@jbrowse/plugin-alignments 1.7.8 → 1.7.11

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -76,15 +76,24 @@ function Formatter(_ref) {
       show = _useState2[0],
       setShow = _useState2[1];
 
+  var _useState3 = (0, _react.useState)(false),
+      _useState4 = (0, _slicedToArray2.default)(_useState3, 2),
+      copied = _useState4[0],
+      setCopied = _useState4[1];
+
   var display = String(value);
 
   if (display.length > 100) {
     return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement("button", {
       type: "button",
       onClick: function onClick() {
-        return (0, _copyToClipboard.default)(display);
+        (0, _copyToClipboard.default)(display);
+        setCopied(true);
+        setTimeout(function () {
+          setCopied(false);
+        }, 700);
       }
-    }, "Copy"), /*#__PURE__*/_react.default.createElement("button", {
+    }, copied ? 'Copied to clipboard' : 'Copy'), /*#__PURE__*/_react.default.createElement("button", {
       type: "button",
       onClick: function onClick() {
         return setShow(function (val) {
@@ -142,7 +151,8 @@ function SupplementaryAlignments(props) {
     return /*#__PURE__*/_react.default.createElement("li", {
       key: "".concat(locString, "-").concat(index)
     }, /*#__PURE__*/_react.default.createElement(_core.Link, {
-      onClick: function onClick() {
+      onClick: function onClick(event) {
+        event.preventDefault();
         var view = model.view;
 
         try {

package/dist/AlignmentsFeatureDetail/index.d.ts

@@ -2,12 +2,37 @@ import PluginManager from '@jbrowse/core/PluginManager';
 declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
+    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
     featureData: import("mobx-state-tree").IType<any, any, any>;
+    formattedFields: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
-    setFeatureData(data: unknown): void;
+    setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+    setFormattedData(feat: Record<string, unknown>): void;
+} & {
+    afterCreate(): void;
+}, {
+    type: "BaseFeatureWidget";
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
+    featureData: import("mobx-state-tree").IType<any, any, any>;
+    formattedFields: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+}>> & import("mobx-state-tree")._NotCustomized, {
+    id: string;
+    type: "BaseFeatureWidget";
+    formattedFields: any;
+    view: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    track: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    finalizedFeatureData: any;
+} & import("mobx-state-tree")._NotCustomized>;
 export default function register(pluginManager: PluginManager): void;
 export { configSchema };

package/dist/AlignmentsFeatureDetail/index.js

@@ -15,12 +15,12 @@ var _react = require("react");
 
 var _configuration = require("@jbrowse/core/configuration");
 
-var _mst = require("@jbrowse/core/util/types/mst");
-
 var _mobxStateTree = require("mobx-state-tree");
 
 var _WidgetType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
 
+var _BaseFeatureWidget = require("@jbrowse/core/BaseFeatureWidget");
+
 function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
 
 function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || (0, _typeof2.default)(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
@@ -29,21 +29,10 @@ var configSchema = (0, _configuration.ConfigurationSchema)('AlignmentsFeatureWid
 exports.configSchema = configSchema;
 
 function stateModelFactory(pluginManager) {
-  return _mobxStateTree.types.model('AlignmentsFeatureWidget', {
-    id: _mst.ElementId,
-    type: _mobxStateTree.types.literal('AlignmentsFeatureWidget'),
-    featureData: _mobxStateTree.types.frozen(),
-    view: _mobxStateTree.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel'))
-  }).actions(function (self) {
-    return {
-      setFeatureData: function setFeatureData(data) {
-        self.featureData = data;
-      },
-      clearFeatureData: function clearFeatureData() {
-        self.featureData = undefined;
-      }
-    };
-  });
+  var baseModel = (0, _BaseFeatureWidget.stateModelFactory)(pluginManager);
+  return _mobxStateTree.types.compose(baseModel, _mobxStateTree.types.model('AlignmentsFeatureWidget', {
+    type: _mobxStateTree.types.literal('AlignmentsFeatureWidget')
+  }));
 }
 
 function register(pluginManager) {

package/dist/BamAdapter/MismatchParser.js

@@ -24,6 +24,7 @@ var _util = require("@jbrowse/core/util");
 var _marked = /*#__PURE__*/_regenerator.default.mark(getNextRefPos);
 
 var mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
+var modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/);
 
 function parseCigar(cigar) {
   return (cigar || '').split(/([MIDNSHPX=])/);
@@ -50,6 +51,7 @@ function cigarToMismatches(ops, seq, ref, qual) {
               start: roffset + j,
               type: 'mismatch',
               base: seq[soffset + j],
+              altbase: ref[roffset + j],
               length: 1
             });
           }
@@ -351,7 +353,7 @@ function getModificationPositions(mm, fseq, fstrand) {
         skips = _mod$split2.slice(1); // regexes based on parse_mm.pl from hts-specs
 
