@jbrowse/plugin-linear-comparative-view 2.16.1 → 2.18.0

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Feature } from '@jbrowse/core/util';
+import type { Feature } from '@jbrowse/core/util';
 export default function LaunchSyntenyViewDialog({ model, feature, trackId, handleClose, }: {
     model: unknown;
     feature: Feature;

package/dist/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js

@@ -29,7 +29,6 @@ const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
-// locals
 const util_2 = require("./util");
 const useStyles = (0, mui_1.makeStyles)()({
     padding: {
@@ -52,7 +51,6 @@ function LaunchSyntenyViewDialog({ model, feature, trackId, handleClose, }) {
                 } })),
         react_1.default.createElement(material_1.DialogActions, null,
             react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
                     ;
                     (async () => {
                         try {

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

@@ -1,6 +1,6 @@
-import { Feature } from '@jbrowse/core/util';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import type { Feature } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import type { IAnyStateTreeNode } from 'mobx-state-tree';
 export declare function navToSynteny({ feature, windowSize: ws, model, trackId, view, horizontallyFlip, }: {
     windowSize: number;
     trackId: string;

package/dist/LGVSyntenyDisplay/components/util.js

@@ -54,7 +54,6 @@ async function navToSynteny({ feature, windowSize: ws, model, trackId, view, hor
         const p = parseCigar(cigar);
         const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart);
         const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart);
-        // avoid multiply by 0 with strand undefined
         const flipper = strand === -1 ? -1 : 1;
         rFeatStart = featStart + fStartX;
         rFeatEnd = featStart + fEndX;

package/dist/LGVSyntenyDisplay/configSchemaF.d.ts

@@ -1,10 +1,10 @@
-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<{
+import type PluginManager from '@jbrowse/core/PluginManager';
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    mouseover: {
+        type: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     defaultRendering: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
@@ -18,11 +18,20 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
         description: string;
         defaultValue: number;
     };
-    colorScheme: {
+    colorBy: {
         type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
-        defaultValue: string;
+        defaultValue: {
+            type: string;
+        };
+    };
+    filterBy: {
+        type: string;
+        description: string;
+        defaultValue: {
+            flagInclude: number;
+            flagExclude: number;
+        };
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     renderer: import("mobx-state-tree").IAnyModelType;

package/dist/LGVSyntenyDisplay/configSchemaF.js

@@ -2,16 +2,19 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
-/**
- * #config LGVSyntenyDisplay
- * extends config
- * - [LinearPileupDisplay](../linearpileupdisplay)
- */
 function configSchemaF(pluginManager) {
-    return (0, configuration_1.ConfigurationSchema)('LGVSyntenyDisplay', {}, {
-        /**
-         * #baseConfiguration
-         */
+    pluginManager.jexl.addFunction('lgvSyntenyTooltip', (f) => {
+        const m = f.get('mate');
+        return [f.get('name') || f.get('id'), (m === null || m === void 0 ? void 0 : m.name) || (m === null || m === void 0 ? void 0 : m.id)]
+            .filter(f => !!f)
+            .join('<br/>');
+    });
+    return (0, configuration_1.ConfigurationSchema)('LGVSyntenyDisplay', {
+        mouseover: {
+            type: 'string',
+            defaultValue: 'jexl:lgvSyntenyTooltip(feature)',
+        },
+    }, {
         baseConfiguration: (0, plugin_alignments_1.linearPileupDisplayConfigSchemaFactory)(pluginManager),
         explicitlyTyped: true,
     });

package/dist/LGVSyntenyDisplay/index.d.ts

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

package/dist/LGVSyntenyDisplay/index.js

@@ -5,9 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LGVSyntenyDisplayF;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const configSchemaF_1 = __importDefault(require("./configSchemaF"));
 const model_1 = __importDefault(require("./model"));
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 function LGVSyntenyDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchemaF_1.default)(pluginManager);

