@jbrowse/plugin-linear-genome-view 2.7.2 → 2.9.0

package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -69,7 +69,11 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
-            features: Map<string, Feature>;
+            features: Map<string, Feature>; /**
+             * #getter
+             * a CompositeMap of `featureId -> feature obj` that
+             * just looks in all the block data for that feature
+             */
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
@@ -128,7 +132,9 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        blockState?: Record<string, any> | undefined; /**
+         * #property
+         */
     }>;
     readonly DisplayBlurb: React.FC<{
         model: {
@@ -136,7 +142,9 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
+            rendererTypeName: string; /**
+             * #getter
+             */
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -144,9 +152,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
-            rendererTypeName: string; /**
-             * #getter
-             */
+            rendererTypeName: string;
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -179,10 +185,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
 } & {
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
-    readonly maxFeatureScreenDensity: any; /**
-     * #property
-     * updated via autorun
-     */
+    readonly maxFeatureScreenDensity: any;
     readonly featureDensityStatsReady: boolean;
     readonly maxAllowableBytes: number;
 } & {
@@ -358,7 +361,11 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
-            features: Map<string, Feature>;
+            features: Map<string, Feature>; /**
+             * #getter
+             * a CompositeMap of `featureId -> feature obj` that
+             * just looks in all the block data for that feature
+             */
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;

package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -1,4 +1,27 @@
 "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 };
 };
@@ -16,7 +39,6 @@ const MenuOpen_1 = __importDefault(require("@mui/icons-material/MenuOpen"));
 const BaseLinearDisplay_1 = require("../components/BaseLinearDisplay");
 const serverSideRenderedBlock_1 = __importDefault(require("./serverSideRenderedBlock"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-const renderSvg_1 = __importDefault(require("./renderSvg"));
 const TrackHeightMixin_1 = __importDefault(require("./TrackHeightMixin"));
 const FeatureDensityMixin_1 = __importDefault(require("./FeatureDensityMixin"));
 /**
@@ -296,7 +318,8 @@ function stateModelFactory() {
          * #method
          */
         async renderSvg(opts) {
-            return (0, renderSvg_1.default)(self, opts);
+            const { renderBaseLinearDisplaySvg } = await Promise.resolve().then(() => __importStar(require('./renderSvg')));
+            return renderBaseLinearDisplaySvg(self, opts);
         },
         afterAttach() {
             // watch the parent's blocks to update our block state when they change,

package/dist/BaseLinearDisplay/models/renderSvg.d.ts

@@ -2,7 +2,7 @@ import React from 'react';
 import { ThemeOptions } from '@mui/material';
 import { ExportSvgOptions } from '../../LinearGenomeView';
 import { BaseLinearDisplayModel } from './BaseLinearDisplayModel';
-export default function renderBaseLinearDisplaySvg(self: BaseLinearDisplayModel, opts: ExportSvgOptions & {
+export declare function renderBaseLinearDisplaySvg(self: BaseLinearDisplayModel, opts: ExportSvgOptions & {
     overrideHeight: number;
     theme: ThemeOptions;
 }): Promise<React.JSX.Element>;

package/dist/BaseLinearDisplay/models/renderSvg.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderBaseLinearDisplaySvg = void 0;
 const react_1 = __importDefault(require("react"));
 const util_1 = require("@jbrowse/core/util");
 const serverSideRenderedBlock_1 = __importStar(require("./serverSideRenderedBlock"));
@@ -79,4 +80,4 @@ async function renderBaseLinearDisplaySvg(self, opts) {
                     react_1.default.createElement(util_1.ReactRendering, { rendering: rendering })))));
     })));
 }
-exports.default = renderBaseLinearDisplaySvg;
+exports.renderBaseLinearDisplaySvg = renderBaseLinearDisplaySvg;

package/dist/BasicTrack/configSchema.d.ts

@@ -58,6 +58,11 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
             defaultValue: number;
             description: string;
         };
+        maxDepth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         config: {

package/dist/FeatureTrack/configSchema.d.ts

@@ -58,6 +58,11 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
             defaultValue: number;
             description: string;
         };
+        maxDepth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         config: {

