@jbrowse/plugin-config 1.6.7 → 1.7.0

package/dist/ConfigurationEditorWidget/index.js

@@ -0,0 +1,45 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.configSchema = exports.HeadingComponent = void 0;
+Object.defineProperty(exports, "stateModelFactory", {
+  enumerable: true,
+  get: function get() {
+    return _model["default"];
+  }
+});
+
+var _mobxReact = require("mobx-react");
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _model = _interopRequireDefault(require("./model"));
+
+var configSchema = (0, _configuration.ConfigurationSchema)('ConfigurationEditorWidget', {});
+exports.configSchema = configSchema;
+var HeadingComponent = (0, _mobxReact.observer)(function (_ref) {
+  var model = _ref.model;
+
+  if (model && model.target) {
+    if (model.target.type) {
+      return "".concat(model.target.type, " settings");
+    }
+
+    if ((0, _mobxStateTree.isStateTreeNode)(model.target)) {
+      var type = (0, _mobxStateTree.getType)(model.target);
+
+      if (type && type.name) {
+        return "".concat(type.name.replace('ConfigurationSchema', ''), " settings");
+      }
+    }
+  }
+
+  return 'Settings';
+});
+exports.HeadingComponent = HeadingComponent;

package/dist/ConfigurationEditorWidget/model.js

@@ -0,0 +1,28 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _mst = require("@jbrowse/core/util/types/mst");
+
+var _default = function _default(pluginManager) {
+  return _mobxStateTree.types.model('ConfigurationEditorWidget', {
+    id: _mst.ElementId,
+    type: _mobxStateTree.types.literal('ConfigurationEditorWidget'),
+    // If you add different types of targets, don't forget to account for that
+    // in the key of ./components/ConfigurationEditor.js
+    target: _mobxStateTree.types.safeReference(pluginManager.pluggableConfigSchemaType('track'))
+  }).actions(function (self) {
+    return {
+      setTarget: function setTarget(newTarget) {
+        self.target = newTarget;
+      }
+    };
+  });
+};
+
+exports["default"] = _default;

