@jbrowse/plugin-linear-genome-view 1.7.8 → 1.7.11

package/dist/LinearGenomeView/components/SearchBox.js

@@ -11,8 +11,6 @@ var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"))
 
 var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
 
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
 var _react = _interopRequireDefault(require("react"));
@@ -21,8 +19,6 @@ var _mobxReact = require("mobx-react");
 
 var _core = require("@material-ui/core");
 
-var _BaseResults = _interopRequireDefault(require("@jbrowse/core/TextSearch/BaseResults"));
-
 var _util = require("@jbrowse/core/util");
 
 var _RefNameAutocomplete = _interopRequireDefault(require("./RefNameAutocomplete"));
@@ -52,101 +48,61 @@ function SearchBox(_ref) {
       rankSearchResults = model.rankSearchResults;
   var assemblyName = assemblyNames[0];
   var assembly = assemblyManager.get(assemblyName);
-  var searchScope = model.searchScope(assemblyName);
-
-  function fetchResults(_x, _x2) {
-    return _fetchResults.apply(this, arguments);
-  } // gets a string as input, or use stored option results from previous query,
+  var searchScope = model.searchScope(assemblyName); // gets a string as input, or use stored option results from previous query,
   // then re-query and
   // 1) if it has multiple results: pop a dialog
   // 2) if it's a single result navigate to it
   // 3) else assume it's a locstring and navigate to it
 
-
-  function _fetchResults() {
-    _fetchResults = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(query, searchType) {
-      var _assembly$allRefNames;
-
-      var textSearchResults, refNameResults;
-      return _regenerator.default.wrap(function _callee$(_context) {
-        while (1) {
-          switch (_context.prev = _context.next) {
-            case 0:
-              if (!textSearchManager) {
-                console.warn('No text search manager');
-              }
-
-              _context.next = 3;
-              return textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
-                queryString: query,
-                searchType: searchType
-              }, searchScope, rankSearchResults);
-
-            case 3:
-              textSearchResults = _context.sent;
-              refNameResults = assembly === null || assembly === void 0 ? void 0 : (_assembly$allRefNames = assembly.allRefNames) === null || _assembly$allRefNames === void 0 ? void 0 : _assembly$allRefNames.filter(function (refName) {
-                return refName.startsWith(query);
-              }).map(function (r) {
-                return new _BaseResults.default({
-                  label: r
-                });
-              }).slice(0, 10);
-              return _context.abrupt("return", (0, _util2.dedupe)([].concat((0, _toConsumableArray2.default)(refNameResults || []), (0, _toConsumableArray2.default)(textSearchResults || [])), function (elt) {
-                return elt.getId();
-              }));
-
-            case 6:
-            case "end":
-              return _context.stop();
-          }
-        }
-      }, _callee);
-    }));
-    return _fetchResults.apply(this, arguments);
-  }
-
-  function handleSelectedRegion(_x3) {
+  function handleSelectedRegion(_x) {
     return _handleSelectedRegion.apply(this, arguments);
   }
 
   function _handleSelectedRegion() {
-    _handleSelectedRegion = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(option) {
+    _handleSelectedRegion = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(option) {
       var trackId, location, label, _location$split, _location$split2, ref, rest, allRefs, results;
 
-      return _regenerator.default.wrap(function _callee2$(_context2) {
+      return _regenerator.default.wrap(function _callee$(_context) {
         while (1) {
-          switch (_context2.prev = _context2.next) {
+          switch (_context.prev = _context.next) {
             case 0:
               trackId = option.getTrackId();
               location = option.getLocation();
               label = option.getLabel();
               _location$split = location.split(':'), _location$split2 = (0, _slicedToArray2.default)(_location$split, 2), ref = _location$split2[0], rest = _location$split2[1];
               allRefs = (assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) || [];
-              _context2.prev = 5;
+              _context.prev = 5;
 
               if (!(allRefs.includes(location) || allRefs.includes(ref) && rest !== undefined && !Number.isNaN(parseInt(rest, 10)))) {
-                _context2.next = 10;
+                _context.next = 10;
                 break;
               }
 
               model.navToLocString(location, assemblyName);
-              _context2.next = 21;
+              _context.next = 21;
               break;
 
             case 10:
-              _context2.next = 12;
-              return fetchResults(label, 'exact');
+              _context.next = 12;
+              return (0, _util2.fetchResults)({
+                queryString: label,
+                searchType: 'exact',
+                searchScope: searchScope,
+                rankSearchResults: rankSearchResults,
+                textSearchManager: textSearchManager,
+                assembly: assembly
+              });
 
