@jbrowse/plugin-linear-comparative-view 3.7.0 → 4.0.1

package/esm/LinearSyntenyView/model.js

@@ -1,17 +1,16 @@
 import { lazy } from 'react';
 import { getSession } from '@jbrowse/core/util';
+import { addDisposer, types } from '@jbrowse/mobx-state-tree';
 import CropFreeIcon from '@mui/icons-material/CropFree';
 import LinkIcon from '@mui/icons-material/Link';
 import PhotoCameraIcon from '@mui/icons-material/PhotoCamera';
 import ShuffleIcon from '@mui/icons-material/Shuffle';
 import VisibilityIcon from '@mui/icons-material/Visibility';
-import { saveAs } from 'file-saver';
-import { observable, transaction } from 'mobx';
-import { types } from 'mobx-state-tree';
-import { Curves } from './components/Icons';
-import baseModel from '../LinearComparativeView/model';
-const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'));
-const DiagonalizationProgressDialog = lazy(() => import('./components/DiagonalizationProgressDialog'));
+import { autorun, observable, when } from 'mobx';
+import { Curves } from "./components/Icons.js";
+import baseModel from "../LinearComparativeView/model.js";
+const ExportSvgDialog = lazy(() => import("./components/ExportSvgDialog.js"));
+const DiagonalizationProgressDialog = lazy(() => import("./components/DiagonalizationProgressDialog.js"));
 export default function stateModelFactory(pluginManager) {
     return types
         .compose('LinearSyntenyView', baseModel(pluginManager), types.model({
@@ -20,9 +19,23 @@ export default function stateModelFactory(pluginManager) {
         drawCIGARMatchesOnly: false,
         drawCurves: false,
         drawLocationMarkers: false,
+        init: types.frozen(),
     }))
         .volatile(() => ({
         importFormSyntenyTrackSelections: observable.array(),
+    }))
+        .views(self => ({
+        get hasSomethingToShow() {
+            return self.views.length > 0 || !!self.init;
+        },
+    }))
+        .views(self => ({
+        get showLoading() {
+            return self.isLoading || (!self.initialized && self.hasSomethingToShow);
+        },
+        get showImportForm() {
+            return !self.hasSomethingToShow;
+        },
     }))
         .actions(self => ({
         importFormRemoveRow(idx) {
@@ -47,19 +60,20 @@ export default function stateModelFactory(pluginManager) {
             self.drawLocationMarkers = arg;
         },
         showAllRegions() {
-            transaction(() => {
-                for (const view of self.views) {
-                    view.showAllRegionsInAssembly();
-                }
-            });
+            for (const view of self.views) {
+                view.showAllRegionsInAssembly();
+            }
+        },
+        setInit(init) {
+            self.init = init;
         },
     }))
         .actions(self => ({
         async exportSvg(opts) {
-            const { renderToSvg } = await import('./svgcomponents/SVGLinearSyntenyView');
+            const { renderToSvg } = await import("./svgcomponents/SVGLinearSyntenyView.js");
             const html = await renderToSvg(self, opts);
-            const blob = new Blob([html], { type: 'image/svg+xml' });
-            saveAs(blob, opts.filename || 'image.svg');
+            const { saveAs } = await import('file-saver-es');
+            saveAs(new Blob([html], { type: 'image/svg+xml' }), opts.filename || 'image.svg');
         },
     }))
         .views(self => {
@@ -197,5 +211,75 @@ export default function stateModelFactory(pluginManager) {
                 ];
             },
         };
+    })
+        .actions(self => ({
+        afterAttach() {
+            addDisposer(self, autorun(async function initAutorun() {
+                const { init, width } = self;
+                if (!width || !init) {
+                    return;
+                }
+                const session = getSession(self);
+                const { assemblyManager } = session;
+                try {
+                    const assemblies = await Promise.all(init.views.map(async (v) => {
+                        const asm = await assemblyManager.waitForAssembly(v.assembly);
+                        if (!asm) {
+                            throw new Error(`Assembly ${v.assembly} failed to load`);
+                        }
+                        return asm;
+                    }));
+                    self.setViews(assemblies.map(asm => ({
+                        type: 'LinearGenomeView',
+                        bpPerPx: 1,
+                        offsetPx: 0,
+                        hideHeader: true,
+                        displayedRegions: asm.regions,
+                    })));
+                    await Promise.all(self.views.map(view => when(() => view.initialized)));
+                    await Promise.all(init.views.map(async (viewInit, idx) => {
+                        const view = self.views[idx];
+                        if (!view) {
+                            return;
+                        }
+                        if (viewInit.loc) {
+                            await view.navToLocString(viewInit.loc, viewInit.assembly);
+                        }
+                        else {
+                            view.showAllRegionsInAssembly(viewInit.assembly);
+                        }
+                        if (viewInit.tracks) {
+                            for (const trackId of viewInit.tracks) {
+                                view.showTrack(trackId);
+                            }
+                        }
+                    }));
+                    if (init.tracks) {
+                        for (const trackId of init.tracks) {
+                            self.showTrack(trackId);
+                        }
+                    }
+                    self.setInit(undefined);
+                }
+                catch (e) {
+                    console.error(e);
+                    session.notifyError(`${e}`, e);
+                    self.setInit(undefined);
+                }
+            }, { name: 'LinearSyntenyViewInit' }));
+        },
+    }))
+        .postProcessSnapshot(snap => {
+        if (!snap) {
+            return snap;
+        }
+        const { init, drawCIGAR, drawCIGARMatchesOnly, drawCurves, drawLocationMarkers, ...rest } = snap;
+        return {
+            ...rest,
+            ...(!drawCIGAR ? { drawCIGAR } : {}),
+            ...(drawCIGARMatchesOnly ? { drawCIGARMatchesOnly } : {}),
+            ...(drawCurves ? { drawCurves } : {}),
+            ...(drawLocationMarkers ? { drawLocationMarkers } : {}),
+        };
     });
 }

