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

package/dist/index.js

@@ -29,6 +29,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.linearBasicDisplayModelFactory = exports.linearBasicDisplayConfigSchemaFactory = exports.SVGRuler = exports.totalHeight = exports.SVGTracks = exports.renderToSvg = exports.SearchBox = exports.RefNameAutocomplete = exports.TooLargeMessage = exports.FeatureDensityMixin = exports.TrackHeightMixin = exports.BaseLinearDisplayComponent = exports.BlockMsg = exports.BaseLinearDisplay = exports.baseLinearDisplayConfigSchema = exports.linearBareDisplayConfigSchemaFactory = void 0;
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const util_1 = require("@jbrowse/core/util");
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
 // icons
 const LineStyle_1 = __importDefault(require("@mui/icons-material/LineStyle"));
 // locals
@@ -39,8 +41,6 @@ const LinearBasicDisplay_1 = __importDefault(require("./LinearBasicDisplay"));
 const FeatureTrack_1 = __importDefault(require("./FeatureTrack"));
 const BasicTrack_1 = __importDefault(require("./BasicTrack"));
 const LaunchLinearGenomeView_1 = __importDefault(require("./LaunchLinearGenomeView"));
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
 class LinearGenomeViewPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);

package/dist/searchUtils.d.ts

@@ -0,0 +1,26 @@
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import { SearchType } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SearchScope } from '@jbrowse/core/TextSearch/TextSearchManager';
+import { TextSearchManager } from '@jbrowse/core/util';
+import { LinearGenomeViewModel } from './LinearGenomeView';
+export declare function navToOption({ option, model, assemblyName, }: {
+    model: LinearGenomeViewModel;
+    option: BaseResult;
+    assemblyName: string;
+}): Promise<void>;
+export declare function handleSelectedRegion({ input, model, assembly, }: {
+    input: string;
+    model: LinearGenomeViewModel;
+    assembly: Assembly;
+}): Promise<void>;
+export declare function checkRef(str: string, allRefs: string[]): boolean;
+export declare function fetchResults({ queryString, searchType, searchScope, rankSearchResults, textSearchManager, assembly, }: {
+    queryString: string;
+    searchScope: SearchScope;
+    rankSearchResults: (results: BaseResult[]) => BaseResult[];
+    searchType?: SearchType;
+    textSearchManager?: TextSearchManager;
+    assembly?: Assembly;
+}): Promise<BaseResult[]>;
+export declare function splitLast(str: string, split: string): [string, string];

package/dist/searchUtils.js

@@ -0,0 +1,90 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.splitLast = exports.fetchResults = exports.checkRef = exports.handleSelectedRegion = exports.navToOption = void 0;
+const util_1 = require("@jbrowse/core/util");
+const BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
+const util_2 = require("@jbrowse/core/util");
+async function navToOption({ option, model, assemblyName, }) {
+    const location = option.getLocation();
+    const trackId = option.getTrackId();
+    if (location) {
+        await model.navToLocString(location, assemblyName);
+        if (trackId) {
+            model.showTrack(trackId);
+        }
+    }
+}
+exports.navToOption = navToOption;
+// 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, model, assembly, }) {
+    const allRefs = (assembly === null || assembly === void 0 ? void 0 : assembly.allRefNamesWithLowerCase) || [];
+    const assemblyName = assembly.name;
+    if (input.split(' ').every(entry => checkRef(entry, allRefs))) {
+        await model.navToLocString(input, assembly.name);
+    }
+    else {
+        const searchScope = model.searchScope(assemblyName);
+        const { textSearchManager } = (0, util_1.getSession)(model);
+        const results = await fetchResults({
+            queryString: input,
+            searchType: 'exact',
+            searchScope,
+            rankSearchResults: model.rankSearchResults,
+            textSearchManager,
+            assembly,
+        });
+        if (results.length > 1) {
+            model.setSearchResults(results, input.toLowerCase(), assemblyName);
+        }
+        else if (results.length === 1) {
+            await navToOption({
+                option: results[0],
+                model,
+                assemblyName,
+            });
+        }
+        else {
+            await model.navToLocString(input, assemblyName);
+        }
+    }
+}
+exports.handleSelectedRegion = handleSelectedRegion;
+function checkRef(str, allRefs) {
+    const [ref, rest] = splitLast(str, ':');
+    return (allRefs.includes(str) ||
+        (allRefs.includes(ref) && !Number.isNaN(Number.parseInt(rest, 10))));
+}
+exports.checkRef = checkRef;
+async function fetchResults({ queryString, searchType, searchScope, rankSearchResults, textSearchManager, assembly, }) {
+    var _a;
+    if (!textSearchManager) {
+        console.warn('No text search manager');
+    }
+    const textSearchResults = await (textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
+        queryString,
+        searchType,
+    }, searchScope, rankSearchResults));
+    const refNameResults = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) === null || _a === void 0 ? void 0 : _a.filter(ref => ref.toLowerCase().startsWith(queryString.toLowerCase())).slice(0, 10).map(r => new BaseResults_1.default({ label: r }));
+    return (0, util_2.dedupe)([...(refNameResults || []), ...(textSearchResults || [])], elt => elt.getId());
+}
+exports.fetchResults = fetchResults;
+// splits on the last instance of a character
+function splitLast(str, split) {
+    const lastIndex = str.lastIndexOf(split);
+    if (lastIndex === -1) {
+        return [str, ''];
+    }
+    else {
+        const before = str.slice(0, lastIndex);
+        const after = str.slice(lastIndex + 1);
+        return [before, after];
+    }
+}
+exports.splitLast = splitLast;

