npm - @jbrowse/plugin-alignments - Versions diffs - 2.17.0 → 3.0.0 - Mend

@jbrowse/plugin-alignments 2.17.0 → 3.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (471) hide show

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts CHANGED Viewed

@@ -1,6 +1,5 @@
-import React from 'react';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
 declare const AlignmentsFeatureDetails: (props: {
     model: AlignmentFeatureWidgetModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default AlignmentsFeatureDetails;

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js CHANGED Viewed

@@ -15,44 +15,45 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+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 react_1 = __importStar(require("react"));
+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 clone_1 = __importDefault(require("clone"));
-const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
-// locals
-const util_1 = require("./util");
-const tagInfo_1 = require("./tagInfo");
-// local components
 const Flags_1 = __importDefault(require("./Flags"));
-const PairLink_1 = __importDefault(require("./PairLink"));
 const Formatter_1 = __importDefault(require("./Formatter"));
-// lazies
+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 AlignmentsFeatureDetails = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     const { featureData } = model;
-    const feat = (0, clone_1.default)(featureData);
+    const feat = structuredClone(featureData);
     const SA = (0, util_1.getTag)('SA', feat);
     const { flags } = feat;
-    return (react_1.default.createElement(material_1.Paper, { "data-testid": "alignment-side-drawer" },
-        react_1.default.createElement(FeatureDetails_1.default, { ...props,
-            // @ts-expect-error
-            descriptions: { ...tagInfo_1.tags, tags: tagInfo_1.tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (react_1.default.createElement(PairLink_1.default, { model: model, locString: value })) : (react_1.default.createElement(Formatter_1.default, { value: value })) }),
-        SA !== undefined ? (react_1.default.createElement(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null,
-        flags & 1 ? (react_1.default.createElement(LinkedPairedAlignments, { model: model, feature: feat })) : null,
-        flags !== undefined ? react_1.default.createElement(Flags_1.default, { feature: feat, ...props }) : null));
+    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 & 1 ? ((0, jsx_runtime_1.jsx)(LinkedPairedAlignments, { model: model, feature: feat })) : null, flags !== undefined ? (0, jsx_runtime_1.jsx)(Flags_1.default, { feature: feat, ...props }) : null] }));
 });
 exports.default = AlignmentsFeatureDetails;

package/dist/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.js CHANGED Viewed

@@ -1,6 +1,5 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = void 0;
-// re-exported for react lazy
 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.js CHANGED Viewed

@@ -1,6 +1,5 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = void 0;
-// re-exported for react lazy
 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 CHANGED Viewed

@@ -1,6 +1,5 @@
-import React from 'react';
 export default function AlignmentFlags(props: {
     feature: {
         flags: number;
     };
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/Flags.js CHANGED Viewed

@@ -4,11 +4,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = AlignmentFlags;
-const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
+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,
@@ -34,11 +34,9 @@ function AlignmentFlags(props) {
     const { classes } = useStyles();
     const { feature } = props;
     const { flags } = feature;
-    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Flags" },
-        react_1.default.createElement(SimpleField_1.default, { name: "Flag", value: flags }),
-        react_1.default.createElement(material_1.FormGroup, null, flagNames.map((name, idx) => {
-            const val = flags & (1 << idx);
-            const key = `${name}_${val}`;
-            return (react_1.default.createElement(material_1.FormControlLabel, { key: key, control: react_1.default.createElement(material_1.Checkbox, { className: classes.compact, checked: Boolean(val), name: name, readOnly: true }), label: name }));
-        }))));
+    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 CHANGED Viewed

@@ -1,4 +1,3 @@
-import React from 'react';
 export default function Formatter({ value }: {
     value: unknown;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/Formatter.js CHANGED Viewed

