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

package/esm/LinearComparativeView/components/Rubberband.js

@@ -1,9 +1,11 @@
-import React, { useRef, useEffect, useState } from 'react';
-import { observer } from 'mobx-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';
+import { transaction } from 'mobx';
+import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import { stringify } from '@jbrowse/core/util';
-import { Menu } from '@jbrowse/core/ui';
 import VerticalGuide from './VerticalGuide';
 const useStyles = makeStyles()(theme => {
     return {
@@ -33,11 +35,9 @@ 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();
-    // clientX and clientY used for anchorPosition for menu
-    // offsetX used for calculations about width of selection
     const [anchorPosition, setAnchorPosition] = useState();
     const [guideX, setGuideX] = useState();
     const controlsRef = useRef(null);
@@ -51,7 +51,6 @@ const LinearComparativeRubberband = observer(function Rubberband({ model, Contro
             }
             let leftPx = startX;
             let rightPx = offsetX;
-            // handles clicking and dragging to the left
             if (rightPx < leftPx) {
                 ;
                 [leftPx, rightPx] = [rightPx, leftPx];
@@ -71,19 +70,19 @@ const LinearComparativeRubberband = observer(function Rubberband({ model, Contro
                 const { clientX, clientY } = event;
                 const ref = controlsRef.current;
                 const offsetX = clientX - ref.getBoundingClientRect().left;
-                // as stated above, store both clientX/Y and offsetX for different
-                // purposes
                 setAnchorPosition({
                     offsetX,
                     clientX,
                     clientY,
                 });
-                model.views.forEach(view => {
-                    const args = computeOffsets(offsetX, view);
-                    if (args) {
-                        const { leftOffset, rightOffset } = args;
-                        view.setOffsets(leftOffset, rightOffset);
-                    }
+                transaction(() => {
+                    model.views.forEach(view => {
+                        const args = computeOffsets(offsetX, view);
+                        if (args) {
+                            const { leftOffset, rightOffset } = args;
+                            view.setOffsets(leftOffset, rightOffset);
+                        }
+                    });
                 });
                 setGuideX(undefined);
             }
@@ -120,8 +119,10 @@ const LinearComparativeRubberband = observer(function Rubberband({ model, Contro
     }
     function mouseOut() {
         setGuideX(undefined);
-        model.views.forEach(view => {
-            view.setOffsets(undefined, undefined);
+        transaction(() => {
+            model.views.forEach(view => {
+                view.setOffsets(undefined, undefined);
+            });
         });
     }
     function handleClose() {
@@ -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);
@@ -146,30 +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) => (
-            /* biome-ignore lint/suspicious/noArrayIndexKey: */
-            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 { LinearComparativeViewModel } from '../model';
+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

@@ -1,7 +1,7 @@
-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';
-import { stringify } from '@jbrowse/core/util';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     guide: {
@@ -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/index.d.ts

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

package/esm/LinearComparativeView/model.d.ts

@@ -1,12 +1,7 @@
-import { Instance, SnapshotIn } from 'mobx-state-tree';
-import { MenuItem } from '@jbrowse/core/ui';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-/**
- * #stateModel LinearComparativeView
- * extends
- * - [BaseViewModel](../baseviewmodel)
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { MenuItem } from '@jbrowse/core/ui';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import type { Instance, SnapshotIn } from 'mobx-state-tree';
 declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -16,7 +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>;
@@ -50,7 +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]>;
     }, {
@@ -71,8 +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;
@@ -82,6 +78,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
         HeaderComponent(): React.FC<any>;
+        readonly assembliesNotFound: string | undefined;
         readonly assemblyErrors: string;
         readonly assembliesInitialized: boolean;
         readonly initialized: boolean;
@@ -118,12 +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;
@@ -140,7 +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;
@@ -162,7 +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;
     } & {
@@ -184,15 +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, }: {
@@ -247,7 +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>>;
@@ -261,81 +258,30 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     setWidth(newWidth: number): void;
     setMinimized(flag: boolean): void;
 } & {
-    /**
-     * #volatile
-     */
     width: number | undefined;
 } & {
-    /**
-     * #getter
-     */
     readonly initialized: boolean;
-    /**
-     * #getter
-     */
     readonly refNames: string[][];
-    /**
-     * #getter
-     */
     readonly assemblyNames: string[];
 } & {
+    afterAttach(): void;
     beforeDestroy(): void;
     onSubviewAction(actionName: string, path: string, args?: unknown[]): void;
-    /**
-     * #action
-     */
     setWidth(newWidth: number): void;
-    /**
-     * #action
-     */
     setViews(views: SnapshotIn<LinearGenomeViewModel>[]): void;
-    /**
-     * #action
-     */
     removeView(view: LinearGenomeViewModel): void;
-    /**
-     * #action
-     */
     setLevelHeight(newHeight: number, level?: number): number;
-    /**
-     * #action
-     */
+    setLinkViews(arg: boolean): void;
     activateTrackSelector(level: number): import("@jbrowse/core/util").Widget;
-    /**
-     * #action
-     */
     toggleTrack(trackId: string, level?: number): void;
-    /**
-     * #action
-     */
     showTrack(trackId: string, level?: number, initialSnapshot?: {}): void;
-    /**
-     * #action
-     */
     hideTrack(trackId: string, level?: number): void;
-    /**
-     * #action
-     */
     squareView(): void;
-    /**
-     * #action
-     */
     clearView(): void;
 } & {
-    /**
-     * #method
-     * includes a subset of view menu options because the full list is a
-     * little overwhelming. overridden by subclasses
-     */
     headerMenuItems(): MenuItem[];
 } & {
-    /**
-     * #method
-     */
     menuItems(): MenuItem[];
-    /**
-     * #method
-     */
     rubberBandMenuItems(): {
         label: string;
         onClick: () => void;
@@ -351,7 +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>;
@@ -385,7 +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]>;
     }, {
@@ -406,8 +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;
@@ -417,6 +364,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
         HeaderComponent(): React.FC<any>;
+        readonly assembliesNotFound: string | undefined;
         readonly assemblyErrors: string;
         readonly assembliesInitialized: boolean;
         readonly initialized: boolean;
@@ -453,12 +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;
@@ -475,7 +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;
@@ -497,7 +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;
     } & {
@@ -519,15 +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, }: {
@@ -582,7 +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>>;