@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/esm/svgExportUtil.d.ts

@@ -0,0 +1,9 @@
+export declare function isReadyOrHasError(display: {
+    renderProps(): {
+        notReady?: boolean;
+    };
+    error?: unknown;
+}): boolean;
+export declare function hasAnySubDisplayError(displays: {
+    error?: unknown;
+}[]): boolean;

package/esm/svgExportUtil.js

@@ -0,0 +1,6 @@
+export function isReadyOrHasError(display) {
+    return !display.renderProps().notReady || !!display.error;
+}
+export function hasAnySubDisplayError(displays) {
+    return displays.some(d => !!d.error);
+}

package/esm/util.d.ts

@@ -1,7 +1,7 @@
 import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { AugmentedRegion, Feature } from '@jbrowse/core/util';
+import type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree';
 import type { IAutorunOptions } from 'mobx';
-import type { IAnyStateTreeNode } from 'mobx-state-tree';
 export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
 export declare const orientationTypes: {
     fr: Record<string, string>;
@@ -16,15 +16,10 @@ export declare const pairMap: {
 };
 export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
 export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
-interface ModificationData {
-    color: string;
-    name: string;
-}
-export declare const modificationData: Record<string, ModificationData>;
 type DisplayModel = IAnyStateTreeNode & {
-    setError: (arg: unknown) => void;
+    setError?: (arg: unknown) => void;
 };
 export declare function createAutorun(self: DisplayModel, cb: () => Promise<void>, opts?: IAutorunOptions): void;
 export declare function randomColor(str: string): string;
 export declare function getColorForModification(str: string): string;
-export {};
+export { modificationData } from './shared/modificationData.ts';

package/esm/util.js

@@ -1,11 +1,11 @@
+import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
-import { addDisposer, isAlive } from 'mobx-state-tree';
 import { firstValueFrom } from 'rxjs';
 import { toArray } from 'rxjs/operators';
+import { modificationData } from "./shared/modificationData.js";
 export function getTagAlt(feature, tag, alt) {
-    var _a;
     const tags = feature.get('tags');
-    return (_a = tags[tag]) !== null && _a !== void 0 ? _a : tags[alt];
+    return tags[tag] ?? tags[alt];
 }
 export const orientationTypes = {
     fr: {
@@ -65,7 +65,6 @@ export function getColorWGBS(strand, base) {
     return '#888';
 }
 export async function fetchSequence(region, adapter) {
-    var _a;
     const { start, end, originalRefName, refName } = region;
     const feats = await firstValueFrom(adapter
         .getFeatures({
@@ -75,30 +74,16 @@ export async function fetchSequence(region, adapter) {
         start,
     })
         .pipe(toArray()));
-    return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
+    return feats[0]?.get('seq');
 }
-export const modificationData = {
-    m: { color: 'rgb(255,0,0)', name: '5mC' },
-    h: { color: 'rgb(255,0,255)', name: '5hmC' },
-    o: { color: 'rgb(111, 78, 129)', name: '8oxoG' },
-    f: { color: 'rgb(246, 200, 95)', name: '5fC' },
-    c: { color: 'rgb(157, 216, 102)', name: '5cac' },
-    g: { color: 'rgb(255, 160, 86)', name: '5hmu' },
-    e: { color: 'rgb(141, 221, 208)', name: '5fU' },
-    b: { color: 'rgb(0,100,47)', name: '5caU' },
-    a: { color: 'rgb(51,0,111)', name: '6mA' },
-    17082: { color: 'rgb(51,153,255)', name: 'pseU' },
-    17596: { color: 'rgb(102,153,0)', name: 'inosine' },
-    21839: { color: 'rgb(153,0,153)', name: '4mC' },
-};
 export function createAutorun(self, cb, opts) {
-    addDisposer(self, autorun(async () => {
+    addDisposer(self, autorun(async function sharedAlignmentsAutorun() {
         try {
             await cb();
         }
         catch (e) {
             if (isAlive(self)) {
-                self.setError(e);
+                self.setError?.(e);
             }
         }
     }, opts));
@@ -111,6 +96,6 @@ export function randomColor(str) {
     return `hsl(${sum * 10}, 20%, 50%)`;
 }
 export function getColorForModification(str) {
-    var _a;
-    return ((_a = modificationData[str]) === null || _a === void 0 ? void 0 : _a.color) || randomColor(str);
+    return modificationData[str]?.color || randomColor(str);
 }
+export { modificationData } from "./shared/modificationData.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "3.6.5",
+  "version": "4.0.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -15,44 +15,28 @@
     "directory": "plugins/alignments"
   },
   "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/alignments",
-    "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/bam": "^6.0.1",
-    "@gmod/cram": "^5.0.4",
-    "@jbrowse/core": "^3.6.5",
-    "@jbrowse/plugin-linear-genome-view": "^3.6.5",
-    "@jbrowse/plugin-wiggle": "^3.6.5",
-    "@jbrowse/sv-core": "^3.6.5",
-    "@mui/icons-material": "^7.0.0",
-    "@mui/material": "^7.0.0",
+    "@gmod/bam": "^7.1.15",
+    "@gmod/cram": "^7.0.3",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/icons-material": "^7.3.6",
+    "@mui/material": "^7.3.6",
+    "@mui/x-charts-vendor": "^8.23.0",
     "canvas2svg": "^1.0.16",
-    "copy-to-clipboard": "^3.3.1",
+    "copy-to-clipboard": "^3.3.3",
     "fast-deep-equal": "^3.1.3",
-    "generic-filehandle2": "^2.0.1",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0",
-    "tss-react": "^4.0.0"
+    "generic-filehandle2": "^2.0.18",
+    "mobx": "^6.15.0",
+    "mobx-react": "^9.2.1",
+    "rxjs": "^7.8.2",
+    "@jbrowse/plugin-linear-genome-view": "^4.0.0",
+    "@jbrowse/sv-core": "^4.0.0",
+    "@jbrowse/plugin-wiggle": "^4.0.0",
+    "@jbrowse/core": "^4.0.0"
   },
   "peerDependencies": {
     "react": ">=18.0.0"
@@ -60,8 +44,19 @@
   "publishConfig": {
     "access": "public"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
-  "gitHead": "354d0a87b757b4d84f824b47507662f6f3a1693f"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/alignments",
+    "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/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -1,5 +0,0 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
-declare const AlignmentsFeatureDetails: (props: {
-    model: AlignmentFeatureWidgetModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default AlignmentsFeatureDetails;

