@jbrowse/plugin-linear-comparative-view 2.15.4 → 2.16.1

package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts

@@ -0,0 +1,14 @@
+import React from 'react';
+import { SimpleFeatureSerialized } from '@jbrowse/core/util';
+interface SyntenyFeatureDetailModel {
+    trackId: string;
+    featureData: SimpleFeatureSerialized;
+    level?: number;
+    view: {
+        type: string;
+    };
+}
+declare const SyntenyFeatureDetail: ({ model, }: {
+    model: SyntenyFeatureDetailModel;
+}) => React.JSX.Element;
+export default SyntenyFeatureDetail;

package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.js

@@ -0,0 +1,100 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+// locals
+const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
+const BaseFeatureDetail_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail"));
+const util_1 = require("@jbrowse/core/util");
+// lazies
+const LaunchSyntenyViewDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../LGVSyntenyDisplay/components/LaunchSyntenyViewDialog'))));
+const CustomLinker = (0, mobx_react_1.observer)(function ({ model, }) {
+    const { featureData, view, level, trackId } = model;
+    return (react_1.default.createElement("ul", null,
+        view.type === 'LinearSyntenyView' ? (react_1.default.createElement("li", null,
+            react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
+                    var _a, _b;
+                    event.preventDefault();
+                    const { views } = view;
+                    if (level !== undefined) {
+                        // level is "pre-known", and stored in the SyntenyFeatureWidget
+                        // model state e.g. when clicking on a feature from a
+                        // LinearSyntenyRendering
+                        (_a = views[level]) === null || _a === void 0 ? void 0 : _a.navTo(featureData);
+                        (_b = views[level + 1]) === null || _b === void 0 ? void 0 : _b.navTo(featureData.mate);
+                    }
+                    else {
+                        // best effort to find the right level. this is triggered for
+                        // example if a user clicks on a feature in a LGVSyntenyDisplay
+                        // in an existing LinearSyntenyView, there is no real proper
+                        // level "pre-known" to this situation
+                        const f1 = featureData;
+                        const f2 = featureData.mate;
+                        const r1 = f1.assemblyName;
+                        const r2 = f2.assemblyName;
+                        const v1 = views.find(view => view.assemblyNames[0] === r1);
+                        const v2 = views.find(view => view.assemblyNames[0] === r2);
+                        if (!v1 || !v2) {
+                            (0, util_1.getSession)(model).notify([
+                                v1
+                                    ? `Unable to find ${(0, util_1.assembleLocString)(f1)} in synteny view`
+                                    : '',
+                                v2
+                                    ? `Unable to find ${(0, util_1.assembleLocString)(f2)} in synteny view`
+                                    : '',
+                            ].join(' ... '));
+                        }
+                        v1 === null || v1 === void 0 ? void 0 : v1.navTo(f1);
+                        v2 === null || v2 === void 0 ? void 0 : v2.navTo(f2);
+                    }
+                } }, "Center view on this feature"))) : null,
+        react_1.default.createElement("li", null,
+            react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
+                    event.preventDefault();
+                    const session = (0, util_1.getSession)(model);
+                    const feature = new util_1.SimpleFeature(featureData);
+                    session.queueDialog(handleClose => [
+                        LaunchSyntenyViewDialog,
+                        {
+                            model,
+                            feature,
+                            trackId,
+                            handleClose,
+                        },
+                    ]);
+                } }, "Launch new linear synteny view on this feature"))));
+});
+const SyntenyFeatureDetail = (0, mobx_react_1.observer)(function ({ model, }) {
+    return (react_1.default.createElement(material_1.Paper, { "data-testid": "alignment-side-drawer" },
+        react_1.default.createElement(BaseFeatureDetail_1.default, { title: "Feature", model: model }),
+        react_1.default.createElement(BaseCard_1.default, { title: "Link to view" },
+            react_1.default.createElement(CustomLinker, { model: model }))));
+});
+exports.default = SyntenyFeatureDetail;

package/dist/SyntenyFeatureDetail/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function SyntenyFeatureWidgetF(pluginManager: PluginManager): void;

package/dist/SyntenyFeatureDetail/index.js

@@ -0,0 +1,56 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SyntenyFeatureWidgetF;
+const react_1 = require("react");
+const configuration_1 = require("@jbrowse/core/configuration");
+const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
+const mobx_state_tree_1 = require("mobx-state-tree");
+const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
+const configSchema = (0, configuration_1.ConfigurationSchema)('SyntenyFeatureWidget', {});
+function stateModelF(pluginManager) {
+    return mobx_state_tree_1.types.compose((0, BaseFeatureWidget_1.stateModelFactory)(pluginManager), mobx_state_tree_1.types.model('SyntenyFeatureWidget', {
+        /**
+         * #property
+         */
+        type: mobx_state_tree_1.types.literal('SyntenyFeatureWidget'),
+        /**
+         * #property
+         */
+        level: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
+    }));
+}
+function SyntenyFeatureWidgetF(pluginManager) {
+    pluginManager.addWidgetType(() => new WidgetType_1.default({
+        name: 'SyntenyFeatureWidget',
+        heading: 'Synteny feature details',
+        configSchema,
+        stateModel: stateModelF(pluginManager),
+        ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SyntenyFeatureDetail')))),
+    }));
+}

