@jbrowse/plugin-grid-bookmark 2.1.0 → 2.1.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/GridBookmarkWidget/components/AssemblySelector.js +13 -14
- package/dist/GridBookmarkWidget/components/AssemblySelector.js.map +1 -1
- package/dist/GridBookmarkWidget/components/ClearBookmarks.js +17 -34
- package/dist/GridBookmarkWidget/components/ClearBookmarks.js.map +1 -1
- package/dist/GridBookmarkWidget/components/DeleteBookmark.js +13 -14
- package/dist/GridBookmarkWidget/components/DeleteBookmark.js.map +1 -1
- package/dist/GridBookmarkWidget/components/DownloadBookmarks.js +20 -37
- package/dist/GridBookmarkWidget/components/DownloadBookmarks.js.map +1 -1
- package/dist/GridBookmarkWidget/components/GridBookmarkWidget.js +45 -91
- package/dist/GridBookmarkWidget/components/GridBookmarkWidget.js.map +1 -1
- package/dist/GridBookmarkWidget/components/ImportBookmarks.js +55 -121
- package/dist/GridBookmarkWidget/components/ImportBookmarks.js.map +1 -1
- package/dist/GridBookmarkWidget/index.js +1 -1
- package/dist/GridBookmarkWidget/index.js.map +1 -1
- package/dist/GridBookmarkWidget/model.js +19 -42
- package/dist/GridBookmarkWidget/model.js.map +1 -1
- package/dist/GridBookmarkWidget/utils.js +50 -104
- package/dist/GridBookmarkWidget/utils.js.map +1 -1
- package/dist/index.js +46 -87
- package/dist/index.js.map +1 -1
- package/package.json +2 -3
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__setModuleDefault(result, mod);
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return result;
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};
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var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
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function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
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return new (P || (P = Promise))(function (resolve, reject) {
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function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
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function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
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function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
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step((generator = generator.apply(thisArg, _arguments || [])).next());
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});
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};
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var __generator = (this && this.__generator) || function (thisArg, body) {
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var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
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return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
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function verb(n) { return function (v) { return step([n, v]); }; }
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function step(op) {
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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;
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if (y = 0, t) op = [op[0] & 2, t.value];
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switch (op[0]) {
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case 0: case 1: t = op; break;
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case 4: _.label++; return { value: op[1], done: false };
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case 5: _.label++; y = op[1]; op = [0]; continue;
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case 7: op = _.ops.pop(); _.trys.pop(); continue;
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default:
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if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
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if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
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if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
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if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
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if (t[2]) _.ops.pop();
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_.trys.pop(); continue;
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}
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op = body.call(thisArg, _);
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} catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
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if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
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}
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};
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var __read = (this && this.__read) || function (o, n) {
