@jbrowse/plugin-linear-comparative-view 2.17.0 → 2.18.0

package/dist/LinearSyntenyView/model.d.ts

@@ -1,7 +1,7 @@
-import React from 'react';
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type React from 'react';
 import { Curves } from './components/Icons';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { Instance } from 'mobx-state-tree';
 export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
     scale?: number;
@@ -18,11 +18,6 @@ export interface ExportSvgOptions {
     themeName?: string;
     trackLabels?: string;
 }
-/**
- * #stateModel LinearSyntenyView
- * extends
- * - [LinearComparativeView](../linearcomparativeview)
- */
 export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -98,6 +93,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
         HeaderComponent(): React.FC<any>;
+        readonly assembliesNotFound: string | undefined;
         readonly assemblyErrors: string;
         readonly assembliesInitialized: boolean;
         readonly initialized: boolean;
@@ -310,29 +306,12 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
 } & {
     afterAttach(): void;
 } & {
-    /**
-     * #action
-     */
     toggleCurves(): void;
-    /**
-     * #action
-     */
     toggleCIGAR(): void;
-    /**
-     * #action
-     */
     showAllRegions(): void;
 } & {
-    /**
-     * #action
-     */
     exportSvg(opts: ExportSvgOptions): Promise<void>;
 } & {
-    /**
-     * #method
-     * includes a subset of view menu options because the full list is a
-     * little overwhelming
-     */
     headerMenuItems(): (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;
         onClick: () => void;
@@ -366,9 +345,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         checked?: undefined;
         type?: undefined;
     })[];
-    /**
-     * #method
-     */
     menuItems(): (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;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
@@ -453,6 +429,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
         HeaderComponent(): React.FC<any>;
+        readonly assembliesNotFound: string | undefined;
         readonly assemblyErrors: string;
         readonly assembliesInitialized: boolean;
         readonly initialized: boolean;

package/dist/LinearSyntenyView/model.js

@@ -28,56 +28,30 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = stateModelFactory;
 const react_1 = require("react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mobx_1 = require("mobx");
 const util_1 = require("@jbrowse/core/util");
-const file_saver_1 = require("file-saver");
-// icons
 const CropFree_1 = __importDefault(require("@mui/icons-material/CropFree"));
-const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
 const PhotoCamera_1 = __importDefault(require("@mui/icons-material/PhotoCamera"));
+const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
+const file_saver_1 = require("file-saver");
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const Icons_1 = require("./components/Icons");
-// locals
 const model_1 = __importDefault(require("../LinearComparativeView/model"));
-// lazies
 const ExportSvgDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ExportSvgDialog'))));
-/**
- * #stateModel LinearSyntenyView
- * extends
- * - [LinearComparativeView](../linearcomparativeview)
- */
 function stateModelFactory(pluginManager) {
     return mobx_state_tree_1.types
         .compose('LinearSyntenyView', (0, model_1.default)(pluginManager), mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('LinearSyntenyView'),
-        /**
-         * #property/
-         */
         drawCIGAR: true,
-        /**
-         * #property
-         */
         drawCurves: false,
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         toggleCurves() {
             self.drawCurves = !self.drawCurves;
         },
-        /**
-         * #action
-         */
         toggleCIGAR() {
             self.drawCIGAR = !self.drawCIGAR;
         },
-        /**
-         * #action
-         */
         showAllRegions() {
             (0, mobx_1.transaction)(() => {
                 for (const view of self.views) {
@@ -87,9 +61,6 @@ function stateModelFactory(pluginManager) {
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         async exportSvg(opts) {
             const { renderToSvg } = await Promise.resolve().then(() => __importStar(require('./svgcomponents/SVGLinearSyntenyView')));
             const html = await renderToSvg(self, opts);
@@ -101,11 +72,6 @@ function stateModelFactory(pluginManager) {
         const superHeaderMenuItems = self.headerMenuItems;
         const superMenuItems = self.menuItems;
         return {
-            /**
-             * #method
-             * includes a subset of view menu options because the full list is a
-             * little overwhelming
-             */
             headerMenuItems() {
                 return [
                     ...superHeaderMenuItems(),
@@ -147,9 +113,6 @@ function stateModelFactory(pluginManager) {
                     },
                 ];
             },
-            /**
-             * #method
-             */
             menuItems() {
                 return [
                     ...superMenuItems(),

