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

package/dist/LinearGenomeView/components/SequenceDialog.js

@@ -1,242 +0,0 @@
-"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);
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-}));
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-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
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-    __setModuleDefault(result, mod);
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-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
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-                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;
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-        try {
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-    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 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),
-    },
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
-    dialogContent: {
-        width: '80em',
-    },
-    textAreaFont: {
-        fontFamily: 'Courier New',
-    },
-}); });
-/**
- * Fetches and returns a list features for a given list of regions
- */
-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) {
-                throw new Error('no offsets on model to use for range');
-            }
-            if (leftOffset.assemblyName !== rightOffset.assemblyName) {
-                throw new Error('not able to fetch sequences from multiple assemblies');
-            }
-            rpcManager = session.rpcManager, assemblyManager = session.assemblyManager;
-            assemblyName = leftOffset.assemblyName || rightOffset.assemblyName || '';
-            assembly = assemblyManager.get(assemblyName);
-            if (!assembly) {
-                throw new Error("assembly ".concat(assemblyName, " not found"));
-            }
-            adapterConfig = (0, configuration_1.getConf)(assembly, ['sequence', 'adapter']);
-            sessionId = 'getSequence';
-            return [2 /*return*/, rpcManager.call(sessionId, 'CoreGetFeatures', {
-                    adapterConfig: adapterConfig,
-                    regions: regions,
-                    sessionId: sessionId,
-                    signal: signal,
-                })];
-        });
-    });
-}
-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"))));
-}
-exports.default = (0, mobx_react_1.observer)(SequenceDialog);
-//# sourceMappingURL=SequenceDialog.js.map

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

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

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

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package/esm/LinearGenomeView/components/VerticalGuides.js.map

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