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var m = typeof Symbol === "function" && o[Symbol.iterator];
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if (!m) return o;
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var i = m.call(o), r, ar = [], e;
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try {
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while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
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}
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catch (error) { e = { error: error }; }
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finally {
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try {
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if (r && !r.done && (m = i["return"])) m.call(i);
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}
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finally { if (e) throw e.error; }
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}
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return ar;
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};
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var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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Object.defineProperty(exports, "__esModule", { value: true });
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const react_1 = __importStar(require("react"));
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const mobx_react_1 = require("mobx-react");
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const util_1 = require("@jbrowse/core/util");
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const AssemblySelector_1 = __importDefault(require("@jbrowse/core/ui/AssemblySelector"));
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const ui_1 = require("@jbrowse/core/ui");
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const io_1 = require("@jbrowse/core/util/io");
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const material_1 = require("@mui/material");
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const mui_1 = require("tss-react/mui");
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const Close_1 = __importDefault(require("@mui/icons-material/Close"));
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const Publish_1 = __importDefault(require("@mui/icons-material/Publish"));
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const useStyles = (0, mui_1.makeStyles)()(() => ({
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closeDialog: {
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position: 'absolute',
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right: 0,
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flexItem: {
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margin: 5,
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},
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})
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function ImportBookmarks(
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var _d = __read((0, react_1.useState)(), 2), error = _d[0], setError = _d[1];
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var _e = __read((0, react_1.useState)(assemblyName || assemblyNames[0]), 2), selectedAsm = _e[0], setSelectedAsm = _e[1];
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}));
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function ImportBookmarks({ model, assemblyName, }) {
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const { classes } = useStyles();
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const session = (0, util_1.getSession)(model);
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const { assemblyNames } = session;
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const [dialogOpen, setDialogOpen] = (0, react_1.useState)(false);
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const [location, setLocation] = (0, react_1.useState)();
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const [error, setError] = (0, react_1.useState)();
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const [selectedAsm, setSelectedAsm] = (0, react_1.useState)(assemblyName || assemblyNames[0]);
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return (react_1.default.createElement(react_1.default.Fragment, null,
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react_1.default.createElement(material_1.Button, { startIcon: react_1.default.createElement(Publish_1.default, null), onClick:
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react_1.default.createElement(material_1.Dialog, { open: dialogOpen, onClose:
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react_1.default.createElement(material_1.Button, { startIcon: react_1.default.createElement(Publish_1.default, null), onClick: () => setDialogOpen(true) }, "Import"),
