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

package/dist/LinearComparativeView/components/LinearComparativeView.js

@@ -3,7 +3,7 @@ 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 mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
 const Header_1 = __importDefault(require("./Header"));
@@ -25,9 +25,6 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
 }));
 const LinearComparativeView = (0, mobx_react_1.observer)(function ({ model, }) {
     const { classes } = useStyles();
-    return (react_1.default.createElement("div", { className: classes.rubberbandContainer },
-        react_1.default.createElement(Header_1.default, { model: model }),
-        react_1.default.createElement(Rubberband_1.default, { model: model, ControlComponent: react_1.default.createElement("div", { className: classes.rubberbandDiv }) }),
-        react_1.default.createElement(LinearComparativeRenderArea_1.default, { model: model })));
+    return ((0, jsx_runtime_1.jsxs)("div", { className: classes.rubberbandContainer, children: [(0, jsx_runtime_1.jsx)(Header_1.default, { model: model }), (0, jsx_runtime_1.jsx)(Rubberband_1.default, { model: model, ControlComponent: (0, jsx_runtime_1.jsx)("div", { className: classes.rubberbandDiv }) }), (0, jsx_runtime_1.jsx)(LinearComparativeRenderArea_1.default, { model: model })] }));
 });
 exports.default = LinearComparativeView;

package/dist/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/dist/LinearComparativeView/components/Rubberband.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 ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
@@ -62,7 +40,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => {
         },
     };
 });
-const LinearComparativeRubberband = (0, mobx_react_1.observer)(function Rubberband({ model, ControlComponent = react_1.default.createElement("div", null), }) {
+const LinearComparativeRubberband = (0, mobx_react_1.observer)(function Rubberband({ model, ControlComponent = (0, jsx_runtime_1.jsx)("div", {}), }) {
     const [startX, setStartX] = (0, react_1.useState)();
     const [currentX, setCurrentX] = (0, react_1.useState)();
     const [anchorPosition, setAnchorPosition] = (0, react_1.useState)();
@@ -163,9 +141,7 @@ const LinearComparativeRubberband = (0, mobx_react_1.observer)(function Rubberba
         handleClose();
     }
     if (startX === undefined) {
-        return (react_1.default.createElement(react_1.default.Fragment, null,
-            guideX !== undefined ? (react_1.default.createElement(VerticalGuide_1.default, { model: model, coordX: guideX })) : null,
-            react_1.default.createElement("div", { ref: controlsRef, className: classes.rubberbandControl, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
+        return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [guideX !== undefined ? ((0, jsx_runtime_1.jsx)(VerticalGuide_1.default, { model: model, coordX: guideX })) : null, (0, jsx_runtime_1.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);
@@ -174,28 +150,21 @@ const LinearComparativeRubberband = (0, mobx_react_1.observer)(function Rubberba
     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_1.default.createElement(react_1.default.Fragment, null,
-        rubberbandRef.current ? (react_1.default.createElement(react_1.default.Fragment, null,
-            react_1.default.createElement(material_1.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_1.default.createElement(material_1.Typography, { key: [JSON.stringify(l), idx, 'left'].join('-') }, (0, util_1.stringify)(l, true))))),
-            react_1.default.createElement(material_1.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_1.default.createElement(material_1.Typography, { key: [JSON.stringify(l), idx, 'right'].join('-') }, (0, util_1.stringify)(l, true))))))) : null,
-        react_1.default.createElement("div", { ref: rubberbandRef, className: classes.rubberband, style: { left, width } },
-            react_1.default.createElement(material_1.Typography, { variant: "h6", className: classes.rubberbandText }, numOfBpSelected.map((n, i) => (react_1.default.createElement(material_1.Typography, { key: `${n}_${i}` }, `${n.toLocaleString('en-US')}bp`))))),
-        react_1.default.createElement("div", { className: classes.rubberbandControl, ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent),
-        anchorPosition ? (react_1.default.createElement(ui_1.Menu, { anchorReference: "anchorPosition", anchorPosition: {
-                left: anchorPosition.clientX,
-                top: anchorPosition.clientY,
-            }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null));
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [rubberbandRef.current ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.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) => ((0, jsx_runtime_1.jsx)(material_1.Typography, { children: (0, util_1.stringify)(l, true) }, [JSON.stringify(l), idx, 'left'].join('-')))) }), (0, jsx_runtime_1.jsx)(material_1.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) => ((0, jsx_runtime_1.jsx)(material_1.Typography, { children: (0, util_1.stringify)(l, true) }, [JSON.stringify(l), idx, 'right'].join('-')))) })] })) : null, (0, jsx_runtime_1.jsx)("div", { ref: rubberbandRef, className: classes.rubberband, style: { left, width }, children: (0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "h6", className: classes.rubberbandText, children: numOfBpSelected.map((n, i) => ((0, jsx_runtime_1.jsx)(material_1.Typography, { children: `${n.toLocaleString('en-US')}bp` }, `${n}_${i}`))) }) }), (0, jsx_runtime_1.jsx)("div", { className: classes.rubberbandControl, ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove, children: ControlComponent }), anchorPosition ? ((0, jsx_runtime_1.jsx)(ui_1.Menu, { anchorReference: "anchorPosition", anchorPosition: {
+                    left: anchorPosition.clientX,
+                    top: anchorPosition.clientY,
+                }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null] }));
 });
 exports.default = LinearComparativeRubberband;

