@jbrowse/sv-core 3.7.0 → 4.0.0

package/{dist/BreakendMultiLevelOptionDialog.d.ts → esm/BreakpointSplitViewChoiceDialog.d.ts}

@@ -1,6 +1,6 @@
 import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-declare const BreakendMultiLevelOptionDialog: ({ session, handleClose, feature, assemblyName, stableViewId, view, }: {
+declare const BreakpointSplitViewChoiceDialog: ({ session, handleClose, feature, assemblyName, stableViewId, view, }: {
     session: AbstractSessionModel;
     handleClose: () => void;
     feature: Feature;
@@ -8,4 +8,4 @@ declare const BreakendMultiLevelOptionDialog: ({ session, handleClose, feature,
     assemblyName: string;
     stableViewId?: string;
 }) => import("react/jsx-runtime").JSX.Element;
-export default BreakendMultiLevelOptionDialog;
+export default BreakpointSplitViewChoiceDialog;

package/esm/BreakpointSplitViewChoiceDialog.js

@@ -0,0 +1,83 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { useLocalStorage } from '@jbrowse/core/util';
+import { getSnapshot } from '@jbrowse/mobx-state-tree';
+import { Button, DialogActions, DialogContent, List, ListItemButton, ListItemIcon, ListItemText, TextField, } from '@mui/material';
+import { observer } from 'mobx-react';
+import Checkbox2 from "./Checkbox2.js";
+import { navToMultiLevelBreak } from "./navToMultiLevelBreak.js";
+import { navToSingleLevelBreak } from "./navToSingleLevelBreak.js";
+function SplitLevelIcon() {
+    return (_jsxs("svg", { width: "24", height: "24", viewBox: "0 0 24 24", children: [_jsx("rect", { x: "2", y: "3", width: "20", height: "8", rx: "1", fill: "currentColor" }), _jsx("rect", { x: "2", y: "13", width: "20", height: "8", rx: "1", fill: "currentColor" })] }));
+}
+function SingleLevelIcon() {
+    return (_jsx("svg", { width: "24", height: "24", viewBox: "0 0 24 24", children: _jsx("rect", { x: "2", y: "8", width: "20", height: "8", rx: "1", fill: "currentColor" }) }));
+}
+const BreakpointSplitViewChoiceDialog = observer(function BreakpointSplitViewChoiceDialog({ session, handleClose, feature, assemblyName, stableViewId, view, }) {
+    const [step, setStep] = useState('choose');
+    const [viewType, setViewType] = useState('split');
+    const [copyTracks, setCopyTracks] = useState(true);
+    const [mirror, setMirror] = useState(true);
+    const [focusOnBreakends, setFocusOnBreakends] = useState(true);
+    const [windowSize, setWindowSize] = useLocalStorage('breakpointWindowSize', '5000');
+    const isSplitLevel = viewType === 'split';
+    const handleLaunch = () => {
+        ;
+        (async () => {
+            try {
+                await (isSplitLevel
+                    ? navToMultiLevelBreak({
+                        stableViewId: stableViewId
+                            ? `${stableViewId}_multilevel`
+                            : undefined,
+                        session,
+                        tracks: copyTracks && view
+                            ? getSnapshot(view.tracks)
+                            : [],
+                        mirror,
+                        feature,
+                        assemblyName,
+                        windowSize: +windowSize || 0,
+                    })
+                    : navToSingleLevelBreak({
+                        feature,
+                        assemblyName,
+                        focusOnBreakends,
+                        session,
+                        stableViewId: stableViewId
+                            ? `${stableViewId}_singlelevel`
+                            : undefined,
+                        tracks: copyTracks ? view?.tracks : undefined,
+                        windowSize: +windowSize || 0,
+                    }));
+            }
+            catch (e) {
+                console.error(e);
+                session.notifyError(`${e}`, e);
+            }
+        })();
+        handleClose();
+    };
+    if (step === 'choose') {
+        return (_jsx(Dialog, { open: true, onClose: handleClose, title: "Open breakpoint split view", children: _jsx(DialogContent, { children: _jsxs(List, { children: [_jsxs(ListItemButton, { onClick: () => {
+                                setViewType('split');
+                                setStep('options');
+                            }, children: [_jsx(ListItemIcon, { children: _jsx(SplitLevelIcon, {}) }), _jsx(ListItemText, { primary: "Split level (top/bottom)", secondary: "Opens two stacked linear genome views, one for each breakend" })] }), _jsxs(ListItemButton, { onClick: () => {
+                                setViewType('single');
+                                setStep('options');
+                            }, children: [_jsx(ListItemIcon, { children: _jsx(SingleLevelIcon, {}) }), _jsx(ListItemText, { primary: "Single level (single row)", secondary: "Opens one linear genome view spanning both breakends" })] })] }) }) }));
+    }
+    return (_jsxs(Dialog, { open: true, onClose: handleClose, title: isSplitLevel ? 'Split level options' : 'Single level options', children: [_jsxs(DialogContent, { children: [view ? (_jsx(Checkbox2, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
+                            setCopyTracks(event.target.checked);
+                        } })) : null, isSplitLevel ? (view && copyTracks ? (_jsx(Checkbox2, { checked: mirror, label: "Mirror the copied tracks", onChange: event => {
+                            setMirror(event.target.checked);
+                        } })) : null) : (_jsx(Checkbox2, { checked: focusOnBreakends, label: "Focus on breakends", onChange: event => {
+                            setFocusOnBreakends(event.target.checked);
+                        } })), _jsx(TextField, { label: "Window size (bp)", value: windowSize, onChange: event => {
+                            setWindowSize(event.target.value);
+                        }, size: "small", style: { marginTop: 8, display: 'block' } })] }), _jsxs(DialogActions, { children: [_jsx(Button, { onClick: () => {
+                            setStep('choose');
+                        }, children: "Back" }), _jsx(Button, { variant: "contained", color: "primary", onClick: handleLaunch, children: "Open" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: handleClose, children: "Cancel" })] })] }));
+});
+export default BreakpointSplitViewChoiceDialog;