 
-    var matches = basemod.match(/([A-Z])([-+])([^,.?]+)([.?])?/);
+    var matches = basemod.match(modificationRegex);
 
     if (!matches) {
       throw new Error('bad format for MM tag');
@@ -426,7 +428,7 @@ function getModificationTypes(mm) {
         _mod$split4 = (0, _slicedToArray2.default)(_mod$split3, 1),
         basemod = _mod$split4[0];
 
-    var matches = basemod.match(/([A-Z])([-+])([^,]+)/);
+    var matches = basemod.match(modificationRegex);
 
     if (!matches) {
       throw new Error('bad format for MM tag');

package/dist/LinearPileupDisplay/model.d.ts

@@ -1,8 +1,8 @@
 /// <reference types="react" />
+import { Instance } from 'mobx-state-tree';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { Feature } from '@jbrowse/core/util';
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
-import { Instance } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
 import { LinearPileupDisplayConfigModel } from './configSchema';
 declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel) => import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -149,7 +149,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     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;
@@ -213,6 +213,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
     modificationTagMap: import("mobx").ObservableMap<string, string>;
+    featureUnderMouseVolatile: Feature | undefined;
     ready: boolean;
 } & {
     setReady(flag: boolean): void;
@@ -225,6 +226,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     }): void;
     updateModificationColorMap(uniqueModifications: string[]): void;
     updateColorTagMap(uniqueTag: string[]): void;
+    setFeatureUnderMouse(feat?: Feature): void;
 } & {
     afterAttach(): void;
     selectFeature(feature: Feature): void;
@@ -233,7 +235,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     toggleSoftClipping(): void;
     toggleMismatchAlpha(): void;
     setConfig(configuration: AnyConfigurationModel): void;
-    setSortedBy(type: string, tag?: string | undefined): void;
+    setSortedBy(type: string, tag?: string): void;
     setFilterBy(filter: {
         flagInclude: number;
         flagExclude: number;
@@ -250,6 +252,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     readonly rendererConfig: any;
     readonly featureHeightSetting: any;
     readonly mismatchAlphaSetting: any;
+    readonly featureUnderMouse: Feature | undefined;
 } & {
     readonly rendererTypeName: string;
     contextMenuItems(): {

package/dist/LinearPileupDisplay/model.js

@@ -21,21 +21,23 @@ var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers
 
 var _react = require("react");
 
+var _mobx = require("mobx");
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _copyToClipboard = _interopRequireDefault(require("copy-to-clipboard"));
+
 var _configuration = require("@jbrowse/core/configuration");
 
 var _tracks = require("@jbrowse/core/util/tracks");
 
 var _util = require("@jbrowse/core/util");
 
-var _Visibility = _interopRequireDefault(require("@material-ui/icons/Visibility"));
-
-var _Icons = require("@jbrowse/core/ui/Icons");
-
 var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
 
-var _mobxStateTree = require("mobx-state-tree");
+var _Visibility = _interopRequireDefault(require("@material-ui/icons/Visibility"));
 
-var _copyToClipboard = _interopRequireDefault(require("copy-to-clipboard"));
+var _Icons = require("@jbrowse/core/ui/Icons");
 
 var _MenuOpen = _interopRequireDefault(require("@material-ui/icons/MenuOpen"));
 
@@ -45,8 +47,6 @@ var _Palette = _interopRequireDefault(require("@material-ui/icons/Palette"));
 
 var _ClearAll = _interopRequireDefault(require("@material-ui/icons/ClearAll"));
 
-var _mobx = require("mobx");
-
 var _LinearPileupDisplayBlurb = _interopRequireDefault(require("./components/LinearPileupDisplayBlurb"));
 
 var _shared = require("../shared");
@@ -61,6 +61,7 @@ function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "functio
 
 function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || (0, _typeof2.default)(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
 
