@jbrowse/sv-core 2.17.0 → 2.18.0

package/dist/BreakendMultiLevelOptionDialog.d.ts

@@ -1,23 +1,12 @@
 import React from 'react';
-import { Feature } from '@jbrowse/core/util';
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-declare const BreakendMultiLevelOptionDialog: ({ model, handleClose, feature, assemblyName, viewType, view, }: {
-    model: unknown;
+declare const BreakendMultiLevelOptionDialog: ({ session, handleClose, feature, assemblyName, stableViewId, view, }: {
+    session: AbstractSessionModel;
     handleClose: () => void;
     feature: Feature;
-    view: LinearGenomeViewModel;
+    view?: LinearGenomeViewModel;
     assemblyName: string;
-    viewType: {
-        getBreakendCoveringRegions: (arg: {
-            feature: Feature;
-            assembly: Assembly;
-        }) => {
-            pos: number;
-            refName: string;
-            mateRefName: string;
-            matePos: number;
-        };
-    };
+    stableViewId?: string;
 }) => React.JSX.Element;
 export default BreakendMultiLevelOptionDialog;

package/dist/BreakendMultiLevelOptionDialog.js

@@ -27,70 +27,78 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
 const mobx_1 = require("mobx");
-const util_1 = require("@jbrowse/core/util");
-// locals
+const mobx_react_1 = require("mobx-react");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const Checkbox2_1 = __importDefault(require("./Checkbox2"));
+const util_1 = require("./util");
 function stripIds(arr) {
     return arr.map(({ id, displays, ...rest }) => ({
         ...rest,
         displays: displays.map(({ id, ...rest }) => rest),
     }));
 }
-const BreakendMultiLevelOptionDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, feature, assemblyName, viewType, view, }) {
+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 (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Multi-level breakpoint split view options" },
         react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement(Checkbox2_1.default, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
-                    setCopyTracks(event.target.checked);
-                } }),
-            copyTracks ? (react_1.default.createElement(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),
+            react_1.default.createElement("div", null, "Launch multi-level breakpoint split view"),
+            view ? (react_1.default.createElement(react_1.default.Fragment, null,
+                react_1.default.createElement(Checkbox2_1.default, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
+                        setCopyTracks(event.target.checked);
+                    } }),
+                copyTracks ? (react_1.default.createElement(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),
         react_1.default.createElement(material_1.DialogActions, null,
             react_1.default.createElement(material_1.Button, { onClick: () => {
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
                     ;
                     (async () => {
-                        const session = (0, util_1.getSession)(model);
                         try {
-                            const asm = await session.assemblyManager.waitForAssembly(assemblyName);
-                            if (!asm) {
+                            const { assemblyManager } = session;
+                            const assembly = await assemblyManager.waitForAssembly(assemblyName);
+                            if (!assembly) {
                                 throw new Error(`assembly ${assemblyName} not found`);
                             }
-                            const { refName, pos, mateRefName, matePos } = viewType.getBreakendCoveringRegions({
+                            const { refName, pos, mateRefName, matePos } = (0, util_1.getBreakendCoveringRegions)({
                                 feature,
-                                assembly: asm,
+                                assembly: assembly,
                             });
-                            const viewTracks = (0, mobx_state_tree_1.getSnapshot)(view.tracks);
-                            const breakpointSplitView = session.addView('BreakpointSplitView', {
-                                type: 'BreakpointSplitView',
-                                displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
-                                views: [
-                                    {
-                                        type: 'LinearGenomeView',
-                                        hideHeader: true,
-                                        tracks: stripIds((0, mobx_state_tree_1.getSnapshot)(view.tracks)),
-                                    },
-                                    {
-                                        type: 'LinearGenomeView',
-                                        hideHeader: true,
-                                        tracks: stripIds(mirror ? [...viewTracks].reverse() : viewTracks),
-                                    },
-                                ],
-                            });
-                            const r1 = asm.regions.find(r => r.refName === refName);
-                            const r2 = asm.regions.find(r => r.refName === mateRefName);
+                            const viewTracks = view
+                                ? (0, mobx_state_tree_1.getSnapshot)(view.tracks)
+                                : [];
+                            let viewInStack = session.views.find(f => f.id === stableViewId);
+                            const displayName = `${feature.get('name') || feature.get('id') || 'breakend'} split detail`;
+                            if (!viewInStack) {
+                                viewInStack = session.addView('BreakpointSplitView', {
+                                    id: stableViewId,
+                                    type: 'BreakpointSplitView',
+                                    displayName,
+                                    views: [
+                                        {
+                                            type: 'LinearGenomeView',
+                                            hideHeader: true,
+                                            tracks: stripIds(viewTracks),
+                                        },
+                                        {
+                                            type: 'LinearGenomeView',
+                                            hideHeader: true,
+                                            tracks: stripIds(mirror ? [...viewTracks].reverse() : viewTracks),
+                                        },
+                                    ],
+                                });
+                            }
+                            viewInStack.setDisplayName(displayName);
+                            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([
-                                breakpointSplitView.views[0].navToLocations([
+                                viewInStack.views[0].navToLocations([
                                     {
                                         refName,
                                         start: r1.start,
@@ -104,7 +112,7 @@ const BreakendMultiLevelOptionDialog = (0, mobx_react_1.observer)(function ({ mo
                                         assemblyName,
                                     },
                                 ]),
-                                breakpointSplitView.views[1].navToLocations([
+                                viewInStack.views[1].navToLocations([
                                     {
                                         refName: mateRefName,
                                         start: r2.start,
@@ -119,16 +127,16 @@ const BreakendMultiLevelOptionDialog = (0, mobx_react_1.observer)(function ({ mo
                                     },
                                 ]),
                             ]);
-                            await (0, mobx_1.when)(() => breakpointSplitView.views[1].initialized &&
-                                breakpointSplitView.views[0].initialized);
-                            breakpointSplitView.views[1].zoomTo(10);
-                            breakpointSplitView.views[0].zoomTo(10);
-                            breakpointSplitView.views[1].centerAt(matePos, mateRefName);
-                            breakpointSplitView.views[0].centerAt(pos, refName);
+                            await (0, mobx_1.when)(() => viewInStack.views[1].initialized &&
+                                viewInStack.views[0].initialized);
+                            viewInStack.views[1].zoomTo(10);
+                            viewInStack.views[0].zoomTo(10);
+                            viewInStack.views[1].centerAt(matePos, mateRefName);
+                            viewInStack.views[0].centerAt(pos, refName);
                         }
                         catch (e) {
                             console.error(e);
-                            session.notify(`${e}`);
+                            session.notifyError(`${e}`, e);
                         }
                     })();
                     handleClose();