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -1,63 +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;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const Flags_1 = __importDefault(require("./Flags"));
-const Formatter_1 = __importDefault(require("./Formatter"));
-const PairLink_1 = __importDefault(require("./PairLink"));
-const tagInfo_1 = require("./tagInfo");
-const util_1 = require("./util");
-const SupplementaryAlignments = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SupplementaryAlignments'))));
-const LinkedPairedAlignments = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LinkedPairedAlignments'))));
-const FeatDefined = (0, mobx_react_1.observer)(function (props) {
-    const { model, feat } = props;
-    const flags = feat.flags;
-    const SA = (0, util_1.getTag)('SA', feat);
-    return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { "data-testid": "alignment-side-drawer", children: [(0, jsx_runtime_1.jsx)(FeatureDetails_1.default, { ...props, descriptions: { tags: tagInfo_1.tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? ((0, jsx_runtime_1.jsx)(PairLink_1.default, { model: model, locString: value })) : ((0, jsx_runtime_1.jsx)(Formatter_1.default, { value: value })) }), SA !== undefined ? ((0, jsx_runtime_1.jsx)(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null, flags != null ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [flags & 1 ? ((0, jsx_runtime_1.jsx)(LinkedPairedAlignments, { model: model, feature: feat })) : null, (0, jsx_runtime_1.jsx)(Flags_1.default, { flags: flags, ...props })] })) : null] }));
-});
-const AlignmentsFeatureDetails = (0, mobx_react_1.observer)(function (props) {
-    const { model } = props;
-    const { featureData } = model;
-    const feat = structuredClone(featureData);
-    return feat ? ((0, jsx_runtime_1.jsx)(FeatDefined, { feat: feat, ...props })) : ((0, jsx_runtime_1.jsx)("div", { children: "No feature loaded, may not be available after page refresh because it was too large for localStorage" }));
-});
-exports.default = AlignmentsFeatureDetails;

package/dist/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.d.ts

@@ -1 +0,0 @@
-export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core';

package/dist/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.js

@@ -1,5 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = void 0;
-var sv_core_1 = require("@jbrowse/sv-core");
-Object.defineProperty(exports, "default", { enumerable: true, get: function () { return sv_core_1.BreakendMultiLevelOptionDialog; } });

package/dist/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.d.ts

@@ -1 +0,0 @@
-export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core';

package/dist/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.js

@@ -1,5 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = void 0;
-var sv_core_1 = require("@jbrowse/sv-core");
-Object.defineProperty(exports, "default", { enumerable: true, get: function () { return sv_core_1.BreakendSingleLevelOptionDialog; } });

package/dist/AlignmentsFeatureDetail/Flags.d.ts

@@ -1,3 +0,0 @@
-export default function AlignmentFlags(props: {
-    flags: number;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/Flags.js

