@jbrowse/plugin-breakpoint-split-view 2.17.0 → 3.0.0

package/dist/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.d.ts

@@ -1,7 +1,10 @@
-import React from 'react';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 declare const BreakpointAlignmentsFeatureDetail: ({ model, }: {
     model: {
-        featureData: Record<string, unknown>;
+        featureData: {
+            feature1: SimpleFeatureSerialized;
+            feature2: SimpleFeatureSerialized;
+        };
     };
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default BreakpointAlignmentsFeatureDetail;

package/dist/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.js

@@ -1,18 +1,12 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
 const BreakpointAlignmentsFeatureDetail = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { feature1, feature2 } = JSON.parse(JSON.stringify(model.featureData));
-    return (react_1.default.createElement(material_1.Paper, { "data-testid": "alignment-side-drawer" },
-        react_1.default.createElement(BaseFeatureDetail_1.BaseCoreDetails, { title: "Feature 1", feature: feature1 }),
-        react_1.default.createElement(BaseFeatureDetail_1.BaseCoreDetails, { title: "Feature 2", feature: feature2 }),
-        react_1.default.createElement(BaseFeatureDetail_1.BaseAttributes, { title: "Feature 1 attributes", feature: feature1 }),
-        react_1.default.createElement(BaseFeatureDetail_1.BaseAttributes, { title: "Feature 2 attributes", feature: feature2 })));
+    const { featureData } = model;
+    const { feature1, feature2 } = structuredClone(featureData);
+    return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { children: [(0, jsx_runtime_1.jsx)(BaseFeatureDetail_1.BaseCoreDetails, { title: "Feature 1", feature: feature1 }), (0, jsx_runtime_1.jsx)(BaseFeatureDetail_1.BaseCoreDetails, { title: "Feature 2", feature: feature2 }), (0, jsx_runtime_1.jsx)(BaseFeatureDetail_1.BaseAttributes, { title: "Feature 1 attributes", feature: feature1 }), (0, jsx_runtime_1.jsx)(BaseFeatureDetail_1.BaseAttributes, { title: "Feature 2 attributes", feature: feature2 })] }));
 });
 exports.default = BreakpointAlignmentsFeatureDetail;

package/dist/BreakpointAlignmentsFeatureDetail/index.d.ts

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

package/dist/BreakpointAlignmentsFeatureDetail/index.js

@@ -15,20 +15,30 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = BreakpointAlignmentsFeatureDetailF;
 const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
+const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const mst_1 = require("@jbrowse/core/util/types/mst");
 const mobx_state_tree_1 = require("mobx-state-tree");
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const configSchema = (0, configuration_1.ConfigurationSchema)('BreakpointAlignmentsWidget', {});
 const stateModel = mobx_state_tree_1.types
     .model('BreakpointAlignmentsWidget', {

package/dist/BreakpointSplitView/BreakpointSplitView.d.ts

@@ -1,52 +1,34 @@
-import { Feature, Region } from '@jbrowse/core/util';
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
-import { IStateTreeNode } from 'mobx-state-tree';
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import { type AbstractSessionModel, type Feature } from '@jbrowse/core/util';
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
 export default class BreakpointSplitViewType extends ViewType {
     getBreakendCoveringRegions({ feature, assembly, }: {
         feature: Feature;
         assembly: Assembly;
     }): {
         pos: number;
-        refName: string | undefined;
-        mateRefName: string | undefined;
-        matePos: number;
+        refName: string;
+        mateRefName: string;
+        matePos: any;
     };
-    singleLevelSnapshotFromBreakendFeature(feature: Feature, view: {
-        displayedRegions: Region[];
-    } & IStateTreeNode): {
-        type: string;
-        views: {
-            type: string;
-            displayedRegions: {
-                start: number;
-                end: number;
-                refName: string;
-                assemblyName: string;
-            }[];
-            hideHeader: boolean;
-            bpPerPx: number;
-            offsetPx: number;
-        }[];
-        displayName: string;
-        featureData: unknown;
-    };
-    snapshotFromBreakendFeature(feature: Feature, view: {
-        displayedRegions: Region[];
-    } & IStateTreeNode): {
-        type: string;
-        views: {
+    singleLevelSnapshotFromBreakendFeature({ feature, session, assemblyName, }: {
+        feature: Feature;
+        session: AbstractSessionModel;
+        assemblyName: string;
+    }): {
+        coverage: {
+            pos: number;
+            refName: string;
+            mateRefName: string;
+            matePos: any;
+        };
+        snap: {
             type: string;
-            displayedRegions: {
-                start: number;
-                end: number;
-                refName: string;
-                assemblyName: string;
+            views: {
+                type: string;
+                displayedRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[];
             }[];
-            hideHeader: boolean;
-            bpPerPx: number;
-            offsetPx: number;
-        }[];
-        displayName: string;
+            displayName: string;
+        };
     };
 }

