@jbrowse/plugin-linear-comparative-view 2.18.0 → 3.0.0

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

@@ -1,8 +1,9 @@
-import React from 'react';
-import type { 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;

package/dist/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js

@@ -1,75 +1,53 @@
 "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;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LaunchSyntenyViewDialog;
-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");
 const mui_1 = require("tss-react/mui");
-const util_2 = require("./util");
+const util_1 = require("./util");
 const useStyles = (0, mui_1.makeStyles)()({
     padding: {
         margin: 10,
         border: '1px solid #ccc',
     },
 });
-function LaunchSyntenyViewDialog({ model, feature, trackId, handleClose, }) {
+function LaunchSyntenyViewDialog({ session, view, feature, trackId, handleClose, }) {
     const { classes } = useStyles();
     const inverted = feature.get('strand') === -1;
+    const hasCIGAR = !!feature.get('CIGAR');
     const [horizontallyFlip, setHorizontallyFlip] = (0, react_1.useState)(inverted);
     const [windowSize, setWindowSize] = (0, react_1.useState)('1000');
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, title: "Launch synteny view", onClose: handleClose },
-        react_1.default.createElement(material_1.DialogContent, null,
-            inverted ? (react_1.default.createElement(material_1.FormControlLabel, { className: classes.padding, control: react_1.default.createElement(material_1.Checkbox, { checked: horizontallyFlip, onChange: event => {
-                        setHorizontallyFlip(event.target.checked);
-                    } }), label: "Note: The feature is inverted in orientation on the target\n            sequence. This will result in the lower panel having genomic\n            coordinates decreasing left to right. Horizontally flip?" })) : null,
-            react_1.default.createElement(material_1.TextField, { label: "Add window size in bp", value: windowSize, onChange: event => {
-                    setWindowSize(event.target.value);
-                } })),
-        react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                    ;
-                    (async () => {
-                        try {
-                            await (0, util_2.navToSynteny)({
-                                feature,
-                                windowSize: +windowSize,
-                                horizontallyFlip,
-                                trackId,
-                                model,
-                            });
-                        }
-                        catch (e) {
-                            console.error(e);
-                            (0, util_1.getSession)(model).notifyError(`${e}`, e);
-                        }
-                    })();
-                    handleClose();
-                } }, "Submit"),
-            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
+    const [useRegionOfInterest, setUseRegionOfInterest] = (0, react_1.useState)(true);
+    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, title: "Launch synteny view", onClose: handleClose, children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [view && hasCIGAR ? ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { className: classes.padding, control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: useRegionOfInterest, onChange: event => {
+                                setUseRegionOfInterest(event.target.checked);
+                            } }), label: "Use CIGAR string to navigate the current visible to the target" })) : null, inverted ? ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { className: classes.padding, control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: horizontallyFlip, onChange: event => {
+                                setHorizontallyFlip(event.target.checked);
+                            } }), label: "Note: The feature is inverted in orientation on the target\n            sequence. This will result in the lower panel having genomic\n            coordinates decreasing left to right. Horizontally flip?" })) : null, (0, jsx_runtime_1.jsx)(material_1.TextField, { label: "Add window size in bp", value: windowSize, onChange: event => {
+                            setWindowSize(event.target.value);
+                        } })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                            ;
+                            (async () => {
+                                try {
+                                    await (0, util_1.navToSynteny)({
+                                        feature,
+                                        windowSize: +windowSize,
+                                        horizontallyFlip,
+                                        trackId,
+                                        session,
+                                        region: useRegionOfInterest
+                                            ? view === null || view === void 0 ? void 0 : view.dynamicBlocks.contentBlocks[0]
+                                            : undefined,
+                                    });
+                                }
+                                catch (e) {
+                                    console.error(e);
+                                    session.notifyError(`${e}`, e);
+                                }
+                            })();
+                            handleClose();
+                        }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                            handleClose();
+                        }, children: "Cancel" })] })] }));
 }