package/esm/Checkbox2.js

@@ -1,12 +1,5 @@
 import { jsx as _jsx } from "react/jsx-runtime";
 import { Checkbox, FormControlLabel } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-const useStyles = makeStyles()({
-    block: {
-        display: 'block',
-    },
-});
 export default function Checkbox2({ checked, disabled, label, onChange, }) {
-    const { classes } = useStyles();
-    return (_jsx(FormControlLabel, { disabled: disabled, className: classes.block, control: _jsx(Checkbox, { checked: checked, onChange: onChange }), label: label }));
+    return (_jsx(FormControlLabel, { disabled: disabled, style: { display: 'block' }, control: _jsx(Checkbox, { checked: checked, onChange: onChange }), label: label }));
 }

package/esm/index.d.ts

@@ -1,5 +1,4 @@
-export { default as BreakendMultiLevelOptionDialog } from './BreakendMultiLevelOptionDialog';
-export { default as BreakendSingleLevelOptionDialog } from './BreakendSingleLevelOptionDialog';
-export * from './util';
-export * from './navToSingleLevelBreak';
-export * from './navToMultiLevelBreak';
+export { default as BreakpointSplitViewChoiceDialog } from './BreakpointSplitViewChoiceDialog.tsx';
+export * from './util.ts';
+export * from './navToSingleLevelBreak.ts';
+export * from './navToMultiLevelBreak.ts';

package/esm/index.js

@@ -1,5 +1,4 @@
-export { default as BreakendMultiLevelOptionDialog } from './BreakendMultiLevelOptionDialog';
-export { default as BreakendSingleLevelOptionDialog } from './BreakendSingleLevelOptionDialog';
-export * from './util';
-export * from './navToSingleLevelBreak';
-export * from './navToMultiLevelBreak';
+export { default as BreakpointSplitViewChoiceDialog } from "./BreakpointSplitViewChoiceDialog.js";
+export * from "./util.js";
+export * from "./navToSingleLevelBreak.js";
+export * from "./navToMultiLevelBreak.js";

package/esm/navToMultiLevelBreak.d.ts

@@ -1,6 +1,6 @@
-import type { Track } from './types';
+import type { Track } from './types.ts';
 import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
-export declare function navToMultiLevelBreak({ stableViewId, feature, assemblyName, session, mirror, tracks: viewTracks, }: {
+export declare function navToMultiLevelBreak({ stableViewId, feature, assemblyName, session, mirror, tracks: viewTracks, windowSize, }: {
     stableViewId?: string;
     feature: Feature;
     assemblyName: string;

package/esm/navToMultiLevelBreak.js

@@ -1,6 +1,6 @@
 import { when } from '@jbrowse/core/util';
-import { getBreakendCoveringRegions, makeTitle, stripIds } from './util';
-export async function navToMultiLevelBreak({ stableViewId, feature, assemblyName, session, mirror, tracks: viewTracks = [], }) {
+import { getBreakendCoveringRegions, makeTitle, splitRegionAtPosition, stripIds, } from "./util.js";
+export async function navToMultiLevelBreak({ stableViewId, feature, assemblyName, session, mirror, tracks: viewTracks = [], windowSize = 0, }) {
     const { assemblyManager } = session;
     const assembly = await assemblyManager.waitForAssembly(assemblyName);
     if (!assembly) {
@@ -37,38 +37,15 @@ export async function navToMultiLevelBreak({ stableViewId, feature, assemblyName
         throw new Error("can't find regions");
     }
     await Promise.all([
-        view.views[0].navToLocations([
-            {
-                refName,
-                start: r1.start,
-                end: pos,
-                assemblyName,
-            },
-            {
-                refName,
-                start: pos + 1,
-                end: r1.end,
-                assemblyName,
-            },
-        ]),
-        view.views[1].navToLocations([
-            {
-                refName: mateRefName,
-                start: r2.start,
-                end: matePos,
-                assemblyName,
-            },
-            {
-                refName: mateRefName,
-                start: matePos + 1,
-                end: r2.end,
-                assemblyName,
-            },
-        ]),
+        view.views[0].navToLocations(splitRegionAtPosition(r1, pos, assemblyName)),
+        view.views[1].navToLocations(splitRegionAtPosition(r2, matePos, assemblyName)),
     ]);
     await when(() => view.views[1].initialized && view.views[0].initialized);
-    view.views[1].zoomTo(10);
-    view.views[0].zoomTo(10);
-    view.views[1].centerAt(matePos, mateRefName);
-    view.views[0].centerAt(pos, refName);
+    const lgv0 = view.views[0];
+    const lgv1 = view.views[1];
+    const bpPerPx = windowSize > 0 ? (windowSize * 2) / lgv0.width : 10;
+    lgv0.zoomTo(bpPerPx);
+    lgv1.zoomTo(bpPerPx);
+    lgv0.centerAt(pos, refName);
+    lgv1.centerAt(matePos, mateRefName);
 }