@@ -1,51 +1,23 @@
 "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 (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __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 });
 exports.default = Formatter;
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-// this 'show more...' used specifically as a formatter on alignments feature
-// details because long SEQ or CRAM files, even a single div full of a ton of
-// data from a long read, can slow down the rest of the app
 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 ? (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement("button", { type: "button", onClick: () => {
-                (0, copy_to_clipboard_1.default)(display);
-                setCopied(true);
-                setTimeout(() => {
-                    setCopied(false);
-                }, 700);
-            } }, copied ? 'Copied to clipboard' : 'Copy'),
-        react_1.default.createElement("button", { type: "button", onClick: () => {
-                setShow(val => !val);
-            } }, show ? 'Show less' : 'Show more'),
-        react_1.default.createElement("div", null, show ? display : `${display.slice(0, 100)}...`))) : (react_1.default.createElement("div", null, display));
+    return display.length > 100 ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("button", { type: "button", onClick: () => {
+                    (0, copy_to_clipboard_1.default)(display);
+                    setCopied(true);
+                    setTimeout(() => {
+                        setCopied(false);
+                    }, 700);
+                }, children: copied ? 'Copied to clipboard' : 'Copy' }), (0, jsx_runtime_1.jsx)("button", { type: "button", onClick: () => {
+                    setShow(val => !val);
+                }, children: show ? 'Show less' : 'Show more' }), (0, jsx_runtime_1.jsx)("div", { children: show ? display : `${display.slice(0, 100)}...` })] })) : ((0, jsx_runtime_1.jsx)("div", { children: display }));
 }

package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.d.ts CHANGED Viewed

@@ -1,9 +1,6 @@
-import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { ViewType } from '@jbrowse/core/pluggableElementTypes';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
-export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, viewType, }: {
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
+export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-    viewType: ViewType;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js CHANGED Viewed

@@ -15,22 +15,32 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+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 react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const util_1 = require("@jbrowse/core/util");
-// lazies
+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, viewType, }) {
+function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }) {
     const session = (0, util_1.getSession)(model);
     const f1 = {
         uniqueId: feature.uniqueId,
@@ -46,47 +56,29 @@ function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, viewType, })
         end: feature.next_pos + 1,
         strand: feature.strand,
     };
-    return (react_1.default.createElement("div", null,
-        react_1.default.createElement(material_1.Typography, null, "Launch split view"),
-        react_1.default.createElement("ul", null,
-            react_1.default.createElement("li", null,
-                f1.refName,
-                ":",
-                (0, util_1.toLocale)(f1.start),
-                " -> ",
-                f2.refName,
-                ":",
-                (0, util_1.toLocale)(f2.start),
-                ' ',
-                react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
-                        event.preventDefault();
-                        session.queueDialog(handleClose => [
-                            BreakendMultiLevelOptionDialog,
-                            {
-                                handleClose,
-                                model,
-                                feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
-                                view: model.view,
-                                assemblyName: model.view.displayedRegions[0].assemblyName,
-                            },
-                        ]);
-                    } }, "(top/bottom)"),
-                ' ',
-                react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
-                        event.preventDefault();
-                        session.queueDialog(handleClose => [
-                            BreakendSingleLevelOptionDialog,
-                            {
-                                handleClose,
-                                model,
-                                feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
-                                view: model.view,
-                                assemblyName: model.view.displayedRegions[0].assemblyName,
-                            },
-                        ]);
-                    } }, "(single row)")))));
+    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 CHANGED Viewed

@@ -1,9 +1,6 @@
-import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { ViewType } from '@jbrowse/core/pluggableElementTypes';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
-export default function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }: {
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
+export default function LaunchBreakpointSplitViewPanel({ model, feature, }: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-    viewType: ViewType;
-}): React.JSX.Element | null;
+}): import("react/jsx-runtime").JSX.Element | null;

package/dist/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js CHANGED Viewed

@@ -15,30 +15,38 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+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 react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
-const util_1 = require("@jbrowse/core/util");
+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");
-// lazies
 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, viewType, }) {
-    const session = (0, util_1.getSession)(model);
+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)(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
@@ -60,51 +68,40 @@ function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
             ret.push([res[i], res[i + 1]]);
         }
     }
-    return ret.length ? (react_1.default.createElement("div", null,
-        react_1.default.createElement(material_1.Typography, null, "Launch split view"),
-        error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null,
-        react_1.default.createElement("ul", null, ret.map((arg, index) => {
-            const [f1, f2] = arg;
-            return (react_1.default.createElement("li", { key: `${JSON.stringify(arg)}-${index}` },
-                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),
-                ' ',
-                react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
-                        event.preventDefault();
-                        session.queueDialog(handleClose => [
-                            BreakendMultiLevelOptionDialog,
-                            {
-                                handleClose,
-                                model,
-                                feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
-                                view: model.view,
-                                assemblyName: model.view.displayedRegions[0].assemblyName,
-                            },
-                        ]);
-                    } }, "(top/bottom)"),
-                ' ',
-                react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
-                        event.preventDefault();
-                        session.queueDialog(handleClose => [
-                            BreakendSingleLevelOptionDialog,
-                            {
-                                handleClose,
-                                model,
-                                feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
-                                view: model.view,
-                                assemblyName: model.view.displayedRegions[0].assemblyName,
-                            },
-                        ]);
-                    } }, "(single row)")));
-        })))) : null;
+    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 CHANGED Viewed