+// async
 var ColorByTagDlg = /*#__PURE__*/(0, _react.lazy)(function () {
   return Promise.resolve().then(function () {
     return _interopRequireWildcard(require('./components/ColorByTag'));
@@ -129,6 +130,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
     return {
       colorTagMap: _mobx.observable.map({}),
       modificationTagMap: _mobx.observable.map({}),
+      featureUnderMouseVolatile: undefined,
       ready: false
     };
   }).actions(function (self) {
@@ -162,7 +164,9 @@ var stateModelFactory = function stateModelFactory(configSchema) {
         });
       },
       updateColorTagMap: function updateColorTagMap(uniqueTag) {
-        // pale color scheme https://cran.r-project.org/web/packages/khroma/vignettes/tol.html e.g. "tol_light"
+        // pale color scheme
+        // https://cran.r-project.org/web/packages/khroma/vignettes/tol.html
+        // e.g. "tol_light"
         var colorPalette = ['#BBCCEE', 'pink', '#CCDDAA', '#EEEEBB', '#FFCCCC', 'lightblue', 'lightgreen', 'tan', '#CCEEFF', 'lightsalmon'];
         uniqueTag.forEach(function (value) {
           if (!self.colorTagMap.has(value)) {
@@ -171,6 +175,9 @@ var stateModelFactory = function stateModelFactory(configSchema) {
             self.colorTagMap.set(value, newColor);
           }
         });
+      },
+      setFeatureUnderMouse: function setFeatureUnderMouse(feat) {
+        self.featureUnderMouseVolatile = feat;
       }
     };
   }).actions(function (self) {
@@ -269,7 +276,75 @@ var stateModelFactory = function stateModelFactory(configSchema) {
           }, _callee, null, [[0, 28]]);
         })), {
           delay: 1000
-        }));
+        })); // autorun synchronizes featureUnderMouse with featureIdUnderMouse
+
+        (0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)( /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
+          var session, _self$featureUnderMou, featureId, sessionId, view, _ref3, feature;
+
+          return _regenerator.default.wrap(function _callee2$(_context2) {
+            while (1) {
+              switch (_context2.prev = _context2.next) {
+                case 0:
+                  session = (0, _util.getSession)(self);
+                  _context2.prev = 1;
+                  featureId = self.featureIdUnderMouse;
+
+                  if (!(((_self$featureUnderMou = self.featureUnderMouse) === null || _self$featureUnderMou === void 0 ? void 0 : _self$featureUnderMou.id()) !== featureId)) {
+                    _context2.next = 15;
+                    break;
+                  }
+
+                  if (featureId) {
+                    _context2.next = 8;
+                    break;
+                  }
+
+                  self.setFeatureUnderMouse(undefined);
+                  _context2.next = 15;
+                  break;
+
+                case 8:
+                  sessionId = (0, _tracks.getRpcSessionId)(self);
+                  view = (0, _util.getContainingView)(self);
+                  _context2.next = 12;
+                  return session.rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
+                    featureId: featureId,
+                    sessionId: sessionId,
+                    layoutId: view.id,
+                    rendererType: 'PileupRenderer'
+                  });
+
+                case 12:
+                  _ref3 = _context2.sent;
+                  feature = _ref3.feature;
+
+                  // check featureIdUnderMouse is still the same as the
+                  // feature.id that was returned e.g. that the user hasn't
+                  // moused over to a new position during the async operation
+                  // above
+                  // @ts-ignore
+                  if (self.featureIdUnderMouse === feature.uniqueId) {
+                    // @ts-ignore
+                    self.setFeatureUnderMouse(new _util.SimpleFeature(feature));
+                  }
+
+                case 15:
+                  _context2.next = 21;
+                  break;
+
+                case 17:
+                  _context2.prev = 17;
+                  _context2.t0 = _context2["catch"](1);
+                  console.error(_context2.t0);
+                  session.notify("".concat(_context2.t0), 'error');
+
+                case 21:
+                case "end":
+                  return _context2.stop();
+              }
+            }
+          }, _callee2, null, [[1, 17]]);
+        }))));
       },
       selectFeature: function selectFeature(feature) {
         var session = (0, _util.getSession)(self);
@@ -307,8 +382,8 @@ var stateModelFactory = function stateModelFactory(configSchema) {
         self.configuration = configuration;
       },
       setSortedBy: function setSortedBy(type, tag) {
-        var _ref2 = (0, _util.getContainingView)(self),
-            centerLineInfo = _ref2.centerLineInfo;
+        var _ref4 = (0, _util.getContainingView)(self),
+            centerLineInfo = _ref4.centerLineInfo;
 
         if (!centerLineInfo) {
           return;
@@ -369,6 +444,10 @@ var stateModelFactory = function stateModelFactory(configSchema) {
 
       get mismatchAlphaSetting() {
         return self.mismatchAlpha !== undefined ? self.mismatchAlpha : (0, _configuration.readConfObject)(this.rendererConfig, 'mismatchAlpha');
+      },
+
+      get featureUnderMouse() {
+        return self.featureUnderMouseVolatile;
       }
 
