@jbrowse/plugin-variants 2.17.0 → 3.0.0

package/esm/MultiLinearVariantMatrixRenderer/makeImageData.js

@@ -0,0 +1,97 @@
+import { getColorAlleleCount, getColorPhased, getColorPhasedWithPhaseSet, } from '../shared/multiVariantColor';
+import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../util';
+const fudgeFactor = 0.6;
+const f2 = fudgeFactor / 2;
+function drawColorAlleleCount(alleles, ctx, x, y, w, h) {
+    ctx.fillStyle = getColorAlleleCount(alleles);
+    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+}
+function drawPhased(alleles, ctx, x, y, w, h, HP, PS) {
+    ctx.fillStyle =
+        PS !== undefined
+            ? getColorPhasedWithPhaseSet(alleles, HP, PS)
+            : getColorPhased(alleles, HP);
+    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+}
+export function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
+    var _a, _b;
+    const { renderingMode: renderingMode, minorAlleleFrequencyFilter, sources, features, } = renderArgs;
+    const { statusCallback = () => { } } = renderArgs;
+    statusCallback('Drawing variant matrix');
+    const h = canvasHeight / sources.length;
+    const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter(features.values(), minorAlleleFrequencyFilter);
+    const arr = [];
+    const m = mafs.length;
+    const w = canvasWidth / m;
+    for (let i = 0; i < m; i++) {
+        const arr2 = [];
+        const f = mafs[i];
+        const hasPhaseSet = f.get('format').includes('PS');
+        if (hasPhaseSet) {
+            const samp = f.get('samples');
+            const x = (i / mafs.length) * canvasWidth;
+            const sln = sources.length;
+            for (let j = 0; j < sln; j++) {
+                const y = (j / sln) * canvasHeight;
+                const { name, HP } = sources[j];
+                const s = samp[name];
+                if (s) {
+                    const genotype = (_a = s.GT) === null || _a === void 0 ? void 0 : _a[0];
+                    if (genotype) {
+                        arr2.push(genotype);
+                        const isPhased = genotype.includes('|');
+                        if (renderingMode === 'phased') {
+                            if (isPhased) {
+                                const PS = (_b = s.PS) === null || _b === void 0 ? void 0 : _b[0];
+                                const alleles = genotype.split('|');
+                                drawPhased(alleles, ctx, x, y, w, h, HP, PS);
+                            }
+                            else {
+                                ctx.fillStyle = 'black';
+                                ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+                            }
+                        }
+                        else {
+                            const alleles = genotype.split(/[/|]/);
+                            drawColorAlleleCount(alleles, ctx, x, y, w, h);
+                        }
+                    }
+                }
+            }
+        }
+        else {
+            const samp = f.get('genotypes');
+            const x = (i / mafs.length) * canvasWidth;
+            const sln = sources.length;
+            const arr2 = [];
+            for (let j = 0; j < sln; j++) {
+                const y = (j / sln) * canvasHeight;
+                const { name, HP } = sources[j];
+                const genotype = samp[name];
+                if (genotype) {
+                    arr2.push(genotype);
+                    const isPhased = genotype.includes('|');
+                    if (renderingMode === 'phased') {
+                        if (isPhased) {
+                            const alleles = genotype.split('|');
+                            drawPhased(alleles, ctx, x, y, w, h, HP);
+                        }
+                        else {
+                            ctx.fillStyle = 'black';
+                            ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+                        }
+                    }
+                    else {
+                        const alleles = genotype.split(/[/|]/);
+                        drawColorAlleleCount(alleles, ctx, x, y, w, h);
+                    }
+                }
+            }
+        }
+        arr.push(arr2);
+    }
+    return {
+        mafs,
+        arr,
+    };
+}