package/esm/LinearSyntenyView/svgcomponents/SVGLinearGenomeView.d.ts

@@ -1,5 +1,5 @@
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export default function SVGLinearGenomeView({ trackLabelOffset, fontSize, textHeight, trackLabels, view, displayResults, rulerHeight, shift, }: {
+export default function SVGLinearGenomeView({ trackLabelOffset, fontSize, textHeight, trackLabels, view, displayResults, rulerHeight, shift, showGridlines, tracksHeight, }: {
     textHeight: number;
     trackLabels: string;
     trackLabelOffset: number;
@@ -8,4 +8,6 @@ export default function SVGLinearGenomeView({ trackLabelOffset, fontSize, textHe
     displayResults: any;
     rulerHeight: number;
     shift: number;
+    showGridlines?: boolean;
+    tracksHeight: number;
 }): import("react/jsx-runtime").JSX.Element;

package/esm/LinearSyntenyView/svgcomponents/SVGLinearGenomeView.js

@@ -1,8 +1,8 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { getFillProps } from '@jbrowse/core/util';
-import { SVGRuler, SVGTracks } from '@jbrowse/plugin-linear-genome-view';
+import { SVGGridlines, SVGRuler, SVGTracks, } from '@jbrowse/plugin-linear-genome-view';
 import { useTheme } from '@mui/material';
-export default function SVGLinearGenomeView({ trackLabelOffset, fontSize, textHeight, trackLabels, view, displayResults, rulerHeight, shift, }) {
+export default function SVGLinearGenomeView({ trackLabelOffset, fontSize, textHeight, trackLabels, view, displayResults, rulerHeight, shift, showGridlines = false, tracksHeight, }) {
     const theme = useTheme();
-    return (_jsxs("g", { transform: `translate(${shift} ${fontSize})`, children: [_jsxs("g", { transform: `translate(${trackLabelOffset})`, children: [_jsx("text", { x: 0, fontSize: fontSize, ...getFillProps(theme.palette.text.primary), children: view.assemblyNames.join(', ') }), _jsx(SVGRuler, { model: displayResults.view, fontSize: fontSize })] }), _jsx("g", { transform: `translate(0 ${rulerHeight + fontSize})`, children: _jsx(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults.view, displayResults: displayResults.data, trackLabelOffset: trackLabelOffset }) })] }));
+    return (_jsxs("g", { transform: `translate(${shift} ${fontSize})`, children: [_jsxs("g", { transform: `translate(${trackLabelOffset})`, children: [_jsx("text", { x: 0, fontSize: fontSize, ...getFillProps(theme.palette.text.primary), children: view.assemblyNames.join(', ') }), _jsx(SVGRuler, { model: displayResults.view, fontSize: fontSize })] }), showGridlines ? (_jsx("g", { transform: `translate(${trackLabelOffset} ${rulerHeight + fontSize})`, children: _jsx(SVGGridlines, { model: displayResults.view, height: tracksHeight }) })) : null, _jsx("g", { transform: `translate(0 ${rulerHeight + fontSize})`, children: _jsx(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults.view, displayResults: displayResults.data, trackLabelOffset: trackLabelOffset }) })] }));
 }