package/dist/LGVSyntenyDisplay/components/util.d.ts

@@ -1,11 +1,14 @@
-import type { Feature } from '@jbrowse/core/util';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import type { IAnyStateTreeNode } from 'mobx-state-tree';
-export declare function navToSynteny({ feature, windowSize: ws, model, trackId, view, horizontallyFlip, }: {
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+export interface SimpleRegion {
+    refName: string;
+    start: number;
+    end: number;
+}
+export declare function navToSynteny({ feature, windowSize: ws, session, trackId, region, horizontallyFlip, }: {
     windowSize: number;
     trackId: string;
     horizontallyFlip: boolean;
     feature: Feature;
-    view?: LinearGenomeViewModel;
-    model: IAnyStateTreeNode;
+    session: AbstractSessionModel;
+    region?: SimpleRegion;
 }): Promise<void>;

package/dist/LGVSyntenyDisplay/components/util.js

@@ -1,12 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.navToSynteny = navToSynteny;
-const util_1 = require("@jbrowse/core/util");
 const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
 const { parseCigar } = plugin_alignments_1.MismatchParser;
-function f(n) {
-    return Math.floor(n);
-}
 function findPosInCigar(cigar, startX) {
     let featX = 0;
     let mateX = 0;
@@ -30,9 +26,7 @@ function findPosInCigar(cigar, startX) {
     }
     return [featX, mateX];
 }
-async function navToSynteny({ feature, windowSize: ws, model, trackId, view, horizontallyFlip, }) {
-    const session = (0, util_1.getSession)(model);
-    const reg = view === null || view === void 0 ? void 0 : view.dynamicBlocks.contentBlocks[0];
+async function navToSynteny({ feature, windowSize: ws, session, trackId, region, horizontallyFlip, }) {
     const cigar = feature.get('CIGAR');
     const strand = feature.get('strand');
     const featRef = feature.get('refName');
@@ -48,9 +42,9 @@ async function navToSynteny({ feature, windowSize: ws, model, trackId, view, hor
     let rMateEnd;
     let rFeatStart;
     let rFeatEnd;
-    if (reg && cigar) {
-        const regStart = reg.start;
-        const regEnd = reg.end;
+    if (region && cigar) {
+        const regStart = region.start;
+        const regEnd = region.end;
         const p = parseCigar(cigar);
         const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart);
         const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart);
@@ -91,10 +85,10 @@ async function navToSynteny({ feature, windowSize: ws, model, trackId, view, hor
             },
         ],
     });
-    const l1 = `${featRef}:${f(rFeatStart - ws)}-${f(rFeatEnd + ws)}`;
+    const l1 = `${featRef}:${Math.floor(rFeatStart - ws)}-${Math.floor(rFeatEnd + ws)}`;
     const m1 = Math.min(rMateStart, rMateEnd);
     const m2 = Math.max(rMateStart, rMateEnd);
-    const l2 = `${mateRef}:${f(m1 - ws)}-${f(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
+    const l2 = `${mateRef}:${Math.floor(m1 - ws)}-${Math.floor(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
     await Promise.all([
         view2.views[0].navToLocString(l1, featAsm),
         view2.views[1].navToLocString(l2, mateAsm),

package/dist/LGVSyntenyDisplay/model.d.ts

@@ -35,7 +35,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -85,6 +85,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     colorBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined>;
     filterBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined>;
     jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LGVSyntenyDisplay">;
     configuration: AnyConfigurationSchemaType;
@@ -179,13 +180,13 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
 } & {
     readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -212,7 +213,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
@@ -223,6 +224,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     readonly filterBy: any;
 } & {
     readonly autorunReady: boolean;
+    readonly hideSmallIndels: boolean | undefined;
 } & {
     setTagsReady(flag: boolean): void;
     setMaxHeight(n?: number): void;
@@ -236,6 +238,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     setConfig(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
     setFilterBy(filter: import("@jbrowse/plugin-alignments/src/shared/types").FilterBy): void;
     setJexlFilters(filters: string[]): void;
+    setHideSmallIndels(arg: boolean): void;
 } & {
     readonly rendererConfig: {
         [x: string]: any;
@@ -271,18 +274,28 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         model: {
             sortedBy?: import("@jbrowse/plugin-alignments/src/shared/types").SortedBy;
         };
-    }) => import("react").JSX.Element | null;
+    }) => import("react/jsx-runtime").JSX.Element | null;
     renderPropsPre(): any;
     colorSchemeSubMenuItems(): {
         label: string;
         onClick: () => void;
     }[];
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        label: string;
+        priority: number;
+        type: string;
+        checked: boolean | undefined;
+        onClick: () => void;
+        icon?: undefined;
+    } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
+        priority?: undefined;
+        type?: undefined;
+        checked?: undefined;
     })[];
 } & {
     renderProps(): any;
@@ -338,7 +351,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -388,5 +401,6 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     colorBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined>;
     filterBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined>;
     jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default stateModelFactory;