package/dist/BreakendSingleLevelOptionDialog.d.ts

@@ -1,23 +1,12 @@
 import React from 'react';
-import { Feature } from '@jbrowse/core/util';
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-declare const BreakendSingleLevelOptionDialog: ({ model, handleClose, feature, assemblyName, viewType, view, }: {
-    model: unknown;
+declare const BreakendSingleLevelOptionDialog: ({ session, handleClose, feature, stableViewId, assemblyName, view, }: {
+    session: AbstractSessionModel;
     handleClose: () => void;
+    stableViewId?: string;
     feature: Feature;
-    view: LinearGenomeViewModel;
+    view?: LinearGenomeViewModel;
     assemblyName: string;
-    viewType: {
-        getBreakendCoveringRegions: (arg: {
-            feature: Feature;
-            assembly: Assembly;
-        }) => {
-            pos: number;
-            refName: string;
-            mateRefName: string;
-            matePos: number;
-        };
-    };
 }) => React.JSX.Element;
 export default BreakendSingleLevelOptionDialog;

package/dist/BreakendSingleLevelOptionDialog.js

@@ -27,71 +27,45 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
-// locals
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const Checkbox2_1 = __importDefault(require("./Checkbox2"));
-function stripIds(arr) {
-    return arr.map(({ id, displays, ...rest }) => ({
-        ...rest,
-        displays: displays.map(({ id, ...rest }) => rest),
-    }));
-}
-const BreakendSingleLevelOptionDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, feature, assemblyName, viewType, view, }) {
+const util_2 = require("./util");
+const BreakendSingleLevelOptionDialog = (0, mobx_react_1.observer)(function ({ session, handleClose, feature, stableViewId, assemblyName, view, }) {
     const [copyTracks, setCopyTracks] = (0, react_1.useState)(true);
     const [windowSize, setWindowSize] = (0, util_1.useLocalStorage)('breakpointWindowSize', '5000');
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Single-level breakpoint split view options" },
         react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement(Checkbox2_1.default, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
+            view ? (react_1.default.createElement(Checkbox2_1.default, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
                     setCopyTracks(event.target.checked);
-                } }),
+                } })) : null,
             react_1.default.createElement(material_1.TextField, { label: "Window size (bp)", value: windowSize, onChange: event => {
                     setWindowSize(event.target.value);
                 } })),
         react_1.default.createElement(material_1.DialogActions, null,
             react_1.default.createElement(material_1.Button, { onClick: () => {
-                    const session = (0, util_1.getSession)(model);
+                    ;
                     (async () => {
                         try {
-                            const assembly = session.assemblyManager.get(assemblyName);
-                            const w = +windowSize;
-                            if (Number.isNaN(w)) {
-                                throw new Error('windowSize not a number');
+                            const { assemblyManager } = session;
+                            const assembly = await assemblyManager.waitForAssembly(assemblyName);
+                            if (!assembly) {
+                                throw new Error(`assembly ${assemblyName} not found`);
                             }
-                            const { refName, pos, mateRefName, matePos } = 
-                            // @ts-expect-error
-                            viewType.getBreakendCoveringRegions({ feature, assembly });
-                            const breakpointSplitView = session.addView('BreakpointSplitView', {
-                                type: 'BreakpointSplitView',
-                                displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
-                                views: [
-                                    {
-                                        type: 'LinearGenomeView',
-                                        tracks: stripIds((0, mobx_state_tree_1.getSnapshot)(view.tracks)),
-                                    },
-                                ],
+                            await (0, util_2.navToSingleLevelBreak)({
+                                feature,
+                                assemblyName,
+                                session,
+                                stableViewId,
+                                tracks: view === null || view === void 0 ? void 0 : view.tracks,
+                                windowSize: +windowSize || 0,
                             });
-                            await breakpointSplitView.views[0].navToLocations((0, util_1.gatherOverlaps)([
-                                {
-                                    refName,
-                                    start: Math.max(0, pos - w),
-                                    end: pos + w,
-                                    assemblyName,
-                                },
-                                {
-                                    refName: mateRefName,
-                                    start: Math.max(0, matePos - w),
-                                    end: matePos + w,
-                                    assemblyName,
-                                },
-                            ], w));
                         }
                         catch (e) {
                             console.error(e);
-                            session.notify(`${e}`);
+                            session.notifyError(`${e}`, e);
                         }
                     })();
                     handleClose();

package/dist/index.d.ts

@@ -1,2 +1,3 @@
 export { default as BreakendMultiLevelOptionDialog } from './BreakendMultiLevelOptionDialog';
 export { default as BreakendSingleLevelOptionDialog } from './BreakendSingleLevelOptionDialog';
+export * from './util';

package/dist/index.js

@@ -1,4 +1,18 @@
 "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 };
 };
@@ -8,3 +22,4 @@ 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);

package/dist/util.d.ts

@@ -0,0 +1,61 @@
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+export interface Display {
+    id: string;
+    [key: string]: unknown;
+}
+export interface Track {
+    id: string;
+    displays: Display[];
+    [key: string]: unknown;
+}
+export declare function getBreakendCoveringRegions({ feature, assembly, }: {
+    feature: Feature;
+    assembly: Assembly;
+}): {
+    pos: number;
+    refName: string;
+    mateRefName: string;
+    matePos: any;
+};
+export declare function singleLevelSnapshotFromBreakendFeature({ 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, }: {
+    stableViewId?: string;
+    feature: Feature;
+    assemblyName: string;
+    windowSize?: number;
+    session: AbstractSessionModel;
+    tracks?: any;
+}): Promise<void>;
+export declare function navToMultiLevelBreak({ stableViewId, feature, assemblyName, session, tracks, }: {
+    stableViewId?: string;
+    feature: Feature;
+    assemblyName: string;
+    windowSize?: number;
+    session: AbstractSessionModel;
+    tracks?: any;
+}): Promise<void>;

