@jbrowse/plugin-breakpoint-split-view 3.6.5 → 4.0.0

package/esm/BreakpointSplitView/model.js

@@ -1,14 +1,12 @@
 import { lazy } from 'react';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { getSession, notEmpty } from '@jbrowse/core/util';
+import { addDisposer, addMiddleware, cast, getPath, types, } from '@jbrowse/mobx-state-tree';
 import LinkIcon from '@mui/icons-material/Link';
 import PhotoCamera from '@mui/icons-material/PhotoCamera';
-import { saveAs } from 'file-saver';
 import { autorun } from 'mobx';
-import { addDisposer, getPath, onAction, types } from 'mobx-state-tree';
-import { getClip } from './getClip';
-import { calc, getBlockFeatures, intersect } from './util';
-const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'));
+import { calc, getBlockFeatures, intersect } from "./util.js";
+const ExportSvgDialog = lazy(() => import("./components/ExportSvgDialog.js"));
 export default function stateModelFactory(pluginManager) {
     const defaultHeight = 400;
     return types
@@ -19,19 +17,32 @@ export default function stateModelFactory(pluginManager) {
         showIntraviewLinks: true,
         linkViews: false,
         interactiveOverlay: true,
+        showHeader: false,
         views: types.array(pluginManager.getViewType('LinearGenomeView')
             .stateModel),
+        init: types.frozen(),
     }))
         .volatile(() => ({
         width: 800,
         matchedTrackFeatures: {},
+    }))
+        .views(self => ({
+        get hasSomethingToShow() {
+            return self.views.length > 0 || !!self.init;
+        },
+        get initialized() {
+            return self.views.length > 0 && self.views.every(v => v.initialized);
+        },
+        get showImportForm() {
+            return !this.hasSomethingToShow;
+        },
     }))
         .views(self => ({
         async exportSvg(opts = {}) {
-            const { renderToSvg } = await import('./svgcomponents/SVGBreakpointSplitView');
+            const { renderToSvg } = await import("./svgcomponents/SVGBreakpointSplitView.js");
             const html = await renderToSvg(self, opts);
-            const blob = new Blob([html], { type: 'image/svg+xml' });
-            saveAs(blob, opts.filename || 'image.svg');
+            const { saveAs } = await import('file-saver-es');
+            saveAs(new Blob([html], { type: 'image/svg+xml' }), opts.filename || 'image.svg');
         },
     }))
         .views(self => ({
@@ -43,40 +54,44 @@ export default function stateModelFactory(pluginManager) {
         getMatchedTracks(trackConfigId) {
             return self.views
                 .map(view => view.getTrack(trackConfigId))
-                .filter(f => !!f);
+                .filter(notEmpty);
         },
         hasTranslocations(trackConfigId) {
-            return [...this.getTrackFeatures(trackConfigId).values()].find(f => f.get('type') === 'translocation');
+            return [...this.getTrackFeatures(trackConfigId).values()].some(f => f.get('type') === 'translocation');
         },
         hasPairedFeatures(trackConfigId) {
-            return [...this.getTrackFeatures(trackConfigId).values()].find(f => f.get('type') === 'paired_feature');
+            return [...this.getTrackFeatures(trackConfigId).values()].some(f => f.get('type') === 'paired_feature');
         },
         getTrackFeatures(trackConfigId) {
-            var _a;
-            return new Map((_a = self.matchedTrackFeatures[trackConfigId]) === null || _a === void 0 ? void 0 : _a.flat().map(f => [f.id(), f]));
+            return new Map(self.matchedTrackFeatures[trackConfigId]
+                ?.flat()
+                .map(f => [f.id(), f]));
         },
         getMatchedFeaturesInLayout(trackConfigId, features) {
             const tracks = this.getMatchedTracks(trackConfigId);
             return features.map(c => c
                 .map(feature => {
-                const level = tracks.findIndex(track => calc(track, feature));
-                return level !== -1
-                    ? {
-                        feature,
-                        layout: calc(tracks[level], feature),
-                        level,
-                        clipPos: getClip(feature.get('CIGAR'), feature.get('strand')),
+                for (const [level, track] of tracks.entries()) {
+                    const layout = calc(track, feature);
+                    if (layout) {
+                        return {
+                            feature,
+                            layout,
+                            level,
+                            clipLengthAtStartOfRead: feature.get('clipLengthAtStartOfRead') ?? 0,
+                        };
                     }
-                    : undefined;
+                }
+                return undefined;
             })
                 .filter(notEmpty));
         },
     }))
         .actions(self => ({
         afterAttach() {
-            addDisposer(self, onAction(self, ({ name, path, args, }) => {
-                if (self.linkViews) {
-                    const actions = [
+            addDisposer(self, addMiddleware(self, (rawCall, next) => {
+                if (rawCall.type === 'action' && rawCall.id === rawCall.rootId) {
+                    const syncActions = [
                         'horizontalScroll',
                         'zoomTo',
                         'setScaleFactor',
@@ -86,20 +101,21 @@ export default function stateModelFactory(pluginManager) {
                         'setTrackLabels',
                         'toggleCenterLine',
                     ];
-                    if (actions.includes(name) && path) {