package/dist/LGVSyntenyDisplay/model.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;
+    };
+})();
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
@@ -50,9 +60,10 @@ function stateModelFactory(schema) {
                                     (0, util_1.getSession)(self).queueDialog(handleClose => [
                                         LaunchSyntenyViewDialog,
                                         {
-                                            model: self,
+                                            view: (0, util_1.getContainingView)(self),
                                             trackId: (0, configuration_1.getConf)((0, util_1.getContainingTrack)(self), 'trackId'),
                                             handleClose,
+                                            session: (0, util_1.getSession)(self),
                                             feature,
                                         },
                                     ]);

package/dist/LinearComparativeView/components/Header.d.ts

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

package/dist/LinearComparativeView/components/Header.js

@@ -1,32 +1,10 @@
 "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 react_1 = require("react");
 const CascadingMenuButton_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenuButton"));
 const Icons_1 = require("@jbrowse/core/ui/Icons");
 const MoreVert_1 = __importDefault(require("@mui/icons-material/MoreVert"));
@@ -45,67 +23,60 @@ const Header = (0, mobx_react_1.observer)(function ({ model, }) {
     const { views } = model;
     const [showSearchBoxes, setShowSearchBoxes] = (0, react_1.useState)(views.length <= 3);
     const [sideBySide, setSideBySide] = (0, react_1.useState)(views.length <= 3);
-    return (react_1.default.createElement(material_1.FormGroup, { row: true },
-        react_1.default.createElement(CascadingMenuButton_1.default, { menuItems: [
-                {
-                    label: 'Synteny track selectors',
-                    type: 'subMenu',
-                    subMenu: views.slice(0, -1).map((_, idx) => ({
-                        label: `Row ${idx + 1}->${idx + 2} (${views[idx].assemblyNames.join(',')}->${views[idx + 1].assemblyNames.join(',')})`,
+    return ((0, jsx_runtime_1.jsxs)(material_1.FormGroup, { row: true, children: [(0, jsx_runtime_1.jsx)(CascadingMenuButton_1.default, { menuItems: [
+                    {
+                        label: 'Synteny track selectors',
+                        type: 'subMenu',
+                        subMenu: views.slice(0, -1).map((_, idx) => ({
+                            label: `Row ${idx + 1}->${idx + 2} (${views[idx].assemblyNames.join(',')}->${views[idx + 1].assemblyNames.join(',')})`,
+                            onClick: () => {
+                                model.activateTrackSelector(idx);
+                            },
+                        })),
+                    },
+                    {
+                        label: 'Row track selectors',
+                        type: 'subMenu',
+                        subMenu: views.map((view, idx) => ({
+                            label: `Row ${idx + 1} track selector (${view.assemblyNames.join(',')})`,
+                            onClick: () => view.activateTrackSelector(),
+                        })),
+                    },
+                ], children: (0, jsx_runtime_1.jsx)(Icons_1.TrackSelector, {}) }), (0, jsx_runtime_1.jsx)(CascadingMenuButton_1.default, { menuItems: [
+                    {
+                        label: 'Row view menus',
+                        type: 'subMenu',
+                        subMenu: views.map((view, idx) => ({
+                            label: `View ${idx + 1} Menu`,
+                            subMenu: view.menuItems(),
+                        })),
+                    },
+                    ...model.headerMenuItems(),
+                ], children: (0, jsx_runtime_1.jsx)(MoreVert_1.default, {}) }), (0, jsx_runtime_1.jsx)(CascadingMenuButton_1.default, { menuItems: [
+                    {
+                        label: 'Show search boxes',
+                        type: 'checkbox',
+                        checked: showSearchBoxes,
                         onClick: () => {
-                            model.activateTrackSelector(idx);
+                            setShowSearchBoxes(!showSearchBoxes);
                         },
-                    })),
-                },
-                {
-                    label: 'Row track selectors',
-                    type: 'subMenu',
-                    subMenu: views.map((view, idx) => ({
-                        label: `Row ${idx + 1} track selector (${view.assemblyNames.join(',')})`,
-                        onClick: () => view.activateTrackSelector(),
-                    })),
-                },
-            ] },
-            react_1.default.createElement(Icons_1.TrackSelector, null)),
-        react_1.default.createElement(CascadingMenuButton_1.default, { menuItems: [
-                {
-                    label: 'Row view menus',
-                    type: 'subMenu',
-                    subMenu: views.map((view, idx) => ({
-                        label: `View ${idx + 1} Menu`,
-                        subMenu: view.menuItems(),
-                    })),
-                },
-                ...model.headerMenuItems(),
-            ] },
-            react_1.default.createElement(MoreVert_1.default, null)),
-        react_1.default.createElement(CascadingMenuButton_1.default, { menuItems: [
-                {
-                    label: 'Show search boxes',
-                    type: 'checkbox',
-                    checked: showSearchBoxes,
-                    onClick: () => {
-                        setShowSearchBoxes(!showSearchBoxes);
                     },
-                },
-                {
-                    label: 'Orientation - Side-by-side',
-                    type: 'radio',
-                    checked: sideBySide,
-                    onClick: () => {
-                        setSideBySide(!sideBySide);
+                    {
+                        label: 'Orientation - Side-by-side',
+                        type: 'radio',
+                        checked: sideBySide,
+                        onClick: () => {
+                            setSideBySide(!sideBySide);
+                        },
                     },
-                },
-                {
-                    label: 'Orientation - Vertical',
-                    type: 'radio',
-                    checked: !sideBySide,
-                    onClick: () => {
-                        setSideBySide(!sideBySide);
+                    {
+                        label: 'Orientation - Vertical',
+                        type: 'radio',
+                        checked: !sideBySide,
+                        onClick: () => {
+                            setSideBySide(!sideBySide);
+                        },
                     },
-                },
-            ] },
-            react_1.default.createElement(Search_1.default, null)),
-        showSearchBoxes ? (react_1.default.createElement("span", { className: sideBySide ? classes.inline : undefined }, views.map(view => (react_1.default.createElement(HeaderSearchBoxes_1.default, { key: view.id, view: view }))))) : null));
+                ], children: (0, jsx_runtime_1.jsx)(Search_1.default, {}) }), showSearchBoxes ? ((0, jsx_runtime_1.jsx)("span", { className: sideBySide ? classes.inline : undefined, children: views.map(view => ((0, jsx_runtime_1.jsx)(HeaderSearchBoxes_1.default, { view: view }, view.id))) })) : null] }));
 });
 exports.default = Header;

