@jbrowse/sv-core 2.18.0 → 3.0.1

package/dist/types.d.ts

@@ -0,0 +1,13 @@
+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

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

package/dist/util.d.ts

@@ -1,14 +1,6 @@
+import type { Track } from './types';
 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;
-}
+import type { Feature } from '@jbrowse/core/util';
 export declare function getBreakendCoveringRegions({ feature, assembly, }: {
     feature: Feature;
     assembly: Assembly;
@@ -18,44 +10,9 @@ export declare function getBreakendCoveringRegions({ feature, assembly, }: {
     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>;
+export declare function stripIds(arr: Track[]): {
+    displays: {
+        [key: string]: unknown;
+    }[];
+}[];
+export declare function makeTitle(f: Feature): string;

package/dist/util.js

@@ -1,19 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getBreakendCoveringRegions = getBreakendCoveringRegions;
-exports.singleLevelSnapshotFromBreakendFeature = singleLevelSnapshotFromBreakendFeature;
-exports.navToSingleLevelBreak = navToSingleLevelBreak;
-exports.navToMultiLevelBreak = navToMultiLevelBreak;
+exports.stripIds = stripIds;
+exports.makeTitle = makeTitle;
 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];
@@ -57,151 +47,12 @@ function getBreakendCoveringRegions({ feature, assembly, }) {
         };
     }
 }
-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');
-    }
+function stripIds(arr) {
+    return arr.map(({ id, displays, ...rest }) => ({
+        ...rest,
+        displays: displays.map(({ id, ...rest }) => rest),
+    }));
 }
-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);
-        });
-    }
+function makeTitle(f) {
+    return `${f.get('name') || f.get('id') || 'breakend'} split detail`;
 }

package/esm/BreakendMultiLevelOptionDialog.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 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, }: {
@@ -8,5 +7,5 @@ declare const BreakendMultiLevelOptionDialog: ({ session, handleClose, feature,
     view?: LinearGenomeViewModel;
     assemblyName: string;
     stableViewId?: string;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default BreakendMultiLevelOptionDialog;

package/esm/BreakendMultiLevelOptionDialog.js

@@ -1,120 +1,41 @@
-import React, { useState } from 'react';
+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 { when } from 'mobx';
 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),
-    }));
-}
+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 (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Multi-level breakpoint split view options" },
-        React.createElement(DialogContent, 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: () => {
-                    ;
-                    (async () => {
-                        try {
-                            const { assemblyManager } = session;
-                            const assembly = await assemblyManager.waitForAssembly(assemblyName);
-                            if (!assembly) {
-                                throw new Error(`assembly ${assemblyName} not found`);
-                            }
-                            const { refName, pos, mateRefName, matePos } = getBreakendCoveringRegions({
-                                feature,
-                                assembly: assembly,
-                            });
-                            const viewTracks = view
-                                ? getSnapshot(view.tracks)
-                                : [];
-                            let viewInStack = session.views.find(f => f.id === stableViewId);
-                            const displayName = `${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([
-                                viewInStack.views[0].navToLocations([
-                                    {
-                                        refName,
-                                        start: r1.start,
-                                        end: pos,
+    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,
-                                    },
-                                    {
-                                        refName,
-                                        start: pos + 1,
-                                        end: r1.end,
-                                        assemblyName,
-                                    },
-                                ]),
-                                viewInStack.views[1].navToLocations([
-                                    {
-                                        refName: mateRefName,
-                                        start: r2.start,
-                                        end: matePos,
-                                        assemblyName,
-                                    },
-                                    {
-                                        refName: mateRefName,
-                                        start: matePos + 1,
-                                        end: r2.end,
-                                        assemblyName,
-                                    },
-                                ]),
-                            ]);
-                            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.notifyError(`${e}`, e);
-                        }
-                    })();
-                    handleClose();
-                }, variant: "contained", color: "primary", autoFocus: true }, "OK"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
+                                    });
+                                }
+                                catch (e) {
+                                    console.error(e);
+                                    session.notifyError(`${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

@@ -1,4 +1,3 @@
-import React from 'react';
 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, }: {
@@ -8,5 +7,5 @@ declare const BreakendSingleLevelOptionDialog: ({ session, handleClose, feature,
     feature: Feature;
     view?: LinearGenomeViewModel;
     assemblyName: string;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default BreakendSingleLevelOptionDialog;

package/esm/BreakendSingleLevelOptionDialog.js

@@ -1,49 +1,48 @@
-import React, { useState } from 'react';
+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 './util';
+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 (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Single-level breakpoint split view options" },
-        React.createElement(DialogContent, null,
-            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: () => {
-                    ;
-                    (async () => {
-                        try {
-                            const { assemblyManager } = session;
-                            const assembly = await assemblyManager.waitForAssembly(assemblyName);
-                            if (!assembly) {
-                                throw new Error(`assembly ${assemblyName} not found`);
-                            }
-                            await navToSingleLevelBreak({
-                                feature,
-                                assemblyName,
-                                session,
-                                stableViewId,
-                                tracks: view === null || view === void 0 ? void 0 : view.tracks,
-                                windowSize: +windowSize || 0,
-                            });
-                        }
-                        catch (e) {
-                            console.error(e);
-                            session.notifyError(`${e}`, e);
-                        }
-                    })();
-                    handleClose();
-                }, variant: "contained", color: "primary", autoFocus: true }, "OK"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
+    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;

package/esm/Checkbox2.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
 export default function Checkbox2({ checked, disabled, label, onChange, }: {
     checked: boolean;
     disabled?: boolean;
     label: string;
     onChange: (event: React.ChangeEvent<HTMLInputElement>) => void;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/Checkbox2.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
 import { Checkbox, FormControlLabel } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
@@ -8,5 +8,5 @@ const useStyles = makeStyles()({
 });
 export default function Checkbox2({ checked, disabled, label, onChange, }) {
     const { classes } = useStyles();
-    return (React.createElement(FormControlLabel, { disabled: disabled, className: classes.block, control: React.createElement(Checkbox, { checked: checked, onChange: onChange }), label: label }));
+    return (_jsx(FormControlLabel, { disabled: disabled, className: classes.block, control: _jsx(Checkbox, { checked: checked, onChange: onChange }), label: label }));
 }

package/esm/index.d.ts

@@ -1,3 +1,5 @@
 export { default as BreakendMultiLevelOptionDialog } from './BreakendMultiLevelOptionDialog';
 export { default as BreakendSingleLevelOptionDialog } from './BreakendSingleLevelOptionDialog';
 export * from './util';
+export * from './navToSingleLevelBreak';
+export * from './navToMultiLevelBreak';

package/esm/index.js

@@ -1,3 +1,5 @@
 export { default as BreakendMultiLevelOptionDialog } from './BreakendMultiLevelOptionDialog';
 export { default as BreakendSingleLevelOptionDialog } from './BreakendSingleLevelOptionDialog';
 export * from './util';
+export * from './navToSingleLevelBreak';
+export * from './navToMultiLevelBreak';

package/esm/navToMultiLevelBreak.d.ts

@@ -0,0 +1,11 @@
+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>;