@jbrowse/plugin-linear-genome-view 2.0.0 → 2.1.2

package/dist/LinearGenomeView/components/SearchBox.js

@@ -1,152 +1,88 @@
 "use strict";
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var react_1 = __importDefault(require("react"));
-var mobx_react_1 = require("mobx-react");
-var material_1 = require("@mui/material");
-var mui_1 = require("tss-react/mui");
-var util_1 = require("@jbrowse/core/util");
+const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const util_1 = require("@jbrowse/core/util");
 // locals
-var RefNameAutocomplete_1 = __importDefault(require("./RefNameAutocomplete"));
-var util_2 = require("./util");
-var __1 = require("..");
-var useStyles = (0, mui_1.makeStyles)()(function () { return ({
+const RefNameAutocomplete_1 = __importDefault(require("./RefNameAutocomplete"));
+const util_2 = require("./util");
+const __1 = require("..");
+const useStyles = (0, mui_1.makeStyles)()(() => ({
     headerRefName: {
         minWidth: 100,
     },
-}); });
-function SearchBox(_a) {
-    var model = _a.model, showHelp = _a.showHelp;
-    var classes = useStyles().classes;
-    var theme = (0, material_1.useTheme)();
-    var session = (0, util_1.getSession)(model);
-    var textSearchManager = session.textSearchManager, assemblyManager = session.assemblyManager;
-    var assemblyNames = model.assemblyNames, rankSearchResults = model.rankSearchResults;
-    var assemblyName = assemblyNames[0];
-    var assembly = assemblyManager.get(assemblyName);
-    var searchScope = model.searchScope(assemblyName);
+}));
+function SearchBox({ model, showHelp, }) {
+    const { classes } = useStyles();
+    const theme = (0, material_1.useTheme)();
+    const session = (0, util_1.getSession)(model);
+    const { textSearchManager, assemblyManager } = session;
+    const { assemblyNames, rankSearchResults } = model;
+    const assemblyName = assemblyNames[0];
+    const assembly = assemblyManager.get(assemblyName);
+    const searchScope = model.searchScope(assemblyName);
     // 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
-    function handleSelectedRegion(option) {
-        return __awaiter(this, void 0, void 0, function () {
-            var trackId, location, label, _a, ref, rest, allRefs, results, e_1;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        trackId = option.getTrackId();
-                        location = option.getLocation();
-                        label = option.getLabel();
-                        _a = __read(location.split(':'), 2), ref = _a[0], rest = _a[1];
-                        allRefs = (assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) || [];
-                        _b.label = 1;
-                    case 1:
-                        _b.trys.push([1, 5, , 6]);
-                        if (!(allRefs.includes(location) ||
-                            (allRefs.includes(ref) &&
-                                rest !== undefined &&
-                                !Number.isNaN(parseInt(rest, 10))))) return [3 /*break*/, 2];
-                        model.navToLocString(location, assemblyName);
-                        return [3 /*break*/, 4];
-                    case 2: return [4 /*yield*/, (0, util_2.fetchResults)({
-                            queryString: label,
-                            searchType: 'exact',
-                            searchScope: searchScope,
-                            rankSearchResults: rankSearchResults,
-                            textSearchManager: textSearchManager,
-                            assembly: assembly,
-                        })];
-                    case 3:
-                        results = _b.sent();
-                        if (results.length > 1) {
-                            model.setSearchResults(results, label.toLowerCase());
-                            return [2 /*return*/];
-                        }
-                        else if (results.length === 1) {
-                            location = results[0].getLocation();
-                            trackId = results[0].getTrackId();
-                        }
-                        model.navToLocString(location, assemblyName);
-                        if (trackId) {
-                            model.showTrack(trackId);
-                        }
-                        _b.label = 4;
-                    case 4: return [3 /*break*/, 6];
-                    case 5:
-                        e_1 = _b.sent();
-                        console.error(e_1);
-                        session.notify("".concat(e_1), 'warning');
-                        return [3 /*break*/, 6];
-                    case 6: return [2 /*return*/];
+    async function handleSelectedRegion(option) {
+        let trackId = option.getTrackId();
+        let location = option.getLocation();
+        const label = option.getLabel();
+        const [ref, rest] = location.split(':');
+        const allRefs = (assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) || [];
+        try {
+            // instead of querying text-index, first:
+            // - check if input matches a refName directly
+            // - or looks like locString
+            // then just navigate as if it were a locString
+            if (allRefs.includes(location) ||
+                (allRefs.includes(ref) &&
+                    rest !== undefined &&
+                    !Number.isNaN(parseInt(rest, 10)))) {
+                model.navToLocString(location, assemblyName);
+            }
+            else {
+                const results = await (0, util_2.fetchResults)({
+                    queryString: label,
+                    searchType: 'exact',
+                    searchScope,
+                    rankSearchResults,
+                    textSearchManager,
+                    assembly,
+                });
+                if (results.length > 1) {
+                    model.setSearchResults(results, label.toLowerCase());
+                    return;
+                }
+                else if (results.length === 1) {
+                    location = results[0].getLocation();
+                    trackId = results[0].getTrackId();
                 }
-            });
-        });
+                model.navToLocString(location, assemblyName);
+                if (trackId) {
+                    model.showTrack(trackId);
+                }
+            }
+        }
+        catch (e) {
+            console.error(e);
+            session.notify(`${e}`, 'warning');
+        }
     }
-    return (react_1.default.createElement(RefNameAutocomplete_1.default, { showHelp: showHelp, onSelect: handleSelectedRegion, assemblyName: assemblyName, fetchResults: function (queryString) {
-            return (0, util_2.fetchResults)({
-                queryString: queryString,
-                searchScope: searchScope,
-                rankSearchResults: rankSearchResults,
-                textSearchManager: textSearchManager,
-                assembly: assembly,
-            });
-        }, model: model, TextFieldProps: {
+    return (react_1.default.createElement(RefNameAutocomplete_1.default, { showHelp: showHelp, onSelect: handleSelectedRegion, assemblyName: assemblyName, fetchResults: queryString => (0, util_2.fetchResults)({
+            queryString,
+            searchScope,
+            rankSearchResults,
+            textSearchManager,
+            assembly,
+        }), model: model, TextFieldProps: {
             variant: 'outlined',
             className: classes.headerRefName,
             style: { margin: __1.SPACING, minWidth: '175px' },

