@jbrowse/core 1.7.4 → 1.7.7

package/ui/App.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
-import { NotificationLevel, SessionWithDrawerWidgets } from '../util';
+import { NotificationLevel, SessionWithDrawerWidgets, SnackAction } from '../util';
 import { MenuItem as JBMenuItem } from './index';
-declare type SnackbarMessage = [string, NotificationLevel];
+declare type SnackbarMessage = [string, NotificationLevel, SnackAction];
 declare const App: ({ session, HeaderButtons, }: {
     HeaderButtons?: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
     session: SessionWithDrawerWidgets & {

package/ui/Icons.d.ts

@@ -1,6 +1,7 @@
 /// <reference types="react" />
 import { SvgIconProps } from '@material-ui/core/SvgIcon';
 export declare function ContentCopy(props: SvgIconProps): JSX.Element;
+export declare function Indexing(props: SvgIconProps): JSX.Element;
 export declare function ContentCut(props: SvgIconProps): JSX.Element;
 export declare function ContentPaste(props: SvgIconProps): JSX.Element;
 export declare function TrackSelector(props: SvgIconProps): JSX.Element;

package/ui/Icons.js

@@ -10,6 +10,7 @@ exports.ContentCopy = ContentCopy;
 exports.ContentCut = ContentCut;
 exports.ContentPaste = ContentPaste;
 exports.DNA = DNA;
+exports.Indexing = Indexing;
 exports.Save = Save;
 exports.SaveAs = SaveAs;
 exports.TrackSelector = TrackSelector;
@@ -23,6 +24,13 @@ function ContentCopy(props) {
   return /*#__PURE__*/_react.default.createElement(_SvgIcon.default, props, /*#__PURE__*/_react.default.createElement("path", {
     d: "M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"
   }));
+} // https://materialdesignicons.com/ text-search icon
+
+
+function Indexing(props) {
+  return /*#__PURE__*/_react.default.createElement(_SvgIcon.default, props, /*#__PURE__*/_react.default.createElement("path", {
+    d: "M19.31 18.9L22.39 22L21 23.39L17.88 20.32C17.19 20.75 16.37 21 15.5 21C13 21 11 19 11 16.5C11 14 13 12 15.5 12C18 12 20 14 20 16.5C20 17.38 19.75 18.21 19.31 18.9M15.5 19C16.88 19 18 17.88 18 16.5C18 15.12 16.88 14 15.5 14C14.12 14 13 15.12 13 16.5C13 17.88 14.12 19 15.5 19M21 4V6H3V4H21M3 16V14H9V16H3M3 11V9H21V11H18.97C17.96 10.37 16.77 10 15.5 10C14.23 10 13.04 10.37 12.03 11H3Z"
+  }));
 }
 
 function ContentCut(props) {

package/ui/Snackbar.d.ts

@@ -1,7 +1,7 @@
 /// <reference types="react" />
 import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { AbstractSessionModel, NotificationLevel } from '../util';
-declare type SnackbarMessage = [string, NotificationLevel];
+import { AbstractSessionModel, NotificationLevel, SnackAction } from '../util';
+declare type SnackbarMessage = [string, NotificationLevel, SnackAction];
 interface SnackbarSession extends AbstractSessionModel {
     snackbarMessages: SnackbarMessage[];
     popSnackbarMessage: () => unknown;

package/ui/Snackbar.js

@@ -74,20 +74,27 @@ function MessageSnackbar(_ref) {
   };
 
   var _ref2 = snackbarMessage || [],
-      _ref3 = (0, _slicedToArray2.default)(_ref2, 2),
+      _ref3 = (0, _slicedToArray2.default)(_ref2, 3),
       message = _ref3[0],
-      level = _ref3[1];
+      level = _ref3[1],
+      action = _ref3[2];
 
