@jbrowse/plugin-data-management 1.7.3 → 1.7.6

package/dist/AddTrackWidget/components/ConfirmTrack.js

@@ -2,12 +2,16 @@
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
+var _typeof = require("@babel/runtime/helpers/typeof");
+
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
 
-var _react = _interopRequireDefault(require("react"));
+var _react = _interopRequireWildcard(require("react"));
 
 var _configuration = require("@jbrowse/core/configuration");
 
@@ -15,16 +19,36 @@ var _util = require("@jbrowse/core/util");
 
 var _core = require("@material-ui/core");
 
+var _Delete = _interopRequireDefault(require("@material-ui/icons/Delete"));
+
+var _Add = _interopRequireDefault(require("@material-ui/icons/Add"));
+
 var _mobxReact = require("mobx-react");
 
 var _mobxStateTree = require("mobx-state-tree");
 
 var _tracks = require("@jbrowse/core/util/tracks");
 
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
+// icons
 var useStyles = (0, _core.makeStyles)(function (theme) {
   return {
     spacing: {
       marginBottom: theme.spacing(3)
+    },
+    paper: {
+      display: 'flex',
+      flexDirection: 'column',
+      padding: theme.spacing(1)
+    },
+    spacer: {
+      height: theme.spacing(8)
+    },
+    card: {
+      marginTop: theme.spacing(1)
     }
   };
 });
@@ -35,11 +59,11 @@ function StatusMessage(_ref) {
   var trackAdapter = _ref.trackAdapter,
       trackType = _ref.trackType;
   var classes = useStyles();
-  return trackAdapter.type === 'SNPCoverageAdapter' ? /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+  return trackAdapter.type === 'SNPCoverageAdapter' ? /*#__PURE__*/_react.default.createElement(_core.Typography, {
     className: classes.spacing
-  }, "Selected ", /*#__PURE__*/_react["default"].createElement("code", null, trackType), ". Using adapter", ' ', /*#__PURE__*/_react["default"].createElement("code", null, trackAdapter.type), " with subadapter", ' ', /*#__PURE__*/_react["default"].createElement("code", null, (_trackAdapter$subadap = trackAdapter.subadapter) === null || _trackAdapter$subadap === void 0 ? void 0 : _trackAdapter$subadap.type), ". Please enter a track name and, if necessary, update the track type.") : /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+  }, "Selected ", /*#__PURE__*/_react.default.createElement("code", null, trackType), ". Using adapter", ' ', /*#__PURE__*/_react.default.createElement("code", null, trackAdapter.type), " with subadapter", ' ', /*#__PURE__*/_react.default.createElement("code", null, (_trackAdapter$subadap = trackAdapter.subadapter) === null || _trackAdapter$subadap === void 0 ? void 0 : _trackAdapter$subadap.type), ". Please enter a track name and, if necessary, update the track type.") : /*#__PURE__*/_react.default.createElement(_core.Typography, {
     className: classes.spacing
-  }, "Using adapter ", /*#__PURE__*/_react["default"].createElement("code", null, trackAdapter.type), " and guessing track type", ' ', /*#__PURE__*/_react["default"].createElement("code", null, trackType), ". Please enter a track name and, if necessary, update the track type.");
+  }, "Using adapter ", /*#__PURE__*/_react.default.createElement("code", null, trackAdapter.type), " and guessing track type", ' ', /*#__PURE__*/_react.default.createElement("code", null, trackType), ". Please enter a track name and, if necessary, update the track type.");
 }
 /**
  * categorizeAdapters takes a list of adapters and sorts their menu item elements under an appropriate ListSubheader
@@ -65,13 +89,13 @@ function categorizeAdapters(adaptersList) {
         var _adapter$adapterMetad3, _adapter$adapterMetad4, _adapter$adapterMetad5, _adapter$adapterMetad6;
 