package/dist/BreakpointSplitView/BreakpointSplitView.js

@@ -3,9 +3,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const util_1 = require("@jbrowse/core/util");
-const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
 const vcf_1 = require("@gmod/vcf");
+const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
+const util_1 = require("@jbrowse/core/util");
 class BreakpointSplitViewType extends ViewType_1.default {
     getBreakendCoveringRegions({ feature, assembly, }) {
         var _a;
@@ -13,81 +13,44 @@ class BreakpointSplitViewType extends ViewType_1.default {
         const bnd = alt ? (0, vcf_1.parseBreakend)(alt) : undefined;
         const startPos = feature.get('start');
         const refName = feature.get('refName');
-        let endPos;
-        let mateRefName;
-        // a VCF breakend feature
+        const f = (ref) => assembly.getCanonicalRefName(ref) || ref;
         if (alt === '<TRA>') {
             const INFO = feature.get('INFO');
-            endPos = INFO.END[0] - 1;
-            mateRefName = INFO.CHR2[0];
+            return {
+                pos: startPos,
+                refName: f(refName),
+                mateRefName: f(INFO.CHR2[0]),
+                matePos: INFO.END[0] - 1,
+            };
         }
         else if (bnd === null || bnd === void 0 ? void 0 : bnd.MatePosition) {
             const matePosition = bnd.MatePosition.split(':');
-            endPos = +matePosition[1] - 1;
-            mateRefName = matePosition[0];
+            return {
+                pos: startPos,
+                refName: f(refName),
+                mateRefName: f(matePosition[0]),
+                matePos: +matePosition[1] - 1,
+            };
         }
         else if (feature.get('mate')) {
-            // a generic 'mate' feature
             const mate = feature.get('mate');
-            mateRefName = mate.refName;
-            endPos = mate.start;
+            return {
+                pos: startPos,
+                refName: f(refName),
+                mateRefName: f(mate.refName),
+                matePos: mate.start,
+            };
         }
         else {
-            endPos = startPos + 1;
-        }
-        if (!mateRefName) {
-            throw new Error(`unable to resolve mate refName ${mateRefName} in reference genome`);
+            return {
+                pos: startPos,
+                refName: f(refName),
+                mateRefName: f(refName),
+                matePos: feature.get('end'),
+            };
         }
-        return {
-            pos: startPos,
-            refName: assembly.getCanonicalRefName(refName),
-            mateRefName: assembly.getCanonicalRefName(mateRefName),
-            matePos: endPos,
-        };
-    }
-    singleLevelSnapshotFromBreakendFeature(feature, view) {
-        const session = (0, util_1.getSession)(view);
-        const bpPerPx = 10;
-        const { assemblyName } = view.displayedRegions[0];
-        const { assemblyManager } = session;
-        const assembly = assemblyManager.get(assemblyName);
-        if (!assembly) {
-            throw new Error(`assembly ${assemblyName} not found`);
-        }
-        if (!assembly.regions) {
-            throw new Error(`assembly ${assemblyName} regions not loaded`);
-        }
-        const { refName, pos: startPos, mateRefName, matePos: endPos, } = this.getBreakendCoveringRegions({
-            feature,
-            assembly,
-        });
-        const topRegion = assembly.regions.find(f => f.refName === refName);
