@jbrowse/plugin-linear-comparative-view 3.7.0 → 4.0.0

package/esm/LinearSyntenyDisplay/drawSynteny.d.ts

@@ -1,4 +1,4 @@
-import type { LinearSyntenyDisplayModel } from './model';
+import type { LinearSyntenyDisplayModel } from './model.ts';
 export declare const MAX_COLOR_RANGE: number;
 export declare function getId(r: number, g: number, b: number, unitMultiplier: number): number;
 export declare function drawCigarClickMap(model: LinearSyntenyDisplayModel, cigarClickMapCanvas: CanvasRenderingContext2D): void;

package/esm/LinearSyntenyDisplay/drawSynteny.js

@@ -1,7 +1,7 @@
 import { category10 } from '@jbrowse/core/ui/colors';
 import { doesIntersect2, getContainingView } from '@jbrowse/core/util';
 import { colord } from '@jbrowse/core/util/colord';
-import { draw, drawLocationMarkers, drawMatchSimple } from './components/util';
+import { draw, drawLocationMarkers, drawMatchSimple, } from "./components/util.js";
 export const MAX_COLOR_RANGE = 255 * 255 * 255;
 function makeColor(idx) {
     const r = Math.floor(idx / (255 * 255)) % 255;
@@ -148,7 +148,6 @@ export function drawCigarClickMap(model, cigarClickMapCanvas) {
     }
 }
 export function drawRef(model, mainCanvas) {
-    var _a;
     const view = getContainingView(model);
     const drawCurves = view.drawCurves;
     const drawCIGAR = view.drawCIGAR;
@@ -377,7 +376,7 @@ export function drawRef(model, mainCanvas) {
             }
         }
     }
-    const ctx2 = (_a = model.clickMapCanvas) === null || _a === void 0 ? void 0 : _a.getContext('2d');
+    const ctx2 = model.clickMapCanvas?.getContext('2d');
     if (!ctx2) {
         return;
     }
@@ -411,14 +410,13 @@ export function drawRef(model, mainCanvas) {
     }
 }
 export function drawMouseoverClickMap(model) {
-    var _a;
     const { level, clickId, mouseoverId } = model;
     const highResolutionScaling = 1;
     const view = getContainingView(model);
     const drawCurves = view.drawCurves;
     const height = model.height;
     const width = view.width;
-    const ctx = (_a = model.mouseoverCanvas) === null || _a === void 0 ? void 0 : _a.getContext('2d');
+    const ctx = model.mouseoverCanvas?.getContext('2d');
     const offsets = view.views.map(v => v.offsetPx);
     if (!ctx) {
         return;

package/esm/LinearSyntenyDisplay/index.js

@@ -1,7 +1,7 @@
 import { lazy } from 'react';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
-import configSchemaF from './configSchemaF';
-import stateModelFactory from './model';
+import configSchemaF from "./configSchemaF.js";
+import stateModelFactory from "./model.js";
 export default function LinearSyntenyDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaF(pluginManager);
@@ -11,7 +11,7 @@ export default function LinearSyntenyDisplayF(pluginManager) {
             stateModel: stateModelFactory(configSchema),
             trackType: 'SyntenyTrack',
             viewType: 'LinearSyntenyViewHelper',
-            ReactComponent: lazy(() => import('./components/Component')),
+            ReactComponent: lazy(() => import("./components/Component.js")),
         });
     });
 }