package/dist/index.js

@@ -11,19 +11,23 @@ const LinearComparativeView_1 = __importDefault(require("./LinearComparativeView
 const LinearSyntenyDisplay_1 = __importDefault(require("./LinearSyntenyDisplay"));
 const LGVSyntenyDisplay_1 = __importDefault(require("./LGVSyntenyDisplay"));
 const LinearSyntenyView_1 = __importDefault(require("./LinearSyntenyView"));
+const LinearSyntenyViewHelper_1 = __importDefault(require("./LinearSyntenyViewHelper"));
 const LaunchLinearSyntenyView_1 = __importDefault(require("./LaunchLinearSyntenyView"));
 const SyntenyTrack_1 = __importDefault(require("./SyntenyTrack"));
 const LinearReadVsRef_1 = __importDefault(require("./LinearReadVsRef"));
+const SyntenyFeatureDetail_1 = __importDefault(require("./SyntenyFeatureDetail"));
 class LinearComparativeViewPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
         this.name = 'LinearComparativeViewPlugin';
     }
     install(pluginManager) {
+        (0, LinearSyntenyViewHelper_1.default)(pluginManager);
         (0, LinearComparativeView_1.default)(pluginManager);
         (0, LinearSyntenyView_1.default)(pluginManager);
         (0, LinearComparativeDisplay_1.default)(pluginManager);
         (0, LinearSyntenyDisplay_1.default)(pluginManager);
+        (0, SyntenyFeatureDetail_1.default)(pluginManager);
         (0, LGVSyntenyDisplay_1.default)(pluginManager);
         (0, LaunchLinearSyntenyView_1.default)(pluginManager);
         (0, SyntenyTrack_1.default)(pluginManager);

package/esm/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.d.ts

@@ -1,7 +1,8 @@
 import React from 'react';
 import { Feature } from '@jbrowse/core/util';
-export default function LaunchSyntenyViewDialog({ model, feature, handleClose, }: {
+export default function LaunchSyntenyViewDialog({ model, feature, trackId, handleClose, }: {
     model: unknown;
     feature: Feature;
+    trackId: string;
     handleClose: () => void;
 }): React.JSX.Element;

package/esm/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js

@@ -2,15 +2,16 @@ import React, { useState } from 'react';
 import { Dialog } from '@jbrowse/core/ui';
 import { getSession } from '@jbrowse/core/util';
 import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, TextField, } from '@mui/material';
-import { navToSynteny } from './util';
 import { makeStyles } from 'tss-react/mui';
+// locals
+import { navToSynteny } from './util';
 const useStyles = makeStyles()({
     padding: {
         margin: 10,
         border: '1px solid #ccc',
     },
 });
-export default function LaunchSyntenyViewDialog({ model, feature, handleClose, }) {
+export default function LaunchSyntenyViewDialog({ model, feature, trackId, handleClose, }) {
     const { classes } = useStyles();
     const inverted = feature.get('strand') === -1;
     const [horizontallyFlip, setHorizontallyFlip] = useState(inverted);
@@ -33,6 +34,7 @@ export default function LaunchSyntenyViewDialog({ model, feature, handleClose, }
                                 feature,
                                 windowSize: +windowSize,
                                 horizontallyFlip,
+                                trackId,
                                 model,
                             });
                         }

package/esm/LGVSyntenyDisplay/components/util.d.ts

@@ -1,8 +1,11 @@
 import { Feature } from '@jbrowse/core/util';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
-export declare function navToSynteny({ feature, windowSize: ws, model, horizontallyFlip, }: {
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+export declare function navToSynteny({ feature, windowSize: ws, model, trackId, view, horizontallyFlip, }: {
     windowSize: number;
+    trackId: string;
     horizontallyFlip: boolean;
     feature: Feature;
+    view?: LinearGenomeViewModel;
     model: IAnyStateTreeNode;
 }): Promise<void>;

