@jbrowse/plugin-wiggle 1.7.11 → 2.1.0

package/dist/index.js

@@ -1,253 +1,145 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-var _exportNames = {
-  WiggleBaseRenderer: true,
-  WiggleRendering: true,
-  linearWiggleDisplayModelFactory: true,
-  LinearWiggleDisplayReactComponent: true,
-  YSCALEBAR_LABEL_OFFSET: true,
-  Tooltip: true
-};
-Object.defineProperty(exports, "LinearWiggleDisplayReactComponent", {
-  enumerable: true,
-  get: function get() {
-    return _LinearWiggleDisplay.ReactComponent;
-  }
-});
-Object.defineProperty(exports, "Tooltip", {
-  enumerable: true,
-  get: function get() {
-    return _Tooltip.Tooltip;
-  }
-});
-Object.defineProperty(exports, "WiggleBaseRenderer", {
-  enumerable: true,
-  get: function get() {
-    return _WiggleBaseRenderer.default;
-  }
-});
-Object.defineProperty(exports, "WiggleRendering", {
-  enumerable: true,
-  get: function get() {
-    return _WiggleRendering.default;
-  }
-});
-Object.defineProperty(exports, "YSCALEBAR_LABEL_OFFSET", {
-  enumerable: true,
-  get: function get() {
-    return _LinearWiggleDisplay.YSCALEBAR_LABEL_OFFSET;
-  }
-});
-exports.default = void 0;
-Object.defineProperty(exports, "linearWiggleDisplayModelFactory", {
-  enumerable: true,
-  get: function get() {
-    return _LinearWiggleDisplay.modelFactory;
-  }
-});
-
-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 _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-
-var _TrackType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
-
-var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _models = require("@jbrowse/core/pluggableElementTypes/models");
-
-var _DisplayType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-
-var _WiggleBaseRenderer = _interopRequireDefault(require("./WiggleBaseRenderer"));
-
-var _WiggleRendering = _interopRequireDefault(require("./WiggleRendering"));
-
-var _BigWigAdapter = require("./BigWigAdapter");
-
-var _DensityRenderer = _interopRequireWildcard(require("./DensityRenderer"));
-
-var utils = _interopRequireWildcard(require("./util"));
-
-Object.keys(utils).forEach(function (key) {
-  if (key === "default" || key === "__esModule") return;
-  if (Object.prototype.hasOwnProperty.call(_exportNames, key)) return;
-  if (key in exports && exports[key] === utils[key]) return;
-  Object.defineProperty(exports, key, {
-    enumerable: true,
-    get: function get() {
-      return utils[key];
+var __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
     }
-  });
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
 });
-
-var _LinearWiggleDisplay = require("./LinearWiggleDisplay");
-
-var _XYPlotRenderer = _interopRequireWildcard(require("./XYPlotRenderer"));
-
-var _LinePlotRenderer = _interopRequireWildcard(require("./LinePlotRenderer"));
-
-var _rpcMethods = require("./WiggleRPC/rpcMethods");
-
-var _tracks = require("@jbrowse/core/util/tracks");
-
-var _Tooltip = require("./LinearWiggleDisplay/components/Tooltip");
-
-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; }
-
-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 WigglePlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2.default)(WigglePlugin, _Plugin);
-
-  var _super = _createSuper(WigglePlugin);
-
-  function WigglePlugin() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, WigglePlugin);
-
-    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-      args[_key] = arguments[_key];
-    }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'WigglePlugin');
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "exports", {
-      LinearWiggleDisplayReactComponent: _LinearWiggleDisplay.ReactComponent,
-      XYPlotRendererReactComponent: _XYPlotRenderer.ReactComponent,
-      XYPlotRenderer: _XYPlotRenderer.default,
-      xyPlotRendererConfigSchema: _XYPlotRenderer.configSchema,
-      utils: utils,
-      WiggleBaseRenderer: _WiggleBaseRenderer.default,
-      linearWiggleDisplayModelFactory: _LinearWiggleDisplay.modelFactory