package/esm/LinearSyntenyDisplay/model.d.ts

@@ -1,6 +1,6 @@
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
-import type { Instance } from 'mobx-state-tree';
+import type { Instance } from '@jbrowse/mobx-state-tree';
 interface Pos {
     offsetPx: number;
 }
@@ -12,40 +12,40 @@ export interface FeatPos {
     f: Feature;
     cigar: string[];
 }
-declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<string>;
-    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"LinearComparativeDisplay">;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"LinearComparativeDisplay">;
     configuration: AnyConfigurationSchemaType;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"LinearSyntenyDisplay">;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"LinearSyntenyDisplay">;
     configuration: AnyConfigurationSchemaType;
-    colorBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    colorBy: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
 }, {
     rendererTypeName: string;
     error: unknown;
-    message: string | undefined;
+    statusMessage: string | undefined;
 } & {
     readonly RenderingComponent: React.FC<{
         model: {
             id: string;
             type: string;
             rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+            statusMessage: string | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            statusMessage: string | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
@@ -54,81 +54,54 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             id: string;
             type: string;
             rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+            statusMessage: string | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            statusMessage: string | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
-    readonly parentTrack: any;
-    renderProps(): any;
-    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: undefined | React.FC<any>;
-    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-    regionCannotBeRendered(): null;
-} & {
-    setMessage(arg?: string): void;
-    setError(error?: unknown): void;
-    setRpcDriverName(rpcDriverName: string): void;
-    reload(): void;
+    readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly parentDisplay: any;
+    readonly effectiveRpcDriverName: any;
 } & {
-    renderInProgress: string | undefined;
-    features: Feature[] | undefined;
-    message: string | undefined;
-    loadingStatus: string | undefined;
-} & {
-    readonly level: number;
-    readonly height: number;
-    renderProps(): {
-        rpcDriverName: string | undefined;
+    renderProps(): any;
+    renderingProps(): {
         displayModel: {
             id: string;
-            type: "LinearComparativeDisplay";
+            type: string;
             rpcDriverName: string | undefined;
-            configuration: {
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                    setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                        [x: string]: any;
-                    } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-                } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
+            statusMessage: string | undefined;
         } & {
             readonly RenderingComponent: React.FC<{
                 model: {
                     id: string;
                     type: string;
                     rpcDriverName: string | undefined;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
                     rendererTypeName: string;
                     error: unknown;
-                    message: string | undefined;
-                } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                    type: import("mobx-state-tree").ISimpleType<string>;
-                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
                 }, {
                     rendererTypeName: string;
                     error: unknown;
-                    message: string | undefined;
-                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
                 onHorizontalScroll?: () => void;
                 blockState?: Record<string, any>;
             }>;
@@ -137,68 +110,51 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     id: string;
                     type: string;
                     rpcDriverName: string | undefined;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
                     rendererTypeName: string;
                     error: unknown;
-                    message: string | undefined;
-                } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                    type: import("mobx-state-tree").ISimpleType<string>;
-                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
                 }, {
                     rendererTypeName: string;
                     error: unknown;
-                    message: string | undefined;
-                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
             }> | null;
             readonly adapterConfig: any;
-            readonly parentTrack: any;
-            renderProps(): any;
-            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-            readonly DisplayMessageComponent: undefined | React.FC<any>;
-            trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-            regionCannotBeRendered(): null;
-        } & {
-            setMessage(arg?: string): void;
-            setError(error?: unknown): void;
-            setRpcDriverName(rpcDriverName: string): void;
-            reload(): void;
-        } & {
-            renderInProgress: string | undefined;
-            features: Feature[] | undefined;
-            message: string | undefined;
-            loadingStatus: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        } & {
-            type: import("mobx-state-tree").ISimpleType<"LinearComparativeDisplay">;
-            configuration: AnyConfigurationSchemaType;
+            readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly parentDisplay: any;
+            readonly effectiveRpcDriverName: any;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
+            statusMessage: string | undefined;
         } & {
             readonly RenderingComponent: React.FC<{
                 model: {
                     id: string;
                     type: string;
                     rpcDriverName: string | undefined;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
                     rendererTypeName: string;
                     error: unknown;
-                    message: string | undefined;
-                } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                    type: import("mobx-state-tree").ISimpleType<string>;
-                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
                 }, {
                     rendererTypeName: string;
                     error: unknown;
-                    message: string | undefined;
-                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
                 onHorizontalScroll?: () => void;
                 blockState?: Record<string, any>;
             }>;
@@ -207,41 +163,45 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     id: string;
                     type: string;
                     rpcDriverName: string | undefined;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
                     rendererTypeName: string;
                     error: unknown;
-                    message: string | undefined;
-                } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                    type: import("mobx-state-tree").ISimpleType<string>;
-                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
                 }, {
                     rendererTypeName: string;
                     error: unknown;
-                    message: string | undefined;
-                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
             }> | null;
             readonly adapterConfig: any;
-            readonly parentTrack: any;
-            renderProps(): any;
-            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-            readonly DisplayMessageComponent: undefined | React.FC<any>;
-            trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-            regionCannotBeRendered(): null;
-        } & {
-            setMessage(arg?: string): void;
-            setError(error?: unknown): void;
-            setRpcDriverName(rpcDriverName: string): void;
-            reload(): void;
-        } & {
-            renderInProgress: string | undefined;
-            features: Feature[] | undefined;
-            message: string | undefined;
-            loadingStatus: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        highResolutionScaling: number;
+            readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly parentDisplay: any;
+            readonly effectiveRpcDriverName: any;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     };
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): null;
+} & {
+    setStatusMessage(arg?: string): void;
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    renderInProgress: string | undefined;
+    features: Feature[] | undefined;
+    message: string | undefined;
+    loadingStatus: string | undefined;
+} & {
+    readonly level: number;
+    readonly height: number;
+    renderProps(): any;
 } & {
     setLoading(newStopToken: string): void;
     setMessage(messageText: string): void;
@@ -285,7 +245,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     };
 } & {
     afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type LinearSyntenyDisplayStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearSyntenyDisplayModel = Instance<LinearSyntenyDisplayStateModel>;
 export default stateModelFactory;

