@jbrowse/plugin-linear-genome-view 1.7.10 → 1.7.11

package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -130,7 +130,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     estimatedRegionStatsP: Promise<Stats> | undefined;
     estimatedRegionStats: Stats | undefined;
 } & {
-    readonly blockType: "staticBlocks" | "dynamicBlocks";
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     /**

package/dist/LinearBareDisplay/model.d.ts

@@ -118,7 +118,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly blockType: "staticBlocks" | "dynamicBlocks";
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;

package/dist/LinearBasicDisplay/model.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { MenuItem } from '@jbrowse/core/ui';
 import { Instance } from 'mobx-state-tree';
@@ -124,7 +123,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly blockType: "staticBlocks" | "dynamicBlocks";
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;

package/dist/LinearBasicDisplay/model.js

@@ -62,7 +62,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
       get showDescriptions() {
         var _self$trackShowDescri;
 
-        return (_self$trackShowDescri = self.trackShowDescriptions) !== null && _self$trackShowDescri !== void 0 ? _self$trackShowDescri : (0, _configuration.getConf)(self, ['renderer', 'showLabels']);
+        return (_self$trackShowDescri = self.trackShowDescriptions) !== null && _self$trackShowDescri !== void 0 ? _self$trackShowDescri : (0, _configuration.getConf)(self, ['renderer', 'showDescriptions']);
       },
 
       get maxHeight() {
@@ -129,7 +129,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
           type: 'checkbox',
           checked: self.showDescriptions,
           onClick: function onClick() {
-            self.toggleShowDescriptions();
+            return self.toggleShowDescriptions();
           }
         }, {
           label: 'Display mode',

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
 declare type LGV = LinearGenomeViewModel;
 declare const LinearGenomeViewHeader: ({ model }: {

package/dist/LinearGenomeView/components/Header.js

@@ -99,13 +99,12 @@ function PanControls(_ref2) {
 var RegionWidth = (0, _mobxReact.observer)(function (_ref3) {
   var model = _ref3.model;
   var classes = useStyles();
-  var coarseTotalBp = model.coarseTotalBp,
-      bpPerPx = model.bpPerPx;
+  var coarseTotalBp = model.coarseTotalBp;
   return /*#__PURE__*/_react.default.createElement(_core.Typography, {
     variant: "body2",
     color: "textSecondary",
     className: classes.bp
-  }, (0, _util.getTickDisplayStr2)(coarseTotalBp, bpPerPx));
+  }, (0, _util.getBpDisplayStr)(coarseTotalBp));
 });
 
 var Controls = function Controls(_ref4) {

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
 declare type LGV = LinearGenomeViewModel;
 declare const ImportForm: ({ model }: {

package/dist/LinearGenomeView/components/ImportForm.js

@@ -11,8 +11,6 @@ var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"))
 
 var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
 var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
@@ -35,6 +33,8 @@ var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
 
 var _RefNameAutocomplete = _interopRequireDefault(require("./RefNameAutocomplete"));
 
+var _util2 = require("./util");
+
 var _ = require("..");
 
 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); }
@@ -98,106 +98,68 @@ var ImportForm = (0, _mobxReact.observer)(function (_ref) {
 
   var option = new _BaseResults.default({
     label: value
-  });
-
-  function fetchResults(_x, _x2) {
-    return _fetchResults.apply(this, arguments);
-  } // gets a string as input, or use stored option results from previous query,
+  }); // 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", [].concat((0, _toConsumableArray2.default)(refNameResults || []), (0, _toConsumableArray2.default)(textSearchResults || [])));
-
-            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(input) {
+    _handleSelectedRegion = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(input) {
       var trackId, location, _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:
               if (option) {
-                _context2.next = 2;
+                _context.next = 2;
                 break;
               }
 
