@jbrowse/plugin-linear-comparative-view 2.9.0 → 2.10.0

package/esm/LinearSyntenyDisplay/components/SyntenyContextMenu.js

@@ -0,0 +1,51 @@
+import React from 'react';
+import { getContainingView, getSession } from '@jbrowse/core/util';
+import { Menu } from '@jbrowse/core/ui';
+export default function SyntenyContextMenu({ model, onClose, anchorEl, }) {
+    const view = getContainingView(model);
+    const { clientX, clientY, feature } = anchorEl;
+    return (React.createElement(Menu, { onMenuItemClick: (event, callback) => {
+            callback(event);
+            onClose();
+        }, anchorEl: {
+            nodeType: 1,
+            getBoundingClientRect: () => {
+                const x = clientX;
+                const y = clientY;
+                return {
+                    top: y,
+                    left: x,
+                    bottom: y,
+                    right: x,
+                    width: 0,
+                    height: 0,
+                    x,
+                    y,
+                    toJSON() { },
+                };
+            },
+        }, onClose: onClose, open: Boolean(anchorEl), menuItems: [
+            {
+                label: 'Center on feature',
+                onClick: () => {
+                    const { f } = feature;
+                    const start = f.get('start');
+                    const end = f.get('end');
+                    const refName = f.get('refName');
+                    const mate = f.get('mate');
+                    view.views[0]
+                        .navToLocString(`${refName}:${start}-${end}`)
+                        .catch(e => {
+                        console.error(e);
+                        getSession(model).notify(`${e}`, 'error');
+                    });
+                    view.views[1]
+                        .navToLocString(`${mate.refName}:${mate.start}-${mate.end}`)
+                        .catch(e => {
+                        console.error(e);
+                        getSession(model).notify(`${e}`, 'error');
+                    });
+                },
+            },
+        ] }));
+}

package/esm/LinearSyntenyDisplay/components/SyntenyTooltip.d.ts

@@ -1,7 +1,5 @@
 import React from 'react';
-declare const SyntenyTooltip: ({ x, y, title, }: {
-    x: number;
-    y: number;
+declare const SyntenyTooltip: ({ title }: {
     title: string;
 }) => React.JSX.Element | null;
 export default SyntenyTooltip;

package/esm/LinearSyntenyDisplay/components/SyntenyTooltip.js

@@ -1,8 +1,8 @@
-import React, { useMemo, useState } from 'react';
+import React from 'react';
 import { observer } from 'mobx-react';
-import { Portal, alpha } from '@mui/material';
+import { Portal, useTheme, alpha } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-import { usePopper } from 'react-popper';
+import { useClientPoint, useFloating, useInteractions, } from '@floating-ui/react';
 import { SanitizedHTML } from '@jbrowse/core/ui';
 function round(value) {
     return Math.round(value * 1e5) / 1e5;
@@ -24,34 +24,22 @@ const useStyles = makeStyles()(theme => ({
         wordWrap: 'break-word',
     },
 }));
-const SyntenyTooltip = observer(function ({ x, y, title, }) {
-    const [width, setWidth] = useState(0);
-    const [anchorEl, setAnchorEl] = useState(null);
+const SyntenyTooltip = observer(function ({ title }) {
+    var _a, _b;
+    const theme = useTheme();
     const { classes } = useStyles();
-    // must be memoized a la https://github.com/popperjs/react-popper/issues/391
-    const virtElement = useMemo(() => ({
-        getBoundingClientRect: () => {
-            return {
-                top: y,
-                left: x + width / 2,
-                bottom: y,
-                right: x,
-                width: 0,
-                height: 0,
-                x,
-                y,
-                toJSON() { },
-            };
-        },
-    }), [x, y, width]);
-    const { styles, attributes } = usePopper(virtElement, anchorEl);
-    return title ? (React.createElement(Portal, null,
-        React.createElement("div", { ref: ref => {
-                setWidth((ref === null || ref === void 0 ? void 0 : ref.getBoundingClientRect().width) || 0);
-                setAnchorEl(ref);
-            }, className: classes.tooltip, 
-            // zIndex needed to go over widget drawer
-            style: { ...styles.popper, zIndex: 100000 }, ...attributes.popper },
+    const { refs, floatingStyles, context } = useFloating({
+        placement: 'right',
+    });
+    const clientPoint = useClientPoint(context);
+    const { getFloatingProps } = useInteractions([clientPoint]);
+    const popperTheme = (_a = theme === null || theme === void 0 ? void 0 : theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
+    return title ? (React.createElement(Portal, { container: (_b = popperTheme === null || popperTheme === void 0 ? void 0 : popperTheme.defaultProps) === null || _b === void 0 ? void 0 : _b.container },
+        React.createElement("div", { className: classes.tooltip, ref: refs.setFloating, style: {
+                ...floatingStyles,
+                zIndex: 100000,
+                pointerEvents: 'none',
+            }, ...getFloatingProps() },
             React.createElement(SanitizedHTML, { html: title })))) : null;
 });
 export default SyntenyTooltip;