-    });
-    return _this;
-  }
-
-  (0, _createClass2.default)(WigglePlugin, [{
-    key: "install",
-    value: function install(pluginManager) {
-      pluginManager.addTrackType(function () {
-        var configSchema = (0, _configuration.ConfigurationSchema)('QuantitativeTrack', {}, {
-          baseConfiguration: (0, _models.createBaseTrackConfig)(pluginManager)
-        });
-        return new _TrackType.default({
-          name: 'QuantitativeTrack',
-          configSchema: configSchema,
-          stateModel: (0, _models.createBaseTrackModel)(pluginManager, 'QuantitativeTrack', configSchema)
-        });
-      });
-      pluginManager.addDisplayType(function () {
-        var configSchema = (0, _LinearWiggleDisplay.configSchemaFactory)(pluginManager);
-        return new _DisplayType.default({
-          name: 'LinearWiggleDisplay',
-          configSchema: configSchema,
-          stateModel: (0, _LinearWiggleDisplay.modelFactory)(pluginManager, configSchema),
-          trackType: 'QuantitativeTrack',
-          viewType: 'LinearGenomeView',
-          ReactComponent: _LinearWiggleDisplay.ReactComponent
-        });
-      });
-      pluginManager.addAdapterType(function () {
-        return new _AdapterType.default({
-          name: 'BigWigAdapter',
-          configSchema: _BigWigAdapter.configSchema,
-          adapterCapabilities: ['hasResolution', 'hasLocalStats', 'hasGlobalStats'],
-          getAdapterClass: function getAdapterClass() {
-            return Promise.resolve().then(function () {
-              return _interopRequireWildcard(require('./BigWigAdapter/BigWigAdapter'));
-            }).then(function (r) {
-              return r.default;
-            });
-          }
-        });
-      });
-      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-        return function (file, index, adapterHint) {
-          var regexGuess = /\.(bw|bigwig)$/i;
-          var adapterName = 'BigWigAdapter';
-          var fileName = (0, _tracks.getFileName)(file);
-          var obj = {
-            type: adapterName,
-            bigWigLocation: file
-          };
-
-          if (regexGuess.test(fileName) && !adapterHint) {
-            return obj;
-          } else if (adapterHint === adapterName) {
-            return obj;
-          }
-
-          return adapterGuesser(file, index, adapterHint);
-        };
-      });
-      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
-        return function (adapterName) {
-          if (adapterName === 'BigWigAdapter') {
-            return 'QuantitativeTrack';
-          }
-
-          return trackTypeGuesser(adapterName);
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.linearWiggleDisplayModelFactory = exports.WiggleBaseRenderer = exports.WiggleRendering = exports.Tooltip = exports.LinearWiggleDisplayReactComponent = void 0;
+var Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+var tracks_1 = require("@jbrowse/core/util/tracks");
+// locals
+var WiggleBaseRenderer_1 = __importDefault(require("./WiggleBaseRenderer"));
+exports.WiggleBaseRenderer = WiggleBaseRenderer_1.default;
+var WiggleRendering_1 = __importDefault(require("./WiggleRendering"));
+exports.WiggleRendering = WiggleRendering_1.default;
+var BigWigAdapter_1 = __importDefault(require("./BigWigAdapter"));
+var QuantitativeTrack_1 = __importDefault(require("./QuantitativeTrack"));
+var MultiQuantitativeTrack_1 = __importDefault(require("./MultiQuantitativeTrack"));
+var MultiWiggleAdapter_1 = __importDefault(require("./MultiWiggleAdapter"));
+var DensityRenderer_1 = __importDefault(require("./DensityRenderer"));
+var XYPlotRenderer_1 = __importDefault(require("./XYPlotRenderer"));
+var LinePlotRenderer_1 = __importDefault(require("./LinePlotRenderer"));
+var LinearWiggleDisplay_1 = __importDefault(require("./LinearWiggleDisplay"));
+var MultiLinearWiggleDisplay_1 = __importDefault(require("./MultiLinearWiggleDisplay"));
