@jbrowse/plugin-linear-comparative-view 2.8.0 → 2.10.0

package/dist/SyntenyTrack/configSchema.js

@@ -4,6 +4,8 @@ const configuration_1 = require("@jbrowse/core/configuration");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 /**
  * #config SyntenyTrack
+ * extends
+ * - [BaseTrack](../basetrack)
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const configSchema = (pluginManager) => (0, configuration_1.ConfigurationSchema)('SyntenyTrack', {}, {

package/esm/LGVSyntenyDisplay/configSchemaF.d.ts

@@ -1,6 +1,8 @@
 import PluginManager from '@jbrowse/core/PluginManager';
 /**
  * #config LGVSyntenyDisplay
+ * extends config
+ * - [LinearPileupDisplay](../linearpileupdisplay)
  */
 declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     defaultRendering: {

package/esm/LGVSyntenyDisplay/configSchemaF.js

@@ -2,6 +2,8 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { linearPileupDisplayConfigSchemaFactory } from '@jbrowse/plugin-alignments';
 /**
  * #config LGVSyntenyDisplay
+ * extends config
+ * - [LinearPileupDisplay](../linearpileupdisplay)
  */
 function configSchemaF(pluginManager) {
     return ConfigurationSchema('LGVSyntenyDisplay', {}, {

package/esm/LGVSyntenyDisplay/model.d.ts

@@ -2,8 +2,11 @@
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 /**
  * #stateModel LGVSyntenyDisplay
- * extends `LinearPileupDisplay`, displays location of "synteny" feature in a
- * plain LGV, allowing linking out to external synteny views
+ * displays location of "synteny" feature in a plain LGV, allowing linking out
+ * to external synteny views
+ *
+ * extends
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
  */
 declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -69,15 +72,15 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         };
         fetchSizeLimit: {
             type: string;
-            defaultValue: number; /**
-             * #property
-             */
+            defaultValue: number;
             description: string;
         };
         height: {
             type: string;
             defaultValue: number;
-            description: string;
+            description: string; /**
+             * #method
+             */
         };
         mouseover: {
             type: string;
@@ -146,7 +149,9 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         model: {
             id: string;
             type: string;
-            rpcDriverName: string | undefined;
+            rpcDriverName: string | undefined; /**
+             * #method
+             */
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
@@ -319,8 +324,14 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
 } & {
     afterAttach(): void;
 } & {
+    /**
+     * #method
+     */
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
 } & {
+    /**
+     * #method
+     */
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
         subMenu: {

package/esm/LGVSyntenyDisplay/model.js

@@ -6,8 +6,11 @@ import { types } from 'mobx-state-tree';
 const LaunchSyntenyViewDialog = lazy(() => import('./components/LaunchSyntenyViewDialog'));
 /**
  * #stateModel LGVSyntenyDisplay
- * extends `LinearPileupDisplay`, displays location of "synteny" feature in a
- * plain LGV, allowing linking out to external synteny views
+ * displays location of "synteny" feature in a plain LGV, allowing linking out
+ * to external synteny views
+ *
+ * extends
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
  */
 function stateModelFactory(schema) {
     return types
@@ -24,6 +27,9 @@ function stateModelFactory(schema) {
         .views(self => {
         const superContextMenuItems = self.contextMenuItems;
         return {
+            /**
+             * #method
+             */
             contextMenuItems() {
                 const feature = self.contextMenuFeature;
                 return [
@@ -52,6 +58,9 @@ function stateModelFactory(schema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, colorSchemeSubMenuItems: superColorSchemeSubMenuItems, } = self;
         return {
+            /**
+             * #method
+             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -65,7 +74,8 @@ function stateModelFactory(schema) {
     })
         .actions(self => ({
         afterCreate() {
-            // use color by stand to help indicate inversions better on first load, otherwise use selected orientation
+            // use color by stand to help indicate inversions better on first load,
+            // otherwise use selected orientation
             if (self.colorBy) {
                 self.setColorScheme({ ...self.colorBy });
             }

package/esm/LaunchLinearSyntenyView.js

@@ -24,8 +24,12 @@ export default function LaunchLinearSyntenyView(pluginManager) {
             const idsNotFound = [];
             await Promise.all(views.map(async (data, idx) => {
                 const view = model.views[idx];
-                const { loc, tracks = [] } = data;
-                await view.navToLocString(loc);
+                const { assembly, loc, tracks = [] } = data;
+                const asm = await assemblyManager.waitForAssembly(assembly);
+                if (!asm) {
+                    throw new Error(`Assembly ${data.assembly} failed to load`);
+                }
+                await view.navToSearchString({ input: loc, assembly: asm });
                 tracks.forEach(track => tryTrack(view, track, idsNotFound));
             }));
             tracks.forEach(track => tryTrack(model, track, idsNotFound));

