@jbrowse/plugin-linear-comparative-view 2.17.0 → 3.0.0

package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -4,19 +4,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderToSvg = renderToSvg;
-const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mobx_1 = require("mobx");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
-const ui_1 = require("@jbrowse/core/ui");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-// locals
+const material_1 = require("@mui/material");
+const mobx_1 = require("mobx");
 const SVGBackground_1 = __importDefault(require("./SVGBackground"));
 const SVGLinearGenomeView_1 = __importDefault(require("./SVGLinearGenomeView"));
 const drawSynteny_1 = require("../../LinearSyntenyDisplay/drawSynteny");
-// render LGV to SVG
 async function renderToSvg(model, opts) {
     var _a;
     await (0, mobx_1.when)(() => model.initialized);
@@ -26,7 +23,6 @@ async function renderToSvg(model, opts) {
     const { width, views, levels } = model;
     const shift = 50;
     const offset = rulerHeight;
-    const { createRootFn } = (0, mobx_state_tree_1.getRoot)(model);
     const heights = views.map(v => (0, plugin_linear_genome_view_1.totalHeight)(v.tracks, textHeight, trackLabels) + offset);
     const totalHeightSvg = (0, util_1.sum)(heights) + (0, util_1.sum)(levels.map(l => l.height)) + 100;
     const displayResults = await Promise.all(views.map(async (view) => ({
@@ -68,7 +64,7 @@ async function renderToSvg(model, opts) {
     const w = width + trackLabelOffset;
     const theme = (0, ui_1.createJBrowseTheme)(themeVar);
     const RenderList = [
-        react_1.default.createElement(SVGLinearGenomeView_1.default, { rulerHeight: rulerHeight, trackLabelOffset: trackLabelOffset, shift: shift, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[0], key: views[0].id, view: views[0], fontSize: fontSize }),
+        (0, jsx_runtime_1.jsx)(SVGLinearGenomeView_1.default, { rulerHeight: rulerHeight, trackLabelOffset: trackLabelOffset, shift: shift, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[0], view: views[0], fontSize: fontSize }, views[0].id),
     ];
     let currOffset = heights[0] + fontSize + rulerHeight;
     for (let i = 1; i < views.length; i++) {
@@ -77,21 +73,8 @@ async function renderToSvg(model, opts) {
         const rendering = renderings[i - 1];
         const height = heights[i];
         const levelHeight = level.height || 0;
-        RenderList.push(react_1.default.createElement("g", { key: view.id, transform: `translate(0 ${currOffset})` },
-            levelHeight ? (react_1.default.createElement("defs", null,
-                react_1.default.createElement("clipPath", { id: `synclip-${i}` },
-                    react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: levelHeight })))) : null,
-            react_1.default.createElement("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})` }, rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => (
-            /* biome-ignore lint/suspicious/noArrayIndexKey: */
-            react_1.default.createElement(util_1.ReactRendering, { key: i, rendering: r })))),
-            react_1.default.createElement("g", { transform: `translate(0 ${levelHeight})` },
-                react_1.default.createElement(SVGLinearGenomeView_1.default, { rulerHeight: rulerHeight, shift: shift, trackLabelOffset: trackLabelOffset, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[i], key: view.id, view: view, fontSize: fontSize }))));
+        RenderList.push((0, jsx_runtime_1.jsxs)("g", { transform: `translate(0 ${currOffset})`, children: [levelHeight ? ((0, jsx_runtime_1.jsx)("defs", { children: (0, jsx_runtime_1.jsx)("clipPath", { id: `synclip-${i}`, children: (0, jsx_runtime_1.jsx)("rect", { x: 0, y: 0, width: width, height: levelHeight }) }) })) : null, (0, jsx_runtime_1.jsx)("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})`, children: rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => ((0, jsx_runtime_1.jsx)(util_1.ReactRendering, { rendering: r }, i))) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${levelHeight})`, children: (0, jsx_runtime_1.jsx)(SVGLinearGenomeView_1.default, { rulerHeight: rulerHeight, shift: shift, trackLabelOffset: trackLabelOffset, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[i], view: view, fontSize: fontSize }, view.id) })] }, view.id));
         currOffset += height + fontSize + rulerHeight + levelHeight;
     }
-    // the xlink namespace is used for rendering <image> tag
-    return (0, util_1.renderToStaticMarkup)(react_1.default.createElement(material_1.ThemeProvider, { theme: theme },
-        react_1.default.createElement(Wrapper, null,
-            react_1.default.createElement("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString() },
-                react_1.default.createElement(SVGBackground_1.default, { width: w, height: totalHeightSvg, shift: shift }),
-                RenderList))), createRootFn);
+    return (0, util_1.renderToStaticMarkup)((0, jsx_runtime_1.jsx)(material_1.ThemeProvider, { theme: theme, children: (0, jsx_runtime_1.jsx)(Wrapper, { children: (0, jsx_runtime_1.jsxs)("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString(), children: [(0, jsx_runtime_1.jsx)(SVGBackground_1.default, { width: w, height: totalHeightSvg, shift: shift }), RenderList] }) }) }));
 }