   return /*#__PURE__*/_react.default.createElement(_core.Snackbar, {
     open: open && !!message,
+    onClose: handleClose
+  }, /*#__PURE__*/_react.default.createElement(_Alert.default, {
     onClose: handleClose,
-    action: /*#__PURE__*/_react.default.createElement(_core.IconButton, {
+    action: action ? /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement(_core.Button, {
+      color: "inherit",
+      onClick: function onClick(e) {
+        action.onClick();
+        handleClose(e);
+      }
+    }, action.name), /*#__PURE__*/_react.default.createElement(_core.IconButton, {
       "aria-label": "close",
       color: "inherit",
       onClick: handleClose
-    }, /*#__PURE__*/_react.default.createElement(_Close.default, null))
-  }, /*#__PURE__*/_react.default.createElement(_Alert.default, {
-    onClose: handleClose,
+    }, /*#__PURE__*/_react.default.createElement(_Close.default, null))) : null,
     severity: level || 'warning'
   }, message));
 }

package/ui/SnackbarModel.d.ts

@@ -1,13 +1,13 @@
 import { IModelType, ModelProperties } from 'mobx-state-tree';
 import { IObservableArray } from 'mobx';
-import { NotificationLevel } from '../util/types';
+import { NotificationLevel, SnackAction } from '../util/types';
 declare function makeExtension(snackbarMessages: IObservableArray<any>): {
     views: {
         readonly snackbarMessages: IObservableArray<any>;
     };
     actions: {
-        notify(message: string, level?: NotificationLevel | undefined): void;
-        pushSnackbarMessage(message: string, level?: NotificationLevel | undefined): number;
+        notify(message: string, level?: NotificationLevel | undefined, action?: SnackAction | undefined): void;
+        pushSnackbarMessage(message: string, level?: NotificationLevel | undefined, action?: SnackAction | undefined): number;
         popSnackbarMessage(): any;
         removeSnackbarMessage(message: string): void;
     };

package/ui/SnackbarModel.js

@@ -17,10 +17,10 @@ function makeExtension(snackbarMessages) {
 
     },
     actions: {
-      notify: function notify(message, level) {
+      notify: function notify(message, level, action) {
         var _this = this;
 
-        this.pushSnackbarMessage(message, level);
+        this.pushSnackbarMessage(message, level, action);
 
         if (level === 'info' || level === 'success') {
           setTimeout(function () {
@@ -28,8 +28,8 @@ function makeExtension(snackbarMessages) {
           }, 5000);
         }
       },
-      pushSnackbarMessage: function pushSnackbarMessage(message, level) {
-        return snackbarMessages.push([message, level]);
+      pushSnackbarMessage: function pushSnackbarMessage(message, level, action) {
+        return snackbarMessages.push([message, level, action]);
       },
       popSnackbarMessage: function popSnackbarMessage() {
         return snackbarMessages.pop();

package/util/index.d.ts

@@ -340,6 +340,7 @@ export declare function viewBpToPx({ refName, coord, regionNumber, self, }: {
     index: number;
     offsetPx: number;
 } | undefined;
+export declare function supportedIndexingAdapters(type: string): boolean;
 export declare function getBpDisplayStr(totalBp: number): string;
 export declare function getViewParams(model: IAnyStateTreeNode, exportSVG?: boolean): {
     offsetPx: number;
@@ -347,3 +348,7 @@ export declare function getViewParams(model: IAnyStateTreeNode, exportSVG?: bool
     start: any;
     end: any;
 };
+export declare function getLayoutId({ sessionId, layoutId, }: {
+    sessionId: string;
+    layoutId: string;
+}): string;

