@jbrowse/plugin-wiggle 2.0.0 → 2.1.2

package/dist/drawxy.js

@@ -0,0 +1,292 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.drawDensity = exports.drawLine = exports.drawXY = void 0;
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const util_2 = require("./util");
+function fillRectCtx(x, y, width, height, ctx, color) {
+    if (width < 0) {
+        x += width;
+        width = -width;
+    }
+    if (height < 0) {
+        y += height;
+        height = -height;
+    }
+    if (color) {
+        ctx.fillStyle = color;
+    }
+    ctx.fillRect(x, y, width, height);
+}
+const fudgeFactor = 0.4;
+const clipHeight = 2;
+function drawXY(ctx, props) {
+    const { features, bpPerPx, regions, scaleOpts, height: unadjustedHeight, config, ticks, displayCrossHatches, offset = 0, colorCallback, Color, } = props;
+    const [region] = regions;
+    const width = (region.end - region.start) / bpPerPx;
+    // 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 filled = (0, configuration_1.readConfObject)(config, 'filled');
+    const clipColor = (0, configuration_1.readConfObject)(config, 'clipColor');
+    const summaryScoreMode = (0, configuration_1.readConfObject)(config, 'summaryScoreMode');
+    const pivotValue = (0, configuration_1.readConfObject)(config, 'bicolorPivotValue');
+    const minSize = (0, configuration_1.readConfObject)(config, 'minSize');
+    const scale = (0, util_2.getScale)({ ...scaleOpts, range: [0, height] });
+    const originY = (0, util_2.getOrigin)(scaleOpts.scaleType);
+    const [niceMin, niceMax] = scale.domain();
+    const toY = (n) => (0, util_1.clamp)(height - (scale(n) || 0), 0, height) + offset;
+    const toOrigin = (n) => toY(originY) - toY(n);
+    const getHeight = (n) => (filled ? toOrigin(n) : Math.max(minSize, 1));
+    let hasClipping = false;
+    let prevLeftPx = 0;
+    const reducedFeatures = [];
+    const crossingOrigin = niceMin < pivotValue && niceMax > pivotValue;
+    // we handle whiskers separately to render max row, min row, and avg in three
+    // passes. this reduces subpixel rendering issues. note: for stylistic
+    // reasons, clipping indicator is only drawn for score, not min/max score
+    if (summaryScoreMode === 'whiskers') {
+        let lastCol;
+        let lastMix;
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
+            if (feature.get('summary')) {
+                const w = rightPx - leftPx + fudgeFactor;
+                const max = feature.get('maxScore');
+                const c = colorCallback(feature, max);
+                const effectiveC = crossingOrigin
+                    ? c
+                    : c === lastCol
+                        ? lastMix
+                        : (lastMix = Color(c).lighten(0.4).toString());
+                fillRectCtx(leftPx, toY(max), w, getHeight(max), ctx, effectiveC);
+                lastCol = c;
+            }
+        }
+        lastMix = undefined;
+        lastCol = undefined;
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
+            const score = feature.get('score');
+            const max = feature.get('maxScore');
+            const min = feature.get('minScore');
+            const summary = feature.get('summary');
+            const c = colorCallback(feature, score);
+            const effectiveC = crossingOrigin && summary
+                ? c === lastCol
+                    ? lastMix
+                    : (lastMix = Color(colorCallback(feature, max))
+                        .mix(Color(colorCallback(feature, min)))
+                        .toString())
+                : c;
+            const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
+            // create reduced features, avoiding multiple features per px
+            if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+                reducedFeatures.push(feature);
+                prevLeftPx = leftPx;
+            }
+            hasClipping = hasClipping || score < niceMin || score > niceMax;
+            fillRectCtx(leftPx, toY(score), w, getHeight(score), ctx, effectiveC);
+            lastCol = c;
+        }
+        lastMix = undefined;
+        lastCol = undefined;
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
+            if (feature.get('summary')) {
+                const min = feature.get('minScore');
+                const c = colorCallback(feature, min);
+                const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
+                const effectiveC = crossingOrigin
+                    ? c
+                    : c === lastCol
+                        ? lastMix
+                        : (lastMix = Color(c).darken(0.4).toString());
+                fillRectCtx(leftPx, toY(min), w, getHeight(min), ctx, effectiveC);
+                lastCol = c;
+            }
+        }
+    }
+    else {