@@ -1,41 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = AlignmentFlags;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-const SimpleField_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField"));
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()({
-    compact: {
-        paddingRight: 0,
-        paddingTop: 0,
-        paddingBottom: 0,
-    },
-});
-const flagNames = [
-    'read paired',
-    'read mapped in proper pair',
-    'read unmapped',
-    'mate unmapped',
-    'read reverse strand',
-    'mate reverse strand',
-    'first in pair',
-    'second in pair',
-    'not primary alignment',
-    'read fails platform/vendor quality checks',
-    'read is PCR or optical duplicate',
-    'supplementary alignment',
-];
-function AlignmentFlags(props) {
-    const { classes } = useStyles();
-    const { flags } = props;
-    return ((0, jsx_runtime_1.jsxs)(BaseCard_1.default, { ...props, title: "Flags", children: [(0, jsx_runtime_1.jsx)(SimpleField_1.default, { name: "Flag", value: flags }), (0, jsx_runtime_1.jsx)(material_1.FormGroup, { children: flagNames.map((name, idx) => {
-                    const val = flags & (1 << idx);
-                    const key = `${name}_${val}`;
-                    return ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { className: classes.compact, checked: Boolean(val), name: name, readOnly: true }), label: name }, key));
-                }) })] }));
-}

package/dist/AlignmentsFeatureDetail/Formatter.d.ts

@@ -1,3 +0,0 @@
-export default function Formatter({ value }: {
-    value: unknown;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/Formatter.js

@@ -1,23 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = Formatter;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-function Formatter({ value }) {
-    const [show, setShow] = (0, react_1.useState)(false);
-    const [copied, setCopied] = (0, react_1.useState)(false);
-    const display = String(value);
-    return display.length > 100 ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("button", { type: "button", onClick: () => {
-                    (0, copy_to_clipboard_1.default)(display);
-                    setCopied(true);
-                    setTimeout(() => {
-                        setCopied(false);
-                    }, 700);
-                }, children: copied ? 'Copied to clipboard' : 'Copy' }), (0, jsx_runtime_1.jsx)("button", { type: "button", onClick: () => {
-                    setShow(val => !val);
-                }, children: show ? 'Show less' : 'Show more' }), (0, jsx_runtime_1.jsx)("div", { children: show ? display : `${display.slice(0, 100)}...` })] })) : ((0, jsx_runtime_1.jsx)("div", { children: display }));
-}

package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.d.ts

@@ -1,6 +0,0 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
-import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }: {
-    model: AlignmentFeatureWidgetModel;
-    feature: SimpleFeatureSerialized;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js

@@ -1,84 +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 = LaunchPairedEndBreakpointSplitViewPanel;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const BreakendMultiLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendMultiLevelOptionDialog'))));
-const BreakendSingleLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendSingleLevelOptionDialog'))));
-function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }) {
-    const session = (0, util_1.getSession)(model);
-    const f1 = {
-        uniqueId: feature.uniqueId,
-        refName: feature.refName,
-        start: feature.start,
-        end: feature.end,
-        strand: feature.strand,
-    };
-    const f2 = {
-        uniqueId: `${feature.id}-mate`,
-        refName: feature.next_ref,
-        start: feature.next_pos,
-        end: feature.next_pos + 1,
-        strand: feature.strand,
-    };
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Launch split view" }), (0, jsx_runtime_1.jsx)("ul", { children: (0, jsx_runtime_1.jsxs)("li", { children: [f1.refName, ":", (0, util_1.toLocale)(f1.start), " -> ", f2.refName, ":", (0, util_1.toLocale)(f2.start), ' ', (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
-                                event.preventDefault();
-                                session.queueDialog(handleClose => [
-                                    BreakendMultiLevelOptionDialog,
-                                    {
-                                        handleClose,
-                                        session,
-                                        feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                                        view: model.view,
-                                        assemblyName: model.view.displayedRegions[0].assemblyName,
-                                    },
-                                ]);
-                            }, children: "(top/bottom)" }), ' ', (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
-                                event.preventDefault();
-                                session.queueDialog(handleClose => [
-                                    BreakendSingleLevelOptionDialog,
-                                    {
-                                        handleClose,
-                                        session,
-                                        feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                                        view: model.view,
-                                        assemblyName: model.view.displayedRegions[0].assemblyName,
-                                    },
-                                ]);
-                            }, children: "(single row)" })] }) })] }));
-}

package/dist/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.d.ts

@@ -1,6 +0,0 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
-import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-export default function LaunchBreakpointSplitViewPanel({ model, feature, }: {
-    model: AlignmentFeatureWidgetModel;
-    feature: SimpleFeatureSerialized;
-}): import("react/jsx-runtime").JSX.Element | null;

