@jbrowse/plugin-alignments 1.6.9 → 1.7.3

package/dist/PileupRPC/rpcMethods.js

@@ -0,0 +1,285 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.PileupGetVisibleModifications = exports.PileupGetGlobalValueForTag = void 0;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
+
+var _get2 = _interopRequireDefault(require("@babel/runtime/helpers/get"));
+
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _dataAdapterCache = require("@jbrowse/core/data_adapters/dataAdapterCache");
+
+var _RpcMethodType3 = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
+
+var _util = require("@jbrowse/core/util");
+
+var _operators = require("rxjs/operators");
+
+var _util2 = require("../util");
+
+var _MismatchParser = require("../BamAdapter/MismatchParser");
+
+function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2["default"])(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2["default"])(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2["default"])(this, result); }; }
+
+function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
+
+var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
+  (0, _inherits2["default"])(PileupGetGlobalValueForTag, _RpcMethodType);
+
+  var _super = _createSuper(PileupGetGlobalValueForTag);
+
+  function PileupGetGlobalValueForTag() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, PileupGetGlobalValueForTag);
+
+    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
+      args[_key] = arguments[_key];
+    }
+
+    _this = _super.call.apply(_super, [this].concat(args));
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "name", 'PileupGetGlobalValueForTag');
+    return _this;
+  }
+
+  (0, _createClass2["default"])(PileupGetGlobalValueForTag, [{
+    key: "serializeArguments",
+    value: function () {
+      var _serializeArguments = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(args, rpcDriverClassName) {
+        var _rootModel$session;
+
+        var rootModel, assemblyManager, renamedArgs;
+        return _regenerator["default"].wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                rootModel = this.pluginManager.rootModel;
+                assemblyManager = rootModel === null || rootModel === void 0 ? void 0 : (_rootModel$session = rootModel.session) === null || _rootModel$session === void 0 ? void 0 : _rootModel$session.assemblyManager;
+
+                if (assemblyManager) {
+                  _context.next = 4;
+                  break;
+                }
+
+                throw new Error('no assembly manager available');
+
+              case 4:
+                _context.next = 6;
+                return (0, _util.renameRegionsIfNeeded)(assemblyManager, args);
+
+              case 6:
+                renamedArgs = _context.sent;
+                return _context.abrupt("return", (0, _get2["default"])((0, _getPrototypeOf2["default"])(PileupGetGlobalValueForTag.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
+
+              case 8:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function serializeArguments(_x, _x2) {
+        return _serializeArguments.apply(this, arguments);
+      }
+
+      return serializeArguments;
+    }()
+  }, {
+    key: "execute",
+    value: function () {
+      var _execute = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(args, rpcDriverClassName) {
+        var deserializedArgs, adapterConfig, sessionId, regions, tag, dataAdapter, features, featuresArray, uniqueValues;
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                _context2.next = 2;
+                return this.deserializeArguments(args, rpcDriverClassName);
+
+              case 2:
+                deserializedArgs = _context2.sent;
+                adapterConfig = deserializedArgs.adapterConfig, sessionId = deserializedArgs.sessionId, regions = deserializedArgs.regions, tag = deserializedArgs.tag;
+                _context2.next = 6;
+                return (0, _dataAdapterCache.getAdapter)(this.pluginManager, sessionId, adapterConfig);
+
+              case 6:
+                dataAdapter = _context2.sent.dataAdapter;
+                features = dataAdapter.getFeaturesInMultipleRegions(regions);
+                _context2.next = 10;
+                return features.pipe((0, _operators.toArray)()).toPromise();
+
+              case 10:
+                featuresArray = _context2.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 _context2.abrupt("return", (0, _toConsumableArray2["default"])(uniqueValues));
+
+              case 14:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function execute(_x3, _x4) {
+        return _execute.apply(this, arguments);
+      }
+
+      return execute;
+    }()
+  }]);
+  return PileupGetGlobalValueForTag;
+}(_RpcMethodType3["default"]);
