npm - @jbrowse/plugin-linear-genome-view - Versions diffs - 2.0.0 → 2.1.2 - Mend

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

Files changed (144) hide show

package/dist/LinearGenomeView/index.js.map CHANGED Viewed

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package/dist/LinearGenomeView/util.js CHANGED Viewed

@@ -1,20 +1,4 @@
 "use strict";
-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;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.makeTicks = exports.chooseGridPitch = void 0;
 /**
@@ -24,9 +8,9 @@ exports.makeTicks = exports.chooseGridPitch = void 0;
  */
 function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
     scale = Math.abs(scale);
-    var minMajorPitchBp = minMajorPitchPx * scale;
-    var majorMagnitude = parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
-    var majorPitch = Math.pow(10, majorMagnitude);
+    const minMajorPitchBp = minMajorPitchPx * scale;
+    const majorMagnitude = parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
+    let majorPitch = 10 ** majorMagnitude;
     while (majorPitch < minMajorPitchBp) {
         majorPitch *= 2;
         if (majorPitch >= minMajorPitchBp) {
@@ -35,8 +19,8 @@ function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
         majorPitch *= 2.5;
     }
     majorPitch = Math.max(majorPitch, 5);
-    var majorPitchPx = majorPitch / scale;
-    var minorPitch = 0;
+    const majorPitchPx = majorPitch / scale;
+    let minorPitch = 0;
     if (!(majorPitch % 10) && majorPitchPx / 10 >= minMinorPitchPx) {
         minorPitch = majorPitch / 10;
     }
@@ -46,37 +30,34 @@ function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
     else if (!(majorPitch % 2) && majorPitchPx / 2 >= minMinorPitchPx) {
         minorPitch = majorPitch / 2;
     }
-    return { majorPitch: majorPitch, minorPitch: minorPitch };
+    return { majorPitch, minorPitch };
 }
 exports.chooseGridPitch = chooseGridPitch;
-function makeTicks(start, end, bpPerPx, emitMajor, emitMinor) {
-    var _a;
-    if (emitMajor === void 0) { emitMajor = true; }
-    if (emitMinor === void 0) { emitMinor = true; }
-    var gridPitch = chooseGridPitch(bpPerPx, 60, 15);
-    var minBase = start;
-    var maxBase = end;
+function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = true) {
+    const gridPitch = chooseGridPitch(bpPerPx, 60, 15);
+    let minBase = start;
+    let maxBase = end;
     if (minBase === null || maxBase === null) {
         return [];
     }
     if (bpPerPx < 0) {
         ;
-        _a = __read([maxBase, minBase], 2), minBase = _a[0], maxBase = _a[1];
+        [minBase, maxBase] = [maxBase, minBase];
     }
     // add 20px additional on the right and left to allow us to draw the ends
     // of labels that lie a little outside our region
     minBase -= Math.abs(20 * bpPerPx) - 1;
     maxBase += Math.abs(20 * bpPerPx) + 1;
-    var iterPitch = gridPitch.minorPitch || gridPitch.majorPitch;
-    var index = 0;
-    var ticks = [];
-    for (var base = Math.ceil(minBase / iterPitch) * iterPitch; base < maxBase; base += iterPitch) {
+    const iterPitch = gridPitch.minorPitch || gridPitch.majorPitch;
+    let index = 0;
+    const ticks = [];
+    for (let base = Math.ceil(minBase / iterPitch) * iterPitch; base < maxBase; base += iterPitch) {
         if (emitMinor && base % (gridPitch.majorPitch * 2)) {
-            ticks.push({ type: 'minor', base: base - 1, index: index });
+            ticks.push({ type: 'minor', base: base - 1, index });
             index += 1;
         }
         else if (emitMajor && !(base % (gridPitch.majorPitch * 2))) {
-            ticks.push({ type: 'major', base: base - 1, index: index });
+            ticks.push({ type: 'major', base: base - 1, index });
             index += 1;
         }
     }

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package/dist/index.js CHANGED Viewed