-              return _context2.abrupt("return");
+              return _context.abrupt("return");
 
             case 2:
               trackId = option.getTrackId();
               location = input || option.getLocation() || '';
               _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 = 6;
+              _context.prev = 6;
 
               if (!(allRefs.includes(location) || allRefs.includes(ref) && rest !== undefined && !Number.isNaN(parseInt(rest, 10)))) {
-                _context2.next = 11;
+                _context.next = 11;
                 break;
               }
 
               model.navToLocString(location, selectedAsm);
-              _context2.next = 22;
+              _context.next = 22;
               break;
 
             case 11:
-              _context2.next = 13;
-              return fetchResults(input, 'exact');
+              _context.next = 13;
+              return (0, _util2.fetchResults)({
+                queryString: input,
+                searchType: 'exact',
+                searchScope: searchScope,
+                rankSearchResults: rankSearchResults,
+                textSearchManager: textSearchManager,
+                assembly: assembly
+              });
 
             case 13:
-              results = _context2.sent;
+              results = _context.sent;
 
               if (!(results.length > 1)) {
-                _context2.next = 19;
+                _context.next = 19;
                 break;
               }
 
               model.setSearchResults(results, input.toLowerCase());
-              return _context2.abrupt("return");
+              return _context.abrupt("return");
 
             case 19:
               if (results.length === 1) {
@@ -213,21 +175,21 @@ var ImportForm = (0, _mobxReact.observer)(function (_ref) {
               }
 
             case 22:
-              _context2.next = 28;
+              _context.next = 28;
               break;
 
             case 24:
-              _context2.prev = 24;
-              _context2.t0 = _context2["catch"](6);
-              console.error(_context2.t0);
-              session.notify("".concat(_context2.t0), 'warning');
+              _context.prev = 24;
+              _context.t0 = _context["catch"](6);
+              console.error(_context.t0);
+              session.notify("".concat(_context.t0), 'warning');
 
             case 28:
             case "end":
-              return _context2.stop();
+              return _context.stop();
           }
         }
-      }, _callee2, null, [[6, 24]]);
+      }, _callee, null, [[6, 24]]);
     }));
     return _handleSelectedRegion.apply(this, arguments);
   }
@@ -276,7 +238,15 @@ var ImportForm = (0, _mobxReact.observer)(function (_ref) {
       color: 'red'
     }
   }) : value ? /*#__PURE__*/_react.default.createElement(_RefNameAutocomplete.default, {
-    fetchResults: fetchResults,
+    fetchResults: function fetchResults(queryString) {
+      return (0, _util2.fetchResults)({
+        queryString: queryString,
+        assembly: assembly,
+        textSearchManager: textSearchManager,
+        rankSearchResults: rankSearchResults,
+        searchScope: searchScope
+      });
+    },
     model: model,
     assemblyName: assemblyError ? undefined : selectedAsm,
     value: value // note: minWidth 270 accomodates full width of helperText

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

@@ -18,7 +18,10 @@ declare const Cytobands: ({ overview, block, assembly, }: {
         error: Error | undefined;
         regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [key: string]: string;
+            [x: string]: string;
+        } | undefined;
+        lowerCaseRefNameAliases: {
+            [x: string]: string;
         } | undefined;
         cytobands: import("@jbrowse/core/util").Feature[] | undefined;
     } & {
@@ -37,17 +40,22 @@ declare const Cytobands: ({ overview, block, assembly, }: {
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("@jbrowse/core/util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            lowerCaseRefNameAliases: {
+                [x: string]: string;
+            };
             cytobands: import("@jbrowse/core/util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("@jbrowse/core/util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
+        }, lowerCaseRefNameAliases: {
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
         afterAttach(): void;
@@ -72,7 +80,10 @@ declare const Cytobands: ({ overview, block, assembly, }: {
         error: Error | undefined;
         regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [key: string]: string;
+            [x: string]: string;
+        } | undefined;
+        lowerCaseRefNameAliases: {
+            [x: string]: string;
         } | undefined;
         cytobands: import("@jbrowse/core/util").Feature[] | undefined;
     } & {
@@ -91,17 +102,22 @@ declare const Cytobands: ({ overview, block, assembly, }: {
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("@jbrowse/core/util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            lowerCaseRefNameAliases: {
+                [x: string]: string;
+            };
             cytobands: import("@jbrowse/core/util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("@jbrowse/core/util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
+        }, lowerCaseRefNameAliases: {
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
         afterAttach(): void;
@@ -122,7 +138,7 @@ declare const Cytobands: ({ overview, block, assembly, }: {
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     block: ContentBlock;
-}) => JSX.Element | null;
+}) => JSX.Element;
 declare function OverviewScaleBar({ model, children, }: {
     model: LGV;
     children: React.ReactNode;

