@jbrowse/core 1.6.9 → 1.7.0

package/ui/App.js

@@ -238,23 +238,19 @@ var App = (0, _mobxReact.observer)(function (_ref2) {
     }
 
     var ReactComponent = viewType.ReactComponent;
-    return (
-      /*#__PURE__*/
-      // @ts-ignore
-      _react.default.createElement(_ViewContainer.default, {
-        key: "view-".concat(view.id),
-        view: view,
-        onClose: function onClose() {
-          return session.removeView(view);
-        }
-      }, /*#__PURE__*/_react.default.createElement(_react.Suspense, {
-        fallback: /*#__PURE__*/_react.default.createElement("div", null, "Loading...")
-      }, /*#__PURE__*/_react.default.createElement(ReactComponent, {
-        model: view,
-        session: session,
-        getTrackType: pluginManager.getTrackType
-      })))
-    );
+    return /*#__PURE__*/_react.default.createElement(_ViewContainer.default, {
+      key: "view-".concat(view.id),
+      view: view,
+      onClose: function onClose() {
+        return session.removeView(view);
+      }
+    }, /*#__PURE__*/_react.default.createElement(_react.Suspense, {
+      fallback: /*#__PURE__*/_react.default.createElement("div", null, "Loading...")
+    }, /*#__PURE__*/_react.default.createElement(ReactComponent, {
+      model: view,
+      session: session,
+      getTrackType: pluginManager.getTrackType
+    })));
   }) : /*#__PURE__*/_react.default.createElement(_core.Paper, {
     className: classes.selectPaper
   }, /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Select a view to launch"), /*#__PURE__*/_react.default.createElement(_core.Select, {

package/ui/AssemblySelector.d.ts

@@ -1,8 +1,11 @@
 /// <reference types="react" />
+import { InputProps as IIP } from '@material-ui/core';
 import { AbstractSessionModel } from '../util';
-declare const AssemblySelector: ({ session, onChange, selected, }: {
+declare const AssemblySelector: ({ session, onChange, selected, InputProps, extra, }: {
     session: AbstractSessionModel;
     onChange: (arg: string) => void;
     selected: string | undefined;
+    InputProps?: IIP | undefined;
+    extra?: unknown;
 }) => JSX.Element;
 export default AssemblySelector;

package/ui/AssemblySelector.js

@@ -2,12 +2,16 @@
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
+var _typeof = require("@babel/runtime/helpers/typeof");
+
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = void 0;
 
-var _react = _interopRequireDefault(require("react"));
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _react = _interopRequireWildcard(require("react"));
 
 var _mobxReact = require("mobx-react");
 
@@ -15,35 +19,92 @@ var _configuration = require("../configuration");
 
 var _core = require("@material-ui/core");
 