package/dist/util.js

@@ -0,0 +1,207 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getBreakendCoveringRegions = getBreakendCoveringRegions;
+exports.singleLevelSnapshotFromBreakendFeature = singleLevelSnapshotFromBreakendFeature;
+exports.navToSingleLevelBreak = navToSingleLevelBreak;
+exports.navToMultiLevelBreak = navToMultiLevelBreak;
+const vcf_1 = require("@gmod/vcf");
+const util_1 = require("@jbrowse/core/util");
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
+function stripIds(arr) {
+    return arr.map(({ id, displays, ...rest }) => ({
+        ...rest,
+        displays: displays.map(({ id, ...rest }) => rest),
+    }));
+}
+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 singleLevelSnapshotFromBreakendFeature({ 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 ${assemblyName} regions not loaded`);
+    }
+    const coverage = getBreakendCoveringRegions({
+        feature,
+        assembly,
+    });
+    const { refName, mateRefName } = coverage;
+    const topRegion = assembly.regions.find(f => f.refName === refName);
+    const bottomRegion = assembly.regions.find(f => f.refName === mateRefName);
+    return {
+        coverage,
+        snap: {
+            type: 'BreakpointSplitView',
+            views: [
+                {
+                    type: 'LinearGenomeView',
+                    displayedRegions: (0, util_1.gatherOverlaps)([
+                        { ...topRegion, assemblyName },
+                        { ...bottomRegion, assemblyName },
+                    ]),
+                },
+            ],
+            displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
+        },
+    };
+}
+async function navToSingleLevelBreak({ stableViewId, feature, assemblyName, session, tracks, windowSize = 0, }) {
+    var _a;
+    const { snap, coverage } = singleLevelSnapshotFromBreakendFeature({
+        feature,
+        assemblyName,
+        session,
+    });
+    const { refName, pos: startPos, mateRefName, matePos: endPos } = coverage;
+    let viewInStack = session.views.find(f => f.id === stableViewId);
+    if (!viewInStack) {
+        viewInStack = session.addView('BreakpointSplitView', {
+            ...snap,
+            views: [
+                {
+                    ...snap.views[0],
+                    tracks: tracks ? stripIds((0, mobx_state_tree_1.getSnapshot)(tracks)) : [],
+                },
+            ],
+        });
+    }
+    else {
+        (_a = viewInStack.views[0]) === null || _a === void 0 ? void 0 : _a.setDisplayedRegions(snap.views[0].displayedRegions);
+        viewInStack.setDisplayName(snap.displayName);
+    }
+    const lgv = viewInStack.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');
+    }
+}
+async function navToMultiLevelBreak({ stableViewId, feature, assemblyName, session, tracks, }) {
+    const bpPerPx = 10;
+    const { assemblyManager } = session;
+    const assembly = assemblyManager.get(assemblyName);
+    if (!assembly) {
+        throw new Error(`assembly ${assemblyName} not found`);
+    }
+    if (!assembly.regions) {
+        throw new Error(`assembly ${assemblyName} regions not loaded`);
+    }
+    const { refName, pos: startPos, mateRefName, matePos: endPos, } = getBreakendCoveringRegions({
+        feature,
+        assembly,
+    });
+    const topRegion = assembly.regions.find(f => f.refName === refName);
+    const bottomRegion = assembly.regions.find(f => f.refName === mateRefName);
+    const topMarkedRegion = [{ ...topRegion }, { ...topRegion }];
+    const bottomMarkedRegion = [{ ...bottomRegion }, { ...bottomRegion }];
+    topMarkedRegion[0].end = startPos;
+    topMarkedRegion[1].start = startPos;
+    bottomMarkedRegion[0].end = endPos;
+    bottomMarkedRegion[1].start = endPos;
+    const snap = {
+        type: 'BreakpointSplitView',
+        views: [
+            {
+                type: 'LinearGenomeView',
+                displayedRegions: topMarkedRegion,
+                hideHeader: true,
+                bpPerPx,
+                offsetPx: (topRegion.start + feature.get('start')) / bpPerPx,
+            },
+            {
+                type: 'LinearGenomeView',
+                displayedRegions: bottomMarkedRegion,
+                hideHeader: true,
+                bpPerPx,
+                tracks,
+                offsetPx: (bottomRegion.start + endPos) / bpPerPx,
+            },
+        ],
+        displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
+    };
+    let viewInStack = session.views.find(f => f.id === stableViewId);
+    if (!viewInStack) {
+        viewInStack = session.addView('BreakpointSplitView', {
+            ...snap,
+            id: stableViewId,
+            views: [
+                {
+                    ...snap.views[0],
+                    tracks: tracks ? stripIds((0, mobx_state_tree_1.getSnapshot)(tracks)) : [],
+                },
+                {
+                    ...snap.views[1],
+                    tracks: (tracks ? stripIds((0, mobx_state_tree_1.getSnapshot)(tracks)) : []).reverse(),
+                },
+            ],
+        });
+    }
+    else {
+        (0, mobx_1.transaction)(() => {
+            for (let i = 0; i < viewInStack.views.length; i++) {
+                const s = snap.views[i];
+                if (s) {
+                    viewInStack.views[i].setDisplayedRegions(s.displayedRegions);
+                    viewInStack.views[i].scrollTo(s.offsetPx - 800);
+                    viewInStack.views[i].zoomTo(s.bpPerPx);
+                }
+            }
+            viewInStack.setDisplayName(snap.displayName);
+        });
+    }
+}

