@jbrowse/plugin-wiggle 1.6.7 → 1.7.0

package/dist/XYPlotRenderer/XYPlotRenderer.js

@@ -0,0 +1,199 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+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 _configuration = require("@jbrowse/core/configuration");
+
+var _util = require("@jbrowse/core/util");
+
+var _color = _interopRequireDefault(require("color"));
+
+var _util2 = require("../util");
+
+var _WiggleBaseRenderer2 = _interopRequireDefault(require("../WiggleBaseRenderer"));
+
+var _model = require("../LinearWiggleDisplay/models/model");
+
+function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it["return"] != null) it["return"](); } finally { if (didErr) throw err; } } }; }
+
+function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
+
+function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
+
+function 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 XYPlotRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
+  (0, _inherits2["default"])(XYPlotRenderer, _WiggleBaseRenderer);
+
+  var _super = _createSuper(XYPlotRenderer);
+
+  function XYPlotRenderer() {
+    (0, _classCallCheck2["default"])(this, XYPlotRenderer);
+    return _super.apply(this, arguments);
+  }
+
+  (0, _createClass2["default"])(XYPlotRenderer, [{
+    key: "draw",
+    value: function draw(ctx, props) {
+      var features = props.features,
+          bpPerPx = props.bpPerPx,
+          regions = props.regions,
+          scaleOpts = props.scaleOpts,
+          unadjustedHeight = props.height,
+          config = props.config,
+          ticks = props.ticks,
+          displayCrossHatches = props.displayCrossHatches;
+
+      var _regions = (0, _slicedToArray2["default"])(regions, 1),
+          region = _regions[0];
+
+      var width = (region.end - region.start) / bpPerPx; // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
+      // wiggle display, and makes the height of the actual drawn area add
+      // "padding" to the top and bottom of the display
+
+      var offset = _model.YSCALEBAR_LABEL_OFFSET;
+      var height = unadjustedHeight - offset * 2;
+      var pivotValue = (0, _configuration.readConfObject)(config, 'bicolorPivotValue');
+      var negColor = (0, _configuration.readConfObject)(config, 'negColor');
+      var posColor = (0, _configuration.readConfObject)(config, 'posColor');
+      var filled = (0, _configuration.readConfObject)(config, 'filled');
+      var clipColor = (0, _configuration.readConfObject)(config, 'clipColor');
+      var highlightColor = (0, _configuration.readConfObject)(config, 'highlightColor');
+      var summaryScoreMode = (0, _configuration.readConfObject)(config, 'summaryScoreMode');
+      var scale = (0, _util2.getScale)(_objectSpread(_objectSpread({}, scaleOpts), {}, {
+        range: [0, height]
+      }));
+      var originY = (0, _util2.getOrigin)(scaleOpts.scaleType);
+
+      var _scale$domain = scale.domain(),
+          _scale$domain2 = (0, _slicedToArray2["default"])(_scale$domain, 2),
+          niceMin = _scale$domain2[0],
+          niceMax = _scale$domain2[1];
+
+      var toY = function toY(n) {
+        return height - (scale(n) || 0) + offset;
+      };
+
+      var toHeight = function toHeight(n) {
+        return toY(originY) - toY(n);
+      };
+
+      var colorCallback = (0, _configuration.readConfObject)(config, 'color') === '#f0f' ? function (_, score) {
+        return score < pivotValue ? negColor : posColor;
+      } : function (feature, _score) {
+        return (0, _configuration.readConfObject)(config, 'color', {
