@jbrowse/plugin-wiggle 1.5.0 → 1.5.4

package/dist/BigWigAdapter/BigWigAdapter.d.ts

@@ -1,5 +1,5 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
@@ -16,7 +16,7 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     refIdToName(refId: number): Promise<any>;
     getGlobalStats(opts?: BaseOptions): Promise<import("@jbrowse/core/util/stats").FeatureStats>;
-    getFeatures(region: NoAssemblyRegion, opts?: WiggleOptions): import("rxjs").Observable<Feature>;
+    getFeatures(region: Region, opts?: WiggleOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }
 export {};

package/dist/LinearWiggleDisplay/components/Tooltip.d.ts

@@ -1,7 +1,10 @@
 import React from 'react';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
 declare type Coord = [number, number];
 declare const Tooltip: ({ model, height, clientMouseCoord, offsetMouseCoord, clientRect, TooltipContents, }: {
-    model: any;
+    model: {
+        featureUnderMouse: Feature;
+    };
     height: number;
     clientMouseCoord: Coord;
     offsetMouseCoord: Coord;
@@ -9,7 +12,9 @@ declare const Tooltip: ({ model, height, clientMouseCoord, offsetMouseCoord, cli
     TooltipContents: React.FC<any>;
 }) => JSX.Element | null;
 declare const WiggleTooltip: (props: {
-    model: any;
+    model: {
+        featureUnderMouse: Feature;
+    };
     height: number;
     offsetMouseCoord: Coord;
     clientMouseCoord: Coord;

package/dist/LinearWiggleDisplay/models/model.d.ts

@@ -170,7 +170,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     }[];
     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>;
 } & {
@@ -244,7 +244,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
 } & {
     reload(): Promise<void>;
     afterAttach(): void;
-    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>;
 }, import("mobx-state-tree")._NotCustomized, {

package/dist/WiggleRendering.d.ts

@@ -10,6 +10,7 @@ declare function WiggleRendering(props: {
     onMouseLeave: Function;
     onMouseMove: Function;
     onFeatureClick: Function;
+    blockKey: string;
 }): JSX.Element;
 declare const _default: typeof WiggleRendering;
 export default _default;

package/dist/index.d.ts

@@ -167,8 +167,8 @@ export default class WigglePlugin extends Plugin {
                 reload(): void;
                 setContextMenuFeature(feature?: import("@jbrowse/core/util/simpleFeature").Feature | undefined): void;
             } & {
-                regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Zoom in to see features";
-                regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
+                regionCannotBeRenderedText(_region: import("@jbrowse/core/util/types").Region): "" | "Zoom in to see features";
+                regionCannotBeRendered(_region: import("@jbrowse/core/util/types").Region): JSX.Element | undefined;
                 trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
                 contextMenuItems(): {
                     label: string;
@@ -177,7 +177,7 @@ export default class WigglePlugin extends Plugin {
                 }[];
                 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>;
             } & {
@@ -251,7 +251,7 @@ export default class WigglePlugin extends Plugin {
             } & {
                 reload(): Promise<void>;
                 afterAttach(): void;
-                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>;
             } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -410,8 +410,8 @@ export default class WigglePlugin extends Plugin {
                 reload(): void;
                 setContextMenuFeature(feature?: import("@jbrowse/core/util/simpleFeature").Feature | undefined): void;
             } & {
-                regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Zoom in to see features";
-                regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
+                regionCannotBeRenderedText(_region: import("@jbrowse/core/util/types").Region): "" | "Zoom in to see features";
+                regionCannotBeRendered(_region: import("@jbrowse/core/util/types").Region): JSX.Element | undefined;
                 trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
                 contextMenuItems(): {
                     label: string;
@@ -420,7 +420,7 @@ export default class WigglePlugin extends Plugin {
                 }[];
                 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>;
             } & {
@@ -494,7 +494,7 @@ export default class WigglePlugin extends Plugin {
             } & {
                 reload(): Promise<void>;
                 afterAttach(): void;
-                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>;
             }, import("mobx-state-tree")._NotCustomized, {
@@ -506,7 +506,7 @@ export default class WigglePlugin extends Plugin {
             } & import("mobx-state-tree")._NotCustomized>>;
         }) => JSX.Element;
         XYPlotRendererReactComponent: (props: {
-            regions: import("@jbrowse/core/util").Region[];
+            regions: import("@jbrowse/core/util/types").Region[];
             features: Map<string, import("@jbrowse/core/util/simpleFeature").Feature>;
             bpPerPx: number;
             width: number;
@@ -514,6 +514,7 @@ export default class WigglePlugin extends Plugin {
             onMouseLeave: Function;
             onMouseMove: Function;
             onFeatureClick: Function;
+            blockKey: string;
         }) => JSX.Element;
         XYPlotRenderer: typeof XYPlotRenderer;
         xyPlotRendererConfigSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
@@ -675,8 +676,8 @@ export default class WigglePlugin extends Plugin {
             reload(): void;
             setContextMenuFeature(feature?: import("@jbrowse/core/util/simpleFeature").Feature | undefined): void;
         } & {
-            regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Zoom in to see features";
-            regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
+            regionCannotBeRenderedText(_region: import("@jbrowse/core/util/types").Region): "" | "Zoom in to see features";
+            regionCannotBeRendered(_region: import("@jbrowse/core/util/types").Region): JSX.Element | undefined;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
             contextMenuItems(): {
                 label: string;
@@ -685,7 +686,7 @@ export default class WigglePlugin extends Plugin {
             }[];
             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>;
         } & {
@@ -759,7 +760,7 @@ export default class WigglePlugin extends Plugin {
         } & {
             reload(): Promise<void>;
             afterAttach(): void;
-            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>;
         }, import("mobx-state-tree")._NotCustomized, {

