@jbrowse/plugin-alignments 2.1.0 → 2.1.2

package/dist/PileupRPC/rpcMethods.js

@@ -1,206 +1,78 @@
 "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 __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 __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
-    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
-        if (ar || !(i in from)) {
-            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
-            ar[i] = from[i];
-        }
-    }
-    return to.concat(ar || Array.prototype.slice.call(from));
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PileupGetVisibleModifications = exports.PileupGetGlobalValueForTag = void 0;
-var dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
-var RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
-var util_1 = require("@jbrowse/core/util");
-var operators_1 = require("rxjs/operators");
-var util_2 = require("../util");
-var MismatchParser_1 = require("../BamAdapter/MismatchParser");
-var PileupGetGlobalValueForTag = /** @class */ (function (_super) {
-    __extends(PileupGetGlobalValueForTag, _super);
-    function PileupGetGlobalValueForTag() {
-        var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this.name = 'PileupGetGlobalValueForTag';
-        return _this;
+const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+const RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
+const util_1 = require("@jbrowse/core/util");
+const operators_1 = require("rxjs/operators");
+const util_2 = require("../util");
+const MismatchParser_1 = require("../BamAdapter/MismatchParser");
+class PileupGetGlobalValueForTag extends RpcMethodType_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'PileupGetGlobalValueForTag';
     }
-    PileupGetGlobalValueForTag.prototype.serializeArguments = function (args, rpcDriverClassName) {
+    async serializeArguments(args, rpcDriverClassName) {
         var _a;
-        return __awaiter(this, void 0, void 0, function () {
-            var rootModel, assemblyManager, renamedArgs;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        rootModel = this.pluginManager.rootModel;
-                        assemblyManager = (_a = rootModel === null || rootModel === void 0 ? void 0 : rootModel.session) === null || _a === void 0 ? void 0 : _a.assemblyManager;
-                        if (!assemblyManager) {
-                            throw new Error('no assembly manager available');
-                        }
-                        return [4 /*yield*/, (0, util_1.renameRegionsIfNeeded)(assemblyManager, args)];
-                    case 1:
-                        renamedArgs = _b.sent();
-                        return [2 /*return*/, _super.prototype.serializeArguments.call(this, renamedArgs, rpcDriverClassName)];
-                }
-            });
-        });
-    };
-    PileupGetGlobalValueForTag.prototype.execute = function (args, rpcDriverClassName) {
-        return __awaiter(this, void 0, void 0, function () {
-            var deserializedArgs, adapterConfig, sessionId, regions, tag, dataAdapter, features, featuresArray, uniqueValues;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.deserializeArguments(args, rpcDriverClassName)];
-                    case 1:
-                        deserializedArgs = _a.sent();
-                        adapterConfig = deserializedArgs.adapterConfig, sessionId = deserializedArgs.sessionId, regions = deserializedArgs.regions, tag = deserializedArgs.tag;
-                        return [4 /*yield*/, (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)];
-                    case 2:
-                        dataAdapter = (_a.sent()).dataAdapter;
-                        features = dataAdapter.getFeaturesInMultipleRegions(regions);
-                        return [4 /*yield*/, features.pipe((0, operators_1.toArray)()).toPromise()];
-                    case 3:
-                        featuresArray = _a.sent();
-                        uniqueValues = new Set();
-                        featuresArray.forEach(function (feature) {
-                            var tags = feature.get('tags');
-                            var val = tags ? tags[tag] : feature.get(tag);
-                            if (val !== undefined) {
-                                uniqueValues.add("".concat(val));
-                            }
-                        });
-                        return [2 /*return*/, __spreadArray([], __read(uniqueValues), false)];
-                }
-            });
+        const { rootModel } = this.pluginManager;
+        const assemblyManager = (_a = rootModel === null || rootModel === void 0 ? void 0 : rootModel.session) === null || _a === void 0 ? void 0 : _a.assemblyManager;
+        if (!assemblyManager) {
+            throw new Error('no assembly manager available');
+        }
+        const renamedArgs = await (0, util_1.renameRegionsIfNeeded)(assemblyManager, args);
+        return super.serializeArguments(renamedArgs, rpcDriverClassName);
+    }
+    async execute(args, rpcDriverClassName) {
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { adapterConfig, sessionId, regions, tag } = deserializedArgs;
+        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
+        const features = dataAdapter.getFeaturesInMultipleRegions(regions);
