@jbrowse/plugin-linear-genome-view 1.7.9 → 2.0.0

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

@@ -0,0 +1 @@
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package/dist/LinearGenomeView/components/SequenceDialog.js

@@ -1,295 +1,242 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
+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;
 });
-exports.default = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _react = _interopRequireWildcard(require("react"));
-
-var _core = require("@material-ui/core");
-
-var _mobxReact = require("mobx-react");
-
-var _fileSaver = require("file-saver");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _copyToClipboard = _interopRequireDefault(require("copy-to-clipboard"));
-
-var _util = require("@jbrowse/core/util");
-
-var _formatFastaStrings = require("@jbrowse/core/util/formatFastaStrings");
-
-var _Icons = require("@jbrowse/core/ui/Icons");
-
-var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
-
-var _GetApp = _interopRequireDefault(require("@material-ui/icons/GetApp"));
-
-function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-
+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 __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 = __importStar(require("react"));
+var mui_1 = require("tss-react/mui");
+var material_1 = require("@mui/material");
+var mobx_react_1 = require("mobx-react");
+var file_saver_1 = require("file-saver");
+var configuration_1 = require("@jbrowse/core/configuration");
+var copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
+var util_1 = require("@jbrowse/core/util");
+var formatFastaStrings_1 = require("@jbrowse/core/util/formatFastaStrings");
 // icons
-var useStyles = (0, _core.makeStyles)(function (theme) {
-  return {
+var Icons_1 = require("@jbrowse/core/ui/Icons");
+var Close_1 = __importDefault(require("@mui/icons-material/Close"));
+var GetApp_1 = __importDefault(require("@mui/icons-material/GetApp"));
+var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
     loadingMessage: {
-      padding: theme.spacing(5)
+        padding: theme.spacing(5),
     },
     closeButton: {
-      position: 'absolute',
-      right: theme.spacing(1),
-      top: theme.spacing(1),
-      color: theme.palette.grey[500]
+        position: 'absolute',
+        right: theme.spacing(1),
+        top: theme.spacing(1),
+        color: theme.palette.grey[500],
     },
     dialogContent: {
-      width: '80em'
+        width: '80em',
     },
     textAreaFont: {
-      fontFamily: 'Courier New'
-    }
-  };
-});
-
+        fontFamily: 'Courier New',
+    },
+}); });
 /**
  * Fetches and returns a list features for a given list of regions
  */
-function fetchSequence(_x, _x2, _x3) {
-  return _fetchSequence.apply(this, arguments);
-}
-
-function _fetchSequence() {
-  _fetchSequence = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(model, regions, signal) {
-    var session, leftOffset, rightOffset, rpcManager, assemblyManager, assemblyName, assembly, adapterConfig, sessionId;
-    return _regenerator.default.wrap(function _callee2$(_context2) {
-      while (1) {
-        switch (_context2.prev = _context2.next) {
-          case 0:
-            session = (0, _util.getSession)(model);
+function fetchSequence(model, regions, signal) {
+    return __awaiter(this, void 0, void 0, function () {
+        var session, leftOffset, rightOffset, rpcManager, assemblyManager, assemblyName, assembly, adapterConfig, sessionId;
+        return __generator(this, function (_a) {
+            session = (0, util_1.getSession)(model);
             leftOffset = model.leftOffset, rightOffset = model.rightOffset;
-
-            if (!(!leftOffset || !rightOffset)) {
-              _context2.next = 4;
-              break;
+            if (!leftOffset || !rightOffset) {
+                throw new Error('no offsets on model to use for range');
             }
-
-            throw new Error('no offsets on model to use for range');
-
-          case 4:
-            if (!(leftOffset.assemblyName !== rightOffset.assemblyName)) {
-              _context2.next = 6;
-              break;
+            if (leftOffset.assemblyName !== rightOffset.assemblyName) {
+                throw new Error('not able to fetch sequences from multiple assemblies');
             }
-
-            throw new Error('not able to fetch sequences from multiple assemblies');
-
-          case 6:
             rpcManager = session.rpcManager, assemblyManager = session.assemblyManager;
             assemblyName = leftOffset.assemblyName || rightOffset.assemblyName || '';
             assembly = assemblyManager.get(assemblyName);
-
-            if (assembly) {
-              _context2.next = 11;
-              break;
