@jbrowse/plugin-linear-genome-view 2.8.0 → 2.9.0

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/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

@@ -12,16 +12,12 @@ 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,
     },
 }));
-function checkRef(str, allRefs) {
-    const [ref, rest] = (0, util_2.splitLast)(str, ':');
-    return (allRefs.includes(str) ||
-        (allRefs.includes(ref) && !Number.isNaN(Number.parseInt(rest, 10))));
-}
 const SearchBox = (0, mobx_react_1.observer)(function ({ model, showHelp, }) {
     const { classes } = useStyles();
     const theme = (0, material_1.useTheme)();
@@ -31,61 +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 {
-            const input = option.getLabel();
-            const allRefs = (assembly === null || assembly === void 0 ? void 0 : assembly.allRefNamesWithLowerCase) || [];
-            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 if (input.split(' ').every(entry => checkRef(entry, allRefs))) {
-                await model.navToLocString(input, assemblyName);
-            }
-            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());
+    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 if (results.length === 1) {
-                    await navToOption(results[0]);
+                else if ((_a = option.results) === null || _a === void 0 ? void 0 : _a.length) {
+                    model.setSearchResults(option.results, option.getLabel());
                 }
-                else {
-                    await model.navToLocString(input, assemblyName);
+                else if (assembly) {
+                    await (0, searchUtils_1.handleSelectedRegion)({
+                        input: option.getLabel(),
+                        assembly,
+                        model,
+                    });
                 }
             }
-        }
-        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