@jbrowse/plugin-sequence 1.6.7 → 1.7.0

package/dist/DivSequenceRenderer/components/DivSequenceRendering.test.js

@@ -0,0 +1,245 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+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 _react = _interopRequireDefault(require("react"));
+
+var _propTypes = _interopRequireDefault(require("prop-types"));
+
+var _react2 = require("@testing-library/react");
+
+var _ui = require("@jbrowse/core/ui");
+
+var _PrecomputedLayout = _interopRequireDefault(require("@jbrowse/core/util/layouts/PrecomputedLayout"));
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+var _core = require("@material-ui/core");
+
+var _DivSequenceRendering = _interopRequireDefault(require("./DivSequenceRendering"));
+
+var _configSchema = _interopRequireDefault(require("../configSchema"));
+
+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; } }
+
+function Rendering(props) {
+  return /*#__PURE__*/_react["default"].createElement(_core.ThemeProvider, {
+    theme: (0, _ui.createJBrowseTheme)()
+  }, /*#__PURE__*/_react["default"].createElement(_DivSequenceRendering["default"], props));
+}
+
+var ErrorCatcher = /*#__PURE__*/function (_React$Component) {
+  (0, _inherits2["default"])(ErrorCatcher, _React$Component);
+
+  var _super = _createSuper(ErrorCatcher);
+
+  function ErrorCatcher(props) {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, ErrorCatcher);
+    _this = _super.call(this, props);
+    _this.state = {
+      hasError: false,
+      errorText: ''
+    };
+    return _this;
+  }
+
+  (0, _createClass2["default"])(ErrorCatcher, [{
+    key: "render",
+    value: function render() {
+      var _this$state = this.state,
+          hasError = _this$state.hasError,
+          errorText = _this$state.errorText;
+
+      if (hasError) {
+        // You can render any custom fallback UI
+        return /*#__PURE__*/_react["default"].createElement("h1", {
+          className: "error"
+        }, errorText);
+      }
+
+      var children = this.props.children;
+      return children;
+    }
+  }], [{
+    key: "getDerivedStateFromError",
+    value: function getDerivedStateFromError(error) {
+      // Update state so the next render will show the fallback UI.
+      return {
+        hasError: true,
+        errorText: String(error)
+      };
+    }
+  }]);
+  return ErrorCatcher;
+}(_react["default"].Component);
+
+ErrorCatcher.propTypes = {
+  children: _propTypes["default"].node.isRequired
+};
+describe('<DivSequenceRendering />', function () {
+  // This just keeps our testing logs clean by not displaying `console.error`s
+  // from errors we intentionally throw in our tests. Hopefully React will
+  // someday provide a way for error boundaries to prevent error logging so we
+  // won't have to do this: https://github.com/facebook/react/issues/15069
+  var originalError = console.error;
+  beforeAll(function () {
+    console.error = function () {
+      for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
+        args[_key] = arguments[_key];
+      }
+
+      if (args[0].includes('feature one did not contain a valid `seq` attribute') || args[0].includes('The above error occurred in the <SequenceDivs> component')) {
+        return;
+      }
+
+      originalError.call.apply(originalError, [console].concat(args));
+    };
+  });
+  afterAll(function () {
+    console.error = originalError;
+  });
+  it('renders with no features', function () {
+    var _render = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(Rendering, {
+      width: 500,
+      height: 500,
+      regions: [{
+        refName: 'zonk',
+        start: 0,
+        end: 300
+      }],
+      layout: new _PrecomputedLayout["default"]({
+        rectangles: {},
+        totalHeight: 20
+      }),
+      config: _configSchema["default"].create(),
+      bpPerPx: 3
+    })),
+        container = _render.container;
+
+    expect(container).toMatchSnapshot();
+  });
+  it('renders with one, zoomed way out', function () {
+    var _render2 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(Rendering, {
+      width: 500,
+      height: 500,
+      regions: [{
+        refName: 'zonk',
+        start: 0,
+        end: 1000
+      }],
+      features: new Map([['one', new _simpleFeature["default"]({
+        uniqueId: 'one',
+        start: 1,
+        end: 3,
+        seq: 'AB'
+      })]]),
+      config: _configSchema["default"].create({}),
+      bpPerPx: 3
+    })),
+        container = _render2.container;
+
+    expect(container).toMatchSnapshot();
+  });
+  it('renders with one feature with no seq, zoomed in, should throw', function () {
+    var _render3 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(ErrorCatcher, null, /*#__PURE__*/_react["default"].createElement(Rendering, {
+      width: 500,
+      height: 500,
+      regions: [{
+        refName: 'zonk',
+        start: 0,
+        end: 1000
+      }],
+      features: new Map([['one', new _simpleFeature["default"]({
+        uniqueId: 'one',
+        start: 1,
+        end: 3
+      })]]),
+      config: _configSchema["default"].create({}),
+      bpPerPx: 0.05
+    }))),
+        container = _render3.container;
+
+    expect(container).toMatchSnapshot();
+  });
+  it('renders with one feature with an incorrect seq, zoomed in, should throw', function () {
+    var _render4 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(ErrorCatcher, null, /*#__PURE__*/_react["default"].createElement(Rendering, {
+      width: 500,
+      height: 500,
+      regions: [{
+        refName: 'zonk',
+        start: 0,
+        end: 1000
+      }],
+      features: new Map([['one', new _simpleFeature["default"]({
+        uniqueId: 'one',
+        start: 1,
+        end: 3,
+        seq: 'ABC'
+      })]]),
+      config: _configSchema["default"].create({}),
+      bpPerPx: 0.05
+    }))),
+        container = _render4.container;
+
+    expect(container).toMatchSnapshot();
+  });
+  it('renders with one feature with a correct seq, zoomed in, should render nicely', function () {
+    var _render5 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(Rendering, {
+      width: 500,
+      height: 500,
+      regions: [{
+        refName: 'zonk',
+        start: 0,
+        end: 1000
+      }],
+      features: new Map([['one', new _simpleFeature["default"]({
+        uniqueId: 'one',
+        start: 1,
+        end: 10,
+        seq: 'ABCDEFGHI'
+      })]]),
+      config: _configSchema["default"].create({}),
+      bpPerPx: 0.05
+    })),
+        container = _render5.container;
+
+    expect(container).toMatchSnapshot();
+  });
+  it('renders with one feature reversed with a correct seq, zoomed in, should render nicely', function () {
+    var _render6 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(Rendering, {
+      width: 500,
+      height: 500,
+      regions: [{
+        refName: 'zonk',
+        start: 0,
+        end: 1000,
+        reversed: true
+      }],
+      features: new Map([['one', new _simpleFeature["default"]({
+        uniqueId: 'one',
+        start: 1,
+        end: 10,
+        seq: 'ABCDEFGHI'
+      })]]),
+      config: _configSchema["default"].create({}),
+      bpPerPx: 0.05
+    })),
+        container = _render6.container;
+
+    expect(container).toMatchSnapshot();
+  });
+});