+          feature: feature
+        });
+      };
+      var crossingOrigin = niceMin < pivotValue && niceMax > pivotValue;
+
+      var _iterator = _createForOfIteratorHelper(features.values()),
+          _step;
+
+      try {
+        for (_iterator.s(); !(_step = _iterator.n()).done;) {
+          var feature = _step.value;
+
+          var _featureSpanPx = (0, _util.featureSpanPx)(feature, region, bpPerPx),
+              _featureSpanPx2 = (0, _slicedToArray2["default"])(_featureSpanPx, 2),
+              leftPx = _featureSpanPx2[0],
+              rightPx = _featureSpanPx2[1];
+
+          var score = feature.get('score');
+          var maxr = feature.get('maxScore');
+          var minr = feature.get('minScore');
+          var lowClipping = score < niceMin;
+          var highClipping = score > niceMax;
+          var w = rightPx - leftPx + 0.4; // fudge factor for subpixel rendering
+
+          var summary = feature.get('summary');
+
+          if (summaryScoreMode === 'max') {
+            score = summary ? maxr : score;
+            ctx.fillStyle = colorCallback(feature, score);
+            ctx.fillRect(leftPx, toY(score), w, filled ? toHeight(score) : 1);
+          } else if (summaryScoreMode === 'min') {
+            score = summary ? minr : score;
+            ctx.fillStyle = colorCallback(feature, score);
+            ctx.fillRect(leftPx, toY(score), w, filled ? toHeight(score) : 1);
+          } else if (summaryScoreMode === 'whiskers') {
+            var c = colorCallback(feature, score);
+
+            if (summary) {
+              ctx.fillStyle = crossingOrigin ? colorCallback(feature, maxr) : (0, _color["default"])(c).lighten(0.6).toString();
+              ctx.fillRect(leftPx, toY(maxr), w, filled ? toHeight(maxr) - toHeight(score) : 1);
+            } // normal
+
+
+            ctx.fillStyle = crossingOrigin && summary ? (0, _color["default"])(colorCallback(feature, maxr)).mix((0, _color["default"])(colorCallback(feature, minr))) : c;
+            ctx.fillRect(leftPx, toY(score), w, filled ? toHeight(score) - (summary ? toHeight(minr) : 0) : 1); // min
+
+            if (summary) {
+              ctx.fillStyle = crossingOrigin ? colorCallback(feature, minr) : (0, _color["default"])(c).darken(0.6).toString();
+              ctx.fillRect(leftPx, toY(minr), w, filled ? toHeight(minr) : 1);
+            }
+          } else {
+            ctx.fillStyle = colorCallback(feature, score);
+            ctx.fillRect(leftPx, toY(score), w, filled ? toHeight(score) : 1);
+          }
+
+          if (highClipping) {
+            ctx.fillStyle = clipColor;
+            ctx.fillRect(leftPx, 0, w, 4);
+          } else if (lowClipping && scaleOpts.scaleType !== 'log') {
+            ctx.fillStyle = clipColor;
+            ctx.fillRect(leftPx, unadjustedHeight - 4, w, 4);
+          }
+
+          if (feature.get('highlighted')) {
+            ctx.fillStyle = highlightColor;
+            ctx.fillRect(leftPx, 0, w, height);
+          }
+        }
+      } catch (err) {
+        _iterator.e(err);
+      } finally {
+        _iterator.f();
+      }
+
+      if (displayCrossHatches) {
+        ctx.lineWidth = 1;
+        ctx.strokeStyle = 'rgba(200,200,200,0.8)';
+        ticks.values.forEach(function (tick) {
+          ctx.beginPath();
+          ctx.moveTo(0, Math.round(toY(tick)));
+          ctx.lineTo(width, Math.round(toY(tick)));
+          ctx.stroke();
+        });
+      }
+    }
+  }]);
+  return XYPlotRenderer;
+}(_WiggleBaseRenderer2["default"]);
+
+exports["default"] = XYPlotRenderer;

