@jbrowse/plugin-sequence 1.6.7 → 1.7.0

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -0,0 +1,228 @@
+"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 _indexedfasta = require("@gmod/indexedfasta");
+
+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 _configuration = require("@jbrowse/core/configuration");
+
+var _abortablePromiseCache = _interopRequireDefault(require("abortable-promise-cache"));
+
+var _QuickLRU = _interopRequireDefault(require("@jbrowse/core/util/QuickLRU"));
+
+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 (_BaseSequenceAdapter) {
+  (0, _inherits2["default"])(_default, _BaseSequenceAdapter);
+
+  var _super = _createSuper(_default);
+
+  function _default(config, getSubAdapter, pluginManager) {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, _default);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "fasta", void 0);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "seqCache", new _abortablePromiseCache["default"]({
+      cache: new _QuickLRU["default"]({
+        maxSize: 200
+      }),
+      fill: function () {
+        var _fill = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(args, signal) {
+          var refName, start, end;
+          return _regenerator["default"].wrap(function _callee$(_context) {
+            while (1) {
+              switch (_context.prev = _context.next) {
+                case 0:
+                  refName = args.refName, start = args.start, end = args.end;
+                  return _context.abrupt("return", _this.fasta.getSequence(refName, start, end, _objectSpread(_objectSpread({}, args), {}, {
+                    signal: signal
+                  })));
+
+                case 2:
+                case "end":
+                  return _context.stop();
+              }
+            }
+          }, _callee);
+        }));
+
+        function fill(_x, _x2) {
+          return _fill.apply(this, arguments);
+        }
+
+        return fill;
+      }()
+    }));
+    var fastaLocation = (0, _configuration.readConfObject)(config, 'fastaLocation');
+    var faiLocation = (0, _configuration.readConfObject)(config, 'faiLocation');
+    var fastaOpts = {
+      fasta: (0, _io.openLocation)(fastaLocation, _this.pluginManager),
+      fai: (0, _io.openLocation)(faiLocation, _this.pluginManager)
+    };
+    _this.fasta = new _indexedfasta.IndexedFasta(fastaOpts);
+    return _this;
+  }
+
+  (0, _createClass2["default"])(_default, [{
+    key: "getRefNames",
+    value: function getRefNames(opts) {
+      return this.fasta.getSequenceNames(opts);
+    }
+  }, {
+    key: "getRegions",
+    value: function () {
+      var _getRegions = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(opts) {
+        var seqSizes;
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                _context2.next = 2;
+                return this.fasta.getSequenceSizes(opts);
+
+              case 2:
+                seqSizes = _context2.sent;
+                return _context2.abrupt("return", Object.keys(seqSizes).map(function (refName) {
+                  return {
+                    refName: refName,
+                    start: 0,
+                    end: seqSizes[refName]
+                  };
+                }));
+
+              case 4:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function getRegions(_x3) {
+        return _getRegions.apply(this, arguments);
+      }
+
+      return getRegions;
+    }()
+  }, {
+    key: "getFeatures",
+    value: function getFeatures(region, opts) {
+      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 size, regionEnd, chunks, chunkSize, s, e, chunkStart, r, seq;
+          return _regenerator["default"].wrap(function _callee3$(_context3) {
+            while (1) {
+              switch (_context3.prev = _context3.next) {
+                case 0:
+                  _context3.next = 2;
+                  return _this2.fasta.getSequenceSize(refName, opts);
+
+                case 2:
+                  size = _context3.sent;
+                  regionEnd = size !== undefined ? Math.min(size, end) : end;
+                  chunks = [];
+                  chunkSize = 128000;
+                  s = start - start % chunkSize;
+                  e = end + (chunkSize - end % chunkSize);
+
+                  for (chunkStart = s; chunkStart < e; chunkStart += chunkSize) {
+                    r = {
+                      refName: refName,
+                      start: chunkStart,
+                      end: chunkStart + chunkSize
+                    };
+                    chunks.push(_this2.seqCache.get(JSON.stringify(r), r, opts === null || opts === void 0 ? void 0 : opts.signal));
+                  }
+
+                  _context3.next = 11;
+                  return Promise.all(chunks);
+
+                case 11:
+                  seq = _context3.sent.join('').slice(start - s).slice(0, end - start);
+
+                  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 14:
+                case "end":
+                  return _context3.stop();
+              }
+            }
+          }, _callee3);
+        }));
+
+        return function (_x4) {
+          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.BaseSequenceAdapter);
+
+exports["default"] = _default;

