@jbrowse/plugin-breakpoint-split-view 2.6.1

package/dist/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js

@@ -0,0 +1,83 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderToSvg = void 0;
+const react_1 = __importDefault(require("react"));
+const server_1 = require("react-dom/server");
+const mobx_1 = require("mobx");
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+const ui_1 = require("@jbrowse/core/ui");
+// locals
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+// locals
+const SVGBackground_1 = __importDefault(require("./SVGBackground"));
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const Overlay_1 = __importDefault(require("../components/Overlay"));
+function getTrackNameMaxLen(views, fontSize, session) {
+    return (0, util_1.max)(views.flatMap(view => view.tracks.map(t => (0, util_1.measureText)((0, tracks_1.getTrackName)(t.configuration, session), fontSize))), 0);
+}
+function getTrackOffsets(view, textOffset, extra = 0) {
+    const offsets = {};
+    let curr = textOffset;
+    for (let i = 0; i < view.tracks.length; i++) {
+        const track = view.tracks[i];
+        offsets[track.configuration.trackId] = curr + extra;
+        curr += track.displays[0].height + textOffset;
+    }
+    return offsets;
+}
+// render LGV to SVG
+async function renderToSvg(model, opts) {
+    var _a;
+    const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', 
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    Wrapper = ({ children }) => react_1.default.createElement(react_1.default.Fragment, null, children), themeName = 'default', } = opts;
+    const session = (0, util_1.getSession)(model);
+    const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
+    const { width, views } = model;
+    const shift = 50;
+    const offset = headerHeight + rulerHeight;
+    const heights = views.map(v => (0, plugin_linear_genome_view_1.totalHeight)(v.tracks, textHeight, trackLabels) + offset);
+    const totalHeightSvg = (0, util_1.sum)(heights) + 100;
+    const displayResults = await Promise.all(views.map(async (view) => ({
+        view,
+        data: await Promise.all(view.tracks.map(async (track) => {
+            const d = track.displays[0];
+            await (0, mobx_1.when)(() => (d.ready !== undefined ? d.ready : true));
+            return { track, result: await d.renderSvg({ ...opts, theme }) };
+        })),
+    })));
+    const trackLabelMaxLen = getTrackNameMaxLen(views, fontSize, session) + 40;
+    const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0;
+    const textOffset = trackLabels === 'offset' ? textHeight : 0;
+    const trackOffsets = [
+        getTrackOffsets(views[0], textOffset, fontSize + offset),
+        getTrackOffsets(views[1], textOffset, fontSize + heights[0] + offset),
+    ];
+    const w = width + trackLabelOffset;
+    const t = (0, ui_1.createJBrowseTheme)(theme);
+    // the xlink namespace is used for rendering <image> tag
+    return (0, server_1.renderToStaticMarkup)(react_1.default.createElement(material_1.ThemeProvider, { theme: t },
+        react_1.default.createElement(Wrapper, null,
+            react_1.default.createElement("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString() },
+                react_1.default.createElement(SVGBackground_1.default, { width: w, height: totalHeightSvg, shift: shift }),
+                react_1.default.createElement("g", { transform: `translate(${shift} ${fontSize})` },
+                    react_1.default.createElement("g", { transform: `translate(${trackLabelOffset})` },
+                        react_1.default.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[0].assemblyNames.join(', ')),
+                        react_1.default.createElement(plugin_linear_genome_view_1.SVGRuler, { model: displayResults[0].view, fontSize: fontSize })),
+                    react_1.default.createElement(plugin_linear_genome_view_1.SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[0].view, displayResults: displayResults[0].data, offset: offset, trackLabelOffset: trackLabelOffset })),
+                react_1.default.createElement("g", { transform: `translate(${shift} ${fontSize + heights[0]})` },
+                    react_1.default.createElement("g", { transform: `translate(${trackLabelOffset})` },
+                        react_1.default.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[1].assemblyNames.join(', ')),
+                        react_1.default.createElement(plugin_linear_genome_view_1.SVGRuler, { model: displayResults[1].view, fontSize: fontSize })),
+                    react_1.default.createElement(plugin_linear_genome_view_1.SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, offset: offset, trackLabelOffset: trackLabelOffset })),
+                react_1.default.createElement("defs", null,
+                    react_1.default.createElement("clipPath", { id: "clip-bsv" },
+                        react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: totalHeightSvg }))),
+                react_1.default.createElement("g", { transform: `translate(${trackLabelOffset + shift})`, clipPath: "url(#clip-bsv)" }, model.matchedTracks.map(track => (react_1.default.createElement(Overlay_1.default, { parentRef: { current: null }, key: track.configuration.trackId, model: model, trackId: track.configuration.trackId, getTrackYPosOverride: (id, level) => trackOffsets[level][id] }))))))));
+}
+exports.renderToSvg = renderToSvg;
+//# sourceMappingURL=SVGBreakpointSplitView.js.map