package/esm/LinearComparativeDisplay/stateModelFactory.d.ts

@@ -4,6 +4,8 @@ import { Instance } from 'mobx-state-tree';
 import { Feature } from '@jbrowse/core/util';
 /**
  * #stateModel LinearComparativeDisplay
+ * extends
+ * - [BaseDisplay](../basedisplay)
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -21,7 +23,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly RenderingComponent: import("react").FC<{
         model: {
             id: string;
-            type: string;
+            type: string; /**
+             * #property
+             */
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
@@ -30,12 +34,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         } & 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>>; /**
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string; /**
              * #action
              * controlled by a reaction
              */
-        }, {
-            rendererTypeName: string;
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -48,10 +52,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string; /**
-             * #action
-             * controlled by a reaction
-             */
+            rendererTypeName: string;
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -67,7 +68,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
-    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType; /**
+     * #action
+     * controlled by a reaction
+     */
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -105,7 +109,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             readonly RenderingComponent: import("react").FC<{
                 model: {
                     id: string;
-                    type: string;
+                    type: string; /**
+                     * #property
+                     */
                     rpcDriverName: string | undefined;
                 } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                     rendererTypeName: string;
@@ -114,12 +120,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                 } & 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>>; /**
+                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string; /**
                      * #action
                      * controlled by a reaction
                      */
-                }, {
-                    rendererTypeName: string;
                     error: unknown;
                     message: string | undefined;
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -132,10 +138,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     type: string;
                     rpcDriverName: string | undefined;
                 } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                    rendererTypeName: string; /**
-                     * #action
-                     * controlled by a reaction
-                     */
+                    rendererTypeName: string;
                     error: unknown;
                     message: string | undefined;
                 } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -151,7 +154,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             readonly adapterConfig: any;
             readonly parentTrack: any;
             renderProps(): any;
-            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType; /**
+             * #action
+             * controlled by a reaction
+             */
             readonly DisplayMessageComponent: import("react").FC<any> | undefined;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
             readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -181,7 +187,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             readonly RenderingComponent: import("react").FC<{
                 model: {
                     id: string;
-                    type: string;
+                    type: string; /**
+                     * #property
+                     */
                     rpcDriverName: string | undefined;
                 } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                     rendererTypeName: string;
@@ -190,12 +198,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                 } & 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>>; /**
+                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string; /**
                      * #action
                      * controlled by a reaction
                      */
-                }, {
-                    rendererTypeName: string;
                     error: unknown;
                     message: string | undefined;
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -208,10 +216,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     type: string;
                     rpcDriverName: string | undefined;
                 } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                    rendererTypeName: string; /**
-                     * #action
-                     * controlled by a reaction
-                     */
+                    rendererTypeName: string;
                     error: unknown;
                     message: string | undefined;
                 } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -227,7 +232,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             readonly adapterConfig: any;
             readonly parentTrack: any;
             renderProps(): any;
-            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType; /**
+             * #action
+             * controlled by a reaction
+             */
             readonly DisplayMessageComponent: import("react").FC<any> | undefined;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
             readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];

package/esm/LinearComparativeDisplay/stateModelFactory.js

@@ -5,6 +5,8 @@ import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models';
 /**
  * #stateModel LinearComparativeDisplay
+ * extends
+ * - [BaseDisplay](../basedisplay)
  */
 function stateModelFactory(configSchema) {
     return types