+var MultiXYPlotRenderer_1 = __importDefault(require("./MultiXYPlotRenderer"));
+var MultiRowXYPlotRenderer_1 = __importDefault(require("./MultiRowXYPlotRenderer"));
+var MultiDensityRenderer_1 = __importDefault(require("./MultiDensityRenderer"));
+var MultiLineRenderer_1 = __importDefault(require("./MultiLineRenderer"));
+var MultiRowLineRenderer_1 = __importDefault(require("./MultiRowLineRenderer"));
+var CreateMultiWiggleExtension_1 = __importDefault(require("./CreateMultiWiggleExtension"));
+var MultiWiggleAddTrackWidget_1 = __importDefault(require("./MultiWiggleAddTrackWidget"));
+var utils = __importStar(require("./util"));
+var rpcMethods_1 = require("./WiggleRPC/rpcMethods");
+var LinearWiggleDisplay_2 = require("./LinearWiggleDisplay");
+Object.defineProperty(exports, "LinearWiggleDisplayReactComponent", { enumerable: true, get: function () { return LinearWiggleDisplay_2.ReactComponent; } });
+Object.defineProperty(exports, "linearWiggleDisplayModelFactory", { enumerable: true, get: function () { return LinearWiggleDisplay_2.modelFactory; } });
+Object.defineProperty(exports, "Tooltip", { enumerable: true, get: function () { return LinearWiggleDisplay_2.Tooltip; } });
+var XYPlotRenderer_2 = require("./XYPlotRenderer");
+var WigglePlugin = /** @class */ (function (_super) {
+    __extends(WigglePlugin, _super);
+    function WigglePlugin() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
+        _this.name = 'WigglePlugin';
+        _this.exports = {
+            LinearWiggleDisplayReactComponent: LinearWiggleDisplay_2.ReactComponent,
+            XYPlotRendererReactComponent: XYPlotRenderer_2.ReactComponent,
+            XYPlotRenderer: XYPlotRenderer_2.XYPlotRenderer,
+            WiggleBaseRenderer: WiggleBaseRenderer_1.default,
+            xyPlotRendererConfigSchema: XYPlotRenderer_2.configSchema,
+            utils: utils,
+            linearWiggleDisplayModelFactory: LinearWiggleDisplay_2.modelFactory,
         };
-      });
-      pluginManager.addRendererType(function () {
-        return new _DensityRenderer.default({
-          name: 'DensityRenderer',
-          ReactComponent: _DensityRenderer.ReactComponent,
-          configSchema: _DensityRenderer.configSchema,
-          pluginManager: pluginManager
-        });
-      });
-      pluginManager.addRendererType(function () {
-        return new _LinePlotRenderer.default({
-          name: 'LinePlotRenderer',
-          ReactComponent: _LinePlotRenderer.ReactComponent,
-          configSchema: _LinePlotRenderer.configSchema,
-          pluginManager: pluginManager
+        return _this;
+    }
+    WigglePlugin.prototype.install = function (pm) {
+        (0, MultiWiggleAdapter_1.default)(pm);
+        (0, BigWigAdapter_1.default)(pm);
+        (0, QuantitativeTrack_1.default)(pm);
+        (0, MultiQuantitativeTrack_1.default)(pm);
+        (0, LinearWiggleDisplay_1.default)(pm);
+        (0, MultiLinearWiggleDisplay_1.default)(pm);
+        (0, LinePlotRenderer_1.default)(pm);
+        (0, XYPlotRenderer_1.default)(pm);
+        (0, DensityRenderer_1.default)(pm);
+        (0, MultiXYPlotRenderer_1.default)(pm);
+        (0, MultiRowXYPlotRenderer_1.default)(pm);
+        (0, MultiDensityRenderer_1.default)(pm);
+        (0, MultiLineRenderer_1.default)(pm);
+        (0, MultiRowLineRenderer_1.default)(pm);
+        (0, MultiWiggleAddTrackWidget_1.default)(pm);
+        (0, CreateMultiWiggleExtension_1.default)(pm);
+        pm.addToExtensionPoint('Core-guessAdapterForLocation', function (cb) {
+            return function (file, index, hint) {
+                var regexGuess = /\.(bw|bigwig)$/i;
+                var adapterName = 'BigWigAdapter';
+                var fileName = (0, tracks_1.getFileName)(file);
+                var obj = {
+                    type: adapterName,
+                    bigWigLocation: file,
+                };
+                if (regexGuess.test(fileName) && !hint) {