             case 12:
-              results = _context2.sent;
+              results = _context.sent;
 
               if (!(results.length > 1)) {
-                _context2.next = 18;
+                _context.next = 18;
                 break;
               }
 
               model.setSearchResults(results, label.toLowerCase());
-              return _context2.abrupt("return");
+              return _context.abrupt("return");
 
             case 18:
               if (results.length === 1) {
@@ -162,21 +118,21 @@ function SearchBox(_ref) {
               }
 
             case 21:
-              _context2.next = 27;
+              _context.next = 27;
               break;
 
             case 23:
-              _context2.prev = 23;
-              _context2.t0 = _context2["catch"](5);
-              console.error(_context2.t0);
-              session.notify("".concat(_context2.t0), 'warning');
+              _context.prev = 23;
+              _context.t0 = _context["catch"](5);
+              console.error(_context.t0);
+              session.notify("".concat(_context.t0), 'warning');
 
             case 27:
             case "end":
-              return _context2.stop();
+              return _context.stop();
           }
         }
-      }, _callee2, null, [[5, 23]]);
+      }, _callee, null, [[5, 23]]);
     }));
     return _handleSelectedRegion.apply(this, arguments);
   }
@@ -185,7 +141,15 @@ function SearchBox(_ref) {
     showHelp: showHelp,
     onSelect: handleSelectedRegion,
     assemblyName: assemblyName,
-    fetchResults: fetchResults,
+    fetchResults: function fetchResults(queryString) {
+      return (0, _util2.fetchResults)({
+        queryString: queryString,
+        searchScope: searchScope,
+        rankSearchResults: rankSearchResults,
+        textSearchManager: textSearchManager,
+        assembly: assembly
+      });
+    },
     model: model,
     TextFieldProps: {
       variant: 'outlined',

package/dist/LinearGenomeView/components/SearchResultsDialog.d.ts

@@ -1,6 +1,6 @@
 /// <reference types="react" />
 import { LinearGenomeViewModel } from '../..';
-export declare const useStyles: (props?: any) => import("@material-ui/styles").ClassNameMap<"closeButton" | "dialogContent">;
+export declare const useStyles: (props?: any) => import("@material-ui/styles").ClassNameMap<"dialogContent" | "closeButton">;
 export default function SearchResultsDialog({ model, optAssemblyName, handleClose, }: {
     model: LinearGenomeViewModel;
     optAssemblyName?: string;

package/dist/LinearGenomeView/components/SearchResultsDialog.js

@@ -146,7 +146,6 @@ function SearchResultsDialog(_ref) {
 
         handleClose();
       },
-      disabled: !getTrackName(result.getTrackId()),
       color: "primary",
       variant: "contained"
     }, "Go")));

package/dist/LinearGenomeView/components/TrackLabel.js

@@ -7,30 +7,32 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.default = void 0;
 
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+var _extends2 = _interopRequireDefault(require("@babel/runtime/helpers/extends"));
 
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
 
 var _react = _interopRequireDefault(require("react"));
 
 var _configuration = require("@jbrowse/core/configuration");
 
-var _ui = require("@jbrowse/core/ui");
+var _CascadingMenu = _interopRequireDefault(require("@jbrowse/core/ui/CascadingMenu"));
 
 var _util = require("@jbrowse/core/util");
 
 var _core = require("@material-ui/core");
 
+var _hooks = require("material-ui-popup-state/hooks");
+
+var _clsx = _interopRequireDefault(require("clsx"));
+
+var _mobxReact = require("mobx-react");
+
 var _MoreVert = _interopRequireDefault(require("@material-ui/icons/MoreVert"));
 
 var _DragIndicator = _interopRequireDefault(require("@material-ui/icons/DragIndicator"));
 
 var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
 
-var _clsx = _interopRequireDefault(require("clsx"));
-
-var _mobxReact = require("mobx-react");
-
 // icons
 var useStyles = (0, _core.makeStyles)(function (theme) {
   return {
@@ -64,30 +66,20 @@ var useStyles = (0, _core.makeStyles)(function (theme) {
   };
 });
 
-var TrackLabel = /*#__PURE__*/_react.default.forwardRef(function (props, ref) {
+var TrackLabel = /*#__PURE__*/_react.default.forwardRef(function (_ref, ref) {
   var _session$getTrackActi;
 