     };
@@ -422,10 +501,12 @@ var stateModelFactory = function stateModelFactory(configSchema) {
             sortedBy = self.sortedBy,
             colorBy = self.colorBy,
             filterBy = self.filterBy,
-            rpcDriverName = self.rpcDriverName;
+            rpcDriverName = self.rpcDriverName,
+            currBpPerPx = self.currBpPerPx,
+            ready = self.ready;
         var superProps = superRenderProps();
         return _objectSpread(_objectSpread({}, superProps), {}, {
-          notReady: superProps.notReady || !self.ready || sortedBy && self.currBpPerPx !== view.bpPerPx,
+          notReady: superProps.notReady || !ready || sortedBy && currBpPerPx !== view.bpPerPx,
           rpcDriverName: rpcDriverName,
           displayModel: self,
           sortedBy: sortedBy,
@@ -436,30 +517,30 @@ var stateModelFactory = function stateModelFactory(configSchema) {
           showSoftClip: self.showSoftClipping,
           config: self.rendererConfig,
           onFeatureClick: function onFeatureClick(_, featureId) {
-            return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-              var session, rpcManager, f, sessionId, _ref3, feature;
+            return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
+              var session, rpcManager, f, sessionId, _ref5, feature;
 
-              return _regenerator.default.wrap(function _callee2$(_context2) {
+              return _regenerator.default.wrap(function _callee3$(_context3) {
                 while (1) {
-                  switch (_context2.prev = _context2.next) {
+                  switch (_context3.prev = _context3.next) {
                     case 0:
                       session = (0, _util.getSession)(self);
                       rpcManager = session.rpcManager;
-                      _context2.prev = 2;
+                      _context3.prev = 2;
                       f = featureId || self.featureIdUnderMouse;
 
                       if (f) {
-                        _context2.next = 8;
+                        _context3.next = 8;
                         break;
                       }
 
                       self.clearFeatureSelection();
-                      _context2.next = 14;
+                      _context3.next = 14;
                       break;
 
                     case 8:
                       sessionId = (0, _tracks.getRpcSessionId)(self);
-                      _context2.next = 11;
+                      _context3.next = 11;
                       return rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
                         featureId: f,
                         sessionId: sessionId,
@@ -468,8 +549,8 @@ var stateModelFactory = function stateModelFactory(configSchema) {
                       });
 
                     case 11:
-                      _ref3 = _context2.sent;
-                      feature = _ref3.feature;
+                      _ref5 = _context3.sent;
+                      feature = _ref5.feature;
 
                       if (feature) {
                         // @ts-ignore
@@ -477,21 +558,21 @@ var stateModelFactory = function stateModelFactory(configSchema) {
                       }
 
                     case 14:
-                      _context2.next = 20;
+                      _context3.next = 20;
                       break;
 
                     case 16:
-                      _context2.prev = 16;
-                      _context2.t0 = _context2["catch"](2);
-                      console.error(_context2.t0);
-                      session.notify("".concat(_context2.t0));
+                      _context3.prev = 16;
+                      _context3.t0 = _context3["catch"](2);
+                      console.error(_context3.t0);
+                      session.notify("".concat(_context3.t0));
 
                     case 20:
                     case "end":
-                      return _context2.stop();
+                      return _context3.stop();
                   }
                 }
-              }, _callee2, null, [[2, 16]]);
+              }, _callee3, null, [[2, 16]]);
             }))();
           },
           onClick: function onClick() {
@@ -499,30 +580,30 @@ var stateModelFactory = function stateModelFactory(configSchema) {
           },
           // similar to click but opens a menu with further options
           onFeatureContextMenu: function onFeatureContextMenu(_, featureId) {
-            return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-              var session, rpcManager, f, sessionId, _ref4, feature;
+            return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
+              var session, rpcManager, f, sessionId, _ref6, feature;
 