package/dist/LinearSyntenyView/svgcomponents/SVGBackground.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SVGBackground;
 const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
 function SVGBackground({ width, height, shift, }) {
     const theme = (0, material_1.useTheme)();
     return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: (0, util_1.stripAlpha)(theme.palette.background.default) }));

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export default function SVGLinearGenomeView({ trackLabelOffset, fontSize, textHeight, trackLabels, view, displayResults, rulerHeight, shift, }: {
     textHeight: number;
     trackLabels: string;

package/dist/LinearSyntenyView/svgcomponents/SVGLinearGenomeView.js

@@ -5,9 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SVGLinearGenomeView;
 const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const material_1 = require("@mui/material");
 function SVGLinearGenomeView({ trackLabelOffset, fontSize, textHeight, trackLabels, view, displayResults, rulerHeight, shift, }) {
     const theme = (0, material_1.useTheme)();
     return (react_1.default.createElement("g", { transform: `translate(${shift} ${fontSize})` },

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

@@ -1,2 +1,2 @@
-import { ExportSvgOptions, LinearSyntenyViewModel } from '../model';
+import type { ExportSvgOptions, LinearSyntenyViewModel } from '../model';
 export declare function renderToSvg(model: LinearSyntenyViewModel, opts: ExportSvgOptions): Promise<string>;

package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -5,18 +5,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderToSvg = renderToSvg;
 const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mobx_1 = require("mobx");
+const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
-const ui_1 = require("@jbrowse/core/ui");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-// locals
+const material_1 = require("@mui/material");
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const SVGBackground_1 = __importDefault(require("./SVGBackground"));
 const SVGLinearGenomeView_1 = __importDefault(require("./SVGLinearGenomeView"));
 const drawSynteny_1 = require("../../LinearSyntenyDisplay/drawSynteny");
-// render LGV to SVG
 async function renderToSvg(model, opts) {
     var _a;
     await (0, mobx_1.when)(() => model.initialized);
@@ -81,14 +79,11 @@ async function renderToSvg(model, opts) {
             levelHeight ? (react_1.default.createElement("defs", null,
                 react_1.default.createElement("clipPath", { id: `synclip-${i}` },
                     react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: levelHeight })))) : null,
-            react_1.default.createElement("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})` }, rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => (
-            /* biome-ignore lint/suspicious/noArrayIndexKey: */
-            react_1.default.createElement(util_1.ReactRendering, { key: i, rendering: r })))),
+            react_1.default.createElement("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})` }, rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => (react_1.default.createElement(util_1.ReactRendering, { key: i, rendering: r })))),
             react_1.default.createElement("g", { transform: `translate(0 ${levelHeight})` },
                 react_1.default.createElement(SVGLinearGenomeView_1.default, { rulerHeight: rulerHeight, shift: shift, trackLabelOffset: trackLabelOffset, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[i], key: view.id, view: view, fontSize: fontSize }))));
         currOffset += height + fontSize + rulerHeight + levelHeight;
     }
-    // the xlink namespace is used for rendering <image> tag
     return (0, util_1.renderToStaticMarkup)(react_1.default.createElement(material_1.ThemeProvider, { theme: theme },
         react_1.default.createElement(Wrapper, null,
             react_1.default.createElement("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() },

