@jbrowse/plugin-linear-comparative-view 2.18.0 → 3.0.1

package/esm/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/esm/LinearComparativeView/components/Header.js

@@ -1,4 +1,5 @@
-import React, { useState } from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
 import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
 import MoreVertIcon from '@mui/icons-material/MoreVert';
@@ -17,67 +18,60 @@ const Header = observer(function ({ model, }) {
     const { views } = model;
     const [showSearchBoxes, setShowSearchBoxes] = useState(views.length <= 3);
     const [sideBySide, setSideBySide] = useState(views.length <= 3);
-    return (React.createElement(FormGroup, { row: true },
-        React.createElement(CascadingMenuButton, { 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 (_jsxs(FormGroup, { row: true, children: [_jsx(CascadingMenuButton, { 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: _jsx(TrackSelectorIcon, {}) }), _jsx(CascadingMenuButton, { menuItems: [
+                    {
+                        label: 'Row view menus',
+                        type: 'subMenu',
+                        subMenu: views.map((view, idx) => ({
+                            label: `View ${idx + 1} Menu`,
+                            subMenu: view.menuItems(),
+                        })),
+                    },
+                    ...model.headerMenuItems(),
+                ], children: _jsx(MoreVertIcon, {}) }), _jsx(CascadingMenuButton, { 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.createElement(TrackSelectorIcon, null)),
-        React.createElement(CascadingMenuButton, { menuItems: [
-                {
-                    label: 'Row view menus',
-                    type: 'subMenu',
-                    subMenu: views.map((view, idx) => ({
-                        label: `View ${idx + 1} Menu`,
-                        subMenu: view.menuItems(),
-                    })),
-                },
-                ...model.headerMenuItems(),
-            ] },
-            React.createElement(MoreVertIcon, null)),
-        React.createElement(CascadingMenuButton, { 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.createElement(SearchIcon, null)),
-        showSearchBoxes ? (React.createElement("span", { className: sideBySide ? classes.inline : undefined }, views.map(view => (React.createElement(HeaderSearchBoxes, { key: view.id, view: view }))))) : null));
+                ], children: _jsx(SearchIcon, {}) }), showSearchBoxes ? (_jsx("span", { className: sideBySide ? classes.inline : undefined, children: views.map(view => (_jsx(HeaderSearchBoxes, { view: view }, view.id))) })) : null] }));
 });
 export default Header;

package/esm/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/esm/LinearComparativeView/components/HeaderSearchBoxes.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { toLocale } from '@jbrowse/core/util';
 import { SearchBox } from '@jbrowse/plugin-linear-genome-view';
 import { Typography } from '@mui/material';
@@ -17,12 +17,6 @@ const useStyles = makeStyles()(() => ({
 const HeaderSearchBoxes = observer(function ({ view, }) {
     const { classes } = useStyles();
     const { assemblyNames, coarseTotalBp } = view;
-    return (React.createElement("span", { className: classes.searchBox },
-        React.createElement(SearchBox, { model: view, showHelp: false }),
-        React.createElement(Typography, { variant: "body2", color: "textSecondary", className: classes.bp },
-            assemblyNames.join(','),
-            " ",
-            toLocale(Math.round(coarseTotalBp)),
-            " bp")));
+    return (_jsxs("span", { className: classes.searchBox, children: [_jsx(SearchBox, { model: view, showHelp: false }), _jsxs(Typography, { variant: "body2", color: "textSecondary", className: classes.bp, children: [assemblyNames.join(','), " ", toLocale(Math.round(coarseTotalBp)), " bp"] })] }));
 });
 export default HeaderSearchBoxes;

package/esm/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/esm/LinearComparativeView/components/LinearComparativeRenderArea.js