package/esm/MultiLinearVariantMatrixRenderer/types.d.ts

@@ -0,0 +1,15 @@
+import type { Source } from '../types';
+import type { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import type { Feature } from '@jbrowse/core/util';
+export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
+    sources: Source[];
+    minorAlleleFrequencyFilter: number;
+    highResolutionScaling: number;
+    height: number;
+    renderingMode: string;
+}
+export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsDeserialized {
+    sources: Source[];
+    features: Map<string, Feature>;
+    renderingMode: string;
+}

package/esm/MultiLinearVariantMatrixRenderer/types.js

@@ -0,0 +1 @@
+export {};

package/esm/MultiLinearVariantRenderer/MultiVariantRenderer.d.ts

@@ -0,0 +1,31 @@
+import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { MultiRenderArgsDeserialized } from './types';
+import type { Feature } from '@jbrowse/core/util';
+export default class MultiVariantBaseRenderer extends FeatureRendererType {
+    supportsSVG: boolean;
+    render(renderProps: MultiRenderArgsDeserialized): Promise<{
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        canvasRecordedData: any;
+        reactElement?: React.ReactElement;
+        html?: string;
+    } | {
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        reactElement: import("react/jsx-runtime").JSX.Element;
+        html?: string;
+    } | {
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        imageData: any;
+        reactElement?: React.ReactElement;
+        html?: string;
+    }>;
+}
+export type { RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';

package/esm/MultiLinearVariantRenderer/MultiVariantRenderer.js

@@ -0,0 +1,34 @@
+import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import { renderToAbstractCanvas } from '@jbrowse/core/util';
+export default class MultiVariantBaseRenderer extends FeatureRendererType {
+    constructor() {
+        super(...arguments);
+        this.supportsSVG = true;
+    }
+    async render(renderProps) {
+        const features = await this.getFeatures(renderProps);
+        const { height, regions, bpPerPx } = renderProps;
+        const region = regions[0];
+        const width = (region.end - region.start) / bpPerPx;
+        const { makeImageData } = await import('./makeImageData');
+        const rest = await renderToAbstractCanvas(width, height, renderProps, ctx => makeImageData(ctx, {
+            ...renderProps,
+            features,
+        }));
+        const results = await super.render({
+            ...renderProps,
+            ...rest,
+            features,
+            height,
+            width,
+        });
+        return {
+            ...results,
+            ...rest,
+            features: new Map(),
+            height,
+            width,
+            containsNoTransferables: true,
+        };
+    }
+}

package/esm/MultiLinearVariantRenderer/MultiVariantRendering.d.ts

@@ -0,0 +1,22 @@
+import RBush from 'rbush';
+import type { Source } from '../types';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
+declare const MultiVariantRendering: (props: {
+    regions: Region[];
+    features: Map<string, Feature>;
+    bpPerPx: number;
+    width: number;
+    height: number;
+    sources: Source[];
+    scrollTop: number;
+    totalHeight: number;
+    rbush: RBush<{
+        genotype: string;
+    }>;
+    displayModel: any;
+    onMouseLeave?: (event: React.MouseEvent) => void;
+    onMouseMove?: (event: React.MouseEvent, arg?: Feature) => void;
+    onFeatureClick?: (event: React.MouseEvent, arg?: Feature) => void;
+}) => import("react/jsx-runtime").JSX.Element;
+export default MultiVariantRendering;