package/dist/LaunchLinearGenomeView/index.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const util_1 = require("@jbrowse/core/util");
+const searchUtils_1 = require("..//searchUtils");
 exports.default = (pluginManager) => {
     pluginManager.addToExtensionPoint('LaunchView-LinearGenomeView', 
     // @ts-expect-error
@@ -16,21 +17,9 @@ exports.default = (pluginManager) => {
             if (!asm) {
                 throw new Error(`Assembly "${assembly}" not found when launching linear genome view`);
             }
-            await view.navToLocString(loc, assembly);
+            await (0, searchUtils_1.handleSelectedRegion)({ input: loc, model: view, assembly: asm });
             const idsNotFound = [];
-            tracks.forEach(track => {
-                try {
-                    view.showTrack(track);
-                }
-                catch (e) {
-                    if (`${e}`.match('Could not resolve identifier')) {
-                        idsNotFound.push(track);
-                    }
-                    else {
-                        throw e;
-                    }
-                }
-            });
+            tracks.forEach(track => tryTrack(view, track, idsNotFound));
             if (idsNotFound.length) {
                 throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
             }
@@ -41,3 +30,16 @@ exports.default = (pluginManager) => {
         }
     });
 };
+function tryTrack(model, trackId, idsNotFound) {
+    try {
+        model.showTrack(trackId);
+    }
+    catch (e) {
+        if (`${e}`.match('Could not resolve identifier')) {
+            idsNotFound.push(trackId);
+        }
+        else {
+            throw e;
+        }
+    }
+}

package/dist/LinearBasicDisplay/model.d.ts

@@ -219,7 +219,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
 } & {
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly blockType: "dynamicBlocks" | "staticBlocks"; /**
+     * #getter
+     */
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;

package/dist/LinearGenomeView/components/CenterLine.js

@@ -30,7 +30,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
     centerLineContainer: {
         background: 'transparent',
         height: '100%',
-        zIndex: 5,
+        zIndex: 5, // above the track but under menu
         position: 'absolute',
         border: `1px ${theme.palette.action.active} dashed`,
         borderTop: 'none',