package/dist/FromConfigAdapter/FromConfigAdapter.js

@@ -0,0 +1,215 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = 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 _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 _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+var _rxjs = require("@jbrowse/core/util/rxjs");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it["return"] != null) it["return"](); } finally { if (didErr) throw err; } } }; }
+
+function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
+
+function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
+
+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; } }
+
+/**
+ * Adapter that just returns the features defined in its `features` configuration
+ * key, like:
+ *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
+ */
+var FromConfigAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
+  (0, _inherits2["default"])(FromConfigAdapter, _BaseFeatureDataAdapt);
+
+  var _super = _createSuper(FromConfigAdapter);
+
+  function FromConfigAdapter(conf, getSubAdapter, pluginManager) {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, FromConfigAdapter);
+    _this = _super.call(this, conf, getSubAdapter, pluginManager);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "features", void 0);
+    var feats = (0, _configuration.readConfObject)(conf, 'features');
+    _this.features = FromConfigAdapter.makeFeatures(feats || []);
+    return _this;
+  }
+
+  (0, _createClass2["default"])(FromConfigAdapter, [{
+    key: "getRefNames",
+    value: function () {
+      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        return _regenerator["default"].wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                return _context.abrupt("return", (0, _toConsumableArray2["default"])(this.features.keys()));
+
+              case 1:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function getRefNames() {
+        return _getRefNames.apply(this, arguments);
+      }
+
+      return getRefNames;
+    }()
+  }, {
+    key: "getRefNameAliases",
+    value: function () {
+      var _getRefNameAliases = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                return _context2.abrupt("return", Array.from(this.features.values()).map(function (featureArray) {
+                  return {
+                    refName: featureArray[0].get('refName'),
+                    aliases: featureArray[0].get('aliases')
+                  };
+                }));
+
+              case 1:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function getRefNameAliases() {
+        return _getRefNameAliases.apply(this, arguments);
+      }
+
+      return getRefNameAliases;
+    }()
+  }, {
+    key: "getFeatures",
+    value: function getFeatures(region) {
+      var _this2 = this;
+
+      var refName = region.refName,
+          start = region.start,
+          end = region.end;
+      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
+        var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(observer) {
+          var features, i, f;
+          return _regenerator["default"].wrap(function _callee3$(_context3) {
+            while (1) {
+              switch (_context3.prev = _context3.next) {
+                case 0:
+                  features = _this2.features.get(refName) || [];
+
+                  for (i = 0; i < features.length; i++) {
+                    f = features[i];
+
+                    if (f.get('end') > start && f.get('start') < end) {
+                      observer.next(f);
+                    }
+                  }
+
+                  observer.complete();
+
+                case 3:
+                case "end":
+                  return _context3.stop();
+              }
+            }
+          }, _callee3);
+        }));
+
+        return function (_x) {
+          return _ref.apply(this, arguments);
+        };
+      }());
+    }
+  }, {
+    key: "freeResources",
+    value: function
+      /* { region } */
+    freeResources() {}
+  }], [{
+    key: "makeFeatures",
+    value: function makeFeatures(fdata) {
+      var features = new Map();
+
+      for (var i = 0; i < fdata.length; i += 1) {
+        if (fdata[i]) {
+          var f = this.makeFeature(fdata[i]);
+          var refName = f.get('refName');
+          var bucket = features.get(refName);
+
+          if (!bucket) {
+            bucket = [];
+            features.set(refName, bucket);
+          }
+
+          bucket.push(f);
+        }
+      } // sort the features on each reference sequence by start coordinate
+
+
+      var _iterator = _createForOfIteratorHelper(features.values()),
+          _step;
+
+      try {
+        for (_iterator.s(); !(_step = _iterator.n()).done;) {
+          var refFeatures = _step.value;
+          refFeatures.sort(function (a, b) {
+            return a.get('start') - b.get('start');
+          });
+        }
+      } catch (err) {
+        _iterator.e(err);
+      } finally {
+        _iterator.f();
+      }
+
+      return features;
+    }
+  }, {
+    key: "makeFeature",
+    value: function makeFeature(data) {
+      return new _simpleFeature["default"](data);
+    }
+  }]);
+  return FromConfigAdapter;
+}(_BaseAdapter.BaseFeatureDataAdapter);
+
+exports["default"] = FromConfigAdapter;

package/dist/FromConfigAdapter/FromConfigAdapter.test.js

@@ -0,0 +1,100 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _operators = require("rxjs/operators");
+
+var _FromConfigAdapter = _interopRequireDefault(require("./FromConfigAdapter"));
+
+var _configSchema = require("./configSchema");
+
+test('adapter can fetch features', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+  var features, adapter, result, featuresArray;
+  return _regenerator["default"].wrap(function _callee$(_context) {
+    while (1) {
+      switch (_context.prev = _context.next) {
+        case 0:
+          features = [{
+            uniqueId: 'one',
+            refName: 'ctgA',
+            start: 20,
+            end: 40
+          }, {
+            uniqueId: 'two',
+            refName: 'ctgB',
+            start: 50,
+            end: 60
+          }];
+          adapter = new _FromConfigAdapter["default"](_configSchema.configSchema.create({
+            features: features
+          }));
+          result = adapter.getFeatures({
+            refName: 'ctgA',
+            start: 0,
+            end: 20000
+          });
+          _context.next = 5;
+          return result.pipe((0, _operators.toArray)()).toPromise();
+
+        case 5:
+          featuresArray = _context.sent;
+          expect(featuresArray.length).toBe(1);
+          expect(featuresArray[0].toJSON()).toEqual(features[0]);
+
+        case 8:
+        case "end":
+          return _context.stop();
+      }
+    }
+  }, _callee);
+})));
+test('adapter can fetch features with subfeatures', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+  var features, adapter, result, featuresArray;
+  return _regenerator["default"].wrap(function _callee2$(_context2) {
+    while (1) {
+      switch (_context2.prev = _context2.next) {
+        case 0:
+          features = [{
+            refName: 'ctgA',
+            uniqueId: 'feat1',
+            start: 200,
+            end: 750,
+            name: 'Feature1',
+            subfeatures: [{
+              uniqueId: 'feat2',
+              start: 225,
+              end: 300,
+              name: 'Feature2'
+            }, {
+              uniqueId: 'feat3',
+              start: 400,
+              end: 600,
+              name: 'Feature3'
+            }]
+          }];
+          adapter = new _FromConfigAdapter["default"](_configSchema.configSchema.create({
+            features: features
+          }));
+          result = adapter.getFeatures({
+            refName: 'ctgA',
+            start: 0,
+            end: 20000
+          });
+          _context2.next = 5;
+          return result.pipe((0, _operators.toArray)()).toPromise();
+
+        case 5:
+          featuresArray = _context2.sent;
+          expect(featuresArray.length).toBe(1);
+
+        case 7:
+        case "end":
+          return _context2.stop();
+      }
+    }
+  }, _callee2);
+})));