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
+            // create reduced features, avoiding multiple features per px
+            if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+                reducedFeatures.push(feature);
+                prevLeftPx = leftPx;
+            }
+            const score = feature.get('score');
+            const c = colorCallback(feature, score);
+            hasClipping = hasClipping || score < niceMin || score > niceMax;
+            const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
+            if (summaryScoreMode === 'max') {
+                const s = feature.get('summary') ? feature.get('maxScore') : score;
+                fillRectCtx(leftPx, toY(s), w, getHeight(s), ctx, c);
+            }
+            else if (summaryScoreMode === 'min') {
+                const s = feature.get('summary') ? feature.get('minScore') : score;
+                fillRectCtx(leftPx, toY(s), w, getHeight(s), ctx, c);
+            }
+            else {
+                fillRectCtx(leftPx, toY(score), w, getHeight(score), ctx, c);
+            }
+        }
+    }
+    // second pass: draw clipping
+    // avoid persisting the red fillstyle with save/restore
+    ctx.save();
+    if (hasClipping) {
+        ctx.fillStyle = clipColor;
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
+            const w = rightPx - leftPx + fudgeFactor;
+            const score = feature.get('score');
+            if (score > niceMax) {
+                fillRectCtx(leftPx, offset, w, clipHeight, ctx);
+            }
+            else if (score < niceMin && scaleOpts.scaleType !== 'log') {
+                fillRectCtx(leftPx, unadjustedHeight, w, clipHeight, ctx);
+            }
+        }
+    }
+    ctx.restore();
+    if (displayCrossHatches) {
+        ctx.lineWidth = 1;
+        ctx.strokeStyle = 'rgba(200,200,200,0.5)';
+        ticks.values.forEach(tick => {
+            ctx.beginPath();
+            ctx.moveTo(0, Math.round(toY(tick)));
+            ctx.lineTo(width, Math.round(toY(tick)));
+            ctx.stroke();
+        });
+    }
+    return { reducedFeatures };
+}
+exports.drawXY = drawXY;
+function drawLine(ctx, props) {
+    const { features, regions, bpPerPx, scaleOpts, height: unadjustedHeight, ticks: { values }, displayCrossHatches, colorCallback, config, offset = 0, } = props;
+    const [region] = regions;
+    const width = (region.end - region.start) / bpPerPx;
+    // 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 = (0, configuration_1.readConfObject)(config, 'clipColor');
+    const scale = (0, util_2.getScale)({ ...scaleOpts, range: [0, height] });
+    const [niceMin, niceMax] = scale.domain();
+    const toY = (n) => (0, util_1.clamp)(height - (scale(n) || 0), 0, height) + offset;
+    let lastVal;
+    let prevLeftPx = 0;
+    const reducedFeatures = [];
+    for (const feature of features.values()) {
+        const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
+        // create reduced features, avoiding multiple features per px
+        if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+            reducedFeatures.push(feature);
+            prevLeftPx = leftPx;
+        }
+        const score = feature.get('score');
+        const lowClipping = score < niceMin;
+        const highClipping = score > niceMax;
+        const w = rightPx - leftPx + fudgeFactor;
+        const c = colorCallback(feature, score);
+        ctx.beginPath();
+        ctx.strokeStyle = c;
+        const startPos = typeof lastVal !== 'undefined' ? lastVal : score;
+        if (!region.reversed) {
+            ctx.moveTo(leftPx, toY(startPos));
+            ctx.lineTo(leftPx, toY(score));
+            ctx.lineTo(rightPx, toY(score));
+        }
+        else {
+            ctx.moveTo(rightPx, toY(startPos));
+            ctx.lineTo(rightPx, toY(score));
+            ctx.lineTo(leftPx, toY(score));
+        }
+        ctx.stroke();
+        lastVal = score;
+        if (highClipping) {
+            ctx.fillStyle = clipColor;
+            ctx.fillRect(leftPx, offset, w, clipHeight);
+        }
+        else if (lowClipping && scaleOpts.scaleType !== 'log') {
+            ctx.fillStyle = clipColor;
+            ctx.fillRect(leftPx, height - clipHeight, w, height);
+        }
+    }
+    if (displayCrossHatches) {
+        ctx.lineWidth = 1;
+        ctx.strokeStyle = 'rgba(200,200,200,0.5)';
+        values.forEach(tick => {
+            ctx.beginPath();
+            ctx.moveTo(0, Math.round(toY(tick)));
+            ctx.lineTo(width, Math.round(toY(tick)));
+            ctx.stroke();
+        });
+    }
+    return { reducedFeatures };
+}
+exports.drawLine = drawLine;
+function drawDensity(ctx, props) {
+    const { features, regions, bpPerPx, scaleOpts, height, config } = props;
+    const [region] = regions;