package/dist/XYPlotRenderer/XYPlotRenderer.test.js

@@ -0,0 +1,83 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+var _offscreenCanvasUtils = require("@jbrowse/core/util/offscreenCanvasUtils");
+
+var _ = _interopRequireWildcard(require("."));
+
+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 || _typeof(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; }
+
+test('several features', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+  var pluginManager, renderer, renderProps, res;
+  return _regenerator["default"].wrap(function _callee$(_context) {
+    while (1) {
+      switch (_context.prev = _context.next) {
+        case 0:
+          pluginManager = {};
+          renderer = new _["default"]({
+            name: 'XYPlotRenderer',
+            ReactComponent: _.ReactComponent,
+            configSchema: _.configSchema,
+            pluginManager: pluginManager
+          });
+          renderProps = {
+            features: [new _simpleFeature["default"]({
+              id: 't1',
+              data: {
+                start: 1,
+                end: 100,
+                score: 1
+              }
+            }), new _simpleFeature["default"]({
+              id: 't2',
+              data: {
+                start: 101,
+                end: 200,
+                score: 2
+              }
+            })],
+            regions: [{
+              end: 100,
+              start: 1
+            }],
+            scaleOpts: {
+              domain: [0, 100],
+              scaleType: 'linear'
+            },
+            config: {},
+            bpPerPx: 3,
+            highResolutionScaling: 1,
+            height: 100,
+            ticks: {
+              values: [0, 100]
+            }
+          };
+          _context.next = 5;
+          return (0, _offscreenCanvasUtils.renderToAbstractCanvas)(1000, 200, renderProps, function (ctx) {
+            return renderer.draw(ctx, renderProps);
+          });
+
+        case 5:
+          res = _context.sent;
+          expect(res).toMatchSnapshot({
+            imageData: expect.any(Object)
+          });
+
+        case 7:
+        case "end":
+          return _context.stop();
+      }
+    }
+  }, _callee);
+})));

package/dist/XYPlotRenderer/index.js

@@ -0,0 +1,34 @@
+"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 _WiggleRendering["default"];
+  }
+});
+exports.configSchema = void 0;
+Object.defineProperty(exports, "default", {
+  enumerable: true,
+  get: function get() {
+    return _XYPlotRenderer["default"];
+  }
+});
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _configSchema = _interopRequireDefault(require("../configSchema"));
+
+var _WiggleRendering = _interopRequireDefault(require("../WiggleRendering"));
+
+var _XYPlotRenderer = _interopRequireDefault(require("./XYPlotRenderer"));
+
+var configSchema = (0, _configuration.ConfigurationSchema)('XYPlotRenderer', {}, {
+  baseConfiguration: _configSchema["default"],
+  explicitlyTyped: true
+});
+exports.configSchema = configSchema;

package/dist/configSchema.js

@@ -0,0 +1,75 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _default = (0, _configuration.ConfigurationSchema)('WiggleRenderer', {
+  color: {
+    type: 'color',
+    description: 'the color of track, overrides posColor and negColor',
+    defaultValue: '#f0f'
+  },
+  posColor: {
+    type: 'color',
+    description: 'the color to use when the score is positive',
+    defaultValue: 'blue'
+  },
+  negColor: {
+    type: 'color',
+    description: 'the color to use when the score is negative',
+    defaultValue: 'red'
+  },
+  highlightColor: {
+    type: 'color',
+    description: 'the color of highlights over the wiggle track',
+    defaultValue: 'rgba(255,255,0,0.5)'
+  },
+  clipColor: {
+    type: 'color',
+    description: 'the color of the clipping marker',
+    defaultValue: 'red'
+  },
+  renderType: {
+    type: 'stringEnum',
+    model: _mobxStateTree.types.enumeration('Rendering type', ['xyplot', 'density', 'line']),
+    description: 'The type of rendering for wiggle data to use',
+    defaultValue: 'xyplot'
+  },
+  filled: {
+    type: 'boolean',
+    description: 'fill in histogram',
+    defaultValue: true
+  },
+  bicolorPivot: {
+    type: 'stringEnum',
+    model: _mobxStateTree.types.enumeration('Scale type', ['numeric', 'mean', 'z_score', 'none']),
+    description: 'type of bicolor pivot',
+    defaultValue: 'numeric'
+  },
+  bicolorPivotValue: {
+    type: 'number',
+    defaultValue: 0,
+    description: 'value to use for bicolor pivot'
+  },
+  summaryScoreMode: {
+    type: 'stringEnum',
+    model: _mobxStateTree.types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
+    description: 'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
+    defaultValue: 'whiskers'
+  },
+  displayCrossHatches: {
+    type: 'boolean',
+    description: 'choose to draw cross hatches (sideways lines)',
+    defaultValue: false
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/declare.d.js