package/esm/LinearSyntenyDisplay/model.js

@@ -1,6 +1,6 @@
 import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
-import baseModelFactory from '../LinearComparativeDisplay/stateModelFactory';
+import { types } from '@jbrowse/mobx-state-tree';
+import baseModelFactory from "../LinearComparativeDisplay/stateModelFactory.js";
 function stateModelFactory(configSchema) {
     return types
         .compose('LinearSyntenyDisplay', baseModelFactory(configSchema), types.model({
@@ -81,7 +81,7 @@ function stateModelFactory(configSchema) {
             ;
             (async () => {
                 try {
-                    const { doAfterAttach } = await import('./afterAttach');
+                    const { doAfterAttach } = await import("./afterAttach.js");
                     doAfterAttach(self);
                 }
                 catch (e) {

package/esm/LinearSyntenyView/components/DiagonalizationProgressDialog.d.ts

@@ -1,4 +1,4 @@
-import type { LinearSyntenyViewModel } from '../model';
+import type { LinearSyntenyViewModel } from '../model.ts';
 declare const DiagonalizationProgressDialog: ({ handleClose, model, }: {
     handleClose: () => void;
     model: LinearSyntenyViewModel;

package/esm/LinearSyntenyView/components/DiagonalizationProgressDialog.js

@@ -5,8 +5,8 @@ import { getSession } from '@jbrowse/core/util';
 import { Button, DialogActions, DialogContent, LinearProgress, Typography, } from '@mui/material';
 import { transaction } from 'mobx';
 import { observer } from 'mobx-react';
-import { diagonalizeRegions } from '../util/diagonalize';
-const DiagonalizationProgressDialog = observer(function ({ handleClose, model, }) {
+import { diagonalizeRegions } from "../util/diagonalize.js";
+const DiagonalizationProgressDialog = observer(function DiagonalizationProgressDialog({ handleClose, model, }) {
     const [progress, setProgress] = useState(0);
     const [message, setMessage] = useState('Initializing...');
     const [error, setError] = useState();

package/esm/LinearSyntenyView/components/ExportSvgDialog.d.ts

@@ -1,4 +1,4 @@
-import type { ExportSvgOptions } from '../types';
+import type { ExportSvgOptions } from '../types.ts';
 export default function ExportSvgDialog({ model, handleClose, }: {
     model: {
         exportSvg(opts: ExportSvgOptions): Promise<void>;

package/esm/LinearSyntenyView/components/ExportSvgDialog.js

@@ -3,7 +3,7 @@ import { useState } from 'react';
 import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
 import { getSession, useLocalStorage } from '@jbrowse/core/util';
 import { Button, Checkbox, CircularProgress, DialogActions, DialogContent, FormControlLabel, MenuItem, Typography, } from '@mui/material';
-import TextField2 from './TextField2';
+import TextField2 from "./TextField2.js";
 function LoadingMessage() {
     return (_jsxs("div", { children: [_jsx(CircularProgress, { size: 20, style: { marginRight: 20 } }), _jsx(Typography, { display: "inline", children: "Creating SVG" })] }));
 }
@@ -14,6 +14,7 @@ export default function ExportSvgDialog({ model, handleClose, }) {
     const session = getSession(model);
     const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
     const [rasterizeLayers, setRasterizeLayers] = useState(offscreenCanvas);
+    const [showGridlines, setShowGridlines] = useSvgLocal('gridlines', false);
     const [loading, setLoading] = useState(false);
     const [filename, setFilename] = useSvgLocal('file', 'jbrowse.svg');
     const [trackLabels, setTrackLabels] = useSvgLocal('tracklabels', 'offset');
@@ -25,7 +26,9 @@ export default function ExportSvgDialog({ model, handleClose, }) {
                             setTrackLabels(event.target.value);
                         }, children: [_jsx(MenuItem, { value: "offset", children: "Offset" }), _jsx(MenuItem, { value: "overlay", children: "Overlay" }), _jsx(MenuItem, { value: "left", children: "Left" }), _jsx(MenuItem, { value: "none", children: "None" })] }), _jsx("br", {}), session.allThemes ? (_jsx(TextField2, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => {
                             setThemeName(event.target.value);
-                        }, children: Object.entries(session.allThemes()).map(([key, val]) => (_jsx(MenuItem, { value: key, children: val.name || '(Unknown name)' }, key))) })) : null, offscreenCanvas ? (_jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: rasterizeLayers, onChange: () => {
+                        }, children: Object.entries(session.allThemes()).map(([key, val]) => (_jsx(MenuItem, { value: key, children: val.name || '(Unknown name)' }, key))) })) : null, _jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: showGridlines, onChange: () => {
+                                setShowGridlines(val => !val);
+                            } }), label: "Show gridlines" }), offscreenCanvas ? (_jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: rasterizeLayers, onChange: () => {
                                 setRasterizeLayers(val => !val);
                             } }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (_jsx(Typography, { children: "Note: rasterizing layers not yet supported in this browser, so SVG size may be large" }))] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
                             handleClose();
@@ -38,6 +41,7 @@ export default function ExportSvgDialog({ model, handleClose, }) {
                                     filename,
                                     themeName,
                                     trackLabels,
+                                    showGridlines,
                                 });
                                 handleClose();
                             }