package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.d.ts

@@ -1,3 +1,3 @@
-import type { LinearSyntenyViewModel } from '../model';
-import type { ExportSvgOptions } from '../types';
+import type { LinearSyntenyViewModel } from '../model.ts';
+import type { ExportSvgOptions } from '../types.ts';
 export declare function renderToSvg(model: LinearSyntenyViewModel, opts: ExportSvgOptions): Promise<string>;

package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -5,15 +5,14 @@ import { getTrackName } from '@jbrowse/core/util/tracks';
 import { totalHeight } from '@jbrowse/plugin-linear-genome-view';
 import { ThemeProvider } from '@mui/material';
 import { when } from 'mobx';
-import SVGBackground from './SVGBackground';
-import SVGLinearGenomeView from './SVGLinearGenomeView';
-import { drawRef } from '../../LinearSyntenyDisplay/drawSynteny';
+import SVGBackground from "./SVGBackground.js";
+import SVGLinearGenomeView from "./SVGLinearGenomeView.js";
+import { drawRef } from "../../LinearSyntenyDisplay/drawSynteny.js";
 export async function renderToSvg(model, opts) {
-    var _a;
     await when(() => model.initialized);
-    const { textHeight = 18, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => children, themeName = 'default', } = opts;
+    const { textHeight = 18, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', showGridlines = false, Wrapper = ({ children }) => children, themeName = 'default', } = opts;
     const session = getSession(model);
-    const themeVar = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
+    const themeVar = session.allThemes?.()[themeName];
     const { width, views, levels } = model;
     const shift = 50;
     const offset = rulerHeight;
@@ -30,35 +29,39 @@ export async function renderToSvg(model, opts) {
             };
         })),
     })));
-    const renderings = await Promise.all(levels.map(async (level) => await Promise.all(level.tracks.map(async (track) => {
-        const d = track.displays[0];
-        await when(() => (d.ready !== undefined ? d.ready : true));
-        const r = await renderToAbstractCanvas(width, level.height, { exportSVG: opts }, ctx => {
-            drawRef(d, ctx);
-            return undefined;
-        });
-        if ('imageData' in r) {
-            throw new Error('found a canvas in svg export, probably a bug');
-        }
-        else if ('canvasRecordedData' in r) {
-            return {
-                html: await getSerializedSvg({
-                    ...r,
-                    width,
-                    height: level.height,
-                }),
-            };
-        }
-        else {
-            return r;
-        }
-    }))));
+    const renderings = await Promise.all(levels.map(async (level) => {
+        const { tracks } = level;
+        return Promise.all(tracks.map(async (track) => {
+            const d = track.displays[0];
+            await when(() => d.ready);
+            const r = await renderToAbstractCanvas(width, level.height, { exportSVG: opts }, ctx => {
+                drawRef(d, ctx);
+                return undefined;
+            });
+            if ('imageData' in r) {
+                throw new Error('found a canvas in svg export, probably a bug');
+            }
+            else if ('canvasRecordedData' in r) {
+                return {
+                    html: await getSerializedSvg({
+                        ...r,
+                        width,
+                        height: level.height,
+                    }),
+                };
+            }
+            else {
+                return r;
+            }
+        }));
+    }));
     const trackLabelMaxLen = max(views.flatMap(view => view.tracks.map(track => measureText(getTrackName(track.configuration, session), fontSize))), 0) + 40;
     const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0;
     const w = width + trackLabelOffset;
     const theme = createJBrowseTheme(themeVar);
+    const tracksHeights = views.map(v => totalHeight(v.tracks, textHeight, trackLabels));
     const RenderList = [
-        _jsx(SVGLinearGenomeView, { rulerHeight: rulerHeight, trackLabelOffset: trackLabelOffset, shift: shift, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[0], view: views[0], fontSize: fontSize }, views[0].id),
+        _jsx(SVGLinearGenomeView, { rulerHeight: rulerHeight, trackLabelOffset: trackLabelOffset, shift: shift, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[0], view: views[0], fontSize: fontSize, showGridlines: showGridlines, tracksHeight: tracksHeights[0] }, views[0].id),
     ];
     let currOffset = heights[0] + fontSize + rulerHeight;
     for (let i = 1; i < views.length; i++) {
@@ -67,7 +70,7 @@ export async function renderToSvg(model, opts) {
         const rendering = renderings[i - 1];
         const height = heights[i];
         const levelHeight = level.height || 0;
-        RenderList.push(_jsxs("g", { transform: `translate(0 ${currOffset})`, children: [levelHeight ? (_jsx("defs", { children: _jsx("clipPath", { id: `synclip-${i}`, children: _jsx("rect", { x: 0, y: 0, width: width, height: levelHeight }) }) })) : null, _jsx("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})`, children: rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => (_jsx(ReactRendering, { rendering: r }, i))) }), _jsx("g", { transform: `translate(0 ${levelHeight})`, children: _jsx(SVGLinearGenomeView, { rulerHeight: rulerHeight, shift: shift, trackLabelOffset: trackLabelOffset, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[i], view: view, fontSize: fontSize }, view.id) })] }, view.id));
+        RenderList.push(_jsxs("g", { transform: `translate(0 ${currOffset})`, children: [levelHeight ? (_jsx("defs", { children: _jsx("clipPath", { id: `synclip-${i}`, children: _jsx("rect", { x: 0, y: 0, width: width, height: levelHeight }) }) })) : null, _jsx("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})`, children: rendering?.map((r, i) => (_jsx(ReactRendering, { rendering: r }, i))) }), _jsx("g", { transform: `translate(0 ${levelHeight})`, children: _jsx(SVGLinearGenomeView, { rulerHeight: rulerHeight, shift: shift, trackLabelOffset: trackLabelOffset, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[i], view: view, fontSize: fontSize, showGridlines: showGridlines, tracksHeight: tracksHeights[i] }, view.id) })] }, view.id));
         currOffset += height + fontSize + rulerHeight + levelHeight;
     }
     return renderToStaticMarkup(_jsx(ThemeProvider, { theme: theme, children: _jsx(Wrapper, { children: _jsxs("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString(), children: [_jsx(SVGBackground, { width: w, height: totalHeightSvg, shift: shift }), RenderList] }) }) }));