@@ -1,19 +1,4 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     var desc = Object.getOwnPropertyDescriptor(m, k);
@@ -37,200 +22,144 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __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 __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SearchBox = exports.RefNameAutocomplete = exports.BaseLinearDisplay = exports.BaseLinearDisplayComponent = exports.renderToSvg = exports.linearBasicDisplayModelFactory = exports.linearBasicDisplayConfigSchemaFactory = exports.linearBareDisplayConfigSchemaFactory = exports.baseLinearDisplayConfigSchema = void 0;
-var react_1 = require("react");
-var mobx_1 = require("mobx");
-var configuration_1 = require("@jbrowse/core/configuration");
-var models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-var TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
-var DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-var ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
-var Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-var util_1 = require("@jbrowse/core/util");
-var LineStyle_1 = __importDefault(require("@mui/icons-material/LineStyle"));
-var BaseLinearDisplay_1 = require("./BaseLinearDisplay");
+const react_1 = require("react");
+const mobx_1 = require("mobx");
+const configuration_1 = require("@jbrowse/core/configuration");
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
+const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
+const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+const util_1 = require("@jbrowse/core/util");
+const LineStyle_1 = __importDefault(require("@mui/icons-material/LineStyle"));
+const BaseLinearDisplay_1 = require("./BaseLinearDisplay");
 Object.defineProperty(exports, "BaseLinearDisplay", { enumerable: true, get: function () { return BaseLinearDisplay_1.BaseLinearDisplay; } });
 Object.defineProperty(exports, "BaseLinearDisplayComponent", { enumerable: true, get: function () { return BaseLinearDisplay_1.BaseLinearDisplayComponent; } });
 Object.defineProperty(exports, "baseLinearDisplayConfigSchema", { enumerable: true, get: function () { return BaseLinearDisplay_1.baseLinearDisplayConfigSchema; } });
-var LinearBareDisplay_1 = require("./LinearBareDisplay");
+const LinearBareDisplay_1 = require("./LinearBareDisplay");
 Object.defineProperty(exports, "linearBareDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearBareDisplay_1.configSchemaFactory; } });
-var LinearGenomeView_1 = require("./LinearGenomeView");
+const LinearGenomeView_1 = require("./LinearGenomeView");
 Object.defineProperty(exports, "renderToSvg", { enumerable: true, get: function () { return LinearGenomeView_1.renderToSvg; } });
 Object.defineProperty(exports, "RefNameAutocomplete", { enumerable: true, get: function () { return LinearGenomeView_1.RefNameAutocomplete; } });
 Object.defineProperty(exports, "SearchBox", { enumerable: true, get: function () { return LinearGenomeView_1.SearchBox; } });
-var LinearBasicDisplay_1 = require("./LinearBasicDisplay");
+const LinearBasicDisplay_1 = require("./LinearBasicDisplay");
 Object.defineProperty(exports, "linearBasicDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearBasicDisplay_1.configSchema; } });
 Object.defineProperty(exports, "linearBasicDisplayModelFactory", { enumerable: true, get: function () { return LinearBasicDisplay_1.modelFactory; } });
-var LinearGenomeViewPlugin = /** @class */ (function (_super) {
-    __extends(LinearGenomeViewPlugin, _super);
-    function LinearGenomeViewPlugin() {
-        var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this.name = 'LinearGenomeViewPlugin';
-        _this.exports = {
+class LinearGenomeViewPlugin extends Plugin_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'LinearGenomeViewPlugin';
+        this.exports = {
             BaseLinearDisplayComponent: BaseLinearDisplay_1.BaseLinearDisplayComponent,
             BaseLinearDisplay: BaseLinearDisplay_1.BaseLinearDisplay,
             baseLinearDisplayConfigSchema: BaseLinearDisplay_1.baseLinearDisplayConfigSchema,
         };
-        return _this;
     }
-    LinearGenomeViewPlugin.prototype.install = function (pluginManager) {
-        var _this = this;
-        pluginManager.addTrackType(function () {
-            var configSchema = (0, configuration_1.ConfigurationSchema)('FeatureTrack', {}, {
+    install(pluginManager) {
+        pluginManager.addTrackType(() => {
+            const configSchema = (0, configuration_1.ConfigurationSchema)('FeatureTrack', {}, {
                 baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager),