package/esm/BreakendMultiLevelOptionDialog.d.ts

@@ -1,23 +1,12 @@
 import React from 'react';
-import { Feature } from '@jbrowse/core/util';
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-declare const BreakendMultiLevelOptionDialog: ({ model, handleClose, feature, assemblyName, viewType, view, }: {
-    model: unknown;
+declare const BreakendMultiLevelOptionDialog: ({ session, handleClose, feature, assemblyName, stableViewId, view, }: {
+    session: AbstractSessionModel;
     handleClose: () => void;
     feature: Feature;
-    view: LinearGenomeViewModel;
+    view?: LinearGenomeViewModel;
     assemblyName: string;
-    viewType: {
-        getBreakendCoveringRegions: (arg: {
-            feature: Feature;
-            assembly: Assembly;
-        }) => {
-            pos: number;
-            refName: string;
-            mateRefName: string;
-            matePos: number;
-        };
-    };
+    stableViewId?: string;
 }) => React.JSX.Element;
 export default BreakendMultiLevelOptionDialog;

package/esm/BreakendMultiLevelOptionDialog.js

@@ -1,68 +1,76 @@
 import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, DialogActions, DialogContent } from '@mui/material';
-import { getSnapshot } from 'mobx-state-tree';
 import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent } from '@mui/material';
 import { when } from 'mobx';
-import { getSession } from '@jbrowse/core/util';
-// locals
+import { observer } from 'mobx-react';
+import { getSnapshot } from 'mobx-state-tree';
 import Checkbox2 from './Checkbox2';
+import { getBreakendCoveringRegions } from './util';
 function stripIds(arr) {
     return arr.map(({ id, displays, ...rest }) => ({
         ...rest,
         displays: displays.map(({ id, ...rest }) => rest),
     }));
 }
-const BreakendMultiLevelOptionDialog = observer(function ({ model, handleClose, feature, assemblyName, viewType, view, }) {
+const BreakendMultiLevelOptionDialog = observer(function ({ session, handleClose, feature, assemblyName, stableViewId, view, }) {
     const [copyTracks, setCopyTracks] = useState(true);
     const [mirror, setMirror] = useState(true);
     return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Multi-level breakpoint split view options" },
         React.createElement(DialogContent, null,
-            React.createElement(Checkbox2, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
-                    setCopyTracks(event.target.checked);
-                } }),
-            copyTracks ? (React.createElement(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),
+            React.createElement("div", null, "Launch multi-level breakpoint split view"),
+            view ? (React.createElement(React.Fragment, null,
+                React.createElement(Checkbox2, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
+                        setCopyTracks(event.target.checked);
+                    } }),
+                copyTracks ? (React.createElement(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),
         React.createElement(DialogActions, null,
             React.createElement(Button, { onClick: () => {
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
                     ;
                     (async () => {
-                        const session = getSession(model);
                         try {
-                            const asm = await session.assemblyManager.waitForAssembly(assemblyName);
-                            if (!asm) {
+                            const { assemblyManager } = session;
+                            const assembly = await assemblyManager.waitForAssembly(assemblyName);
+                            if (!assembly) {
                                 throw new Error(`assembly ${assemblyName} not found`);
                             }
-                            const { refName, pos, mateRefName, matePos } = viewType.getBreakendCoveringRegions({
+                            const { refName, pos, mateRefName, matePos } = getBreakendCoveringRegions({
                                 feature,
-                                assembly: asm,
+                                assembly: assembly,
                             });
-                            const viewTracks = getSnapshot(view.tracks);
-                            const breakpointSplitView = session.addView('BreakpointSplitView', {
-                                type: 'BreakpointSplitView',
-                                displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
-                                views: [
-                                    {
-                                        type: 'LinearGenomeView',