package/dist/LinearSyntenyView/types.d.ts

@@ -0,0 +1,12 @@
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { SnapshotIn } from 'mobx-state-tree';
+export type Conf = SnapshotIn<AnyConfigurationModel>;
+export type ImportFormSyntenyTrack = {
+    type: 'preConfigured';
+    value: string;
+} | {
+    type: 'userOpened';
+    value: Conf;
+} | {
+    type: 'none';
+};

package/dist/LinearSyntenyView/types.js

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

package/dist/LinearSyntenyViewHelper/index.d.ts

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

package/dist/LinearSyntenyViewHelper/index.js

@@ -4,11 +4,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LinearSyntenyViewF;
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
 const stateModelFactory_1 = require("./stateModelFactory");
 function UnusedComponent() {
-    return react_1.default.createElement("div", null);
+    return (0, jsx_runtime_1.jsx)("div", {});
 }
 function LinearSyntenyViewF(pluginManager) {
     pluginManager.addViewType(() => {

package/dist/LinearSyntenyViewHelper/stateModelFactory.d.ts

@@ -1,5 +1,5 @@
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { Instance } from 'mobx-state-tree';
 export declare function linearSyntenyViewHelperModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").IType<string | undefined, string, string>;
@@ -7,21 +7,9 @@ export declare function linearSyntenyViewHelperModelFactory(pluginManager: Plugi
     height: import("mobx-state-tree").IType<number | undefined, number, number>;
     level: import("mobx-state-tree").ISimpleType<number>;
 }, {
-    /**
-     * #action
-     */
     setHeight(n: number): number;
-    /**
-     * #action
-     */
     showTrack(trackId: string, initialSnapshot?: {}): void;
-    /**
-     * #action
-     */
     hideTrack(trackId: string): number;
-    /**
-     * #action
-     */
     toggleTrack(trackId: string): boolean;
 } & {
     readonly assemblyNames: (string | undefined)[];

package/dist/LinearSyntenyViewHelper/stateModelFactory.js

@@ -1,44 +1,23 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.linearSyntenyViewHelperModelFactory = linearSyntenyViewHelperModelFactory;
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mobx_1 = require("mobx");
 const mst_1 = require("@jbrowse/core/util/types/mst");
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 function linearSyntenyViewHelperModelFactory(pluginManager) {
     return mobx_state_tree_1.types
         .model('LinearSyntenyViewHelper', {
-        /**
-         * #property
-         */
         id: mst_1.ElementId,
-        /**
-         * #property
-         */
         type: 'LinearSyntenyViewHelper',
-        /**
-         * #property
-         */
         tracks: mobx_state_tree_1.types.array(pluginManager.pluggableMstType('track', 'stateModel')),
-        /**
-         * #property
-         */
         height: 100,
-        /**
-         * #property
-         */
         level: mobx_state_tree_1.types.number,
     })
         .actions(self => ({
-        /**
-         * #action
-         */
         setHeight(n) {
             self.height = n;
             return self.height;
         },
-        /**
-         * #action
-         */
         showTrack(trackId, initialSnapshot = {}) {
             const schema = pluginManager.pluggableConfigSchemaType('track');
             const configuration = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
@@ -67,9 +46,6 @@ function linearSyntenyViewHelperModelFactory(pluginManager) {
                 ],
             }));
         },
-        /**
-         * #action
-         */
         hideTrack(trackId) {
             const schema = pluginManager.pluggableConfigSchemaType('track');
             const config = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
@@ -81,9 +57,6 @@ function linearSyntenyViewHelperModelFactory(pluginManager) {
             });
             return shownTracks.length;
         },
-        /**
-         * #action
-         */
         toggleTrack(trackId) {
             const hiddenCount = this.hideTrack(trackId);
             if (!hiddenCount) {