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.test.js

@@ -0,0 +1,71 @@
+"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 _IndexedFastaAdapter = _interopRequireDefault(require("./IndexedFastaAdapter"));
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+test('adapter can fetch sequence from volvox.fa', /*#__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 _IndexedFastaAdapter["default"](_configSchema["default"].create({
+            fastaLocation: {
+              localPath: require.resolve('../../test_data/volvox.fa'),
+              locationType: 'LocalPathLocation'
+            },
+            faiLocation: {
+              localPath: require.resolve('../../test_data/volvox.fa.fai'),
+              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);
+})));

package/dist/IndexedFastaAdapter/configSchema.js

@@ -0,0 +1,29 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _default = (0, _configuration.ConfigurationSchema)('IndexedFastaAdapter', {
+  fastaLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/seq.fa',
+      locationType: 'UriLocation'
+    }
+  },
+  faiLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/seq.fa.fai',
+      locationType: 'UriLocation'
+    }
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/IndexedFastaAdapter/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/LinearReferenceSequenceDisplay/configSchema.js

@@ -0,0 +1,18 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.configSchema = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _DivSequenceRenderer = require("../DivSequenceRenderer");
+
+var configSchema = (0, _configuration.ConfigurationSchema)('LinearReferenceSequenceDisplay', {
+  renderer: _DivSequenceRenderer.configSchema
+}, {
+  explicitIdentifier: 'displayId',
+  explicitlyTyped: true
+});
+exports.configSchema = configSchema;

package/dist/LinearReferenceSequenceDisplay/index.js

@@ -0,0 +1,21 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "configSchema", {
+  enumerable: true,
+  get: function get() {
+    return _configSchema.configSchema;
+  }
+});
+Object.defineProperty(exports, "modelFactory", {
+  enumerable: true,
+  get: function get() {
+    return _model.modelFactory;
+  }
+});
+
+var _configSchema = require("./configSchema");
+
+var _model = require("./model");

package/dist/LinearReferenceSequenceDisplay/model.d.ts

@@ -25,7 +25,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
         renderInProgress: AbortController | undefined;
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | ((props: any) => import("react").ReactElement<any, any> | null) | (new (props: any) => import("react").Component<any, any, any>)> | undefined;
-        features: Map<string, import("@jbrowse/core/util/simpleFeature").Feature> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
         error: unknown;
@@ -43,7 +43,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | ((props: any) => import("react").ReactElement<any, any> | null) | (new (props: any) => import("react").Component<any, any, any>)>;
-            features: Map<string, import("@jbrowse/core/util/simpleFeature").Feature>;
+            features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
@@ -117,7 +117,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     currBpPerPx: number;
     message: string;
     featureIdUnderMouse: string | undefined;
-    contextMenuFeature: import("@jbrowse/core/util/simpleFeature").Feature | undefined;
+    contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
     scrollTop: number;
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
@@ -130,8 +130,8 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     readonly selectedFeatureId: string | undefined;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
 } & {
-    readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util/simpleFeature").Feature>;
-    readonly featureUnderMouse: import("@jbrowse/core/util/simpleFeature").Feature | undefined;
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): any;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
@@ -158,11 +158,11 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util/simpleFeature").Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature: string | undefined): void;
     reload(): void;
-    setContextMenuFeature(feature?: import("@jbrowse/core/util/simpleFeature").Feature | undefined): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
@@ -180,7 +180,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     }[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").ExportSvgOptions & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
     }): Promise<JSX.Element>;
 } & {

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();
+          }
+        }];
+      }
+    };
+  });
+}