-                        this.onSubviewAction(name, path, args);
+                    if (self.linkViews && syncActions.includes(rawCall.name)) {
+                        const sourcePath = getPath(rawCall.context);
+                        next(rawCall);
+                        for (const view of self.views) {
+                            const viewPath = getPath(view);
+                            if (viewPath !== sourcePath) {
+                                view[rawCall.name](rawCall.args[0]);
+                            }
+                        }
+                        return;
                     }
                 }
+                next(rawCall);
             }));
         },
-        onSubviewAction(actionName, path, args) {
-            for (const view of self.views) {
-                const ret = getPath(view);
-                if (!ret.endsWith(path)) {
-                    view[actionName](args === null || args === void 0 ? void 0 : args[0]);
-                }
-            }
-        },
         setWidth(newWidth) {
             self.width = newWidth;
             for (const v of self.views) {
@@ -115,21 +131,42 @@ export default function stateModelFactory(pluginManager) {
         setLinkViews(arg) {
             self.linkViews = arg;
         },
+        setShowHeader(arg) {
+            self.showHeader = arg;
+        },
         setMatchedTrackFeatures(obj) {
             self.matchedTrackFeatures = obj;
         },
         reverseViewOrder() {
             self.views.reverse();
         },
+        setInit(init) {
+            self.init = init;
+        },
+        setViews(viewInits) {
+            self.views = cast(viewInits.map(viewInit => ({
+                type: 'LinearGenomeView',
+                hideHeader: true,
+                init: viewInit,
+            })));
+        },
     }))
         .actions(self => ({
         afterAttach() {
+            addDisposer(self, autorun(function breakpointSplitViewInitAutorun() {
+                const { init, width } = self;
+                if (!width || !init) {
+                    return;
+                }
+                self.setViews(init.views);
+                self.setInit(undefined);
+            }, { name: 'BreakpointSplitViewInit' }));
             addDisposer(self, autorun(async () => {
                 try {
                     if (!self.views.every(view => view.initialized)) {
                         return;
                     }
-                    if (self.matchedTracks.some(track => { var _a, _b; return (_b = (_a = track.displays[0]).notReady) === null || _b === void 0 ? void 0 : _b.call(_a); })) {
+                    if (self.matchedTracks.some(track => track.displays[0].notReady?.())) {
                         return;
                     }
                     self.setMatchedTrackFeatures(Object.fromEntries(await Promise.all(self.matchedTracks.map(async (track) => [
@@ -141,15 +178,16 @@ export default function stateModelFactory(pluginManager) {
                     console.error(e);
                     getSession(self).notifyError(`${e}`, e);
                 }
+            }, {
+                name: 'BreakpointFeatureFetcher',
+                delay: 1000,
             }));
         },
         menuItems() {
             return [
-                ...self.views
-                    .map((view, idx) => [idx, view.menuItems()])
-                    .map(f => ({
-                    label: `Row ${f[0] + 1} view menu`,
-                    subMenu: f[1],
+                ...self.views.map((view, idx) => ({
+                    label: `Row ${idx + 1} view menu`,
+                    subMenu: view.menuItems(),
                 })),
                 ...(self.views.length > 1
                     ? [
@@ -161,6 +199,14 @@ export default function stateModelFactory(pluginManager) {
                         },
                     ]
                     : []),
+                {
+                    label: 'Show header',
+                    type: 'checkbox',
+                    checked: self.showHeader,
+                    onClick: () => {
+                        self.setShowHeader(!self.showHeader);
+                    },
+                },
                 {
                     label: 'Show intra-view links',
                     type: 'checkbox',
@@ -201,5 +247,35 @@ export default function stateModelFactory(pluginManager) {
                 },
             ];
         },
-    }));
+        rubberBandMenuItems() {
+            return [
+                {
+                    label: 'Zoom to region(s)',
+                    onClick: () => {
+                        for (const view of self.views) {
+                            const { leftOffset, rightOffset } = view;
+                            if (leftOffset && rightOffset) {
+                                view.moveTo(leftOffset, rightOffset);
+                            }
+                        }
+                    },
+                },
+            ];
+        },
+    }))
+        .postProcessSnapshot(snap => {
+        if (!snap) {
+            return snap;
+        }
+        const { init, height, trackSelectorType, showIntraviewLinks, linkViews, interactiveOverlay, showHeader, ...rest } = snap;
+        return {
+            ...rest,
+            ...(height !== 400 ? { height } : {}),
+            ...(trackSelectorType !== 'hierarchical' ? { trackSelectorType } : {}),
+            ...(!showIntraviewLinks ? { showIntraviewLinks } : {}),
+            ...(linkViews ? { linkViews } : {}),
+            ...(!interactiveOverlay ? { interactiveOverlay } : {}),
+            ...(showHeader ? { showHeader } : {}),
+        };
+    });
 }