package/dist/LinearSyntenyViewHelper/index.d.ts

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

package/dist/LinearSyntenyViewHelper/stateModelFactory.d.ts

@@ -1,5 +1,5 @@
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
+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>;
@@ -7,21 +7,9 @@ export declare function linearSyntenyViewHelperModelFactory(pluginManager: Plugi
     height: import("mobx-state-tree").IType<number | undefined, number, number>;
     level: import("mobx-state-tree").ISimpleType<number>;
 }, {
-    /**
-     * #action
-     */
     setHeight(n: number): number;
-    /**
-     * #action
-     */
     showTrack(trackId: string, initialSnapshot?: {}): void;
-    /**
-     * #action
-     */
     hideTrack(trackId: string): number;
-    /**
-     * #action
-     */
     toggleTrack(trackId: string): boolean;
 } & {
     readonly assemblyNames: (string | undefined)[];

package/dist/LinearSyntenyViewHelper/stateModelFactory.js

@@ -1,44 +1,23 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.linearSyntenyViewHelperModelFactory = linearSyntenyViewHelperModelFactory;
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mobx_1 = require("mobx");
 const mst_1 = require("@jbrowse/core/util/types/mst");
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 function linearSyntenyViewHelperModelFactory(pluginManager) {
     return mobx_state_tree_1.types
         .model('LinearSyntenyViewHelper', {
-        /**
-         * #property
-         */
         id: mst_1.ElementId,
-        /**
-         * #property
-         */
         type: 'LinearSyntenyViewHelper',
-        /**
-         * #property
-         */
         tracks: mobx_state_tree_1.types.array(pluginManager.pluggableMstType('track', 'stateModel')),
-        /**
-         * #property
-         */
         height: 100,
-        /**
-         * #property
-         */
         level: mobx_state_tree_1.types.number,
     })
         .actions(self => ({
-        /**
-         * #action
-         */
         setHeight(n) {
             self.height = n;
             return self.height;
         },
-        /**
-         * #action
-         */
         showTrack(trackId, initialSnapshot = {}) {
             const schema = pluginManager.pluggableConfigSchemaType('track');
             const configuration = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
@@ -67,9 +46,6 @@ function linearSyntenyViewHelperModelFactory(pluginManager) {
                 ],
             }));
         },
-        /**
-         * #action
-         */
         hideTrack(trackId) {
             const schema = pluginManager.pluggableConfigSchemaType('track');
             const config = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
@@ -81,9 +57,6 @@ function linearSyntenyViewHelperModelFactory(pluginManager) {
             });
             return shownTracks.length;
         },
-        /**
-         * #action
-         */
         toggleTrack(trackId) {
             const hiddenCount = this.hideTrack(trackId);
             if (!hiddenCount) {

package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 interface SyntenyFeatureDetailModel {
     trackId: string;
     featureData: SimpleFeatureSerialized;

package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.js

@@ -27,13 +27,11 @@ var __importDefault = (this && this.__importDefault) || function (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 BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 const util_1 = require("@jbrowse/core/util");
-// lazies
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 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;
@@ -44,17 +42,10 @@ const CustomLinker = (0, mobx_react_1.observer)(function ({ model, }) {
                     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;
@@ -92,7 +83,7 @@ const CustomLinker = (0, mobx_react_1.observer)(function ({ model, }) {
                 } }, "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" },
+    return (react_1.default.createElement(material_1.Paper, null,
         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 }))));

package/dist/SyntenyFeatureDetail/index.d.ts

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

package/dist/SyntenyFeatureDetail/index.js

@@ -28,20 +28,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SyntenyFeatureWidgetF;
 const react_1 = require("react");
+const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
 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),
     }));
 }

package/dist/SyntenyTrack/configSchema.d.ts

@@ -1,4 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+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<{
     name: {
         description: string;

package/dist/SyntenyTrack/configSchema.js

@@ -2,16 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 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
+function x() { }
 const configSchema = (pluginManager) => (0, configuration_1.ConfigurationSchema)('SyntenyTrack', {}, {
-    /**
-     * #baseConfiguration
-     */
     baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager),
 });
 exports.default = configSchema;

package/dist/SyntenyTrack/index.d.ts

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

package/dist/SyntenyTrack/index.js

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = registerSyntenyTrack;
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const configSchema_1 = __importDefault(require("./configSchema"));
 function registerSyntenyTrack(pluginManager) {
     pluginManager.addTrackType(() => {