         currentCategory = (_adapter$adapterMetad3 = adapter.adapterMetadata) === null || _adapter$adapterMetad3 === void 0 ? void 0 : _adapter$adapterMetad3.category;
-        items.push( /*#__PURE__*/_react["default"].createElement(_core.ListSubheader, {
+        items.push( /*#__PURE__*/_react.default.createElement(_core.ListSubheader, {
           key: (_adapter$adapterMetad4 = adapter.adapterMetadata) === null || _adapter$adapterMetad4 === void 0 ? void 0 : _adapter$adapterMetad4.category,
           value: (_adapter$adapterMetad5 = adapter.adapterMetadata) === null || _adapter$adapterMetad5 === void 0 ? void 0 : _adapter$adapterMetad5.category
         }, (_adapter$adapterMetad6 = adapter.adapterMetadata) === null || _adapter$adapterMetad6 === void 0 ? void 0 : _adapter$adapterMetad6.category));
       }
 
-      items.push( /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
+      items.push( /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
         key: adapter.name,
         value: adapter.name
       }, (_adapter$adapterMetad7 = adapter.adapterMetadata) !== null && _adapter$adapterMetad7 !== void 0 && _adapter$adapterMetad7.displayName ? (_adapter$adapterMetad8 = adapter.adapterMetadata) === null || _adapter$adapterMetad8 === void 0 ? void 0 : _adapter$adapterMetad8.displayName : adapter.name));
@@ -88,14 +112,113 @@ function getTrackTypes(pluginManager) {
   return pluginManager.getElementTypesInGroup('track');
 }
 
-var TrackAdapterSelector = (0, _mobxReact.observer)(function (_ref2) {
+var TextIndexingConfig = (0, _mobxReact.observer)(function (_ref2) {
   var model = _ref2.model;
   var classes = useStyles();
+
+  var _useState = (0, _react.useState)(''),
+      _useState2 = (0, _slicedToArray2.default)(_useState, 2),
+      value1 = _useState2[0],
+      setValue1 = _useState2[1];
+
+  var _useState3 = (0, _react.useState)(''),
+      _useState4 = (0, _slicedToArray2.default)(_useState3, 2),
+      value2 = _useState4[0],
+      setValue2 = _useState4[1];
+
+  var _useState5 = (0, _react.useState)(['Name', 'ID']),
+      _useState6 = (0, _slicedToArray2.default)(_useState5, 2),
+      attributes = _useState6[0],
+      setAttributes = _useState6[1];
+
+  var _useState7 = (0, _react.useState)(['CDS', 'exon']),
+      _useState8 = (0, _slicedToArray2.default)(_useState7, 2),
+      exclude = _useState8[0],
+      setExclude = _useState8[1];
+
+  var sections = [{
+    label: 'Indexing attributes',
+    values: attributes
+  }, {
+    label: 'Feature types to exclude',
+    values: exclude
+  }];
+  (0, _react.useEffect)(function () {
+    model.setTextIndexingConf({
+      attributes: attributes,
+      exclude: exclude
+    });
+  }, [model, attributes, exclude]);
+  return /*#__PURE__*/_react.default.createElement(_core.Paper, {
+    className: classes.paper
