@jbrowse/plugin-sequence 1.6.9 → 1.7.3

package/dist/LinearReferenceSequenceDisplay/model.js

@@ -0,0 +1,102 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.modelFactory = modelFactory;
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _util = require("@jbrowse/core/util");
+
+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 modelFactory(configSchema) {
+  return _mobxStateTree.types.compose('LinearReferenceSequenceDisplay', _pluginLinearGenomeView.BaseLinearDisplay, _mobxStateTree.types.model({
+    type: _mobxStateTree.types.literal('LinearReferenceSequenceDisplay'),
+    configuration: (0, _configuration.ConfigurationReference)(configSchema),
+    showForward: _mobxStateTree.types.optional(_mobxStateTree.types["boolean"], true),
+    showReverse: _mobxStateTree.types.optional(_mobxStateTree.types["boolean"], true),
+    showTranslation: _mobxStateTree.types.optional(_mobxStateTree.types["boolean"], true),
+    height: 180
+  })).views(function (self) {
+    var superRenderProps = self.renderProps;
+    return {
+      renderProps: function renderProps() {
+        var showForward = self.showForward,
+            showReverse = self.showReverse,
+            showTranslation = self.showTranslation;
+        return _objectSpread(_objectSpread({}, superRenderProps()), {}, {
+          rpcDriverName: self.rpcDriverName,
+          config: self.configuration.renderer,
+          showForward: showForward,
+          showReverse: showReverse,
+          showTranslation: showTranslation
+        });
+      },
+      regionCannotBeRendered: function regionCannotBeRendered() {
+        var view = (0, _util.getContainingView)(self);
+
+        if (view && view.bpPerPx >= 1) {
+          return 'Zoom in to see sequence';
+        }
+
+        return undefined;
+      },
+
+      get rendererTypeName() {
+        return self.configuration.renderer.type;
+      }
+
+    };
+  }).actions(function (self) {
+    return {
+      toggleShowForward: function toggleShowForward() {
+        self.showForward = !self.showForward;
+      },
+      toggleShowReverse: function toggleShowReverse() {
+        self.showReverse = !self.showReverse;
+      },
+      toggleShowTranslation: function toggleShowTranslation() {
+        self.showTranslation = !self.showTranslation;
+      }
+    };
+  }).views(function (self) {
+    return {
+      trackMenuItems: function trackMenuItems() {
+        return [{
+          label: 'Show forward',
+          type: 'checkbox',
+          checked: self.showForward,
+          onClick: function onClick() {
+            self.toggleShowForward();
+          }
+        }, {
+          label: 'Show reverse',
+          type: 'checkbox',
+          checked: self.showReverse,
+          onClick: function onClick() {
+            self.toggleShowReverse();
+          }
+        }, {
+          label: 'Show translation',
+          type: 'checkbox',
+          checked: self.showTranslation,
+          onClick: function onClick() {
+            self.toggleShowTranslation();
+          }
+        }];
+      }
+    };
+  });
+}

package/dist/TwoBitAdapter/TwoBitAdapter.d.ts

@@ -1,26 +1,26 @@
-import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-export default class TwoBitAdapter extends BaseSequenceAdapter {
-    private twobit;
-    protected chromSizesData: Promise<Record<string, number> | undefined>;
-    private initChromSizes;
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    getRefNames(): Promise<string[]>;
-    getRegions(): Promise<NoAssemblyRegion[]>;
-    /**
-     * Fetch features for a certain region
-     * @param param -
-     * @returns Observable of Feature objects in the region
-     */
-    getFeatures({ refName, start, end }: NoAssemblyRegion): import("rxjs").Observable<Feature>;
-    /**
-     * 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
-     */
-    freeResources(): void;
-}
+import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class TwoBitAdapter extends BaseSequenceAdapter {
+    private twobit;
+    protected chromSizesData: Promise<Record<string, number> | undefined>;
+    private initChromSizes;
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    getRefNames(): Promise<string[]>;
+    getRegions(): Promise<NoAssemblyRegion[]>;
+    /**
+     * Fetch features for a certain region
+     * @param param -
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures({ refName, start, end }: NoAssemblyRegion): import("rxjs").Observable<Feature>;
+    /**
+     * 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
+     */
+    freeResources(): void;
+}