package/dist/LinearGenomeView/components/OverviewScaleBar.js

@@ -150,15 +150,11 @@ var colorMap = {
   stalk: 'rgb(127,127,127)',
   acen: '#800'
 };
-var Cytobands = (0, _mobxReact.observer)(function (_ref2) {
+
+function getCytobands(assembly, refName) {
   var _assembly$cytobands;
 
-  var overview = _ref2.overview,
-      block = _ref2.block,
-      assembly = _ref2.assembly;
-  var offsetPx = block.offsetPx,
-      reversed = block.reversed;
-  var cytobands = assembly === null || assembly === void 0 ? void 0 : (_assembly$cytobands = assembly.cytobands) === null || _assembly$cytobands === void 0 ? void 0 : _assembly$cytobands.map(function (f) {
+  return (assembly === null || assembly === void 0 ? void 0 : (_assembly$cytobands = assembly.cytobands) === null || _assembly$cytobands === void 0 ? void 0 : _assembly$cytobands.map(function (f) {
     return {
       refName: assembly.getCanonicalRefName(f.get('refName')),
       start: f.get('start'),
@@ -166,8 +162,18 @@ var Cytobands = (0, _mobxReact.observer)(function (_ref2) {
       type: f.get('type')
     };
   }).filter(function (f) {
-    return f.refName === block.refName;
-  }).map(function (f) {
+    return f.refName === refName;
+  })) || [];
+}
+
+var Cytobands = (0, _mobxReact.observer)(function (_ref2) {
+  var overview = _ref2.overview,
+      block = _ref2.block,
+      assembly = _ref2.assembly;
+  var offsetPx = block.offsetPx,
+      reversed = block.reversed;
+  var cytobands = getCytobands(assembly, block.refName);
+  var coords = cytobands.map(function (f) {
     var refName = f.refName,
         start = f.start,
         end = f.end,
@@ -184,9 +190,9 @@ var Cytobands = (0, _mobxReact.observer)(function (_ref2) {
   var lcap = reversed ? arr.length - 1 : 0;
   var rcap = reversed ? 0 : arr.length - 1;
   var firstCent = true;
-  return cytobands ? /*#__PURE__*/_react.default.createElement("g", {
+  return /*#__PURE__*/_react.default.createElement("g", {
     transform: "translate(-".concat(offsetPx, ")")
-  }, cytobands.map(function (_ref3, index) {
+  }, coords.map(function (_ref3, index) {
     var _ref4 = (0, _slicedToArray2.default)(_ref3, 3),
         start = _ref4[0],
         end = _ref4[1],
@@ -233,7 +239,7 @@ var Cytobands = (0, _mobxReact.observer)(function (_ref2) {
         fill: colorMap[type]
       });
     }
-  })) : null;
+  }));
 });
 exports.Cytobands = Cytobands;
 var OverviewBox = (0, _mobxReact.observer)(function (_ref5) {
@@ -266,20 +272,21 @@ var OverviewBox = (0, _mobxReact.observer)(function (_ref5) {
     tickLabels.push(reversed ? end - offsetLabel : start + offsetLabel);
   }
 