+    const pivot = (0, configuration_1.readConfObject)(config, 'bicolorPivot');
+    const pivotValue = (0, configuration_1.readConfObject)(config, 'bicolorPivotValue');
+    const negColor = (0, configuration_1.readConfObject)(config, 'negColor');
+    const posColor = (0, configuration_1.readConfObject)(config, 'posColor');
+    const color = (0, configuration_1.readConfObject)(config, 'color');
+    const clipColor = (0, configuration_1.readConfObject)(config, 'clipColor');
+    const crossing = pivot !== 'none' && scaleOpts.scaleType !== 'log';
+    const scale = (0, util_2.getScale)({
+        ...scaleOpts,
+        pivotValue: crossing ? pivotValue : undefined,
+        range: crossing ? [negColor, 'white', posColor] : ['white', posColor],
+    });
+    const scale2 = (0, util_2.getScale)({ ...scaleOpts, range: [0, height] });
+    let cb;
+    if (color === '#f0f') {
+        cb = (_feature, score) => scale(score);
+    }
+    else {
+        cb = (feature, score) => (0, configuration_1.readConfObject)(config, 'color', { feature, score });
+    }
+    const [niceMin, niceMax] = scale2.domain();
+    let prevLeftPx = 0;
+    let hasClipping = false;
+    const reducedFeatures = [];
+    for (const feature of features.values()) {
+        const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
+        // create reduced features, avoiding multiple features per px
+        if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+            reducedFeatures.push(feature);
+            prevLeftPx = leftPx;
+        }
+        const score = feature.get('score');
+        hasClipping = hasClipping || score > niceMax || score < niceMin;
+        const w = rightPx - leftPx + fudgeFactor;
+        ctx.fillStyle = cb(feature, score);
+        ctx.fillRect(leftPx, 0, w, height);
+    }
+    // second pass: draw clipping
+    // avoid persisting the red fillstyle with save/restore
+    ctx.save();
+    if (hasClipping) {
+        ctx.fillStyle = clipColor;
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
+            const w = rightPx - leftPx + fudgeFactor;
+            const score = feature.get('score');
+            if (score > niceMax) {
+                fillRectCtx(leftPx, 0, w, clipHeight, ctx);
+            }
+            else if (score < niceMin && scaleOpts.scaleType !== 'log') {
+                fillRectCtx(leftPx, 0, w, clipHeight, ctx);
+            }
+        }
+    }
+    ctx.restore();
+    return { reducedFeatures };
+}
+exports.drawDensity = drawDensity;
+//# sourceMappingURL=drawxy.js.map

package/dist/drawxy.js.map

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package/dist/index.d.ts

@@ -4,11 +4,12 @@ import PluginManager from '@jbrowse/core/PluginManager';
 import WiggleBaseRenderer from './WiggleBaseRenderer';
 import WiggleRendering from './WiggleRendering';
 import * as utils from './util';
-import { modelFactory as linearWiggleDisplayModelFactory, ReactComponent as LinearWiggleDisplayReactComponent, YSCALEBAR_LABEL_OFFSET } from './LinearWiggleDisplay';
-import XYPlotRenderer from './XYPlotRenderer';
+import { ReactComponent as LinearWiggleDisplayReactComponent, modelFactory as linearWiggleDisplayModelFactory, Tooltip } from './LinearWiggleDisplay';
+import { TooltipContentsComponent } from './Tooltip';
+import { XYPlotRenderer } from './XYPlotRenderer';
 export default class WigglePlugin extends Plugin {
     name: string;
-    install(pluginManager: PluginManager): void;
+    install(pm: PluginManager): void;
     exports: {
         LinearWiggleDisplayReactComponent: (props: {
             model: {
@@ -113,6 +114,7 @@ export default class WigglePlugin extends Plugin {
                 selectedRendering: string;
                 resolution: number;
                 fill: boolean | undefined;
+                minSize: number | undefined;
                 color: string | undefined;
                 posColor: string | undefined;
                 negColor: string | undefined;
@@ -261,7 +263,7 @@ export default class WigglePlugin extends Plugin {
                 };
                 statsFetchInProgress: AbortController | undefined;
             } & {
-                updateStats({ scoreMin, scoreMax, }: {
+                updateStats(stats: {
                     scoreMin: number;
                     scoreMax: number;
                 }): void;
@@ -271,7 +273,7 @@ export default class WigglePlugin extends Plugin {
                 setLoading(aborter: AbortController): void;
                 selectFeature(feature: import("@jbrowse/core/util").Feature): void;
                 setResolution(res: number): void;
-                setFill(fill: boolean): void;
+                setFill(fill: number): void;
                 toggleLogScale(): void;
                 setScaleType(scale?: string | undefined): void;
                 setSummaryScoreMode(val: string): void;