package/esm/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/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -10,7 +10,6 @@ import MenuOpenIcon from '@mui/icons-material/MenuOpen';
 import { Tooltip } from '../components/BaseLinearDisplay';
 import BlockState from './serverSideRenderedBlock';
 import configSchema from './configSchema';
-import renderBaseLinearDisplaySvg from './renderSvg';
 import TrackHeightMixin from './TrackHeightMixin';
 import FeatureDensityMixin from './FeatureDensityMixin';
 /**
@@ -290,6 +289,7 @@ function stateModelFactory() {
          * #method
          */
         async renderSvg(opts) {
+            const { renderBaseLinearDisplaySvg } = await import('./renderSvg');
             return renderBaseLinearDisplaySvg(self, opts);
         },
         afterAttach() {

package/esm/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/esm/BaseLinearDisplay/models/renderSvg.js

@@ -2,7 +2,7 @@ import React from 'react';
 import { getContainingView, getViewParams, ReactRendering, } from '@jbrowse/core/util';
 import BlockState, { renderBlockData } from './serverSideRenderedBlock';
 import { getId } from './util';
-export default async function renderBaseLinearDisplaySvg(self, opts) {
+export async function renderBaseLinearDisplaySvg(self, opts) {
     const { height, id } = self;
     const { overrideHeight } = opts;
     const view = getContainingView(self);

package/esm/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/esm/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/esm/LaunchLinearGenomeView/index.js

@@ -1,4 +1,5 @@
 import { when } from '@jbrowse/core/util';
+import { handleSelectedRegion } from '..//searchUtils';
 export default (pluginManager) => {
     pluginManager.addToExtensionPoint('LaunchView-LinearGenomeView', 
     // @ts-expect-error
@@ -14,21 +15,9 @@ export default (pluginManager) => {
             if (!asm) {
                 throw new Error(`Assembly "${assembly}" not found when launching linear genome view`);
             }
-            await view.navToLocString(loc, assembly);
+            await handleSelectedRegion({ input: loc, model: view, assembly: asm });
             const idsNotFound = [];
-            tracks.forEach(track => {
-                try {
-                    view.showTrack(track);
-                }
-                catch (e) {
-                    if (`${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: ${idsNotFound.join(',')}`);
             }
@@ -39,3 +28,16 @@ export default (pluginManager) => {
         }
     });
 };
+function tryTrack(model, trackId, idsNotFound) {
+    try {
+        model.showTrack(trackId);
+    }
+    catch (e) {
+        if (`${e}`.match('Could not resolve identifier')) {
+            idsNotFound.push(trackId);
+        }
+        else {
+            throw e;
+        }
+    }
+}

package/esm/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/esm/LinearGenomeView/components/CenterLine.js

@@ -5,7 +5,7 @@ const useStyles = 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/esm/LinearGenomeView/components/ImportForm.js