package/esm/MultiLinearVariantRenderer/MultiVariantRendering.js

@@ -0,0 +1,47 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { useMemo, useRef } from 'react';
+import { PrerenderedCanvas } from '@jbrowse/core/ui';
+import { observer } from 'mobx-react';
+import RBush from 'rbush';
+const MultiVariantRendering = observer(function (props) {
+    const { totalHeight, scrollTop } = props;
+    const { rbush, displayModel } = props;
+    const ref = useRef(null);
+    const rbush2 = useMemo(() => new RBush().fromJSON(rbush), [rbush]);
+    function getFeatureUnderMouse(eventClientX, eventClientY) {
+        var _a;
+        let offsetX = 0;
+        let offsetY = 0;
+        if (ref.current) {
+            const r = ref.current.getBoundingClientRect();
+            offsetX = eventClientX - r.left;
+            offsetY = eventClientY - r.top;
+        }
+        const ret = rbush2.search({
+            minX: offsetX,
+            maxX: offsetX + 3,
+            minY: offsetY,
+            maxY: offsetY + 3,
+        });
+        return (_a = ret[0]) === null || _a === void 0 ? void 0 : _a.genotype;
+    }
+    return (_jsx("div", { ref: ref, onMouseMove: e => {
+            var _a;
+            return (_a = displayModel.setHoveredGenotype) === null || _a === void 0 ? void 0 : _a.call(displayModel, getFeatureUnderMouse(e.clientX, e.clientY));
+        }, onMouseLeave: () => {
+            var _a;
+            (_a = displayModel.setHoveredGenotype) === null || _a === void 0 ? void 0 : _a.call(displayModel, undefined);
+        }, onMouseOut: () => {
+            var _a;
+            (_a = displayModel.setHoveredGenotype) === null || _a === void 0 ? void 0 : _a.call(displayModel, undefined);
+        }, style: {
+            overflow: 'visible',
+            position: 'relative',
+            height: totalHeight,
+        }, children: _jsx(PrerenderedCanvas, { ...props, style: {
+                position: 'absolute',
+                left: 0,
+                top: scrollTop,
+            } }) }));
+});
+export default MultiVariantRendering;

package/esm/MultiLinearVariantRenderer/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default configSchema;

package/esm/MultiLinearVariantRenderer/configSchema.js

@@ -0,0 +1,6 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+function x() { }
+const configSchema = ConfigurationSchema('MultiVariantRenderer', {}, {
+    explicitlyTyped: true,
+});
+export default configSchema;

package/esm/MultiLinearVariantRenderer/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function MultiVariantRendererF(pluginManager: PluginManager): void;

package/esm/MultiLinearVariantRenderer/index.js

@@ -0,0 +1,13 @@
+import MultiVariantRenderer from './MultiVariantRenderer';
+import ReactComponent from './MultiVariantRendering';
+import configSchema from './configSchema';
+export default function MultiVariantRendererF(pluginManager) {
+    pluginManager.addRendererType(() => {
+        return new MultiVariantRenderer({
+            name: 'MultiVariantRenderer',
+            ReactComponent,
+            configSchema,
+            pluginManager,
+        });
+    });
+}

package/esm/MultiLinearVariantRenderer/makeImageData.d.ts

@@ -0,0 +1,4 @@
+import type { MultiRenderArgsDeserialized } from './types';
+export declare function makeImageData(ctx: CanvasRenderingContext2D, props: MultiRenderArgsDeserialized): Promise<{
+    rbush: any;
+}>;