+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; }
+
 var useStyles = (0, _core.makeStyles)(function () {
   return {
     importFormEntry: {
       minWidth: 180
     }
   };
-});
+}); // Hook from https://usehooks.com/useLocalStorage/
+
+function useLocalStorage(key, initialValue) {
+  var _useState = (0, _react.useState)(function () {
+    if (typeof window === 'undefined') {
+      return initialValue;
+    }
+
+    try {
+      var item = window.localStorage.getItem(key);
+      return item ? JSON.parse(item) : initialValue;
+    } catch (error) {
+      console.error(error);
+      return initialValue;
+    }
+  }),
+      _useState2 = (0, _slicedToArray2.default)(_useState, 2),
+      storedValue = _useState2[0],
+      setStoredValue = _useState2[1];
+
+  var setValue = function setValue(value) {
+    try {
+      var valueToStore = value instanceof Function ? value(storedValue) : value;
+      setStoredValue(valueToStore);
+
+      if (typeof window !== 'undefined') {
+        window.localStorage.setItem(key, JSON.stringify(valueToStore));
+      }
+    } catch (error) {
+      console.error(error);
+    }
+  };
+
+  return [storedValue, setValue];
+}
+
 var AssemblySelector = (0, _mobxReact.observer)(function (_ref) {
   var session = _ref.session,
-      _onChange = _ref.onChange,
-      selected = _ref.selected;
+      onChange = _ref.onChange,
+      selected = _ref.selected,
+      InputProps = _ref.InputProps,
+      _ref$extra = _ref.extra,
+      extra = _ref$extra === void 0 ? 0 : _ref$extra;
   var classes = useStyles();
   var assemblyNames = session.assemblyNames,
-      assemblyManager = session.assemblyManager;
+      assemblyManager = session.assemblyManager; // constructs a localstorage key based on host/path/config to help
+  // remember. non-config assists usage with e.g. embedded apps
+
+  var config = new URLSearchParams(window.location.search).get('config');
+
+  var _useLocalStorage = useLocalStorage("lastAssembly-".concat([window.location.host + window.location.pathname, config, extra].join('-')), selected),
+      _useLocalStorage2 = (0, _slicedToArray2.default)(_useLocalStorage, 2),
+      lastSelected = _useLocalStorage2[0],
+      setLastSelected = _useLocalStorage2[1];
+
+  var selection = assemblyNames.includes(lastSelected || '') ? lastSelected : selected;
+  (0, _react.useEffect)(function () {
+    if (selection && selection !== selected) {
+      onChange(selection);
+    }
+  }, [selection, onChange, selected]);
   var error = assemblyNames.length ? '' : 'No configured assemblies';
   return /*#__PURE__*/_react.default.createElement(_core.TextField, {
     select: true,
     label: "Assembly",
     variant: "outlined",
-    margin: "normal",
     helperText: error || 'Select assembly to view',
-    value: error ? '' : selected,
+    value: error ? '' : selection,
     inputProps: {
       'data-testid': 'assembly-selector'
     },
     onChange: function onChange(event) {
-      return _onChange(event.target.value);
+      return setLastSelected(event.target.value);
     },
     error: !!error,
+    InputProps: InputProps,
     disabled: !!error,
     className: classes.importFormEntry
   }, assemblyNames.map(function (name) {

package/ui/PrerenderedCanvas.js

@@ -11,8 +11,6 @@ exports.default = void 0;
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
 var _propTypes = _interopRequireDefault(require("prop-types"));
 
 var _react = _interopRequireWildcard(require("react"));
@@ -53,30 +51,7 @@ function PrerenderedCanvas(props) {
       return;
     }
 
-    if (imageData.commands) {
-      imageData.commands.forEach(function (command) {
-        if (command.type === 'strokeStyle') {
-          context.strokeStyle = command.style;
-        } else if (command.type === 'fillStyle') {
-          context.fillStyle = command.style;
-        } else if (command.type === 'font') {
-          context.font = command.style;
-        } else {
-          // @ts-ignore
-          context[command.type].apply(context, (0, _toConsumableArray2.default)(command.args));
-        }
-      });
-    } else if (imageData instanceof _offscreenCanvasPonyfill.ImageBitmapType) {
-      context.drawImage(imageData, 0, 0);
-    } else if (imageData.dataURL) {
-      var img = new Image();
-
-      img.onload = function () {
-        return context.drawImage(img, 0, 0);
-      };
-
-      img.src = imageData.dataURL;
-    }
+    (0, _offscreenCanvasPonyfill.drawImageOntoCanvasContext)(imageData, context);
   }, [imageData]);
   var softClipString = showSoftClip ? '_softclipped' : '';
   var blockKeyStr = blockKey ? '_' + blockKey : '';

package/ui/ViewContainer.d.ts

@@ -1,9 +1,9 @@
 import React from 'react';
 import { IBaseViewModel } from '../pluggableElementTypes/models';
-declare const _default: React.ComponentType<{
+declare const ViewContainer: ({ view, onClose, style, children, }: {
     view: IBaseViewModel;
-    style: React.CSSProperties;
-    children: React.ReactNode;
     onClose: () => void;
-} & import("react-sizeme").WithSizeProps>;
-export default _default;
+    style?: React.CSSProperties | undefined;
+    children: React.ReactNode;
+}) => JSX.Element;
+export default ViewContainer;

package/ui/ViewContainer.js

@@ -23,7 +23,7 @@ var _mobxReact = require("mobx-react");
 
 var _mobxStateTree = require("mobx-state-tree");
 