@@ -6,9 +6,8 @@ import { Button, FormControl, Container, Grid, CircularProgress, } from '@mui/ma
 import { ErrorMessage, AssemblySelector } from '@jbrowse/core/ui';
 // icons
 import CloseIcon from '@mui/icons-material/Close';
-// locals
-import RefNameAutocomplete from './RefNameAutocomplete';
-import { fetchResults, splitLast } from './util';
+import { handleSelectedRegion, navToOption } from '../../searchUtils';
+import ImportFormRefNameAutocomplete from './ImportFormRefNameAutocomplete';
 const useStyles = makeStyles()(theme => ({
     importFormContainer: {
         padding: theme.spacing(2),
@@ -24,11 +23,10 @@ const LinearGenomeViewImportForm = observer(function ({ model, }) {
     var _a;
     const { classes } = useStyles();
     const session = getSession(model);
-    const { assemblyNames, assemblyManager, textSearchManager } = session;
-    const { rankSearchResults, error } = model;
+    const { assemblyNames, assemblyManager } = session;
+    const { error } = model;
     const [selectedAsm, setSelectedAsm] = useState(assemblyNames[0]);
     const [option, setOption] = useState();
-    const searchScope = model.searchScope(selectedAsm);
     const assembly = assemblyManager.get(selectedAsm);
     const assemblyError = assemblyNames.length
         ? assembly === null || assembly === void 0 ? void 0 : assembly.error
@@ -46,74 +44,37 @@ const LinearGenomeViewImportForm = observer(function ({ model, }) {
     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] = 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 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(`${e}`, 'warning');
-        }
-    }
     // implementation notes:
     // having this wrapped in a form allows intuitive use of enter key to submit
     return (React.createElement("div", { className: classes.container },
         displayError ? React.createElement(ErrorMessage, { error: displayError }) : null,
         React.createElement(Container, { className: classes.importFormContainer },
             React.createElement("form", { onSubmit: async (event) => {
+                    var _a;
                     event.preventDefault();
                     model.setError(undefined);
                     if (value) {
                         // has it's own error handling
-                        await handleSelectedRegion(value);
+                        try {
+                            if ((option === null || option === void 0 ? void 0 : option.getDisplayString()) === value &&
+                                option.hasLocation()) {
+                                await navToOption({
+                                    option,
+                                    model,
+                                    assemblyName: selectedAsm,
+                                });
+                            }
+                            else if ((_a = option === null || option === void 0 ? void 0 : option.results) === null || _a === void 0 ? void 0 : _a.length) {
+                                model.setSearchResults(option.results, option.getLabel(), selectedAsm);
+                            }
+                            else if (assembly) {
+                                await handleSelectedRegion({ input: value, assembly, model });
+                            }
+                        }
+                        catch (e) {
+                            console.error(e);
+                            session.notify(`${e}`, 'warning');
+                        }
                     }
                 } },
                 React.createElement(Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center" },
@@ -121,16 +82,7 @@ const LinearGenomeViewImportForm = observer(function ({ model, }) {
                         React.createElement(FormControl, null,
                             React.createElement(AssemblySelector, { onChange: val => setSelectedAsm(val), localStorageKey: "lgv", session: session, selected: selectedAsm }))),
                     React.createElement(Grid, { item: true }, selectedAsm ? (assemblyError ? (React.createElement(CloseIcon, { style: { color: 'red' } })) : assemblyLoaded ? (React.createElement(FormControl, null,
-                        React.createElement(RefNameAutocomplete, { fetchResults: queryString => 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.createElement(CircularProgress, { size: 20, disableShrink: true }))) : null),
+                        React.createElement(ImportFormRefNameAutocomplete, { value: value, setValue: setValue, selectedAsm: selectedAsm, setOption: setOption, model: model }))) : (React.createElement(CircularProgress, { size: 20, disableShrink: true }))) : null),
                     React.createElement(Grid, { item: true },
                         React.createElement(FormControl, null,
                             React.createElement(Button, { type: "submit", disabled: !value, className: classes.button, variant: "contained", color: "primary" }, "Open")),

package/esm/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/esm/LinearGenomeView/components/ImportFormRefNameAutocomplete.js

@@ -0,0 +1,24 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { getSession } from '@jbrowse/core/util';
+// locals
+import RefNameAutocomplete from './RefNameAutocomplete';
+import { fetchResults } from './util';
+const ImportFormRefNameAutocomplete = observer(function ({ model, selectedAsm, value, setValue, setOption, }) {
+    const session = getSession(model);
+    const { assemblyManager, textSearchManager } = session;
+    const { rankSearchResults } = model;
+    const searchScope = model.searchScope(selectedAsm);
+    const assembly = assemblyManager.get(selectedAsm);
+    return (React.createElement(RefNameAutocomplete, { fetchResults: queryString => 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',
+        } }));
+});
+export default ImportFormRefNameAutocomplete;

package/esm/LinearGenomeView/components/OverviewScalebar.js

@@ -195,7 +195,7 @@ const OverviewScalebar = 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/esm/LinearGenomeView/components/SearchBox.js

@@ -5,8 +5,9 @@ import { makeStyles } from 'tss-react/mui';
 import { getSession } from '@jbrowse/core/util';
 // locals
 import RefNameAutocomplete from './RefNameAutocomplete';
-import { fetchResults, splitLast } from './util';
+import { fetchResults } from './util';
 import { SPACING, WIDGET_HEIGHT } from '..';
+import { handleSelectedRegion, navToOption } from '../../searchUtils';
 const useStyles = makeStyles()(() => ({
     headerRefName: {
         minWidth: 100,
@@ -21,65 +22,28 @@ const SearchBox = 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] = 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.createElement(RefNameAutocomplete, { showHelp: showHelp, onSelect: async (option) => {
+            var _a;
+            try {
+                if (option.hasLocation()) {
+                    await navToOption({ option, model, assemblyName });
                 }
-                else {
-                    const results = await 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 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(`${e}`, 'warning');
-        }
-    }
-    return (React.createElement(RefNameAutocomplete, { showHelp: showHelp, onSelect: handleSelectedRegion, assemblyName: assemblyName, fetchResults: queryString => fetchResults({
+            catch (e) {
+                console.error(e);
+                getSession(model).notify(`${e}`, 'warning');
+            }
+        }, assemblyName: assemblyName, fetchResults: queryString => fetchResults({
             queryString,
             searchScope,
             rankSearchResults,

package/esm/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