package/dist/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js

@@ -1,107 +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 = LaunchBreakpointSplitViewPanel;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const getSAFeatures_1 = require("./getSAFeatures");
-const BreakendMultiLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendMultiLevelOptionDialog'))));
-const BreakendSingleLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendSingleLevelOptionDialog'))));
-function LaunchBreakpointSplitViewPanel({ model, feature, }) {
-    const { view } = model;
-    const [res, setRes] = (0, react_1.useState)();
-    const [error, setError] = (0, react_1.useState)();
-    (0, react_1.useEffect)(() => {
-        ;
-        (async () => {
-            try {
-                const feats = await (0, getSAFeatures_1.getSAFeatures)({
-                    view,
-                    feature: new util_1.SimpleFeature(feature),
-                });
-                setRes(feats);
-            }
-            catch (e) {
-                setError(e);
-                console.error(e);
-            }
-        })();
-    }, [feature, view]);
-    const ret = [];
-    if (res) {
-        for (let i = 0; i < res.length - 1; i++) {
-            ret.push([res[i], res[i + 1]]);
-        }
-    }
-    return ret.length ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Launch split view" }), error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null, (0, jsx_runtime_1.jsx)("ul", { children: ret.map((arg, index) => {
-                    const [f1, f2] = arg;
-                    return ((0, jsx_runtime_1.jsxs)("li", { children: [f1.refName, ":", (0, util_1.toLocale)(f1.strand === 1 ? f1.end : f1.start), " ->", ' ', f2.refName, ":", (0, util_1.toLocale)(f2.strand === 1 ? f2.start : f2.end), ' ', (0, jsx_runtime_1.jsx)(TopBottomSplitViewLink, { model: model, f1: f1, f2: f2 }), ' ', (0, jsx_runtime_1.jsx)(SideBySideViewLink, { model: model, f1: f1, f2: f2 })] }, `${JSON.stringify(arg)}-${index}`));
-                }) })] })) : null;
-}
-function TopBottomSplitViewLink({ model, f1, f2, }) {
-    return ((0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
-            event.preventDefault();
-            const session = (0, util_1.getSession)(model);
-            session.queueDialog(handleClose => [
-                BreakendMultiLevelOptionDialog,
-                {
-                    handleClose,
-                    session,
-                    feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                    view: model.view,
-                    assemblyName: model.view.displayedRegions[0].assemblyName,
-                },
-            ]);
-        }, children: "(top/bottom)" }));
-}
-function SideBySideViewLink({ model, f1, f2, }) {
-    return ((0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
-            event.preventDefault();
-            const session = (0, util_1.getSession)(model);
-            session.queueDialog(handleClose => [
-                BreakendSingleLevelOptionDialog,
-                {
-                    handleClose,
-                    session,
-                    feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                    view: model.view,
-                    assemblyName: model.view.displayedRegions[0].assemblyName,
-                },
-            ]);
-        }, children: "(single row)" }));
-}

package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts

@@ -1,6 +0,0 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
-import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-export default function SuppAlignments(props: {
-    model: AlignmentFeatureWidgetModel;
-    feature: SimpleFeatureSerialized;
-}): import("react/jsx-runtime").JSX.Element | null;

package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.js

@@ -1,22 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SuppAlignments;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-const util_1 = require("@jbrowse/core/util");
-const LaunchPairedEndBreakpointSplitViewPanel_1 = __importDefault(require("./LaunchPairedEndBreakpointSplitViewPanel"));
-function SuppAlignments(props) {
-    const { model, feature } = props;
-    const session = (0, util_1.getSession)(model);
-    const { pluginManager } = (0, util_1.getEnv)(session);
-    let hasBreakendSplitView = false;
-    try {
-        hasBreakendSplitView = !!pluginManager.getViewType('BreakpointSplitView');
-    }
-    catch (e) {
-    }
-    return hasBreakendSplitView ? ((0, jsx_runtime_1.jsx)(BaseCard_1.default, { ...props, title: "Paired alignments", children: (0, jsx_runtime_1.jsx)(LaunchPairedEndBreakpointSplitViewPanel_1.default, { model: model, feature: feature }) })) : null;
-}

package/dist/AlignmentsFeatureDetail/PairLink.d.ts

@@ -1,5 +0,0 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
-export default function PairLink({ locString, model, }: {
-    locString: string;
-    model: AlignmentFeatureWidgetModel;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/PairLink.js

@@ -1,12 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = PairLink;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const material_1 = require("@mui/material");
-const util_1 = require("./util");
-function PairLink({ locString, model, }) {
-    return ((0, jsx_runtime_1.jsx)(material_1.Link, { onClick: event => {
-            event.preventDefault();
-            (0, util_1.navToLoc)(locString, model);
-        }, href: "#", children: locString }));
-}

package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts

@@ -1,7 +0,0 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
-import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-export default function SupplementaryAlignments(props: {
-    tag: string;
-    model: AlignmentFeatureWidgetModel;
-    feature: SimpleFeatureSerialized;
-}): import("react/jsx-runtime").JSX.Element;