+        const featuresArray = await features.pipe((0, operators_1.toArray)()).toPromise();
+        const uniqueValues = new Set();
+        featuresArray.forEach(feature => {
+            const tags = feature.get('tags');
+            const val = tags ? tags[tag] : feature.get(tag);
+            if (val !== undefined) {
+                uniqueValues.add(`${val}`);
+            }
         });
-    };
-    return PileupGetGlobalValueForTag;
-}(RpcMethodType_1.default));
+        return [...uniqueValues];
+    }
+}
 exports.PileupGetGlobalValueForTag = PileupGetGlobalValueForTag;
-var PileupGetVisibleModifications = /** @class */ (function (_super) {
-    __extends(PileupGetVisibleModifications, _super);
-    function PileupGetVisibleModifications() {
-        var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this.name = 'PileupGetVisibleModifications';
-        return _this;
+class PileupGetVisibleModifications extends RpcMethodType_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'PileupGetVisibleModifications';
     }
-    PileupGetVisibleModifications.prototype.serializeArguments = function (args, rpcDriverClassName) {
+    async serializeArguments(args, rpcDriverClassName) {
         var _a;
-        return __awaiter(this, void 0, void 0, function () {
-            var rootModel, assemblyManager, renamedArgs;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        rootModel = this.pluginManager.rootModel;
-                        assemblyManager = (_a = rootModel === null || rootModel === void 0 ? void 0 : rootModel.session) === null || _a === void 0 ? void 0 : _a.assemblyManager;
-                        if (!assemblyManager) {
-                            throw new Error('no assembly manager available');
-                        }
-                        return [4 /*yield*/, (0, util_1.renameRegionsIfNeeded)(assemblyManager, args)];
-                    case 1:
-                        renamedArgs = _b.sent();
-                        return [2 /*return*/, _super.prototype.serializeArguments.call(this, renamedArgs, rpcDriverClassName)];
-                }
-            });
-        });
-    };
-    PileupGetVisibleModifications.prototype.execute = function (args, rpcDriverClassName) {
-        return __awaiter(this, void 0, void 0, function () {
-            var deserializedArgs, adapterConfig, sessionId, regions, dataAdapter, features, featuresArray, uniqueValues;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.deserializeArguments(args, rpcDriverClassName)];
-                    case 1:
-                        deserializedArgs = _a.sent();
-                        adapterConfig = deserializedArgs.adapterConfig, sessionId = deserializedArgs.sessionId, regions = deserializedArgs.regions;
-                        return [4 /*yield*/, (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)];
-                    case 2:
-                        dataAdapter = (_a.sent()).dataAdapter;
-                        features = dataAdapter.getFeaturesInMultipleRegions(regions);
-                        return [4 /*yield*/, features.pipe((0, operators_1.toArray)()).toPromise()];
-                    case 3:
-                        featuresArray = _a.sent();
-                        uniqueValues = new Set();
-                        featuresArray.forEach(function (feature) {
-                            var val = (0, util_2.getTagAlt)(feature, 'MM', 'Mm') || '';
-                            if (val !== undefined) {
-                                (0, MismatchParser_1.getModificationTypes)(val).forEach(function (t) { return uniqueValues.add(t); });
-                            }
-                        });
-                        return [2 /*return*/, __spreadArray([], __read(uniqueValues), false)];
-                }
-            });
+        const { rootModel } = this.pluginManager;
+        const assemblyManager = (_a = rootModel === null || rootModel === void 0 ? void 0 : rootModel.session) === null || _a === void 0 ? void 0 : _a.assemblyManager;
+        if (!assemblyManager) {
+            throw new Error('no assembly manager available');
+        }
+        const renamedArgs = await (0, util_1.renameRegionsIfNeeded)(assemblyManager, args);
+        return super.serializeArguments(renamedArgs, rpcDriverClassName);
+    }
+    async execute(args, rpcDriverClassName) {
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { adapterConfig, sessionId, regions } = deserializedArgs;
+        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
+        const features = dataAdapter.getFeaturesInMultipleRegions(regions);
+        const featuresArray = await features.pipe((0, operators_1.toArray)()).toPromise();
+        const uniqueValues = new Set();
+        featuresArray.forEach(feature => {
+            const val = (0, util_2.getTagAlt)(feature, 'MM', 'Mm') || '';
+            if (val !== undefined) {
+                (0, MismatchParser_1.getModificationTypes)(val).forEach(t => uniqueValues.add(t));
+            }
         });
-    };
-    return PileupGetVisibleModifications;
-}(RpcMethodType_1.default));
+        return [...uniqueValues];
+    }
+}
 exports.PileupGetVisibleModifications = PileupGetVisibleModifications;
 //# sourceMappingURL=rpcMethods.js.map