package/util/index.js

@@ -56,8 +56,10 @@ var _exportNames = {
   objectHash: true,
   bytesForRegions: true,
   viewBpToPx: true,
+  supportedIndexingAdapters: true,
   getBpDisplayStr: true,
   getViewParams: true,
+  getLayoutId: true,
   SimpleFeature: true,
   isFeature: true
 };
@@ -87,6 +89,7 @@ exports.getBpDisplayStr = getBpDisplayStr;
 exports.getContainingDisplay = getContainingDisplay;
 exports.getContainingTrack = getContainingTrack;
 exports.getContainingView = getContainingView;
+exports.getLayoutId = getLayoutId;
 exports.getSession = getSession;
 exports.getViewParams = getViewParams;
 exports.hashCode = hashCode;
@@ -114,6 +117,7 @@ exports.renameRegionsIfNeeded = renameRegionsIfNeeded;
 exports.revcom = revcom;
 exports.springAnimate = springAnimate;
 exports.stringify = stringify;
+exports.supportedIndexingAdapters = supportedIndexingAdapters;
 exports.updateStatus = updateStatus;
 exports.useDebounce = useDebounce;
 exports.useDebouncedCallback = useDebouncedCallback;
@@ -1005,7 +1009,7 @@ function _renameRegionsIfNeeded() {
             _context3.t0 = Object;
             _context3.next = 7;
             return Promise.all(assemblyNames.map( /*#__PURE__*/function () {
-              var _ref5 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(assemblyName) {
+              var _ref6 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(assemblyName) {
                 return _regenerator.default.wrap(function _callee2$(_context2) {
                   while (1) {
                     switch (_context2.prev = _context2.next) {
@@ -1027,7 +1031,7 @@ function _renameRegionsIfNeeded() {
               }));
 
               return function (_x10) {
-                return _ref5.apply(this, arguments);
+                return _ref6.apply(this, arguments);
               };
             }()));
 
@@ -1397,6 +1401,12 @@ function viewBpToPx(_ref4) {
   }
 
   return undefined;
+} // supported adapter types by text indexer
+//  ensure that this matches the method found in @jbrowse/text-indexing/util
+
+
+function supportedIndexingAdapters(type) {
+  return ['Gff3TabixAdapter', 'VcfTabixAdapter', 'Gff3Adapter', 'VcfAdapter'].includes(type);
 }
 
 function getBpDisplayStr(totalBp) {
@@ -1429,4 +1439,10 @@ function getViewParams(model, exportSVG) {
     start: b.start,
     end: b.end
   };
+}
+
+function getLayoutId(_ref5) {
+  var sessionId = _ref5.sessionId,
+      layoutId = _ref5.layoutId;
+  return sessionId + '-' + layoutId;
 }

package/util/layouts/BaseLayout.d.ts

@@ -12,12 +12,12 @@ export interface Rectangle<T> {
     top: number | null;
     h: number;
     originalHeight: number;
-    data?: Record<string, T>;
+    data?: T;
 }
 export interface BaseLayout<T> {
-    addRect(id: string, left: number, right: number, height: number, data?: Record<string, T>): number | null;
+    addRect(id: string, left: number, right: number, height: number, data?: unknown): number | null;
     collides(rect: Rectangle<T>, top: number): boolean;
-    addRectToBitmap(rect: Rectangle<T>, data: Record<string, T>): void;
+    addRectToBitmap(rect: Rectangle<T>, data: unknown): void;
     getRectangles(): Map<string, RectTuple>;
     discardRange(left: number, right: number): void;
     serializeRegion(region: {

package/util/layouts/GranularRectLayout.d.ts

@@ -20,7 +20,7 @@ export default class GranularRectLayout<T> implements BaseLayout<T> {
      * @returns top position for the rect, or Null if laying
      *  out the rect would exceed maxHeight
      */
-    addRect(id: string, left: number, right: number, height: number, data?: Record<string, T>): number | null;
+    addRect(id: string, left: number, right: number, height: number, data?: T): number | null;
     collides(rect: Rectangle<T>, top: number): boolean;
     /**
      * make a subarray if it does not exist
@@ -35,6 +35,7 @@ export default class GranularRectLayout<T> implements BaseLayout<T> {
     hasSeen(id: string): boolean;
     getByCoord(x: number, y: number): Record<string, T> | string | undefined;
     getByID(id: string): RectTuple | undefined;
+    getDataByID(id: string): unknown;
     cleanup(): void;
     getTotalHeight(): number;
     get totalHeight(): number;

