@jbrowse/core 1.5.7 → 1.6.1

package/configuration/util.js

@@ -1,6 +1,6 @@
 "use strict";
 
-var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
 Object.defineProperty(exports, "__esModule", {
   value: true
@@ -13,9 +13,9 @@ exports.isConfigurationSchemaType = isConfigurationSchemaType;
 exports.isConfigurationSlotType = isConfigurationSlotType;
 exports.readConfObject = readConfObject;
 
-var _typeof2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/typeof.js"));
+var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 
-var _toConsumableArray2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/toConsumableArray.js"));
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
 
 var _mobxStateTree = require("mobx-state-tree");
 
@@ -154,7 +154,7 @@ function getTypeNamesFromExplicitlyTypedUnion(maybeUnionType) {
           throw new Error("invalid config schema type ".concat(type));
         }
 
-        typeNames.push.apply(typeNames, (0, _toConsumableArray2["default"])(typeName));
+        typeNames.push.apply(typeNames, (0, _toConsumableArray2.default)(typeName));
       });
       return typeNames;
     }
@@ -217,5 +217,5 @@ function isConfigurationModel(thing) {
 }
 
 function isConfigurationSlotType(thing) {
-  return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'isJBrowseConfigurationSlot' in thing;
+  return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'isJBrowseConfigurationSlot' in thing;
 }

package/data_adapters/BaseAdapter.d.ts

@@ -24,7 +24,9 @@ export interface BaseArgs {
 export interface AnyAdapter {
     new (config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager | undefined): AnyDataAdapter;
 }
-export declare type AnyDataAdapter = BaseAdapter | BaseFeatureDataAdapter | BaseRefNameAliasAdapter | BaseTextSearchAdapter | RegionsAdapter | SequenceAdapter;
+export declare type AnyDataAdapter = BaseAdapter | BaseFeatureDataAdapter | BaseRefNameAliasAdapter | BaseTextSearchAdapter | RegionsAdapter | BaseSequenceAdapter;
+export interface SequenceAdapter extends BaseFeatureDataAdapter, RegionsAdapter {
+}
 export declare abstract class BaseAdapter {
     config: AnyConfigurationModel;
     getSubAdapter?: getSubAdapterType | undefined;
@@ -39,6 +41,11 @@ export declare abstract class BaseAdapter {
      */
     abstract freeResources(region: Region): void;
 }
+export interface Stats {
+    featureDensity?: number;
+    fetchSizeLimit?: number;
+    bytes?: number;
+}
 /**
  * Base class for feature adapters to extend. Defines some methods that
  * subclasses must implement.
@@ -101,13 +108,18 @@ export declare abstract class BaseFeatureDataAdapter extends BaseAdapter {
     hasDataForRefName(refName: string, opts?: BaseOptions): Promise<boolean>;
     getRegionStats(region: Region, opts?: BaseOptions): Promise<import("../util/stats").FeatureStats>;
     getMultiRegionStats(regions?: Region[], opts?: BaseOptions): Promise<import("../util/stats").FeatureStats>;
+    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<Stats>;
 }
 export interface RegionsAdapter extends BaseAdapter {
     getRegions(opts: BaseOptions): Promise<NoAssemblyRegion[]>;
 }
-export interface SequenceAdapter extends BaseFeatureDataAdapter, RegionsAdapter {
+export declare abstract class BaseSequenceAdapter extends BaseFeatureDataAdapter implements RegionsAdapter {
+    estimateRegionsStats(): Promise<{
+        featureDensity: number;
+    }>;
+    abstract getRegions(opts: BaseOptions): Promise<NoAssemblyRegion[]>;
 }
-export declare function isSequenceAdapter(thing: AnyDataAdapter): thing is SequenceAdapter;
+export declare function isSequenceAdapter(thing: AnyDataAdapter): thing is BaseSequenceAdapter;
 export declare function isRegionsAdapter(thing: AnyDataAdapter): thing is RegionsAdapter;
 export declare function isFeatureAdapter(thing: AnyDataAdapter): thing is BaseFeatureDataAdapter;
 export interface Alias {

package/data_adapters/BaseAdapter.js

@@ -1,30 +1,34 @@
 "use strict";
 
-var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.BaseFeatureDataAdapter = exports.BaseAdapter = void 0;
+exports.BaseSequenceAdapter = exports.BaseFeatureDataAdapter = exports.BaseAdapter = void 0;
 exports.isFeatureAdapter = isFeatureAdapter;
 exports.isRefNameAliasAdapter = isRefNameAliasAdapter;
 exports.isRegionsAdapter = isRegionsAdapter;
 exports.isSequenceAdapter = isSequenceAdapter;
 exports.isTextSearchAdapter = isTextSearchAdapter;
 