+  var track = _ref.track,
+      className = _ref.className;
   var classes = useStyles();
-
-  var _React$useState = _react.default.useState(null),
-      _React$useState2 = (0, _slicedToArray2.default)(_React$useState, 2),
-      anchorEl = _React$useState2[0],
-      setAnchorEl = _React$useState2[1];
-
-  var track = props.track,
-      className = props.className;
   var view = (0, _util.getContainingView)(track);
   var session = (0, _util.getSession)(track);
   var trackConf = track.configuration;
   var trackId = (0, _configuration.getConf)(track, 'trackId');
-
-  var handleClick = function handleClick(event) {
-    setAnchorEl(event.currentTarget);
-  };
-
-  var handleClose = function handleClose() {
-    setAnchorEl(null);
-  };
+  var popupState = (0, _hooks.usePopupState)({
+    popupId: 'trackLabelMenu',
+    variant: 'popover'
+  });
 
   var onDragStart = function onDragStart(event) {
     var target = event.target;
@@ -108,12 +100,7 @@ var TrackLabel = /*#__PURE__*/_react.default.forwardRef(function (props, ref) {
     var r = session.assemblies.find(function (a) {
       return a.sequence === trackConf;
     });
-    trackName = (0, _configuration.readConfObject)(trackConf, 'name') || (r ? "Reference Sequence (".concat((0, _configuration.readConfObject)(r, 'name'), ")") : 'Reference Sequence');
-  }
-
-  function handleMenuItemClick(_, callback) {
-    callback();
-    handleClose();
+    trackName = trackName || (r ? "Reference Sequence (".concat((0, _configuration.readConfObject)(r, 'name'), ")") : 'Reference Sequence');
   }
 
   var items = [].concat((0, _toConsumableArray2.default)(((_session$getTrackActi = session.getTrackActionMenuItems) === null || _session$getTrackActi === void 0 ? void 0 : _session$getTrackActi.call(session, trackConf)) || []), (0, _toConsumableArray2.default)(track.trackMenuItems())).sort(function (a, b) {
@@ -141,21 +128,18 @@ var TrackLabel = /*#__PURE__*/_react.default.forwardRef(function (props, ref) {
     variant: "body1",
     component: "span",
     className: classes.trackName
-  }, trackName), /*#__PURE__*/_react.default.createElement(_core.IconButton, {
-    "aria-controls": "simple-menu",
-    "aria-haspopup": "true",
-    onClick: handleClick,
+  }, trackName), /*#__PURE__*/_react.default.createElement(_core.IconButton, (0, _extends2.default)({}, (0, _hooks.bindTrigger)(popupState), {
     className: classes.iconButton,
     color: "secondary",
     "data-testid": "track_menu_icon",
     disabled: !items.length
-  }, /*#__PURE__*/_react.default.createElement(_MoreVert.default, null))), /*#__PURE__*/_react.default.createElement(_ui.Menu, {
-    anchorEl: anchorEl,
-    onMenuItemClick: handleMenuItemClick,
-    open: Boolean(anchorEl),
-    onClose: handleClose,
-    menuItems: items
-  }));
+  }), /*#__PURE__*/_react.default.createElement(_MoreVert.default, null))), /*#__PURE__*/_react.default.createElement(_CascadingMenu.default, (0, _extends2.default)({}, (0, _hooks.bindPopover)(popupState), {
+    onMenuItemClick: function onMenuItemClick(_, callback) {
+      return callback();
+    },
+    menuItems: items,
+    popupState: popupState
+  })));
 });
 
 var _default = (0, _mobxReact.observer)(TrackLabel);

package/dist/LinearGenomeView/components/util.d.ts

@@ -1,2 +1,14 @@
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import { SearchType } from '@jbrowse/core/data_adapters/BaseAdapter';
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+import { SearchScope } from '@jbrowse/core/TextSearch/TextSearchManager';
+import { TextSearchManager } from '@jbrowse/core/util';
 export declare function dedupe(results: BaseResult[] | undefined, cb: (result: BaseResult) => string): BaseResult[];
+export declare function fetchResults({ queryString, searchType, searchScope, rankSearchResults, textSearchManager, assembly, }: {
+    queryString: string;
+    searchScope: SearchScope;
+    rankSearchResults: (results: BaseResult[]) => BaseResult[];
+    searchType?: SearchType;
+    textSearchManager?: TextSearchManager;
+    assembly?: Assembly;
+}): Promise<BaseResult[]>;

package/dist/LinearGenomeView/components/util.js

@@ -1,9 +1,20 @@
 "use strict";
 