package/esm/LGVSyntenyDisplay/components/util.js

@@ -1,4 +1,4 @@
-import { getSession, getContainingTrack, getContainingView, } from '@jbrowse/core/util';
+import { getSession } from '@jbrowse/core/util';
 import { MismatchParser } from '@jbrowse/plugin-alignments';
 const { parseCigar } = MismatchParser;
 function f(n) {
@@ -27,18 +27,13 @@ function findPosInCigar(cigar, startX) {
     }
     return [featX, mateX];
 }
-export async function navToSynteny({ feature, windowSize: ws, model, horizontallyFlip, }) {
+export async function navToSynteny({ feature, windowSize: ws, model, trackId, view, horizontallyFlip, }) {
     const session = getSession(model);
-    const track = getContainingTrack(model);
-    const view = getContainingView(model);
-    const reg = view.dynamicBlocks.contentBlocks[0];
-    if (!reg) {
-        throw new Error('no visible region');
-    }
+    const reg = view === null || view === void 0 ? void 0 : view.dynamicBlocks.contentBlocks[0];
     const cigar = feature.get('CIGAR');
     const strand = feature.get('strand');
-    const regStart = reg.start;
-    const regEnd = reg.end;
+    const featRef = feature.get('refName');
+    const featAsm = feature.get('assemblyName');
     const featStart = feature.get('start');
     const featEnd = feature.get('end');
     const mate = feature.get('mate');
@@ -46,13 +41,13 @@ export async function navToSynteny({ feature, windowSize: ws, model, horizontall
     const mateEnd = mate.end;
     const mateAsm = mate.assemblyName;
     const mateRef = mate.refName;
-    const featAsm = reg.assemblyName;
-    const featRef = reg.refName;
     let rMateStart;
     let rMateEnd;
     let rFeatStart;
     let rFeatEnd;
-    if (cigar) {
+    if (reg && cigar) {
+        const regStart = reg.start;
+        const regEnd = reg.end;
         const p = parseCigar(cigar);
         const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart);
         const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart);
@@ -69,17 +64,14 @@ export async function navToSynteny({ feature, windowSize: ws, model, horizontall
         rMateStart = mateStart;
         rMateEnd = mateEnd;
     }
-    const trackId = track.configuration.trackId;
     const view2 = session.addView('LinearSyntenyView', {
         type: 'LinearSyntenyView',
         views: [
             {
-                id: `${Math.random()}`,
                 type: 'LinearGenomeView',
                 hideHeader: true,
             },
             {
-                id: `${Math.random()}`,
                 type: 'LinearGenomeView',
                 hideHeader: true,
             },

package/esm/LGVSyntenyDisplay/model.d.ts

@@ -1,4 +1,5 @@
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import { Feature } from '@jbrowse/core/util';
 /**
  * #stateModel LGVSyntenyDisplay
  * displays location of "synteny" feature in a plain LGV, allowing linking out
@@ -10,7 +11,14 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 declare function stateModelFactory(schema: 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>>;
+    rpcDriverName: import("mobx-state-tree" /**
+     * #stateModel LGVSyntenyDisplay
+     * displays location of "synteny" feature in a plain LGV, allowing linking out
+     * to external synteny views
+     *
+     * extends
+     * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
+     */).IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
@@ -38,7 +46,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         renderInProgress: AbortController | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
-        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+        features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
         error: unknown;
@@ -63,7 +71,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: React.ReactElement;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
+            features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
@@ -223,7 +231,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
-    contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
+    contextMenuFeature: undefined | Feature;
 } & {
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -233,19 +241,19 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
 } & {
-    readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
-    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
+    readonly featureUnderMouse: Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
-    navToFeature(feature: import("@jbrowse/core/util").Feature): void;
+    selectFeature(feature: Feature): void;
+    navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
-    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
+    setContextMenuFeature(feature?: Feature): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -257,7 +265,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
-    featureUnderMouseVolatile: undefined | import("@jbrowse/core/util").Feature;
+    featureUnderMouseVolatile: undefined | Feature;
     tagsReady: boolean;
 } & {
     readonly autorunReady: boolean;
@@ -272,9 +280,9 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         extra?: import("@jbrowse/plugin-alignments/src/shared/color").ExtraColorBy;
     }): void;
     updateColorTagMap(uniqueTag: string[]): void;
-    setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
-    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
+    setFeatureUnderMouse(feat?: Feature): void;
+    selectFeature(feature: Feature): void;
+    copyFeatureToClipboard(feature: Feature): void;
     setConfig(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
     setFilterBy(filter: import("@jbrowse/plugin-alignments/src/shared").IFilter): void;
     setJexlFilters(filters: string[]): void;
@@ -293,7 +301,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
 } & {
     readonly maxHeight: any;
     readonly featureHeightSetting: any;
-    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly featureUnderMouse: Feature | undefined;
     renderReady(): boolean;
     readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
 } & {
@@ -352,6 +360,10 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         }[];
     })[];
 } & {
+    /**
+     * #action
+     */
+    selectFeature(feature: Feature): void;
     afterCreate(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default stateModelFactory;