package/dist/plugin-wiggle.cjs.development.js

@@ -52,14 +52,9 @@ function ownKeys(object, enumerableOnly) {
 
   if (Object.getOwnPropertySymbols) {
     var symbols = Object.getOwnPropertySymbols(object);
-
-    if (enumerableOnly) {
-      symbols = symbols.filter(function (sym) {
-        return Object.getOwnPropertyDescriptor(object, sym).enumerable;
-      });
-    }
-
-    keys.push.apply(keys, symbols);
+    enumerableOnly && (symbols = symbols.filter(function (sym) {
+      return Object.getOwnPropertyDescriptor(object, sym).enumerable;
+    })), keys.push.apply(keys, symbols);
   }
 
   return keys;
@@ -67,19 +62,12 @@ function ownKeys(object, enumerableOnly) {
 
 function _objectSpread2(target) {
   for (var i = 1; i < arguments.length; i++) {
-    var source = arguments[i] != null ? arguments[i] : {};
-
-    if (i % 2) {
-      ownKeys(Object(source), true).forEach(function (key) {
-        _defineProperty(target, key, source[key]);
-      });
-    } else if (Object.getOwnPropertyDescriptors) {
-      Object.defineProperties(target, Object.getOwnPropertyDescriptors(source));
-    } else {
-      ownKeys(Object(source)).forEach(function (key) {
-        Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key));
-      });
-    }
+    var source = null != arguments[i] ? arguments[i] : {};
+    i % 2 ? ownKeys(Object(source), !0).forEach(function (key) {
+      _defineProperty(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;
@@ -140,6 +128,9 @@ function _defineProperties(target, props) {
 function _createClass(Constructor, protoProps, staticProps) {
   if (protoProps) _defineProperties(Constructor.prototype, protoProps);
   if (staticProps) _defineProperties(Constructor, staticProps);
+  Object.defineProperty(Constructor, "prototype", {
+    writable: false
+  });
   return Constructor;
 }
 
@@ -163,12 +154,15 @@ function _inherits(subClass, superClass) {
     throw new TypeError("Super expression must either be null or a function");
   }
 