package/esm/navToSingleLevelBreak.js

@@ -1,6 +1,6 @@
 import { gatherOverlaps, getSession, when } from '@jbrowse/core/util';
-import { getSnapshot } from 'mobx-state-tree';
-import { getBreakendCoveringRegions, makeTitle, stripIds } from './util';
+import { getSnapshot } from '@jbrowse/mobx-state-tree';
+import { getBreakendCoveringRegions, makeTitle, stripIds } from "./util.js";
 export function singleLevelFocusedSnapshotFromBreakendFeature({ feature, session, assemblyName, windowSize = 0, }) {
     const { assemblyManager } = session;
     const assembly = assemblyManager.get(assemblyName);
@@ -27,7 +27,7 @@ export function singleLevelFocusedSnapshotFromBreakendFeature({ feature, session
                     displayedRegions: gatherOverlaps([
                         {
                             ...topRegion,
-                            end: coverage.pos + windowSize,
+                            end: coverage.pos + 1 + windowSize,
                             assemblyName,
                         },
                         {
@@ -76,7 +76,6 @@ export function singleLevelEncompassingSnapshotFromBreakendFeature({ feature, se
     };
 }
 export async function navToSingleLevelBreak({ stableViewId, feature, assemblyName, session, tracks, windowSize = 0, focusOnBreakends, }) {
-    var _a;
     const { snap, coverage } = focusOnBreakends
         ? singleLevelFocusedSnapshotFromBreakendFeature({
             feature,
@@ -103,29 +102,37 @@ export async function navToSingleLevelBreak({ stableViewId, feature, assemblyNam
         });
     }
     else {
-        (_a = view.views[0]) === null || _a === void 0 ? void 0 : _a.setDisplayedRegions(snap.views[0].displayedRegions);
+        view.views[0]?.setDisplayedRegions(snap.views[0].displayedRegions);
         view.setDisplayName(snap.displayName);
     }
     const lgv = view.views[0];
     await when(() => lgv.initialized);
-    const l0 = lgv.bpToPx({
-        coord: Math.max(0, startPos - windowSize),
-        refName,
-    });
-    const r0 = lgv.bpToPx({
-        coord: endPos + windowSize,
-        refName: mateRefName,
-    });
-    if (l0 && r0) {
-        lgv.moveTo({
-            ...l0,
-            offset: l0.offsetPx,
-        }, {
-            ...r0,
-            offset: r0.offsetPx,
-        });
+    if (focusOnBreakends) {
+        lgv.zoomTo(10);
+        const l0 = lgv.bpToPx({ coord: startPos, refName });
+        const r0 = lgv.bpToPx({ coord: endPos, refName: mateRefName });
+        if (l0 && r0) {
+            const midPx = (l0.offsetPx + r0.offsetPx) / 2;
+            lgv.scrollTo(Math.round(midPx - lgv.width / 2));
+        }
+        else {
+            getSession(lgv).notify('Unable to navigate to breakpoint');
+        }
     }
     else {
-        getSession(lgv).notify('Unable to navigate to breakpoint');
+        const l0 = lgv.bpToPx({
+            coord: Math.max(0, startPos - windowSize),
+            refName,
+        });
+        const r0 = lgv.bpToPx({
+            coord: endPos + windowSize,
+            refName: mateRefName,
+        });
+        if (l0 && r0) {
+            lgv.moveTo({ ...l0, offset: l0.offsetPx }, { ...r0, offset: r0.offsetPx });
+        }
+        else {
+            getSession(lgv).notify('Unable to navigate to breakpoint');
+        }
     }
 }

package/esm/util.d.ts

@@ -1,4 +1,4 @@
-import type { Track } from './types';
+import type { Track } from './types.ts';
 import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
 import type { Feature } from '@jbrowse/core/util';
 export declare function getBreakendCoveringRegions({ feature, assembly, }: {
@@ -16,3 +16,22 @@ export declare function stripIds(arr: Track[]): {
     }[];
 }[];
 export declare function makeTitle(f: Feature): string;
+export interface Region {
+    refName: string;
+    start: number;
+    end: number;
+    assemblyName?: string;
+}
+export interface ViewWithAssemblyNames {
+    assemblyNames: string[];
+}
+export declare function getAssemblyName(view?: ViewWithAssemblyNames): string | undefined;
+export declare function splitRegionAtPosition<T extends {
+    refName: string;
+    start: number;
+    end: number;
+}>(region: T, pos: number, assemblyName?: string): [T & {
+    assemblyName?: string;
+}, T & {
+    assemblyName?: string;
+}];