package/dist/LinearGenomeView/components/ImportForm.js

@@ -34,9 +34,8 @@ const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
 // icons
 const Close_1 = __importDefault(require("@mui/icons-material/Close"));
-// locals
-const RefNameAutocomplete_1 = __importDefault(require("./RefNameAutocomplete"));
-const util_2 = require("./util");
+const searchUtils_1 = require("../../searchUtils");
+const ImportFormRefNameAutocomplete_1 = __importDefault(require("./ImportFormRefNameAutocomplete"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     importFormContainer: {
         padding: theme.spacing(2),
@@ -52,11 +51,10 @@ const LinearGenomeViewImportForm = (0, mobx_react_1.observer)(function ({ model,
     var _a;
     const { classes } = useStyles();
     const session = (0, util_1.getSession)(model);
-    const { assemblyNames, assemblyManager, textSearchManager } = session;
-    const { rankSearchResults, error } = model;
+    const { assemblyNames, assemblyManager } = session;
+    const { error } = model;
     const [selectedAsm, setSelectedAsm] = (0, react_1.useState)(assemblyNames[0]);
     const [option, setOption] = (0, react_1.useState)();
-    const searchScope = model.searchScope(selectedAsm);
     const assembly = assemblyManager.get(selectedAsm);
     const assemblyError = assemblyNames.length
         ? assembly === null || assembly === void 0 ? void 0 : assembly.error
@@ -74,74 +72,37 @@ const LinearGenomeViewImportForm = (0, mobx_react_1.observer)(function ({ model,
     (0, react_1.useEffect)(() => {
         setValue(r0);
     }, [r0, selectedAsm]);
-    async function navToOption(option) {
-        const location = option.getLocation();
-        const trackId = option.getTrackId();
-        if (location) {
-            await model.navToLocString(location, selectedAsm);
-            if (trackId) {
-                model.showTrack(trackId);
-            }
-        }
-    }
-    // gets a string as input, or use stored option results from previous query,
-    // then re-query and
-    // 1) if it has multiple results: pop a dialog
-    // 2) if it's a single result navigate to it
-    // 3) else assume it's a locstring and navigate to it
-    async function handleSelectedRegion(input) {
-        var _a;
-        try {
-            if ((option === null || option === void 0 ? void 0 : option.getDisplayString()) === input && option.hasLocation()) {
-                await navToOption(option);
-            }
-            else if ((_a = option === null || option === void 0 ? void 0 : option.results) === null || _a === void 0 ? void 0 : _a.length) {
-                model.setSearchResults(option.results, option.getLabel(), selectedAsm);
-            }
-            else {
-                const [ref, rest] = (0, util_2.splitLast)(input, ':');
-                const allRefs = (assembly === null || assembly === void 0 ? void 0 : assembly.allRefNamesWithLowerCase) || [];
-                if (allRefs.includes(input) ||
-                    (allRefs.includes(ref) && !Number.isNaN(Number.parseInt(rest, 10)))) {
-                    await model.navToLocString(input, selectedAsm);
-                }
-                else {
-                    const results = await (0, util_2.fetchResults)({
-                        queryString: input,
-                        searchType: 'exact',
-                        searchScope,
-                        rankSearchResults,
-                        textSearchManager,
-                        assembly,
-                    });
-                    if (results.length > 1) {
-                        model.setSearchResults(results, input.toLowerCase(), selectedAsm);
-                    }
-                    else if (results.length === 1) {
-                        await navToOption(results[0]);
-                    }
-                    else {
-                        await model.navToLocString(input, selectedAsm);
-                    }
-                }
-            }
-        }
-        catch (e) {
-            console.error(e);
-            session.notify(`${e}`, 'warning');
-        }
-    }
     // implementation notes:
     // having this wrapped in a form allows intuitive use of enter key to submit
     return (react_1.default.createElement("div", { className: classes.container },
         displayError ? react_1.default.createElement(ui_1.ErrorMessage, { error: displayError }) : null,
         react_1.default.createElement(material_1.Container, { className: classes.importFormContainer },
             react_1.default.createElement("form", { onSubmit: async (event) => {
+                    var _a;
                     event.preventDefault();
                     model.setError(undefined);
                     if (value) {
                         // has it's own error handling
-                        await handleSelectedRegion(value);
+                        try {
+                            if ((option === null || option === void 0 ? void 0 : option.getDisplayString()) === value &&
+                                option.hasLocation()) {
+                                await (0, searchUtils_1.navToOption)({
+                                    option,
+                                    model,
+                                    assemblyName: selectedAsm,
+                                });
+                            }
+                            else if ((_a = option === null || option === void 0 ? void 0 : option.results) === null || _a === void 0 ? void 0 : _a.length) {
+                                model.setSearchResults(option.results, option.getLabel(), selectedAsm);
+                            }
+                            else if (assembly) {
+                                await (0, searchUtils_1.handleSelectedRegion)({ input: value, assembly, model });
+                            }
+                        }
+                        catch (e) {
+                            console.error(e);
+                            session.notify(`${e}`, 'warning');
+                        }
                     }
                 } },
                 react_1.default.createElement(material_1.Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center" },
@@ -149,16 +110,7 @@ const LinearGenomeViewImportForm = (0, mobx_react_1.observer)(function ({ model,
                         react_1.default.createElement(material_1.FormControl, null,
                             react_1.default.createElement(ui_1.AssemblySelector, { onChange: val => setSelectedAsm(val), localStorageKey: "lgv", session: session, selected: selectedAsm }))),
                     react_1.default.createElement(material_1.Grid, { item: true }, selectedAsm ? (assemblyError ? (react_1.default.createElement(Close_1.default, { style: { color: 'red' } })) : assemblyLoaded ? (react_1.default.createElement(material_1.FormControl, null,
-                        react_1.default.createElement(RefNameAutocomplete_1.default, { fetchResults: queryString => (0, util_2.fetchResults)({
-                                queryString,
-                                assembly,
-                                textSearchManager,
-                                rankSearchResults,
-                                searchScope,
-                            }), model: model, assemblyName: selectedAsm, value: value, minWidth: 270, onChange: str => setValue(str), onSelect: val => setOption(val), TextFieldProps: {
-                                variant: 'outlined',
-                                helperText: 'Enter sequence name, feature name, or location',
-                            } }))) : (react_1.default.createElement(material_1.CircularProgress, { size: 20, disableShrink: true }))) : null),
+                        react_1.default.createElement(ImportFormRefNameAutocomplete_1.default, { value: value, setValue: setValue, selectedAsm: selectedAsm, setOption: setOption, model: model }))) : (react_1.default.createElement(material_1.CircularProgress, { size: 20, disableShrink: true }))) : null),
                     react_1.default.createElement(material_1.Grid, { item: true },
                         react_1.default.createElement(material_1.FormControl, null,
                             react_1.default.createElement(material_1.Button, { type: "submit", disabled: !value, className: classes.button, variant: "contained", color: "primary" }, "Open")),