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class LinearComparativeViewPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -6,16 +6,16 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const util_1 = require("@jbrowse/core/util");
 const CalendarViewDay_1 = __importDefault(require("@mui/icons-material/CalendarViewDay"));
+const LGVSyntenyDisplay_1 = __importDefault(require("./LGVSyntenyDisplay"));
+const LaunchLinearSyntenyView_1 = __importDefault(require("./LaunchLinearSyntenyView"));
 const LinearComparativeDisplay_1 = __importDefault(require("./LinearComparativeDisplay"));
 const LinearComparativeView_1 = __importDefault(require("./LinearComparativeView"));
+const LinearReadVsRef_1 = __importDefault(require("./LinearReadVsRef"));
 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"));
+const SyntenyTrack_1 = __importDefault(require("./SyntenyTrack"));
 class LinearComparativeViewPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);

package/dist/util.d.ts

@@ -1,5 +1,5 @@
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { Region } from '@jbrowse/core/util/types';
 export type LayoutRecord = [number, number, number, number];
 export interface ReducedLinearGenomeView {
     bpPerPx: number;

package/dist/util.js

@@ -26,18 +26,14 @@ function getTrackPos(view, trackConfigId) {
     const idx = view.tracks.findIndex(t => t.configuration === trackConfigId);
     let accum = 0;
     for (let i = 0; i < idx; i += 1) {
-        accum += view.tracks[i].height + 3; // +1px for trackresizehandle
+        accum += view.tracks[i].height + 3;
     }
     return accum;
 }
-// Uses bpToPx to get the screen pixel coordinates but ignores some conditions
-// where bpToPx could return undefined
 function getPxFromCoordinate(view, refName, coord) {
     var _a;
     return (((_a = bpToPx(view, { refName, coord })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - view.offsetPx;
 }
-// Retrieves the y-position of a layout record in a track
-// If track not found returns 0
 function overlayYPos(trackConfigId, level, views, c, cond) {
     const track = views[level].tracks.find(t => t.configuration === trackConfigId);
     const ypos = track
@@ -47,11 +43,6 @@ function overlayYPos(trackConfigId, level, views, c, cond) {
         : 0;
     return ypos + (cond ? cheight(c) : 0);
 }
-// Returns the pixel screen position of a refName:coord input, or undefined if
-// the input could not be located. Uses view.displayedRegions as a representation
-// of what is on the screen
-//
-// Note: does not consider that this refName:coord input could multi-match
 function bpToPx(view, { refName, coord }) {
     let offsetBp = 0;
     const index = view.displayedRegions.findIndex(r => {
@@ -71,7 +62,6 @@ function bpToPx(view, { refName, coord }) {
     }
     return undefined;
 }
-// Returns either 0 or height depending on condition
 function interstitialYPos(cond, height) {
     return cond ? 0 : height;
 }

package/esm/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/esm/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js

@@ -3,7 +3,6 @@ import { Dialog } from '@jbrowse/core/ui';
 import { getSession } from '@jbrowse/core/util';
 import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, TextField, } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-// locals
 import { navToSynteny } from './util';
 const useStyles = makeStyles()({
     padding: {
@@ -26,7 +25,6 @@ export default function LaunchSyntenyViewDialog({ model, feature, trackId, handl
                 } })),
         React.createElement(DialogActions, null,
             React.createElement(Button, { variant: "contained", onClick: () => {
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
                     ;
                     (async () => {
                         try {

package/esm/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/esm/LGVSyntenyDisplay/components/util.js

@@ -51,7 +51,6 @@ export async function navToSynteny({ feature, windowSize: ws, model, trackId, vi
         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/esm/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;