@@ -284,6 +286,7 @@ export default class WigglePlugin extends Plugin {
             } & {
                 readonly TooltipComponent: import("react").FC<{}>;
                 readonly adapterTypeName: any;
+                readonly rendererTypeNameSimple: any;
                 readonly rendererTypeName: string;
                 readonly filters: undefined;
                 readonly scaleType: any;
@@ -310,18 +313,36 @@ export default class WigglePlugin extends Plugin {
                 readonly autoscaleType: any;
                 readonly displayCrossHatchesSetting: any;
             } & {
-                readonly ticks: any;
+                readonly ticks: {
+                    range: number[];
+                    values: number[];
+                    format: (d: import("d3-scale").NumberValue) => string;
+                    position: import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
+                };
+                readonly adapterCapabilities: string[];
             } & {
                 renderProps(): any;
-                readonly adapterCapabilities: string[];
                 readonly hasResolution: boolean;
                 readonly hasGlobalStats: boolean;
+                readonly fillSetting: 2 | 1 | 0;
             } & {
                 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;
+                    subMenu: {
+                        label: string;
+                        type: string;
+                        checked: boolean;
+                        onClick: () => void;
+                    }[];
+                    type?: undefined;
+                    checked?: undefined;
+                    onClick?: undefined;
+                } | {
                     type: string;
                     label: string;
                     checked: any;
                     onClick: () => void;
+                    subMenu?: undefined;
                 })[];
             } & {
                 reload(): Promise<void>;
@@ -389,6 +410,7 @@ export default class WigglePlugin extends Plugin {
                 selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
                 resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
                 fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+                minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
                 color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
                 posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
                 negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -534,7 +556,7 @@ export default class WigglePlugin extends Plugin {
                 };
                 statsFetchInProgress: AbortController | undefined;
             } & {
-                updateStats({ scoreMin, scoreMax, }: {
+                updateStats(stats: {
                     scoreMin: number;
                     scoreMax: number;
                 }): void;
@@ -544,7 +566,7 @@ export default class WigglePlugin extends Plugin {
                 setLoading(aborter: AbortController): void;
                 selectFeature(feature: import("@jbrowse/core/util").Feature): void;
                 setResolution(res: number): void;
-                setFill(fill: boolean): void;
+                setFill(fill: number): void;
                 toggleLogScale(): void;
                 setScaleType(scale?: string | undefined): void;
                 setSummaryScoreMode(val: string): void;
@@ -557,6 +579,7 @@ export default class WigglePlugin extends Plugin {
             } & {
                 readonly TooltipComponent: import("react").FC<{}>;
                 readonly adapterTypeName: any;
+                readonly rendererTypeNameSimple: any;
                 readonly rendererTypeName: string;
                 readonly filters: undefined;
                 readonly scaleType: any;
@@ -583,18 +606,36 @@ export default class WigglePlugin extends Plugin {
                 readonly autoscaleType: any;
                 readonly displayCrossHatchesSetting: any;
             } & {
-                readonly ticks: any;
+                readonly ticks: {
+                    range: number[];
+                    values: number[];
+                    format: (d: import("d3-scale").NumberValue) => string;
+                    position: import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
+                };
+                readonly adapterCapabilities: string[];
             } & {
                 renderProps(): any;
-                readonly adapterCapabilities: string[];
                 readonly hasResolution: boolean;
                 readonly hasGlobalStats: boolean;
+                readonly fillSetting: 2 | 1 | 0;
             } & {
                 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;
+                    subMenu: {