-var _reactSizeme = require("react-sizeme");
+var _reactUseMeasure = _interopRequireDefault(require("react-use-measure"));
 
 var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
 
@@ -114,16 +114,20 @@ var ViewMenu = (0, _mobxReact.observer)(function (_ref) {
     menuItems: model.menuItems()
   })) : null;
 });
-
-var _default = (0, _reactSizeme.withSize)()((0, _mobxReact.observer)(function (_ref2) {
+var ViewContainer = (0, _mobxReact.observer)(function (_ref2) {
   var view = _ref2.view,
       onClose = _ref2.onClose,
       style = _ref2.style,
-      children = _ref2.children,
-      width = _ref2.size.width;
+      children = _ref2.children;
   var classes = useStyles();
   var theme = (0, _core.useTheme)();
   var padWidth = theme.spacing(1);
+
+  var _useMeasure = (0, _reactUseMeasure.default)(),
+      _useMeasure2 = (0, _slicedToArray2.default)(_useMeasure, 2),
+      ref = _useMeasure2[0],
+      width = _useMeasure2[1].width;
+
   (0, _react.useEffect)(function () {
     if (width && (0, _mobxStateTree.isAlive)(view)) {
       view.setWidth(width - padWidth * 2);
@@ -141,6 +145,7 @@ var _default = (0, _reactSizeme.withSize)()((0, _mobxReact.observer)(function (_
     });
   }, []);
   return /*#__PURE__*/_react.default.createElement(_core.Paper, {
+    ref: ref,
     elevation: 12,
     className: classes.viewContainer,
     style: _objectSpread(_objectSpread({}, style), {}, {
@@ -193,6 +198,6 @@ var _default = (0, _reactSizeme.withSize)()((0, _mobxReact.observer)(function (_
   }, /*#__PURE__*/_react.default.createElement(_Close.default, {
     className: classes.icon
   }))), /*#__PURE__*/_react.default.createElement(_core.Paper, null, children));
-}));
-
+});
+var _default = ViewContainer;
 exports.default = _default;

package/util/index.d.ts

@@ -228,7 +228,7 @@ export declare function stringify({ refName, coord, oob, }: {
 export declare const isElectron: boolean;
 export declare function revcom(seqString: string): string;
 export declare const complement: (seqString: string) => string;
-export declare function blobToDataURL(blob: Blob): Promise<unknown>;
+export declare function blobToDataURL(blob: Blob): Promise<string>;
 export declare const rIC: (((callback: IdleRequestCallback, options?: IdleRequestOptions | undefined) => number) & typeof requestIdleCallback) | ((cb: Function) => any);
 export declare function measureText(str: unknown, fontSize?: number): number;
 export declare const defaultStarts: string[];
@@ -341,3 +341,9 @@ export declare function viewBpToPx({ refName, coord, regionNumber, self, }: {
     offsetPx: number;
 } | undefined;
 export declare function getBpDisplayStr(totalBp: number): string;
+export declare function getViewParams(model: IAnyStateTreeNode, exportSVG?: boolean): {
+    offsetPx: number;
+    offsetPx1: number;
+    start: any;
+    end: any;
+};

package/util/index.js

@@ -57,6 +57,7 @@ var _exportNames = {
   bytesForRegions: true,
   viewBpToPx: true,
   getBpDisplayStr: true,
+  getViewParams: true,
   SimpleFeature: true,
   isFeature: true
 };
@@ -87,6 +88,7 @@ exports.getContainingDisplay = getContainingDisplay;
 exports.getContainingTrack = getContainingTrack;
 exports.getContainingView = getContainingView;
 exports.getSession = getSession;
+exports.getViewParams = getViewParams;
 exports.hashCode = hashCode;
 exports.isElectron = exports.inProduction = exports.inDevelopment = void 0;
 Object.defineProperty(exports, "isFeature", {
@@ -1409,4 +1411,22 @@ function getBpDisplayStr(totalBp) {
   }
 