package/dist/LinearGenomeView/components/SearchBox.js.map

@@ -1 +1 @@
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+{"version":3,"file":"SearchBox.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/SearchBox.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,4CAA+C;AAC/C,uCAA0C;AAC1C,6CAA+C;AAG/C,SAAS;AACT,gFAAuD;AACvD,iCAAqC;AACrC,0BAAkE;AAElE,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,GAAG,EAAE,CAAC,CAAC;IACpC,aAAa,EAAE;QACb,QAAQ,EAAE,GAAG;KACd;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,SAAS,CAAC,EACjB,KAAK,EACL,QAAQ,GAIT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,KAAK,GAAG,IAAA,mBAAQ,GAAE,CAAA;IACxB,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IAEjC,MAAM,EAAE,iBAAiB,EAAE,eAAe,EAAE,GAAG,OAAO,CAAA;IACtD,MAAM,EAAE,aAAa,EAAE,iBAAiB,EAAE,GAAG,KAAK,CAAA;IAClD,MAAM,YAAY,GAAG,aAAa,CAAC,CAAC,CAAC,CAAA;IACrC,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAClD,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,YAAY,CAAC,CAAA;IAEnD,4EAA4E;IAC5E,oBAAoB;IACpB,8CAA8C;IAC9C,4CAA4C;IAC5C,qDAAqD;IACrD,KAAK,UAAU,oBAAoB,CAAC,MAAkB;QACpD,IAAI,OAAO,GAAG,MAAM,CAAC,UAAU,EAAE,CAAA;QACjC,IAAI,QAAQ,GAAG,MAAM,CAAC,WAAW,EAAE,CAAA;QACnC,MAAM,KAAK,GAAG,MAAM,CAAC,QAAQ,EAAE,CAAA;QAC/B,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QACvC,MAAM,OAAO,GAAG,CAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,KAAI,EAAE,CAAA;QAC3C,IAAI;YACF,yCAAyC;YACzC,8CAA8C;YAC9C,4BAA4B;YAC5B,+CAA+C;YAC/C,IACE,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAC;gBAC1B,CAAC,OAAO,CAAC,QAAQ,CAAC,GAAG,CAAC;oBACpB,IAAI,KAAK,SAAS;oBAClB,CAAC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,EACpC;gBACA,KAAK,CAAC,cAAc,CAAC,QAAQ,EAAE,YAAY,CAAC,CAAA;aAC7C;iBAAM;gBACL,MAAM,OAAO,GAAG,MAAM,IAAA,mBAAY,EAAC;oBACjC,WAAW,EAAE,KAAK;oBAClB,UAAU,EAAE,OAAO;oBACnB,WAAW;oBACX,iBAAiB;oBACjB,iBAAiB;oBACjB,QAAQ;iBACT,CAAC,CAAA;gBACF,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;oBACtB,KAAK,CAAC,gBAAgB,CAAC,OAAO,EAAE,KAAK,CAAC,WAAW,EAAE,CAAC,CAAA;oBACpD,OAAM;iBACP;qBAAM,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE;oBAC/B,QAAQ,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAA;oBACnC,OAAO,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,UAAU,EAAE,CAAA;iBAClC;gBAED,KAAK,CAAC,cAAc,CAAC,QAAQ,EAAE,YAAY,CAAC,CAAA;gBAC5C,IAAI,OAAO,EAAE;oBACX,KAAK,CAAC,SAAS,CAAC,OAAO,CAAC,CAAA;iBACzB;aACF;SACF;QAAC,OAAO,CAAC,EAAE;YACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,EAAE,SAAS,CAAC,CAAA;SAClC;IACH,CAAC;IACD,OAAO,CACL,8BAAC,6BAAmB,IAClB,QAAQ,EAAE,QAAQ,EAClB,QAAQ,EAAE,oBAAoB,EAC9B,YAAY,EAAE,YAAY,EAC1B,YAAY,EAAE,WAAW,CAAC,EAAE,CAC1B,IAAA,mBAAY,EAAC;YACX,WAAW;YACX,WAAW;YACX,iBAAiB;YACjB,iBAAiB;YACjB,QAAQ;SACT,CAAC,EAEJ,KAAK,EAAE,KAAK,EACZ,cAAc,EAAE;YACd,OAAO,EAAE,UAAU;YACnB,SAAS,EAAE,OAAO,CAAC,aAAa;YAChC,KAAK,EAAE,EAAE,MAAM,EAAE,WAAO,EAAE,QAAQ,EAAE,OAAO,EAAE;YAC7C,UAAU,EAAE;gBACV,KAAK,EAAE;oBACL,OAAO,EAAE,CAAC;oBACV,MAAM,EAAE,iBAAa;oBACrB,UAAU,EAAE,IAAA,gBAAK,EAAC,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK,EAAE,GAAG,CAAC;iBACvD;aACF;SACF,GACD,CACH,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,SAAS,CAAC,CAAA"}

