@jbrowse/plugin-alignments 2.18.0 → 3.0.1

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
 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

@@ -15,18 +15,29 @@ 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");
@@ -43,10 +54,6 @@ const AlignmentsFeatureDetails = (0, mobx_react_1.observer)(function (props) {
     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, descriptions: { 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/Flags.d.ts

@@ -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

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = AlignmentFlags;
-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 SimpleField_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField"));
 const material_1 = require("@mui/material");
@@ -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

@@ -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

@@ -1,48 +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"));
 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

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

package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js

@@ -15,16 +15,27 @@ 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 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'))));
@@ -45,43 +56,29 @@ function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }) {
         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,
-                                session,
-                                feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                                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,
-                                session,
-                                feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                                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

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

package/dist/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js

@@ -15,16 +15,27 @@ 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 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");
@@ -57,28 +68,13 @@ function LaunchBreakpointSplitViewPanel({ model, feature, }) {
             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(TopBottomSplitViewLink, { model: model, f1: f1, f2: f2 }),
-                ' ',
-                react_1.default.createElement(SideBySideViewLink, { model: model, f1: f1, f2: f2 })));
-        })))) : 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 (react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
+    return ((0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
             event.preventDefault();
             const session = (0, util_1.getSession)(model);
             session.queueDialog(handleClose => [
@@ -91,10 +87,10 @@ function TopBottomSplitViewLink({ model, f1, f2, }) {
                     assemblyName: model.view.displayedRegions[0].assemblyName,
                 },
             ]);
-        } }, "(top/bottom)"));
+        }, children: "(top/bottom)" }));
 }
 function SideBySideViewLink({ model, f1, f2, }) {
-    return (react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
+    return ((0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
             event.preventDefault();
             const session = (0, util_1.getSession)(model);
             session.queueDialog(handleClose => [
@@ -107,5 +103,5 @@ function SideBySideViewLink({ model, f1, f2, }) {
                     assemblyName: model.view.displayedRegions[0].assemblyName,
                 },
             ]);
-        } }, "(single row)"));
+        }, children: "(single row)" }));
 }

package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
 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

@@ -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"));
@@ -18,5 +18,5 @@ function SuppAlignments(props) {
     }
     catch (e) {
     }
-    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Paired alignments" }, hasBreakendSplitView ? (react_1.default.createElement(LaunchPairedEndBreakpointSplitViewPanel_1.default, { 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

@@ -1,6 +1,5 @@
-import React from 'react';
 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

@@ -1,15 +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();
             (0, util_1.navToLoc)(locString, model);
-        }, href: "#" }, locString));
+        }, href: "#", children: locString }));
 }

package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts

@@ -1,8 +1,7 @@
-import React from 'react';
 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

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SupplementaryAlignments;
-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 LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1 = __importDefault(require("./LaunchSupplementaryAlignmentBreakpointSplitViewPanel"));
@@ -19,7 +19,5 @@ function SupplementaryAlignments(props) {
     }
     catch (e) {
     }
-    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Supplementary alignments" },
-        react_1.default.createElement(SupplementaryAlignmentsLocStrings_1.default, { model: model, tag: tag }),
-        hasBreakendSplitView ? (react_1.default.createElement(LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1.default, { 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] }));
 }

package/dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.d.ts

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

package/dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.js

@@ -1,35 +1,29 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SupplementaryAlignmentsLocStrings;
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const material_1 = require("@mui/material");
 const MismatchParser_1 = require("../MismatchParser");
 const util_1 = require("./util");
 function SupplementaryAlignmentsLocStrings({ tag, model, }) {
-    return (react_1.default.createElement("div", null,
-        react_1.default.createElement(material_1.Typography, null, "List of supplementary alignment locations"),
-        react_1.default.createElement("ul", null, tag
-            .split(';')
-            .filter(SA => !!SA)
-            .map((SA, idx) => {
-            const [saRef, saStart, saStrand, saCigar] = SA.split(',');
-            const saLength = (0, MismatchParser_1.getLengthOnRef)(saCigar);
-            const extra = Math.floor(saLength / 5);
-            const start = +saStart;
-            const end = +saStart + saLength;
-            const sp = start - extra;
-            const ep = end + extra;
-            const locString = `${saRef}:${Math.max(1, sp)}-${ep}`;
-            const displayStart = start.toLocaleString('en-US');
-            const displayEnd = end.toLocaleString('en-US');
-            const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`;
-            return (react_1.default.createElement("li", { key: `${locString}-${idx}` },
-                react_1.default.createElement(material_1.Link, { href: "#", onClick: async (event) => {
-                        event.preventDefault();
-                        (0, util_1.navToLoc)(locString, model);
-                    } }, displayString)));
-        }))));
+    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "List of supplementary alignment locations" }), (0, jsx_runtime_1.jsx)("ul", { children: tag
+                    .split(';')
+                    .filter(SA => !!SA)
+                    .map((SA, idx) => {
+                    const [saRef, saStart, saStrand, saCigar] = SA.split(',');
+                    const saLength = (0, MismatchParser_1.getLengthOnRef)(saCigar);
+                    const extra = Math.floor(saLength / 5);
+                    const start = +saStart;
+                    const end = +saStart + saLength;
+                    const sp = start - extra;
+                    const ep = end + extra;
+                    const locString = `${saRef}:${Math.max(1, sp)}-${ep}`;
+                    const displayStart = start.toLocaleString('en-US');
+                    const displayEnd = end.toLocaleString('en-US');
+                    const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`;
+                    return ((0, jsx_runtime_1.jsx)("li", { children: (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: async (event) => {
+                                event.preventDefault();
+                                (0, util_1.navToLoc)(locString, model);
+                            }, children: displayString }) }, `${locString}-${idx}`));
+                }) })] }));
 }

package/dist/AlignmentsFeatureDetail/index.js

@@ -15,13 +15,23 @@ 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 };
 };

package/dist/BamAdapter/index.js

@@ -15,13 +15,23 @@ 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 };
 };