package/esm/LinearSyntenyView/types.d.ts

@@ -1,6 +1,6 @@
 import type React from 'react';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { SnapshotIn } from 'mobx-state-tree';
+import type { SnapshotIn } from '@jbrowse/mobx-state-tree';
 export type Conf = SnapshotIn<AnyConfigurationModel>;
 export type ImportFormSyntenyTrack = {
     type: 'preConfigured';
@@ -11,6 +11,14 @@ export type ImportFormSyntenyTrack = {
 } | {
     type: 'none';
 };
+export interface LinearSyntenyViewInit {
+    views: {
+        loc?: string;
+        assembly: string;
+        tracks?: string[];
+    }[];
+    tracks?: string[];
+}
 export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
     scale?: number;
@@ -26,4 +34,5 @@ export interface ExportSvgOptions {
     cytobandHeight?: number;
     themeName?: string;
     trackLabels?: string;
+    showGridlines?: boolean;
 }

package/esm/LinearSyntenyViewHelper/index.js

@@ -1,6 +1,6 @@
 import { jsx as _jsx } from "react/jsx-runtime";
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
-import { linearSyntenyViewHelperModelFactory } from './stateModelFactory';
+import { linearSyntenyViewHelperModelFactory } from "./stateModelFactory.js";
 function UnusedComponent() {
     return _jsx("div", {});
 }