+            if (!assembly) {
+                throw new Error("assembly ".concat(assemblyName, " not found"));
             }
-
-            throw new Error("assembly ".concat(assemblyName, " not found"));
-
-          case 11:
-            adapterConfig = (0, _configuration.getConf)(assembly, ['sequence', 'adapter']);
+            adapterConfig = (0, configuration_1.getConf)(assembly, ['sequence', 'adapter']);
             sessionId = 'getSequence';
-            return _context2.abrupt("return", rpcManager.call(sessionId, 'CoreGetFeatures', {
-              adapterConfig: adapterConfig,
-              regions: regions,
-              sessionId: sessionId,
-              signal: signal
-            }));
-
-          case 14:
-          case "end":
-            return _context2.stop();
-        }
-      }
-    }, _callee2);
-  }));
-  return _fetchSequence.apply(this, arguments);
+            return [2 /*return*/, rpcManager.call(sessionId, 'CoreGetFeatures', {
+                    adapterConfig: adapterConfig,
+                    regions: regions,
+                    sessionId: sessionId,
+                    signal: signal,
+                })];
+        });
+    });
 }
-
-function SequenceDialog(_ref) {
-  var model = _ref.model,
-      handleClose = _ref.handleClose;
-  var classes = useStyles();
-  var session = (0, _util.getSession)(model);
-
-  var _useState = (0, _react.useState)(),
-      _useState2 = (0, _slicedToArray2.default)(_useState, 2),
-      error = _useState2[0],
-      setError = _useState2[1];
-
-  var _useState3 = (0, _react.useState)(),
-      _useState4 = (0, _slicedToArray2.default)(_useState3, 2),
-      sequence = _useState4[0],
-      setSequence = _useState4[1];
-
-  var loading = Boolean(sequence === undefined);
-  var leftOffset = model.leftOffset,
-      rightOffset = model.rightOffset; // avoid infinite looping of useEffect
-  // random note: the current selected region can't be a computed because it
-  // uses action on base1dview even though it's on the ephemeral base1dview
-
-  var regionsSelected = (0, _react.useMemo)(function () {
-    return model.getSelectedRegions(leftOffset, rightOffset);
-  }, [model, leftOffset, rightOffset]);
-  (0, _react.useEffect)(function () {
-    var active = true;
-    var controller = new AbortController();
-    (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-      var chunks;
-      return _regenerator.default.wrap(function _callee$(_context) {
-        while (1) {
-          switch (_context.prev = _context.next) {
-            case 0:
-              _context.prev = 0;
-
-              if (!(regionsSelected.length > 0)) {
-                _context.next = 8;
-                break;
-              }
-
-              _context.next = 4;
-              return fetchSequence(model, regionsSelected, controller.signal);
-
-            case 4:
-              chunks = _context.sent;
-
-              if (active) {
-                setSequence((0, _formatFastaStrings.formatSeqFasta)(chunks.filter(function (f) {
-                  return !!f;
-                }).map(function (chunk) {
-                  var chunkSeq = chunk.get('seq');
-                  var chunkRefName = chunk.get('refName');
-                  var chunkStart = chunk.get('start') + 1;
-                  var chunkEnd = chunk.get('end');
-                  var chunkLocstring = "".concat(chunkRefName, ":").concat(chunkStart, "-").concat(chunkEnd);
-
-                  if ((chunkSeq === null || chunkSeq === void 0 ? void 0 : chunkSeq.length) !== chunkEnd - chunkStart + 1) {
-                    throw new Error("".concat(chunkLocstring, " returned ").concat(chunkSeq.length.toLocaleString(), " bases, but should have returned ").concat((chunkEnd - chunkStart).toLocaleString()));
-                  }
-
-                  return {
-                    header: chunkLocstring,
-                    seq: chunkSeq
-                  };
-                })));
-              }
-
-              _context.next = 9;
-              break;
-
-            case 8:
-              throw new Error('Selected region is out of bounds');
-
-            case 9:
-              _context.next = 15;
-              break;
-
-            case 11:
-              _context.prev = 11;
-              _context.t0 = _context["catch"](0);
-              console.error(_context.t0);
-
-              if (active) {
-                setError(_context.t0);
-              }
-
-            case 15:
-            case "end":
-              return _context.stop();
-          }
-        }
-      }, _callee, null, [[0, 11]]);
-    }))();
-    return function () {
-      controller.abort();
-      active = false;
-    };
-  }, [model, session, regionsSelected, setSequence]);