package/esm/MultiLinearVariantRenderer/makeImageData.js

@@ -0,0 +1,61 @@
+import { featureSpanPx } from '@jbrowse/core/util';
+import RBush from 'rbush';
+import { getColorAlleleCount, getColorPhased, } from '../shared/multiVariantColor';
+import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../util';
+const fudgeFactor = 0.6;
+const f2 = fudgeFactor / 2;
+function drawColorAlleleCount(alleles, ctx, x, y, w, h) {
+    ctx.fillStyle = getColorAlleleCount(alleles);
+    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+}
+function drawPhased(alleles, ctx, x, y, w, h, HP) {
+    ctx.fillStyle = getColorPhased(alleles, HP);
+    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+}
+export async function makeImageData(ctx, props) {
+    const { scrollTop, minorAlleleFrequencyFilter, sources, rowHeight, features, regions, bpPerPx, renderingMode, } = props;
+    const region = regions[0];
+    const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter(features.values(), minorAlleleFrequencyFilter);
+    const rbush = new RBush();
+    for (const feature of mafs) {
+        const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+        const w = Math.max(Math.round(rightPx - leftPx), 2);
+        const samp = feature.get('genotypes');
+        let y = -scrollTop;
+        const s = sources.length;
+        for (let j = 0; j < s; j++) {
+            const { name, HP } = sources[j];
+            const genotype = samp[name];
+            const x = Math.floor(leftPx);
+            const h = Math.max(rowHeight, 1);
+            if (genotype) {
+                rbush.insert({
+                    minX: x - f2,
+                    maxX: x + w + f2,
+                    minY: y - f2,
+                    maxY: y + h + f2,
+                    genotype,
+                });
+                const isPhased = genotype.includes('|');
+                if (renderingMode === 'phased') {
+                    if (isPhased) {
+                        const alleles = genotype.split('|');
+                        drawPhased(alleles, ctx, x, y, w, h, HP);
+                    }
+                    else {
+                        ctx.fillStyle = 'black';
+                        ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+                    }
+                }
+                else {
+                    const alleles = genotype.split(/[/|]/);
+                    drawColorAlleleCount(alleles, ctx, x, y, w, h);
+                }
+            }
+            y += rowHeight;
+        }
+    }
+    return {
+        rbush: rbush.toJSON(),
+    };
+}

package/esm/MultiLinearVariantRenderer/types.d.ts

@@ -0,0 +1,19 @@
+import type { Source } from '../types';
+import type { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { Feature } from '@jbrowse/core/util';
+import type { ThemeOptions } from '@mui/material';
+export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
+    bpPerPx: number;
+    height: number;
+    highResolutionScaling: number;
+    themeOptions: ThemeOptions;
+}
+export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+}
+export interface MultiRenderArgsDeserialized extends RenderArgsDeserializedWithFeatures {
+    sources: Source[];
+    rowHeight: number;
+    scrollTop: number;
+    minorAlleleFrequencyFilter: number;
+}

package/esm/MultiLinearVariantRenderer/types.js

@@ -0,0 +1 @@
+export {};

package/esm/MultiVariantBaseRenderer.d.ts

@@ -0,0 +1,46 @@
+import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { Source } from './types';
+import type { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { Feature } from '@jbrowse/core/util';
+import type { ThemeOptions } from '@mui/material';
+export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
+    bpPerPx: number;
+    height: number;
+    highResolutionScaling: number;
+    themeOptions: ThemeOptions;
+}
+export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+}
+export interface MultiRenderArgsDeserialized extends RenderArgsDeserializedWithFeatures {
+    sources: Source[];
+}
+export default abstract class MultiVariantBaseRenderer extends FeatureRendererType {
+    supportsSVG: boolean;
+    render(renderProps: RenderArgsDeserialized): Promise<{
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        canvasRecordedData: any;
+        reactElement?: React.ReactElement;
+        html?: string;
+    } | {
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        reactElement: import("react/jsx-runtime").JSX.Element;
+        html?: string;
+    } | {
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        imageData: any;
+        reactElement?: React.ReactElement;
+        html?: string;
+    }>;
+    abstract draw<T extends RenderArgsDeserializedWithFeatures>(ctx: CanvasRenderingContext2D, props: T): Promise<Record<string, unknown> | undefined>;
+}
+export type { RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';

package/esm/MultiVariantBaseRenderer.js

@@ -0,0 +1,33 @@
+import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import { renderToAbstractCanvas } from '@jbrowse/core/util';
+export default class MultiVariantBaseRenderer extends FeatureRendererType {
+    constructor() {
+        super(...arguments);
+        this.supportsSVG = true;
+    }
+    async render(renderProps) {
+        const features = await this.getFeatures(renderProps);
+        const { height, regions, bpPerPx } = renderProps;
+        const region = regions[0];
+        const width = (region.end - region.start) / bpPerPx;
+        const rest = await renderToAbstractCanvas(width, height, renderProps, ctx => this.draw(ctx, {
+            ...renderProps,
+            features,
+        }));
+        const results = await super.render({
+            ...renderProps,
+            ...rest,
+            features,
+            height,
+            width,
+        });
+        return {
+            ...results,
+            ...rest,
+            features: new Map(),
+            height,
+            width,
+            containsNoTransferables: true,
+        };
+    }
+}