package/esm/util.js

@@ -1,7 +1,6 @@
 import { parseBreakend } from '@gmod/vcf';
 export function getBreakendCoveringRegions({ feature, assembly, }) {
-    var _a;
-    const alt = (_a = feature.get('ALT')) === null || _a === void 0 ? void 0 : _a[0];
+    const alt = feature.get('ALT')?.[0];
     const bnd = alt ? parseBreakend(alt) : undefined;
     const startPos = feature.get('start');
     const refName = feature.get('refName');
@@ -15,7 +14,7 @@ export function getBreakendCoveringRegions({ feature, assembly, }) {
             matePos: INFO.END[0] - 1,
         };
     }
-    else if (bnd === null || bnd === void 0 ? void 0 : bnd.MatePosition) {
+    else if (bnd?.MatePosition) {
         const matePosition = bnd.MatePosition.split(':');
         return {
             pos: startPos,
@@ -26,11 +25,15 @@ export function getBreakendCoveringRegions({ feature, assembly, }) {
     }
     else if (feature.get('mate')) {
         const mate = feature.get('mate');
+        const strand = feature.get('strand');
+        const mateStrand = mate.strand;
+        const pos = strand === 1 ? feature.get('end') : startPos;
+        const matePos = mateStrand === 1 ? mate.start : (mate.end ?? mate.start);
         return {
-            pos: startPos,
+            pos,
             refName: f(refName),
             mateRefName: f(mate.refName),
-            matePos: mate.start,
+            matePos,
         };
     }
     else {
@@ -51,3 +54,20 @@ export function stripIds(arr) {
 export function makeTitle(f) {
     return `${f.get('name') || f.get('id') || 'breakend'} split detail`;
 }
+export function getAssemblyName(view) {
+    return view?.assemblyNames[0];
+}
+export function splitRegionAtPosition(region, pos, assemblyName) {
+    return [
+        {
+            ...region,
+            end: pos + 1,
+            ...(assemblyName !== undefined && { assemblyName }),
+        },
+        {
+            ...region,
+            start: pos,
+            ...(assemblyName !== undefined && { assemblyName }),
+        },
+    ];
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/sv-core",
-  "version": "3.7.0",
+  "version": "4.0.0",
   "description": "JBrowse 2 code shared between sv type code",
   "keywords": [
     "jbrowse",
@@ -18,39 +18,18 @@
     "directory": "packages/sv-core"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "distModule": "esm/index.js",
-  "srcMain": "src/index.ts",
-  "srcModule": "src/index.ts",
-  "main": "dist/index.js",
-  "module": "esm/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "build": "npm run build:esm && npm run build:commonjs",
-    "test": "cd ../..; jest --passWithNoTests packages/sv-core",
-    "clean": "rimraf dist esm *.tsbuildinfo",
-    "prebuild": "yarn clean",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js"
-  },
   "dependencies": {
-    "@gmod/vcf": "^6.0.8",
-    "@jbrowse/core": "^3.7.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.7.0",
-    "@mui/icons-material": "^7.0.0",
-    "@mui/material": "^7.0.0",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0",
-    "tss-react": "^4.0.0"
+    "@gmod/vcf": "^6.1.0",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/material": "^7.3.6",
+    "mobx": "^6.15.0",
+    "mobx-react": "^9.2.1",
+    "@jbrowse/core": "^4.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^4.0.0"
   },
   "peerDependencies": {
     "react": ">=18.0.0",
@@ -59,5 +38,19 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "build": "pnpm build:esm",
+    "test": "cd ../..; jest --passWithNoTests packages/sv-core",
+    "clean": "rimraf esm *.tsbuildinfo",
+    "prebuild": "pnpm clean"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/BreakendMultiLevelOptionDialog.js

@@ -1,46 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const Checkbox2_1 = __importDefault(require("./Checkbox2"));
-const navToMultiLevelBreak_1 = require("./navToMultiLevelBreak");
-const BreakendMultiLevelOptionDialog = (0, mobx_react_1.observer)(function ({ session, handleClose, feature, assemblyName, stableViewId, view, }) {
-    const [copyTracks, setCopyTracks] = (0, react_1.useState)(true);
-    const [mirror, setMirror] = (0, react_1.useState)(true);
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Multi-level breakpoint split view options", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)("div", { children: "Launch multi-level breakpoint split view" }), view ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(Checkbox2_1.default, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
-                                    setCopyTracks(event.target.checked);
-                                } }), copyTracks ? ((0, jsx_runtime_1.jsx)(Checkbox2_1.default, { checked: mirror, disabled: !copyTracks, label: "Mirror the copied tracks (only available if copying tracks and using two level)", onChange: event => {
-                                    setMirror(event.target.checked);
-                                } })) : null] })) : null] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
-                            ;
-                            (async () => {
-                                try {
-                                    await (0, navToMultiLevelBreak_1.navToMultiLevelBreak)({
-                                        stableViewId,
-                                        session,
-                                        tracks: copyTracks && view
-                                            ? (0, mobx_state_tree_1.getSnapshot)(view.tracks)
-                                            : [],
-                                        mirror,
-                                        feature,
-                                        assemblyName,
-                                    });
-                                }
-                                catch (e) {
-                                    console.error(e);
-                                    session.notifyError(`${e}`, e);
-                                }
-                            })();
-                            handleClose();
-                        }, variant: "contained", color: "primary", autoFocus: true, children: "OK" }), (0, jsx_runtime_1.jsx)(material_1.Button, { color: "secondary", variant: "contained", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-});
-exports.default = BreakendMultiLevelOptionDialog;

package/dist/BreakendSingleLevelOptionDialog.d.ts

@@ -1,11 +0,0 @@
-import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-declare const BreakendSingleLevelOptionDialog: ({ session, handleClose, feature, stableViewId, assemblyName, view, }: {
-    session: AbstractSessionModel;
-    handleClose: () => void;
-    stableViewId?: string;
-    feature: Feature;
-    view?: LinearGenomeViewModel;
-    assemblyName: string;
-}) => import("react/jsx-runtime").JSX.Element;
-export default BreakendSingleLevelOptionDialog;

package/dist/BreakendSingleLevelOptionDialog.js

@@ -1,53 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const Checkbox2_1 = __importDefault(require("./Checkbox2"));
-const navToSingleLevelBreak_1 = require("./navToSingleLevelBreak");
-const BreakendSingleLevelOptionDialog = (0, mobx_react_1.observer)(function ({ session, handleClose, feature, stableViewId, assemblyName, view, }) {
-    const [copyTracks, setCopyTracks] = (0, react_1.useState)(true);
-    const [focusOnBreakends, setFocusOnBreakends] = (0, react_1.useState)(true);
-    const [windowSize, setWindowSize] = (0, util_1.useLocalStorage)('breakpointWindowSize', '5000');
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Single-level breakpoint split view options", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [view ? ((0, jsx_runtime_1.jsx)(Checkbox2_1.default, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
-                            setCopyTracks(event.target.checked);
-                        } })) : null, (0, jsx_runtime_1.jsx)(Checkbox2_1.default, { checked: copyTracks, label: "Focus on breakends", onChange: event => {
-                            setFocusOnBreakends(event.target.checked);
-                        } }), (0, jsx_runtime_1.jsx)(material_1.TextField, { label: "Window size (bp)", value: windowSize, onChange: event => {
-                            setWindowSize(event.target.value);
-                        } })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
-                            ;
-                            (async () => {
-                                try {
-                                    const { assemblyManager } = session;
-                                    const assembly = await assemblyManager.waitForAssembly(assemblyName);
-                                    if (!assembly) {
-                                        throw new Error(`assembly ${assemblyName} not found`);
-                                    }
-                                    await (0, navToSingleLevelBreak_1.navToSingleLevelBreak)({
-                                        feature,
-                                        assemblyName,
-                                        focusOnBreakends,
-                                        session,
-                                        stableViewId,
-                                        tracks: view === null || view === void 0 ? void 0 : view.tracks,
-                                        windowSize: +windowSize || 0,
-                                    });
-                                }
-                                catch (e) {
-                                    console.error(e);
-                                    session.notifyError(`${e}`, e);
-                                }
-                            })();
-                            handleClose();
-                        }, variant: "contained", color: "primary", autoFocus: true, children: "OK" }), (0, jsx_runtime_1.jsx)(material_1.Button, { color: "secondary", variant: "contained", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-});
-exports.default = BreakendSingleLevelOptionDialog;

package/dist/Checkbox2.d.ts

@@ -1,6 +0,0 @@
-export default function Checkbox2({ checked, disabled, label, onChange, }: {
-    checked: boolean;
-    disabled?: boolean;
-    label: string;
-    onChange: (event: React.ChangeEvent<HTMLInputElement>) => void;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/Checkbox2.js

@@ -1,15 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = Checkbox2;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()({
-    block: {
-        display: 'block',
-    },
-});
-function Checkbox2({ checked, disabled, label, onChange, }) {
-    const { classes } = useStyles();
-    return ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { disabled: disabled, className: classes.block, control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: checked, onChange: onChange }), label: label }));
-}

package/dist/index.d.ts

@@ -1,5 +0,0 @@
-export { default as BreakendMultiLevelOptionDialog } from './BreakendMultiLevelOptionDialog';
-export { default as BreakendSingleLevelOptionDialog } from './BreakendSingleLevelOptionDialog';
-export * from './util';
-export * from './navToSingleLevelBreak';
-export * from './navToMultiLevelBreak';

package/dist/index.js

@@ -1,27 +0,0 @@
-"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 __exportStar = (this && this.__exportStar) || function(m, exports) {
-    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
-};
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.BreakendSingleLevelOptionDialog = exports.BreakendMultiLevelOptionDialog = void 0;
-var BreakendMultiLevelOptionDialog_1 = require("./BreakendMultiLevelOptionDialog");
-Object.defineProperty(exports, "BreakendMultiLevelOptionDialog", { enumerable: true, get: function () { return __importDefault(BreakendMultiLevelOptionDialog_1).default; } });
-var BreakendSingleLevelOptionDialog_1 = require("./BreakendSingleLevelOptionDialog");
-Object.defineProperty(exports, "BreakendSingleLevelOptionDialog", { enumerable: true, get: function () { return __importDefault(BreakendSingleLevelOptionDialog_1).default; } });
-__exportStar(require("./util"), exports);
-__exportStar(require("./navToSingleLevelBreak"), exports);
-__exportStar(require("./navToMultiLevelBreak"), exports);

package/dist/navToMultiLevelBreak.d.ts

@@ -1,11 +0,0 @@
-import type { Track } from './types';
-import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
-export declare function navToMultiLevelBreak({ stableViewId, feature, assemblyName, session, mirror, tracks: viewTracks, }: {
-    stableViewId?: string;
-    feature: Feature;
-    assemblyName: string;
-    windowSize?: number;
-    session: AbstractSessionModel;
-    mirror?: boolean;
-    tracks?: Track[];
-}): Promise<void>;

package/dist/navToMultiLevelBreak.js

@@ -1,77 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.navToMultiLevelBreak = navToMultiLevelBreak;
-const util_1 = require("@jbrowse/core/util");
-const util_2 = require("./util");
-async function navToMultiLevelBreak({ stableViewId, feature, assemblyName, session, mirror, tracks: viewTracks = [], }) {
-    const { assemblyManager } = session;
-    const assembly = await assemblyManager.waitForAssembly(assemblyName);
-    if (!assembly) {
-        throw new Error(`assembly ${assemblyName} not found`);
-    }
-    const { refName, pos, mateRefName, matePos } = (0, util_2.getBreakendCoveringRegions)({
-        feature,
-        assembly: assembly,
-    });
-    let view = session.views.find(f => f.id === stableViewId);
-    if (!view) {
-        view = session.addView('BreakpointSplitView', {
-            id: stableViewId,
-            type: 'BreakpointSplitView',
-            displayName: (0, util_2.makeTitle)(feature),
-            views: [
-                {
-                    type: 'LinearGenomeView',
-                    hideHeader: true,
-                    tracks: (0, util_2.stripIds)(viewTracks),
-                },
-                {
-                    type: 'LinearGenomeView',
-                    hideHeader: true,
-                    tracks: (0, util_2.stripIds)(mirror ? [...viewTracks].reverse() : viewTracks),
-                },
-            ],
-        });
-    }
-    view.setDisplayName((0, util_2.makeTitle)(feature));
-    const r1 = assembly.regions.find(r => r.refName === refName);
-    const r2 = assembly.regions.find(r => r.refName === mateRefName);
-    if (!r1 || !r2) {
-        throw new Error("can't find regions");
-    }
-    await Promise.all([
-        view.views[0].navToLocations([
-            {
-                refName,
-                start: r1.start,
-                end: pos,
-                assemblyName,
-            },
-            {
-                refName,
-                start: pos + 1,
-                end: r1.end,
-                assemblyName,
-            },
-        ]),
-        view.views[1].navToLocations([
-            {
-                refName: mateRefName,
-                start: r2.start,
-                end: matePos,
-                assemblyName,
-            },
-            {
-                refName: mateRefName,
-                start: matePos + 1,
-                end: r2.end,
-                assemblyName,
-            },
-        ]),
-    ]);
-    await (0, util_1.when)(() => view.views[1].initialized && view.views[0].initialized);
-    view.views[1].zoomTo(10);
-    view.views[0].zoomTo(10);
-    view.views[1].centerAt(matePos, mateRefName);
-    view.views[0].centerAt(pos, refName);
-}

package/dist/navToSingleLevelBreak.d.ts

@@ -1,61 +0,0 @@
-import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
-export declare function singleLevelFocusedSnapshotFromBreakendFeature({ feature, session, assemblyName, windowSize, }: {
-    feature: Feature;
-    session: AbstractSessionModel;
-    assemblyName: string;
-    windowSize?: number;
-}): {
-    coverage: {
-        pos: number;
-        refName: string;
-        mateRefName: string;
-        matePos: any;
-    };
-    snap: {
-        type: string;
-        views: {
-            type: string;
-            displayedRegions: {
-                end: number;
-                assemblyName: string;
-                start: number;
-                refName: string;
-            }[];
-        }[];
-        displayName: string;
-    };
-};
-export declare function singleLevelEncompassingSnapshotFromBreakendFeature({ feature, session, assemblyName, }: {
-    feature: Feature;
-    session: AbstractSessionModel;
-    assemblyName: string;
-}): {
-    coverage: {
-        pos: number;
-        refName: string;
-        mateRefName: string;
-        matePos: any;
-    };
-    snap: {
-        type: string;
-        views: {
-            type: string;
-            displayedRegions: {
-                assemblyName: string;
-                start: number;
-                end: number;
-                refName: string;
-            }[];
-        }[];
-        displayName: string;
-    };
-};
-export declare function navToSingleLevelBreak({ stableViewId, feature, assemblyName, session, tracks, windowSize, focusOnBreakends, }: {
-    stableViewId?: string;
-    feature: Feature;
-    assemblyName: string;
-    windowSize?: number;
-    session: AbstractSessionModel;
-    tracks?: any;
-    focusOnBreakends?: boolean;
-}): Promise<void>;

package/dist/navToSingleLevelBreak.js

@@ -1,136 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.singleLevelFocusedSnapshotFromBreakendFeature = singleLevelFocusedSnapshotFromBreakendFeature;
-exports.singleLevelEncompassingSnapshotFromBreakendFeature = singleLevelEncompassingSnapshotFromBreakendFeature;
-exports.navToSingleLevelBreak = navToSingleLevelBreak;
-const util_1 = require("@jbrowse/core/util");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_2 = require("./util");
-function singleLevelFocusedSnapshotFromBreakendFeature({ feature, session, assemblyName, windowSize = 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 coverage = (0, util_2.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);
-    return {
-        coverage,
-        snap: {
-            type: 'BreakpointSplitView',
-            views: [
-                {
-                    type: 'LinearGenomeView',
-                    displayedRegions: (0, util_1.gatherOverlaps)([
-                        {
-                            ...topRegion,
-                            end: coverage.pos + windowSize,
-                            assemblyName,
-                        },
-                        {
-                            ...bottomRegion,
-                            start: coverage.matePos - windowSize,
-                            assemblyName,
-                        },
-                    ]),
-                },
-            ],
-            displayName: (0, util_2.makeTitle)(feature),
-        },
-    };
-}
-function singleLevelEncompassingSnapshotFromBreakendFeature({ feature, session, assemblyName, }) {
-    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 coverage = (0, util_2.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);
-    return {
-        coverage,
-        snap: {
-            type: 'BreakpointSplitView',
-            views: [
-                {
-                    type: 'LinearGenomeView',
-                    displayedRegions: (0, util_1.gatherOverlaps)([
-                        { ...topRegion, assemblyName },
-                        { ...bottomRegion, assemblyName },
-                    ]),
-                },
-            ],
-            displayName: (0, util_2.makeTitle)(feature),
-        },
-    };
-}
-async function navToSingleLevelBreak({ stableViewId, feature, assemblyName, session, tracks, windowSize = 0, focusOnBreakends, }) {
-    var _a;
-    const { snap, coverage } = focusOnBreakends
-        ? singleLevelFocusedSnapshotFromBreakendFeature({
-            feature,
-            assemblyName,
-            session,
-            windowSize,
-        })
-        : singleLevelEncompassingSnapshotFromBreakendFeature({
-            feature,
-            assemblyName,
-            session,
-        });
-    const { refName, pos: startPos, mateRefName, matePos: endPos } = coverage;
-    let view = session.views.find(f => f.id === stableViewId);
-    if (!view) {
-        view = session.addView('BreakpointSplitView', {
-            ...snap,
-            views: [
-                {
-                    ...snap.views[0],
-                    tracks: tracks ? (0, util_2.stripIds)((0, mobx_state_tree_1.getSnapshot)(tracks)) : [],
-                },
-            ],
-        });
-    }
-    else {
-        (_a = view.views[0]) === null || _a === void 0 ? void 0 : _a.setDisplayedRegions(snap.views[0].displayedRegions);
-        view.setDisplayName(snap.displayName);
-    }
-    const lgv = view.views[0];
-    await (0, util_1.when)(() => lgv.initialized);
-    const l0 = lgv.bpToPx({
-        coord: Math.max(0, startPos - windowSize),
-        refName,
-    });
-    const r0 = lgv.bpToPx({
-        coord: endPos + windowSize,
-        refName: mateRefName,
-    });
-    if (l0 && r0) {
-        lgv.moveTo({
-            ...l0,
-            offset: l0.offsetPx,
-        }, {
-            ...r0,
-            offset: r0.offsetPx,
-        });
-    }
-    else {
-        (0, util_1.getSession)(lgv).notify('Unable to navigate to breakpoint');
-    }
-}

package/dist/types.d.ts

@@ -1,13 +0,0 @@
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export interface Display {
-    id: string;
-    [key: string]: unknown;
-}
-export interface Track {
-    id: string;
-    displays: Display[];
-    [key: string]: unknown;
-}
-export interface BreakpointSplitView {
-    views: LinearGenomeViewModel[];
-}

package/dist/types.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/util.d.ts

@@ -1,18 +0,0 @@
-import type { Track } from './types';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-import type { Feature } from '@jbrowse/core/util';
-export declare function getBreakendCoveringRegions({ feature, assembly, }: {
-    feature: Feature;
-    assembly: Assembly;
-}): {
-    pos: number;
-    refName: string;
-    mateRefName: string;
-    matePos: any;
-};
-export declare function stripIds(arr: Track[]): {
-    displays: {
-        [key: string]: unknown;
-    }[];
-}[];
-export declare function makeTitle(f: Feature): string;

package/dist/util.js

@@ -1,58 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getBreakendCoveringRegions = getBreakendCoveringRegions;
-exports.stripIds = stripIds;
-exports.makeTitle = makeTitle;
-const vcf_1 = require("@gmod/vcf");
-function getBreakendCoveringRegions({ feature, assembly, }) {
-    var _a;
-    const alt = (_a = feature.get('ALT')) === null || _a === void 0 ? void 0 : _a[0];
-    const bnd = alt ? (0, vcf_1.parseBreakend)(alt) : undefined;
-    const startPos = feature.get('start');
-    const refName = feature.get('refName');
-    const f = (ref) => assembly.getCanonicalRefName(ref) || ref;
-    if (alt === '<TRA>') {
-        const INFO = feature.get('INFO');
-        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(':');
-        return {
-            pos: startPos,
-            refName: f(refName),
-            mateRefName: f(matePosition[0]),
-            matePos: +matePosition[1] - 1,
-        };
-    }
-    else if (feature.get('mate')) {
-        const mate = feature.get('mate');
-        return {
-            pos: startPos,
-            refName: f(refName),
-            mateRefName: f(mate.refName),
-            matePos: mate.start,
-        };
-    }
-    else {
-        return {
-            pos: startPos,
-            refName: f(refName),
-            mateRefName: f(refName),
-            matePos: feature.get('end'),
-        };
-    }
-}
-function stripIds(arr) {
-    return arr.map(({ id, displays, ...rest }) => ({
-        ...rest,
-        displays: displays.map(({ id, ...rest }) => rest),
-    }));
-}
-function makeTitle(f) {
-    return `${f.get('name') || f.get('id') || 'breakend'} split detail`;
-}

package/esm/BreakendMultiLevelOptionDialog.d.ts

@@ -1,11 +0,0 @@
-import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-declare const BreakendMultiLevelOptionDialog: ({ session, handleClose, feature, assemblyName, stableViewId, view, }: {
-    session: AbstractSessionModel;
-    handleClose: () => void;
-    feature: Feature;
-    view?: LinearGenomeViewModel;
-    assemblyName: string;
-    stableViewId?: string;
-}) => import("react/jsx-runtime").JSX.Element;
-export default BreakendMultiLevelOptionDialog;