package/dist/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js.map

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package/dist/BreakpointSplitView/util.d.ts

@@ -0,0 +1,18 @@
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import { LayoutRecord } from './model';
+type LGV = LinearGenomeViewModel;
+interface Display {
+    height: number;
+    scrollTop: number;
+    SNPCoverageDisplay?: {
+        height: number;
+    };
+}
+interface Track {
+    displays: Display[];
+}
+export declare function getPxFromCoordinate(view: LGV, refName: string, coord: number): number;
+export declare function yPos(trackId: string, level: number, views: LGV[], tracks: Track[], c: LayoutRecord, getYPosOverride?: (trackId: string, level: number) => number): number;
+export declare const useNextFrame: (variable: unknown) => void;
+export declare function intersect<T>(cb: (l: T) => string, a1?: T[], a2?: T[], ...rest: T[][]): T[];
+export {};

package/dist/BreakpointSplitView/util.js

@@ -0,0 +1,56 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.intersect = exports.useNextFrame = exports.yPos = exports.getPxFromCoordinate = void 0;
+const react_1 = require("react");
+const util_1 = require("@jbrowse/core/util");
+const [, TOP, , BOTTOM] = [0, 1, 2, 3];
+function cheight(chunk) {
+    return chunk[BOTTOM] - chunk[TOP];
+}
+function heightFromSpecificLevel(views, trackId, level, getYPosOverride) {
+    var _a;
+    return getYPosOverride
+        ? getYPosOverride(trackId, level)
+        : ((_a = views[level].trackRefs[trackId]) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect().top) || 0;
+}
+function getPxFromCoordinate(view, refName, coord) {
+    return ((view.bpToPx({ refName, coord }) || {}).offsetPx || 0) - view.offsetPx;
+}
+exports.getPxFromCoordinate = getPxFromCoordinate;
+// get's the yposition of a layout record in a track
+function yPos(trackId, level, views, tracks, c, getYPosOverride) {
+    const display = tracks[level].displays[0];
+    const min = 0;
+    const max = display.height;
+    let offset = 0;
+    const { SNPCoverageDisplay } = display;
+    if (SNPCoverageDisplay) {
+        offset = SNPCoverageDisplay.height;
+    }
+    const yPos = getYPosOverride ? 0 : display.scrollTop;
+    return ((0, util_1.clamp)(c[TOP] - yPos + cheight(c) / 2 + offset, min, max) +
+        heightFromSpecificLevel(views, trackId, level, getYPosOverride) +
+        display.scrollTop);
+}
+exports.yPos = yPos;
+// we combo a useEffect and useState combo to force rerender on snap changing.
+// the setup of this being a useEffect+useState makes it re-render once the
+// useEffect is called, which is generally the "next frame". If we removed the
+// below use
+const useNextFrame = (variable) => {
+    const [, setNextFrameState] = (0, react_1.useState)();
+    (0, react_1.useEffect)(() => {
+        setNextFrameState(variable);
+    }, [variable]);
+};
+exports.useNextFrame = useNextFrame;
+// https://stackoverflow.com/a/49186706/2129219 the array-intersection package
+// on npm has a large kb size, and we are just intersecting open track ids so
+// simple is better
+function intersect(cb, a1 = [], a2 = [], ...rest) {
+    const ids = new Set(a2.map(elt => cb(elt)));
+    const a12 = a1.filter(value => ids.has(cb(value)));
+    return rest.length === 0 ? a12 : intersect(cb, a12, ...rest);
+}
+exports.intersect = intersect;
+//# sourceMappingURL=util.js.map