package/esm/StructuralVariantChordRenderer/Chord.d.ts

@@ -1,23 +1,6 @@
-import React from 'react';
-import { Feature } from '@jbrowse/core/util';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export interface Region {
-    end: number;
-    start: number;
-    refName: string;
-    elided?: false;
-}
-export interface ElidedRegion {
-    elided: true;
-    regions: Region[];
-}
-export type AnyRegion = Region | ElidedRegion;
-export interface Block {
-    flipped: boolean;
-    bpPerRadian: number;
-    startRadians: number;
-    region: AnyRegion;
-}
+import type { AnyRegion, Block } from './types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 declare const Chord: ({ feature, blocksForRefs, radius, config, bezierRadius, selected, onClick, }: {
     feature: Feature;
     blocksForRefs: Record<string, Block>;
@@ -26,5 +9,5 @@ declare const Chord: ({ feature, blocksForRefs, radius, config, bezierRadius, se
     bezierRadius: number;
     selected: boolean;
     onClick: (feat: Feature, reg: AnyRegion, end: AnyRegion, evt: unknown) => void;
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default Chord;

package/esm/StructuralVariantChordRenderer/Chord.js

@@ -1,8 +1,9 @@
-import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { polarToCartesian, getStrokeProps } from '@jbrowse/core/util';
-import { readConfObject, } from '@jbrowse/core/configuration';
+import { jsx as _jsx } from "react/jsx-runtime";
+import { useState } from 'react';
 import { parseBreakend } from '@gmod/vcf';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { getStrokeProps, polarToCartesian } from '@jbrowse/core/util';
+import { observer } from 'mobx-react';
 function bpToRadians(block, pos) {
     const blockStart = block.region.elided ? 0 : block.region.start;
     const blockEnd = block.region.elided ? 0 : block.region.end;
@@ -12,7 +13,6 @@ function bpToRadians(block, pos) {
 const Chord = observer(function Chord({ feature, blocksForRefs, radius, config, bezierRadius, selected, onClick, }) {
     var _a, _b, _c, _d, _e;
     const [hovered, setHovered] = useState(false);
-    // find the blocks that our start and end points belong to
     const startBlock = blocksForRefs[feature.get('refName')];
     if (!startBlock) {
         return null;
@@ -31,28 +31,25 @@ const Chord = observer(function Chord({ feature, blocksForRefs, radius, config,
     const bnd = alt && parseBreakend(alt);
     const startPos = feature.get('start');
     if (bnd) {
-        // VCF BND
         const matePosition = bnd.MatePosition.split(':');
         endPosition = +matePosition[1];
         endBlock = blocksForRefs[matePosition[0]];
     }
     else if (alt === '<TRA>') {
-        // VCF TRA
         const chr2 = (_c = (_b = feature.get('INFO')) === null || _b === void 0 ? void 0 : _b.CHR2) === null || _c === void 0 ? void 0 : _c[0];
         const end = (_e = (_d = feature.get('INFO')) === null || _d === void 0 ? void 0 : _d.END) === null || _e === void 0 ? void 0 : _e[0];
         endPosition = Number.parseInt(end, 10);
         endBlock = blocksForRefs[chr2];
     }
     else if (svType === 'mate') {
-        // generic simplefeatures arcs
         const mate = feature.get('mate');
         const chr2 = mate.refName;
         endPosition = mate.start;
         endBlock = blocksForRefs[chr2];
     }
     else {
-        console.warn('unknown sv type', svType);
-        endPosition = startPos + 1;
+        endBlock = startBlock;
+        endPosition = feature.get('end');
     }
     if (endBlock) {
         const startRadians = bpToRadians(startBlock, startPos);
@@ -66,7 +63,7 @@ const Chord = observer(function Chord({ feature, blocksForRefs, radius, config,
         const hoverStrokeColor = readConfObject(config, 'strokeColorHover', {
             feature,
         });
-        return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, cursor: "crosshair", fill: "none", d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), ...getStrokeProps(hovered ? hoverStrokeColor : strokeColor), strokeWidth: hovered ? 3 : 1, onClick: evt => {
+        return (_jsx("path", { "data-testid": `chord-${feature.id()}`, cursor: "crosshair", fill: "none", d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), ...getStrokeProps(hovered ? hoverStrokeColor : strokeColor), strokeWidth: hovered ? 3 : 1, onClick: evt => {
                 onClick(feature, startBlock.region, endBlock.region, evt);
             }, onMouseOver: () => {
                 if (!selected) {