-var _index = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/regenerator/index.js"));
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
-var _toConsumableArray2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/toConsumableArray.js"));
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
-var _inherits2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/inherits.js"));
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
 
-var _createSuper2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createSuper.js"));
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
 
-var _createClass2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createClass.js"));
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
 
-var _classCallCheck2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
 var _rxjs = require("rxjs");
 
@@ -42,21 +46,29 @@ var _stats = require("../util/stats");
 
 var _idMaker = _interopRequireDefault(require("../util/idMaker"));
 
-var BaseAdapter = /*#__PURE__*/(0, _createClass2["default"])(function BaseAdapter() {
+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 BaseAdapter = /*#__PURE__*/(0, _createClass2.default)(function BaseAdapter() {
   var config = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : (0, _configurationSchema.ConfigurationSchema)('empty', {}).create();
   var getSubAdapter = arguments.length > 1 ? arguments[1] : undefined;
   var pluginManager = arguments.length > 2 ? arguments[2] : undefined;
-  (0, _classCallCheck2["default"])(this, BaseAdapter);
+  (0, _classCallCheck2.default)(this, BaseAdapter);
   this.config = config;
   this.getSubAdapter = getSubAdapter;
   this.pluginManager = pluginManager;
-  this.id = void 0;
+  (0, _defineProperty2.default)(this, "id", void 0);
 
   // note: we use switch on jest here for more simple feature IDs
   // in test environment
   if (typeof jest === 'undefined') {
     var data = (0, _mobxStateTree.isStateTreeNode)(config) ? (0, _mobxStateTree.getSnapshot)(config) : config;
-    this.id = "".concat((0, _idMaker["default"])(data));
+    this.id = "".concat((0, _idMaker.default)(data));
   } else {
     this.id = 'test';
   }
@@ -67,25 +79,24 @@ var BaseAdapter = /*#__PURE__*/(0, _createClass2["default"])(function BaseAdapte
  * @param region - Region
  */
 );
+exports.BaseAdapter = BaseAdapter;
+(0, _defineProperty2.default)(BaseAdapter, "capabilities", []);
+
 /**
  * Base class for feature adapters to extend. Defines some methods that
  * subclasses must implement.
  */
-
-exports.BaseAdapter = BaseAdapter;
-BaseAdapter.capabilities = [];
-
 var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
-  (0, _inherits2["default"])(BaseFeatureDataAdapter, _BaseAdapter);
+  (0, _inherits2.default)(BaseFeatureDataAdapter, _BaseAdapter);
 
-  var _super = (0, _createSuper2["default"])(BaseFeatureDataAdapter);
+  var _super = _createSuper(BaseFeatureDataAdapter);
 
   function BaseFeatureDataAdapter() {
-    (0, _classCallCheck2["default"])(this, BaseFeatureDataAdapter);
+    (0, _classCallCheck2.default)(this, BaseFeatureDataAdapter);
     return _super.apply(this, arguments);
   }
 
-  (0, _createClass2["default"])(BaseFeatureDataAdapter, [{
+  (0, _createClass2.default)(BaseFeatureDataAdapter, [{
     key: "getHeader",
     value: // public abstract getFeatures(
     //   region: Region,
@@ -108,8 +119,8 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
      * object
      */
     function () {
-      var _getHeader = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee(_opts) {
-        return _index["default"].wrap(function _callee$(_context) {
+      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(_opts) {
+        return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -137,8 +148,8 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
   }, {
     key: "getMetadata",
     value: function () {
-      var _getMetadata = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee2(_opts) {
-        return _index["default"].wrap(function _callee2$(_context2) {
+      var _getMetadata = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(_opts) {
+        return _regenerator.default.wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
@@ -170,9 +181,9 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
 
       var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
       return (0, _rxjs2.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee3(observer) {
+        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(observer) {
           var hasData;
-          return _index["default"].wrap(function _callee3$(_context3) {
+          return _regenerator.default.wrap(function _callee3$(_context3) {
             while (1) {
               switch (_context3.prev = _context3.next) {
                 case 0:
@@ -184,7 +195,6 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
                   (0, _util.checkAbortSignal)(opts.signal);
 
                   if (!hasData) {
-                    // console.warn(`no data for ${region.refName}`)
                     observer.complete();
                   } else {
                     _this.getFeatures(region, opts).pipe((0, _operators.takeUntil)((0, _util.observeAbortSignal)(opts.signal))).subscribe(observer);
@@ -226,11 +236,11 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
 