package/esm/LinearSyntenyViewHelper/stateModelFactory.d.ts

@@ -1,18 +1,18 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-import type { Instance } from 'mobx-state-tree';
-export declare function linearSyntenyViewHelperModelFactory(pluginManager: PluginManager): 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>;
-    tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
-    height: import("mobx-state-tree").IType<number | undefined, number, number>;
-    level: import("mobx-state-tree").ISimpleType<number>;
+import type { Instance } from '@jbrowse/mobx-state-tree';
+export declare function linearSyntenyViewHelperModelFactory(pluginManager: PluginManager): 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").IType<string | undefined, string, string>;
+    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    height: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    level: import("@jbrowse/mobx-state-tree").ISimpleType<number>;
 }, {
     setHeight(n: number): number;
-    showTrack(trackId: string, initialSnapshot?: {}): void;
-    hideTrack(trackId: string): number;
-    toggleTrack(trackId: string): boolean;
+    showTrack(trackId: string, initialSnapshot?: {}): any;
+    hideTrack(trackId: string): 0 | 1;
+    toggleTrack(trackId: string): void;
 } & {
     readonly assemblyNames: (string | undefined)[];
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type LinearSyntenyViewHelperStateModel = ReturnType<typeof linearSyntenyViewHelperModelFactory>;
 export type LinearSyntenyViewHelperModel = Instance<LinearSyntenyViewHelperStateModel>;

package/esm/LinearSyntenyViewHelper/stateModelFactory.js

@@ -1,6 +1,6 @@
+import { hideTrackGeneric, showTrackGeneric, toggleTrackGeneric, } from '@jbrowse/core/util/tracks';
 import { ElementId } from '@jbrowse/core/util/types/mst';
-import { transaction } from 'mobx';
-import { getParent, getRoot, resolveIdentifier, types } from 'mobx-state-tree';
+import { getParent, types } from '@jbrowse/mobx-state-tree';
 export function linearSyntenyViewHelperModelFactory(pluginManager) {
     return types
         .model('LinearSyntenyViewHelper', {
@@ -16,51 +16,13 @@ export function linearSyntenyViewHelperModelFactory(pluginManager) {
             return self.height;
         },
         showTrack(trackId, initialSnapshot = {}) {
-            const schema = pluginManager.pluggableConfigSchemaType('track');
-            const configuration = resolveIdentifier(schema, getRoot(self), trackId);
-            if (!configuration) {
-                throw new Error(`track not found ${trackId}`);
-            }
-            const trackType = pluginManager.getTrackType(configuration.type);
-            if (!trackType) {
-                throw new Error(`unknown track type ${configuration.type}`);
-            }
-            const viewType = pluginManager.getViewType(self.type);
-            const supportedDisplays = new Set(viewType.displayTypes.map(d => d.name));
-            const displayConf = configuration.displays.find((d) => supportedDisplays.has(d.type));
-            if (!displayConf) {
-                throw new Error(`could not find a compatible display for view type ${self.type}`);
-            }
-            self.tracks.push(trackType.stateModel.create({
-                ...initialSnapshot,
-                type: configuration.type,
-                configuration,
-                displays: [
-                    {
-                        type: displayConf.type,
-                        configuration: displayConf,
-                    },
-                ],
-            }));
+            return showTrackGeneric(self, trackId, initialSnapshot);
         },
         hideTrack(trackId) {
-            const schema = pluginManager.pluggableConfigSchemaType('track');
-            const config = resolveIdentifier(schema, getRoot(self), trackId);
-            const shownTracks = self.tracks.filter(t => t.configuration === config);
-            transaction(() => {
-                for (const t of shownTracks) {
-                    self.tracks.remove(t);
-                }
-            });
-            return shownTracks.length;
+            return hideTrackGeneric(self, trackId);
         },
         toggleTrack(trackId) {
-            const hiddenCount = this.hideTrack(trackId);
-            if (!hiddenCount) {
-                this.showTrack(trackId);
-                return true;
-            }
-            return false;
+            toggleTrackGeneric(self, trackId);
         },
     }))
         .views(self => ({