+                    return obj;
+                }
+                else if (hint === adapterName) {
+                    return obj;
+                }
+                return cb(file, index, hint);
+            };
         });
-      });
-      pluginManager.addRendererType(function () {
-        return new _XYPlotRenderer.default({
-          name: 'XYPlotRenderer',
-          ReactComponent: _XYPlotRenderer.ReactComponent,
-          configSchema: _XYPlotRenderer.configSchema,
-          pluginManager: pluginManager
+        pm.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+            return function (adapterName) {
+                if (adapterName === 'BigWigAdapter') {
+                    return 'QuantitativeTrack';
+                }
+                return trackTypeGuesser(adapterName);
+            };
         });
-      });
-      pluginManager.addRpcMethod(function () {
-        return new _rpcMethods.WiggleGetGlobalStats(pluginManager);
-      });
-      pluginManager.addRpcMethod(function () {
-        return new _rpcMethods.WiggleGetMultiRegionStats(pluginManager);
-      });
-    }
-  }]);
-  return WigglePlugin;
-}(_Plugin2.default);
-
-exports.default = WigglePlugin;
+        pm.addRpcMethod(function () { return new rpcMethods_1.WiggleGetGlobalStats(pm); });
+        pm.addRpcMethod(function () { return new rpcMethods_1.WiggleGetMultiRegionStats(pm); });
+        pm.addRpcMethod(function () { return new rpcMethods_1.MultiWiggleGetSources(pm); });
+    };
+    return WigglePlugin;
+}(Plugin_1.default));
+exports.default = WigglePlugin;
+__exportStar(require("./util"), exports);
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
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package/dist/util.d.ts

@@ -1,3 +1,6 @@
+import { FeatureStats } from '@jbrowse/core/util/stats';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare const YSCALEBAR_LABEL_OFFSET = 5;
 export interface ScaleOpts {
     domain: number[];
     range: number[];
@@ -5,6 +8,11 @@ export interface ScaleOpts {
     pivotValue?: number;
     inverted: boolean;
 }
+export interface Source {
+    name: string;
+    color?: string;
+    group?: string;
+}
 /**
  * produces a d3-scale from arguments. applies a "nice domain" adjustment
  *
@@ -16,7 +24,7 @@ export interface ScaleOpts {
  *   - pivotValue (number)
  *   - inverted (boolean)
  */
-export declare function getScale({ domain, range, scaleType, pivotValue, inverted, }: ScaleOpts): import("d3-scale").ScaleLinear<number, number> | import("d3-scale").ScaleQuantize<number>;
+export declare function getScale({ domain, range, scaleType, pivotValue, inverted, }: ScaleOpts): import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
 /**
  * gets the origin for drawing the graph. for linear this is 0, for log this is arbitrarily set to log(1)==0
  *
@@ -39,3 +47,28 @@ export declare function getNiceDomain({ scaleType, domain, bounds, }: {
     domain: number[];
     bounds: number[];
 }): [number, number];
+export declare function groupBy<T>(array: T[], predicate: (v: T) => string): {
+    [key: string]: T[];
+};
+export declare function getStats(self: {
+    adapterConfig: AnyConfigurationModel;
+    autoscaleType: string;
+    setMessage: (str: string) => void;
+}, opts: {
+    headers?: Record<string, string>;
+    signal?: AbortSignal;
+    filters?: string[];
+}): Promise<FeatureStats>;
+export declare function statsAutorun(self: {
+    estimatedStatsReady: boolean;
+    regionTooLarge: boolean;
+    setLoading: (aborter: AbortController) => void;
+    setError: (error: unknown) => void;
+    updateStats: (stats: FeatureStats, statsRegion: string) => void;
+    renderProps: () => Record<string, unknown>;
+    adapterConfig: AnyConfigurationModel;
+    autoscaleType: string;
+    setMessage: (str: string) => void;
+}): void;
+export declare function toP(s?: number): number;
+export declare function round(value: number): number;