package/dist/LinearGenomeView/components/ImportFormRefNameAutocomplete.d.ts

@@ -0,0 +1,12 @@
+import React from 'react';
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+import { LinearGenomeViewModel } from '..';
+type LGV = LinearGenomeViewModel;
+declare const ImportFormRefNameAutocomplete: ({ model, selectedAsm, value, setValue, setOption, }: {
+    value: string;
+    setValue: (arg: string) => void;
+    model: LGV;
+    selectedAsm: string;
+    setOption: (arg: BaseResult) => void;
+}) => React.JSX.Element;
+export default ImportFormRefNameAutocomplete;

package/dist/LinearGenomeView/components/ImportFormRefNameAutocomplete.js

@@ -0,0 +1,29 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+const util_1 = require("@jbrowse/core/util");
+// locals
+const RefNameAutocomplete_1 = __importDefault(require("./RefNameAutocomplete"));
+const util_2 = require("./util");
+const ImportFormRefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, selectedAsm, value, setValue, setOption, }) {
+    const session = (0, util_1.getSession)(model);
+    const { assemblyManager, textSearchManager } = session;
+    const { rankSearchResults } = model;
+    const searchScope = model.searchScope(selectedAsm);
+    const assembly = assemblyManager.get(selectedAsm);
+    return (react_1.default.createElement(RefNameAutocomplete_1.default, { fetchResults: queryString => (0, util_2.fetchResults)({
+            queryString,
+            assembly,
+            textSearchManager,
+            rankSearchResults,
+            searchScope,
+        }), model: model, assemblyName: selectedAsm, value: value, minWidth: 270, onChange: str => setValue(str), onSelect: val => setOption(val), TextFieldProps: {
+            variant: 'outlined',
+            helperText: 'Enter sequence name, feature name, or location',
+        } }));
+});
+exports.default = ImportFormRefNameAutocomplete;

package/dist/LinearGenomeView/components/OverviewScalebar.js

@@ -225,7 +225,7 @@ const OverviewScalebar = (0, mobx_react_1.observer)(function ({ model, children,
         overview.showAllRegions();
         return overview;
     }, [
-        JSON.stringify(displayedRegions),
+        JSON.stringify(displayedRegions), // eslint-disable-line react-hooks/exhaustive-deps
         model.minimumBlockWidth,
         modWidth,
         displayedRegions,