   return str;
+}
+
+function getViewParams(model, exportSVG) {
+  // @ts-ignore
+  var _getContainingView = getContainingView(model),
+      dynamicBlocks = _getContainingView.dynamicBlocks,
+      staticBlocks = _getContainingView.staticBlocks,
+      offsetPx = _getContainingView.offsetPx;
+
+  var block = (dynamicBlocks === null || dynamicBlocks === void 0 ? void 0 : dynamicBlocks.contentBlocks[0]) || {};
+  var staticblock = (staticBlocks === null || staticBlocks === void 0 ? void 0 : staticBlocks.contentBlocks[0]) || {};
+  var staticblock1 = (staticBlocks === null || staticBlocks === void 0 ? void 0 : staticBlocks.contentBlocks[1]) || {};
+  return {
+    offsetPx: exportSVG ? 0 : offsetPx - staticblock.offsetPx,
+    offsetPx1: exportSVG ? 0 : offsetPx - staticblock1.offsetPx,
+    start: block.start,
+    end: block.end
+  };
 }

package/util/io/index.js

@@ -30,6 +30,8 @@ var _tracks = require("../tracks");
 
 var _detectNode = _interopRequireDefault(require("detect-node"));
 
+var _util = require("@jbrowse/core/util");
+
 function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
 
 function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
@@ -52,7 +54,7 @@ function openLocation(location, pluginManager) {
       throw new Error('No local path provided');
     }
 
-    if (_detectNode.default) {
+    if (_detectNode.default || _util.isElectron) {
       return new _genericFilehandle.LocalFile(location.localPath);
     } else {
       throw new Error("can't use local files in the browser");

package/util/layouts/BaseLayout.d.ts

@@ -2,6 +2,7 @@ export declare type RectTuple = [number, number, number, number];
 export interface SerializedLayout {
     rectangles: Record<string, RectTuple>;
     totalHeight: number;
+    containsNoTransferables: true;
     maxHeightReached: boolean;
 }
 export interface Rectangle<T> {

package/util/layouts/GranularRectLayout.js

@@ -580,6 +580,7 @@ var GranularRectLayout = /*#__PURE__*/function () {
 
       return {
         rectangles: regionRectangles,
+        containsNoTransferables: true,
         totalHeight: this.getTotalHeight(),
         maxHeightReached: maxHeightReached
       };
@@ -590,6 +591,7 @@ var GranularRectLayout = /*#__PURE__*/function () {
       var rectangles = (0, _index.objectFromEntries)(this.getRectangles());
       return {
         rectangles: rectangles,
+        containsNoTransferables: true,
         totalHeight: this.getTotalHeight(),
         maxHeightReached: this.maxHeightReached
       };

package/util/layouts/PrecomputedLayout.js

@@ -118,7 +118,8 @@ var PrecomputedLayout = /*#__PURE__*/function () {
       return {
         rectangles: (0, _.objectFromEntries)(this.rectangles),
         totalHeight: this.totalHeight,
-        maxHeightReached: false
+        maxHeightReached: false,
+        containsNoTransferables: true
       };
     }
   }]);

package/util/offscreenCanvas/Canvas2DContextShim/Canvas2DContextShim.test.d.ts

@@ -0,0 +1 @@
+export {};

package/util/offscreenCanvas/Canvas2DContextShim/Canvas2DContextShim.test.js

@@ -0,0 +1,15 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _ = _interopRequireDefault(require("."));
+
+test('serialize a single command and read back out', function () {
+  var ctx = new _.default(100, 100);
+  ctx.arc(20, 21, 22, 23, 24);
+  var cmds = Array.from(ctx.getCommands());
+  expect(cmds).toEqual([{
+    name: 'arc',
+    args: [20, 21, 22, 23, 24]
+  }]);
+});