package/dist/LinearGenomeView/components/SearchResultsDialog.js

@@ -3,13 +3,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var react_1 = __importDefault(require("react"));
-var mui_1 = require("tss-react/mui");
-var mobx_state_tree_1 = require("mobx-state-tree");
-var util_1 = require("@jbrowse/core/util");
-var material_1 = require("@mui/material");
-var Close_1 = __importDefault(require("@mui/icons-material/Close"));
-var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
+const react_1 = __importDefault(require("react"));
+const mui_1 = require("tss-react/mui");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
     dialogContent: {
         width: '80em',
     },
@@ -19,32 +19,31 @@ var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
         top: theme.spacing(1),
         color: theme.palette.grey[500],
     },
-}); });
-function SearchResultsDialog(_a) {
-    var _b, _c;
-    var model = _a.model, optAssemblyName = _a.optAssemblyName, handleClose = _a.handleClose;
-    var classes = useStyles().classes;
-    var session = (0, util_1.getSession)(model);
-    var pluginManager = (0, mobx_state_tree_1.getEnv)(session).pluginManager;
-    var assemblyManager = session.assemblyManager;
-    var assemblyName = optAssemblyName;
+}));
+function SearchResultsDialog({ model, optAssemblyName, handleClose, }) {
+    var _a, _b;
+    const { classes } = useStyles();
+    const session = (0, util_1.getSession)(model);
+    const { pluginManager } = (0, mobx_state_tree_1.getEnv)(session);
+    const { assemblyManager } = session;
+    let assemblyName = optAssemblyName;
     if (model.displayedRegions.length > 0) {
-        assemblyName = (_b = model.displayedRegions[0]) === null || _b === void 0 ? void 0 : _b.assemblyName;
+        assemblyName = (_a = model.displayedRegions[0]) === null || _a === void 0 ? void 0 : _a.assemblyName;
     }
     if (!assemblyName) {
-        throw new Error("Assembly name not found");
+        throw new Error(`Assembly name not found`);
     }
-    var assembly = assemblyManager.get(assemblyName);
+    const assembly = assemblyManager.get(assemblyName);
     if (!assembly) {
-        throw new Error("assembly ".concat(assemblyName, " not found"));
+        throw new Error(`assembly ${assemblyName} not found`);
     }
     if (!assembly.regions) {
-        throw new Error("assembly ".concat(assemblyName, " regions not loaded"));
+        throw new Error(`assembly ${assemblyName} regions not loaded`);
     }
-    var assemblyRegions = assembly.regions;
+    const assemblyRegions = assembly.regions;
     function handleClick(location) {
         try {
-            var newRegion = assemblyRegions.find(function (region) { return location === region.refName; });
+            const newRegion = assemblyRegions.find(region => location === region.refName);
             if (newRegion) {
                 model.setDisplayedRegions([newRegion]);
                 // we use showAllRegions after setDisplayedRegions to make the entire
@@ -57,14 +56,14 @@ function SearchResultsDialog(_a) {
         }
         catch (e) {
             console.warn(e);
-            session.notify("".concat(e), 'warning');
+            session.notify(`${e}`, 'warning');
         }
     }
     function getTrackName(trackId) {
         var _a;
         if (trackId) {
-            var trackConfigSchema = pluginManager.pluggableConfigSchemaType('track');
-            var configuration = (0, mobx_state_tree_1.resolveIdentifier)(trackConfigSchema, (0, mobx_state_tree_1.getRoot)(model), trackId);
+            const trackConfigSchema = pluginManager.pluggableConfigSchemaType('track');
+            const configuration = (0, mobx_state_tree_1.resolveIdentifier)(trackConfigSchema, (0, mobx_state_tree_1.getRoot)(model), trackId);
             if (configuration) {
                 return (_a = configuration.name) === null || _a === void 0 ? void 0 : _a.value;
             }
@@ -74,12 +73,12 @@ function SearchResultsDialog(_a) {
     return (react_1.default.createElement(material_1.Dialog, { open: true, maxWidth: "xl", onClose: handleClose },