package/esm/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.d.ts

@@ -1,5 +1,5 @@
-import type { BreakpointViewModel } from '../model';
-import type { ExportSvgOptions } from '../types';
+import type { BreakpointViewModel } from '../model.ts';
+import type { ExportSvgOptions } from '../types.ts';
 type BSV = BreakpointViewModel;
 export declare function renderToSvg(model: BSV, opts: ExportSvgOptions): Promise<string>;
 export {};

package/esm/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js

@@ -1,17 +1,16 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { createJBrowseTheme } from '@jbrowse/core/ui';
 import { getSession, renderToStaticMarkup, sum } from '@jbrowse/core/util';
-import { SVGRuler, SVGTracks, totalHeight, } from '@jbrowse/plugin-linear-genome-view';
+import { SVGGridlines, SVGRuler, SVGTracks, totalHeight, } from '@jbrowse/plugin-linear-genome-view';
 import { ThemeProvider } from '@mui/material';
 import { when } from 'mobx';
-import SVGBackground from './SVGBackground';
-import { getTrackNameMaxLen, getTrackOffsets } from './util';
-import Overlay from '../components/Overlay';
+import SVGBackground from "./SVGBackground.js";
+import { getTrackNameMaxLen, getTrackOffsets } from "./util.js";
+import Overlay from "../components/Overlay.js";
 export async function renderToSvg(model, opts) {
-    var _a;
-    const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => children, themeName = 'default', } = opts;
+    const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', showGridlines = false, Wrapper = ({ children }) => children, themeName = 'default', } = opts;
     const session = getSession(model);
-    const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
+    const theme = session.allThemes?.()[themeName];
     const { width, views } = model;
     const shift = 50;
     const offset = headerHeight + rulerHeight;
@@ -31,5 +30,6 @@ export async function renderToSvg(model, opts) {
     const trackOffsets = views.map((view, idx) => getTrackOffsets(view, textOffset, fontSize + (idx > 0 ? heights[idx - 1] : 0) + offset));
     const w = width + trackLabelOffset;
     const t = createJBrowseTheme(theme);
-    return renderToStaticMarkup(_jsx(ThemeProvider, { theme: t, children: _jsx(Wrapper, { children: _jsxs("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString(), children: [_jsx(SVGBackground, { width: w, height: totalHeightSvg, shift: shift }), views[0] ? (_jsxs("g", { transform: `translate(${shift} ${fontSize})`, children: [_jsxs("g", { transform: `translate(${trackLabelOffset})`, children: [_jsx("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary, children: views[0].assemblyNames.join(', ') }), _jsx(SVGRuler, { model: displayResults[0].view, fontSize: fontSize })] }), _jsx("g", { transform: `translate(0 ${offset})`, children: _jsx(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[0].view, displayResults: displayResults[0].data, trackLabelOffset: trackLabelOffset }) })] })) : null, views[1] ? (_jsxs("g", { transform: `translate(${shift} ${fontSize + heights[0]})`, children: [_jsxs("g", { transform: `translate(${trackLabelOffset})`, children: [_jsx("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary, children: views[1].assemblyNames.join(', ') }), _jsx(SVGRuler, { model: displayResults[1].view, fontSize: fontSize })] }), _jsx("g", { transform: `translate(0 ${offset})`, children: _jsx(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, trackLabelOffset: trackLabelOffset }) })] })) : null, _jsx("defs", { children: _jsx("clipPath", { id: "clip-bsv", children: _jsx("rect", { x: 0, y: 0, width: width, height: totalHeightSvg }) }) }), _jsx("g", { transform: `translate(${trackLabelOffset + shift})`, clipPath: "url(#clip-bsv)", children: model.matchedTracks.map(track => (_jsx(Overlay, { parentRef: { current: null }, model: model, trackId: track.configuration.trackId, getTrackYPosOverride: (id, level) => trackOffsets[level][id] }, track.configuration.trackId))) })] }) }) }));
+    const tracksHeights = views.map(v => totalHeight(v.tracks, textHeight, trackLabels));
+    return renderToStaticMarkup(_jsx(ThemeProvider, { theme: t, children: _jsx(Wrapper, { children: _jsxs("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString(), children: [_jsx(SVGBackground, { width: w, height: totalHeightSvg, shift: shift }), views[0] ? (_jsxs("g", { transform: `translate(${shift} ${fontSize})`, children: [_jsxs("g", { transform: `translate(${trackLabelOffset})`, children: [_jsx("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary, children: views[0].assemblyNames.join(', ') }), _jsx(SVGRuler, { model: displayResults[0].view, fontSize: fontSize })] }), showGridlines ? (_jsx("g", { transform: `translate(${trackLabelOffset} ${offset})`, children: _jsx(SVGGridlines, { model: displayResults[0].view, height: tracksHeights[0] }) })) : null, _jsx("g", { transform: `translate(0 ${offset})`, children: _jsx(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[0].view, displayResults: displayResults[0].data, trackLabelOffset: trackLabelOffset }) })] })) : null, views[1] ? (_jsxs("g", { transform: `translate(${shift} ${fontSize + heights[0]})`, children: [_jsxs("g", { transform: `translate(${trackLabelOffset})`, children: [_jsx("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary, children: views[1].assemblyNames.join(', ') }), _jsx(SVGRuler, { model: displayResults[1].view, fontSize: fontSize })] }), showGridlines ? (_jsx("g", { transform: `translate(${trackLabelOffset} ${offset})`, children: _jsx(SVGGridlines, { model: displayResults[1].view, height: tracksHeights[1] }) })) : null, _jsx("g", { transform: `translate(0 ${offset})`, children: _jsx(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, trackLabelOffset: trackLabelOffset }) })] })) : null, _jsx("defs", { children: _jsx("clipPath", { id: "clip-bsv", children: _jsx("rect", { x: 0, y: 0, width: width, height: totalHeightSvg }) }) }), _jsx("g", { transform: `translate(${trackLabelOffset + shift})`, clipPath: "url(#clip-bsv)", children: model.matchedTracks.map(track => (_jsx(Overlay, { parentRef: { current: null }, model: model, trackId: track.configuration.trackId, getTrackYPosOverride: (id, level) => trackOffsets[level][id] }, track.configuration.trackId))) })] }) }) }));
 }

package/esm/BreakpointSplitView/types.d.ts

@@ -12,6 +12,14 @@ export interface ExportSvgOptions {
     cytobandHeight?: number;
     trackLabels?: string;
     themeName?: string;
+    showGridlines?: boolean;
+}
+export interface BreakpointSplitViewInit {
+    views: {
+        loc?: string;
+        assembly: string;
+        tracks?: string[];
+    }[];
 }
 export interface Breakend {
     MateDirection: string;

package/esm/BreakpointSplitView/util.d.ts

@@ -1,4 +1,4 @@
-import type { LayoutRecord } from './types';
+import type { LayoutRecord } from './types.ts';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';