-              return _regenerator.default.wrap(function _callee3$(_context3) {
+              return _regenerator.default.wrap(function _callee4$(_context4) {
                 while (1) {
-                  switch (_context3.prev = _context3.next) {
+                  switch (_context4.prev = _context4.next) {
                     case 0:
                       session = (0, _util.getSession)(self);
                       rpcManager = session.rpcManager;
-                      _context3.prev = 2;
+                      _context4.prev = 2;
                       f = featureId || self.featureIdUnderMouse;
 
                       if (f) {
-                        _context3.next = 8;
+                        _context4.next = 8;
                         break;
                       }
 
                       self.clearFeatureSelection();
-                      _context3.next = 14;
+                      _context4.next = 14;
                       break;
 
                     case 8:
                       sessionId = (0, _tracks.getRpcSessionId)(self);
-                      _context3.next = 11;
+                      _context4.next = 11;
                       return rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
                         featureId: f,
                         sessionId: sessionId,
@@ -531,8 +612,8 @@ var stateModelFactory = function stateModelFactory(configSchema) {
                       });
 
                     case 11:
-                      _ref4 = _context3.sent;
-                      feature = _ref4.feature;
+                      _ref6 = _context4.sent;
+                      feature = _ref6.feature;
 
                       if (feature) {
                         // @ts-ignore
@@ -540,21 +621,21 @@ var stateModelFactory = function stateModelFactory(configSchema) {
                       }
 
                     case 14:
-                      _context3.next = 20;
+                      _context4.next = 20;
                       break;
 
                     case 16:
-                      _context3.prev = 16;
-                      _context3.t0 = _context3["catch"](2);
-                      console.error(_context3.t0);
-                      session.notify("".concat(_context3.t0));
+                      _context4.prev = 16;
+                      _context4.t0 = _context4["catch"](2);
+                      console.error(_context4.t0);
+                      session.notify("".concat(_context4.t0));
 
                     case 20:
                     case "end":
-                      return _context3.stop();
+                      return _context4.stop();
                   }
                 }
-              }, _callee3, null, [[2, 16]]);
+              }, _callee4, null, [[2, 16]]);
             }))();
           }
         });
@@ -587,10 +668,10 @@ var stateModelFactory = function stateModelFactory(configSchema) {
           })), [{
             label: 'Sort by tag...',
             onClick: function onClick() {
-              (0, _util.getSession)(self).queueDialog(function (doneCallback) {
+              (0, _util.getSession)(self).queueDialog(function (handleClose) {
                 return [SortByTagDlg, {
                   model: self,
-                  handleClose: doneCallback
+                  handleClose: handleClose
                 }];
               });
             }

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -11,42 +11,63 @@ var _extends2 = _interopRequireDefault(require("@babel/runtime/helpers/extends")
 
 var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
 
+var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
+
 var _react = _interopRequireDefault(require("react"));
 
 var _mobxReact = require("mobx-react");
 
 var _pluginWiggle = require("@jbrowse/plugin-wiggle");
 
-/* eslint-disable @typescript-eslint/no-explicit-any */
+var _excluded = ["refbase", "all", "total", "ref", "-1", "1", "0"];
+
 var en = function en(n) {
   return n.toLocaleString('en-US');
 };
 