-  var sequenceTooLarge = sequence ? sequence.length > 1000000 : false;
-  return /*#__PURE__*/_react.default.createElement(_core.Dialog, {
-    "data-testid": "sequence-dialog",
-    maxWidth: "xl",
-    open: true,
-    onClose: handleClose,
-    "aria-labelledby": "alert-dialog-title",
-    "aria-describedby": "alert-dialog-description"
-  }, /*#__PURE__*/_react.default.createElement(_core.DialogTitle, {
-    id: "alert-dialog-title"
-  }, "Reference sequence", handleClose ? /*#__PURE__*/_react.default.createElement(_core.IconButton, {
-    "data-testid": "close-seqDialog",
-    className: classes.closeButton,
-    onClick: function onClick() {
-      handleClose();
-      model.setOffsets(undefined, undefined);
-    }
-  }, /*#__PURE__*/_react.default.createElement(_Close.default, null)) : null), /*#__PURE__*/_react.default.createElement(_core.Divider, null), /*#__PURE__*/_react.default.createElement(_core.DialogContent, null, error ? /*#__PURE__*/_react.default.createElement(_core.Typography, {
-    color: "error"
-  }, "".concat(error)) : null, loading && !error ? /*#__PURE__*/_react.default.createElement(_core.Container, null, "Retrieving reference sequence...", /*#__PURE__*/_react.default.createElement(_core.CircularProgress, {
-    style: {
-      marginLeft: 10
-    },
-    size: 20,
-    disableShrink: true
-  })) : null, /*#__PURE__*/_react.default.createElement(_core.TextField, {
-    "data-testid": "rubberband-sequence",
-    variant: "outlined",
-    multiline: true,
-    minRows: 5,
-    disabled: sequenceTooLarge,
-    className: classes.dialogContent,
-    fullWidth: true,
-    value: sequenceTooLarge ? 'Reference sequence too large to display, use the download FASTA button' : sequence,
-    InputProps: {
-      readOnly: true,
-      classes: {
-        input: classes.textAreaFont
-      }
-    }
-  })), /*#__PURE__*/_react.default.createElement(_core.DialogActions, null, /*#__PURE__*/_react.default.createElement(_core.Button, {
-    onClick: function onClick() {
-      (0, _copyToClipboard.default)(sequence || '');
-      session.notify('Copied to clipboard', 'success');
-    },
-    disabled: loading || !!error || sequenceTooLarge,
-    color: "primary",
-    startIcon: /*#__PURE__*/_react.default.createElement(_Icons.ContentCopy, null)
-  }, "Copy to clipboard"), /*#__PURE__*/_react.default.createElement(_core.Button, {
-    onClick: function onClick() {
-      var seqFastaFile = new Blob([sequence || ''], {
-        type: 'text/x-fasta;charset=utf-8'
-      });
-      (0, _fileSaver.saveAs)(seqFastaFile, 'jbrowse_ref_seq.fa');
-    },
-    disabled: loading || !!error,
-    color: "primary",
-    startIcon: /*#__PURE__*/_react.default.createElement(_GetApp.default, null)
-  }, "Download FASTA"), /*#__PURE__*/_react.default.createElement(_core.Button, {
-    onClick: handleClose,
-    color: "primary",
-    autoFocus: true
-  }, "Close")));
+function SequenceDialog(_a) {
+    var _this = this;
+    var model = _a.model, handleClose = _a.handleClose;
+    var classes = useStyles().classes;
+    var session = (0, util_1.getSession)(model);
+    var _b = __read((0, react_1.useState)(), 2), error = _b[0], setError = _b[1];
+    var _c = __read((0, react_1.useState)(), 2), sequence = _c[0], setSequence = _c[1];
+    var loading = Boolean(sequence === undefined);
+    var leftOffset = model.leftOffset, rightOffset = model.rightOffset;
+    // avoid infinite looping of useEffect
+    // random note: the current selected region can't be a computed because it
+    // uses action on base1dview even though it's on the ephemeral base1dview
+    var regionsSelected = (0, react_1.useMemo)(function () { return model.getSelectedRegions(leftOffset, rightOffset); }, [model, leftOffset, rightOffset]);
+    (0, react_1.useEffect)(function () {
+        var active = true;
+        var controller = new AbortController();
+        (function () { return __awaiter(_this, void 0, void 0, function () {
+            var chunks, e_1;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        _a.trys.push([0, 4, , 5]);
+                        if (!(regionsSelected.length > 0)) return [3 /*break*/, 2];
+                        return [4 /*yield*/, fetchSequence(model, regionsSelected, controller.signal)];
+                    case 1:
+                        chunks = _a.sent();
+                        if (active) {
+                            setSequence((0, formatFastaStrings_1.formatSeqFasta)(chunks
+                                .filter(function (f) { return !!f; })
+                                .map(function (chunk) {
+                                var chunkSeq = chunk.get('seq');
+                                var chunkRefName = chunk.get('refName');