package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyOpenCustomTrack.d.ts

@@ -1,4 +1,4 @@
-import type { LinearSyntenyViewModel } from '../../model';
+import type { LinearSyntenyViewModel } from '../../model.ts';
 declare const ImportSyntenyOpenCustomTrack: ({ model, assembly1, assembly2, selectedRow, }: {
     model: LinearSyntenyViewModel;
     assembly1: string;

package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyOpenCustomTrack.js

@@ -3,10 +3,10 @@ import { useEffect, useState } from 'react';
 import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
 import { FormControlLabel, Grid, Paper, Radio, RadioGroup, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
-import { getAdapter } from './getAdapter';
-import { AnchorsSelector, PifGzSelector, StandardFormatSelector, } from './selectors';
-import { basename, extName, getName, stripGz } from './util';
-const ImportSyntenyOpenCustomTrack = observer(function ({ model, assembly1, assembly2, selectedRow, }) {
+import { getAdapter } from "./getAdapter.js";
+import { AnchorsSelector, PifGzSelector, StandardFormatSelector, } from "./selectors/index.js";
+import { basename, extName, getName, stripGz } from "./util.js";
+const ImportSyntenyOpenCustomTrack = observer(function ImportSyntenyOpenCustomTrack({ model, assembly1, assembly2, selectedRow, }) {
     const [swap, setSwap] = useState(false);
     const [bed2Location, setBed2Location] = useState();
     const [bed1Location, setBed1Location] = useState();

package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyPreConfigured.d.ts

@@ -1,4 +1,4 @@
-import type { LinearSyntenyViewModel } from '../../model';
+import type { LinearSyntenyViewModel } from '../../model.ts';
 declare const ImportSyntenyTrackSelector: ({ model, selectedRow, assembly1, assembly2, }: {
     model: LinearSyntenyViewModel;
     selectedRow: number;

package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyPreConfigured.js

@@ -6,11 +6,10 @@ import { getSession } from '@jbrowse/core/util';
 import { getTrackName } from '@jbrowse/core/util/tracks';
 import { MenuItem, Paper, Select, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
-const ImportSyntenyTrackSelector = observer(function ({ model, selectedRow, assembly1, assembly2, }) {
-    var _a;
+const ImportSyntenyTrackSelector = observer(function ImportSyntenyTrackSelector({ model, selectedRow, assembly1, assembly2, }) {
     const session = getSession(model);
     const { importFormSyntenyTrackSelections } = model;
-    const { tracks = [], sessionTracks = [] } = session;
+    const { tracks, sessionTracks = [] } = session;
     const allTracks = [...tracks, ...sessionTracks];
     const filteredTracks = allTracks.filter(track => {
         const assemblyNames = readConfObject(track, 'assemblyNames');
@@ -18,9 +17,9 @@ const ImportSyntenyTrackSelector = observer(function ({ model, selectedRow, asse
             assemblyNames.includes(assembly2) &&
             track.type.includes('Synteny'));
     });
-    const resetTrack = ((_a = filteredTracks[0]) === null || _a === void 0 ? void 0 : _a.trackId) || '';
+    const resetTrack = filteredTracks[0]?.trackId || '';
     const r = importFormSyntenyTrackSelections[selectedRow];
-    const value = (r === null || r === void 0 ? void 0 : r.type) === 'preConfigured' ? r.value : undefined;
+    const value = r?.type === 'preConfigured' ? r.value : undefined;
     useEffect(() => {
         model.setImportFormSyntenyTrack(selectedRow, {
             type: 'preConfigured',