package/dist/LGVSyntenyDisplay/model.d.ts

@@ -1,24 +1,9 @@
-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
- * to external synteny views
- *
- * extends
- * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
- */
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 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" /**
-     * #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>>;
+    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
@@ -27,23 +12,12 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree" /**
-             * #property
-             */).IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, Feature> | undefined;
@@ -67,15 +41,9 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -114,29 +82,11 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-        type: import("mobx-state-tree").ISimpleType<string>;
-        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        extra: import("mobx-state-tree").IType<any, any, any>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-        flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-        flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-            tag: import("mobx-state-tree").ISimpleType<string>;
-            value: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    colorBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined>;
+    filterBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined>;
     jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
 } & {
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"LGVSyntenyDisplay">;
-    /**
-     * #property
-     */
     configuration: AnyConfigurationSchemaType;
 }, {
     rendererTypeName: string;
@@ -227,6 +177,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
@@ -267,6 +218,9 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     colorTagMap: import("mobx").ObservableMap<string, string>;
     featureUnderMouseVolatile: undefined | Feature;
     tagsReady: boolean;
+} & {
+    readonly colorBy: any;
+    readonly filterBy: any;
 } & {
     readonly autorunReady: boolean;
 } & {
@@ -274,17 +228,13 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     setMaxHeight(n?: number): void;
     setFeatureHeight(n?: number): void;
     setNoSpacing(flag?: boolean): void;
-    setColorScheme(colorScheme: {
-        type: string;
-        tag?: string;
-        extra?: import("@jbrowse/plugin-alignments/src/shared/color").ExtraColorBy;
-    }): void;
+    setColorScheme(colorScheme: import("@jbrowse/plugin-alignments/src/shared/types").ColorBy): void;
     updateColorTagMap(uniqueTag: string[]): 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;
+    setFilterBy(filter: import("@jbrowse/plugin-alignments/src/shared/types").FilterBy): void;
     setJexlFilters(filters: string[]): void;
 } & {
     readonly rendererConfig: {
@@ -319,12 +269,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     })[];
     readonly DisplayBlurb: ({ model, }: {
         model: {
-            sortedBy?: {
-                pos: number;
-                refName: number;
-                type: string;
-                tag?: string;
-            };
+            sortedBy?: import("@jbrowse/plugin-alignments/src/shared/types").SortedBy;
         };
     }) => import("react").JSX.Element | null;
     renderPropsPre(): any;
@@ -344,14 +289,8 @@ 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: {
@@ -360,10 +299,94 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         }[];
     })[];
 } & {
-    /**
-     * #action
-     */
     selectFeature(feature: Feature): void;
     afterCreate(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, {
+    type: string;
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    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>>;
+} & {
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
+        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        stopToken: string | undefined;
+        filled: boolean;
+        reactElement: React.ReactElement | undefined;
+        features: Map<string, Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: React.ReactNode;
+                filled?: boolean;
+                status?: string;
+                reactElement?: React.ReactElement;
+            };
+        }) => import("react").JSX.Element | undefined;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(newStopToken: string): void;
+        setMessage(messageText: string): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
+} & {
+    configuration: AnyConfigurationSchemaType;
+    featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    colorBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined>;
+    filterBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined>;
+    jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
+}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default stateModelFactory;

package/dist/LGVSyntenyDisplay/model.js

@@ -29,32 +29,15 @@ const util_1 = require("@jbrowse/core/util");
 const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const LaunchSyntenyViewDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/LaunchSyntenyViewDialog'))));
-/**
- * #stateModel LGVSyntenyDisplay
- * displays location of "synteny" feature in a plain LGV, allowing linking out
- * to external synteny views
- *
- * extends
- * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
- */
 function stateModelFactory(schema) {
     return mobx_state_tree_1.types
         .compose('LGVSyntenyDisplay', (0, plugin_alignments_1.SharedLinearPileupDisplayMixin)(schema), mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('LGVSyntenyDisplay'),
-        /**
-         * #property
-         */
         configuration: (0, configuration_1.ConfigurationReference)(schema),
     }))
         .views(self => {
         const superContextMenuItems = self.contextMenuItems;
         return {
-            /**
-             * #method
-             */
             contextMenuItems() {
                 const feature = self.contextMenuFeature;
                 return [
@@ -84,9 +67,6 @@ function stateModelFactory(schema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, colorSchemeSubMenuItems: superColorSchemeSubMenuItems, } = self;
         return {
-            /**
-             * #method
-             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -99,9 +79,6 @@ function stateModelFactory(schema) {
         };
     })
         .actions(self => ({
-        /**
-         * #action
-         */
         selectFeature(feature) {
             const session = (0, util_1.getSession)(self);
             if ((0, util_1.isSessionModelWithWidgets)(session)) {
@@ -121,12 +98,7 @@ function stateModelFactory(schema) {
             session.setSelection(feature);
         },
         afterCreate() {
-            // use color by stand to help indicate inversions better on first load,
-            // otherwise use selected orientation
-            if (self.colorBy) {
-                self.setColorScheme({ ...self.colorBy });
-            }
-            else {
+            if (!self.colorBySetting && self.colorBy.type === 'normal') {
                 self.setColorScheme({ type: 'strand' });
             }
         },

package/dist/LaunchLinearSyntenyView.d.ts

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

package/dist/LaunchLinearSyntenyView.js

@@ -7,9 +7,7 @@ function makeMultiDimArray(str) {
     return Array.isArray(str[0]) ? str : [str];
 }
 function LaunchLinearSyntenyView(pluginManager) {
-    pluginManager.addToExtensionPoint('LaunchView-LinearSyntenyView', 
-    // @ts-expect-error
-    async ({ session, views, tracks = [], }) => {
+    pluginManager.addToExtensionPoint('LaunchView-LinearSyntenyView', async ({ session, views, tracks = [], }) => {
         try {
             const { assemblyManager } = session;
             const model = session.addView('LinearSyntenyView', {});

package/dist/LinearComparativeDisplay/configSchemaF.d.ts

@@ -1,5 +1,2 @@
-/**
- * #config LinearComparativeDisplay
- */
 declare function configSchemaFactory(_pluginManager: any): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 export default configSchemaFactory;

package/dist/LinearComparativeDisplay/configSchemaF.js

@@ -1,15 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config LinearComparativeDisplay
- */
 function configSchemaFactory(_pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('LinearComparativeDisplay', {}, {
         explicitlyTyped: true,
-        /**
-         * #identifier
-         */
         explicitIdentifier: 'displayId',
     });
 }

package/dist/LinearComparativeDisplay/index.d.ts

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