-                                        hideHeader: true,
-                                        tracks: stripIds(getSnapshot(view.tracks)),
-                                    },
-                                    {
-                                        type: 'LinearGenomeView',
-                                        hideHeader: true,
-                                        tracks: stripIds(mirror ? [...viewTracks].reverse() : viewTracks),
-                                    },
-                                ],
-                            });
-                            const r1 = asm.regions.find(r => r.refName === refName);
-                            const r2 = asm.regions.find(r => r.refName === mateRefName);
+                            const viewTracks = view
+                                ? getSnapshot(view.tracks)
+                                : [];
+                            let viewInStack = session.views.find(f => f.id === stableViewId);
+                            const displayName = `${feature.get('name') || feature.get('id') || 'breakend'} split detail`;
+                            if (!viewInStack) {
+                                viewInStack = session.addView('BreakpointSplitView', {
+                                    id: stableViewId,
+                                    type: 'BreakpointSplitView',
+                                    displayName,
+                                    views: [
+                                        {
+                                            type: 'LinearGenomeView',
+                                            hideHeader: true,
+                                            tracks: stripIds(viewTracks),
+                                        },
+                                        {
+                                            type: 'LinearGenomeView',
+                                            hideHeader: true,
+                                            tracks: stripIds(mirror ? [...viewTracks].reverse() : viewTracks),
+                                        },
+                                    ],
+                                });
+                            }
+                            viewInStack.setDisplayName(displayName);
+                            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([
-                                breakpointSplitView.views[0].navToLocations([
+                                viewInStack.views[0].navToLocations([
                                     {
                                         refName,
                                         start: r1.start,
@@ -76,7 +84,7 @@ const BreakendMultiLevelOptionDialog = observer(function ({ model, handleClose,
                                         assemblyName,
                                     },
                                 ]),
-                                breakpointSplitView.views[1].navToLocations([
+                                viewInStack.views[1].navToLocations([
                                     {
                                         refName: mateRefName,
                                         start: r2.start,
@@ -91,16 +99,16 @@ const BreakendMultiLevelOptionDialog = observer(function ({ model, handleClose,
                                     },
                                 ]),
                             ]);
-                            await when(() => breakpointSplitView.views[1].initialized &&
-                                breakpointSplitView.views[0].initialized);
-                            breakpointSplitView.views[1].zoomTo(10);
-                            breakpointSplitView.views[0].zoomTo(10);
-                            breakpointSplitView.views[1].centerAt(matePos, mateRefName);
-                            breakpointSplitView.views[0].centerAt(pos, refName);
+                            await when(() => viewInStack.views[1].initialized &&
+                                viewInStack.views[0].initialized);
+                            viewInStack.views[1].zoomTo(10);
+                            viewInStack.views[0].zoomTo(10);
+                            viewInStack.views[1].centerAt(matePos, mateRefName);
+                            viewInStack.views[0].centerAt(pos, refName);
                         }
                         catch (e) {
                             console.error(e);
-                            session.notify(`${e}`);
+                            session.notifyError(`${e}`, e);
                         }
                     })();
                     handleClose();