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.dedupe = dedupe;
+exports.fetchResults = fetchResults;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _BaseResults = _interopRequireDefault(require("@jbrowse/core/TextSearch/BaseResults"));
 
 function dedupe() {
   var results = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : [];
@@ -13,4 +24,52 @@ function dedupe() {
       return cb(t) === cb(elt);
     });
   });
+}
+
+function fetchResults(_x) {
+  return _fetchResults.apply(this, arguments);
+}
+
+function _fetchResults() {
+  _fetchResults = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(_ref) {
+    var _assembly$allRefNames;
+
+    var queryString, searchType, searchScope, rankSearchResults, textSearchManager, assembly, textSearchResults, refNameResults;
+    return _regenerator.default.wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            queryString = _ref.queryString, searchType = _ref.searchType, searchScope = _ref.searchScope, rankSearchResults = _ref.rankSearchResults, textSearchManager = _ref.textSearchManager, assembly = _ref.assembly;
+
+            if (!textSearchManager) {
+              console.warn('No text search manager');
+            }
+
+            _context.next = 4;
+            return textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
+              queryString: queryString,
+              searchType: searchType
+            }, searchScope, rankSearchResults);
+
+          case 4:
+            textSearchResults = _context.sent;
+            refNameResults = assembly === null || assembly === void 0 ? void 0 : (_assembly$allRefNames = assembly.allRefNames) === null || _assembly$allRefNames === void 0 ? void 0 : _assembly$allRefNames.filter(function (ref) {
+              return ref.toLowerCase().startsWith(queryString.toLowerCase());
+            }).slice(0, 10).map(function (r) {
+              return new _BaseResults.default({
+                label: r
+              });
+            });
+            return _context.abrupt("return", dedupe([].concat((0, _toConsumableArray2.default)(refNameResults || []), (0, _toConsumableArray2.default)(textSearchResults || [])), function (elt) {
+              return elt.getId();
+            }));
+
+          case 7:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee);
+  }));
+  return _fetchResults.apply(this, arguments);
 }

package/dist/LinearGenomeView/index.d.ts

@@ -20,6 +20,7 @@ export interface BpOffset {
 }
 export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
+    filename?: string;
 }
 export interface NavLocation {
     refName: string;
@@ -55,6 +56,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
     hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<"hierarchical">, [undefined]>;
     trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -86,6 +88,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 } & {
     readonly width: number;
     readonly interRegionPaddingWidth: number;
+    readonly assemblyNames: string[];
 } & {
     readonly assemblyErrors: string;
     readonly assembliesInitialized: boolean;
@@ -105,19 +108,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly minOffset: number;
     readonly displayedRegionsTotalPx: number;
     renderProps(): any;
-    readonly assemblyNames: string[];
     searchScope(assemblyName: string): {
         assemblyName: string;
         includeAggregateIndexes: boolean;
         tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
     };
-    /**
-     * @param refName - refName of the displayedRegion
-     * @param coord - coordinate at the displayed Region
-     * @param regionNumber - optional param used as identifier when
-     * there are multiple displayedRegions with the same refName
-     * @returns offsetPx of the displayed region that it lands in
-     */
     bpToPx({ refName, coord, regionNumber, }: {
         refName: string;
         coord: number;
@@ -163,6 +158,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setError(error: Error | undefined): void;
     toggleHeader(): void;
     toggleHeaderOverview(): void;
+    toggleNoTracksActive(): void;
     scrollTo(offsetPx: number): number;
     zoomTo(bpPerPx: number): number;
     setOffsets(left: undefined | BpOffset, right: undefined | BpOffset): void;
@@ -180,7 +176,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     toggleCenterLine(): void;
     setDisplayedRegions(regions: Region[]): void;
     activateTrackSelector(): import("@jbrowse/core/util").Widget;
-    navToLocString(locString: string, optAssemblyName?: string | undefined): void;
+    navToLocString(locString: string, optAssemblyName?: string): void;
     /**
      * Navigate to a location based on its refName and optionally start, end,
      * and assemblyName. Can handle if there are multiple displayedRegions
@@ -245,8 +241,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     centerAt(bp: number, refName: string, regionIndex: number): void;
     center(): void;
     showAllRegions(): void;
-    showAllRegionsInAssembly(assemblyName?: string | undefined): void;
-    setDraggingTrackId(idx?: string | undefined): void;
+    showAllRegionsInAssembly(assemblyName?: string): void;
+    setDraggingTrackId(idx?: string): void;
     setScaleFactor(factor: number): void;
 } & {
     slide: (viewWidths: number) => void;