@@ -1,7 +1,6 @@
-import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function SuppAlignments(props: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.js CHANGED Viewed

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SuppAlignments;
-const react_1 = __importDefault(require("react"));
+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"));
@@ -12,12 +12,11 @@ function SuppAlignments(props) {
     const { model, feature } = props;
     const session = (0, util_1.getSession)(model);
     const { pluginManager } = (0, util_1.getEnv)(session);
-    let viewType;
+    let hasBreakendSplitView = false;
     try {
-        viewType = pluginManager.getViewType('BreakpointSplitView');
+        hasBreakendSplitView = !!pluginManager.getViewType('BreakpointSplitView');
     }
     catch (e) {
-        // ignore
     }
-    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Supplementary alignments" }, viewType ? (react_1.default.createElement(LaunchPairedEndBreakpointSplitViewPanel_1.default, { viewType: viewType, model: model, feature: feature })) : null));
+    return ((0, jsx_runtime_1.jsx)(BaseCard_1.default, { ...props, title: "Paired alignments", children: hasBreakendSplitView ? ((0, jsx_runtime_1.jsx)(LaunchPairedEndBreakpointSplitViewPanel_1.default, { model: model, feature: feature })) : null }));
 }

package/dist/AlignmentsFeatureDetail/PairLink.d.ts CHANGED Viewed

@@ -1,6 +1,5 @@
-import React from 'react';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
 export default function PairLink({ locString, model, }: {
     locString: string;
     model: AlignmentFeatureWidgetModel;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/PairLink.js CHANGED Viewed

@@ -1,16 +1,12 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = PairLink;
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const material_1 = require("@mui/material");
 const util_1 = require("./util");
 function PairLink({ locString, model, }) {
-    return (react_1.default.createElement(material_1.Link, { onClick: event => {
+    return ((0, jsx_runtime_1.jsx)(material_1.Link, { onClick: event => {
             event.preventDefault();
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             (0, util_1.navToLoc)(locString, model);
-        }, href: "#" }, locString));
+        }, href: "#", children: locString }));
 }

package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts CHANGED Viewed

@@ -1,8 +1,7 @@
-import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function SupplementaryAlignments(props: {
     tag: string;
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.js CHANGED Viewed

@@ -4,23 +4,20 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SupplementaryAlignments;
-const react_1 = __importDefault(require("react"));
-const util_1 = require("@jbrowse/core/util");
+const jsx_runtime_1 = require("react/jsx-runtime");
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-const SupplementaryAlignmentsLocStrings_1 = __importDefault(require("./SupplementaryAlignmentsLocStrings"));
+const util_1 = require("@jbrowse/core/util");
 const LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1 = __importDefault(require("./LaunchSupplementaryAlignmentBreakpointSplitViewPanel"));
+const SupplementaryAlignmentsLocStrings_1 = __importDefault(require("./SupplementaryAlignmentsLocStrings"));
 function SupplementaryAlignments(props) {
     const { model, tag, feature } = props;
     const session = (0, util_1.getSession)(model);
     const { pluginManager } = (0, util_1.getEnv)(session);
-    let viewType;
+    let hasBreakendSplitView = false;
     try {
-        viewType = pluginManager.getViewType('BreakpointSplitView');
+        hasBreakendSplitView = !!pluginManager.getViewType('BreakpointSplitView');
     }
     catch (e) {
-        // ignore
     }
-    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Supplementary alignments" },
-        react_1.default.createElement(SupplementaryAlignmentsLocStrings_1.default, { model: model, tag: tag }),
-        viewType ? (react_1.default.createElement(LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1.default, { viewType: viewType, model: model, feature: feature })) : null));
+    return ((0, jsx_runtime_1.jsxs)(BaseCard_1.default, { ...props, title: "Supplementary alignments", children: [(0, jsx_runtime_1.jsx)(SupplementaryAlignmentsLocStrings_1.default, { model: model, tag: tag }), hasBreakendSplitView ? ((0, jsx_runtime_1.jsx)(LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1.default, { model: model, feature: feature })) : null] }));
 }