+  var canDisplayCytobands = showCytobands && getCytobands(assembly, block.refName).length;
   return /*#__PURE__*/_react.default.createElement("div", null, /*#__PURE__*/_react.default.createElement(_core.Typography, {
     style: {
       left: block.offsetPx + 3,
-      color: showCytobands ? 'black' : refNameColor
+      color: canDisplayCytobands ? 'black' : refNameColor
     },
     className: classes.scaleBarRefName
   }, refName), /*#__PURE__*/_react.default.createElement("div", {
-    className: (0, _clsx.default)(classes.scaleBarContig, showCytobands ? undefined : reversed ? classes.scaleBarContigReverse : classes.scaleBarContigForward, !showCytobands ? classes.scaleBarBorder : undefined),
+    className: (0, _clsx.default)(classes.scaleBarContig, canDisplayCytobands ? undefined : reversed ? classes.scaleBarContigReverse : classes.scaleBarContigForward, !canDisplayCytobands ? classes.scaleBarBorder : undefined),
     style: {
       left: block.offsetPx + cytobandOffset,
       width: block.widthPx,
       borderColor: refNameColor
     }
-  }, !showCytobands ? tickLabels.map(function (tickLabel, labelIdx) {
+  }, !canDisplayCytobands ? tickLabels.map(function (tickLabel, labelIdx) {
     return /*#__PURE__*/_react.default.createElement(_core.Typography, {
       key: "".concat(JSON.stringify(block), "-").concat(tickLabel, "-").concat(labelIdx),
       className: classes.scaleBarLabel,
@@ -290,7 +297,7 @@ var OverviewBox = (0, _mobxReact.observer)(function (_ref5) {
         color: refNameColor
       }
     }, (0, _util.getTickDisplayStr)(tickLabel, bpPerPx));
-  }) : null, showCytobands ? /*#__PURE__*/_react.default.createElement("svg", {
+  }) : null, canDisplayCytobands ? /*#__PURE__*/_react.default.createElement("svg", {
     style: {
       width: '100%'
     }

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/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/index.d.ts

@@ -124,7 +124,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
                 estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
             } & {
-                readonly blockType: "staticBlocks" | "dynamicBlocks";
+                readonly blockType: "dynamicBlocks" | "staticBlocks";
                 readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
             } & {
                 readonly renderDelay: number;
@@ -300,7 +300,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
                 estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
             } & {
-                readonly blockType: "staticBlocks" | "dynamicBlocks";
+                readonly blockType: "dynamicBlocks" | "staticBlocks";
                 readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
             } & {
                 readonly renderDelay: number;
@@ -486,7 +486,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
             estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
         } & {
-            readonly blockType: "staticBlocks" | "dynamicBlocks";
+            readonly blockType: "dynamicBlocks" | "staticBlocks";
             readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
         } & {
             readonly renderDelay: number;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "1.7.10",
+  "version": "1.7.11",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "02d8c1e88e5603ea5855faed4ccb814e28071b32"
+  "gitHead": "5c21beb48a21f08b0091d293f09ac99174c48f77"
 }

package/src/LinearBasicDisplay/model.ts

@@ -42,7 +42,7 @@ const stateModelFactory = (configSchema: AnyConfigurationSchemaType) =>
       get showDescriptions() {
         return (
           self.trackShowDescriptions ??
-          getConf(self, ['renderer', 'showLabels'])
+          getConf(self, ['renderer', 'showDescriptions'])
         )
       },
 
@@ -116,9 +116,7 @@ const stateModelFactory = (configSchema: AnyConfigurationSchemaType) =>
               icon: VisibilityIcon,
               type: 'checkbox',
               checked: self.showDescriptions,
-              onClick: () => {
-                self.toggleShowDescriptions()
-              },
+              onClick: () => self.toggleShowDescriptions(),
             },
             {
               label: 'Display mode',

package/src/LinearGenomeView/components/Header.tsx

@@ -7,7 +7,7 @@ import {
   makeStyles,
   alpha,
 } from '@material-ui/core'
-import { getTickDisplayStr2 } from '@jbrowse/core/util'
+import { getBpDisplayStr } from '@jbrowse/core/util'
 import SearchBox from './SearchBox'
 