package/util/layouts/GranularRectLayout.js

@@ -150,8 +150,7 @@ var LayoutRow = /*#__PURE__*/function () {
 
       var oLeft = left - this.rowState.offset;
       var oRight = right - this.rowState.offset;
-      var currLength = this.rowState.bits.length; // console.log(oRight, this.rowState.bits.length)
-      // expand rightward if necessary
+      var currLength = this.rowState.bits.length; // expand rightward if necessary
 
       if (oRight >= this.rowState.bits.length) {
         var additionalLength = oRight + 1;
@@ -179,18 +178,14 @@ var LayoutRow = /*#__PURE__*/function () {
       }
 
       oRight = right - this.rowState.offset;
-      oLeft = left - this.rowState.offset; // set the bits in the bitmask
-      // if (oLeft < 0) debugger
-      // if (oRight < 0) debugger
-      // if (oRight <= oLeft) debugger
-      // if (oRight > this.rowState.bits.length) debugger
+      oLeft = left - this.rowState.offset;
+      var w = oRight - oLeft;
 
-      if (oRight - oLeft > maxFeaturePitchWidth) {
-        console.warn("Layout X pitch set too low, feature spans ".concat(oRight - oLeft, " bits in a single row."), rect, data);
+      if (w > maxFeaturePitchWidth) {
+        console.warn("Layout X pitch set too low, feature spans ".concat(w, " bits in a single row."), rect, data);
       }
 
       for (var x = oLeft; x < oRight; x += 1) {
-        // if (this.rowState.bits[x] && this.rowState.bits[x].get('name') !== data.get('name')) debugger
         this.rowState.bits[x] = data;
       }
 
@@ -200,8 +195,7 @@ var LayoutRow = /*#__PURE__*/function () {
 
       if (right > this.rowState.max) {
         this.rowState.max = right;
-      } // // this.log(`added ${leftX} - ${rightX}`)
-
+      }
     }
     /**
      *  Given a range of interbase coordinates, deletes all data dealing with that range
@@ -435,8 +429,7 @@ var GranularRectLayout = /*#__PURE__*/function () {
         return;
       }
 
-      var data = rect.data || rect.id;
-      var bitmap = this.bitmap;
+      var data = rect.id;
       var yEnd = rect.top + rect.h;
 
       if (rect.r - rect.l > maxFeaturePitchWidth) {
@@ -446,11 +439,11 @@ var GranularRectLayout = /*#__PURE__*/function () {
         // along the genome at the same zoom level.  but most users will not do
         // that.  hopefully.
         for (var y = rect.top; y < yEnd; y += 1) {
-          this.autovivifyRow(bitmap, y).setAllFilled(data);
+          this.autovivifyRow(this.bitmap, y).setAllFilled(data);
         }
       } else {
         for (var _y = rect.top; _y < yEnd; _y += 1) {
-          this.autovivifyRow(bitmap, _y).addRect(rect, data);
+          this.autovivifyRow(this.bitmap, _y).addRect(rect, data);
         }
       }
     }
@@ -505,6 +498,13 @@ var GranularRectLayout = /*#__PURE__*/function () {
 
       return undefined;
     }
+  }, {
+    key: "getDataByID",
+    value: function getDataByID(id) {
+      var _this$rectangles$get;
+
+      return (_this$rectangles$get = this.rectangles.get(id)) === null || _this$rectangles$get === void 0 ? void 0 : _this$rectangles$get.data;
+    }
   }, {
     key: "cleanup",
     value: function cleanup() {}

package/util/layouts/GranularRectLayout.test.js

@@ -90,18 +90,10 @@ describe('GranularRectLayout', function () {
       maxHeight: 600
     });
     expect(l.getByCoord(50000, 0)).toEqual(undefined);
-    l.addRect('test1', 0, 100000000, 1, {
-      id: 'feat1'
-    });
-    expect(l.getByCoord(50000, 0)).toEqual({
-      id: 'feat1'
-    });
-    l.addRect('test2', 0, 1000, 1, {
-      id: 'feat2'
-    });
-    expect(l.getByCoord(500, 1)).toEqual({
-      id: 'feat2'
-    });
+    l.addRect('test1', 0, 100000000, 1, 'feat1');
+    expect(l.getByCoord(50000, 0)).toEqual('test1');
+    l.addRect('test2', 0, 1000, 1, 'feat2');
+    expect(l.getByCoord(500, 1)).toEqual('test2');
     expect(l.rectangles.size).toBe(2);
   });
 });