package/esm/BreakendSingleLevelOptionDialog.d.ts

@@ -1,23 +1,12 @@
 import React from 'react';
-import { Feature } from '@jbrowse/core/util';
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-declare const BreakendSingleLevelOptionDialog: ({ model, handleClose, feature, assemblyName, viewType, view, }: {
-    model: unknown;
+declare const BreakendSingleLevelOptionDialog: ({ session, handleClose, feature, stableViewId, assemblyName, view, }: {
+    session: AbstractSessionModel;
     handleClose: () => void;
+    stableViewId?: string;
     feature: Feature;
-    view: LinearGenomeViewModel;
+    view?: LinearGenomeViewModel;
     assemblyName: string;
-    viewType: {
-        getBreakendCoveringRegions: (arg: {
-            feature: Feature;
-            assembly: Assembly;
-        }) => {
-            pos: number;
-            refName: string;
-            mateRefName: string;
-            matePos: number;
-        };
-    };
 }) => React.JSX.Element;
 export default BreakendSingleLevelOptionDialog;

package/esm/BreakendSingleLevelOptionDialog.js

@@ -1,69 +1,43 @@
 import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, DialogActions, DialogContent, TextField } from '@mui/material';
-import { getSnapshot } from 'mobx-state-tree';
 import { Dialog } from '@jbrowse/core/ui';
-import { getSession, gatherOverlaps, useLocalStorage, } from '@jbrowse/core/util';
-// locals
+import { useLocalStorage } from '@jbrowse/core/util';
+import { Button, DialogActions, DialogContent, TextField } from '@mui/material';
+import { observer } from 'mobx-react';
 import Checkbox2 from './Checkbox2';
-function stripIds(arr) {
-    return arr.map(({ id, displays, ...rest }) => ({
-        ...rest,
-        displays: displays.map(({ id, ...rest }) => rest),
-    }));
-}
-const BreakendSingleLevelOptionDialog = observer(function ({ model, handleClose, feature, assemblyName, viewType, view, }) {
+import { navToSingleLevelBreak } from './util';
+const BreakendSingleLevelOptionDialog = observer(function ({ session, handleClose, feature, stableViewId, assemblyName, view, }) {
     const [copyTracks, setCopyTracks] = useState(true);
     const [windowSize, setWindowSize] = useLocalStorage('breakpointWindowSize', '5000');
     return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Single-level breakpoint split view options" },
         React.createElement(DialogContent, null,
-            React.createElement(Checkbox2, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
+            view ? (React.createElement(Checkbox2, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
                     setCopyTracks(event.target.checked);
-                } }),
+                } })) : null,
             React.createElement(TextField, { label: "Window size (bp)", value: windowSize, onChange: event => {
                     setWindowSize(event.target.value);
                 } })),
         React.createElement(DialogActions, null,
             React.createElement(Button, { onClick: () => {
-                    const session = getSession(model);
+                    ;
                     (async () => {
                         try {
-                            const assembly = session.assemblyManager.get(assemblyName);
-                            const w = +windowSize;
-                            if (Number.isNaN(w)) {
-                                throw new Error('windowSize not a number');
+                            const { assemblyManager } = session;
+                            const assembly = await assemblyManager.waitForAssembly(assemblyName);
+                            if (!assembly) {
+                                throw new Error(`assembly ${assemblyName} not found`);
                             }
-                            const { refName, pos, mateRefName, matePos } = 
-                            // @ts-expect-error
-                            viewType.getBreakendCoveringRegions({ feature, assembly });
-                            const breakpointSplitView = session.addView('BreakpointSplitView', {
-                                type: 'BreakpointSplitView',
-                                displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
-                                views: [
-                                    {
-                                        type: 'LinearGenomeView',
-                                        tracks: stripIds(getSnapshot(view.tracks)),
-                                    },
-                                ],
+                            await navToSingleLevelBreak({
+                                feature,
+                                assemblyName,
+                                session,
+                                stableViewId,
+                                tracks: view === null || view === void 0 ? void 0 : view.tracks,
+                                windowSize: +windowSize || 0,
                             });
-                            await breakpointSplitView.views[0].navToLocations(gatherOverlaps([
-                                {
-                                    refName,
-                                    start: Math.max(0, pos - w),
-                                    end: pos + w,
-                                    assemblyName,
-                                },
-                                {
-                                    refName: mateRefName,
-                                    start: Math.max(0, matePos - w),
-                                    end: matePos + w,
-                                    assemblyName,
-                                },
-                            ], w));
                         }
                         catch (e) {
                             console.error(e);
-                            session.notify(`${e}`);
+                            session.notifyError(`${e}`, e);
                         }
                     })();
                     handleClose();