 // icons
@@ -98,10 +98,10 @@ function PanControls({ model }: { model: LGV }) {
 
 const RegionWidth = observer(({ model }: { model: LGV }) => {
   const classes = useStyles()
-  const { coarseTotalBp, bpPerPx } = model
+  const { coarseTotalBp } = model
   return (
     <Typography variant="body2" color="textSecondary" className={classes.bp}>
-      {getTickDisplayStr2(coarseTotalBp, bpPerPx)}
+      {getBpDisplayStr(coarseTotalBp)}
     </Typography>
   )
 })

package/src/LinearGenomeView/components/ImportForm.tsx

@@ -8,7 +8,6 @@ import {
   Grid,
   makeStyles,
 } from '@material-ui/core'
-import { SearchType } from '@jbrowse/core/data_adapters/BaseAdapter'
 import ErrorMessage from '@jbrowse/core/ui/ErrorMessage'
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
 import AssemblySelector from '@jbrowse/core/ui/AssemblySelector'
@@ -16,6 +15,7 @@ import CloseIcon from '@material-ui/icons/Close'
 
 // locals
 import RefNameAutocomplete from './RefNameAutocomplete'
+import { fetchResults } from './util'
 import { LinearGenomeViewModel, WIDGET_HEIGHT } from '..'
 const SearchResultsDialog = lazy(() => import('./SearchResultsDialog'))
 
@@ -57,28 +57,6 @@ const ImportForm = observer(({ model }: { model: LGV }) => {
     label: value,
   })
 
-  async function fetchResults(query: string, searchType?: SearchType) {
-    if (!textSearchManager) {
-      console.warn('No text search manager')
-    }
-
-    const textSearchResults = await textSearchManager?.search(
-      {
-        queryString: query,
-        searchType,
-      },
-      searchScope,
-      rankSearchResults,
-    )
-
-    const refNameResults = assembly?.allRefNames
-      ?.filter(refName => refName.startsWith(query))
-      .map(r => new BaseResult({ label: r }))
-      .slice(0, 10)
-
-    return [...(refNameResults || []), ...(textSearchResults || [])]
-  }
-
   // 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
@@ -105,7 +83,14 @@ const ImportForm = observer(({ model }: { model: LGV }) => {
       ) {
         model.navToLocString(location, selectedAsm)
       } else {
-        const results = await fetchResults(input, 'exact')
+        const results = await fetchResults({
+          queryString: input,
+          searchType: 'exact',
+          searchScope,
+          rankSearchResults,
+          textSearchManager,
+          assembly,
+        })
         if (results.length > 1) {
           model.setSearchResults(results, input.toLowerCase())
           return
@@ -165,7 +150,15 @@ const ImportForm = observer(({ model }: { model: LGV }) => {
                   <CloseIcon style={{ color: 'red' }} />
                 ) : value ? (
                   <RefNameAutocomplete
-                    fetchResults={fetchResults}
+                    fetchResults={queryString =>
+                      fetchResults({
+                        queryString,
+                        assembly,
+                        textSearchManager,
+                        rankSearchResults,
+                        searchScope,
+                      })
+                    }
                     model={model}
                     assemblyName={assemblyError ? undefined : selectedAsm}
                     value={value}

package/src/LinearGenomeView/components/OverviewScaleBar.tsx

@@ -170,6 +170,19 @@ const colorMap: { [key: string]: string | undefined } = {
   acen: '#800',
 }
 