package/dist/PileupRPC/rpcMethods.js.map

@@ -1 +1 @@
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package/dist/PileupRenderer/PileupLayoutSession.js

@@ -1,61 +1,39 @@
 "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 __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PileupLayoutSession = void 0;
-var fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
-var BoxRendererType_1 = require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType");
-var configuration_1 = require("@jbrowse/core/configuration");
+const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
+const BoxRendererType_1 = require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType");
+const configuration_1 = require("@jbrowse/core/configuration");
 // Sorting and revealing soft clip changes the layout of Pileup renderer
 // Adds extra conditions to see if cached layout is valid
-var PileupLayoutSession = /** @class */ (function (_super) {
-    __extends(PileupLayoutSession, _super);
-    function PileupLayoutSession(args) {
-        var _this = _super.call(this, args) || this;
-        _this.showSoftClip = false;
-        _this.config = args.config;
-        return _this;
+class PileupLayoutSession extends BoxRendererType_1.LayoutSession {
+    constructor(args) {
+        super(args);
+        this.showSoftClip = false;
+        this.config = args.config;
     }
-    PileupLayoutSession.prototype.cachedLayoutIsValid = function (cachedLayout) {
-        return (_super.prototype.cachedLayoutIsValid.call(this, cachedLayout) &&
+    cachedLayoutIsValid(cachedLayout) {
+        return (super.cachedLayoutIsValid(cachedLayout) &&
             this.showSoftClip === cachedLayout.showSoftClip &&
             (0, fast_deep_equal_1.default)(this.sortedBy, cachedLayout.sortedBy) &&
             (0, fast_deep_equal_1.default)(this.filterBy, cachedLayout.filterBy));
-    };
-    Object.defineProperty(PileupLayoutSession.prototype, "layout", {
-        get: function () {
-            if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
-                this.cachedLayout = {
-                    layout: this.makeLayout(),
-                    config: (0, configuration_1.readConfObject)(this.config),
-                    filters: this.filters,
-                    filterBy: this.filterBy,
-                    sortedBy: this.sortedBy,
-                    showSoftClip: this.showSoftClip,
-                };
-            }
-            return this.cachedLayout.layout;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    return PileupLayoutSession;
-}(BoxRendererType_1.LayoutSession));
+    }
+    get layout() {
+        if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
+            this.cachedLayout = {
+                layout: this.makeLayout(),
+                config: (0, configuration_1.readConfObject)(this.config),
+                filters: this.filters,
+                filterBy: this.filterBy,
+                sortedBy: this.sortedBy,
+                showSoftClip: this.showSoftClip,
+            };
+        }
+        return this.cachedLayout.layout;
+    }
+}
 exports.PileupLayoutSession = PileupLayoutSession;
 //# sourceMappingURL=PileupLayoutSession.js.map

package/dist/PileupRenderer/PileupLayoutSession.js.map

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