+
+exports.PileupGetGlobalValueForTag = PileupGetGlobalValueForTag;
+
+var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
+  (0, _inherits2["default"])(PileupGetVisibleModifications, _RpcMethodType2);
+
+  var _super2 = _createSuper(PileupGetVisibleModifications);
+
+  function PileupGetVisibleModifications() {
+    var _this2;
+
+    (0, _classCallCheck2["default"])(this, PileupGetVisibleModifications);
+
+    for (var _len2 = arguments.length, args = new Array(_len2), _key2 = 0; _key2 < _len2; _key2++) {
+      args[_key2] = arguments[_key2];
+    }
+
+    _this2 = _super2.call.apply(_super2, [this].concat(args));
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this2), "name", 'PileupGetVisibleModifications');
+    return _this2;
+  }
+
+  (0, _createClass2["default"])(PileupGetVisibleModifications, [{
+    key: "serializeArguments",
+    value: function () {
+      var _serializeArguments2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(args, rpcDriverClassName) {
+        var _rootModel$session2;
+
+        var rootModel, assemblyManager, renamedArgs;
+        return _regenerator["default"].wrap(function _callee3$(_context3) {
+          while (1) {
+            switch (_context3.prev = _context3.next) {
+              case 0:
+                rootModel = this.pluginManager.rootModel;
+                assemblyManager = rootModel === null || rootModel === void 0 ? void 0 : (_rootModel$session2 = rootModel.session) === null || _rootModel$session2 === void 0 ? void 0 : _rootModel$session2.assemblyManager;
+
+                if (assemblyManager) {
+                  _context3.next = 4;
+                  break;
+                }
+
+                throw new Error('no assembly manager available');
+
+              case 4:
+                _context3.next = 6;
+                return (0, _util.renameRegionsIfNeeded)(assemblyManager, args);
+
+              case 6:
+                renamedArgs = _context3.sent;
+                return _context3.abrupt("return", (0, _get2["default"])((0, _getPrototypeOf2["default"])(PileupGetVisibleModifications.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
+
+              case 8:
+              case "end":
+                return _context3.stop();
+            }
+          }
+        }, _callee3, this);
+      }));
+
+      function serializeArguments(_x5, _x6) {
+        return _serializeArguments2.apply(this, arguments);
+      }
+
+      return serializeArguments;
+    }()
+  }, {
+    key: "execute",
+    value: function () {
+      var _execute2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(args, rpcDriverClassName) {
+        var deserializedArgs, adapterConfig, sessionId, regions, dataAdapter, features, featuresArray, uniqueValues;
+        return _regenerator["default"].wrap(function _callee4$(_context4) {
+          while (1) {
+            switch (_context4.prev = _context4.next) {
+              case 0:
+                _context4.next = 2;
+                return this.deserializeArguments(args, rpcDriverClassName);
+
+              case 2:
+                deserializedArgs = _context4.sent;
+                adapterConfig = deserializedArgs.adapterConfig, sessionId = deserializedArgs.sessionId, regions = deserializedArgs.regions;
+                _context4.next = 6;
+                return (0, _dataAdapterCache.getAdapter)(this.pluginManager, sessionId, adapterConfig);
+
+              case 6:
+                dataAdapter = _context4.sent.dataAdapter;
+                features = dataAdapter.getFeaturesInMultipleRegions(regions);
+                _context4.next = 10;
+                return features.pipe((0, _operators.toArray)()).toPromise();
+
+              case 10:
+                featuresArray = _context4.sent;
+                uniqueValues = new Set();
+                featuresArray.forEach(function (feature) {
+                  var val = (0, _util2.getTagAlt)(feature, 'MM', 'Mm') || '';
+
+                  if (val !== undefined) {
+                    (0, _MismatchParser.getModificationTypes)(val).forEach(function (t) {
+                      return uniqueValues.add(t);
+                    });
+                  }
+                });
+                return _context4.abrupt("return", (0, _toConsumableArray2["default"])(uniqueValues));
+
+              case 14:
+              case "end":
+                return _context4.stop();
+            }
+          }
+        }, _callee4, this);
+      }));
+
+      function execute(_x7, _x8) {
+        return _execute2.apply(this, arguments);
+      }
+
+      return execute;
+    }()
+  }]);
+  return PileupGetVisibleModifications;
+}(_RpcMethodType3["default"]);
+
+exports.PileupGetVisibleModifications = PileupGetVisibleModifications;