package/esm/BreakpointSplitView/util.js

@@ -7,28 +7,20 @@ function cheight(chunk) {
     return chunk[BOTTOM] - chunk[TOP];
 }
 export function heightFromSpecificLevel(views, trackId, level, getYPosOverride) {
-    var _a;
     return getYPosOverride
         ? getYPosOverride(trackId, level)
-        : ((_a = views[level].trackRefs[trackId]) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect().top) || 0;
+        : views[level].trackRefs[trackId]?.getBoundingClientRect().top || 0;
 }
 export function getPxFromCoordinate(view, refName, coord) {
-    var _a;
-    return (((_a = view.bpToPx({ refName, coord })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - view.offsetPx;
+    return (view.bpToPx({ refName, coord })?.offsetPx || 0) - view.offsetPx;
 }
 export function yPos(trackId, level, views, tracks, c, getYPosOverride) {
     const display = tracks[level].displays[0];
-    const min = 0;
     const max = display.height;
-    let offset = 0;
-    const { SNPCoverageDisplay } = display;
-    if (SNPCoverageDisplay) {
-        offset = SNPCoverageDisplay.height;
-    }
-    const yPos = getYPosOverride ? 0 : display.scrollTop;
-    return (clamp(c[TOP] - yPos + cheight(c) / 2 + offset, min, max) +
-        heightFromSpecificLevel(views, trackId, level, getYPosOverride) +
-        display.scrollTop);
+    const offset = display.SNPCoverageDisplay?.height ?? 0;
+    const scrollTop = getYPosOverride ? 0 : display.scrollTop;
+    return (clamp(c[TOP] - scrollTop + cheight(c) / 2 + offset, offset, max) +
+        heightFromSpecificLevel(views, trackId, level, getYPosOverride));
 }
 export const useNextFrame = (variable) => {
     const [, setNextFrameState] = useState();
@@ -42,14 +34,13 @@ export function intersect(cb, a1 = [], a2 = [], ...rest) {
     return rest.length === 0 ? a12 : intersect(cb, a12, ...rest);
 }
 export function calc(track, f) {
-    var _a, _b;
-    return (_b = (_a = track.displays[0]).searchFeatureByID) === null || _b === void 0 ? void 0 : _b.call(_a, f.id());
+    return track.displays[0].searchFeatureByID?.(f.id());
 }
 export async function getBlockFeatures(model, track) {
     const { views } = model;
     const { rpcManager } = getSession(model);
     const sessionId = getRpcSessionId(track);
-    return Promise.all(views.flatMap(async (view) => (await rpcManager.call(sessionId, 'CoreGetFeatures', {
+    return Promise.all(views.flatMap(async (view) => (await rpcManager.call(sessionId, 'BreakpointGetFeatures', {
         adapterConfig: getConf(track, ['adapter']),
         sessionId,
         regions: view.staticBlocks.contentBlocks,

package/esm/LaunchBreakpointSplitView/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function LaunchBreakpointSplitViewF(pluginManager: PluginManager): void;

package/esm/LaunchBreakpointSplitView/index.js

@@ -0,0 +1,12 @@
+export default function LaunchBreakpointSplitViewF(pluginManager) {
+    pluginManager.addToExtensionPoint('LaunchView-BreakpointSplitView', async ({ session, views, }) => {
+        if (views.length < 2) {
+            throw new Error('BreakpointSplitView requires at least 2 views to be specified');
+        }
+        session.addView('BreakpointSplitView', {
+            init: {
+                views,
+            },
+        });
+    });
+}

package/esm/index.js

@@ -1,14 +1,15 @@
 import Plugin from '@jbrowse/core/Plugin';
-import BreakpointAlignmentsWidgetF from './BreakpointAlignmentsFeatureDetail';
-import BreakpointSplitViewF from './BreakpointSplitView';
+import BreakpointAlignmentsWidgetF from "./BreakpointAlignmentsFeatureDetail/index.js";
+import BreakpointGetFeaturesF from "./BreakpointGetFeatures/index.js";
+import BreakpointSplitViewF from "./BreakpointSplitView/index.js";
+import LaunchBreakpointSplitViewF from "./LaunchBreakpointSplitView/index.js";
 export default class BreakpointSplitViewPlugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'BreakpointSplitViewPlugin';
-    }
+    name = 'BreakpointSplitViewPlugin';
     install(pluginManager) {
         BreakpointSplitViewF(pluginManager);
         BreakpointAlignmentsWidgetF(pluginManager);
+        LaunchBreakpointSplitViewF(pluginManager);
+        BreakpointGetFeaturesF(pluginManager);
     }
     configure() { }
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-breakpoint-split-view",
-  "version": "3.6.5",
+  "version": "4.0.0",
   "description": "JBrowse 2 breakpoint detail split view",
   "keywords": [
     "jbrowse",
@@ -15,48 +15,42 @@
     "directory": "plugins/breakpoint-split-view"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "test": "cd ../..; jest --passWithNoTests plugins/breakpoint-split-view",
-    "prepublishOnly": "yarn test",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js",
-    "prebuild": "npm run clean",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "clean": "rimraf dist esm *.tsbuildinfo"
-  },
   "dependencies": {
-    "@gmod/vcf": "^6.0.8",
-    "@jbrowse/core": "^3.6.5",
-    "@jbrowse/plugin-linear-genome-view": "^3.6.5",
-    "@mui/icons-material": "^7.0.0",
-    "@mui/material": "^7.0.0",
-    "@types/file-saver": "^2.0.1",
-    "file-saver": "^2.0.0",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "tss-react": "^4.0.0"
+    "@gmod/vcf": "^6.1.0",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/icons-material": "^7.3.6",
+    "@mui/material": "^7.3.6",
+    "@types/file-saver-es": "^2.0.3",
+    "file-saver-es": "^2.0.5",
+    "mobx": "^6.15.0",
+    "mobx-react": "^9.2.1",
+    "@jbrowse/core": "^4.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^4.0.0"
   },
   "peerDependencies": {
     "react": ">=16.8.4",
     "react-dom": ">=16.8.4"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "354d0a87b757b4d84f824b47507662f6f3a1693f"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/breakpoint-split-view",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "clean": "rimraf esm *.tsbuildinfo"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.d.ts