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react_1.default.createElement(material_1.Dialog, { open: dialogOpen, onClose: () => setDialogOpen(false), maxWidth: "xl" },
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react_1.default.createElement(material_1.DialogTitle, null,
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"Import bookmarks",
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react_1.default.createElement(material_1.IconButton, { className: classes.closeDialog, "aria-label": "close-dialog", onClick:
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react_1.default.createElement(material_1.IconButton, { className: classes.closeDialog, "aria-label": "close-dialog", onClick: () => setDialogOpen(false) },
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react_1.default.createElement(Close_1.default, null))),
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react_1.default.createElement(material_1.DialogContent, null,
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react_1.default.createElement(material_1.Typography, null, "Choose a BED format file to import. The first 4 columns will be used"),
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react_1.default.createElement(ui_1.FileSelector, { location: location, setLocation: setLocation, name: "File" }),
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react_1.default.createElement(material_1.Typography, null, "Select assembly that your data belongs to"),
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react_1.default.createElement(AssemblySelector_1.default, { onChange:
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error ? (react_1.default.createElement(material_1.Typography, { color: "error", variant: "h6" },
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react_1.default.createElement(AssemblySelector_1.default, { onChange: val => setSelectedAsm(val), session: session, selected: selectedAsm }),
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error ? (react_1.default.createElement(material_1.Typography, { color: "error", variant: "h6" }, `${error}`)) : null),
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react_1.default.createElement(material_1.DialogActions, null,
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react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick:
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react_1.default.createElement(material_1.Button, { className: classes.flexItem, "data-testid": "dialogImport", variant: "contained", color: "primary", disabled: !location, startIcon: react_1.default.createElement(Publish_1.default, null), onClick:
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case 0:
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_a.trys.push([0, 2, , 3]);
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if (!location) {
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return [2 /*return*/];
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}
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return [4 /*yield*/, (0, io_1.openLocation)(location).readFile('utf8')];
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case 1:
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data = _a.sent();
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regions = data
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.split('\n')
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.filter(function (f) { return !!f.trim(); })
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.filter(function (f) {
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return !f.startsWith('#') &&
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!f.startsWith('browser');
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})
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.map(function (line) {
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var _a = __read(line.split('\t'), 4), refName = _a[0], start = _a[1], end = _a[2], name = _a[3];
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return {
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assemblyName: selectedAsm,
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refName: refName,
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start: +start,
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end: +end,
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label: name === '.' ? undefined : name,
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};
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});
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model.importBookmarks(regions);
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setDialogOpen(false);
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return [3 /*break*/, 3];
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case 2:
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e_1 = _a.sent();
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console.error(e_1);
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setError(e_1);