package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelectorArea.d.ts

@@ -1,4 +1,14 @@
-import type { LinearSyntenyViewModel } from '../../model';
+import type { LinearSyntenyViewModel } from '../../model.ts';
+export interface LinearSyntenyImportFormSyntenyOption {
+    value: string;
+    label: string;
+    ReactComponent: React.FC<{
+        model: LinearSyntenyViewModel;
+        assembly1: string;
+        assembly2: string;
+        selectedRow: number;
+    }>;
+}
 export default function ImportSyntenyTrackSelectorArea({ model, assembly1, assembly2, selectedRow, }: {
     model: LinearSyntenyViewModel;
     assembly1: string;

package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelectorArea.js

@@ -1,16 +1,20 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useEffect, useState } from 'react';
+import { getEnv } from '@jbrowse/core/util';
 import { FormControl, FormControlLabel, Radio, RadioGroup } from '@mui/material';
-import ImportCustomTrack from './ImportSyntenyOpenCustomTrack';
-import ImportSyntenyTrackSelector from './ImportSyntenyPreConfigured';
+import ImportCustomTrack from "./ImportSyntenyOpenCustomTrack.js";
+import ImportSyntenyTrackSelector from "./ImportSyntenyPreConfigured.js";
 export default function ImportSyntenyTrackSelectorArea({ model, assembly1, assembly2, selectedRow, }) {
+    const { pluginManager } = getEnv(model);
     const [choice, setChoice] = useState('tracklist');
+    const customOptions = pluginManager.evaluateExtensionPoint('LinearSyntenyView-ImportFormSyntenyOptions', [], { model, assembly1, assembly2, selectedRow });
+    const selectedCustomOption = customOptions.find(opt => opt.value === choice);
     useEffect(() => {
-        if (choice === 'none') {
+        if (choice === 'none' || choice === 'custom') {
             model.setImportFormSyntenyTrack(selectedRow, { type: 'none' });
         }
     }, [choice, model, selectedRow]);
     return (_jsxs("div", { children: [_jsx(FormControl, { children: _jsxs(RadioGroup, { row: true, value: choice, "aria-labelledby": "group-label", onChange: event => {
                         setChoice(event.target.value);
-                    }, children: [_jsx(FormControlLabel, { value: "none", control: _jsx(Radio, {}), label: "None" }), _jsx(FormControlLabel, { value: "tracklist", control: _jsx(Radio, {}), label: "Existing track" }), _jsx(FormControlLabel, { value: "custom", control: _jsx(Radio, {}), label: "New track" })] }) }), choice === 'custom' ? (_jsx(ImportCustomTrack, { model: model, selectedRow: selectedRow, assembly2: assembly2, assembly1: assembly1 })) : null, choice === 'tracklist' ? (_jsx(ImportSyntenyTrackSelector, { model: model, selectedRow: selectedRow, assembly1: assembly1, assembly2: assembly2 })) : null] }));
+                    }, children: [_jsx(FormControlLabel, { value: "none", control: _jsx(Radio, {}), label: "None" }), _jsx(FormControlLabel, { value: "tracklist", control: _jsx(Radio, {}), label: "Existing track" }), _jsx(FormControlLabel, { value: "custom", control: _jsx(Radio, {}), label: "New track" }), customOptions.map(opt => (_jsx(FormControlLabel, { value: opt.value, control: _jsx(Radio, {}), label: opt.label }, opt.value)))] }) }), choice === 'custom' ? (_jsx(ImportCustomTrack, { model: model, selectedRow: selectedRow, assembly2: assembly2, assembly1: assembly1 })) : null, choice === 'tracklist' ? (_jsx(ImportSyntenyTrackSelector, { model: model, selectedRow: selectedRow, assembly1: assembly1, assembly2: assembly2 })) : null, selectedCustomOption ? (_jsx(selectedCustomOption.ReactComponent, { model: model, assembly1: assembly1, assembly2: assembly2, selectedRow: selectedRow })) : null] }));
 }

package/esm/LinearSyntenyView/components/ImportForm/LeftPanel.d.ts

@@ -1,4 +1,4 @@
-import type { LinearSyntenyViewModel } from '../../model';
+import type { LinearSyntenyViewModel } from '../../model.ts';
 declare const LeftPanel: ({ model, selectedAssemblyNames, setSelectedAssemblyNames, selectedRow, setSelectedRow, defaultAssemblyName, onLaunch, }: {
     model: LinearSyntenyViewModel;
     selectedAssemblyNames: string[];