package/dist/LinearGenomeView/index.js

@@ -155,6 +155,7 @@ function stateModelFactory(pluginManager) {
     tracks: _mobxStateTree.types.array(pluginManager.pluggableMstType('track', 'stateModel')),
     hideHeader: false,
     hideHeaderOverview: false,
+    hideNoTracksActive: false,
     trackSelectorType: _mobxStateTree.types.optional(_mobxStateTree.types.enumeration(['hierarchical']), 'hierarchical'),
     trackLabels: _mobxStateTree.types.optional(_mobxStateTree.types.string, function () {
       return localStorageGetItem('lgv-trackLabels') || 'overlapping';
@@ -199,6 +200,12 @@ function stateModelFactory(pluginManager) {
 
       get interRegionPaddingWidth() {
         return INTER_REGION_PADDING_WIDTH;
+      },
+
+      get assemblyNames() {
+        return (0, _toConsumableArray2.default)(new Set(self.displayedRegions.map(function (region) {
+          return region.assemblyName;
+        })));
       }
 
     };
@@ -208,7 +215,8 @@ function stateModelFactory(pluginManager) {
         var _getSession = (0, _util.getSession)(self),
             assemblyManager = _getSession.assemblyManager;
 
-        return this.assemblyNames.map(function (a) {
+        var assemblyNames = self.assemblyNames;
+        return assemblyNames.map(function (a) {
           var _assemblyManager$get;
 
           return (_assemblyManager$get = assemblyManager.get(a)) === null || _assemblyManager$get === void 0 ? void 0 : _assemblyManager$get.error;
@@ -221,7 +229,8 @@ function stateModelFactory(pluginManager) {
         var _getSession2 = (0, _util.getSession)(self),
             assemblyManager = _getSession2.assemblyManager;
 
-        return this.assemblyNames.every(function (a) {
+        var assemblyNames = self.assemblyNames;
+        return assemblyNames.every(function (a) {
           var _assemblyManager$get2;
 
           return (_assemblyManager$get2 = assemblyManager.get(a)) === null || _assemblyManager$get2 === void 0 ? void 0 : _assemblyManager$get2.initialized;
@@ -312,13 +321,6 @@ function stateModelFactory(pluginManager) {
           highResolutionScaling: (0, _configuration.getConf)((0, _util.getSession)(self), 'highResolutionScaling')
         });
       },
-
-      get assemblyNames() {
-        return (0, _toConsumableArray2.default)(new Set(self.displayedRegions.map(function (region) {
-          return region.assemblyName;
-        })));
-      },
-
       searchScope: function searchScope(assemblyName) {
         return {
           assemblyName: assemblyName,
@@ -326,14 +328,6 @@ function stateModelFactory(pluginManager) {
           tracks: self.tracks
         };
       },
-
-      /**
-       * @param refName - refName of the displayedRegion
-       * @param coord - coordinate at the displayed Region
-       * @param regionNumber - optional param used as identifier when
-       * there are multiple displayedRegions with the same refName
-       * @returns offsetPx of the displayed region that it lands in
-       */
       bpToPx: function bpToPx(_ref) {
         var refName = _ref.refName,
             coord = _ref.coord,
@@ -432,10 +426,8 @@ function stateModelFactory(pluginManager) {
           return track.configuration.trackId;
         });
         results.forEach(function (result) {
-          if (openTrackIds !== []) {
-            if (openTrackIds.includes(result.trackId)) {
-              result.updateScore(result.getScore() + 1);
-            }
+          if (openTrackIds.includes(result.trackId)) {
+            result.updateScore(result.getScore() + 1);
           }
         });
         return results;
@@ -509,6 +501,9 @@ function stateModelFactory(pluginManager) {
       toggleHeaderOverview: function toggleHeaderOverview() {
         self.hideHeaderOverview = !self.hideHeaderOverview;
       },
+      toggleNoTracksActive: function toggleNoTracksActive() {
+        self.hideNoTracksActive = !self.hideNoTracksActive;
+      },
       scrollTo: function scrollTo(offsetPx) {
         var newOffsetPx = (0, _util.clamp)(offsetPx, self.minOffset, self.maxOffset);
         self.offsetPx = newOffsetPx;
@@ -692,6 +687,8 @@ function stateModelFactory(pluginManager) {
         throw new Error("invalid track selector type ".concat(self.trackSelectorType));
       },
       navToLocString: function navToLocString(locString, optAssemblyName) {
+        var _parsedLocStrings;
+
         var assemblyNames = self.assemblyNames;
 