                 explicitIdentifier: 'trackId',
             });
             return new TrackType_1.default({
                 name: 'FeatureTrack',
-                configSchema: configSchema,
+                configSchema,
                 stateModel: (0, models_1.createBaseTrackModel)(pluginManager, 'FeatureTrack', configSchema),
             });
         });
-        pluginManager.addTrackType(function () {
-            var configSchema = (0, configuration_1.ConfigurationSchema)('BasicTrack', {}, {
+        pluginManager.addTrackType(() => {
+            const configSchema = (0, configuration_1.ConfigurationSchema)('BasicTrack', {}, {
                 baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager),
                 explicitIdentifier: 'trackId',
             });
             return new TrackType_1.default({
                 name: 'BasicTrack',
-                configSchema: configSchema,
+                configSchema,
                 stateModel: (0, models_1.createBaseTrackModel)(pluginManager, 'BasicTrack', configSchema),
             });
         });
-        pluginManager.addDisplayType(function () {
-            var configSchema = (0, LinearBareDisplay_1.configSchemaFactory)(pluginManager);
+        pluginManager.addDisplayType(() => {
+            const configSchema = (0, LinearBareDisplay_1.configSchemaFactory)(pluginManager);
             return new DisplayType_1.default({
                 name: 'LinearBareDisplay',
-                configSchema: configSchema,
+                configSchema,
                 stateModel: (0, LinearBareDisplay_1.stateModelFactory)(configSchema),
                 trackType: 'BasicTrack',
                 viewType: 'LinearGenomeView',
                 ReactComponent: BaseLinearDisplay_1.BaseLinearDisplayComponent,
             });
         });
-        pluginManager.addDisplayType(function () {
-            var configSchema = (0, LinearBasicDisplay_1.configSchema)(pluginManager);
+        pluginManager.addDisplayType(() => {
+            const configSchema = (0, LinearBasicDisplay_1.configSchema)(pluginManager);
             return new DisplayType_1.default({
                 name: 'LinearBasicDisplay',
-                configSchema: configSchema,
+                configSchema,
                 stateModel: (0, LinearBasicDisplay_1.modelFactory)(configSchema),
                 trackType: 'FeatureTrack',
                 viewType: 'LinearGenomeView',
                 ReactComponent: BaseLinearDisplay_1.BaseLinearDisplayComponent,
             });
         });
-        pluginManager.addViewType(function () {
-            return new ViewType_1.default({
-                name: 'LinearGenomeView',
-                stateModel: (0, LinearGenomeView_1.stateModelFactory)(pluginManager),
-                ReactComponent: (0, react_1.lazy)(function () { return Promise.resolve().then(function () { return __importStar(require('./LinearGenomeView/components/LinearGenomeView')); }); }),
-            });
-        });
+        pluginManager.addViewType(() => new ViewType_1.default({
+            name: 'LinearGenomeView',
+            stateModel: (0, LinearGenomeView_1.stateModelFactory)(pluginManager),
+            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LinearGenomeView/components/LinearGenomeView')))),
+        }));
         pluginManager.addToExtensionPoint('LaunchView-LinearGenomeView',
         // @ts-ignore
-        function (_a) {
-            var session = _a.session, assembly = _a.assembly, loc = _a.loc, _b = _a.tracks, tracks = _b === void 0 ? [] : _b;
-            return __awaiter(_this, void 0, void 0, function () {
-                var assemblyManager, view_1, asm, idsNotFound_1, e_1;
-                return __generator(this, function (_c) {
-                    switch (_c.label) {
-                        case 0:
-                            _c.trys.push([0, 3, , 4]);
-                            assemblyManager = session.assemblyManager;
-                            view_1 = session.addView('LinearGenomeView', {});
-                            return [4 /*yield*/, (0, mobx_1.when)(function () { return !!view_1.volatileWidth; })];
-                        case 1:
-                            _c.sent();
-                            if (!assembly) {
-                                throw new Error('No assembly provided when launching linear genome view');
-                            }
-                            return [4 /*yield*/, assemblyManager.waitForAssembly(assembly)];
-                        case 2:
-                            asm = _c.sent();
-                            if (!asm) {
-                                throw new Error("Assembly \"".concat(assembly, "\" not found when launching linear genome view"));
-                            }
-                            view_1.navToLocString(loc, assembly);
-                            idsNotFound_1 = [];
-                            tracks.forEach(function (track) {
-                                try {
-                                    view_1.showTrack(track);
-                                }
-                                catch (e) {
-                                    if ("".concat(e).match('Could not resolve identifier')) {
-                                        idsNotFound_1.push(track);
-                                    }
-                                    else {
-                                        throw e;
-                                    }
-                                }
-                            });
-                            if (idsNotFound_1.length) {
-                                throw new Error("Could not resolve identifiers: ".concat(idsNotFound_1.join(',')));
-                            }
-                            return [3 /*break*/, 4];
-                        case 3:
-                            e_1 = _c.sent();
-                            session.notify("".concat(e_1), 'error');
-                            throw e_1;
-                        case 4: return [2 /*return*/];
+        async ({ session, assembly, loc, tracks = [], }) => {
+            try {
+                const { assemblyManager } = session;
+                const view = session.addView('LinearGenomeView', {});
+                await (0, mobx_1.when)(() => !!view.volatileWidth);
+                if (!assembly) {
+                    throw new Error('No assembly provided when launching linear genome view');
+                }
+                const asm = await assemblyManager.waitForAssembly(assembly);
+                if (!asm) {
+                    throw new Error(`Assembly "${assembly}" not found when launching linear genome view`);
+                }
+                view.navToLocString(loc, assembly);
+                const idsNotFound = [];
+                tracks.forEach(track => {
+                    try {
+                        view.showTrack(track);
+                    }
+                    catch (e) {
+                        if (`${e}`.match('Could not resolve identifier')) {
+                            idsNotFound.push(track);
+                        }
+                        else {
+                            throw e;
+                        }
                     }
                 });
-            });
+                if (idsNotFound.length) {
+                    throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
+                }
+            }
+            catch (e) {
+                session.notify(`${e}`, 'error');
+                throw e;
+            }
         });
-    };
-    LinearGenomeViewPlugin.prototype.configure = function (pluginManager) {
+    }
+    configure(pluginManager) {
         if ((0, util_1.isAbstractMenuManager)(pluginManager.rootModel)) {
             pluginManager.rootModel.appendToSubMenu(['Add'], {
                 label: 'Linear genome view',
                 icon: LineStyle_1.default,
-                onClick: function (session) {
+                onClick: (session) => {
                     session.addView('LinearGenomeView', {});
                 },
             });
         }
-    };
-    return LinearGenomeViewPlugin;
-}(Plugin_1.default));
+    }
+}
 exports.default = LinearGenomeViewPlugin;
 //# sourceMappingURL=index.js.map

package/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/BaseLinearDisplay/components/BaseLinearDisplay.js CHANGED Viewed

@@ -61,7 +61,7 @@ const BaseLinearDisplay = observer((props) => {
                 },
             }, anchorReference: "anchorPosition", anchorPosition: contextCoord
                 ? { top: contextCoord[1], left: contextCoord[0] }
-                : undefined, style: { zIndex: theme.zIndex.tooltip }, menuItems: contextMenuItems(), "data-testid": "base_linear_display_context_menu" })));
+                : undefined, style: { zIndex: theme.zIndex.tooltip }, menuItems: contextMenuItems() })));
 });
 export default BaseLinearDisplay;
 export { Tooltip };

package/esm/BaseLinearDisplay/components/BaseLinearDisplay.js.map CHANGED Viewed

	@@ -1 +1 @@
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