         react_1.default.createElement(material_1.DialogTitle, null,
             "Search results",
-            handleClose ? (react_1.default.createElement(material_1.IconButton, { "data-testid": "close-resultsDialog", className: classes.closeButton, onClick: function () {
+            handleClose ? (react_1.default.createElement(material_1.IconButton, { "data-testid": "close-resultsDialog", className: classes.closeButton, onClick: () => {
                     handleClose();
                 }, size: "large" },
                 react_1.default.createElement(Close_1.default, null))) : null),
         react_1.default.createElement(material_1.Divider, null),
-        react_1.default.createElement(material_1.DialogContent, null, !((_c = model.searchResults) === null || _c === void 0 ? void 0 : _c.length) ? (react_1.default.createElement(material_1.Typography, null,
+        react_1.default.createElement(material_1.DialogContent, null, !((_b = model.searchResults) === null || _b === void 0 ? void 0 : _b.length) ? (react_1.default.createElement(material_1.Typography, null,
             "No results found for ",
             react_1.default.createElement("b", null, model.searchQuery))) : (react_1.default.createElement(react_1.default.Fragment, null,
             react_1.default.createElement(material_1.Typography, null,
@@ -93,22 +92,22 @@ function SearchResultsDialog(_a) {
                             react_1.default.createElement(material_1.TableCell, { align: "right" }, "Location"),
                             react_1.default.createElement(material_1.TableCell, { align: "right" }, "Track"),
                             react_1.default.createElement(material_1.TableCell, { align: "right" }))),
-                    react_1.default.createElement(material_1.TableBody, null, model.searchResults.map(function (result) { return (react_1.default.createElement(material_1.TableRow, { key: "".concat(result.getId()) },
+                    react_1.default.createElement(material_1.TableBody, null, model.searchResults.map(result => (react_1.default.createElement(material_1.TableRow, { key: `${result.getId()}` },
                         react_1.default.createElement(material_1.TableCell, { component: "th", scope: "row" }, result.getLabel()),
                         react_1.default.createElement(material_1.TableCell, { align: "right" }, result.getLocation()),
                         react_1.default.createElement(material_1.TableCell, { align: "right" }, getTrackName(result.getTrackId()) || 'N/A'),
                         react_1.default.createElement(material_1.TableCell, { align: "right" },
-                            react_1.default.createElement(material_1.Button, { onClick: function () {
+                            react_1.default.createElement(material_1.Button, { onClick: () => {
                                     handleClick(result.getLocation());
-                                    var resultTrackId = result.getTrackId();
+                                    const resultTrackId = result.getTrackId();
                                     if (resultTrackId) {
                                         model.showTrack(resultTrackId);
                                     }
                                     handleClose();
-                                }, color: "primary", variant: "contained" }, "Go")))); }))))))),
+                                }, color: "primary", variant: "contained" }, "Go"))))))))))),
         react_1.default.createElement(material_1.Divider, null),
         react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { onClick: function () { return handleClose(); }, color: "primary" }, "Cancel"))));
+            react_1.default.createElement(material_1.Button, { onClick: () => handleClose(), color: "primary" }, "Cancel"))));
 }
 exports.default = SearchResultsDialog;
 //# sourceMappingURL=SearchResultsDialog.js.map

package/dist/LinearGenomeView/components/SearchResultsDialog.js.map

@@ -1 +1 @@
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package/dist/LinearGenomeView/components/SequenceSearchDialog.js