@@ -1,8 +1,9 @@
-import React from 'react';
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { getConf } from '@jbrowse/core/configuration';
 import { ResizeHandle } from '@jbrowse/core/ui';
 import { getEnv } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
+import { Fragment } from 'react/jsx-runtime';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     container: {
@@ -20,30 +21,24 @@ const useStyles = makeStyles()({
 function View({ view }) {
     const { pluginManager } = getEnv(view);
     const { ReactComponent } = pluginManager.getViewType(view.type);
-    return React.createElement(ReactComponent, { model: view });
+    return _jsx(ReactComponent, { model: view });
 }
 const LinearComparativeRenderArea = observer(function ({ model, }) {
     const { classes } = useStyles();
     const { views, levels } = model;
-    return (React.createElement("div", { className: classes.container }, views.map((view, i) => (React.createElement(React.Fragment, { key: view.id },
-        i > 0 ? (React.createElement(React.Fragment, null,
-            React.createElement("div", { className: classes.container },
-                React.createElement(Overlays, { model: model, level: i - 1 })),
-            React.createElement(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.createElement(View, { view: view }))))));
+    return (_jsx("div", { className: classes.container, children: views.map((view, i) => (_jsxs(Fragment, { children: [i > 0 ? (_jsxs(_Fragment, { children: [_jsx("div", { className: classes.container, children: _jsx(Overlays, { model: model, level: i - 1 }) }), _jsx(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, _jsx(View, { view: view })] }, view.id))) }));
 });
 const Overlays = observer(function ({ model, level, }) {
     var _a;
     const { classes } = useStyles();
-    return (React.createElement(React.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 = getConf(track, 'trackId');
-        return RenderingComponent ? (React.createElement("div", { className: classes.overlay, key: trackId, style: {
-                height: display.height,
-                overflow: 'hidden',
-            } },
-            React.createElement(RenderingComponent, { model: display }))) : null;
-    })));
+    return (_jsx(_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 = getConf(track, 'trackId');
+            return RenderingComponent ? (_jsx("div", { className: classes.overlay, style: {
+                    height: display.height,
+                    overflow: 'hidden',
+                }, children: _jsx(RenderingComponent, { model: display }) }, trackId)) : null;
+        }) }));
 });
 export default LinearComparativeRenderArea;

package/esm/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;

package/esm/LinearComparativeView/components/LinearComparativeView.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import Header from './Header';
@@ -20,9 +20,6 @@ const useStyles = makeStyles()(theme => ({
 }));
 const LinearComparativeView = observer(function ({ model, }) {
     const { classes } = useStyles();
-    return (React.createElement("div", { className: classes.rubberbandContainer },
-        React.createElement(Header, { model: model }),
-        React.createElement(Rubberband, { model: model, ControlComponent: React.createElement("div", { className: classes.rubberbandDiv }) }),
-        React.createElement(LinearComparativeRenderArea, { model: model })));
+    return (_jsxs("div", { className: classes.rubberbandContainer, children: [_jsx(Header, { model: model }), _jsx(Rubberband, { model: model, ControlComponent: _jsx("div", { className: classes.rubberbandDiv }) }), _jsx(LinearComparativeRenderArea, { model: model })] }));
 });
 export default LinearComparativeView;

package/esm/LinearComparativeView/components/Rubberband.d.ts

@@ -1,8 +1,7 @@
-import React from 'react';
 import type { LinearComparativeViewModel } from '../model';
 type LCV = LinearComparativeViewModel;
 declare const LinearComparativeRubberband: ({ model, ControlComponent, }: {
     model: LCV;
     ControlComponent?: React.ReactElement;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default LinearComparativeRubberband;