package/dist/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/dist/LinearComparativeView/components/VerticalGuide.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 material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
@@ -22,12 +19,11 @@ const useStyles = (0, mui_1.makeStyles)()({
 });
 const VerticalGuide = (0, mobx_react_1.observer)(function ({ model, coordX, }) {
     const { classes } = useStyles();
-    return (react_1.default.createElement(material_1.Tooltip, { open: true, placement: "top", title: model.views
+    return ((0, jsx_runtime_1.jsx)(material_1.Tooltip, { open: true, placement: "top", title: model.views
             .map(view => view.pxToBp(coordX))
-            .map((elt, idx) => (react_1.default.createElement(material_1.Typography, { className: classes.sm, key: [JSON.stringify(elt), idx].join('-') }, (0, util_1.stringify)(elt, true)))), arrow: true },
-        react_1.default.createElement("div", { className: classes.guide, style: {
+            .map((elt, idx) => ((0, jsx_runtime_1.jsx)(material_1.Typography, { className: classes.sm, children: (0, util_1.stringify)(elt, true) }, [JSON.stringify(elt), idx].join('-')))), arrow: true, children: (0, jsx_runtime_1.jsx)("div", { className: classes.guide, style: {
                 left: coordX,
                 background: 'red',
-            } })));
+            } }) }));
 });
 exports.default = VerticalGuide;

package/dist/LinearComparativeView/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/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>>;

package/dist/LinearComparativeView/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;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -43,7 +53,8 @@ function stateModelFactory(pluginManager) {
         type: mobx_state_tree_1.types.literal('LinearComparativeView'),
         trackSelectorType: 'hierarchical',
         showIntraviewLinks: true,
-        interactToggled: false,
+        linkViews: false,
+        interactiveOverlay: false,
         levels: mobx_state_tree_1.types.array(LinearSyntenyViewHelper),
         views: mobx_state_tree_1.types.array(pluginManager.getViewType('LinearGenomeView')
             .stateModel),
@@ -68,6 +79,21 @@ function stateModelFactory(pluginManager) {
         },
     }))
         .actions(self => ({
+        afterAttach() {
+            const actions = new Set([
+                'horizontalScroll',
+                'zoomTo',
+                'setScaleFactor',
+            ]);
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_state_tree_1.onAction)(self, param => {
+                if (self.linkViews) {
+                    const { name, path, args } = param;
+                    if (actions.has(name) && path) {
+                        this.onSubviewAction(name, path, args);
+                    }
+                }
+            }));
+        },
         beforeDestroy() {
             var _a;
             const session = (0, util_1.getSession)(self);
@@ -97,6 +123,9 @@ function stateModelFactory(pluginManager) {
             l.setHeight(newHeight);
             return l.height;
         },
+        setLinkViews(arg) {
+            self.linkViews = arg;
+        },
         activateTrackSelector(level) {
             if (self.trackSelectorType === 'hierarchical') {
                 const session = (0, util_1.getSession)(self);

package/dist/LinearReadVsRef/LinearReadVsRef.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
 import type { Feature } from '@jbrowse/core/util';
 export default function ReadVsRefDialog({ track, feature: preFeature, handleClose, }: {
     feature: Feature;
     handleClose: () => void;
     track: any;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/LinearReadVsRef/LinearReadVsRef.js