+  }, /*#__PURE__*/_react.default.createElement(_core.InputLabel, null, "Indexing configuration"), sections.map(function (section, index) {
+    return /*#__PURE__*/_react.default.createElement(_core.Card, {
+      raised: true,
+      key: section.label,
+      className: classes.card
+    }, /*#__PURE__*/_react.default.createElement(_core.CardContent, null, /*#__PURE__*/_react.default.createElement(_core.InputLabel, null, section.label), /*#__PURE__*/_react.default.createElement(_core.List, {
+      disablePadding: true
+    }, section.values.map(function (val, idx) {
+      return /*#__PURE__*/_react.default.createElement(_core.ListItem, {
+        key: idx,
+        disableGutters: true
+      }, /*#__PURE__*/_react.default.createElement(_core.TextField, {
+        value: val,
+        InputProps: {
+          endAdornment: /*#__PURE__*/_react.default.createElement(_core.InputAdornment, {
+            position: "end"
+          }, /*#__PURE__*/_react.default.createElement(_core.IconButton, {
+            color: "secondary",
+            onClick: function onClick() {
+              var newAttr = section.values.filter(function (a, i) {
+                return i !== idx;
+              });
+              index === 0 ? setAttributes(newAttr) : setExclude(newAttr);
+            }
+          }, /*#__PURE__*/_react.default.createElement(_Delete.default, null)))
+        }
+      }));
+    }), /*#__PURE__*/_react.default.createElement(_core.ListItem, {
+      disableGutters: true
+    }, /*#__PURE__*/_react.default.createElement(_core.TextField, {
+      value: index === 0 ? value1 : value2,
+      placeholder: "add new",
+      onChange: function onChange(event) {
+        index === 0 ? setValue1(event.target.value) : setValue2(event.target.value);
+      },
+      InputProps: {
+        endAdornment: /*#__PURE__*/_react.default.createElement(_core.InputAdornment, {
+          position: "end"
+        }, /*#__PURE__*/_react.default.createElement(_core.IconButton, {
+          onClick: function onClick() {
+            if (index === 0) {
+              var newAttr = attributes;
+              newAttr.push(value1);
+              setAttributes(newAttr);
+              setValue1('');
+            } else {
+              var newFeat = exclude;
+              newFeat.push(value2);
+              setExclude(newFeat);
+              setValue2('');
+            }
+          },
+          disabled: index === 0 ? value1 === '' : value2 === '',
+          color: "secondary",
+          "data-testid": "stringArrayAdd-Feat"
+        }, /*#__PURE__*/_react.default.createElement(_Add.default, null)))
+      }
+    })))));
+  }));
+});
+var TrackAdapterSelector = (0, _mobxReact.observer)(function (_ref3) {
+  var model = _ref3.model;
+  var classes = useStyles();
   var session = (0, _util.getSession)(model);
   var trackAdapter = model.trackAdapter; // prettier-ignore
 