package/esm/index.d.ts

@@ -1,2 +1,3 @@
 export { default as BreakendMultiLevelOptionDialog } from './BreakendMultiLevelOptionDialog';
 export { default as BreakendSingleLevelOptionDialog } from './BreakendSingleLevelOptionDialog';
+export * from './util';

package/esm/index.js

@@ -1,2 +1,3 @@
 export { default as BreakendMultiLevelOptionDialog } from './BreakendMultiLevelOptionDialog';
 export { default as BreakendSingleLevelOptionDialog } from './BreakendSingleLevelOptionDialog';
+export * from './util';

package/esm/util.d.ts

@@ -0,0 +1,61 @@
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+export interface Display {
+    id: string;
+    [key: string]: unknown;
+}
+export interface Track {
+    id: string;
+    displays: Display[];
+    [key: string]: unknown;
+}
+export declare function getBreakendCoveringRegions({ feature, assembly, }: {
+    feature: Feature;
+    assembly: Assembly;
+}): {
+    pos: number;
+    refName: string;
+    mateRefName: string;
+    matePos: any;
+};
+export declare function singleLevelSnapshotFromBreakendFeature({ 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, }: {
+    stableViewId?: string;
+    feature: Feature;
+    assemblyName: string;
+    windowSize?: number;
+    session: AbstractSessionModel;
+    tracks?: any;
+}): Promise<void>;
+export declare function navToMultiLevelBreak({ stableViewId, feature, assemblyName, session, tracks, }: {
+    stableViewId?: string;
+    feature: Feature;
+    assemblyName: string;
+    windowSize?: number;
+    session: AbstractSessionModel;
+    tracks?: any;
+}): Promise<void>;