package/esm/BreakendMultiLevelOptionDialog.js

@@ -1,41 +0,0 @@
-import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
-import { useState } from 'react';
-import { Dialog } from '@jbrowse/core/ui';
-import { Button, DialogActions, DialogContent } from '@mui/material';
-import { observer } from 'mobx-react';
-import { getSnapshot } from 'mobx-state-tree';
-import Checkbox2 from './Checkbox2';
-import { navToMultiLevelBreak } from './navToMultiLevelBreak';
-const BreakendMultiLevelOptionDialog = observer(function ({ session, handleClose, feature, assemblyName, stableViewId, view, }) {
-    const [copyTracks, setCopyTracks] = useState(true);
-    const [mirror, setMirror] = useState(true);
-    return (_jsxs(Dialog, { open: true, onClose: handleClose, title: "Multi-level breakpoint split view options", children: [_jsxs(DialogContent, { children: [_jsx("div", { children: "Launch multi-level breakpoint split view" }), view ? (_jsxs(_Fragment, { children: [_jsx(Checkbox2, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
-                                    setCopyTracks(event.target.checked);
-                                } }), copyTracks ? (_jsx(Checkbox2, { checked: mirror, disabled: !copyTracks, label: "Mirror the copied tracks (only available if copying tracks and using two level)", onChange: event => {
-                                    setMirror(event.target.checked);
-                                } })) : null] })) : null] }), _jsxs(DialogActions, { children: [_jsx(Button, { onClick: () => {
-                            ;
-                            (async () => {
-                                try {
-                                    await navToMultiLevelBreak({
-                                        stableViewId,
-                                        session,
-                                        tracks: copyTracks && view
-                                            ? getSnapshot(view.tracks)
-                                            : [],
-                                        mirror,
-                                        feature,
-                                        assemblyName,
-                                    });
-                                }
-                                catch (e) {
-                                    console.error(e);
-                                    session.notifyError(`${e}`, e);
-                                }
-                            })();
-                            handleClose();
-                        }, variant: "contained", color: "primary", autoFocus: true, children: "OK" }), _jsx(Button, { color: "secondary", variant: "contained", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-});
-export default BreakendMultiLevelOptionDialog;

package/esm/BreakendSingleLevelOptionDialog.d.ts

@@ -1,11 +0,0 @@
-import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-declare const BreakendSingleLevelOptionDialog: ({ session, handleClose, feature, stableViewId, assemblyName, view, }: {
-    session: AbstractSessionModel;
-    handleClose: () => void;
-    stableViewId?: string;
-    feature: Feature;
-    view?: LinearGenomeViewModel;
-    assemblyName: string;
-}) => import("react/jsx-runtime").JSX.Element;
-export default BreakendSingleLevelOptionDialog;

package/esm/BreakendSingleLevelOptionDialog.js

@@ -1,48 +0,0 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { useState } from 'react';
-import { Dialog } from '@jbrowse/core/ui';
-import { useLocalStorage } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent, TextField } from '@mui/material';
-import { observer } from 'mobx-react';
-import Checkbox2 from './Checkbox2';
-import { navToSingleLevelBreak } from './navToSingleLevelBreak';
-const BreakendSingleLevelOptionDialog = observer(function ({ session, handleClose, feature, stableViewId, assemblyName, view, }) {
-    const [copyTracks, setCopyTracks] = useState(true);
-    const [focusOnBreakends, setFocusOnBreakends] = useState(true);
-    const [windowSize, setWindowSize] = useLocalStorage('breakpointWindowSize', '5000');
-    return (_jsxs(Dialog, { open: true, onClose: handleClose, title: "Single-level breakpoint split view options", children: [_jsxs(DialogContent, { children: [view ? (_jsx(Checkbox2, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
-                            setCopyTracks(event.target.checked);
-                        } })) : null, _jsx(Checkbox2, { checked: copyTracks, label: "Focus on breakends", onChange: event => {
-                            setFocusOnBreakends(event.target.checked);
-                        } }), _jsx(TextField, { label: "Window size (bp)", value: windowSize, onChange: event => {
-                            setWindowSize(event.target.value);
-                        } })] }), _jsxs(DialogActions, { children: [_jsx(Button, { onClick: () => {
-                            ;
-                            (async () => {
-                                try {
-                                    const { assemblyManager } = session;
-                                    const assembly = await assemblyManager.waitForAssembly(assemblyName);
-                                    if (!assembly) {
-                                        throw new Error(`assembly ${assemblyName} not found`);
-                                    }
-                                    await navToSingleLevelBreak({
-                                        feature,
-                                        assemblyName,
-                                        focusOnBreakends,
-                                        session,
-                                        stableViewId,
-                                        tracks: view === null || view === void 0 ? void 0 : view.tracks,
-                                        windowSize: +windowSize || 0,
-                                    });
-                                }
-                                catch (e) {
-                                    console.error(e);
-                                    session.notifyError(`${e}`, e);
-                                }
-                            })();
-                            handleClose();
-                        }, variant: "contained", color: "primary", autoFocus: true, children: "OK" }), _jsx(Button, { color: "secondary", variant: "contained", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-});
-export default BreakendSingleLevelOptionDialog;