       var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
 
-      var obs = _rxjs.merge.apply(void 0, (0, _toConsumableArray2["default"])(regions.map(function (region) {
+      var obs = _rxjs.merge.apply(void 0, (0, _toConsumableArray2.default)(regions.map(function (region) {
         return (0, _rxjs2.ObservableCreate)( /*#__PURE__*/function () {
-          var _ref2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee4(observer) {
+          var _ref2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(observer) {
             var hasData;
-            return _index["default"].wrap(function _callee4$(_context4) {
+            return _regenerator.default.wrap(function _callee4$(_context4) {
               while (1) {
                 switch (_context4.prev = _context4.next) {
                   case 0:
@@ -242,7 +252,6 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
                     (0, _util.checkAbortSignal)(opts.signal);
 
                     if (!hasData) {
-                      // console.warn(`no data for ${region.refName}`)
                       observer.complete();
                     } else {
                       _this2.getFeatures(region, opts).subscribe(observer);
@@ -277,11 +286,11 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
   }, {
     key: "hasDataForRefName",
     value: function () {
-      var _hasDataForRefName = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee5(refName) {
+      var _hasDataForRefName = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(refName) {
         var opts,
             refNames,
             _args5 = arguments;
-        return _index["default"].wrap(function _callee5$(_context5) {
+        return _regenerator.default.wrap(function _callee5$(_context5) {
           while (1) {
             switch (_context5.prev = _context5.next) {
               case 0:
@@ -310,9 +319,9 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
   }, {
     key: "getRegionStats",
     value: function () {
-      var _getRegionStats = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee6(region, opts) {
+      var _getRegionStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(region, opts) {
         var feats;
-        return _index["default"].wrap(function _callee6$(_context6) {
+        return _regenerator.default.wrap(function _callee6$(_context6) {
           while (1) {
             switch (_context6.prev = _context6.next) {
               case 0:
@@ -336,7 +345,7 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
   }, {
     key: "getMultiRegionStats",
     value: function () {
-      var _getMultiRegionStats = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee7() {
+      var _getMultiRegionStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7() {
         var _this3 = this;
 
         var regions,
@@ -349,7 +358,7 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
             featureCount,
             basesCovered,
             _args7 = arguments;
-        return _index["default"].wrap(function _callee7$(_context7) {
+        return _regenerator.default.wrap(function _callee7$(_context7) {
           while (1) {
             switch (_context7.prev = _context7.next) {
               case 0:
@@ -371,35 +380,27 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
 
               case 6:
                 feats = _context7.sent;
-                scoreMax = feats.map(function (s) {
-                  return s.scoreMax;
-                }).reduce(function (acc, curr) {
-                  return Math.max(acc, curr);
-                });
-                scoreMin = feats.map(function (s) {
-                  return s.scoreMin;
-                }).reduce(function (acc, curr) {
-                  return Math.min(acc, curr);
+                scoreMax = feats.map(function (a) {
+                  return a.scoreMax;
+                }).reduce(function (a, b) {
+                  return Math.max(a, b);
                 });
-                scoreSum = feats.map(function (s) {
-                  return s.scoreSum;
+                scoreMin = feats.map(function (a) {
+                  return a.scoreMin;
                 }).reduce(function (a, b) {
-                  return a + b;
+                  return Math.min(a, b);
+                });
+                scoreSum = feats.reduce(function (a, b) {
+                  return a + b.scoreSum;
                 }, 0);
-                scoreSumSquares = feats.map(function (s) {
-                  return s.scoreSumSquares;
-                }).reduce(function (a, b) {
-                  return a + b;
+                scoreSumSquares = feats.reduce(function (a, b) {
+                  return a + b.scoreSumSquares;
                 }, 0);
-                featureCount = feats.map(function (s) {
-                  return s.featureCount;
-                }).reduce(function (a, b) {
-                  return a + b;
+                featureCount = feats.reduce(function (a, b) {
+                  return a + b.featureCount;
                 }, 0);
-                basesCovered = feats.map(function (s) {
-                  return s.basesCovered;
-                }).reduce(function (a, b) {
-                  return a + b;
+                basesCovered = feats.reduce(function (a, b) {
+                  return a + b.basesCovered;
                 }, 0);
                 return _context7.abrupt("return", (0, _stats.rectifyStats)({
                   scoreMin: scoreMin,
@@ -424,12 +425,165 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
 