package/esm/LinearComparativeView/model.d.ts

@@ -5,6 +5,8 @@ import PluginManager from '@jbrowse/core/PluginManager';
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 /**
  * #stateModel LinearComparativeView
+ * extends
+ * - [BaseViewModel](../baseviewmodel)
  */
 declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -34,9 +36,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
             end: import("mobx-state-tree").ISimpleType<number>;
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
-            /**
-             * #property
-             */
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
             setRefName(newRefName: string): void;
@@ -64,7 +63,9 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         draggingTrackId: string | undefined;
         volatileError: unknown;
         afterDisplayedRegionsSetCallbacks: Function[];
-        scaleFactor: number;
+        scaleFactor: number; /**
+         * #action
+         */
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
@@ -123,7 +124,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     } & {
         moveTrack(movingId: string, targetId: string): void;
         closeView(): void;
-        toggleTrack(trackId: string): void;
+        toggleTrack(trackId: string): boolean;
         setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
         toggleCenterLine(): void;
         setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -173,6 +174,140 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     } & {
         moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
         navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+        navToSearchString({ input, assembly, }: {
+            input: string;
+            assembly: {
+                configuration: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                error: unknown;
+                loaded: boolean;
+                loadingP: Promise<void> | undefined;
+                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: {
+                    [x: string]: string | undefined;
+                } | undefined;
+                lowerCaseRefNameAliases: {
+                    [x: string]: string | undefined;
+                } | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly initialized: boolean;
+                /**
+                 * #property
+                 */
+                readonly name: string;
+                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                readonly aliases: string[];
+                readonly displayName: string | undefined;
+                hasName(name: string): boolean;
+                readonly allAliases: string[];
+                readonly allRefNames: string[] | undefined;
+                readonly lowerCaseRefNames: string[] | undefined;
+                readonly allRefNamesWithLowerCase: string[] | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+                readonly refNameColors: string[];
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                isValidRefName(refName: string): boolean;
+            } & {
+                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
+                setError(e: unknown): void;
+                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
+                setRefNameAliases(aliases: {
+                    [x: string]: string | undefined;
+                }, lcAliases: {
+                    [x: string]: string | undefined;
+                }): void;
+                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setLoadingP(p?: Promise<void> | undefined): void;
+                load(): Promise<void>;
+                loadPre(): Promise<void>;
+            } & {
+                getAdapterMapEntry(adapterConf: {
+                    [x: string]: unknown;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                    [x: string]: string | undefined;
+                }>;
+                getReverseRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                    [x: string]: string | undefined;
+                }>;
+            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+            }, {
+                error: unknown;
+                loaded: boolean;
+                loadingP: Promise<void> | undefined;
+                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: {
+                    [x: string]: string | undefined;
+                } | undefined;
+                lowerCaseRefNameAliases: {
+                    [x: string]: string | undefined;
+                } | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly initialized: boolean;
+                /**
+                 * #property
+                 */
+                readonly name: string;
+                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                readonly aliases: string[];
+                readonly displayName: string | undefined;
+                hasName(name: string): boolean;
+                readonly allAliases: string[];
+                readonly allRefNames: string[] | undefined;
+                readonly lowerCaseRefNames: string[] | undefined;
+                readonly allRefNamesWithLowerCase: string[] | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+                readonly refNameColors: string[];
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                isValidRefName(refName: string): boolean;
+            } & {
+                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
+                setError(e: unknown): void;
+                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
+                setRefNameAliases(aliases: {
+                    [x: string]: string | undefined;
+                }, lcAliases: {
+                    [x: string]: string | undefined;
+                }): void;
+                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setLoadingP(p?: Promise<void> | undefined): void;
+                load(): Promise<void>;
+                loadPre(): Promise<void>;
+            } & {
+                getAdapterMapEntry(adapterConf: {
+                    [x: string]: unknown;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                    [x: string]: string | undefined;
+                }>;
+                getReverseRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                    [x: string]: string | undefined;
+                }>;
+            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }): Promise<void>;
         navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
         navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
         navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
@@ -277,7 +412,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     /**
      * #action
      */
-    toggleTrack(trackId: string): void;
+    toggleTrack(trackId: string): boolean;
     /**
      * #action
      */

package/esm/LinearComparativeView/model.js

@@ -12,6 +12,8 @@ import FolderOpenIcon from '@mui/icons-material/FolderOpen';
 const ReturnToImportFormDialog = lazy(() => import('@jbrowse/core/ui/ReturnToImportFormDialog'));
 /**
  * #stateModel LinearComparativeView
+ * extends
+ * - [BaseViewModel](../baseviewmodel)
  */
 function stateModelFactory(pluginManager) {
     return types
@@ -186,12 +188,12 @@ function stateModelFactory(pluginManager) {
          * #action
          */
         toggleTrack(trackId) {
-            // if we have any tracks with that configuration, turn them off
             const hiddenCount = this.hideTrack(trackId);
-            // if none had that configuration, turn one on
             if (!hiddenCount) {
                 this.showTrack(trackId);
+                return true;
             }
+            return false;
         },
         /**
          * #action

package/esm/LinearReadVsRef/LinearReadVsRef.js

@@ -144,7 +144,7 @@ export default function ReadVsRefDialog({ track, feature: preFeature, handleClos
                             {
                                 start: 0,
                                 end: totalLength,
-                                seq: featSeq || '',
+                                seq: featSeq || '', // can be empty if user clicks secondary read
                                 refName: readName,
                                 uniqueId: `${Math.random()}`,
                             },

package/esm/LinearReadVsRef/index.js

@@ -1,8 +1,9 @@
+import { lazy } from 'react';
 import { getSession, getContainingTrack } from '@jbrowse/core/util';
 // icons
 import AddIcon from '@mui/icons-material/Add';
 // locals
-import ReadVsRefDialog from './LinearReadVsRef';
+const ReadVsRefDialog = lazy(() => import('./LinearReadVsRef'));
 function isDisplay(elt) {
     return elt.name === 'LinearPileupDisplay';
 }