package/dist/SyntenyFeatureDetail/LinkToSyntenyView.d.ts

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

package/dist/SyntenyFeatureDetail/LinkToSyntenyView.js

@@ -0,0 +1,87 @@
+"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 });
+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 mobx_react_1 = require("mobx-react");
+const LaunchSyntenyViewDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../LGVSyntenyDisplay/components/LaunchSyntenyViewDialog'))));
+const LinkToSyntenyView = (0, mobx_react_1.observer)(function ({ model, }) {
+    const { featureData, view, level, trackId } = model;
+    return ((0, jsx_runtime_1.jsxs)("ul", { children: [view.type === 'LinearSyntenyView' ? ((0, jsx_runtime_1.jsx)("li", { children: (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
+                        var _a, _b;
+                        event.preventDefault();
+                        const { views } = view;
+                        if (level !== undefined) {
+                            (_a = views[level]) === null || _a === void 0 ? void 0 : _a.navTo(featureData);
+                            (_b = views[level + 1]) === null || _b === void 0 ? void 0 : _b.navTo(featureData.mate);
+                        }
+                        else {
+                            const f1 = featureData;
+                            const f2 = featureData.mate;
+                            const r1 = f1.assemblyName;
+                            const r2 = f2.assemblyName;
+                            const v1 = views.find(view => view.assemblyNames[0] === r1);
+                            const v2 = views.find(view => view.assemblyNames[0] === r2);
+                            if (!v1 || !v2) {
+                                (0, util_1.getSession)(model).notify([
+                                    v1
+                                        ? `Unable to find ${(0, util_1.assembleLocString)(f1)} in synteny view`
+                                        : '',
+                                    v2
+                                        ? `Unable to find ${(0, util_1.assembleLocString)(f2)} in synteny view`
+                                        : '',
+                                ].join(' ... '));
+                            }
+                            v1 === null || v1 === void 0 ? void 0 : v1.navTo(f1);
+                            v2 === null || v2 === void 0 ? void 0 : v2.navTo(f2);
+                        }
+                    }, children: "Center view on this feature" }) })) : null, (0, jsx_runtime_1.jsx)("li", { children: (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: event => {
+                        event.preventDefault();
+                        const feature = new util_1.SimpleFeature(featureData);
+                        const session = (0, util_1.getSession)(model);
+                        session.queueDialog(handleClose => [
+                            LaunchSyntenyViewDialog,
+                            {
+                                session,
+                                feature,
+                                trackId,
+                                handleClose,
+                            },
+                        ]);
+                    }, children: "Launch new linear synteny view on this feature" }) })] }));
+});
+exports.default = LinkToSyntenyView;

package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts

@@ -1,14 +1,5 @@
-import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-interface SyntenyFeatureDetailModel {
-    trackId: string;
-    featureData: SimpleFeatureSerialized;
-    level?: number;
-    view: {
-        type: string;
-    };
-}
+import type { SyntenyFeatureDetailModel } from './types';
 declare const SyntenyFeatureDetail: ({ model, }: {
     model: SyntenyFeatureDetailModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default SyntenyFeatureDetail;