   var adapters = getAdapterTypes((0, _mobxStateTree.getEnv)(session).pluginManager);
-  return /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+  return /*#__PURE__*/_react.default.createElement(_core.TextField, {
     className: classes.spacing,
     value: (trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) !== 'UNKNOWN' ? trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type : '',
     label: "adapterType",
@@ -119,7 +242,7 @@ var TrackAdapterSelector = (0, _mobxReact.observer)(function (_ref2) {
   }).map(function (elt) {
     var _elt$adapterMetadata3, _elt$adapterMetadata4;
 
-    return /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
+    return /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
       key: elt.name,
       value: elt.name
     }, (_elt$adapterMetadata3 = elt.adapterMetadata) !== null && _elt$adapterMetadata3 !== void 0 && _elt$adapterMetadata3.displayName ? (_elt$adapterMetadata4 = elt.adapterMetadata) === null || _elt$adapterMetadata4 === void 0 ? void 0 : _elt$adapterMetadata4.displayName : elt.name);
@@ -130,31 +253,31 @@ var TrackAdapterSelector = (0, _mobxReact.observer)(function (_ref2) {
   })));
 });
 
-function UnknownAdapterPrompt(_ref3) {
-  var model = _ref3.model;
+function UnknownAdapterPrompt(_ref4) {
+  var model = _ref4.model;
   var classes = useStyles();
-  return /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement(_core.Typography, {
     className: classes.spacing
-  }, "JBrowse was not able to guess the adapter type for this data, but it may be in the list below. If not, you can", ' ', /*#__PURE__*/_react["default"].createElement(_core.Link, {
+  }, "JBrowse was not able to guess the adapter type for this data, but it may be in the list below. If not, you can", ' ', /*#__PURE__*/_react.default.createElement(_core.Link, {
     href: "https://github.com/GMOD/jbrowse-components/releases",
     target: "_blank",
     rel: "noopener noreferrer"
-  }, "check for new releases"), ' ', "of JBrowse to see if they support this data type or", ' ', /*#__PURE__*/_react["default"].createElement(_core.Link, {
+  }, "check for new releases"), ' ', "of JBrowse to see if they support this data type or", ' ', /*#__PURE__*/_react.default.createElement(_core.Link, {
     href: "https://github.com/GMOD/jbrowse-components/issues/new",
     target: "_blank",
     rel: "noopener noreferrer"
-  }, "file an issue"), ' ', "and add a feature request for this data type."), /*#__PURE__*/_react["default"].createElement(TrackAdapterSelector, {
+  }, "file an issue"), ' ', "and add a feature request for this data type."), /*#__PURE__*/_react.default.createElement(TrackAdapterSelector, {
     model: model
   }));
 }
 
-var TrackTypeSelector = (0, _mobxReact.observer)(function (_ref4) {
-  var model = _ref4.model;
+var TrackTypeSelector = (0, _mobxReact.observer)(function (_ref5) {
+  var model = _ref5.model;
   var classes = useStyles();
   var session = (0, _util.getSession)(model);
   var trackType = model.trackType;
   var trackTypes = getTrackTypes((0, _mobxStateTree.getEnv)(session).pluginManager);
-  return /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+  return /*#__PURE__*/_react.default.createElement(_core.TextField, {
     className: classes.spacing,
     value: trackType,
     label: "trackType",
@@ -170,19 +293,19 @@ var TrackTypeSelector = (0, _mobxReact.observer)(function (_ref4) {
         'data-testid': 'trackTypeSelect'
       }
     }
-  }, trackTypes.map(function (_ref5) {
-    var name = _ref5.name;
-    return /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
+  }, trackTypes.map(function (_ref6) {
+    var name = _ref6.name;
+    return /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
       key: name,
       value: name
     }, name);
   }));
 });
-var TrackAssemblySelector = (0, _mobxReact.observer)(function (_ref6) {
-  var model = _ref6.model;
+var TrackAssemblySelector = (0, _mobxReact.observer)(function (_ref7) {
+  var model = _ref7.model;
   var session = (0, _util.getSession)(model);
   var assembly = model.assembly;
-  return /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+  return /*#__PURE__*/_react.default.createElement(_core.TextField, {
     value: assembly,
     label: "assemblyName",
     helperText: "Assembly to which the track will be added",
@@ -200,16 +323,22 @@ var TrackAssemblySelector = (0, _mobxReact.observer)(function (_ref6) {
   }, session.assemblies.map(function (conf) {
     return (0, _configuration.readConfObject)(conf, 'name');
   }).map(function (name) {
-    return /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
+    return /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
       key: name,
       value: name
     }, name);
   }));
 });
 
-function ConfirmTrack(_ref7) {
-  var model = _ref7.model;
+function ConfirmTrack(_ref8) {
+  var model = _ref8.model;
   var classes = useStyles();
+
+  var _useState9 = (0, _react.useState)(true),
+      _useState10 = (0, _slicedToArray2.default)(_useState9, 2),
+      check = _useState10[0],
+      setCheck = _useState10[1];
+
   var trackName = model.trackName,
       trackAdapter = model.trackAdapter,
       trackType = model.trackType,
@@ -217,13 +346,13 @@ function ConfirmTrack(_ref7) {
       adapterHint = model.adapterHint;
 