package/dist/LinearComparativeView/components/HeaderSearchBoxes.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 declare const HeaderSearchBoxes: ({ view, }: {
     view: LinearGenomeViewModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default HeaderSearchBoxes;

package/dist/LinearComparativeView/components/HeaderSearchBoxes.js

@@ -1,9 +1,6 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const util_1 = require("@jbrowse/core/util");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const material_1 = require("@mui/material");
@@ -22,12 +19,6 @@ const useStyles = (0, mui_1.makeStyles)()(() => ({
 const HeaderSearchBoxes = (0, mobx_react_1.observer)(function ({ view, }) {
     const { classes } = useStyles();
     const { assemblyNames, coarseTotalBp } = view;
-    return (react_1.default.createElement("span", { className: classes.searchBox },
-        react_1.default.createElement(plugin_linear_genome_view_1.SearchBox, { model: view, showHelp: false }),
-        react_1.default.createElement(material_1.Typography, { variant: "body2", color: "textSecondary", className: classes.bp },
-            assemblyNames.join(','),
-            " ",
-            (0, util_1.toLocale)(Math.round(coarseTotalBp)),
-            " bp")));
+    return ((0, jsx_runtime_1.jsxs)("span", { className: classes.searchBox, children: [(0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.SearchBox, { model: view, showHelp: false }), (0, jsx_runtime_1.jsxs)(material_1.Typography, { variant: "body2", color: "textSecondary", className: classes.bp, children: [assemblyNames.join(','), " ", (0, util_1.toLocale)(Math.round(coarseTotalBp)), " bp"] })] }));
 });
 exports.default = HeaderSearchBoxes;