package/esm/SyntenyFeatureDetail/Formatter.js

@@ -1,11 +1,11 @@
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { useState } from 'react';
-import copy from 'copy-to-clipboard';
 export default function Formatter({ value }) {
     const [show, setShow] = useState(false);
     const [copied, setCopied] = useState(false);
     const display = String(value);
-    return display.length > 100 ? (_jsxs(_Fragment, { children: [_jsx("button", { type: "button", onClick: () => {
+    return display.length > 100 ? (_jsxs(_Fragment, { children: [_jsx("button", { type: "button", onClick: async () => {
+                    const { default: copy } = await import('copy-to-clipboard');
                     copy(display);
                     setCopied(true);
                     setTimeout(() => {

package/esm/SyntenyFeatureDetail/LinkToSyntenyView.d.ts

@@ -1,4 +1,4 @@
-import type { SyntenyFeatureDetailModel } from './types';
+import type { SyntenyFeatureDetailModel } from './types.ts';
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 declare const LinkToSyntenyView: ({ model, feat, }: {
     model: SyntenyFeatureDetailModel;

package/esm/SyntenyFeatureDetail/LinkToSyntenyView.js

@@ -3,16 +3,15 @@ import { lazy } from 'react';
 import { SimpleFeature, assembleLocString, getSession, } from '@jbrowse/core/util';
 import { Link } from '@mui/material';
 import { observer } from 'mobx-react';
-const LaunchSyntenyViewDialog = lazy(() => import('../LGVSyntenyDisplay/components/LaunchSyntenyViewDialog'));
-const LinkToSyntenyView = observer(function ({ model, feat, }) {
+const LaunchSyntenyViewDialog = lazy(() => import("../LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js"));
+const LinkToSyntenyView = observer(function LinkToSyntenyView({ model, feat, }) {
     const { view, level, trackId } = model;
     return (_jsxs("ul", { children: [view.type === 'LinearSyntenyView' ? (_jsx("li", { children: _jsx(Link, { href: "#", onClick: event => {
-                        var _a, _b;
                         event.preventDefault();
                         const { views } = view;
                         if (level !== undefined) {
-                            (_a = views[level]) === null || _a === void 0 ? void 0 : _a.navTo(feat);
-                            (_b = views[level + 1]) === null || _b === void 0 ? void 0 : _b.navTo(feat.mate);
+                            views[level]?.navTo(feat);
+                            views[level + 1]?.navTo(feat.mate);
                         }
                         else {
                             const f1 = feat;
@@ -31,8 +30,8 @@ const LinkToSyntenyView = observer(function ({ model, feat, }) {
                                         : '',
                                 ].join(' ... '));
                             }
-                            v1 === null || v1 === void 0 ? void 0 : v1.navTo(f1);
-                            v2 === null || v2 === void 0 ? void 0 : v2.navTo(f2);
+                            v1?.navTo(f1);
+                            v2?.navTo(f2);
                         }
                     }, children: "Center view on this feature" }) })) : null, _jsx("li", { children: _jsx(Link, { href: "#", onClick: event => {
                         event.preventDefault();

package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts

@@ -1,4 +1,4 @@
-import type { SyntenyFeatureDetailModel } from './types';
+import type { SyntenyFeatureDetailModel } from './types.ts';
 declare const SyntenyFeatureDetail: (props: {
     model: SyntenyFeatureDetailModel;
 }) => import("react/jsx-runtime").JSX.Element;

package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.js

@@ -3,9 +3,9 @@ import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard
 import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
-import Formatter from './Formatter';
-import LinkToSyntenyView from './LinkToSyntenyView';
-const SyntenyFeatureDetail = observer(function (props) {
+import Formatter from "./Formatter.js";
+import LinkToSyntenyView from "./LinkToSyntenyView.js";
+const SyntenyFeatureDetail = observer(function SyntenyFeatureDetail(props) {
     const { model } = props;
     const { featureData } = model;
     const feat = structuredClone(featureData);