+                        label: string;
+                        type: string;
+                        checked: boolean;
+                        onClick: () => void;
+                    }[];
+                    type?: undefined;
+                    checked?: undefined;
+                    onClick?: undefined;
+                } | {
                     type: string;
                     label: string;
                     checked: any;
                     onClick: () => void;
+                    subMenu?: undefined;
                 })[];
             } & {
                 reload(): Promise<void>;
@@ -623,9 +664,9 @@ export default class WigglePlugin extends Plugin {
             blockKey: string;
         }) => JSX.Element;
         XYPlotRenderer: typeof XYPlotRenderer;
+        WiggleBaseRenderer: typeof WiggleBaseRenderer;
         xyPlotRendererConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
         utils: typeof utils;
-        WiggleBaseRenderer: typeof WiggleBaseRenderer;
         linearWiggleDisplayModelFactory: (pluginManager: PluginManager, configSchema: import("@jbrowse/core/configuration").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>;
@@ -686,6 +727,7 @@ export default class WigglePlugin extends Plugin {
             selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
             fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+            minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
             color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
             posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
             negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -831,7 +873,7 @@ export default class WigglePlugin extends Plugin {
             };
             statsFetchInProgress: AbortController | undefined;
         } & {
-            updateStats({ scoreMin, scoreMax, }: {
+            updateStats(stats: {
                 scoreMin: number;
                 scoreMax: number;
             }): void;
@@ -841,7 +883,7 @@ export default class WigglePlugin extends Plugin {
             setLoading(aborter: AbortController): void;
             selectFeature(feature: import("@jbrowse/core/util").Feature): void;
             setResolution(res: number): void;
-            setFill(fill: boolean): void;
+            setFill(fill: number): void;
             toggleLogScale(): void;
             setScaleType(scale?: string | undefined): void;
             setSummaryScoreMode(val: string): void;
@@ -854,6 +896,7 @@ export default class WigglePlugin extends Plugin {
         } & {
             readonly TooltipComponent: import("react").FC<{}>;
             readonly adapterTypeName: any;
+            readonly rendererTypeNameSimple: any;
             readonly rendererTypeName: string;
             readonly filters: undefined;
             readonly scaleType: any;
@@ -880,18 +923,36 @@ export default class WigglePlugin extends Plugin {
             readonly autoscaleType: any;
             readonly displayCrossHatchesSetting: any;
         } & {
-            readonly ticks: any;
+            readonly ticks: {
+                range: number[];
+                values: number[];
+                format: (d: import("d3-scale").NumberValue) => string;
+                position: import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
+            };
+            readonly adapterCapabilities: string[];
         } & {
             renderProps(): any;
-            readonly adapterCapabilities: string[];
             readonly hasResolution: boolean;
             readonly hasGlobalStats: boolean;
+            readonly fillSetting: 2 | 1 | 0;
         } & {
             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;
+                subMenu: {
+                    label: string;
+                    type: string;
+                    checked: boolean;
+                    onClick: () => void;
+                }[];
+                type?: undefined;
+                checked?: undefined;
+                onClick?: undefined;
+            } | {
                 type: string;
                 label: string;
                 checked: any;
                 onClick: () => void;
+                subMenu?: undefined;
             })[];
         } & {
             reload(): Promise<void>;
@@ -910,8 +971,5 @@ export default class WigglePlugin extends Plugin {
     };
 }
 export * from './util';
-export { WiggleRendering };
-export { WiggleBaseRenderer };
-export { LinearWiggleDisplayReactComponent, linearWiggleDisplayModelFactory };
-export { Tooltip } from './LinearWiggleDisplay/components/Tooltip';
-export { YSCALEBAR_LABEL_OFFSET };
+export { LinearWiggleDisplayReactComponent, Tooltip, WiggleRendering, WiggleBaseRenderer, linearWiggleDisplayModelFactory, };
+export type { TooltipContentsComponent };