package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.js

@@ -1,100 +1,15 @@
 "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 });
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const BaseFeatureDetail_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail"));
+const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
-// locals
-const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-const BaseFeatureDetail_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail"));
-const util_1 = require("@jbrowse/core/util");
-// lazies
-const LaunchSyntenyViewDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../LGVSyntenyDisplay/components/LaunchSyntenyViewDialog'))));
-const CustomLinker = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { featureData, view, level, trackId } = model;
-    return (react_1.default.createElement("ul", null,
-        view.type === 'LinearSyntenyView' ? (react_1.default.createElement("li", null,
-            react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
-                    var _a, _b;
-                    event.preventDefault();
-                    const { views } = view;
-                    if (level !== undefined) {
-                        // level is "pre-known", and stored in the SyntenyFeatureWidget
-                        // model state e.g. when clicking on a feature from a
-                        // LinearSyntenyRendering
-                        (_a = views[level]) === null || _a === void 0 ? void 0 : _a.navTo(featureData);
-                        (_b = views[level + 1]) === null || _b === void 0 ? void 0 : _b.navTo(featureData.mate);
-                    }
-                    else {
-                        // best effort to find the right level. this is triggered for
-                        // example if a user clicks on a feature in a LGVSyntenyDisplay
-                        // in an existing LinearSyntenyView, there is no real proper
-                        // level "pre-known" to this situation
-                        const f1 = featureData;
-                        const f2 = featureData.mate;
-                        const r1 = f1.assemblyName;
-                        const r2 = f2.assemblyName;
-                        const v1 = views.find(view => view.assemblyNames[0] === r1);
-                        const v2 = views.find(view => view.assemblyNames[0] === r2);
-                        if (!v1 || !v2) {
-                            (0, util_1.getSession)(model).notify([
-                                v1
-                                    ? `Unable to find ${(0, util_1.assembleLocString)(f1)} in synteny view`
-                                    : '',
-                                v2
-                                    ? `Unable to find ${(0, util_1.assembleLocString)(f2)} in synteny view`
-                                    : '',
-                            ].join(' ... '));
-                        }
-                        v1 === null || v1 === void 0 ? void 0 : v1.navTo(f1);
-                        v2 === null || v2 === void 0 ? void 0 : v2.navTo(f2);
-                    }
-                } }, "Center view on this feature"))) : null,
-        react_1.default.createElement("li", null,
-            react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
-                    event.preventDefault();
-                    const session = (0, util_1.getSession)(model);
-                    const feature = new util_1.SimpleFeature(featureData);
-                    session.queueDialog(handleClose => [
-                        LaunchSyntenyViewDialog,
-                        {
-                            model,
-                            feature,
-                            trackId,
-                            handleClose,
-                        },
-                    ]);
-                } }, "Launch new linear synteny view on this feature"))));
-});
+const LinkToSyntenyView_1 = __importDefault(require("./LinkToSyntenyView"));
 const SyntenyFeatureDetail = (0, mobx_react_1.observer)(function ({ model, }) {
-    return (react_1.default.createElement(material_1.Paper, { "data-testid": "alignment-side-drawer" },
-        react_1.default.createElement(BaseFeatureDetail_1.default, { title: "Feature", model: model }),
-        react_1.default.createElement(BaseCard_1.default, { title: "Link to view" },
-            react_1.default.createElement(CustomLinker, { model: model }))));
+    return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { children: [(0, jsx_runtime_1.jsx)(BaseFeatureDetail_1.default, { title: "Feature", model: model }), (0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: "Link to view", children: (0, jsx_runtime_1.jsx)(LinkToSyntenyView_1.default, { model: model }) })] }));
 });
 exports.default = SyntenyFeatureDetail;

package/dist/SyntenyFeatureDetail/index.d.ts

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

package/dist/SyntenyFeatureDetail/index.js

@@ -15,33 +15,37 @@ 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 });
 exports.default = SyntenyFeatureWidgetF;
 const react_1 = require("react");
+const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
 const configuration_1 = require("@jbrowse/core/configuration");
 const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
 const mobx_state_tree_1 = require("mobx-state-tree");
-const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
 const configSchema = (0, configuration_1.ConfigurationSchema)('SyntenyFeatureWidget', {});
 function stateModelF(pluginManager) {
     return mobx_state_tree_1.types.compose((0, BaseFeatureWidget_1.stateModelFactory)(pluginManager), mobx_state_tree_1.types.model('SyntenyFeatureWidget', {
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('SyntenyFeatureWidget'),
-        /**
-         * #property
-         */
         level: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
     }));
 }

package/dist/SyntenyFeatureDetail/types.d.ts

@@ -0,0 +1,9 @@
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
+export interface SyntenyFeatureDetailModel {
+    trackId: string;
+    featureData: SimpleFeatureSerialized;
+    level?: number;
+    view: {
+        type: string;
+    };
+}

package/dist/SyntenyFeatureDetail/types.js

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

package/dist/SyntenyTrack/configSchema.d.ts

@@ -1,4 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         description: string;

package/dist/SyntenyTrack/configSchema.js

@@ -2,16 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-/**
- * #config SyntenyTrack
- * extends
- * - [BaseTrack](../basetrack)
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = (pluginManager) => (0, configuration_1.ConfigurationSchema)('SyntenyTrack', {}, {
-    /**
-     * #baseConfiguration
-     */
     baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager),
 });
 exports.default = configSchema;

package/dist/SyntenyTrack/index.d.ts

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

package/dist/SyntenyTrack/index.js

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = registerSyntenyTrack;
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const configSchema_1 = __importDefault(require("./configSchema"));
 function registerSyntenyTrack(pluginManager) {
     pluginManager.addTrackType(() => {