package/esm/LGVSyntenyDisplay/model.js

@@ -1,6 +1,6 @@
 import { lazy } from 'react';
-import { ConfigurationReference, } from '@jbrowse/core/configuration';
-import { getSession } from '@jbrowse/core/util';
+import { ConfigurationReference, getConf, } from '@jbrowse/core/configuration';
+import { getContainingTrack, getContainingView, getSession, isSessionModelWithWidgets, } from '@jbrowse/core/util';
 import { SharedLinearPileupDisplayMixin } from '@jbrowse/plugin-alignments';
 import { types } from 'mobx-state-tree';
 const LaunchSyntenyViewDialog = lazy(() => import('./components/LaunchSyntenyViewDialog'));
@@ -37,12 +37,13 @@ function stateModelFactory(schema) {
                     ...(feature
                         ? [
                             {
-                                label: 'Open synteny view for this position',
+                                label: 'Launch synteny view for this position',
                                 onClick: () => {
                                     getSession(self).queueDialog(handleClose => [
                                         LaunchSyntenyViewDialog,
                                         {
                                             model: self,
+                                            trackId: getConf(getContainingTrack(self), 'trackId'),
                                             handleClose,
                                             feature,
                                         },
@@ -73,6 +74,27 @@ function stateModelFactory(schema) {
         };
     })
         .actions(self => ({
+        /**
+         * #action
+         */
+        selectFeature(feature) {
+            const session = getSession(self);
+            if (isSessionModelWithWidgets(session)) {
+                const r2 = getContainingView(self);
+                let r3 = r2;
+                try {
+                    r3 = getContainingView(r3);
+                }
+                catch (e) { }
+                const featureWidget = session.addWidget('SyntenyFeatureWidget', 'syntenyFeature', {
+                    featureData: feature.toJSON(),
+                    view: r3,
+                    track: getContainingTrack(self),
+                });
+                session.showWidget(featureWidget);
+            }
+            session.setSelection(feature);
+        },
         afterCreate() {
             // use color by stand to help indicate inversions better on first load,
             // otherwise use selected orientation

package/esm/LaunchLinearSyntenyView.js

@@ -1,4 +1,8 @@
+import { notEmpty } from '@jbrowse/core/util';
 import { when } from 'mobx';
+function makeMultiDimArray(str) {
+    return Array.isArray(str[0]) ? str : [str];
+}
 export default function LaunchLinearSyntenyView(pluginManager) {
     pluginManager.addToExtensionPoint('LaunchView-LinearSyntenyView', 
     // @ts-expect-error
@@ -21,7 +25,7 @@ export default function LaunchLinearSyntenyView(pluginManager) {
                 };
             })));
             await Promise.all(model.views.map(view => when(() => view.initialized)));
-            const idsNotFound = [];
+            let idsNotFound = [];
             await Promise.all(views.map(async (data, idx) => {
                 const view = model.views[idx];
                 const { assembly, loc, tracks = [] } = data;
@@ -30,14 +34,23 @@ export default function LaunchLinearSyntenyView(pluginManager) {
                     throw new Error(`Assembly ${data.assembly} failed to load`);
                 }
                 await view.navToSearchString({ input: loc, assembly: asm });
-                tracks.forEach(track => {
-                    tryTrack(view, track, idsNotFound);
-                });
+                idsNotFound = [
+                    ...idsNotFound,
+                    ...tracks.map(trackId => tryTrackLGV({
+                        model: view,
+                        trackId,
+                    })),
+                ];
             }));
-            tracks.forEach(track => {
-                tryTrack(model, track, idsNotFound);
-            });
-            if (idsNotFound.length) {
+            idsNotFound = [
+                ...idsNotFound,
+                ...makeMultiDimArray(tracks).flatMap((trackSet, level) => trackSet.map(trackId => tryTrackSynteny({
+                    model,
+                    trackId,
+                    level,
+                }))),
+            ];
+            if (idsNotFound.filter(notEmpty).length) {
                 throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
             }
         }
@@ -47,16 +60,33 @@ export default function LaunchLinearSyntenyView(pluginManager) {
         }
     });
 }
-function tryTrack(model, trackId, idsNotFound) {
+function tryTrackLGV({ model, trackId, }) {
     try {
         model.showTrack(trackId);
     }
     catch (e) {
-        if (/Could not resolve identifier/.exec(`${e}`)) {
-            idsNotFound.push(trackId);
+        if (/Could not resolve identifier/.exec(`${e}`) ||
+            /track not found/.exec(`${e}`)) {
+            return trackId;
+        }
+        else {
+            throw e;
+        }
+    }
+    return undefined;
+}
+function tryTrackSynteny({ model, trackId, level, }) {
+    try {
+        model.showTrack(trackId, level);
+    }
+    catch (e) {
+        if (/Could not resolve identifier/.exec(`${e}`) ||
+            /track not found/.exec(`${e}`)) {
+            return trackId;
         }
         else {
             throw e;
         }
     }
+    return undefined;
 }