package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
-import { Feature } from '@jbrowse/core/util';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { Block, AnyRegion } from './Chord';
+import type { AnyRegion, Block } from './types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 declare const StructuralVariantChordsReactComponent: ({ features, config, blockDefinitions, radius, bezierRadius, displayModel, onChordClick, }: {
     features: Map<string, Feature>;
     radius: number;
@@ -13,5 +12,5 @@ declare const StructuralVariantChordsReactComponent: ({ features, config, blockD
     blockDefinitions: Block[];
     bezierRadius: number;
     onChordClick: (feature: Feature, reg: AnyRegion, endBlock: AnyRegion, evt: unknown) => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default StructuralVariantChordsReactComponent;

package/esm/StructuralVariantChordRenderer/ReactComponent.js

@@ -1,6 +1,6 @@
-import React, { useMemo } from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
+import { useMemo } from 'react';
 import { observer } from 'mobx-react';
-// locals
 import Chord from './Chord';
 const StructuralVariantChordsReactComponent = observer(function ({ features, config, blockDefinitions, radius, bezierRadius, displayModel, onChordClick, }) {
     const { selectedFeatureId } = displayModel || {};
@@ -16,10 +16,10 @@ const StructuralVariantChordsReactComponent = observer(function ({ features, con
         }
         return blocksForRefs;
     }, [blockDefinitions]);
-    return (React.createElement("g", { "data-testid": "structuralVariantChordRenderer" }, [...features.values()].map(feature => {
-        const id = feature.id();
-        const selected = String(selectedFeatureId) === String(id);
-        return (React.createElement(Chord, { key: id, feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
-    })));
+    return (_jsx("g", { "data-testid": "structuralVariantChordRenderer", children: [...features.values()].map(feature => {
+            const id = feature.id();
+            const selected = String(selectedFeatureId) === String(id);
+            return (_jsx(Chord, { feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }, id));
+        }) }));
 });
 export default StructuralVariantChordsReactComponent;

package/esm/StructuralVariantChordRenderer/configSchema.d.ts

@@ -1,25 +1,16 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     strokeColor: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     strokeColorSelected: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     strokeColorHover: {
         type: string;
         description: string;

package/esm/StructuralVariantChordRenderer/configSchema.js

@@ -1,30 +1,18 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config StructuralVariantChordRenderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = ConfigurationSchema('StructuralVariantChordRenderer', {
-    /**
-     * #slot
-     */
     strokeColor: {
         type: 'color',
         description: 'the line color of each arc',
         defaultValue: 'rgba(255,133,0,0.32)',
         contextVariable: ['feature'],
     },
-    /**
-     * #slot
-     */
     strokeColorSelected: {
         type: 'color',
         description: 'the line color of an arc that has been selected',
         defaultValue: 'black',
         contextVariable: ['feature'],
     },
-    /**
-     * #slot
-     */
     strokeColorHover: {
         type: 'color',
         description: 'the line color of an arc that is being hovered over with the mouse',