package/dist/BreakpointSplitView/util.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -0,0 +1,7 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+import Plugin from '@jbrowse/core/Plugin';
+export default class BreakpointSplitViewPlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+    configure(): void;
+}

package/dist/index.js

@@ -0,0 +1,21 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+const BreakpointAlignmentsFeatureDetail_1 = __importDefault(require("./BreakpointAlignmentsFeatureDetail"));
+const BreakpointSplitView_1 = __importDefault(require("./BreakpointSplitView"));
+class BreakpointSplitViewPlugin extends Plugin_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'BreakpointSplitViewPlugin';
+    }
+    install(pluginManager) {
+        (0, BreakpointSplitView_1.default)(pluginManager);
+        (0, BreakpointAlignmentsFeatureDetail_1.default)(pluginManager);
+    }
+    configure() { }
+}
+exports.default = BreakpointSplitViewPlugin;
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;AACA,kEAAyC;AACzC,4GAA6E;AAC7E,gFAAwD;AAExD,MAAqB,yBAA0B,SAAQ,gBAAM;IAA7D;;QACE,SAAI,GAAG,2BAA2B,CAAA;IAQpC,CAAC;IANC,OAAO,CAAC,aAA4B;QAClC,IAAA,6BAAoB,EAAC,aAAa,CAAC,CAAA;QACnC,IAAA,2CAA2B,EAAC,aAAa,CAAC,CAAA;IAC5C,CAAC;IAED,SAAS,KAAI,CAAC;CACf;AATD,4CASC"}

package/esm/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.d.ts

@@ -0,0 +1,5 @@
+import React from 'react';
+declare const BreakpointAlignmentsFeatureDetail: ({ model }: {
+    model: any;
+}) => React.JSX.Element;
+export default BreakpointAlignmentsFeatureDetail;

package/esm/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.js

@@ -0,0 +1,16 @@
+import Paper from '@mui/material/Paper';
+import { observer } from 'mobx-react';
+import React from 'react';
+import { BaseCoreDetails, BaseAttributes, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+const BreakpointAlignmentsFeatureDetail = observer(
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+({ model }) => {
+    const { feature1, feature2 } = JSON.parse(JSON.stringify(model.featureData));
+    return (React.createElement(Paper, { "data-testid": "alignment-side-drawer" },
+        React.createElement(BaseCoreDetails, { title: "Feature 1", feature: feature1 }),
+        React.createElement(BaseCoreDetails, { title: "Feature 2", feature: feature2 }),
+        React.createElement(BaseAttributes, { title: "Feature 1 attributes", feature: feature1 }),
+        React.createElement(BaseAttributes, { title: "Feature 2 attributes", feature: feature2 })));
+});
+export default BreakpointAlignmentsFeatureDetail;
+//# sourceMappingURL=BreakpointAlignmentsFeatureDetail.js.map

package/esm/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"BreakpointAlignmentsFeatureDetail.js","sourceRoot":"","sources":["../../src/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,qBAAqB,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EACL,eAAe,EACf,cAAc,GACf,MAAM,mDAAmD,CAAA;AAE1D,MAAM,iCAAiC,GAAG,QAAQ;AAChD,8DAA8D;AAC9D,CAAC,EAAE,KAAK,EAAkB,EAAE,EAAE;IAC5B,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAA;IAC5E,OAAO,CACL,oBAAC,KAAK,mBAAa,uBAAuB;QACxC,oBAAC,eAAe,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAE,QAAQ,GAAI;QACxD,oBAAC,eAAe,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAE,QAAQ,GAAI;QACxD,oBAAC,cAAc,IAAC,KAAK,EAAC,sBAAsB,EAAC,OAAO,EAAE,QAAQ,GAAI;QAClE,oBAAC,cAAc,IAAC,KAAK,EAAC,sBAAsB,EAAC,OAAO,EAAE,QAAQ,GAAI,CAC5D,CACT,CAAA;AACH,CAAC,CACF,CAAA;AAED,eAAe,iCAAiC,CAAA"}

package/esm/BreakpointAlignmentsFeatureDetail/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/BreakpointAlignmentsFeatureDetail/index.js