package/dist/DivSequenceRenderer/configSchema.js

@@ -0,0 +1,20 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _default = (0, _configuration.ConfigurationSchema)('DivSequenceRenderer', {
+  height: {
+    type: 'number',
+    description: 'height in pixels of each line of sequence',
+    defaultValue: 16
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/DivSequenceRenderer/index.js

@@ -0,0 +1,23 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "ReactComponent", {
+  enumerable: true,
+  get: function get() {
+    return _DivSequenceRendering["default"];
+  }
+});
+Object.defineProperty(exports, "configSchema", {
+  enumerable: true,
+  get: function get() {
+    return _configSchema["default"];
+  }
+});
+
+var _DivSequenceRendering = _interopRequireDefault(require("./components/DivSequenceRendering"));
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));

package/dist/GCContentAdapter/GCContentAdapter.js

@@ -0,0 +1,261 @@
+"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 _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 _rxjs = require("@jbrowse/core/util/rxjs");
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _operators = require("rxjs/operators");
+
+function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
+
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
+
+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 _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
+  (0, _inherits2["default"])(_default, _BaseFeatureDataAdapt);
+
+  var _super = _createSuper(_default);
+
+  function _default() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, _default);
+
+    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), "windowSize", 1000);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "windowDelta", 1000);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "gcMode", 'content');
+    return _this;
+  }
+
+  (0, _createClass2["default"])(_default, [{
+    key: "configure",
+    value: function () {
+      var _configure = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        var _this$getSubAdapter;
+
+        var sequenceAdapter, dataAdapter;
+        return _regenerator["default"].wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                // instantiate the sequence adapter
+                sequenceAdapter = (0, _configuration.readConfObject)(this.config, 'sequenceAdapter');
+                _context.next = 3;
+                return (_this$getSubAdapter = this.getSubAdapter) === null || _this$getSubAdapter === void 0 ? void 0 : _this$getSubAdapter.call(this, sequenceAdapter);
+
+              case 3:
+                dataAdapter = _context.sent;
+
+                if (dataAdapter) {
+                  _context.next = 6;
+                  break;
+                }
+
+                throw new Error('Error getting subadapter');
+
+              case 6:
+                return _context.abrupt("return", dataAdapter.dataAdapter);
+
+              case 7:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function configure() {
+        return _configure.apply(this, arguments);
+      }
+
+      return configure;
+    }()
+  }, {
+    key: "getRefNames",
+    value: function () {
+      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+        var sequenceAdapter;
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                _context2.next = 2;
+                return this.configure();
+
+              case 2:
+                sequenceAdapter = _context2.sent;
+                return _context2.abrupt("return", sequenceAdapter.getRefNames());
+
+              case 4:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function getRefNames() {
+        return _getRefNames.apply(this, arguments);
+      }
+
+      return getRefNames;
+    }()
+    /**
+     * Fetch features for a certain region
+     * @param param -
+     * @returns Observable of Feature objects in the region
+     */
+
+  }, {
+    key: "getFeatures",
+    value: function getFeatures(query, opts) {
+      var _this2 = this;
+
+      this.windowSize = 1000;
+      this.windowDelta = 1000;
+      this.gcMode = 'content';
+      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
+        var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(observer) {
+          var _feats$;
+
+          var sequenceAdapter, hw, f, queryStart, queryEnd, ret, feats, residues, i, r, nc, ng, len, j, pos, score;
+          return _regenerator["default"].wrap(function _callee3$(_context3) {
+            while (1) {
+              switch (_context3.prev = _context3.next) {
+                case 0:
+                  _context3.next = 2;
+                  return _this2.configure();
+
+                case 2:
+                  sequenceAdapter = _context3.sent;
+                  hw = _this2.windowSize === 1 ? 1 : _this2.windowSize / 2; // Half the window size
+
+                  f = _this2.windowSize === 1;
+                  queryStart = query.start, queryEnd = query.end;
+                  queryStart = Math.max(0, queryStart - hw);
+                  queryEnd += hw;
+
+                  if (!(queryEnd < 0 || queryStart > queryEnd)) {
+                    _context3.next = 11;
+                    break;
+                  }
+
+                  observer.complete();
+                  return _context3.abrupt("return");
+
+                case 11:
+                  ret = sequenceAdapter.getFeatures(_objectSpread(_objectSpread({}, query), {}, {
+                    start: queryStart,
+                    end: queryEnd
+                  }));
+                  _context3.next = 14;
+                  return ret.pipe((0, _operators.toArray)()).toPromise();
+
+                case 14:
+                  feats = _context3.sent;
+                  residues = ((_feats$ = feats[0]) === null || _feats$ === void 0 ? void 0 : _feats$.get('seq')) || '';
+
+                  for (i = hw; i < residues.length - hw; i += _this2.windowDelta) {
+                    r = f ? residues[i] : residues.slice(i - hw, i + hw);
+                    nc = 0;
+                    ng = 0;
+                    len = 0;
+
+                    for (j = 0; j < r.length; j++) {
+                      if (r[j] === 'c' || r[j] === 'C') {
+                        nc++;
+                      } else if (r[j] === 'g' || r[j] === 'G') {
+                        ng++;
+                      }
+
+                      if (r[j] !== 'N') {
+                        len++;
+                      }
+                    }
+
+                    pos = queryStart;
+                    score = void 0;
+
+                    if (_this2.gcMode === 'content') {
+                      score = (ng + nc) / (len || 1);
+                    } else if (_this2.gcMode === 'skew') {
+                      score = (ng - nc) / (ng + nc || 1);
+                    }
+
+                    observer.next(new _simpleFeature["default"]({
+                      uniqueId: "".concat(_this2.id, "_").concat(pos + i),
+                      start: pos + i,
+                      end: pos + i + _this2.windowDelta,
+                      score: score
+                    }));
+                  }
+
+                  observer.complete();
+
+                case 18:
+                case "end":
+                  return _context3.stop();
+              }
+            }
+          }, _callee3);
+        }));
+
+        return function (_x) {
+          return _ref.apply(this, arguments);
+        };
+      }());
+    }
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+
+  }, {
+    key: "freeResources",
+    value: function
+      /* { region } */
+    freeResources() {}
+  }]);
+  return _default;
+}(_BaseAdapter.BaseFeatureDataAdapter);
+
+exports["default"] = _default;
+(0, _defineProperty2["default"])(_default, "capabilities", ['hasLocalStats']);

package/dist/GCContentAdapter/configSchema.js

@@ -0,0 +1,18 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _default = function _default(pluginManager) {
+  return (0, _configuration.ConfigurationSchema)('GCContentAdapter', {
+    sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter')
+  }, {
+    explicitlyTyped: true
+  });
+};
+
+exports["default"] = _default;

package/dist/GCContentAdapter/index.js

@@ -0,0 +1,31 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || (0, _typeof2["default"])(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
+var _default = function _default(pluginManager) {
+  return {
+    configSchema: pluginManager.load(_configSchema["default"]),
+    getAdapterClass: function getAdapterClass() {
+      return Promise.resolve().then(function () {
+        return _interopRequireWildcard(require('./GCContentAdapter'));
+      }).then(function (r) {
+        return r["default"];
+      });
+    }
+  };
+};
+
+exports["default"] = _default;

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -15,11 +15,6 @@ export default class extends BaseSequenceAdapter {
         start: number;
         end: number;
     }[]>;
-    /**
-     * Fetch features for a certain region
-     * @param param -
-     * @returns Observable of Feature objects in the region
-     */
     getFeatures(region: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region