package/util/layouts/MultiLayout.d.ts

@@ -9,6 +9,7 @@ export default class MultiLayout<SUB_LAYOUT_CLASS extends BaseLayout<T>, T> {
      * `{ layout1: new GranularRectLayout(), layout2: new GranularRectLayout() ...}`
      */
     constructor(SubLayoutClass: new (...args: any[]) => SUB_LAYOUT_CLASS, layoutArgs?: Record<string, any>);
+    getDataByID(id: string): unknown;
     getSublayout(layoutName: string): SUB_LAYOUT_CLASS;
     addRect(layoutName: string, id: string, left: number, right: number, height: number, data?: Record<string, T>): number | null;
     discardRange(layoutName: string, left: number, right: number): void | undefined;

package/util/layouts/MultiLayout.js

@@ -39,6 +39,30 @@ var MultiLayout = /*#__PURE__*/function () {
   }
 
   (0, _createClass2.default)(MultiLayout, [{
+    key: "getDataByID",
+    value: function getDataByID(id) {
+      var _iterator = _createForOfIteratorHelper(this.subLayouts.values()),
+          _step;
+
+      try {
+        for (_iterator.s(); !(_step = _iterator.n()).done;) {
+          var layout = _step.value;
+          // @ts-ignore
+          var r = layout.getDataByID(id);
+
+          if (r) {
+            return r;
+          }
+        }
+      } catch (err) {
+        _iterator.e(err);
+      } finally {
+        _iterator.f();
+      }
+
+      return undefined;
+    }
+  }, {
     key: "getSublayout",
     value: function getSublayout(layoutName) {
       var subLayout = this.subLayouts.get(layoutName);
@@ -68,21 +92,21 @@ var MultiLayout = /*#__PURE__*/function () {
     value: function toJSON() {
       var data = {};
 
-      var _iterator = _createForOfIteratorHelper(this.subLayouts.entries()),
-          _step;
+      var _iterator2 = _createForOfIteratorHelper(this.subLayouts.entries()),
+          _step2;
 
       try {
-        for (_iterator.s(); !(_step = _iterator.n()).done;) {
-          var _step$value = (0, _slicedToArray2.default)(_step.value, 2),
-              layoutName = _step$value[0],
-              sublayout = _step$value[1];
+        for (_iterator2.s(); !(_step2 = _iterator2.n()).done;) {
+          var _step2$value = (0, _slicedToArray2.default)(_step2.value, 2),
+              layoutName = _step2$value[0],
+              sublayout = _step2$value[1];
 
           data[layoutName] = sublayout.toJSON();
         }
       } catch (err) {
-        _iterator.e(err);
+        _iterator2.e(err);
       } finally {
-        _iterator.f();
+        _iterator2.f();
       }
 
       return data;

package/util/types/index.d.ts

@@ -17,6 +17,10 @@ export interface AbstractViewContainer extends IAnyStateTreeNode {
 }
 export declare function isViewContainer(thing: unknown): thing is AbstractViewContainer;
 export declare type NotificationLevel = 'error' | 'info' | 'warning' | 'success';
+export interface SnackAction {
+    name: string;
+    onClick: () => void;
+}
 export declare type AssemblyManager = Instance<ReturnType<typeof assemblyManager>>;
 export type { TextSearchManager };
 export interface BasePlugin {
@@ -47,7 +51,7 @@ export interface AbstractSessionModel extends AbstractViewContainer {
     assemblies: AnyConfigurationModel[];
     selection?: unknown;
     duplicateCurrentSession?(): void;
-    notify(message: string, level?: NotificationLevel): void;
+    notify(message: string, level?: NotificationLevel, action?: SnackAction): void;
     assemblyManager: AssemblyManager;
     version: string;
     getTrackActionMenuItems?: Function;