const pivot = readConfObject(config, 'bicolorPivot');
+        const pivotValue = readConfObject(config, 'bicolorPivotValue');
+        const negColor = readConfObject(config, 'negColor');
+        const posColor = readConfObject(config, 'posColor');
+        const color = readConfObject(config, 'color');
+        let colorCallback;
+        if (color === '#f0f') {
+            const colorScale = pivot !== 'none'
+                ? getScale({
+                    ...scaleOpts,
+                    pivotValue,
+                    range: [negColor, 'white', posColor],
+                })
+                : getScale({ ...scaleOpts, range: ['white', posColor] });
+            colorCallback = (feature) => colorScale(feature.get('score'));
+        }
+        else {
+            colorCallback = (feature) => readConfObject(config, 'color', { feature });
+        }
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+            const w = rightPx - leftPx + 0.3; // fudge factor for subpixel rendering
+            ctx.fillStyle = colorCallback(feature);
+            ctx.fillRect(leftPx, 0, w, height);
+        }
+    }
+}
+export const configSchema = ConfigurationSchema('DensityRenderer', {}, { baseConfiguration: ConfigSchema, explicitlyTyped: true });
+//# sourceMappingURL=index.js.map

package/esm/DensityRenderer/index.js.map

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package/esm/LinePlotRenderer/LinePlotRenderer.d.ts

@@ -0,0 +1,4 @@
+export default class LinePlotRenderer extends WiggleBaseRenderer {
+    draw(ctx: any, props: any): Promise<void>;
+}
+import WiggleBaseRenderer from "../WiggleBaseRenderer";

package/esm/LinePlotRenderer/LinePlotRenderer.js

@@ -0,0 +1,71 @@
+import { readConfObject } from '@jbrowse/core/configuration';
+import { featureSpanPx } from '@jbrowse/core/util';
+import { getScale } from '../util';
+import WiggleBaseRenderer from '../WiggleBaseRenderer';
+import { YSCALEBAR_LABEL_OFFSET } from '../LinearWiggleDisplay/models/model';
+export default class LinePlotRenderer extends WiggleBaseRenderer {
+    async draw(ctx, props) {
+        const { features, regions, bpPerPx, scaleOpts, height: unadjustedHeight, ticks: { values }, displayCrossHatches, config, } = props;
+        const [region] = regions;
+        const width = (region.end - region.start) / bpPerPx;
+        const offset = YSCALEBAR_LABEL_OFFSET;
+        // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
+        // wiggle display, and makes the height of the actual drawn area add
+        // "padding" to the top and bottom of the display
+        const height = unadjustedHeight - offset * 2;
+        const clipColor = readConfObject(config, 'clipColor');
+        const highlightColor = readConfObject(config, 'highlightColor');
+        const scale = getScale({ ...scaleOpts, range: [0, height] });
+        const [niceMin, niceMax] = scale.domain();
+        const toY = rawscore => height - scale(rawscore) + offset;
+        const colorCallback = readConfObject(config, 'color') === '#f0f'
+            ? () => 'grey'
+            : feature => readConfObject(config, 'color', { feature });
+        let lastVal;
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+            const score = feature.get('score');
+            const lowClipping = score < niceMin;
+            const highClipping = score > niceMax;
+            const w = rightPx - leftPx + 0.3; // fudge factor for subpixel rendering
+            const c = colorCallback(feature);
+            ctx.strokeStyle = c;
+            ctx.beginPath();
+            if (!region.reversed) {
+                ctx.moveTo(leftPx, toY(typeof lastVal !== 'undefined' ? lastVal : score));
+                ctx.lineTo(leftPx, toY(score));
+                ctx.lineTo(rightPx, toY(score));
+            }
+            else {
+                ctx.moveTo(rightPx, toY(typeof lastVal !== 'undefined' ? lastVal : score));
+                ctx.lineTo(rightPx, toY(score));
+                ctx.lineTo(leftPx, toY(score));
+            }
+            ctx.stroke();
+            lastVal = score;
+            if (highClipping) {
+                ctx.fillStyle = clipColor;
+                ctx.fillRect(leftPx, 0, w, 4);
+            }
+            else if (lowClipping && scaleOpts.scaleType !== 'log') {
+                ctx.fillStyle = clipColor;
+                ctx.fillRect(leftPx, height - 4, w, height);
+            }
+            if (feature.get('highlighted')) {
+                ctx.fillStyle = highlightColor;
+                ctx.fillRect(leftPx, 0, w, height);
+            }
+        }
+        if (displayCrossHatches) {
+            ctx.lineWidth = 1;
+            ctx.strokeStyle = 'rgba(200,200,200,0.8)';
+            values.forEach(tick => {
+                ctx.beginPath();
+                ctx.moveTo(0, Math.round(toY(tick)));
+                ctx.lineTo(width, Math.round(toY(tick)));
+                ctx.stroke();
+            });
+        }
+    }
+}
+//# sourceMappingURL=LinePlotRenderer.js.map

package/esm/LinePlotRenderer/LinePlotRenderer.js.map

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package/esm/LinePlotRenderer/index.d.ts

@@ -0,0 +1,3 @@
+export { default as ReactComponent } from "../WiggleRendering";
+export { default } from "./LinePlotRenderer";
+export const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/LinePlotRenderer/index.js

@@ -0,0 +1,12 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import ConfigSchema from '../configSchema';
+export { default as ReactComponent } from '../WiggleRendering';
+export { default } from './LinePlotRenderer';
+export const configSchema = ConfigurationSchema('LinePlotRenderer', {
+    displayCrossHatches: {
+        type: 'boolean',
+        description: 'choose to draw cross hatches (sideways lines)',
+        defaultValue: false,
+    },
+}, { baseConfiguration: ConfigSchema, explicitlyTyped: true });
+//# sourceMappingURL=index.js.map

package/esm/LinePlotRenderer/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinePlotRenderer/index.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,YAAY,MAAM,iBAAiB,CAAA;AAE1C,OAAO,EAAE,OAAO,IAAI,cAAc,EAAE,MAAM,oBAAoB,CAAA;AAC9D,OAAO,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAA;AAE5C,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAC7C,kBAAkB,EAClB;IACE,mBAAmB,EAAE;QACnB,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,+CAA+C;QAC5D,YAAY,EAAE,KAAK;KACpB;CACF,EACD,EAAE,iBAAiB,EAAE,YAAY,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA"}

package/esm/LinearWiggleDisplay/components/SetColorDialog.d.ts

@@ -0,0 +1,10 @@
+/// <reference types="react" />
+export default function SetColorDialog({ model, handleClose, }: {
+    model: {
+        color: number;
+        setColor: (arg?: string) => void;
+        setPosColor: (arg?: string) => void;
+        setNegColor: (arg?: string) => void;
+    };
+    handleClose: () => void;
+}): JSX.Element;