package/dist/LinearComparativeView/components/LinearComparativeRenderArea.d.ts

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

package/dist/LinearComparativeView/components/LinearComparativeRenderArea.js

@@ -1,13 +1,11 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const mobx_react_1 = require("mobx-react");
+const jsx_runtime_2 = require("react/jsx-runtime");
 const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()({
     container: {
@@ -25,30 +23,24 @@ const useStyles = (0, mui_1.makeStyles)()({
 function View({ view }) {
     const { pluginManager } = (0, util_1.getEnv)(view);
     const { ReactComponent } = pluginManager.getViewType(view.type);
-    return react_1.default.createElement(ReactComponent, { model: view });
+    return (0, jsx_runtime_1.jsx)(ReactComponent, { model: view });
 }
 const LinearComparativeRenderArea = (0, mobx_react_1.observer)(function ({ model, }) {
     const { classes } = useStyles();
     const { views, levels } = model;
-    return (react_1.default.createElement("div", { className: classes.container }, views.map((view, i) => (react_1.default.createElement(react_1.default.Fragment, { key: view.id },
-        i > 0 ? (react_1.default.createElement(react_1.default.Fragment, null,
-            react_1.default.createElement("div", { className: classes.container },
-                react_1.default.createElement(Overlays, { model: model, level: i - 1 })),
-            react_1.default.createElement(ui_1.ResizeHandle, { onDrag: n => { var _a, _b; return (_a = levels[i - 1]) === null || _a === void 0 ? void 0 : _a.setHeight((((_b = levels[i - 1]) === null || _b === void 0 ? void 0 : _b.height) || 0) + n); }, className: classes.resizeHandle }))) : null,
-        react_1.default.createElement(View, { view: view }))))));
+    return ((0, jsx_runtime_1.jsx)("div", { className: classes.container, children: views.map((view, i) => ((0, jsx_runtime_1.jsxs)(jsx_runtime_2.Fragment, { children: [i > 0 ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", { className: classes.container, children: (0, jsx_runtime_1.jsx)(Overlays, { model: model, level: i - 1 }) }), (0, jsx_runtime_1.jsx)(ui_1.ResizeHandle, { onDrag: n => { var _a, _b; return (_a = levels[i - 1]) === null || _a === void 0 ? void 0 : _a.setHeight((((_b = levels[i - 1]) === null || _b === void 0 ? void 0 : _b.height) || 0) + n); }, className: classes.resizeHandle })] })) : null, (0, jsx_runtime_1.jsx)(View, { view: view })] }, view.id))) }));
 });
 const Overlays = (0, mobx_react_1.observer)(function ({ model, level, }) {
     var _a;
     const { classes } = useStyles();
-    return (react_1.default.createElement(react_1.default.Fragment, null, (_a = model.levels[level]) === null || _a === void 0 ? void 0 : _a.tracks.map(track => {
-        const [display] = track.displays;
-        const { RenderingComponent } = display;
-        const trackId = (0, configuration_1.getConf)(track, 'trackId');
-        return RenderingComponent ? (react_1.default.createElement("div", { className: classes.overlay, key: trackId, style: {
-                height: display.height,
-                overflow: 'hidden',
-            } },
-            react_1.default.createElement(RenderingComponent, { model: display }))) : null;
-    })));
+    return ((0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (_a = model.levels[level]) === null || _a === void 0 ? void 0 : _a.tracks.map(track => {
+            const [display] = track.displays;
+            const { RenderingComponent } = display;
+            const trackId = (0, configuration_1.getConf)(track, 'trackId');
+            return RenderingComponent ? ((0, jsx_runtime_1.jsx)("div", { className: classes.overlay, style: {
+                    height: display.height,
+                    overflow: 'hidden',
+                }, children: (0, jsx_runtime_1.jsx)(RenderingComponent, { model: display }) }, trackId)) : null;
+        }) }));
 });
 exports.default = LinearComparativeRenderArea;

package/dist/LinearComparativeView/components/LinearComparativeView.d.ts

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