+function getCytobands(assembly: Assembly | undefined, refName: string) {
+  return (
+    assembly?.cytobands
+      ?.map(f => ({
+        refName: assembly.getCanonicalRefName(f.get('refName')),
+        start: f.get('start'),
+        end: f.get('end'),
+        type: f.get('type'),
+      }))
+      .filter(f => f.refName === refName) || []
+  )
+}
+
 const Cytobands = observer(
   ({
     overview,
@@ -181,37 +194,30 @@ const Cytobands = observer(
     block: ContentBlock
   }) => {
     const { offsetPx, reversed } = block
-    const cytobands = assembly?.cytobands
-      ?.map(f => ({
-        refName: assembly.getCanonicalRefName(f.get('refName')),
-        start: f.get('start'),
-        end: f.get('end'),
-        type: f.get('type'),
-      }))
-      .filter(f => f.refName === block.refName)
-      .map(f => {
-        const { refName, start, end, type } = f
-        return [
-          overview.bpToPx({
-            refName,
-            coord: start,
-          }),
-          overview.bpToPx({
-            refName,
-            coord: end,
-          }),
-          type,
-        ]
-      })
+    const cytobands = getCytobands(assembly, block.refName)
+    const coords = cytobands.map(f => {
+      const { refName, start, end, type } = f
+      return [
+        overview.bpToPx({
+          refName,
+          coord: start,
+        }),
+        overview.bpToPx({
+          refName,
+          coord: end,
+        }),
+        type,
+      ]
+    })
 
     const arr = cytobands || []
     const lcap = reversed ? arr.length - 1 : 0
     const rcap = reversed ? 0 : arr.length - 1
 
     let firstCent = true
-    return cytobands ? (
+    return (
       <g transform={`translate(-${offsetPx})`}>
-        {cytobands.map(([start, end, type], index) => {
+        {coords.map(([start, end, type], index) => {
           const key = `${start}-${end}-${type}`
           if (type === 'acen' && firstCent) {
             firstCent = false
@@ -283,7 +289,7 @@ const Cytobands = observer(
           }
         })}
       </g>
-    ) : null
+    )
   },
 )
 
@@ -313,13 +319,16 @@ const OverviewBox = observer(
       tickLabels.push(reversed ? end - offsetLabel : start + offsetLabel)
     }
 
+    const canDisplayCytobands =
+      showCytobands && getCytobands(assembly, block.refName).length
+
     return (
       <div>
         {/* name of sequence */}
         <Typography
           style={{
             left: block.offsetPx + 3,
-            color: showCytobands ? 'black' : refNameColor,
+            color: canDisplayCytobands ? 'black' : refNameColor,
           }}
           className={classes.scaleBarRefName}
         >
@@ -328,12 +337,12 @@ const OverviewBox = observer(
         <div
           className={clsx(
             classes.scaleBarContig,
-            showCytobands
+            canDisplayCytobands
               ? undefined
               : reversed
               ? classes.scaleBarContigReverse
               : classes.scaleBarContigForward,
-            !showCytobands ? classes.scaleBarBorder : undefined,
+            !canDisplayCytobands ? classes.scaleBarBorder : undefined,
           )}
           style={{
             left: block.offsetPx + cytobandOffset,
@@ -341,7 +350,7 @@ const OverviewBox = observer(
             borderColor: refNameColor,
           }}
         >
-          {!showCytobands
+          {!canDisplayCytobands
             ? tickLabels.map((tickLabel, labelIdx) => (
                 <Typography
                   key={`${JSON.stringify(block)}-${tickLabel}-${labelIdx}`}
@@ -358,7 +367,7 @@ const OverviewBox = observer(
               ))
             : null}
 
-          {showCytobands ? (
+          {canDisplayCytobands ? (
             <svg style={{ width: '100%' }}>
               <Cytobands
                 overview={overview}

package/src/LinearGenomeView/components/SearchBox.tsx

@@ -3,11 +3,10 @@ import { observer } from 'mobx-react'
 import { makeStyles, useTheme, alpha } from '@material-ui/core'
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
 import { getSession } from '@jbrowse/core/util'
-import { SearchType } from '@jbrowse/core/data_adapters/BaseAdapter'
 