package/esm/LinearComparativeView/components/Rubberband.js

@@ -1,4 +1,5 @@
-import React, { useEffect, useRef, useState } from 'react';
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { useEffect, useRef, useState } from 'react';
 import { Menu } from '@jbrowse/core/ui';
 import { stringify } from '@jbrowse/core/util';
 import { Popover, Typography, alpha } from '@mui/material';
@@ -34,7 +35,7 @@ const useStyles = makeStyles()(theme => {
         },
     };
 });
-const LinearComparativeRubberband = observer(function Rubberband({ model, ControlComponent = React.createElement("div", null), }) {
+const LinearComparativeRubberband = observer(function Rubberband({ model, ControlComponent = _jsx("div", {}), }) {
     const [startX, setStartX] = useState();
     const [currentX, setCurrentX] = useState();
     const [anchorPosition, setAnchorPosition] = useState();
@@ -135,9 +136,7 @@ const LinearComparativeRubberband = observer(function Rubberband({ model, Contro
         handleClose();
     }
     if (startX === undefined) {
-        return (React.createElement(React.Fragment, null,
-            guideX !== undefined ? (React.createElement(VerticalGuide, { model: model, coordX: guideX })) : null,
-            React.createElement("div", { ref: controlsRef, className: classes.rubberbandControl, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
+        return (_jsxs(_Fragment, { children: [guideX !== undefined ? (_jsx(VerticalGuide, { model: model, coordX: guideX })) : null, _jsx("div", { ref: controlsRef, className: classes.rubberbandControl, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove, children: ControlComponent })] }));
     }
     const right = anchorPosition ? anchorPosition.offsetX : currentX || 0;
     const left = Math.min(right, startX);
@@ -146,28 +145,21 @@ const LinearComparativeRubberband = observer(function Rubberband({ model, Contro
     const leftBpOffset = views.map(view => view.pxToBp(left));
     const rightBpOffset = views.map(view => view.pxToBp(left + width));
     const numOfBpSelected = views.map(view => Math.ceil(width * view.bpPerPx));
-    return (React.createElement(React.Fragment, null,
-        rubberbandRef.current ? (React.createElement(React.Fragment, null,
-            React.createElement(Popover, { className: classes.popover, classes: { paper: classes.paper }, open: true, anchorEl: rubberbandRef.current, anchorOrigin: {
-                    vertical: 'top',
-                    horizontal: 'left',
-                }, transformOrigin: {
-                    vertical: 'bottom',
-                    horizontal: 'right',
-                }, keepMounted: true, disableRestoreFocus: true }, leftBpOffset.map((l, idx) => (React.createElement(Typography, { key: [JSON.stringify(l), idx, 'left'].join('-') }, stringify(l, true))))),
-            React.createElement(Popover, { className: classes.popover, classes: { paper: classes.paper }, open: true, anchorEl: rubberbandRef.current, anchorOrigin: {
-                    vertical: 'top',
-                    horizontal: 'right',
-                }, transformOrigin: {
-                    vertical: 'bottom',
-                    horizontal: 'left',
-                }, keepMounted: true, disableRestoreFocus: true }, rightBpOffset.map((l, idx) => (React.createElement(Typography, { key: [JSON.stringify(l), idx, 'right'].join('-') }, stringify(l, true))))))) : null,
-        React.createElement("div", { ref: rubberbandRef, className: classes.rubberband, style: { left, width } },
-            React.createElement(Typography, { variant: "h6", className: classes.rubberbandText }, numOfBpSelected.map((n, i) => (React.createElement(Typography, { key: `${n}_${i}` }, `${n.toLocaleString('en-US')}bp`))))),
-        React.createElement("div", { className: classes.rubberbandControl, ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent),
-        anchorPosition ? (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
-                left: anchorPosition.clientX,
-                top: anchorPosition.clientY,
-            }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null));
+    return (_jsxs(_Fragment, { children: [rubberbandRef.current ? (_jsxs(_Fragment, { children: [_jsx(Popover, { className: classes.popover, classes: { paper: classes.paper }, open: true, anchorEl: rubberbandRef.current, anchorOrigin: {
+                            vertical: 'top',
+                            horizontal: 'left',
+                        }, transformOrigin: {
+                            vertical: 'bottom',
+                            horizontal: 'right',
+                        }, keepMounted: true, disableRestoreFocus: true, children: leftBpOffset.map((l, idx) => (_jsx(Typography, { children: stringify(l, true) }, [JSON.stringify(l), idx, 'left'].join('-')))) }), _jsx(Popover, { className: classes.popover, classes: { paper: classes.paper }, open: true, anchorEl: rubberbandRef.current, anchorOrigin: {
+                            vertical: 'top',
+                            horizontal: 'right',
+                        }, transformOrigin: {
+                            vertical: 'bottom',
+                            horizontal: 'left',
+                        }, keepMounted: true, disableRestoreFocus: true, children: rightBpOffset.map((l, idx) => (_jsx(Typography, { children: stringify(l, true) }, [JSON.stringify(l), idx, 'right'].join('-')))) })] })) : null, _jsx("div", { ref: rubberbandRef, className: classes.rubberband, style: { left, width }, children: _jsx(Typography, { variant: "h6", className: classes.rubberbandText, children: numOfBpSelected.map((n, i) => (_jsx(Typography, { children: `${n.toLocaleString('en-US')}bp` }, `${n}_${i}`))) }) }), _jsx("div", { className: classes.rubberbandControl, ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove, children: ControlComponent }), anchorPosition ? (_jsx(Menu, { anchorReference: "anchorPosition", anchorPosition: {
+                    left: anchorPosition.clientX,
+                    top: anchorPosition.clientY,
+                }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null] }));
 });
 export default LinearComparativeRubberband;

package/esm/LinearComparativeView/components/VerticalGuide.d.ts

@@ -1,8 +1,7 @@
-import React from 'react';
 import type { LinearComparativeViewModel } from '../model';
 type LCV = LinearComparativeViewModel;
 declare const VerticalGuide: ({ model, coordX, }: {
     model: LCV;
     coordX: number;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default VerticalGuide;

package/esm/LinearComparativeView/components/VerticalGuide.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
 import { stringify } from '@jbrowse/core/util';
 import { Tooltip, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
@@ -17,12 +17,11 @@ const useStyles = makeStyles()({
 });
 const VerticalGuide = observer(function ({ model, coordX, }) {
     const { classes } = useStyles();
-    return (React.createElement(Tooltip, { open: true, placement: "top", title: model.views
+    return (_jsx(Tooltip, { open: true, placement: "top", title: model.views
             .map(view => view.pxToBp(coordX))
-            .map((elt, idx) => (React.createElement(Typography, { className: classes.sm, key: [JSON.stringify(elt), idx].join('-') }, stringify(elt, true)))), arrow: true },
-        React.createElement("div", { className: classes.guide, style: {
+            .map((elt, idx) => (_jsx(Typography, { className: classes.sm, children: stringify(elt, true) }, [JSON.stringify(elt), idx].join('-')))), arrow: true, children: _jsx("div", { className: classes.guide, style: {
                 left: coordX,
                 background: 'red',
-            } })));
+            } }) }));
 });
 export default VerticalGuide;