         var _getSession3 = (0, _util.getSession)(self),
@@ -699,14 +696,38 @@ function stateModelFactory(pluginManager) {
 
         var isValidRefName = assemblyManager.isValidRefName;
         var assemblyName = optAssemblyName || assemblyNames[0];
-        var parsedLocStrings = locString.split(' ').filter(function (f) {
-          return !!f.trim();
-        }).map(function (l) {
-          return (0, _util.parseLocString)(l, function (ref) {
-            return isValidRefName(ref, assemblyName);
+        var parsedLocStrings;
+        var inputs = locString.split(/(\s+)/).map(function (f) {
+          return f.trim();
+        }).filter(function (f) {
+          return !!f;
+        }); // first try interpreting as a whitespace-separated sequence of
+        // multiple locstrings
+
+        try {
+          parsedLocStrings = inputs.map(function (l) {
+            return (0, _util.parseLocString)(l, function (ref) {
+              return isValidRefName(ref, assemblyName);
+            });
           });
-        });
-        var locations = parsedLocStrings.map(function (region) {
+        } catch (e) {
+          // if this fails, try interpreting as a whitespace-separated refname,
+          // start, end if start and end are integer inputs
+          var _inputs = (0, _slicedToArray2.default)(inputs, 3),
+              refName = _inputs[0],
+              start = _inputs[1],
+              end = _inputs[2];
+
+          if ("".concat(e).match(/Unknown reference sequence/) && Number.isInteger(+start) && Number.isInteger(+end)) {
+            parsedLocStrings = [(0, _util.parseLocString)(refName + ':' + start + '..' + end, function (ref) {
+              return isValidRefName(ref, assemblyName);
+            })];
+          } else {
+            throw e;
+          }
+        }
+
+        var locations = (_parsedLocStrings = parsedLocStrings) === null || _parsedLocStrings === void 0 ? void 0 : _parsedLocStrings.map(function (region) {
           var asmName = region.assemblyName || assemblyName;
           var asm = assemblyManager.get(asmName);
           var refName = region.refName;
@@ -746,12 +767,12 @@ function stateModelFactory(pluginManager) {
           this.setDisplayedRegions([_objectSpread({
             reversed: loc.reversed
           }, loc.parentRegion)]);
-          var start = loc.start,
-              end = loc.end,
+          var _start = loc.start,
+              _end = loc.end,
               parentRegion = loc.parentRegion;
           this.navTo(_objectSpread(_objectSpread({}, loc), {}, {
-            start: (0, _util.clamp)(start !== null && start !== void 0 ? start : 0, 0, parentRegion.end),
-            end: (0, _util.clamp)(end !== null && end !== void 0 ? end : parentRegion.end, 0, parentRegion.end)
+            start: (0, _util.clamp)(_start !== null && _start !== void 0 ? _start : 0, 0, parentRegion.end),
+            end: (0, _util.clamp)(_end !== null && _end !== void 0 ? _end : parentRegion.end, 0, parentRegion.end)
           }));
         } else {
           this.setDisplayedRegions( // @ts-ignore
@@ -1230,6 +1251,12 @@ function stateModelFactory(pluginManager) {
           checked: !self.hideHeaderOverview,
           onClick: self.toggleHeaderOverview,
           disabled: self.hideHeader
+        }, {
+          label: 'Show no tracks active button',
+          icon: _Visibility.default,
+          type: 'checkbox',
+          checked: !self.hideNoTracksActive,
+          onClick: self.toggleNoTracksActive
         }, {
           label: 'Track labels',
           icon: _Label.default,
@@ -1380,7 +1407,7 @@ function stateModelFactory(pluginManager) {
                   blob = new Blob([html], {
                     type: 'image/svg+xml'
                   });
-                  (0, _fileSaver.saveAs)(blob, 'image.svg');
+                  (0, _fileSaver.saveAs)(blob, opts.filename || 'image.svg');
 
                 case 6:
                 case "end":