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return [3 /*break*/, 3];
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case 3: return [2 /*return*/];
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react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => setDialogOpen(false) }, "Cancel"),
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react_1.default.createElement(material_1.Button, { className: classes.flexItem, "data-testid": "dialogImport", variant: "contained", color: "primary", disabled: !location, startIcon: react_1.default.createElement(Publish_1.default, null), onClick: async () => {
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try {
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if (!location) {
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return;
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}
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const data = await (0, io_1.openLocation)(location).readFile('utf8');
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const regions = data
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.split('\n')
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.filter(f => !!f.trim())
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.filter(f => !f.startsWith('#') &&
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!f.startsWith('track') &&
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.map(line => {
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const [refName, start, end, name] = line.split('\t');
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return {
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assemblyName: selectedAsm,
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refName,
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start: +start,
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end: +end,
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label: name === '.' ? undefined : name,
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};
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});
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model.importBookmarks(regions);
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setDialogOpen(false);
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}
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catch (e) {
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console.error(e);
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setError(e);
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}
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} }, "Import")))));
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}
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exports.default = (0, mobx_react_1.observer)(ImportBookmarks);
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//# sourceMappingURL=ImportBookmarks.js.map
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{"version":3,"file":"ImportBookmarks.js","sourceRoot":"","sources":["../../../src/GridBookmarkWidget/components/ImportBookmarks.tsx"],"names":[],"mappings":"
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{"version":3,"file":"ImportBookmarks.js","sourceRoot":"","sources":["../../../src/GridBookmarkWidget/components/ImportBookmarks.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,6CAA+C;AAC/C,yFAAgE;AAEhE,yCAA+C;AAC/C,8CAAoD;AACpD,4CAQsB;AACtB,uCAA0C;AAC1C,sEAAiD;AACjD,0EAAoD;AAGpD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,GAAG,EAAE,CAAC,CAAC;IACpC,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,CAAC;QACR,GAAG,EAAE,CAAC;KACP;IACD,eAAe,EAAE;QACf,MAAM,EAAE,EAAE;KACX;IACD,QAAQ,EAAE;QACR,MAAM,EAAE,CAAC;KACV;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,eAAe,CAAC,EACvB,KAAK,EACL,YAAY,GAIb;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,aAAa,EAAE,GAAG,OAAO,CAAA;IACjC,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IACnD,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,IAAA,gBAAQ,GAAgB,CAAA;IACxD,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,IAAA,gBAAQ,GAAW,CAAA;IAC7C,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,IAAA,gBAAQ,EAC5C,YAAY,IAAI,aAAa,CAAC,CAAC,CAAC,CACjC,CAAA;IAED,OAAO,CACL;QACE,8BAAC,iBAAM,IAAC,SAAS,EAAE,8BAAC,iBAAU,OAAG,EAAE,OAAO,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,IAAI,CAAC,aAE5D;QACT,8BAAC,iBAAM,IACL,IAAI,EAAE,UAAU,EAChB,OAAO,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,KAAK,CAAC,EACnC,QAAQ,EAAC,IAAI;YAEb,8BAAC,sBAAW;;gBAEV,8BAAC,qBAAU,IACT,SAAS,EAAE,OAAO,CAAC,WAAW,gBACnB,cAAc,EACzB,OAAO,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,KAAK,CAAC;oBAEnC,8BAAC,eAAS,OAAG,CACF,CACD;YACd,8BAAC,wBAAa;gBACZ,8BAAC,qBAAU,+EAEE;gBAEb,8BAAC,iBAAY,IACX,QAAQ,EAAE,QAAQ,EAClB,WAAW,EAAE,WAAW,EACxB,IAAI,EAAC,MAAM,GACX;gBACF,8BAAC,qBAAU,oDAAuD;gBAClE,8BAAC,0BAAgB,IACf,QAAQ,EAAE,GAAG,CAAC,EAAE,CAAC,cAAc,CAAC,GAAG,CAAC,EACpC,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,WAAW,GACrB;gBACD,KAAK,CAAC,CAAC,CAAC,CACP,8BAAC,qBAAU,IAAC,KAAK,EAAC,OAAO,EAAC,OAAO,EAAC,IAAI,IAAE,GAAG,KAAK,EAAE,CAAc,CACjE,CAAC,CAAC,CAAC,IAAI,CACM;YAChB,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,KAAK,CAAC,aAG5B;gBACT,8BAAC,iBAAM,IACL,SAAS,EAAE,OAAO,CAAC,QAAQ,iBACf,cAAc,EAC1B,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,QAAQ,EAAE,CAAC,QAAQ,EACnB,SAAS,EAAE,8BAAC,iBAAU,OAAG,EACzB,OAAO,EAAE,KAAK,IAAI,EAAE;wBAClB,IAAI;4BACF,IAAI,CAAC,QAAQ,EAAE;gCACb,OAAM;6BACP;4BACD,MAAM,IAAI,GAAG,MAAM,IAAA,iBAAY,EAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;4BAC1D,MAAM,OAAO,GAAG,IAAI;iCACjB,KAAK,CAAC,IAAI,CAAC;iCACX,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;iCACvB,MAAM,CACL,CAAC,CAAC,EAAE,CACF,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC;gCAClB,CAAC,CAAC,CAAC,UAAU,CAAC,OAAO,CAAC;gCACtB,CAAC,CAAC,CAAC,UAAU,CAAC,SAAS,CAAC,CAC3B;iCACA,GAAG,CAAC,IAAI,CAAC,EAAE;gCACV,MAAM,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gCACpD,OAAO;oCACL,YAAY,EAAE,WAAW;oCACzB,OAAO;oCACP,KAAK,EAAE,CAAC,KAAK;oCACb,GAAG,EAAE,CAAC,GAAG;oCACT,KAAK,EAAE,IAAI,KAAK,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI;iCACvC,CAAA;4BACH,CAAC,CAAC,CAAA;4BACJ,KAAK,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;4BAC9B,aAAa,CAAC,KAAK,CAAC,CAAA;yBACrB;wBAAC,OAAO,CAAC,EAAE;4BACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;yBACZ;oBACH,CAAC,aAGM,CACK,CACT,CACR,CACJ,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,eAAe,CAAC,CAAA"}
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GridBookmarkWidget/index.js"],"names":[],"mappings":";;;;;;AAAA
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GridBookmarkWidget/index.js"],"names":[],"mappings":";;;;;;AAAA,+DAAiE;AACjE,iCAAsD;AAA7C,2HAAA,OAAO,OAAqB;AACxB,QAAA,YAAY,GAAG,IAAA,mCAAmB,EAAC,oBAAoB,EAAE,EAAE,CAAC,CAAA"}
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.compose(mst_1.Region, mobx_state_tree_1.types.model('Label', { label: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, '') }))
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{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/GridBookmarkWidget/model.ts"],"names":[],"mappings":"
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{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/GridBookmarkWidget/model.ts"],"names":[],"mappings":";;AAAA,qDAAuD;AAGvD,sDAA+E;AAE/E,MAAM,kBAAkB,GAAG,uBAAK;KAC7B,OAAO,CACN,YAAW,EACX,uBAAK,CAAC,KAAK,CAAC,OAAO,EAAE,EAAE,KAAK,EAAE,uBAAK,CAAC,QAAQ,CAAC,uBAAK,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE,CAAC,CAClE;KACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAChB,QAAQ,CAAC,KAAa;QACpB,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;IACpB,CAAC;CACF,CAAC,CAAC,CAAA;AAEL,SAAwB,CAAC,CAAC,aAA4B;IACpD,OAAO,uBAAK;SACT,KAAK,CAAC,mBAAmB,EAAE;QAC1B,EAAE,EAAE,eAAS;QACb,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,oBAAoB,CAAC;QACzC,IAAI,EAAE,uBAAK,CAAC,aAAa,CACvB,aAAa,CAAC,gBAAgB,CAAC,MAAM,EAAE,YAAY,CAAC,CACrD;QACD,iBAAiB,EAAE,uBAAK,CAAC,KAAK,CAAC,kBAAkB,CAAC;QAClD,qBAAqB,EAAE,EAAE;KAC1B,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,eAAe,CAAC,OAAiB;YAC/B,IAAI,CAAC,iBAAiB,GAAG,IAAA,sBAAI,EAAC,IAAI,CAAC,iBAAiB,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,CAAA;QACvE,CAAC;QACD,WAAW,CAAC,MAAc;YACxB,IAAI,CAAC,iBAAiB,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACrC,CAAC;QACD,cAAc,CAAC,KAAa;YAC1B,IAAI,CAAC,iBAAiB,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,CAAC,CAAA;QACzC,CAAC;QACD,iBAAiB;YACf,IAAI,CAAC,iBAAiB,CAAC,KAAK,EAAE,CAAA;QAChC,CAAC;QACD,mBAAmB,CAAC,KAAa,EAAE,KAAa;;YAC9C,MAAA,IAAI,CAAC,iBAAiB,CAAC,KAAK,CAAC,0CAAE,QAAQ,CAAC,KAAK,CAAC,CAAA;QAChD,CAAC;QACD,mBAAmB,CAAC,QAAgB;YAClC,IAAI,CAAC,qBAAqB,GAAG,QAAQ,CAAA;QACvC,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd,IAAI,gBAAgB;YAClB,OAAO,CACL,IAAI,CAAC,qBAAqB;gBAC1B,CAAC,IAAI,CAAC,iBAAiB,CAAC,MAAM;oBAC5B,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC,CAAC,CAAC,YAAY;oBACxC,CAAC,CAAC,EAAE,CAAC,CACR,CAAA;QACH,CAAC;QACD,IAAI,UAAU;YACZ,OAAO;gBACL,GAAG,IAAI,GAAG,CAAC,IAAI,CAAC,iBAAiB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,YAAY,CAAC,CAAC;aACtE,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AA9CD,oBA8CC"}
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53
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-
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54
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-
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55
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-
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56
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-
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57
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-
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58
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-
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59
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-
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|