   if (model.unsupported) {
-    return /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+    return /*#__PURE__*/_react.default.createElement(_core.Typography, {
       className: classes.spacing
-    }, "This version of JBrowse cannot display data of this type. It is possible, however, that there is a newer version that can display them. You can", ' ', /*#__PURE__*/_react["default"].createElement(_core.Link, {
+    }, "This version of JBrowse cannot display data of this type. It is possible, however, that there is a newer version that can display them. You can", ' ', /*#__PURE__*/_react.default.createElement(_core.Link, {
       href: "https://github.com/GMOD/jbrowse-components/releases",
       target: "_blank",
       rel: "noopener noreferrer"
-    }, "check for new releases"), ' ', "of JBrowse or", ' ', /*#__PURE__*/_react["default"].createElement(_core.Link, {
+    }, "check for new releases"), ' ', "of JBrowse or", ' ', /*#__PURE__*/_react.default.createElement(_core.Link, {
       href: "https://github.com/GMOD/jbrowse-components/issues/new",
       target: "_blank",
       rel: "noopener noreferrer"
@@ -231,7 +360,7 @@ function ConfirmTrack(_ref7) {
   }
 
   if ((trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) === _tracks.UNKNOWN) {
-    return /*#__PURE__*/_react["default"].createElement(UnknownAdapterPrompt, {
+    return /*#__PURE__*/_react.default.createElement(UnknownAdapterPrompt, {
       model: model
     });
   }
@@ -241,17 +370,18 @@ function ConfirmTrack(_ref7) {
   }
 
   if (!(trackAdapter !== null && trackAdapter !== void 0 && trackAdapter.type)) {
-    return /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Could not recognize this data type.");
+    return /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Could not recognize this data type.");
   }
 
-  return /*#__PURE__*/_react["default"].createElement("div", null, trackAdapter ? /*#__PURE__*/_react["default"].createElement(StatusMessage, {
+  var supportedForIndexing = (0, _util.supportedIndexingAdapters)(trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type);
+  return /*#__PURE__*/_react.default.createElement("div", null, trackAdapter ? /*#__PURE__*/_react.default.createElement(StatusMessage, {
     trackAdapter: trackAdapter,
     trackType: trackType
-  }) : null, warningMessage ? /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+  }) : null, warningMessage ? /*#__PURE__*/_react.default.createElement(_core.Typography, {
     style: {
       color: 'orange'
     }
-  }, warningMessage) : null, /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+  }, warningMessage) : null, /*#__PURE__*/_react.default.createElement(_core.TextField, {
     className: classes.spacing,
     label: "trackName",
     helperText: "A name for this track",
@@ -263,15 +393,26 @@ function ConfirmTrack(_ref7) {
     inputProps: {
       'data-testid': 'trackNameInput'
     }
-  }), /*#__PURE__*/_react["default"].createElement(TrackAdapterSelector, {
+  }), /*#__PURE__*/_react.default.createElement(TrackAdapterSelector, {
     model: model
-  }), /*#__PURE__*/_react["default"].createElement(TrackTypeSelector, {
+  }), /*#__PURE__*/_react.default.createElement(TrackTypeSelector, {
     model: model
-  }), /*#__PURE__*/_react["default"].createElement(TrackAssemblySelector, {
+  }), /*#__PURE__*/_react.default.createElement(TrackAssemblySelector, {
     model: model
-  }));
+  }), _util.isElectron && supportedForIndexing && /*#__PURE__*/_react.default.createElement(_core.FormControl, null, /*#__PURE__*/_react.default.createElement(_core.FormControlLabel, {
+    label: 'Index track for text searching?',
+    control: /*#__PURE__*/_react.default.createElement(_core.Checkbox, {
+      checked: check,
+      onChange: function onChange(e) {
+        setCheck(e.target.checked);
+        model.setTextIndexTrack(e.target.checked);
+      }
+    })
+  })), _util.isElectron && check && supportedForIndexing ? /*#__PURE__*/_react.default.createElement(TextIndexingConfig, {
+    model: model
+  }) : null);
 }
 
 var _default = (0, _mobxReact.observer)(ConfirmTrack);
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/AddTrackWidget/components/TrackSourceSelect.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _react = _interopRequireDefault(require("react"));
 