package/dist/FromConfigAdapter/FromConfigRegionsAdapter.js

@@ -0,0 +1,154 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+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 _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 _BaseAdapter2 = require("@jbrowse/core/data_adapters/BaseAdapter");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _FromConfigAdapter = _interopRequireDefault(require("./FromConfigAdapter"));
+
+function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it["return"] != null) it["return"](); } finally { if (didErr) throw err; } } }; }
+
+function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
+
+function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
+
+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; } }
+
+/**
+ * Adapter that just returns the features defined in its `features` configuration
+ * key, like:
+ *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
+ */
+var FromConfigRegionsAdapter = /*#__PURE__*/function (_BaseAdapter) {
+  (0, _inherits2["default"])(FromConfigRegionsAdapter, _BaseAdapter);
+
+  var _super = _createSuper(FromConfigRegionsAdapter);
+
+  function FromConfigRegionsAdapter(config, getSubAdapter, pluginManager) {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, FromConfigRegionsAdapter);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "features", void 0);
+    var features = (0, _configuration.readConfObject)(config, 'features');
+    _this.features = _FromConfigAdapter["default"].makeFeatures(features || []);
+    return _this;
+  }
+  /**
+   * Get refName, start, and end for all features after collapsing any overlaps
+   */
+
+
+  (0, _createClass2["default"])(FromConfigRegionsAdapter, [{
+    key: "getRegions",
+    value: function () {
+      var _getRegions = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        var regions, _iterator, _step, _step$value, refName, features, currentRegion, _iterator2, _step2, feature;
+
+        return _regenerator["default"].wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                regions = []; // recall: features are stored in this object sorted by start coordinate
+
+                _iterator = _createForOfIteratorHelper(this.features);
+
+                try {
+                  for (_iterator.s(); !(_step = _iterator.n()).done;) {
+                    _step$value = (0, _slicedToArray2["default"])(_step.value, 2), refName = _step$value[0], features = _step$value[1];
+                    currentRegion = void 0;
+                    _iterator2 = _createForOfIteratorHelper(features);
+
+                    try {
+                      for (_iterator2.s(); !(_step2 = _iterator2.n()).done;) {
+                        feature = _step2.value;
+
+                        if (currentRegion && currentRegion.end >= feature.get('start') && currentRegion.start <= feature.get('end')) {
+                          currentRegion.end = feature.get('end');
+                        } else {
+                          if (currentRegion) {
+                            regions.push(currentRegion);
+                          }
+
+                          currentRegion = {
+                            refName: refName,
+                            start: feature.get('start'),
+                            end: feature.get('end')
+                          };
+                        }
+                      }
+                    } catch (err) {
+                      _iterator2.e(err);
+                    } finally {
+                      _iterator2.f();
+                    }
+
+                    if (currentRegion) {
+                      regions.push(currentRegion);
+                    }
+                  } // sort the regions by refName
+
+                } catch (err) {
+                  _iterator.e(err);
+                } finally {
+                  _iterator.f();
+                }
+
+                regions.sort(function (a, b) {
+                  return a.refName.localeCompare(b.refName);
+                });
+                return _context.abrupt("return", regions);
+
+              case 5:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function getRegions() {
+        return _getRegions.apply(this, arguments);
+      }
+
+      return getRegions;
+    }()
+  }, {
+    key: "freeResources",
+    value: function
+      /* { region } */
+    freeResources() {}
+  }]);
+  return FromConfigRegionsAdapter;
+}(_BaseAdapter2.BaseAdapter);
+
+exports["default"] = FromConfigRegionsAdapter;