@@ -0,0 +1,32 @@
+import { lazy } from 'react';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { ElementId } from '@jbrowse/core/util/types/mst';
+import { types } from 'mobx-state-tree';
+import { WidgetType } from '@jbrowse/core/pluggableElementTypes';
+const configSchema = ConfigurationSchema('BreakpointAlignmentsWidget', {});
+const stateModel = types
+    .model('BreakpointAlignmentsWidget', {
+    id: ElementId,
+    type: types.literal('BreakpointAlignmentsWidget'),
+    featureData: types.frozen(),
+})
+    .actions(self => ({
+    setFeatureData(data) {
+        self.featureData = data;
+    },
+    clearFeatureData() {
+        self.featureData = undefined;
+    },
+}));
+export default (pluginManager) => {
+    pluginManager.addWidgetType(() => {
+        return new WidgetType({
+            name: 'BreakpointAlignmentsWidget',
+            heading: 'Breakpoint feature details',
+            configSchema,
+            stateModel,
+            ReactComponent: lazy(() => import('./BreakpointAlignmentsFeatureDetail')),
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/BreakpointAlignmentsFeatureDetail/index.js.map

@@ -0,0 +1 @@
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package/esm/BreakpointSplitView/BreakpointSplitView.d.ts

@@ -0,0 +1,23 @@
+import { Feature } from '@jbrowse/core/util';
+import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+type LGV = LinearGenomeViewModel;
+export default class BreakpointSplitViewType extends ViewType {
+    snapshotFromBreakendFeature(feature: Feature, view: LGV): {
+        type: string;
+        views: {
+            type: string;
+            displayedRegions: {
+                start: number;
+                end: number;
+                refName: string;
+                assemblyName: string;
+            }[];
+            hideHeader: boolean;
+            bpPerPx: number;
+            offsetPx: number;
+        }[];
+        displayName: string;
+    };
+}
+export {};

package/esm/BreakpointSplitView/BreakpointSplitView.js

@@ -0,0 +1,86 @@
+import { getSession } from '@jbrowse/core/util';
+import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
+import { parseBreakend } from '@gmod/vcf';
+export default class BreakpointSplitViewType extends ViewType {
+    snapshotFromBreakendFeature(feature, view) {
+        var _a;
+        const alt = (_a = feature.get('ALT')) === null || _a === void 0 ? void 0 : _a[0];
+        const bnd = alt ? parseBreakend(alt) : undefined;
+        const startPos = feature.get('start');
+        let endPos;
+        const bpPerPx = 10;
+        // TODO: Figure this out for multiple assembly names
+        const { assemblyName } = view.displayedRegions[0];
+        const { assemblyManager } = getSession(view);
+        const assembly = assemblyManager.get(assemblyName);
+        if (!assembly) {
+            throw new Error(`assembly ${assemblyName} not found`);
+        }
+        if (!assembly.regions) {
+            throw new Error(`assembly ${assemblyName} regions not loaded`);
+        }
+        const { getCanonicalRefName } = assembly;
+        const featureRefName = getCanonicalRefName(feature.get('refName'));
+        const topRegion = assembly.regions.find(f => f.refName === featureRefName);
+        let mateRefName;
+        let startMod = 0;
+        let endMod = 0;
+        // a VCF breakend feature
+        if (alt === '<TRA>') {
+            const INFO = feature.get('INFO');
+            endPos = INFO.END[0] - 1;
+            mateRefName = getCanonicalRefName(INFO.CHR2[0]);
+        }
+        else if (bnd === null || bnd === void 0 ? void 0 : bnd.MatePosition) {
+            const matePosition = bnd.MatePosition.split(':');
+            endPos = +matePosition[1] - 1;
+            mateRefName = getCanonicalRefName(matePosition[0]);
+            if (bnd.Join === 'left') {
+                startMod = -1;
+            }
+            if (bnd.MateDirection === 'left') {
+                endMod = -1;
+            }
+        }
+        else if (feature.get('mate')) {
+            // a generic 'mate' feature
+            const mate = feature.get('mate');
+            mateRefName = getCanonicalRefName(mate.refName);
+            endPos = mate.start;
+        }
+        if (!mateRefName) {
+            throw new Error(`unable to resolve mate refName ${mateRefName} in reference genome`);
+        }
+        const bottomRegion = assembly.regions.find(f => f.refName === mateRefName);
+        if (!topRegion || !bottomRegion) {
+            throw new Error(`unable to find the refName for the top or bottom of the breakpoint view`);
+        }
+        const topMarkedRegion = [{ ...topRegion }, { ...topRegion }];
+        const bottomMarkedRegion = [{ ...bottomRegion }, { ...bottomRegion }];
+        topMarkedRegion[0].end = startPos + startMod;
+        topMarkedRegion[1].start = startPos + startMod;
+        bottomMarkedRegion[0].end = endPos + endMod;
+        bottomMarkedRegion[1].start = endPos + endMod;
+        return {
+            type: 'BreakpointSplitView',
+            views: [
+                {
+                    type: 'LinearGenomeView',
+                    displayedRegions: topMarkedRegion,
+                    hideHeader: true,
+                    bpPerPx,
+                    offsetPx: (topRegion.start + feature.get('start')) / bpPerPx,
+                },
+                {
+                    type: 'LinearGenomeView',
+                    displayedRegions: bottomMarkedRegion,
+                    hideHeader: true,
+                    bpPerPx,
+                    offsetPx: (bottomRegion.start + endPos) / bpPerPx,
+                },
+            ],
+            displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
+        };
+    }
+}
+//# sourceMappingURL=BreakpointSplitView.js.map