-        const bottomRegion = assembly.regions.find(f => f.refName === mateRefName);
-        const topMarkedRegion = [{ ...topRegion }, { ...topRegion }];
-        const bottomMarkedRegion = [{ ...bottomRegion }, { ...bottomRegion }];
-        topMarkedRegion[0].end = startPos;
-        topMarkedRegion[1].start = startPos;
-        bottomMarkedRegion[0].end = endPos;
-        bottomMarkedRegion[1].start = endPos;
-        return {
-            type: 'BreakpointSplitView',
-            views: [
-                {
-                    type: 'LinearGenomeView',
-                    displayedRegions: topMarkedRegion,
-                    hideHeader: true,
-                    bpPerPx,
-                    offsetPx: (topRegion.start + feature.get('start')) / bpPerPx,
-                },
-            ],
-            displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
-            featureData: undefined,
-        };
     }
-    snapshotFromBreakendFeature(feature, view) {
-        const session = (0, util_1.getSession)(view);
-        const bpPerPx = 10;
-        const { assemblyName } = view.displayedRegions[0];
+    singleLevelSnapshotFromBreakendFeature({ feature, session, assemblyName, }) {
         const { assemblyManager } = session;
         const assembly = assemblyManager.get(assemblyName);
         if (!assembly) {
@@ -96,37 +59,25 @@ class BreakpointSplitViewType extends ViewType_1.default {
         if (!assembly.regions) {
             throw new Error(`assembly ${assemblyName} regions not loaded`);
         }
-        const { refName, pos: startPos, mateRefName, matePos: endPos, } = this.getBreakendCoveringRegions({
+        const coverage = this.getBreakendCoveringRegions({
             feature,
             assembly,
         });
+        const { refName, mateRefName } = coverage;
         const topRegion = assembly.regions.find(f => f.refName === refName);
         const bottomRegion = assembly.regions.find(f => f.refName === mateRefName);
-        const topMarkedRegion = [{ ...topRegion }, { ...topRegion }];
-        const bottomMarkedRegion = [{ ...bottomRegion }, { ...bottomRegion }];
-        topMarkedRegion[0].end = startPos;
-        topMarkedRegion[1].start = startPos;
-        bottomMarkedRegion[0].end = endPos;
-        bottomMarkedRegion[1].start = endPos;
         return {
-            type: 'BreakpointSplitView',
-            views: [
-                {
-                    type: 'LinearGenomeView',
-                    displayedRegions: topMarkedRegion,
-                    hideHeader: true,
-                    bpPerPx,
-                    offsetPx: (topRegion.start + feature.get('start')) / bpPerPx,
-                },
-                {
-                    type: 'LinearGenomeView',
-                    displayedRegions: bottomMarkedRegion,
-                    hideHeader: true,
-                    bpPerPx,
-                    offsetPx: (bottomRegion.start + endPos) / bpPerPx,
-                },
-            ],
-            displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
+            coverage,
+            snap: {
+                type: 'BreakpointSplitView',
+                views: [
+                    {
+                        type: 'LinearGenomeView',
+                        displayedRegions: (0, util_1.gatherOverlaps)([topRegion, bottomRegion]),
+                    },
+                ],
+                displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
+            },
         };
     }
 }