@@ -1,30 +1,8 @@
 "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 = ReadVsRefDialog;
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
@@ -257,16 +235,7 @@ function ReadVsRefDialog({ track, feature: preFeature, handleClose, }) {
             setError(e);
         }
     }
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set window size" },
-        react_1.default.createElement(material_1.DialogContent, null, error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : !primaryFeature ? (react_1.default.createElement("div", null,
-            react_1.default.createElement(material_1.Typography, null, "To accurately perform comparison we are fetching the primary alignment. Loading primary feature..."),
-            react_1.default.createElement(material_1.CircularProgress, null))) : (react_1.default.createElement("div", { className: classes.root },
-            primaryFeature.get('flags') & 256 ? (react_1.default.createElement(material_1.Typography, { style: { color: 'orange' } }, "Note: You selected a secondary alignment (which generally does not have SA tags or SEQ fields) so do a full reconstruction of the alignment")) : null,
-            react_1.default.createElement(material_1.Typography, null, "Show an extra window size around each part of the split alignment. Using a larger value can allow you to see more genomic context."),
-            react_1.default.createElement(material_1.TextField, { value: windowSize, onChange: event => {
-                    setWindowSize(event.target.value);
-                }, label: "Set window size" })))),
-        react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: handleClose }, "Cancel"),
-            react_1.default.createElement(material_1.Button, { disabled: !primaryFeature, variant: "contained", color: "primary", onClick: onSubmit }, "Submit"))));
+    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set window size", children: [(0, jsx_runtime_1.jsx)(material_1.DialogContent, { children: error ? ((0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: `${error}` })) : !primaryFeature ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "To accurately perform comparison we are fetching the primary alignment. Loading primary feature..." }), (0, jsx_runtime_1.jsx)(material_1.CircularProgress, {})] })) : ((0, jsx_runtime_1.jsxs)("div", { className: classes.root, children: [primaryFeature.get('flags') & 256 ? ((0, jsx_runtime_1.jsx)(material_1.Typography, { style: { color: 'orange' }, children: "Note: You selected a secondary alignment (which generally does not have SA tags or SEQ fields) so do a full reconstruction of the alignment" })) : null, (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Show an extra window size around each part of the split alignment. Using a larger value can allow you to see more genomic context." }), (0, jsx_runtime_1.jsx)(material_1.TextField, { value: windowSize, onChange: event => {
+                                setWindowSize(event.target.value);
+                            }, label: "Set window size" })] })) }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: handleClose, children: "Cancel" }), (0, jsx_runtime_1.jsx)(material_1.Button, { disabled: !primaryFeature, variant: "contained", color: "primary", onClick: onSubmit, children: "Submit" })] })] }));
 }

package/dist/LinearReadVsRef/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/LinearSyntenyDisplay/afterAttach.js

@@ -11,7 +11,8 @@ function doAfterAttach(self) {
     (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
         var _a, _b;
         const view = (0, util_1.getContainingView)(self);
-        if (!view.initialized) {
+        if (!view.initialized ||
+            !view.views.every(a => a.displayedRegions.length > 0 && a.initialized)) {
             return;
         }
         const ctx1 = (_a = self.mainCanvas) === null || _a === void 0 ? void 0 : _a.getContext('2d');
@@ -27,7 +28,8 @@ function doAfterAttach(self) {
     }));
     (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
         const view = (0, util_1.getContainingView)(self);
-        if (!view.initialized) {
+        if (!view.initialized ||
+            !view.views.every(a => a.displayedRegions.length > 0 && a.initialized)) {
             return;
         }
         (0, drawSynteny_1.drawMouseoverSynteny)(self);
@@ -38,7 +40,8 @@ function doAfterAttach(self) {
             bpPerPx: view.views.map(v => v.bpPerPx),
             displayedRegions: JSON.stringify(view.views.map(v => v.displayedRegions)),
             features: self.features,
-            initialized: view.initialized,
+            initialized: view.initialized &&
+                view.views.every(a => a.displayedRegions.length > 0 && a.initialized),
         };
     }, ({ initialized }) => {
         if (!initialized) {