package/esm/SyntenyFeatureDetail/index.js

@@ -2,7 +2,7 @@ import { lazy } from 'react';
 import { stateModelFactory as BaseFeatureWidgetStateModelF } from '@jbrowse/core/BaseFeatureWidget';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
-import { types } from 'mobx-state-tree';
+import { types } from '@jbrowse/mobx-state-tree';
 const configSchema = ConfigurationSchema('SyntenyFeatureWidget', {});
 function stateModelF(pluginManager) {
     return types.compose(BaseFeatureWidgetStateModelF(pluginManager), types.model('SyntenyFeatureWidget', {
@@ -16,6 +16,6 @@ export default function SyntenyFeatureWidgetF(pluginManager) {
         heading: 'Synteny feature details',
         configSchema,
         stateModel: stateModelF(pluginManager),
-        ReactComponent: lazy(() => import('./SyntenyFeatureDetail')),
+        ReactComponent: lazy(() => import("./SyntenyFeatureDetail.js")),
     }));
 }

package/esm/SyntenyTrack/configSchema.d.ts

@@ -1,5 +1,5 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const configSchema: (pluginManager: PluginManager) => import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         description: string;
         type: string;
@@ -25,8 +25,13 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
         description: string;
         defaultValue: {};
     };
-    adapter: import("mobx-state-tree").IAnyModelType;
-    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    rpcDriverName: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    textSearching: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         indexingAttributes: {
             type: string;
             description: string;
@@ -37,10 +42,10 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
             description: string;
             defaultValue: string[];
         };
-        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        textSearchAdapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    formatDetails: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         feature: {
             type: string;
             description: string;
@@ -63,8 +68,8 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
             defaultValue: number;
             description: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         config: {
             type: string;
             description: string;
@@ -75,6 +80,6 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
             type: string;
             defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
 export default configSchema;

package/esm/SyntenyTrack/index.js

@@ -1,6 +1,6 @@
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
 import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
-import configSchemaF from './configSchema';
+import configSchemaF from "./configSchema.js";
 export default function registerSyntenyTrack(pluginManager) {
     pluginManager.addTrackType(() => {
         const configSchema = configSchemaF(pluginManager);

package/esm/index.d.ts

@@ -1,5 +1,7 @@
 import Plugin from '@jbrowse/core/Plugin';
 import type PluginManager from '@jbrowse/core/PluginManager';
+export type { LinearSyntenyImportFormSyntenyOption } from './LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelectorArea.tsx';
+export type { LinearSyntenyViewModel } from './LinearSyntenyView/model.ts';
 export default class LinearComparativeViewPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,21 +1,18 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { isAbstractMenuManager } from '@jbrowse/core/util';
 import CalendarIcon from '@mui/icons-material/CalendarViewDay';
-import LGVSyntenyDisplayF from './LGVSyntenyDisplay';
-import LaunchLinearSyntenyViewF from './LaunchLinearSyntenyView';
-import LinearComparativeDisplayF from './LinearComparativeDisplay';
-import LinearComparativeViewF from './LinearComparativeView';
-import LinearReadVsRefMenuItemF from './LinearReadVsRef';
-import LinearSyntenyDisplayF from './LinearSyntenyDisplay';
-import LinearSyntenyViewF from './LinearSyntenyView';
-import LinearSyntenyViewHelperF from './LinearSyntenyViewHelper';
-import SyntenyFeatureWidgetF from './SyntenyFeatureDetail';
-import SyntenyTrackF from './SyntenyTrack';
+import LGVSyntenyDisplayF from "./LGVSyntenyDisplay/index.js";
+import LaunchLinearSyntenyViewF from "./LaunchLinearSyntenyView.js";
+import LinearComparativeDisplayF from "./LinearComparativeDisplay/index.js";
+import LinearComparativeViewF from "./LinearComparativeView/index.js";
+import LinearReadVsRefMenuItemF from "./LinearReadVsRef/index.js";
+import LinearSyntenyDisplayF from "./LinearSyntenyDisplay/index.js";
+import LinearSyntenyViewF from "./LinearSyntenyView/index.js";
+import LinearSyntenyViewHelperF from "./LinearSyntenyViewHelper/index.js";
+import SyntenyFeatureWidgetF from "./SyntenyFeatureDetail/index.js";
+import SyntenyTrackF from "./SyntenyTrack/index.js";
 export default class LinearComparativeViewPlugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'LinearComparativeViewPlugin';
-    }
+    name = 'LinearComparativeViewPlugin';
     install(pluginManager) {
         LinearSyntenyViewHelperF(pluginManager);
         LinearComparativeViewF(pluginManager);