60
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-
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61
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-
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|
62
|
-
|
|
63
|
-
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|
64
|
-
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
|
|
71
|
-
|
|
72
|
-
canonicalRefName_1 = assembly.getCanonicalRefName(refName);
|
|
73
|
-
newDisplayedRegion = void 0;
|
|
74
|
-
if (regions) {
|
|
75
|
-
newDisplayedRegion = regions.find(function (region) { return region.refName === canonicalRefName_1; });
|
|
76
|
-
}
|
|
77
|
-
view_1 = session_1.addView('LinearGenomeView', {
|
|
78
|
-
displayName: selectedAssembly,
|
|
79
|
-
});
|
|
80
|
-
return [4 /*yield*/, (0, util_1.when)(function () { return view_1.initialized; })];
|
|
81
|
-
case 4:
|
|
82
|
-
_a.sent();
|
|
83
|
-
view_1.setDisplayedRegions([
|
|
84
|
-
JSON.parse(JSON.stringify(newDisplayedRegion)),
|
|
85
|
-
]);
|
|
86
|
-
view_1.navToLocString(locString);
|
|
87
|
-
return [3 /*break*/, 6];
|
|
88
|
-
case 5:
|
|
89
|
-
e_1 = _a.sent();
|
|
90
|
-
session_1.notify("".concat(e_1), 'error');
|
|
91
|
-
return [3 /*break*/, 6];
|
|
92
|
-
case 6: return [2 /*return*/];
|
|
4
|
+
const file_saver_1 = require("file-saver");
|
|
5
|
+
const util_1 = require("@jbrowse/core/util");
|
|
6
|
+
async function navToBookmark(locString, views, model) {
|
|
7
|
+
const { selectedAssembly } = model;
|
|
8
|
+
const lgv = views.find(view => view.type === 'LinearGenomeView' &&
|
|
9
|
+
// @ts-ignore
|
|
10
|
+
view.assemblyNames[0] === selectedAssembly);
|
|
11
|
+
if (lgv) {
|
|
12
|
+
lgv.navToLocString(locString);
|
|
13
|
+
}
|
|
14
|
+
else {
|
|
15
|
+
const session = (0, util_1.getSession)(model);
|
|
16
|
+
const { assemblyManager } = session;
|
|
17
|
+
const assembly = await assemblyManager.waitForAssembly(selectedAssembly);
|
|
18
|
+
if (assembly) {
|
|
19
|
+
try {
|
|
20
|
+
const loc = (0, util_1.parseLocString)(locString, refName => session.assemblyManager.isValidRefName(refName, selectedAssembly));
|
|
21
|
+
const { refName } = loc;
|
|
22
|
+
const { regions } = assembly;
|
|
23
|
+
const canonicalRefName = assembly.getCanonicalRefName(refName);
|
|
24
|
+
let newDisplayedRegion;
|
|
25
|
+
if (regions) {
|
|
26
|
+
newDisplayedRegion = regions.find(region => region.refName === canonicalRefName);
|
|
27
|
+
}
|
|
28
|
+
const view = session.addView('LinearGenomeView', {
|
|
29
|
+
displayName: selectedAssembly,
|
|
30
|
+
});
|
|
31
|
+
await (0, util_1.when)(() => view.initialized);
|
|
32
|
+
view.setDisplayedRegions([
|
|
33
|
+
JSON.parse(JSON.stringify(newDisplayedRegion)),
|
|
34
|
+
]);
|
|
35
|
+
view.navToLocString(locString);
|
|
93
36
|
}
|
|
94
|
-
|
|
95
|
-
|
|
37
|
+
catch (e) {
|
|
38
|
+
session.notify(`${e}`, 'error');
|
|
39
|
+
}
|
|
40
|
+
}
|
|
41
|
+
}
|
|
96
42
|
}
|
|
97
43
|
exports.navToBookmark = navToBookmark;
|
|
98
44
|
function downloadBookmarkFile(bookmarkedRegions, fileFormat, model) {
|
|
99
|
-
|
|
100
|
-
|
|
45
|
+
const { selectedAssembly } = model;
|
|
46
|
+
const fileHeader = fileFormat === 'TSV'
|
|
101
47
|
? 'chrom\tstart\tend\tlabel\tassembly_name\tcoord_range\n'
|
|
102
48
|
: '';
|
|
103
|
-
|
|
104
|
-
.map(
|
|
105
|
-
|
|
106
|
-
|
|
107
|
-
|
|
49
|
+
const fileContents = bookmarkedRegions
|
|
50
|
+
.map(b => {
|
|
51
|
+
const { label } = b;
|
|
52
|
+
const labelVal = label === '' ? '.' : label;
|
|
53
|
+
const locString = (0, util_1.assembleLocString)(b);
|
|
108
54
|
if (fileFormat === 'BED') {
|
|
109
55
|
if (b.assemblyName === selectedAssembly || selectedAssembly === 'all') {
|
|
110
56
|
// the "name" column (column 4) in a BED has a max of 255 characters
|
|
111
57
|
// according to the new spec: https://github.com/samtools/hts-specs/pull/570
|
|
112
|
-
return
|
|
58
|
+
return `${b.refName}\t${b.start}\t${b.end}\t${labelVal.slice(0, 255)}\n`;
|
|
113
59
|
}
|
|
114
60
|
return '';
|
|
115
61
|
}
|
|
116
62
|
else {
|
|
117
|
-
return
|
|
63
|
+
return `${b.refName}\t${b.start + 1}\t${b.end}\t${labelVal}\t${b.assemblyName}\t${locString}\n`;
|
|
118
64
|
}
|
|
119
65
|
})
|
|
120
|
-
.reduce(
|
|
121
|
-
|
|
66
|
+
.reduce((a, b) => a + b, fileHeader);
|
|
67
|
+
const blob = new Blob([fileContents || ''], {
|
|
122
68
|
type: fileFormat === 'BED'
|
|
123
69
|
? 'text/x-bed;charset=utf-8'
|
|
124
70
|
: 'text/tab-separated-values;charset=utf-8',
|
|
125
71
|
});
|
|
126
|
-
|
|
72
|
+
let fileName;
|
|
127
73
|
if (fileFormat === 'BED') {
|
|
128
|
-
fileName =
|
|
74
|
+
fileName = `jbrowse_bookmarks_${selectedAssembly}.bed`;
|
|
129
75
|
}
|
|
130
76
|
else {
|
|
131
77
|
fileName = 'jbrowse_bookmarks.tsv';
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"utils.js","sourceRoot":"","sources":["../../src/GridBookmarkWidget/utils.ts"],"names":[],"mappings":"
|
|
1
|
+
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|