package/esm/LinearSyntenyDisplay/model.d.ts

@@ -5,7 +5,7 @@ import { Feature } from '@jbrowse/core/util';
 interface Pos {
     offsetPx: number;
 }
-interface FeatPos {
+export interface FeatPos {
     p11: Pos;
     p12: Pos;
     p21: Pos;
@@ -15,7 +15,8 @@ interface FeatPos {
 }
 /**
  * #stateModel LinearSyntenyDisplay
- * extends `LinearComparativeDisplay` model
+ * extends
+ * - [LinearComparativeDisplay](../linearcomparativedisplay)
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -77,17 +78,20 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
-         * #action
-         */
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
-    renderProps(): any;
+    renderProps(): any; /**
+     * #getter
+     */
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[]; /**
+     * #getter
+     * used for synteny svg rendering
+     */
     regionCannotBeRendered(): null;
 } & {
     setMessage(arg?: string | undefined): void;
@@ -154,17 +158,20 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     rendererTypeName: string;
                     error: unknown;
                     message: string | undefined;
-                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
-                 * #action
-                 */
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: any;
-            renderProps(): any;
+            renderProps(): any; /**
+             * #getter
+             */
             readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
             readonly DisplayMessageComponent: import("react").FC<any> | undefined;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[]; /**
+             * #getter
+             * used for synteny svg rendering
+             */
             regionCannotBeRendered(): null;
         } & {
             setMessage(arg?: string | undefined): void;
@@ -226,17 +233,20 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     rendererTypeName: string;
                     error: unknown;
                     message: string | undefined;
-                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
-                 * #action
-                 */
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: any;
-            renderProps(): any;
+            renderProps(): any; /**
+             * #getter
+             */
             readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
             readonly DisplayMessageComponent: import("react").FC<any> | undefined;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[]; /**
+             * #getter
+             * used for synteny svg rendering
+             */
             regionCannotBeRendered(): null;
         } & {
             setMessage(arg?: string | undefined): void;

package/esm/LinearSyntenyDisplay/model.js

@@ -4,7 +4,8 @@ import { getConf, ConfigurationReference, } from '@jbrowse/core/configuration';
 import baseModelFactory from '../LinearComparativeDisplay/stateModelFactory';
 /**
  * #stateModel LinearSyntenyDisplay
- * extends `LinearComparativeDisplay` model
+ * extends
+ * - [LinearComparativeDisplay](../linearcomparativedisplay)
  */
 function stateModelFactory(configSchema) {
     return types

package/esm/LinearSyntenyView/model.d.ts

@@ -6,7 +6,9 @@ export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
     scale?: number;
     filename?: string;
-    Wrapper?: React.FC<any>;
+    Wrapper?: React.FC<{
+        children: React.ReactNode;
+    }>;
     fontSize?: number;
     rulerHeight?: number;
     textHeight?: number;
@@ -18,7 +20,8 @@ export interface ExportSvgOptions {
 }
 /**
  * #stateModel LinearSyntenyView
- * extends the `LinearComparativeView` base model
+ * extends
+ * - [LinearComparativeView](../linearcomparativeview)
  */
 export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -45,10 +48,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>; /**
+             * #property/
+             */
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
+             * #action
+             */
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -203,11 +210,11 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             } & {
                 getConf(arg: string): any;
             } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
-                 * #property
+                readonly initialized: boolean; /**
+                 * #property/
                  */
+                readonly name: string;
+                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
                 readonly displayName: string | undefined;
                 hasName(name: string): boolean;
@@ -237,11 +244,17 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
-                getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getAdapterMapEntry(adapterConf: {
+                    [x: string]: unknown;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
-                getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getReverseRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
             } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -261,11 +274,11 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             } & {
                 getConf(arg: string): any;
             } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
-                 * #property
+                readonly initialized: boolean; /**
+                 * #property/
                  */
+                readonly name: string;
+                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
                 readonly displayName: string | undefined;
                 hasName(name: string): boolean;
@@ -295,11 +308,17 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
-                getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getAdapterMapEntry(adapterConf: {
+                    [x: string]: unknown;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
-                getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getReverseRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
             }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -380,10 +399,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>; /**
+             * #property/
+             */
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
+             * #action
+             */
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -407,19 +430,27 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         displayedRegions: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>; /**
+             * #property/
+             */
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
+             * #action
+             */
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>; /**
+             * #property/
+             */
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
+             * #action
+             */
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
@@ -574,11 +605,11 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             } & {
                 getConf(arg: string): any;
             } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
-                 * #property
+                readonly initialized: boolean; /**
+                 * #property/
                  */
+                readonly name: string;
+                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
                 readonly displayName: string | undefined;
                 hasName(name: string): boolean;
@@ -608,11 +639,17 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
-                getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getAdapterMapEntry(adapterConf: {
+                    [x: string]: unknown;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
-                getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getReverseRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
             } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -632,11 +669,11 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             } & {
                 getConf(arg: string): any;
             } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
-                 * #property
+                readonly initialized: boolean; /**
+                 * #property/
                  */
+                readonly name: string;
+                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
                 readonly displayName: string | undefined;
                 hasName(name: string): boolean;
@@ -666,11 +703,17 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
-                getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getAdapterMapEntry(adapterConf: {
+                    [x: string]: unknown;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
-                getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getReverseRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
             }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -725,10 +768,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>; /**
+             * #property/
+             */
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
+             * #action
+             */
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -883,11 +930,11 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             } & {
                 getConf(arg: string): any;
             } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
-                 * #property
+                readonly initialized: boolean; /**
+                 * #property/
                  */
+                readonly name: string;
+                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
                 readonly displayName: string | undefined;
                 hasName(name: string): boolean;
@@ -917,11 +964,17 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
-                getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getAdapterMapEntry(adapterConf: {
+                    [x: string]: unknown;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
-                getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getReverseRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
             } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -941,11 +994,11 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             } & {
                 getConf(arg: string): any;
             } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
-                 * #property
+                readonly initialized: boolean; /**
+                 * #property/
                  */
+                readonly name: string;
+                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
                 readonly displayName: string | undefined;
                 hasName(name: string): boolean;
@@ -975,11 +1028,17 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
-                getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getAdapterMapEntry(adapterConf: {
+                    [x: string]: unknown;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
-                getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                getReverseRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                     [x: string]: string | undefined;
                 }>;
             }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -1056,6 +1115,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
      */
     showAllRegions(): void;
 } & {
+    /**
+     * #action
+     */
     exportSvg(opts: ExportSvgOptions): Promise<void>;
 } & {
     /**
@@ -1105,6 +1167,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         checked?: undefined;
         type?: undefined;
     })[];
+    /**
+     * #method
+     */
     menuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {

package/esm/LinearSyntenyView/model.js

@@ -15,7 +15,8 @@ import baseModel from '../LinearComparativeView/model';
 const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'));
 /**
  * #stateModel LinearSyntenyView
- * extends the `LinearComparativeView` base model
+ * extends
+ * - [LinearComparativeView](../linearcomparativeview)
  */
 export default function stateModelFactory(pluginManager) {
     return types
@@ -56,6 +57,9 @@ export default function stateModelFactory(pluginManager) {
         },
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
         async exportSvg(opts) {
             const { renderToSvg } = await import('./svgcomponents/SVGLinearSyntenyView');
             const html = await renderToSvg(self, opts);
@@ -120,6 +124,9 @@ export default function stateModelFactory(pluginManager) {
                     },
                 ];
             },
+            /**
+             * #method
+             */
             menuItems() {
                 return [
                     ...superMenuItems(),

package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -1,8 +1,8 @@
 import React from 'react';
 import { ThemeProvider } from '@mui/material';
-import { renderToStaticMarkup } from 'react-dom/server';
+import { getRoot } from 'mobx-state-tree';
 import { when } from 'mobx';
-import { getSession, getSerializedSvg, max, measureText, ReactRendering, renderToAbstractCanvas, sum, } from '@jbrowse/core/util';
+import { getSession, getSerializedSvg, max, measureText, ReactRendering, renderToAbstractCanvas, renderToStaticMarkup, sum, } from '@jbrowse/core/util';
 import { getTrackName } from '@jbrowse/core/util/tracks';
 import { createJBrowseTheme } from '@jbrowse/core/ui';
 import { SVGTracks, SVGRuler, totalHeight, } from '@jbrowse/plugin-linear-genome-view';
@@ -13,14 +13,14 @@ import { drawRef } from '../../LinearSyntenyDisplay/drawSynteny';
 export async function renderToSvg(model, opts) {
     var _a;
     await when(() => model.initialized);
-    const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', 
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    Wrapper = ({ children }) => React.createElement(React.Fragment, null, children), themeName = 'default', } = opts;
+    const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => React.createElement(React.Fragment, null, children), themeName = 'default', } = opts;
     const session = getSession(model);
     const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
     const { width, views, middleComparativeHeight: synH, tracks } = model;
     const shift = 50;
     const offset = headerHeight + rulerHeight;
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const { createRootFn } = getRoot(model);
     const heights = views.map(v => totalHeight(v.tracks, textHeight, trackLabels) + offset);
     const totalHeightSvg = sum(heights) + synH + 100;
     const displayResults = await Promise.all(views.map(async (view) => ({
@@ -73,5 +73,5 @@ export async function renderToSvg(model, opts) {
                     React.createElement("g", { transform: `translate(${trackLabelOffset})` },
                         React.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[1].assemblyNames.join(', ')),
                         React.createElement(SVGRuler, { model: displayResults[1].view, fontSize: fontSize })),
-                    React.createElement(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, offset: offset, trackLabelOffset: trackLabelOffset }))))));
+                    React.createElement(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, offset: offset, trackLabelOffset: trackLabelOffset }))))), createRootFn);
 }