       return getMultiRegionStats;
     }()
+  }, {
+    key: "estimateRegionsStats",
+    value: function () {
+      var _estimateRegionsStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee10(regions, opts) {
+        var _this4 = this;
+
+        var region, lastTime, statsFromInterval, maybeRecordStats;
+        return _regenerator.default.wrap(function _callee10$(_context10) {
+          while (1) {
+            switch (_context10.prev = _context10.next) {
+              case 0:
+                region = regions[0];
+                lastTime = +Date.now();
+
+                statsFromInterval = /*#__PURE__*/function () {
+                  var _ref3 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(length, expansionTime) {
+                    var start, end, sampleCenter, query, features;
+                    return _regenerator.default.wrap(function _callee8$(_context8) {
+                      while (1) {
+                        switch (_context8.prev = _context8.next) {
+                          case 0:
+                            start = region.start, end = region.end;
+                            sampleCenter = start * 0.75 + end * 0.25;
+                            query = _objectSpread(_objectSpread({}, region), {}, {
+                              start: Math.max(0, Math.round(sampleCenter - length / 2)),
+                              end: Math.min(Math.round(sampleCenter + length / 2), end)
+                            });
+                            _context8.next = 5;
+                            return _this4.getFeatures(query, opts).pipe((0, _operators.toArray)()).toPromise();
+
+                          case 5:
+                            features = _context8.sent;
+                            return _context8.abrupt("return", maybeRecordStats(length, {
+                              featureDensity: features.length / length
+                            }, features.length, expansionTime));
+
+                          case 7:
+                          case "end":
+                            return _context8.stop();
+                        }
+                      }
+                    }, _callee8);
+                  }));
+
+                  return function statsFromInterval(_x10, _x11) {
+                    return _ref3.apply(this, arguments);
+                  };
+                }();
+
+                maybeRecordStats = /*#__PURE__*/function () {
+                  var _ref4 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee9(interval, stats, statsSampleFeatures, expansionTime) {
+                    var refLen, currTime;
+                    return _regenerator.default.wrap(function _callee9$(_context9) {
+                      while (1) {
+                        switch (_context9.prev = _context9.next) {
+                          case 0:
+                            refLen = region.end - region.start;
+
+                            if (!(statsSampleFeatures >= 70 || interval * 2 > refLen)) {
+                              _context9.next = 5;
+                              break;
+                            }
+
+                            return _context9.abrupt("return", stats);
+
+                          case 5:
+                            if (!(expansionTime <= 5000)) {
+                              _context9.next = 12;
+                              break;
+                            }
+
+                            currTime = +Date.now();
+                            expansionTime += currTime - lastTime;
+                            lastTime = currTime;
+                            return _context9.abrupt("return", statsFromInterval(interval * 2, expansionTime));
+
+                          case 12:
+                            console.warn("Stats estimation reached timeout, or didn't get enough features");
+                            return _context9.abrupt("return", {
+                              featureDensity: Infinity
+                            });
+
+                          case 14:
+                          case "end":
+                            return _context9.stop();
+                        }
+                      }
+                    }, _callee9);
+                  }));
+
+                  return function maybeRecordStats(_x12, _x13, _x14, _x15) {
+                    return _ref4.apply(this, arguments);
+                  };
+                }();
+
+                return _context10.abrupt("return", statsFromInterval(1000, 0));
+
+              case 5:
+              case "end":
+                return _context10.stop();
+            }
+          }
+        }, _callee10);
+      }));
+
+      function estimateRegionsStats(_x8, _x9) {
+        return _estimateRegionsStats.apply(this, arguments);
+      }
+
+      return estimateRegionsStats;
+    }()
   }]);
   return BaseFeatureDataAdapter;
 }(BaseAdapter);
 
 exports.BaseFeatureDataAdapter = BaseFeatureDataAdapter;
 
+var BaseSequenceAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
+  (0, _inherits2.default)(BaseSequenceAdapter, _BaseFeatureDataAdapt);
+
+  var _super2 = _createSuper(BaseSequenceAdapter);
+
+  function BaseSequenceAdapter() {
+    (0, _classCallCheck2.default)(this, BaseSequenceAdapter);
+    return _super2.apply(this, arguments);
+  }
+
+  (0, _createClass2.default)(BaseSequenceAdapter, [{
+    key: "estimateRegionsStats",
+    value: function () {
+      var _estimateRegionsStats2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee11() {
+        return _regenerator.default.wrap(function _callee11$(_context11) {
+          while (1) {
+            switch (_context11.prev = _context11.next) {
+              case 0:
+                return _context11.abrupt("return", {
+                  featureDensity: 0
+                });
+
+              case 1:
+              case "end":
+                return _context11.stop();
+            }
+          }
+        }, _callee11);
+      }));
+
+      function estimateRegionsStats() {
+        return _estimateRegionsStats2.apply(this, arguments);
+      }
+
+      return estimateRegionsStats;
+    }()
+  }]);
+  return BaseSequenceAdapter;
+}(BaseFeatureDataAdapter);
+
+exports.BaseSequenceAdapter = BaseSequenceAdapter;
+
 function isSequenceAdapter(thing) {
   return 'getRegions' in thing && 'getFeatures' in thing;
 }

package/data_adapters/BaseAdapter.test.js

@@ -1,18 +1,20 @@
 "use strict";
 