package/dist/PileupRenderer/PileupLayoutSession.d.ts

@@ -1,29 +1,29 @@
-import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
-import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
-export interface PileupLayoutSessionProps {
-    config: AnyConfigurationModel;
-    bpPerPx: number;
-    filters: SerializableFilterChain;
-    sortedBy: unknown;
-    showSoftClip: unknown;
-}
-declare type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
-interface CachedPileupLayout {
-    layout: MyMultiLayout;
-    config: AnyConfigurationModel;
-    filters: SerializableFilterChain;
-    sortedBy: unknown;
-    showSoftClip: boolean;
-}
-export declare class PileupLayoutSession extends LayoutSession {
-    sortedBy: unknown;
-    showSoftClip: boolean;
-    constructor(args: PileupLayoutSessionProps);
-    cachedLayoutIsValid(cachedLayout: CachedPileupLayout): boolean;
-    cachedLayout: CachedPileupLayout | undefined;
-    get layout(): MyMultiLayout;
-}
-export {};
+import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
+import GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
+import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
+export interface PileupLayoutSessionProps {
+    config: AnyConfigurationModel;
+    bpPerPx: number;
+    filters: SerializableFilterChain;
+    sortedBy: unknown;
+    showSoftClip: unknown;
+}
+declare type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
+interface CachedPileupLayout {
+    layout: MyMultiLayout;
+    config: AnyConfigurationModel;
+    filters: SerializableFilterChain;
+    sortedBy: unknown;
+    showSoftClip: boolean;
+}
+export declare class PileupLayoutSession extends LayoutSession {
+    sortedBy: unknown;
+    showSoftClip: boolean;
+    constructor(args: PileupLayoutSessionProps);
+    cachedLayoutIsValid(cachedLayout: CachedPileupLayout): boolean;
+    cachedLayout: CachedPileupLayout | undefined;
+    get layout(): MyMultiLayout;
+}
+export {};

package/dist/PileupRenderer/PileupLayoutSession.js

@@ -0,0 +1,79 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.PileupLayoutSession = void 0;
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
+
+var _get2 = _interopRequireDefault(require("@babel/runtime/helpers/get"));
+
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _fastDeepEqual = _interopRequireDefault(require("fast-deep-equal"));
+
+var _BoxRendererType = require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2["default"])(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2["default"])(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2["default"])(this, result); }; }
+
+function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
+
+// Sorting and revealing soft clip changes the layout of Pileup renderer
+// Adds extra conditions to see if cached layout is valid
+var PileupLayoutSession = /*#__PURE__*/function (_LayoutSession) {
+  (0, _inherits2["default"])(PileupLayoutSession, _LayoutSession);
+
+  var _super = _createSuper(PileupLayoutSession);
+
+  function PileupLayoutSession(args) {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, PileupLayoutSession);
+    _this = _super.call(this, args);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "sortedBy", void 0);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "showSoftClip", false);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "cachedLayout", void 0);
+    _this.config = args.config;
+    return _this;
+  }
+
+  (0, _createClass2["default"])(PileupLayoutSession, [{
+    key: "cachedLayoutIsValid",
+    value: function cachedLayoutIsValid(cachedLayout) {
+      return (0, _get2["default"])((0, _getPrototypeOf2["default"])(PileupLayoutSession.prototype), "cachedLayoutIsValid", this).call(this, cachedLayout) && this.showSoftClip === cachedLayout.showSoftClip && (0, _fastDeepEqual["default"])(this.sortedBy, cachedLayout.sortedBy);
+    }
+  }, {
+    key: "layout",
+    get: function get() {
+      if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
+        this.cachedLayout = {
+          layout: this.makeLayout(),
+          config: (0, _configuration.readConfObject)(this.config),
+          filters: this.filters,
+          sortedBy: this.sortedBy,
+          showSoftClip: this.showSoftClip
+        };
+      }
+
+      return this.cachedLayout.layout;
+    }
+  }]);
+  return PileupLayoutSession;
+}(_BoxRendererType.LayoutSession);
+
+exports.PileupLayoutSession = PileupLayoutSession;