+                                var chunkStart = chunk.get('start') + 1;
+                                var chunkEnd = chunk.get('end');
+                                var chunkLocstring = "".concat(chunkRefName, ":").concat(chunkStart, "-").concat(chunkEnd);
+                                if ((chunkSeq === null || chunkSeq === void 0 ? void 0 : chunkSeq.length) !== chunkEnd - chunkStart + 1) {
+                                    throw new Error("".concat(chunkLocstring, " returned ").concat(chunkSeq.length.toLocaleString(), " bases, but should have returned ").concat((chunkEnd - chunkStart).toLocaleString()));
+                                }
+                                return { header: chunkLocstring, seq: chunkSeq };
+                            })));
+                        }
+                        return [3 /*break*/, 3];
+                    case 2: throw new Error('Selected region is out of bounds');
+                    case 3: return [3 /*break*/, 5];
+                    case 4:
+                        e_1 = _a.sent();
+                        console.error(e_1);
+                        if (active) {
+                            setError(e_1);
+                        }
+                        return [3 /*break*/, 5];
+                    case 5: return [2 /*return*/];
+                }
+            });
+        }); })();
+        return function () {
+            controller.abort();
+            active = false;
+        };
+    }, [model, session, regionsSelected, setSequence]);
+    var sequenceTooLarge = sequence ? sequence.length > 1000000 : false;
+    return (react_1.default.createElement(material_1.Dialog, { "data-testid": "sequence-dialog", maxWidth: "xl", open: true, onClose: handleClose, "aria-labelledby": "alert-dialog-title", "aria-describedby": "alert-dialog-description" },
+        react_1.default.createElement(material_1.DialogTitle, { id: "alert-dialog-title" },
+            "Reference sequence",
+            handleClose ? (react_1.default.createElement(material_1.IconButton, { "data-testid": "close-seqDialog", className: classes.closeButton, onClick: function () {
+                    handleClose();
+                    model.setOffsets(undefined, undefined);
+                }, 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,
+            error ? react_1.default.createElement(material_1.Typography, { color: "error" }, "".concat(error)) : null,
+            loading && !error ? (react_1.default.createElement(material_1.Container, null,
+                "Retrieving reference sequence...",
+                react_1.default.createElement(material_1.CircularProgress, { style: {
+                        marginLeft: 10,
+                    }, size: 20, disableShrink: true }))) : null,
+            react_1.default.createElement(material_1.TextField, { "data-testid": "rubberband-sequence", variant: "outlined", multiline: true, minRows: 5, disabled: sequenceTooLarge, className: classes.dialogContent, fullWidth: true, value: sequenceTooLarge
+                    ? 'Reference sequence too large to display, use the download FASTA button'
+                    : sequence, InputProps: {
+                    readOnly: true,
+                    classes: {
+                        input: classes.textAreaFont,
+                    },
+                } })),
+        react_1.default.createElement(material_1.DialogActions, null,
+            react_1.default.createElement(material_1.Button, { onClick: function () {
+                    (0, copy_to_clipboard_1.default)(sequence || '');
+                    session.notify('Copied to clipboard', 'success');
+                }, disabled: loading || !!error || sequenceTooLarge, color: "primary", startIcon: react_1.default.createElement(Icons_1.ContentCopy, null) }, "Copy to clipboard"),
+            react_1.default.createElement(material_1.Button, { onClick: function () {
+                    var seqFastaFile = new Blob([sequence || ''], {
+                        type: 'text/x-fasta;charset=utf-8',
+                    });
+                    (0, file_saver_1.saveAs)(seqFastaFile, 'jbrowse_ref_seq.fa');
+                }, disabled: loading || !!error, color: "primary", startIcon: react_1.default.createElement(GetApp_1.default, null) }, "Download FASTA"),
+            react_1.default.createElement(material_1.Button, { onClick: handleClose, color: "primary", autoFocus: true }, "Close"))));
 }
-
-var _default = (0, _mobxReact.observer)(SequenceDialog);
-
-exports.default = _default;
+exports.default = (0, mobx_react_1.observer)(SequenceDialog);
+//# sourceMappingURL=SequenceDialog.js.map

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

@@ -0,0 +1 @@
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