package/dist/BreakpointSplitView/components/AlignmentConnections.d.ts

@@ -1,9 +1,8 @@
-import React from 'react';
-import { BreakpointViewModel } from '../model';
+import type { BreakpointViewModel } from '../model';
 declare const AlignmentConnections: ({ model, trackId, parentRef, getTrackYPosOverride, }: {
     model: BreakpointViewModel;
     trackId: string;
-    parentRef: React.RefObject<SVGSVGElement>;
+    parentRef: React.RefObject<SVGSVGElement | null>;
     getTrackYPosOverride?: (trackId: string, level: number) => number;
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default AlignmentConnections;

package/dist/BreakpointSplitView/components/AlignmentConnections.js

@@ -1,40 +1,17 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const mobx_state_tree_1 = require("mobx-state-tree");
-const material_1 = require("@mui/material");
-const util_1 = require("@jbrowse/core/util");
-// locals
 const util_2 = require("./util");
 const util_3 = require("../util");
 const getOrientationColor_1 = require("./getOrientationColor");
 const [LEFT, , RIGHT] = [0, 1, 2, 3];
 const AlignmentConnections = (0, mobx_react_1.observer)(function ({ model, trackId, parentRef, getTrackYPosOverride, }) {
-    const { views, showIntraviewLinks } = model;
+    const { interactiveOverlay, views, showIntraviewLinks } = model;
     const theme = (0, material_1.useTheme)();
     const session = (0, util_1.getSession)(model);
     const snap = (0, mobx_state_tree_1.getSnapshot)(model);
@@ -61,104 +38,96 @@ const AlignmentConnections = (0, mobx_react_1.observer)(function ({ model, track
         const rect = parentRef.current.getBoundingClientRect();
         yOffset = rect.top;
     }
-    return assembly ? (react_1.default.createElement("g", { 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 row
-            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 ${f1ref || f2ref}`);
-            }
-            const r = {
-                pair_orientation: f1.get('pair_orientation'),
-            };
-            const s1 = f1.get('strand');
-            const s2 = f2.get('strand');
-            const sameRef = f1ref === f2ref;
-            const checkOrientation = sameRef;
-            let orientationColor = '';
-            let isAbnormal = false;
-            if (checkOrientation) {
-                if (hasPaired) {
-                    orientationColor = (0, getOrientationColor_1.getPairedOrientationColor)(r);
-                    isAbnormal = (0, getOrientationColor_1.isAbnormalOrientation)(r);
+    return assembly ? ((0, jsx_runtime_1.jsx)("g", { fill: "none", "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId, children: layoutMatches.map(chunk => {
+            const ret = [];
+            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;
                 }
-                else {
-                    orientationColor = (0, getOrientationColor_1.getLongReadOrientationColorOrDefault)(s1, s2);
-                    isAbnormal = (0, getOrientationColor_1.getLongReadOrientationAbnormal)(s1, s2);
+                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 r = {
+                    pair_orientation: f1.get('pair_orientation'),
+                };
+                const s1 = f1.get('strand');
+                const s2 = f2.get('strand');
+                const sameRef = f1ref === f2ref;
+                const checkOrientation = sameRef;
+                let orientationColor = '';
+                let isAbnormal = false;
+                if (checkOrientation) {
+                    if (hasPaired) {
+                        orientationColor = (0, getOrientationColor_1.getPairedOrientationColor)(r);
+                        isAbnormal = (0, getOrientationColor_1.isAbnormalOrientation)(r);
+                    }
+                    else {
+                        orientationColor = (0, getOrientationColor_1.getLongReadOrientationColorOrDefault)(s1, s2);
+                        isAbnormal = (0, getOrientationColor_1.getLongReadOrientationAbnormal)(s1, s2);
+                    }
+                }
+                const p1 = c1[s1 === -1 ? LEFT : RIGHT];
+                const sn1 = s2 === -1;
+                const p2 = hasPaired ? c2[sn1 ? LEFT : RIGHT] : c2[sn1 ? RIGHT : LEFT];
+                const x1 = (0, util_3.getPxFromCoordinate)(views[level1], f1ref, p1);
+                const x2 = (0, util_3.getPxFromCoordinate)(views[level2], f2ref, p2);
+                const reversed1 = views[level1].pxToBp(x1).reversed;
+                const reversed2 = views[level2].pxToBp(x2).reversed;
+                const rf1 = reversed1 ? -1 : 1;
+                const rf2 = reversed2 ? -1 : 1;
+                const tracks = views.map(v => v.getTrack(trackId));
+                const y1 = (0, util_3.yPos)(trackId, level1, views, tracks, c1, getTrackYPosOverride) -