package/esm/LinearComparativeView/model.d.ts

@@ -11,7 +11,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     type: import("mobx-state-tree").ISimpleType<"LinearComparativeView">;
     trackSelectorType: import("mobx-state-tree").IType<string | undefined, string, string>;
     showIntraviewLinks: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    interactToggled: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    linkViews: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    interactiveOverlay: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     levels: import("mobx-state-tree").IArrayType<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>;
@@ -45,7 +46,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }, {
@@ -66,8 +67,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
-        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
-        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
+        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
+        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
     } & {
         readonly trackLabelsSetting: any;
         readonly width: number;
@@ -114,12 +115,12 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setHideHeaderOverview(b: boolean): void;
         setHideNoTracksActive(b: boolean): void;
         setShowGridlines(b: boolean): void;
-        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
-        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType[]): void;
-        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
+        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
+        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
+        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
         scrollTo(offsetPx: number): number;
         zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
-        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
         setNewView(bpPerPx: number, offsetPx: number): void;
         horizontallyFlip(): void;
@@ -136,7 +137,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setShowCenterLine(b: boolean): void;
         setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
         activateTrackSelector(): import("@jbrowse/core/util").Widget;
-        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): {
+        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
             start: number;
             end: number;
             type: string;
@@ -158,7 +159,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setDraggingTrackId(idx?: string): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
-        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
+        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
     } & {
         slide: (viewWidths: number) => void;
     } & {
@@ -180,15 +181,15 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
         afterAttach(): void;
     } & {
-        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         navToLocString(input: string, optAssemblyName?: string): Promise<void>;
         navToSearchString({ input, assembly, }: {
             input: string;
             assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
         }): Promise<void>;
         navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
-        navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
-        navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
+        navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
+        navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
     } & {
         rubberBandMenuItems(): MenuItem[];
         bpToPx({ refName, coord, regionNumber, }: {
@@ -243,7 +244,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }>>, import("mobx-state-tree")._NotCustomized>>;
@@ -263,12 +264,14 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     readonly refNames: string[][];
     readonly assemblyNames: string[];
 } & {
+    afterAttach(): void;
     beforeDestroy(): void;
     onSubviewAction(actionName: string, path: string, args?: unknown[]): void;
     setWidth(newWidth: number): void;
     setViews(views: SnapshotIn<LinearGenomeViewModel>[]): void;
     removeView(view: LinearGenomeViewModel): void;
     setLevelHeight(newHeight: number, level?: number): number;
+    setLinkViews(arg: boolean): void;
     activateTrackSelector(level: number): import("@jbrowse/core/util").Widget;
     toggleTrack(trackId: string, level?: number): void;
     showTrack(trackId: string, level?: number, initialSnapshot?: {}): void;
@@ -294,7 +297,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     type: import("mobx-state-tree").ISimpleType<"LinearComparativeView">;
     trackSelectorType: import("mobx-state-tree").IType<string | undefined, string, string>;
     showIntraviewLinks: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    interactToggled: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    linkViews: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    interactiveOverlay: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     levels: import("mobx-state-tree").IArrayType<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>;
@@ -328,7 +332,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }, {
@@ -349,8 +353,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
-        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
-        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
+        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
+        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
     } & {
         readonly trackLabelsSetting: any;
         readonly width: number;
@@ -397,12 +401,12 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setHideHeaderOverview(b: boolean): void;
         setHideNoTracksActive(b: boolean): void;
         setShowGridlines(b: boolean): void;
-        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
-        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType[]): void;
-        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
+        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
+        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
+        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
         scrollTo(offsetPx: number): number;
         zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
-        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
         setNewView(bpPerPx: number, offsetPx: number): void;
         horizontallyFlip(): void;
@@ -419,7 +423,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setShowCenterLine(b: boolean): void;
         setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
         activateTrackSelector(): import("@jbrowse/core/util").Widget;
-        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): {
+        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
             start: number;
             end: number;
             type: string;
@@ -441,7 +445,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setDraggingTrackId(idx?: string): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
-        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
+        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
     } & {
         slide: (viewWidths: number) => void;
     } & {
@@ -463,15 +467,15 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
         afterAttach(): void;
     } & {
-        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         navToLocString(input: string, optAssemblyName?: string): Promise<void>;
         navToSearchString({ input, assembly, }: {
             input: string;
             assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
         }): Promise<void>;
         navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
-        navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
-        navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
+        navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
+        navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
     } & {
         rubberBandMenuItems(): MenuItem[];
         bpToPx({ refName, coord, regionNumber, }: {
@@ -526,7 +530,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }>>, import("mobx-state-tree")._NotCustomized>>;