package/esm/util.js

@@ -0,0 +1,201 @@
+import { parseBreakend } from '@gmod/vcf';
+import { gatherOverlaps, getSession, when } from '@jbrowse/core/util';
+import { transaction } from 'mobx';
+import { getSnapshot } from 'mobx-state-tree';
+function stripIds(arr) {
+    return arr.map(({ id, displays, ...rest }) => ({
+        ...rest,
+        displays: displays.map(({ id, ...rest }) => rest),
+    }));
+}
+export function getBreakendCoveringRegions({ feature, assembly, }) {
+    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');
+    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'),
+        };
+    }
+}
+export function singleLevelSnapshotFromBreakendFeature({ 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 ${assemblyName} regions not loaded`);
+    }
+    const coverage = getBreakendCoveringRegions({
+        feature,
+        assembly,
+    });
+    const { refName, mateRefName } = coverage;
+    const topRegion = assembly.regions.find(f => f.refName === refName);
+    const bottomRegion = assembly.regions.find(f => f.refName === mateRefName);
+    return {
+        coverage,
+        snap: {
+            type: 'BreakpointSplitView',
+            views: [
+                {
+                    type: 'LinearGenomeView',
+                    displayedRegions: gatherOverlaps([
+                        { ...topRegion, assemblyName },
+                        { ...bottomRegion, assemblyName },
+                    ]),
+                },
+            ],
+            displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
+        },
+    };
+}
+export async function navToSingleLevelBreak({ stableViewId, feature, assemblyName, session, tracks, windowSize = 0, }) {
+    var _a;
+    const { snap, coverage } = singleLevelSnapshotFromBreakendFeature({
+        feature,
+        assemblyName,
+        session,
+    });
+    const { refName, pos: startPos, mateRefName, matePos: endPos } = coverage;
+    let viewInStack = session.views.find(f => f.id === stableViewId);
+    if (!viewInStack) {
+        viewInStack = session.addView('BreakpointSplitView', {
+            ...snap,
+            views: [
+                {
+                    ...snap.views[0],
+                    tracks: tracks ? stripIds(getSnapshot(tracks)) : [],
+                },
+            ],
+        });
+    }
+    else {
+        (_a = viewInStack.views[0]) === null || _a === void 0 ? void 0 : _a.setDisplayedRegions(snap.views[0].displayedRegions);
+        viewInStack.setDisplayName(snap.displayName);
+    }
+    const lgv = viewInStack.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 });
+    }
+    else {
+        getSession(lgv).notify('Unable to navigate to breakpoint');
+    }
+}
+export async function navToMultiLevelBreak({ stableViewId, feature, assemblyName, session, tracks, }) {
+    const bpPerPx = 10;
+    const { assemblyManager } = session;
+    const assembly = assemblyManager.get(assemblyName);
+    if (!assembly) {
+        throw new Error(`assembly ${assemblyName} not found`);
+    }
+    if (!assembly.regions) {
+        throw new Error(`assembly ${assemblyName} regions not loaded`);
+    }
+    const { refName, pos: startPos, mateRefName, matePos: endPos, } = getBreakendCoveringRegions({
+        feature,
+        assembly,
+    });
+    const topRegion = assembly.regions.find(f => f.refName === refName);
+    const bottomRegion = assembly.regions.find(f => f.refName === mateRefName);
+    const topMarkedRegion = [{ ...topRegion }, { ...topRegion }];
+    const bottomMarkedRegion = [{ ...bottomRegion }, { ...bottomRegion }];
+    topMarkedRegion[0].end = startPos;
+    topMarkedRegion[1].start = startPos;
+    bottomMarkedRegion[0].end = endPos;
+    bottomMarkedRegion[1].start = endPos;
+    const snap = {
+        type: 'BreakpointSplitView',
+        views: [
+            {
+                type: 'LinearGenomeView',
+                displayedRegions: topMarkedRegion,
+                hideHeader: true,
+                bpPerPx,
+                offsetPx: (topRegion.start + feature.get('start')) / bpPerPx,
+            },
+            {
+                type: 'LinearGenomeView',
+                displayedRegions: bottomMarkedRegion,
+                hideHeader: true,
+                bpPerPx,
+                tracks,
+                offsetPx: (bottomRegion.start + endPos) / bpPerPx,
+            },
+        ],
+        displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
+    };
+    let viewInStack = session.views.find(f => f.id === stableViewId);
+    if (!viewInStack) {
+        viewInStack = session.addView('BreakpointSplitView', {
+            ...snap,
+            id: stableViewId,
+            views: [
+                {
+                    ...snap.views[0],
+                    tracks: tracks ? stripIds(getSnapshot(tracks)) : [],
+                },
+                {
+                    ...snap.views[1],
+                    tracks: (tracks ? stripIds(getSnapshot(tracks)) : []).reverse(),
+                },
+            ],
+        });
+    }
+    else {
+        transaction(() => {
+            for (let i = 0; i < viewInStack.views.length; i++) {
+                const s = snap.views[i];
+                if (s) {
+                    viewInStack.views[i].setDisplayedRegions(s.displayedRegions);
+                    viewInStack.views[i].scrollTo(s.offsetPx - 800);
+                    viewInStack.views[i].zoomTo(s.bpPerPx);
+                }
+            }
+            viewInStack.setDisplayName(snap.displayName);
+        });
+    }
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/sv-core",
-  "version": "2.17.0",
+  "version": "2.18.0",
   "description": "JBrowse 2 code shared between sv type code",
   "keywords": [
     "jbrowse",
@@ -41,7 +41,9 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@jbrowse/plugin-linear-genome-view": "^2.17.0",
+    "@gmod/vcf": "^6.0.0",
+    "@jbrowse/core": "^2.18.0",
+    "@jbrowse/plugin-linear-genome-view": "^2.18.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0"
   },
@@ -57,5 +59,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }