@jbrowse/plugin-alignments 1.7.0 → 1.7.4

package/dist/LinearPileupDisplay/model.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 _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 
@@ -55,11 +55,11 @@ var _excluded = ["uniqueId"];
 
 function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
 
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
 
 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; }
+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; }
 
 var ColorByTagDlg = /*#__PURE__*/(0, _react.lazy)(function () {
   return Promise.resolve().then(function () {
@@ -100,10 +100,10 @@ var stateModelFactory = function stateModelFactory(configSchema) {
     configuration: (0, _configuration.ConfigurationReference)(configSchema),
     showSoftClipping: false,
     featureHeight: _mobxStateTree.types.maybe(_mobxStateTree.types.number),
-    noSpacing: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
-    fadeLikelihood: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
+    noSpacing: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
+    fadeLikelihood: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
     trackMaxHeight: _mobxStateTree.types.maybe(_mobxStateTree.types.number),
-    mismatchAlpha: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
+    mismatchAlpha: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
     sortedBy: _mobxStateTree.types.maybe(_mobxStateTree.types.model({
       type: _mobxStateTree.types.string,
       pos: _mobxStateTree.types.number,
@@ -125,7 +125,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
         value: _mobxStateTree.types.string
       }))
     }), {})
-  }))["volatile"](function () {
+  })).volatile(function () {
     return {
       colorTagMap: _mobx.observable.map({}),
       modificationTagMap: _mobx.observable.map({}),
@@ -155,7 +155,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
         var colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
         uniqueModifications.forEach(function (value) {
           if (!self.modificationTagMap.has(value)) {
-            var totalKeys = (0, _toConsumableArray2["default"])(self.modificationTagMap.keys()).length;
+            var totalKeys = (0, _toConsumableArray2.default)(self.modificationTagMap.keys()).length;
             var newColor = colorPalette[totalKeys];
             self.modificationTagMap.set(value, newColor);
           }
@@ -166,7 +166,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
         var colorPalette = ['#BBCCEE', 'pink', '#CCDDAA', '#EEEEBB', '#FFCCCC', 'lightblue', 'lightgreen', 'tan', '#CCEEFF', 'lightsalmon'];
         uniqueTag.forEach(function (value) {
           if (!self.colorTagMap.has(value)) {
-            var totalKeys = (0, _toConsumableArray2["default"])(self.colorTagMap.keys()).length;
+            var totalKeys = (0, _toConsumableArray2.default)(self.colorTagMap.keys()).length;
             var newColor = colorPalette[totalKeys];
             self.colorTagMap.set(value, newColor);
           }
@@ -176,10 +176,10 @@ var stateModelFactory = function stateModelFactory(configSchema) {
   }).actions(function (self) {
     return {
       afterAttach: function afterAttach() {
-        (0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)( /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        (0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)( /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
           var _getSession, rpcManager, sortedBy, colorBy, view, uniqueTagSet, uniqueModificationsSet, pos, refName, assemblyName, region;
 
-          return _regenerator["default"].wrap(function _callee$(_context) {
+          return _regenerator.default.wrap(function _callee$(_context) {
             while (1) {
               switch (_context.prev = _context.next) {
                 case 0:
@@ -287,10 +287,10 @@ var stateModelFactory = function stateModelFactory(configSchema) {
       copyFeatureToClipboard: function copyFeatureToClipboard(feature) {
         var _feature$toJSON = feature.toJSON(),
             uniqueId = _feature$toJSON.uniqueId,
-            rest = (0, _objectWithoutProperties2["default"])(_feature$toJSON, _excluded);
+            rest = (0, _objectWithoutProperties2.default)(_feature$toJSON, _excluded);
 
         var session = (0, _util.getSession)(self);
-        (0, _copyToClipboard["default"])(JSON.stringify(rest, null, 4));
+        (0, _copyToClipboard.default)(JSON.stringify(rest, null, 4));
         session.notify('Copied to clipboard', 'success');
       },
       toggleSoftClipping: function toggleSoftClipping() {
@@ -387,7 +387,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
         var feat = self.contextMenuFeature;
         var contextMenuItems = feat ? [{
           label: 'Open feature details',
-          icon: _MenuOpen["default"],
+          icon: _MenuOpen.default,
           onClick: function onClick() {
             self.clearFeatureSelection();
 
@@ -408,7 +408,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
       },
 
       get DisplayBlurb() {
-        return _LinearPileupDisplayBlurb["default"];
+        return _LinearPileupDisplayBlurb.default;
       },
 
       renderProps: function renderProps() {
@@ -434,9 +434,9 @@ var stateModelFactory = function stateModelFactory(configSchema) {
         });
       },
       trackMenuItems: function trackMenuItems() {
-        return [].concat((0, _toConsumableArray2["default"])(superTrackMenuItems()), [{
+        return [].concat((0, _toConsumableArray2.default)(superTrackMenuItems()), [{
           label: 'Show soft clipping',
-          icon: _Visibility["default"],
+          icon: _Visibility.default,
           type: 'checkbox',
           checked: self.showSoftClipping,
           onClick: function onClick() {
@@ -449,9 +449,9 @@ var stateModelFactory = function stateModelFactory(configSchema) {
           }
         }, {
           label: 'Sort by',
-          icon: _Sort["default"],
+          icon: _Sort.default,
           disabled: self.showSoftClipping,
-          subMenu: [].concat((0, _toConsumableArray2["default"])(['Start location', 'Read strand', 'Base pair'].map(function (option) {
+          subMenu: [].concat((0, _toConsumableArray2.default)(['Start location', 'Read strand', 'Base pair'].map(function (option) {
             return {
               label: option,
               onClick: function onClick() {
@@ -476,7 +476,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
           }])
         }, {
           label: 'Color scheme',
-          icon: _Palette["default"],
+          icon: _Palette.default,
           subMenu: [{
             label: 'Normal',
             onClick: function onClick() {
@@ -556,7 +556,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
           }]
         }, {
           label: 'Filter by',
-          icon: _ClearAll["default"],
+          icon: _ClearAll.default,
           onClick: function onClick() {
             (0, _util.getSession)(self).queueDialog(function (doneCallback) {
               return [FilterByTagDlg, {
@@ -599,4 +599,4 @@ var stateModelFactory = function stateModelFactory(configSchema) {
 };
 
 var _default = stateModelFactory;
-exports["default"] = _default;
+exports.default = _default;

package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts

@@ -1,10 +1,10 @@
-/// <reference types="react" />
-declare type Coord = [number, number];
-declare const SNPCoverageTooltip: (props: {
-    model: any;
-    height: number;
-    offsetMouseCoord: Coord;
-    clientMouseCoord: Coord;
-    clientRect?: DOMRect;
-}) => JSX.Element | null;
-export default SNPCoverageTooltip;
+/// <reference types="react" />
+declare type Coord = [number, number];
+declare const SNPCoverageTooltip: (props: {
+    model: any;
+    height: number;
+    offsetMouseCoord: Coord;
+    clientMouseCoord: Coord;
+    clientRect?: DOMRect;
+}) => JSX.Element | null;
+export default SNPCoverageTooltip;

package/dist/LinearSNPCoverageDisplay/components/Tooltip.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 _extends2 = _interopRequireDefault(require("@babel/runtime/helpers/extends"));
 
@@ -22,7 +22,7 @@ var en = function en(n) {
   return n.toLocaleString('en-US');
 };
 
-var TooltipContents = /*#__PURE__*/_react["default"].forwardRef(function (_ref, ref) {
+var TooltipContents = /*#__PURE__*/_react.default.forwardRef(function (_ref, ref) {
   var feature = _ref.feature;
   var start = feature.get('start');
   var end = feature.get('end');
@@ -32,22 +32,22 @@ var TooltipContents = /*#__PURE__*/_react["default"].forwardRef(function (_ref,
     return !!f;
   }).join(':');
   var total = info === null || info === void 0 ? void 0 : info.total;
-  return /*#__PURE__*/_react["default"].createElement("div", {
+  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, total), /*#__PURE__*/_react["default"].createElement("td", null)), Object.entries(info).map(function (_ref2) {
-    var _ref3 = (0, _slicedToArray2["default"])(_ref2, 2),
+  }, /*#__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, total), /*#__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];
 
     return Object.entries(entry).map(function (_ref4) {
-      var _ref5 = (0, _slicedToArray2["default"])(_ref4, 2),
+      var _ref5 = (0, _slicedToArray2.default)(_ref4, 2),
           base = _ref5[0],
           score = _ref5[1];
 
       var strands = score.strands;
-      return /*#__PURE__*/_react["default"].createElement("tr", {
+      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, strands['-1'] ? "".concat(strands['-1'], "(-)") : '', strands['1'] ? "".concat(strands['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' ? '---' : "".concat(Math.floor(score.total / (total || score.total || 1) * 100), "%")), /*#__PURE__*/_react.default.createElement("td", null, strands['-1'] ? "".concat(strands['-1'], "(-)") : '', strands['1'] ? "".concat(strands['1'], "(+)") : ''), /*#__PURE__*/_react.default.createElement("td", null, key));
     });
   }))));
 });
@@ -55,9 +55,9 @@ var TooltipContents = /*#__PURE__*/_react["default"].forwardRef(function (_ref,
 var SNPCoverageTooltip = (0, _mobxReact.observer)(function (props) {
   var model = props.model;
   var feat = model.featureUnderMouse;
-  return feat && feat.get('type') === 'skip' ? null : /*#__PURE__*/_react["default"].createElement(_pluginWiggle.Tooltip, (0, _extends2["default"])({
+  return feat && feat.get('type') === 'skip' ? null : /*#__PURE__*/_react.default.createElement(_pluginWiggle.Tooltip, (0, _extends2.default)({
     TooltipContents: TooltipContents
   }, props));
 });
 var _default = SNPCoverageTooltip;
-exports["default"] = _default;
+exports.default = _default;

package/dist/LinearSNPCoverageDisplay/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-export default function register(pluginManager: PluginManager): void;
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function register(pluginManager: PluginManager): void;

package/dist/LinearSNPCoverageDisplay/index.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = register;
+exports.default = register;
 
 var _configSchema = _interopRequireDefault(require("./models/configSchema"));
 
@@ -17,11 +17,11 @@ var _DisplayType = _interopRequireDefault(require("@jbrowse/core/pluggableElemen
 
 function register(pluginManager) {
   pluginManager.addDisplayType(function () {
-    var configSchema = (0, _configSchema["default"])(pluginManager);
-    return new _DisplayType["default"]({
+    var configSchema = (0, _configSchema.default)(pluginManager);
+    return new _DisplayType.default({
       name: 'LinearSNPCoverageDisplay',
       configSchema: configSchema,
-      stateModel: (0, _model["default"])(pluginManager, configSchema),
+      stateModel: (0, _model.default)(pluginManager, configSchema),
       trackType: 'AlignmentsTrack',
       viewType: 'LinearGenomeView',
       ReactComponent: _pluginWiggle.LinearWiggleDisplayReactComponent

package/dist/LinearSNPCoverageDisplay/models/configSchema.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/dist/LinearSNPCoverageDisplay/models/configSchema.js

@@ -3,7 +3,7 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = SNPCoverageConfigFactory;
+exports.default = SNPCoverageConfigFactory;
 
 var _configuration = require("@jbrowse/core/configuration");
 

package/dist/LinearSNPCoverageDisplay/models/configSchema.test.js

@@ -20,7 +20,7 @@ var _SNPCoverageRenderer = _interopRequireDefault(require("../../SNPCoverageRend
 
 var _configSchema = _interopRequireDefault(require("./configSchema"));
 
-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; } }
 
@@ -33,26 +33,26 @@ afterEach(function () {
 }); // change renderer
 
 var SNPCoverageRendererPlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2["default"])(SNPCoverageRendererPlugin, _Plugin);
+  (0, _inherits2.default)(SNPCoverageRendererPlugin, _Plugin);
 
   var _super = _createSuper(SNPCoverageRendererPlugin);
 
   function SNPCoverageRendererPlugin() {
-    (0, _classCallCheck2["default"])(this, SNPCoverageRendererPlugin);
+    (0, _classCallCheck2.default)(this, SNPCoverageRendererPlugin);
     return _super.apply(this, arguments);
   }
 
-  (0, _createClass2["default"])(SNPCoverageRendererPlugin, [{
+  (0, _createClass2.default)(SNPCoverageRendererPlugin, [{
     key: "install",
     value: function install(pluginManager) {
-      (0, _SNPCoverageRenderer["default"])(pluginManager);
+      (0, _SNPCoverageRenderer.default)(pluginManager);
     }
   }]);
   return SNPCoverageRendererPlugin;
-}(_Plugin2["default"]);
+}(_Plugin2.default);
 
 test('has a type attr', function () {
-  var configSchema = (0, _configSchema["default"])(new _PluginManager["default"]([new SNPCoverageRendererPlugin()]).createPluggableElements().configure());
+  var configSchema = (0, _configSchema.default)(new _PluginManager.default([new SNPCoverageRendererPlugin()]).createPluggableElements().configure());
   var config = configSchema.create({
     type: 'LinearSNPCoverageDisplay',
     displayId: 'display1',