@jbrowse/plugin-linear-genome-view 2.1.0 → 2.1.2

package/src/LinearGenomeView/index.tsx

@@ -1,3 +1,4 @@
+import { lazy } from 'react'
 import { getConf, AnyConfigurationModel } from '@jbrowse/core/configuration'
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'
 import { Region } from '@jbrowse/core/util/types'
@@ -53,6 +54,10 @@ import RefNameAutocomplete from './components/RefNameAutocomplete'
 import SearchBox from './components/SearchBox'
 import ExportSvgDlg from './components/ExportSvgDialog'
 
+const SequenceSearchDialog = lazy(
+  () => import('./components/SequenceSearchDialog'),
+)
+
 export interface BpOffset {
   refName?: string
   index: number
@@ -396,21 +401,18 @@ export function stateModelFactory(pluginManager: PluginManager) {
         return newBpPerPx
       },
 
-      setOffsets(left: undefined | BpOffset, right: undefined | BpOffset) {
+      setOffsets(left?: BpOffset, right?: BpOffset) {
         // sets offsets used in the get sequence dialog
         self.leftOffset = left
         self.rightOffset = right
       },
 
-      setSearchResults(
-        results: BaseResult[] | undefined,
-        query: string | undefined,
-      ) {
+      setSearchResults(results?: BaseResult[], query?: string) {
         self.searchResults = results
         self.searchQuery = query
       },
 
-      setSequenceDialogOpen(open: boolean) {
+      setGetSequenceDialogOpen(open: boolean) {
         self.seqDialogDisplayed = open
       },
 
@@ -561,8 +563,7 @@ export function stateModelFactory(pluginManager: PluginManager) {
       getSelectedRegions(leftOffset?: BpOffset, rightOffset?: BpOffset) {
         const snap = getSnapshot(self)
         const simView = Base1DView.create({
-          // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
-          ...(snap as Omit<typeof self, symbol>),
+          ...snap,
           interRegionPaddingWidth: self.interRegionPaddingWidth,
         })
 
@@ -718,6 +719,15 @@ export function stateModelFactory(pluginManager: PluginManager) {
             },
             icon: FolderOpenIcon,
           },
+          {
+            label: 'Sequence search',
+            onClick: () => {
+              getSession(self).queueDialog(handleClose => [
+                SequenceSearchDialog,
+                { model: self, handleClose },
+              ])
+            },
+          },
           {
             label: 'Export SVG',
             icon: PhotoCameraIcon,
@@ -774,12 +784,23 @@ export function stateModelFactory(pluginManager: PluginManager) {
             onClick: self.toggleNoTracksActive,
           },
           {
-            label: 'Show gridlines',
+            label: 'Show guidelines',
             icon: VisibilityIcon,
             type: 'checkbox',
             checked: self.showGridlines,
             onClick: self.toggleShowGridlines,
           },
+          ...(canShowCytobands
+            ? [
+                {
+                  label: 'Show ideogram',
+                  icon: VisibilityIcon,
+                  type: 'checkbox' as const,
+                  checked: self.showCytobands,
+                  onClick: () => self.setShowCytobands(!showCytobands),
+                },
+              ]
+            : []),
           {
             label: 'Track labels',
             icon: LabelIcon,
@@ -807,16 +828,6 @@ export function stateModelFactory(pluginManager: PluginManager) {
               },
             ],
           },
-          ...(canShowCytobands
-            ? [
-                {
-                  label: showCytobands ? 'Hide ideogram' : 'Show ideograms',
-                  onClick: () => {
-                    self.setShowCytobands(!showCytobands)
-                  },
-                },
-              ]
-            : []),
         ]
 
         // add track's view level menu options
@@ -826,9 +837,7 @@ export function stateModelFactory(pluginManager: PluginManager) {
               { type: 'divider' },
               { type: 'subHeader', label: key },
             )
-            value.forEach(action => {
-              menuItems.push(action)
-            })
+            value.forEach(action => menuItems.push(action))
           }
         }
 
@@ -1164,9 +1173,7 @@ export function stateModelFactory(pluginManager: PluginManager) {
           {
             label: 'Get sequence',
             icon: MenuOpenIcon,
-            onClick: () => {
-              self.setSequenceDialogOpen(true)
-            },
+            onClick: () => self.setGetSequenceDialogOpen(true),
           },
         ]
       },

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);
-    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 __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 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, variant: "contained" }, "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/esm/LinearGenomeView/components/SequenceDialog.js.map

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