package/util/offscreenCanvas/Canvas2DContextShim/context.d.ts

@@ -0,0 +1,56 @@
+/// <reference types="react" />
+/// <reference types="offscreencanvas" />
+import { Command } from './types';
+/** get the params type of real method in OffscreenCanvasRenderingContext2D */
+declare type RealP<METHODNAME extends keyof OffscreenCanvasRenderingContext2D> = OffscreenCanvasRenderingContext2D[METHODNAME] extends (...arg0: any[]) => any ? Parameters<OffscreenCanvasRenderingContext2D[METHODNAME]> : never;
+/** get the return type of real method in OffscreenCanvasRenderingContext2D */
+declare type RealRet<METHODNAME extends keyof OffscreenCanvasRenderingContext2D> = OffscreenCanvasRenderingContext2D[METHODNAME] extends (...arg0: any[]) => any ? ReturnType<OffscreenCanvasRenderingContext2D[METHODNAME]> : never;
+/** get the type of the params of a method of the canvas shim */
+export declare type ShimP<METHODNAME extends keyof OffscreenCanvasRenderingContext2DShim> = OffscreenCanvasRenderingContext2DShim[METHODNAME] extends (...arg0: any[]) => any ? Parameters<OffscreenCanvasRenderingContext2DShim[METHODNAME]> : never;
+/** decode all the commands in the given buffer and replay them onto the given context */
+export declare function replayCommandsOntoContext(targetContext: CanvasRenderingContext2D, encodedCommands: Iterable<Command>): void;
+export default class OffscreenCanvasRenderingContext2DShim {
+    width: number;
+    height: number;
+    currentFont: string;
+    currentStrokeStyle: string;
+    currentFillStyle: string;
+    recordedCommands: Command[];
+    constructor(width: number, height: number);
+    private pushMethodCall;
+    private pushSetterCall;
+    getSerializedCommands(): Command[];
+    getSerializedSvg(): JSX.Element;
+    getCommands(): Command[];
+    set strokeStyle(style: string);
+    set fillStyle(style: string);
+    set font(style: string);
+    arc(...args: RealP<'arc'>): RealRet<'arc'>;
+    arcTo(...args: RealP<'arcTo'>): RealRet<'arcTo'>;
+    beginPath(...args: RealP<'beginPath'>): RealRet<'beginPath'>;
+    clearRect(...args: RealP<'clearRect'>): RealRet<'clearRect'>;
+    closePath(...args: RealP<'closePath'>): RealRet<'closePath'>;
+    ellipse(...args: RealP<'ellipse'>): RealRet<'ellipse'>;
+    fill(...args: RealP<'fill'>): RealRet<'fill'>;
+    fillRect(...args: RealP<'fillRect'>): RealRet<'fillRect'>;
+    fillText(...args: RealP<'fillText'>): RealRet<'fillText'>;
+    lineTo(...args: RealP<'lineTo'>): RealRet<'lineTo'>;
+    measureText(...args: RealP<'measureText'>): {
+        width: number;
+        height: number;
+    };
+    moveTo(...args: RealP<'moveTo'>): RealRet<'moveTo'>;
+    quadraticCurveTo(...args: RealP<'quadraticCurveTo'>): RealRet<'quadraticCurveTo'>;
+    rect(...args: RealP<'rect'>): RealRet<'rect'>;
+    restore(...args: RealP<'restore'>): RealRet<'restore'>;
+    rotate(...args: RealP<'rotate'>): RealRet<'rotate'>;
+    save(...args: RealP<'save'>): RealRet<'save'>;
+    setTransform(...args: RealP<'setTransform'>): RealRet<'setTransform'>;
+    scale(...args: RealP<'scale'>): RealRet<'scale'>;
+    stroke(): RealRet<'stroke'>;
+    strokeRect(...args: RealP<'strokeRect'>): RealRet<'strokeRect'>;
+    strokeText(...args: RealP<'strokeText'>): RealRet<'strokeText'>;
+    transform(...args: RealP<'transform'>): RealRet<'transform'>;
+    translate(...args: RealP<'translate'>): RealRet<'translate'>;
+}
+export {};