package/esm/BreakpointSplitView/BreakpointSplitView.js.map

@@ -0,0 +1 @@
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package/esm/BreakpointSplitView/components/AlignmentConnections.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { BreakpointViewModel } from '../model';
+declare const AlignmentConnections: ({ model, trackId, parentRef, getTrackYPosOverride, }: {
+    model: BreakpointViewModel;
+    trackId: string;
+    parentRef: React.RefObject<SVGSVGElement>;
+    getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
+}) => React.JSX.Element | null;
+export default AlignmentConnections;

package/esm/BreakpointSplitView/components/AlignmentConnections.js

@@ -0,0 +1,108 @@
+import React, { useMemo, useState } from 'react';
+import { observer } from 'mobx-react';
+import { getSnapshot } from 'mobx-state-tree';
+import { useTheme } from '@mui/material';
+import { getSession } from '@jbrowse/core/util';
+// locals
+import { getBadlyPairedAlignments, getMatchedAlignmentFeatures, hasPairedReads, } from './util';
+import { yPos, useNextFrame, getPxFromCoordinate } from '../util';
+const [LEFT, , RIGHT] = [0, 1, 2, 3];
+const AlignmentConnections = observer(function ({ model, trackId, parentRef, getTrackYPosOverride, }) {
+    const { views, showIntraviewLinks } = model;
+    const theme = useTheme();
+    const session = getSession(model);
+    const snap = getSnapshot(model);
+    const { assemblyManager } = session;
+    const assembly = assemblyManager.get(views[0].assemblyNames[0]);
+    useNextFrame(snap);
+    const allFeatures = model.getTrackFeatures(trackId);
+    const hasPaired = useMemo(() => hasPairedReads(allFeatures), [allFeatures]);
+    const layoutMatches = useMemo(() => {
+        const layoutMatches = model.getMatchedFeaturesInLayout(trackId, hasPaired
+            ? getBadlyPairedAlignments(allFeatures)
+            : getMatchedAlignmentFeatures(allFeatures));
+        if (!hasPaired) {
+            layoutMatches.forEach(m => {
+                m.sort((a, b) => a.feature.get('clipPos') - b.feature.get('clipPos'));
+            });
+        }
+        return layoutMatches;
+    }, [allFeatures, trackId, hasPaired, model]);
+    const [mouseoverElt, setMouseoverElt] = useState();
+    let yOffset = 0;
+    if (parentRef.current) {
+        const rect = parentRef.current.getBoundingClientRect();
+        yOffset = rect.top;
+    }
+    if (!assembly) {
+        return null;
+    }
+    return (React.createElement("g", { stroke: theme.palette.text.disabled, fill: "none", "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId }, layoutMatches.map(chunk => {
+        const ret = [];
+        // we follow a path in the list of chunks, not from top to bottom, just in series
+        // following x1,y1 -> x2,y2
+        for (let i = 0; i < chunk.length - 1; i++) {
+            const { layout: c1, feature: f1, level: level1 } = chunk[i];
+            const { layout: c2, feature: f2, level: level2 } = chunk[i + 1];
+            if (!c1 || !c2) {
+                console.warn('received null layout for a overlay feature');
+                return null;
+            }
+            // disable rendering connections in a single level
+            if (!showIntraviewLinks && level1 === level2) {
+                return null;
+            }