-var TooltipContents = /*#__PURE__*/_react.default.forwardRef(function (_ref, ref) {
+var toP = function toP() {
+  var s = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : 0;
+  return +(+s).toFixed(1);
+};
+
+var pct = function pct(n, total) {
+  return "".concat(toP(n / (total || 1) * 100), "%");
+};
+
+var TooltipContents = /*#__PURE__*/_react.default.forwardRef(function (_ref, reactRef) {
   var feature = _ref.feature;
   var start = feature.get('start');
   var end = feature.get('end');
   var name = feature.get('refName');
-  var info = feature.get('snpinfo');
+
+  var _ref2 = feature.get('snpinfo'),
+      refbase = _ref2.refbase,
+      all = _ref2.all,
+      total = _ref2.total,
+      ref = _ref2.ref,
+      rn1 = _ref2['-1'],
+      r1 = _ref2['1'],
+      r0 = _ref2['0'],
+      info = (0, _objectWithoutProperties2.default)(_ref2, _excluded);
+
   var loc = [name, start === end ? en(start) : "".concat(en(start), "..").concat(en(end))].filter(function (f) {
     return !!f;
   }).join(':');
-  var total = info === null || info === void 0 ? void 0 : info.total;
   return /*#__PURE__*/_react.default.createElement("div", {
-    ref: ref
-  }, /*#__PURE__*/_react.default.createElement("table", null, /*#__PURE__*/_react.default.createElement("caption", null, loc), /*#__PURE__*/_react.default.createElement("thead", null, /*#__PURE__*/_react.default.createElement("tr", null, /*#__PURE__*/_react.default.createElement("th", null, "Base"), /*#__PURE__*/_react.default.createElement("th", null, "Count"), /*#__PURE__*/_react.default.createElement("th", null, "% of Total"), /*#__PURE__*/_react.default.createElement("th", null, "Strands"), /*#__PURE__*/_react.default.createElement("th", null, "Source"))), /*#__PURE__*/_react.default.createElement("tbody", null, /*#__PURE__*/_react.default.createElement("tr", null, /*#__PURE__*/_react.default.createElement("td", null, "Total"), /*#__PURE__*/_react.default.createElement("td", null, info.total)), /*#__PURE__*/_react.default.createElement("tr", null, /*#__PURE__*/_react.default.createElement("td", null, "REF"), /*#__PURE__*/_react.default.createElement("td", null, info.ref), /*#__PURE__*/_react.default.createElement("td", null, info['-1'] ? "".concat(info['-1'], "(-)") : '', info['1'] ? "".concat(info['1'], "(+)") : ''), /*#__PURE__*/_react.default.createElement("td", null)), Object.entries(info).map(function (_ref2) {
-    var _ref3 = (0, _slicedToArray2.default)(_ref2, 2),
-        key = _ref3[0],
-        entry = _ref3[1];
+    ref: reactRef
+  }, /*#__PURE__*/_react.default.createElement("table", null, /*#__PURE__*/_react.default.createElement("caption", null, loc), /*#__PURE__*/_react.default.createElement("thead", null, /*#__PURE__*/_react.default.createElement("tr", null, /*#__PURE__*/_react.default.createElement("th", null, "Base"), /*#__PURE__*/_react.default.createElement("th", null, "Count"), /*#__PURE__*/_react.default.createElement("th", null, "% of Total"), /*#__PURE__*/_react.default.createElement("th", null, "Strands"), /*#__PURE__*/_react.default.createElement("th", null, "Source"))), /*#__PURE__*/_react.default.createElement("tbody", null, /*#__PURE__*/_react.default.createElement("tr", null, /*#__PURE__*/_react.default.createElement("td", null, "Total"), /*#__PURE__*/_react.default.createElement("td", null, all)), /*#__PURE__*/_react.default.createElement("tr", null, /*#__PURE__*/_react.default.createElement("td", null, "REF ", refbase ? "(".concat(refbase.toUpperCase(), ")") : ''), /*#__PURE__*/_react.default.createElement("td", null, ref), /*#__PURE__*/_react.default.createElement("td", null, pct(ref, all)), /*#__PURE__*/_react.default.createElement("td", null, rn1 ? "".concat(rn1, "(-)") : '', r1 ? "".concat(r1, "(+)") : ''), /*#__PURE__*/_react.default.createElement("td", null)), Object.entries(info).map(function (_ref3) {
+    var _ref4 = (0, _slicedToArray2.default)(_ref3, 2),
+        key = _ref4[0],
+        entry = _ref4[1];
 
-    return Object.entries(entry).map(function (_ref4) {
-      var _ref5 = (0, _slicedToArray2.default)(_ref4, 2),
-          base = _ref5[0],
-          score = _ref5[1];
+    return Object.entries(entry).map(function (_ref5) {
+      var _ref6 = (0, _slicedToArray2.default)(_ref5, 2),
+          base = _ref6[0],
+          score = _ref6[1];
 
       return /*#__PURE__*/_react.default.createElement("tr", {
         key: base
-      }, /*#__PURE__*/_react.default.createElement("td", null, base.toUpperCase()), /*#__PURE__*/_react.default.createElement("td", null, score.total), /*#__PURE__*/_react.default.createElement("td", null, base === 'total' || base === 'skip' ? '---' : "".concat(Math.floor(score.total / (total || score.total || 1) * 100), "%")), /*#__PURE__*/_react.default.createElement("td", null, score['-1'] ? "".concat(score['-1'], "(-)") : '', score['1'] ? "".concat(score['1'], "(+)") : ''), /*#__PURE__*/_react.default.createElement("td", null, key));
+      }, /*#__PURE__*/_react.default.createElement("td", null, base.toUpperCase()), /*#__PURE__*/_react.default.createElement("td", null, score.total), /*#__PURE__*/_react.default.createElement("td", null, base === 'total' || base === 'skip' ? '---' : pct(score.total, all)), /*#__PURE__*/_react.default.createElement("td", null, score['-1'] ? "".concat(score['-1'], "(-)") : '', score['1'] ? "".concat(score['1'], "(+)") : ''), /*#__PURE__*/_react.default.createElement("td", null, key));
     });
   }))));
 });