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class LinearComparativeViewPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -6,16 +6,16 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const util_1 = require("@jbrowse/core/util");
 const CalendarViewDay_1 = __importDefault(require("@mui/icons-material/CalendarViewDay"));
+const LGVSyntenyDisplay_1 = __importDefault(require("./LGVSyntenyDisplay"));
+const LaunchLinearSyntenyView_1 = __importDefault(require("./LaunchLinearSyntenyView"));
 const LinearComparativeDisplay_1 = __importDefault(require("./LinearComparativeDisplay"));
 const LinearComparativeView_1 = __importDefault(require("./LinearComparativeView"));
+const LinearReadVsRef_1 = __importDefault(require("./LinearReadVsRef"));
 const LinearSyntenyDisplay_1 = __importDefault(require("./LinearSyntenyDisplay"));
-const LGVSyntenyDisplay_1 = __importDefault(require("./LGVSyntenyDisplay"));
 const LinearSyntenyView_1 = __importDefault(require("./LinearSyntenyView"));
 const LinearSyntenyViewHelper_1 = __importDefault(require("./LinearSyntenyViewHelper"));
-const LaunchLinearSyntenyView_1 = __importDefault(require("./LaunchLinearSyntenyView"));
-const SyntenyTrack_1 = __importDefault(require("./SyntenyTrack"));
-const LinearReadVsRef_1 = __importDefault(require("./LinearReadVsRef"));
 const SyntenyFeatureDetail_1 = __importDefault(require("./SyntenyFeatureDetail"));
+const SyntenyTrack_1 = __importDefault(require("./SyntenyTrack"));
 class LinearComparativeViewPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);

package/dist/util.d.ts

@@ -1,5 +1,5 @@
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { Region } from '@jbrowse/core/util/types';
 export type LayoutRecord = [number, number, number, number];
 export interface ReducedLinearGenomeView {
     bpPerPx: number;

package/dist/util.js

@@ -26,18 +26,14 @@ function getTrackPos(view, trackConfigId) {
     const idx = view.tracks.findIndex(t => t.configuration === trackConfigId);
     let accum = 0;
     for (let i = 0; i < idx; i += 1) {
-        accum += view.tracks[i].height + 3; // +1px for trackresizehandle
+        accum += view.tracks[i].height + 3;
     }
     return accum;
 }
-// Uses bpToPx to get the screen pixel coordinates but ignores some conditions
-// where bpToPx could return undefined
 function getPxFromCoordinate(view, refName, coord) {
     var _a;
     return (((_a = bpToPx(view, { refName, coord })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - view.offsetPx;
 }
-// Retrieves the y-position of a layout record in a track
-// If track not found returns 0
 function overlayYPos(trackConfigId, level, views, c, cond) {
     const track = views[level].tracks.find(t => t.configuration === trackConfigId);
     const ypos = track
@@ -47,11 +43,6 @@ function overlayYPos(trackConfigId, level, views, c, cond) {
         : 0;
     return ypos + (cond ? cheight(c) : 0);
 }
-// Returns the pixel screen position of a refName:coord input, or undefined if
-// the input could not be located. Uses view.displayedRegions as a representation
-// of what is on the screen
-//
-// Note: does not consider that this refName:coord input could multi-match
 function bpToPx(view, { refName, coord }) {
     let offsetBp = 0;
     const index = view.displayedRegions.findIndex(r => {
@@ -71,7 +62,6 @@ function bpToPx(view, { refName, coord }) {
     }
     return undefined;
 }
-// Returns either 0 or height depending on condition
 function interstitialYPos(cond, height) {
     return cond ? 0 : height;
 }

package/esm/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.d.ts

@@ -1,8 +1,9 @@
-import React from 'react';
-import { Feature } from '@jbrowse/core/util';
-export default function LaunchSyntenyViewDialog({ model, feature, trackId, handleClose, }: {
-    model: unknown;
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+export default function LaunchSyntenyViewDialog({ session, view, feature, trackId, handleClose, }: {
+    session: AbstractSessionModel;
+    view?: LinearGenomeViewModel;
     feature: Feature;
     trackId: string;
     handleClose: () => void;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;