+            const f1ref = assembly.getCanonicalRefName(f1.get('refName'));
+            const f2ref = assembly.getCanonicalRefName(f2.get('refName'));
+            if (!f1ref || !f2ref) {
+                throw new Error(`unable to find ref for ${f1ref || f2ref}`);
+            }
+            const s1 = f1.get('strand');
+            const s2 = f2.get('strand');
+            const p1 = c1[s1 === -1 ? LEFT : RIGHT];
+            const sn1 = s2 === -1;
+            const p2 = hasPaired ? c2[sn1 ? LEFT : RIGHT] : c2[sn1 ? RIGHT : LEFT];
+            const x1 = getPxFromCoordinate(views[level1], f1ref, p1);
+            const x2 = getPxFromCoordinate(views[level2], f2ref, p2);
+            const reversed1 = views[level1].pxToBp(x1).reversed;
+            const reversed2 = views[level2].pxToBp(x2).reversed;
+            const tracks = views.map(v => v.getTrack(trackId));
+            const y1 = yPos(trackId, level1, views, tracks, c1, getTrackYPosOverride) -
+                yOffset;
+            const y2 = yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
+                yOffset;
+            // possible todo: use totalCurveHeight to possibly make alternative
+            // squiggle if the S is too small
+            const path = [
+                'M',
+                x1,
+                y1,
+                'C',
+                x1 + 200 * f1.get('strand') * (reversed1 ? -1 : 1),
+                y1,
+                x2 -
+                    200 *
+                        f2.get('strand') *
+                        (reversed2 ? -1 : 1) *
+                        (hasPaired ? -1 : 1),
+                y2,
+                x2,
+                y2,
+            ].join(' ');
+            const id = `${f1.id()}-${f2.id()}`;
+            ret.push(React.createElement("path", { d: path, key: id, "data-testid": "r1", strokeWidth: mouseoverElt === id ? 5 : 1, onClick: () => {
+                    var _a, _b;
+                    const featureWidget = (_a = session.addWidget) === null || _a === void 0 ? void 0 : _a.call(session, 'BreakpointAlignmentsWidget', 'breakpointAlignments', {
+                        featureData: {
+                            feature1: (allFeatures.get(f1.id()) || { toJSON: () => { } }).toJSON(),
+                            feature2: (allFeatures.get(f2.id()) || { toJSON: () => { } }).toJSON(),
+                        },
+                    });
+                    (_b = session.showWidget) === null || _b === void 0 ? void 0 : _b.call(session, featureWidget);
+                }, onMouseOver: () => setMouseoverElt(id), onMouseOut: () => setMouseoverElt(undefined) }));
+        }
+        return ret;
+    })));
+});
+export default AlignmentConnections;
+//# sourceMappingURL=AlignmentConnections.js.map

package/esm/BreakpointSplitView/components/AlignmentConnections.js.map

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package/esm/BreakpointSplitView/components/Breakends.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { BreakpointViewModel } from '../model';
+declare const Breakends: ({ model, trackId, parentRef: ref, getTrackYPosOverride, }: {
+    model: BreakpointViewModel;
+    trackId: string;
+    parentRef: React.RefObject<SVGSVGElement>;
+    getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
+}) => React.JSX.Element | null;
+export default Breakends;