package/dist/TwoBitAdapter/TwoBitAdapter.js

@@ -0,0 +1,289 @@
+"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 _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
+
+var _io = require("@jbrowse/core/util/io");
+
+var _rxjs = require("@jbrowse/core/util/rxjs");
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+var _twobit = require("@gmod/twobit");
+
+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; } }
+
+var TwoBitAdapter = /*#__PURE__*/function (_BaseSequenceAdapter) {
+  (0, _inherits2["default"])(TwoBitAdapter, _BaseSequenceAdapter);
+
+  var _super = _createSuper(TwoBitAdapter);
+
+  function TwoBitAdapter(config, getSubAdapter, pluginManager) {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, TwoBitAdapter);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "twobit", void 0);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "chromSizesData", void 0);
+    _this.chromSizesData = _this.initChromSizes();
+    _this.twobit = new _twobit.TwoBitFile({
+      filehandle: (0, _io.openLocation)((0, _configuration.readConfObject)(config, 'twoBitLocation'), _this.pluginManager)
+    });
+    return _this;
+  }
+
+  (0, _createClass2["default"])(TwoBitAdapter, [{
+    key: "initChromSizes",
+    value: // the chromSizesData can be used to speed up loading since TwoBit has to do
+    // many range requests at startup to perform the getRegions request
+    function () {
+      var _initChromSizes = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        var conf, file, data;
+        return _regenerator["default"].wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                conf = (0, _configuration.readConfObject)(this.config, 'chromSizesLocation'); // check against default and empty in case someone makes the field blank in
+                // config editor, may want better way to check "optional config slots" in
+                // future
+
+                if (!(conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '')) {
+                  _context.next = 7;
+                  break;
+                }
+
+                file = (0, _io.openLocation)(conf, this.pluginManager);
+                _context.next = 5;
+                return file.readFile('utf8');
+
+              case 5:
+                data = _context.sent;
+                return _context.abrupt("return", Object.fromEntries(data === null || data === void 0 ? void 0 : data.split('\n').filter(function (line) {
+                  return !!line.trim();
+                }).map(function (line) {
+                  var _line$split = line.split('\t'),
+                      _line$split2 = (0, _slicedToArray2["default"])(_line$split, 2),
+                      name = _line$split2[0],
+                      length = _line$split2[1];
+
+                  return [name, +length];
+                })));
+
+              case 7:
+                return _context.abrupt("return", undefined);
+
+              case 8:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function initChromSizes() {
+        return _initChromSizes.apply(this, arguments);
+      }
+
+      return initChromSizes;
+    }()
+  }, {
+    key: "getRefNames",
+    value: function () {
+      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+        var chromSizesData;
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                _context2.next = 2;
+                return this.chromSizesData;
+
+              case 2:
+                chromSizesData = _context2.sent;
+
+                if (!chromSizesData) {
+                  _context2.next = 5;
+                  break;
+                }
+
+                return _context2.abrupt("return", Object.keys(chromSizesData));
+
+              case 5:
+                return _context2.abrupt("return", this.twobit.getSequenceNames());
+
+              case 6:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function getRefNames() {
+        return _getRefNames.apply(this, arguments);
+      }
+
+      return getRefNames;
+    }()
+  }, {
+    key: "getRegions",
+    value: function () {
+      var _getRegions = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
+        var chromSizesData, refSizes;
+        return _regenerator["default"].wrap(function _callee3$(_context3) {
+          while (1) {
+            switch (_context3.prev = _context3.next) {
+              case 0:
+                _context3.next = 2;
+                return this.chromSizesData;
+
+              case 2:
+                chromSizesData = _context3.sent;
+
+                if (!chromSizesData) {
+                  _context3.next = 5;
+                  break;
+                }
+
+                return _context3.abrupt("return", Object.keys(chromSizesData).map(function (refName) {
+                  return {
+                    refName: refName,
+                    start: 0,
+                    end: chromSizesData[refName]
+                  };
+                }));
+
+              case 5:
+                _context3.next = 7;
+                return this.twobit.getSequenceSizes();
+
+              case 7:
+                refSizes = _context3.sent;
+                return _context3.abrupt("return", Object.keys(refSizes).map(function (refName) {
+                  return {
+                    refName: refName,
+                    start: 0,
+                    end: refSizes[refName]
+                  };
+                }));
+
+              case 9:
+              case "end":
+                return _context3.stop();
+            }
+          }
+        }, _callee3, this);
+      }));
+
+      function getRegions() {
+        return _getRegions.apply(this, arguments);
+      }
+
+      return getRegions;
+    }()
+    /**
+     * Fetch features for a certain region
+     * @param param -
+     * @returns Observable of Feature objects in the region
+     */
+
+  }, {
+    key: "getFeatures",
+    value: function getFeatures(_ref) {
+      var _this2 = this;
+
+      var refName = _ref.refName,
+          start = _ref.start,
+          end = _ref.end;
+      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
+        var _ref2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(observer) {
+          var size, regionEnd, seq;
+          return _regenerator["default"].wrap(function _callee4$(_context4) {
+            while (1) {
+              switch (_context4.prev = _context4.next) {
+                case 0:
+                  _context4.next = 2;
+                  return _this2.twobit.getSequenceSize(refName);
+
+                case 2:
+                  size = _context4.sent;
+                  regionEnd = size !== undefined ? Math.min(size, end) : end;
+                  _context4.next = 6;
+                  return _this2.twobit.getSequence(refName, start, regionEnd);
+
+                case 6:
+                  seq = _context4.sent;
+
+                  if (seq) {
+                    observer.next(new _simpleFeature["default"]({
+                      id: "".concat(refName, " ").concat(start, "-").concat(regionEnd),
+                      data: {
+                        refName: refName,
+                        start: start,
+                        end: regionEnd,
+                        seq: seq
+                      }
+                    }));
+                  }
+
+                  observer.complete();
+
+                case 9:
+                case "end":
+                  return _context4.stop();
+              }
+            }
+          }, _callee4);
+        }));
+
+        return function (_x) {
+          return _ref2.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 TwoBitAdapter;
+}(_BaseAdapter.BaseSequenceAdapter);
+
+exports["default"] = TwoBitAdapter;