+                    yOffset;
+                const y2 = (0, util_3.yPos)(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
+                    yOffset;
+                const sameLevel = level1 === level2;
+                const abnormalSpecialRenderFlag = sameLevel && isAbnormal;
+                const trackHeight = abnormalSpecialRenderFlag
+                    ? tracks[level1].displays[0].height
+                    : 0;
+                const pf1 = hasPaired ? -1 : 1;
+                const y0 = (0, util_3.heightFromSpecificLevel)(views, trackId, level1, getTrackYPosOverride);
+                const path = [
+                    'M',
+                    x1,
+                    y1,
+                    'C',
+                    x1 + 200 * f1.get('strand') * rf1,
+                    abnormalSpecialRenderFlag
+                        ? Math.min(y0 - yOffset + trackHeight, y1 + trackHeight)
+                        : y1,
+                    x2 - 200 * f2.get('strand') * rf2 * pf1,
+                    abnormalSpecialRenderFlag
+                        ? Math.min(y0 - yOffset + trackHeight, y2 + trackHeight)
+                        : y2,
+                    x2,
+                    y2,
+                ].join(' ');
+                const id = `${f1.id()}-${f2.id()}`;
+                ret.push((0, jsx_runtime_1.jsx)("path", { d: path, "data-testid": "r1", pointerEvents: interactiveOverlay ? 'auto' : undefined, strokeWidth: mouseoverElt === id ? 5 : 1, ...(0, util_1.getStrokeProps)(orientationColor || theme.palette.text.disabled), 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);
+                    } }, id));
             }
-            const p1 = c1[s1 === -1 ? LEFT : RIGHT];
-            const sn1 = s2 === -1;
-            const p2 = hasPaired ? c2[sn1 ? LEFT : RIGHT] : c2[sn1 ? RIGHT : LEFT];
-            const x1 = (0, util_3.getPxFromCoordinate)(views[level1], f1ref, p1);
-            const x2 = (0, util_3.getPxFromCoordinate)(views[level2], f2ref, p2);
-            const reversed1 = views[level1].pxToBp(x1).reversed;
-            const reversed2 = views[level2].pxToBp(x2).reversed;
-            const rf1 = reversed1 ? -1 : 1;
-            const rf2 = reversed2 ? -1 : 1;
-            const tracks = views.map(v => v.getTrack(trackId));
-            const y1 = (0, util_3.yPos)(trackId, level1, views, tracks, c1, getTrackYPosOverride) -
-                yOffset;
-            const y2 = (0, util_3.yPos)(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
-                yOffset;
-            const sameLevel = level1 === level2;
-            const abnormalSpecialRenderFlag = sameLevel && isAbnormal;
-            const trackHeight = abnormalSpecialRenderFlag
-                ? tracks[level1].displays[0].height
-                : 0;
-            const pf1 = hasPaired ? -1 : 1;
-            const y0 = (0, util_3.heightFromSpecificLevel)(views, trackId, level1, getTrackYPosOverride);
-            // possible todo: use totalCurveHeight to possibly make alternative
-            // squiggle if the S is too small
-            const path = [
-                'M',
-                x1,
-                y1,
-                'C',
-                // first bezier x,y
-                x1 + 200 * f1.get('strand') * rf1,
-                abnormalSpecialRenderFlag
-                    ? Math.min(y0 - yOffset + trackHeight, y1 + trackHeight)
-                    : y1,
-                // second bezier x,y
-                x2 - 200 * f2.get('strand') * rf2 * pf1,
-                abnormalSpecialRenderFlag
-                    ? Math.min(y0 - yOffset + trackHeight, y2 + trackHeight)
-                    : y2,
-                // third bezier x,y
-                x2,
-                y2,
-            ].join(' ');
-            const id = `${f1.id()}-${f2.id()}`;
-            ret.push(react_1.default.createElement("path", { d: path, key: id, "data-testid": "r1", strokeWidth: mouseoverElt === id ? 5 : 1, ...(0, util_1.getStrokeProps)(orientationColor || theme.palette.text.disabled), 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;
-    }))) : null;
+            return ret;
+        }) })) : null;
 });
 exports.default = AlignmentConnections;

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

@@ -1,9 +1,8 @@
-import React from 'react';
-import { BreakpointViewModel } from '../model';
+import type { BreakpointViewModel } from '../model';
 declare const Breakends: ({ model, trackId, parentRef: ref, getTrackYPosOverride, }: {
     model: BreakpointViewModel;
     trackId: string;
-    parentRef: React.RefObject<SVGSVGElement>;
+    parentRef: React.RefObject<SVGSVGElement | null>;
     getTrackYPosOverride?: (trackId: string, level: number) => number;
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default Breakends;