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

package/dist/index.d.ts

@@ -36,7 +36,7 @@ export default class WigglePlugin extends Plugin {
                     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;
@@ -54,7 +54,7 @@ export default class WigglePlugin extends Plugin {
                     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;
@@ -139,7 +139,7 @@ export default class WigglePlugin extends Plugin {
                 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;
@@ -152,8 +152,8 @@ export default class WigglePlugin extends Plugin {
                 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;
@@ -180,11 +180,11 @@ export default class WigglePlugin extends Plugin {
                 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;
@@ -222,7 +222,7 @@ export default class WigglePlugin extends Plugin {
                 setPosColor(color: string): void;
                 setNegColor(color: string): void;
                 setLoading(aborter: AbortController): void;
-                selectFeature(feature: import("@jbrowse/core/util/simpleFeature").Feature): void;
+                selectFeature(feature: import("@jbrowse/core/util").Feature): void;
                 setResolution(res: number): void;
                 setFill(fill: boolean): void;
                 toggleLogScale(): void;
@@ -307,7 +307,7 @@ export default class WigglePlugin extends Plugin {
                     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;
@@ -325,7 +325,7 @@ export default class WigglePlugin extends Plugin {
                     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;
@@ -410,7 +410,7 @@ export default class WigglePlugin extends Plugin {
                 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;
@@ -423,8 +423,8 @@ export default class WigglePlugin extends Plugin {
                 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;
@@ -451,11 +451,11 @@ export default class WigglePlugin extends Plugin {
                 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;
@@ -493,7 +493,7 @@ export default class WigglePlugin extends Plugin {
                 setPosColor(color: string): void;
                 setNegColor(color: string): void;
                 setLoading(aborter: AbortController): void;
-                selectFeature(feature: import("@jbrowse/core/util/simpleFeature").Feature): void;
+                selectFeature(feature: import("@jbrowse/core/util").Feature): void;
                 setResolution(res: number): void;
                 setFill(fill: boolean): void;
                 toggleLogScale(): void;
@@ -564,7 +564,7 @@ export default class WigglePlugin extends Plugin {
         }) => JSX.Element;
         XYPlotRendererReactComponent: (props: {
             regions: import("@jbrowse/core/util/types").Region[];
-            features: Map<string, import("@jbrowse/core/util/simpleFeature").Feature>;
+            features: Map<string, import("@jbrowse/core/util").Feature>;
             bpPerPx: number;
             width: number;
             height: number;
@@ -602,7 +602,7 @@ export default class WigglePlugin extends Plugin {
                 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;
@@ -620,7 +620,7 @@ export default class WigglePlugin extends Plugin {
                 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;
@@ -705,7 +705,7 @@ export default class WigglePlugin extends Plugin {
             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;
@@ -718,8 +718,8 @@ export default class WigglePlugin extends Plugin {
             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;
@@ -746,11 +746,11 @@ export default class WigglePlugin extends Plugin {
             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;
@@ -788,7 +788,7 @@ export default class WigglePlugin extends Plugin {
             setPosColor(color: string): void;
             setNegColor(color: string): void;
             setLoading(aborter: AbortController): void;
-            selectFeature(feature: import("@jbrowse/core/util/simpleFeature").Feature): void;
+            selectFeature(feature: import("@jbrowse/core/util").Feature): void;
             setResolution(res: number): void;
             setFill(fill: boolean): void;
             toggleLogScale(): void;