@@ -1,10 +0,0 @@
-import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-declare const BreakpointAlignmentsFeatureDetail: ({ model, }: {
-    model: {
-        featureData: {
-            feature1: SimpleFeatureSerialized;
-            feature2: SimpleFeatureSerialized;
-        };
-    };
-}) => import("react/jsx-runtime").JSX.Element;
-export default BreakpointAlignmentsFeatureDetail;

package/dist/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.js

@@ -1,12 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const BreakpointAlignmentsFeatureDetail = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { featureData } = model;
-    const { feature1, feature2 } = structuredClone(featureData);
-    return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { children: [(0, jsx_runtime_1.jsx)(BaseFeatureDetail_1.BaseCoreDetails, { title: "Feature 1", feature: feature1 }), (0, jsx_runtime_1.jsx)(BaseFeatureDetail_1.BaseCoreDetails, { title: "Feature 2", feature: feature2 }), (0, jsx_runtime_1.jsx)(BaseFeatureDetail_1.BaseAttributes, { title: "Feature 1 attributes", feature: feature1 }), (0, jsx_runtime_1.jsx)(BaseFeatureDetail_1.BaseAttributes, { title: "Feature 2 attributes", feature: feature2 })] }));
-});
-exports.default = BreakpointAlignmentsFeatureDetail;

package/dist/BreakpointAlignmentsFeatureDetail/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function BreakpointAlignmentsFeatureDetailF(pluginManager: PluginManager): void;

package/dist/BreakpointAlignmentsFeatureDetail/index.js

@@ -1,67 +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 __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = BreakpointAlignmentsFeatureDetailF;
-const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const mst_1 = require("@jbrowse/core/util/types/mst");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const configSchema = (0, configuration_1.ConfigurationSchema)('BreakpointAlignmentsWidget', {});
-const stateModel = mobx_state_tree_1.types
-    .model('BreakpointAlignmentsWidget', {
-    id: mst_1.ElementId,
-    type: mobx_state_tree_1.types.literal('BreakpointAlignmentsWidget'),
-    featureData: mobx_state_tree_1.types.frozen(),
-})
-    .actions(self => ({
-    setFeatureData(data) {
-        self.featureData = data;
-    },
-    clearFeatureData() {
-        self.featureData = undefined;
-    },
-}));
-function BreakpointAlignmentsFeatureDetailF(pluginManager) {
-    pluginManager.addWidgetType(() => {
-        return new pluggableElementTypes_1.WidgetType({
-            name: 'BreakpointAlignmentsWidget',
-            heading: 'Breakpoint feature details',
-            configSchema,
-            stateModel,
-            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakpointAlignmentsFeatureDetail')))),
-        });
-    });
-}

package/dist/BreakpointSplitView/BreakpointSplitView.d.ts

@@ -1,34 +0,0 @@
-import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
-import { type AbstractSessionModel, type Feature } from '@jbrowse/core/util';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-export default class BreakpointSplitViewType extends ViewType {
-    getBreakendCoveringRegions({ feature, assembly, }: {
-        feature: Feature;
-        assembly: Assembly;
-    }): {
-        pos: number;
-        refName: string;
-        mateRefName: string;
-        matePos: any;
-    };
-    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: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[];
-            }[];
-            displayName: string;
-        };
-    };
-}