package/dist/TwoBitAdapter/TwoBitAdapter.test.js

@@ -0,0 +1,94 @@
+"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 _TwoBitAdapter = _interopRequireDefault(require("./TwoBitAdapter"));
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+test('adapter can fetch features from volvox.2bit', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+  var adapter, features, featuresArray, features2, featuresArray2, features3, featuresArray3;
+  return _regenerator["default"].wrap(function _callee$(_context) {
+    while (1) {
+      switch (_context.prev = _context.next) {
+        case 0:
+          adapter = new _TwoBitAdapter["default"](_configSchema["default"].create({
+            twoBitLocation: {
+              localPath: require.resolve('../../test_data/volvox.2bit'),
+              locationType: 'LocalPathLocation'
+            }
+          }));
+          features = adapter.getFeatures({
+            refName: 'ctgA',
+            start: 0,
+            end: 20000
+          });
+          _context.next = 4;
+          return features.pipe((0, _operators.toArray)()).toPromise();
+
+        case 4:
+          featuresArray = _context.sent;
+          expect(featuresArray).toMatchSnapshot();
+          features2 = adapter.getFeatures({
+            refName: 'ctgA',
+            start: 45000,
+            end: 55000
+          });
+          _context.next = 9;
+          return features2.pipe((0, _operators.toArray)()).toPromise();
+
+        case 9:
+          featuresArray2 = _context.sent;
+          expect(featuresArray2[0].get('end')).toBe(50001);
+          features3 = adapter.getFeatures({
+            refName: 'ctgC',
+            start: 0,
+            end: 20000
+          });
+          _context.next = 14;
+          return features3.pipe((0, _operators.toArray)()).toPromise();
+
+        case 14:
+          featuresArray3 = _context.sent;
+          expect(featuresArray3).toMatchSnapshot();
+
+        case 16:
+        case "end":
+          return _context.stop();
+      }
+    }
+  }, _callee);
+})));
+test('adapter can fetch regions from with chrom.sizes', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+  var adapter;
+  return _regenerator["default"].wrap(function _callee2$(_context2) {
+    while (1) {
+      switch (_context2.prev = _context2.next) {
+        case 0:
+          adapter = new _TwoBitAdapter["default"](_configSchema["default"].create({
+            chromSizesLocation: {
+              localPath: require.resolve('../../test_data/volvox.chrom.sizes'),
+              locationType: 'LocalPathLocation'
+            }
+          }));
+          _context2.t0 = expect;
+          _context2.next = 4;
+          return adapter.getRegions();
+
+        case 4:
+          _context2.t1 = _context2.sent;
+          (0, _context2.t0)(_context2.t1).toMatchSnapshot();
+
+        case 6:
+        case "end":
+          return _context2.stop();
+      }
+    }
+  }, _callee2);
+})));

package/dist/TwoBitAdapter/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/TwoBitAdapter/configSchema.js

@@ -0,0 +1,30 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _default = (0, _configuration.ConfigurationSchema)('TwoBitAdapter', {
+  twoBitLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/my.2bit',
+      locationType: 'UriLocation'
+    }
+  },
+  chromSizesLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/default.chrom.sizes',
+      locationType: 'UriLocation'
+    },
+    description: 'An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time'
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/TwoBitAdapter/index.d.ts

@@ -1 +1 @@
-export { default as configSchema } from './configSchema';
+export { default as configSchema } from './configSchema';

package/dist/TwoBitAdapter/index.js

@@ -0,0 +1,15 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "configSchema", {
+  enumerable: true,
+  get: function get() {
+    return _configSchema["default"];
+  }
+});
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));

package/dist/declare.d.js

@@ -0,0 +1 @@
+"use strict";

package/dist/index.d.ts

@@ -1,6 +1,6 @@
-import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
-export default class SequencePlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-}
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class SequencePlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}