-var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-var _index = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/regenerator/index.js"));
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
-var _classCallCheck2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
-var _createClass2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createClass.js"));
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
 
-var _inherits2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/inherits.js"));
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
 
-var _createSuper2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createSuper.js"));
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
 var _operators = require("rxjs/operators");
 
@@ -24,28 +26,32 @@ var _simpleFeature = _interopRequireDefault(require("../util/simpleFeature"));
 
 var _configurationSchema = require("../configuration/configurationSchema");
 
+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; } }
+
 describe('base data adapter', function () {
-  it('properly propagates errors in feature fetching', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee2() {
+  it('properly propagates errors in feature fetching', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
     var Adapter, adapter, features, featuresArray;
-    return _index["default"].wrap(function _callee2$(_context2) {
+    return _regenerator.default.wrap(function _callee2$(_context2) {
       while (1) {
         switch (_context2.prev = _context2.next) {
           case 0:
             Adapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-              (0, _inherits2["default"])(Adapter, _BaseFeatureDataAdapt);
+              (0, _inherits2.default)(Adapter, _BaseFeatureDataAdapt);
 
-              var _super = (0, _createSuper2["default"])(Adapter);
+              var _super = _createSuper(Adapter);
 
               function Adapter() {
-                (0, _classCallCheck2["default"])(this, Adapter);
+                (0, _classCallCheck2.default)(this, Adapter);
                 return _super.apply(this, arguments);
               }
 
-              (0, _createClass2["default"])(Adapter, [{
+              (0, _createClass2.default)(Adapter, [{
                 key: "getRefNames",
                 value: function () {
-                  var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee() {
-                    return _index["default"].wrap(function _callee$(_context) {
+                  var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
+                    return _regenerator.default.wrap(function _callee$(_context) {
                       while (1) {
                         switch (_context.prev = _context.next) {
                           case 0:
@@ -96,27 +102,27 @@ describe('base data adapter', function () {
       }
     }, _callee2);
   })));
-  it('retrieves features', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee4() {
+  it('retrieves features', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
     var Adapter, adapter, features, featuresArray, features2, featuresArray2;
-    return _index["default"].wrap(function _callee4$(_context4) {
+    return _regenerator.default.wrap(function _callee4$(_context4) {
       while (1) {
         switch (_context4.prev = _context4.next) {
           case 0:
             Adapter = /*#__PURE__*/function (_BaseFeatureDataAdapt2) {
-              (0, _inherits2["default"])(Adapter, _BaseFeatureDataAdapt2);
+              (0, _inherits2.default)(Adapter, _BaseFeatureDataAdapt2);
 
-              var _super2 = (0, _createSuper2["default"])(Adapter);
+              var _super2 = _createSuper(Adapter);
 
               function Adapter() {
-                (0, _classCallCheck2["default"])(this, Adapter);
+                (0, _classCallCheck2.default)(this, Adapter);
                 return _super2.apply(this, arguments);
               }
 
-              (0, _createClass2["default"])(Adapter, [{
+              (0, _createClass2.default)(Adapter, [{
                 key: "getRefNames",
                 value: function () {
-                  var _getRefNames2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee3() {
-                    return _index["default"].wrap(function _callee3$(_context3) {
+                  var _getRefNames2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
+                    return _regenerator.default.wrap(function _callee3$(_context3) {
                       while (1) {
                         switch (_context3.prev = _context3.next) {
                           case 0:
@@ -141,7 +147,7 @@ describe('base data adapter', function () {
                 value: function getFeatures(region) {
                   return (0, _rxjs.ObservableCreate)(function (observer) {
                     if (region.refName === 'ctgA') {
-                      observer.next(new _simpleFeature["default"]({
+                      observer.next(new _simpleFeature.default({
                         uniqueId: 'testFeature',
                         start: 100,
                         end: 200

package/data_adapters/CytobandAdapter.d.ts

@@ -1,4 +1,4 @@
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import SimpleFeature from '../util/simpleFeature';
 import { BaseAdapter } from './BaseAdapter';
 declare const configSchema: import("../configuration/configurationSchema").AnyConfigurationSchemaType;
 declare class CytobandAdapter extends BaseAdapter {