-  subClass.prototype = Object.create(superClass && superClass.prototype, {
-    constructor: {
-      value: subClass,
-      writable: true,
-      configurable: true
-    }
+  Object.defineProperty(subClass, "prototype", {
+    value: Object.create(superClass && superClass.prototype, {
+      constructor: {
+        value: subClass,
+        writable: true,
+        configurable: true
+      }
+    }),
+    writable: false
   });
   if (superClass) _setPrototypeOf(subClass, superClass);
 }
@@ -248,7 +242,7 @@ function _superPropBase(object, property) {
   return object;
 }
 
-function _get(target, property, receiver) {
+function _get() {
   if (typeof Reflect !== "undefined" && Reflect.get) {
     _get = Reflect.get;
   } else {
@@ -259,14 +253,14 @@ function _get(target, property, receiver) {
       var desc = Object.getOwnPropertyDescriptor(base, property);
 
       if (desc.get) {
-        return desc.get.call(receiver);
+        return desc.get.call(arguments.length < 3 ? target : receiver);
       }
 
       return desc.value;
     };
   }
 
-  return _get(target, property, receiver || target);
+  return _get.apply(this, arguments);
 }
 
 function _slicedToArray(arr, i) {
@@ -1674,7 +1668,7 @@ function WiggleConfigFactory(pluginManager) {
 
 function toP() {
   var s = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : 0;
-  return parseFloat(s.toPrecision(6));
+  return +(+s).toPrecision(6);
 }
 
 function round(value) {
@@ -1700,8 +1694,7 @@ var useStyles = /*#__PURE__*/core.makeStyles(function (theme) {
       fontSize: theme.typography.pxToRem(10),
       lineHeight: "".concat(round(14 / 10), "em"),
       maxWidth: 300,
-      wordWrap: 'break-word',
-      fontWeight: theme.typography.fontWeightMedium
+      wordWrap: 'break-word'
     },
     hoverVertical: {
       background: '#333',
@@ -1737,7 +1730,6 @@ var Tooltip = /*#__PURE__*/mobxReact.observer(function (_ref2) {
       clientRect = _ref2.clientRect,
       TooltipContents = _ref2.TooltipContents;
   var featureUnderMouse = model.featureUnderMouse;
-  var classes = useStyles();
 
   var _useState = React.useState(0),
       _useState2 = _slicedToArray(_useState, 2),
@@ -1746,9 +1738,10 @@ var Tooltip = /*#__PURE__*/mobxReact.observer(function (_ref2) {
 
   var _useState3 = React.useState(null),
       _useState4 = _slicedToArray(_useState3, 2),
-      popperElement = _useState4[0],
-      setPopperElement = _useState4[1]; // must be memoized a la https://github.com/popperjs/react-popper/issues/391
+      anchorEl = _useState4[0],
+      setAnchorEl = _useState4[1];
 
+  var classes = useStyles(); // must be memoized a la https://github.com/popperjs/react-popper/issues/391
 
   var virtElement = React.useMemo(function () {
     return {
@@ -1770,12 +1763,12 @@ var Tooltip = /*#__PURE__*/mobxReact.observer(function (_ref2) {
     };
   }, [clientRect === null || clientRect === void 0 ? void 0 : clientRect.top, clientMouseCoord, width]);
 
-  var _usePopper = reactPopper.usePopper(virtElement, popperElement),
+  var _usePopper = reactPopper.usePopper(virtElement, anchorEl),
       styles = _usePopper.styles,
       attributes = _usePopper.attributes;
 
   return featureUnderMouse ? React__default.createElement(React__default.Fragment, null, React__default.createElement(core.Portal, null, React__default.createElement("div", Object.assign({
-    ref: setPopperElement,
+    ref: setAnchorEl,
     className: classes.tooltip,
     // zIndex needed to go over widget drawer
     style: _objectSpread2(_objectSpread2({}, styles.popper), {}, {
@@ -3074,6 +3067,31 @@ var WigglePlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.(bw|bigwig)$/i;
+          var adapterName = 'BigWigAdapter';
+          var fileName = tracks.getFileName(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bigWigLocation: file
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'BigWigAdapter') {
+            return 'QuantitativeTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
       pluginManager.addRendererType(function () {
         return new DensityRenderer({
           name: 'DensityRenderer',