 // locals
 import RefNameAutocomplete from './RefNameAutocomplete'
-import { dedupe } from './util'
+import { fetchResults } from './util'
 import { LinearGenomeViewModel, SPACING, WIDGET_HEIGHT } from '..'
 
 const useStyles = makeStyles(() => ({
@@ -33,31 +32,6 @@ function SearchBox({
   const assembly = assemblyManager.get(assemblyName)
   const searchScope = model.searchScope(assemblyName)
 
-  async function fetchResults(query: string, searchType?: SearchType) {
-    if (!textSearchManager) {
-      console.warn('No text search manager')
-    }
-
-    const textSearchResults = await textSearchManager?.search(
-      {
-        queryString: query,
-        searchType,
-      },
-      searchScope,
-      rankSearchResults,
-    )
-
-    const refNameResults = assembly?.allRefNames
-      ?.filter(refName => refName.startsWith(query))
-      .map(r => new BaseResult({ label: r }))
-      .slice(0, 10)
-
-    return dedupe(
-      [...(refNameResults || []), ...(textSearchResults || [])],
-      elt => elt.getId(),
-    )
-  }
-
   // 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
@@ -82,7 +56,14 @@ function SearchBox({
       ) {
         model.navToLocString(location, assemblyName)
       } else {
-        const results = await fetchResults(label, 'exact')
+        const results = await fetchResults({
+          queryString: label,
+          searchType: 'exact',
+          searchScope,
+          rankSearchResults,
+          textSearchManager,
+          assembly,
+        })
         if (results.length > 1) {
           model.setSearchResults(results, label.toLowerCase())
           return
@@ -106,7 +87,15 @@ function SearchBox({
       showHelp={showHelp}
       onSelect={handleSelectedRegion}
       assemblyName={assemblyName}
-      fetchResults={fetchResults}
+      fetchResults={queryString =>
+        fetchResults({
+          queryString,
+          searchScope,
+          rankSearchResults,
+          textSearchManager,
+          assembly,
+        })
+      }
       model={model}
       TextFieldProps={{
         variant: 'outlined',

package/src/LinearGenomeView/components/SearchResultsDialog.tsx

@@ -156,7 +156,6 @@ export default function SearchResultsDialog({
                             }
                             handleClose()
                           }}
-                          disabled={!getTrackName(result.getTrackId())}
                           color="primary"
                           variant="contained"
                         >

package/src/LinearGenomeView/components/util.ts

@@ -1,4 +1,8 @@
+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 function dedupe(
   results: BaseResult[] = [],
@@ -8,3 +12,42 @@ export function dedupe(
     (elt, idx, self) => idx === self.findIndex(t => cb(t) === cb(elt)),
   )
 }
+
+export async function fetchResults({
+  queryString,
+  searchType,
+  searchScope,
+  rankSearchResults,
+  textSearchManager,
+  assembly,
+}: {
+  queryString: string
+  searchScope: SearchScope
+  rankSearchResults: (results: BaseResult[]) => BaseResult[]
+  searchType?: SearchType
+  textSearchManager?: TextSearchManager
+  assembly?: Assembly
+}) {
+  if (!textSearchManager) {
+    console.warn('No text search manager')
+  }
+
+  const textSearchResults = await textSearchManager?.search(
+    {
+      queryString,
+      searchType,
+    },
+    searchScope,
+    rankSearchResults,
+  )
+
+  const refNameResults = assembly?.allRefNames
+    ?.filter(ref => ref.toLowerCase().startsWith(queryString.toLowerCase()))
+    .slice(0, 10)
+    .map(r => new BaseResult({ label: r }))
+
+  return dedupe(
+    [...(refNameResults || []), ...(textSearchResults || [])],
+    elt => elt.getId(),
+  )
+}