@@ -0,0 +1,104 @@
+"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 };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mui_1 = require("tss-react/mui");
+const mobx_react_1 = require("mobx-react");
+const util_1 = require("@jbrowse/core/util");
+// icons
+const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    closeButton: {
+        position: 'absolute',
+        right: theme.spacing(1),
+        top: theme.spacing(1),
+        color: theme.palette.grey[500],
+    },
+    dialogContent: {
+        width: '40em',
+    },
+}));
+function SequenceDialog({ model, handleClose, }) {
+    const { classes } = useStyles();
+    const [value, setValue] = (0, react_1.useState)('');
+    const [searchForward, setSearchForward] = (0, react_1.useState)(true);
+    const [searchReverse, setSearchReverse] = (0, react_1.useState)(true);
+    const [caseInsensitive, setCaseInsensitive] = (0, react_1.useState)(true);
+    let error;
+    try {
+        new RegExp(value);
+    }
+    catch (e) {
+        error = e;
+    }
+    return (react_1.default.createElement(material_1.Dialog, { maxWidth: "xl", open: true, onClose: handleClose },
+        react_1.default.createElement(material_1.DialogTitle, null,
+            "Sequence search",
+            handleClose ? (react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => handleClose(), size: "large" },
+                react_1.default.createElement(Close_1.default, null))) : null),
+        react_1.default.createElement(material_1.Divider, null),
+        react_1.default.createElement(material_1.DialogContent, { className: classes.dialogContent },
+            react_1.default.createElement(material_1.Typography, null, "Supply a sequence to search for. A track will be created with the resulting matches once submitted. You can also supply regex style expressions e.g. AACT(C|T)."),
+            react_1.default.createElement(material_1.TextField, { value: value, onChange: e => setValue(e.target.value), helperText: "Sequence search pattern" }),
+            react_1.default.createElement(material_1.FormGroup, null,
+                react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: searchForward, onChange: event => setSearchForward(event.target.checked) }), label: "Search forward strand" }),
+                react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: searchReverse, onChange: event => setSearchReverse(event.target.checked) }), label: "Search reverse strand" }),
+                react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: caseInsensitive, onChange: event => setCaseInsensitive(event.target.checked) }), label: "Case insensitive" })),
+            error ? react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`) : null),
+        react_1.default.createElement(material_1.DialogActions, null,
+            react_1.default.createElement(material_1.Button, { onClick: () => {
+                    var _a;
+                    if (value) {
+                        const trackId = `sequence_search_${+Date.now()}`;
+                        const session = (0, util_1.getSession)(model);
+                        const { assemblyManager } = session;
+                        const assemblyName = model.assemblyNames[0];
+                        session.addTrackConf({
+                            trackId,
+                            name: `Sequence search ${value}`,
+                            assemblyNames: [assemblyName],
+                            type: 'FeatureTrack',
+                            adapter: {
+                                type: 'SequenceSearchAdapter',
+                                search: value,
+                                searchForward,
+                                searchReverse,
+                                caseInsensitive,
+                                sequenceAdapter: (0, mobx_state_tree_1.getSnapshot)((_a = assemblyManager.get(assemblyName)) === null || _a === void 0 ? void 0 : _a.configuration.sequence.adapter),
+                            },
+                        });
+                        model.toggleTrack(trackId);
+                    }
+                    handleClose();
+                }, variant: "contained", color: "primary" }, "Submit"),
+            react_1.default.createElement(material_1.Button, { onClick: () => handleClose(), variant: "contained", color: "secondary" }, "Close"))));
+}
+exports.default = (0, mobx_react_1.observer)(SequenceDialog);
+//# sourceMappingURL=SequenceSearchDialog.js.map

package/dist/LinearGenomeView/components/SequenceSearchDialog.js.map

@@ -0,0 +1 @@
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package/dist/LinearGenomeView/components/TrackContainer.d.ts

@@ -1,8 +1,9 @@
 /// <reference types="react" />
 import { BaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { LinearGenomeViewModel } from '..';
+declare type LGV = LinearGenomeViewModel;
 declare function TrackContainer({ model, track, }: {
-    model: LinearGenomeViewModel;
+    model: LGV;
     track: BaseTrackModel;
 }): JSX.Element;
 declare const _default: typeof TrackContainer;