@@ -34,18 +34,18 @@ function TrackSourceSelect(_ref) {
   var model = _ref.model;
   var classes = useStyles();
   var rootModel = (0, _mobxStateTree.getRoot)(model);
-  return /*#__PURE__*/_react["default"].createElement(_core.Paper, {
+  return /*#__PURE__*/_react.default.createElement(_core.Paper, {
     className: classes.paper
-  }, /*#__PURE__*/_react["default"].createElement(_ui.FileSelector, {
+  }, /*#__PURE__*/_react.default.createElement(_ui.FileSelector, {
     name: "Main file",
     description: "",
     location: model.trackData,
     setLocation: model.setTrackData,
     setName: model.setTrackName,
     rootModel: rootModel
-  }), /*#__PURE__*/_react["default"].createElement("div", {
+  }), /*#__PURE__*/_react.default.createElement("div", {
     className: classes.spacer
-  }), /*#__PURE__*/_react["default"].createElement(_ui.FileSelector, {
+  }), /*#__PURE__*/_react.default.createElement(_ui.FileSelector, {
     name: "Index file",
     description: "(Optional) The URL of the index file is automatically inferred from the URL of the main file if it is not supplied.",
     location: model.indexTrackData,
@@ -57,4 +57,4 @@ function TrackSourceSelect(_ref) {
 
 var _default = (0, _mobxReact.observer)(TrackSourceSelect);
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/AddTrackWidget/index.js

@@ -9,7 +9,7 @@ exports.configSchema = void 0;
 Object.defineProperty(exports, "stateModelFactory", {
   enumerable: true,
   get: function get() {
-    return _model["default"];
+    return _model.default;
   }
 });
 

package/dist/AddTrackWidget/index.test.js

@@ -36,19 +36,19 @@ var _pluginVariants = _interopRequireDefault(require("@jbrowse/plugin-variants")
 
 var _pluginHic = _interopRequireDefault(require("@jbrowse/plugin-hic"));
 
-function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2["default"])(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2["default"])(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2["default"])(this, result); }; }
+function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
 
 function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
 
 function standardInitializer() {
-  var pluginManager = new _PluginManager["default"]([new FakeViewPlugin(), new _pluginAlignments["default"](), new _pluginSvg["default"](), new _pluginVariants["default"](), new _pluginHic["default"]()]);
+  var pluginManager = new _PluginManager.default([new FakeViewPlugin(), new _pluginAlignments.default(), new _pluginSvg.default(), new _pluginVariants.default(), new _pluginHic.default()]);
   pluginManager.createPluggableElements();
   pluginManager.configure();
 
   var SessionModel = _mobxStateTree.types.model({
     view: FakeViewModel,
-    widget: (0, _model["default"])(pluginManager)
-  })["volatile"](function () {
+    widget: (0, _model.default)(pluginManager)
+  }).volatile(function () {
     return {
       rpcManager: {},
       configuration: {}
@@ -89,40 +89,40 @@ var FakeViewModel = _mobxStateTree.types.model('FakeView', {
 
 
 var FakeViewPlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2["default"])(FakeViewPlugin, _Plugin);
+  (0, _inherits2.default)(FakeViewPlugin, _Plugin);
 
   var _super = _createSuper(FakeViewPlugin);
 
   function FakeViewPlugin() {
     var _this;
 
-    (0, _classCallCheck2["default"])(this, FakeViewPlugin);
+    (0, _classCallCheck2.default)(this, FakeViewPlugin);
 
     for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
       args[_key] = arguments[_key];
     }
 
     _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "name", 'FakeViewPlugin');
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'FakeViewPlugin');
     return _this;
   }
 