package/dist/LinearGenomeView/components/SearchBox.js

@@ -12,6 +12,7 @@ const util_1 = require("@jbrowse/core/util");
 const RefNameAutocomplete_1 = __importDefault(require("./RefNameAutocomplete"));
 const util_2 = require("./util");
 const __1 = require("..");
+const searchUtils_1 = require("../../searchUtils");
 const useStyles = (0, mui_1.makeStyles)()(() => ({
     headerRefName: {
         minWidth: 100,
@@ -26,65 +27,28 @@ const SearchBox = (0, mobx_react_1.observer)(function ({ model, showHelp, }) {
     const assemblyName = assemblyNames[0];
     const assembly = assemblyManager.get(assemblyName);
     const searchScope = model.searchScope(assemblyName);
-    async function navToOption(option) {
-        const location = option.getLocation();
-        const trackId = option.getTrackId();
-        if (location) {
-            await model.navToLocString(location, assemblyName);
-            if (trackId) {
-                model.showTrack(trackId);
-            }
-        }
-    }
-    // gets a string as input, or use stored option results from previous query,
-    // then re-query and
-    // 1) if it has multiple results: pop a dialog
-    // 2) if it's a single result navigate to it
-    // 3) else assume it's a locstring and navigate to it
-    async function handleSelectedRegion(option) {
-        var _a;
-        try {
-            if (option.hasLocation()) {
-                await navToOption(option);
-            }
-            else if ((_a = option.results) === null || _a === void 0 ? void 0 : _a.length) {
-                model.setSearchResults(option.results, option.getLabel());
-            }
-            else {
-                const input = option.getLabel();
-                const [ref, rest] = (0, util_2.splitLast)(input, ':');
-                const allRefs = (assembly === null || assembly === void 0 ? void 0 : assembly.allRefNamesWithLowerCase) || [];
-                if (allRefs.includes(input) ||
-                    (allRefs.includes(ref) && !Number.isNaN(Number.parseInt(rest, 10)))) {
-                    await model.navToLocString(input, assemblyName);
+    return (react_1.default.createElement(RefNameAutocomplete_1.default, { showHelp: showHelp, onSelect: async (option) => {
+            var _a;
+            try {
+                if (option.hasLocation()) {
+                    await (0, searchUtils_1.navToOption)({ option, model, assemblyName });
                 }
-                else {
-                    const results = await (0, util_2.fetchResults)({
-                        queryString: input,
-                        searchType: 'exact',
-                        searchScope,
-                        rankSearchResults,
-                        textSearchManager,
+                else if ((_a = option.results) === null || _a === void 0 ? void 0 : _a.length) {
+                    model.setSearchResults(option.results, option.getLabel());
+                }
+                else if (assembly) {
+                    await (0, searchUtils_1.handleSelectedRegion)({
+                        input: option.getLabel(),
                         assembly,
+                        model,
                     });
-                    if (results.length > 1) {
-                        model.setSearchResults(results, input.toLowerCase());
-                    }
-                    else if (results.length === 1) {
-                        await navToOption(results[0]);
-                    }
-                    else {
-                        await model.navToLocString(input, assemblyName);
-                    }
                 }
             }
-        }
-        catch (e) {
-            console.error(e);
-            session.notify(`${e}`, 'warning');
-        }
-    }
-    return (react_1.default.createElement(RefNameAutocomplete_1.default, { showHelp: showHelp, onSelect: handleSelectedRegion, assemblyName: assemblyName, fetchResults: queryString => (0, util_2.fetchResults)({
+            catch (e) {
+                console.error(e);
+                (0, util_1.getSession)(model).notify(`${e}`, 'warning');
+            }
+        }, assemblyName: assemblyName, fetchResults: queryString => (0, util_2.fetchResults)({
             queryString,
             searchScope,
             rankSearchResults,

package/dist/LinearGenomeView/model.d.ts

@@ -6,6 +6,7 @@ import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import { BlockSet, BaseBlock } from '@jbrowse/core/util/blockTypes';
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
 export interface BpOffset {
     refName?: string;
     index: number;
@@ -292,7 +293,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    toggleTrack(trackId: string): void;
+    toggleTrack(trackId: string): boolean;
     /**
      * #action
      */
@@ -463,6 +464,16 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * navigating to the locstring
      */
     navToLocString(input: string, optAssemblyName?: string): Promise<void>;
+    /**
+     * #action
+     * Performs a text index search, and navigates to it immediately if a
+     * single result is returned. Will pop up a search dialog if multiple
+     * results are returned
+     */
+    navToSearchString({ input, assembly, }: {
+        input: string;
+        assembly: Assembly;
+    }): Promise<void>;
     /**
      * #action
      * Similar to `navToLocString`, but accepts parsed location objects

package/dist/LinearGenomeView/model.js

@@ -53,6 +53,7 @@ const MenuOpen_1 = __importDefault(require("@mui/icons-material/MenuOpen"));
 const MiniControls_1 = __importDefault(require("./components/MiniControls"));
 const Header_1 = __importDefault(require("./components/Header"));
 const util_2 = require("./util");
+const searchUtils_1 = require("../searchUtils");
 // lazies
 const ReturnToImportFormDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@jbrowse/core/ui/ReturnToImportFormDialog'))));
 const SequenceSearchDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SequenceSearchDialog'))));
@@ -624,7 +625,9 @@ function stateModelFactory(pluginManager) {
             // if none had that configuration, turn one on
             if (!hiddenCount) {
                 self.showTrack(trackId);
+                return true;
             }
+            return false;
         },
         /**
          * #action
@@ -1106,6 +1109,19 @@ function stateModelFactory(pluginManager) {
             }
             return this.navToLocations((0, util_2.parseLocStrings)(input, assemblyName, isValidRefName), assemblyName);
         },
+        /**
+         * #action
+         * Performs a text index search, and navigates to it immediately if a
+         * single result is returned. Will pop up a search dialog if multiple
+         * results are returned
+         */
+        async navToSearchString({ input, assembly, }) {
+            await (0, searchUtils_1.handleSelectedRegion)({
+                input,
+                assembly,
+                model: self,
+            });
+        },
         /**
          * #action
          * Similar to `navToLocString`, but accepts parsed location objects