-  (0, _createClass2["default"])(FakeViewPlugin, [{
+  (0, _createClass2.default)(FakeViewPlugin, [{
     key: "install",
     value: function install(pluginManager) {
       pluginManager.addViewType(function () {
-        return new _ViewType["default"]({
+        return new _ViewType.default({
           name: 'FakeView',
           stateModel: FakeViewModel,
           ReactComponent: function ReactComponent() {
-            return /*#__PURE__*/_react["default"].createElement("div", null, "Hello world");
+            return /*#__PURE__*/_react.default.createElement("div", null, "Hello world");
           }
         });
       });
     }
   }]);
   return FakeViewPlugin;
-}(_Plugin2["default"]);
+}(_Plugin2.default);
 
 describe('tests on an LGV type system with view.assemblyNames, using URL', function () {
   var session;
@@ -180,13 +180,13 @@ describe('tests on an LGV type system with view.assemblyNames, using URL', funct
 describe('tests on an view without view.assemblyNames', function () {
   var session;
   beforeEach(function () {
-    var pluginManager = new _PluginManager["default"]([new FakeViewPlugin()]);
+    var pluginManager = new _PluginManager.default([new FakeViewPlugin()]);
     pluginManager.createPluggableElements();
     pluginManager.configure();
 
     var SessionModel = _mobxStateTree.types.model({
       view: FakeViewModel,
-      widget: (0, _model["default"])(pluginManager)
+      widget: (0, _model.default)(pluginManager)
     }); // no assemblyNames on the view, just in case some view does not implement
     // view.assemblyNames (it is just a convenience)
 

package/dist/AddTrackWidget/model.d.ts

@@ -1,6 +1,10 @@
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { FileLocation } from '@jbrowse/core/util/types';
+interface IndexingAttr {
+    attributes: string[];
+    exclude: string[];
+}
 export default function f(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<"AddTrackWidget">;
@@ -13,9 +17,13 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
     altTrackName: string;
     altTrackType: string;
     adapterHint: string;
+    textIndexTrack: boolean;
+    textIndexingConf: IndexingAttr | undefined;
 } & {
     setAdapterHint(obj: string): void;
     setTrackSource(str: string): void;
+    setTextIndexingConf(conf: IndexingAttr): void;
+    setTextIndexTrack(flag: boolean): void;
     setTrackData(obj: FileLocation): void;
     setIndexTrackData(obj: FileLocation): void;
     setAssembly(str: string): void;
@@ -40,3 +48,4 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export declare type AddTrackStateModel = ReturnType<typeof f>;
 export declare type AddTrackModel = Instance<AddTrackStateModel>;
+export {};

package/dist/AddTrackWidget/model.js

@@ -3,7 +3,7 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = f;
+exports.default = f;
 
 var _mobxStateTree = require("mobx-state-tree");
 
@@ -27,7 +27,7 @@ function f(pluginManager) {
     id: _mst.ElementId,
     type: _mobxStateTree.types.literal('AddTrackWidget'),
     view: _mobxStateTree.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel'))
-  })["volatile"](function () {
+  }).volatile(function () {
     return {
       trackSource: 'fromFile',
       trackData: undefined,
@@ -36,7 +36,9 @@ function f(pluginManager) {
       altAssemblyName: '',
       altTrackName: '',
       altTrackType: '',
-      adapterHint: ''
+      adapterHint: '',
+      textIndexTrack: true,
+      textIndexingConf: undefined
     };
   }).actions(function (self) {
     return {
@@ -46,6 +48,12 @@ function f(pluginManager) {
       setTrackSource: function setTrackSource(str) {
         self.trackSource = str;
       },
+      setTextIndexingConf: function setTextIndexingConf(conf) {
+        self.textIndexingConf = conf;
+      },
+      setTextIndexTrack: function setTextIndexTrack(flag) {
+        self.textIndexTrack = flag;
+      },
       setTrackData: function setTrackData(obj) {
         self.trackData = obj;
       },
@@ -69,6 +77,8 @@ function f(pluginManager) {
         self.adapterHint = '';
         self.indexTrackData = undefined;
         self.trackData = undefined;
+        self.textIndexingConf = undefined;
+        self.textIndexTrack = false;
       }
     };
   }).views(function (self) {