@jbrowse/plugin-linear-genome-view 1.7.11 → 2.0.0

package/dist/LinearGenomeView/components/ZoomControls.js

@@ -1,92 +1,77 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
 });
-exports.default = void 0;
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _react = _interopRequireWildcard(require("react"));
-
-var _mobxReact = require("mobx-react");
-
-var _IconButton = _interopRequireDefault(require("@material-ui/core/IconButton"));
-
-var _Slider = _interopRequireDefault(require("@material-ui/core/Slider"));
-
-var _styles = require("@material-ui/core/styles");
-
-var _ZoomIn = _interopRequireDefault(require("@material-ui/icons/ZoomIn"));
-
-var _ZoomOut = _interopRequireDefault(require("@material-ui/icons/ZoomOut"));
-
-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; }
-
-var useStyles = (0, _styles.makeStyles)({
-  container: {
-    display: 'flex',
-    flexDirection: 'row',
-    alignItems: 'center'
-  },
-  slider: {
-    width: 70
-  }
-});
-
-function ZoomControls(_ref) {
-  var model = _ref.model;
-  var classes = useStyles();
-  var maxBpPerPx = model.maxBpPerPx,
-      minBpPerPx = model.minBpPerPx,
-      bpPerPx = model.bpPerPx,
-      scaleFactor = model.scaleFactor;
-
-  var _useState = (0, _react.useState)(-Math.log2(bpPerPx) * 100),
-      _useState2 = (0, _slicedToArray2.default)(_useState, 2),
-      value = _useState2[0],
-      setValue = _useState2[1];
-
-  (0, _react.useEffect)(function () {
-    setValue(-Math.log2(bpPerPx) * 100);
-  }, [setValue, bpPerPx]);
-  return /*#__PURE__*/_react.default.createElement("div", {
-    className: classes.container
-  }, /*#__PURE__*/_react.default.createElement(_IconButton.default, {
-    "data-testid": "zoom_out",
-    onClick: function onClick() {
-      model.zoom(bpPerPx * 2);
-    },
-    disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1,
-    color: "secondary"
-  }, /*#__PURE__*/_react.default.createElement(_ZoomOut.default, null)), /*#__PURE__*/_react.default.createElement(_Slider.default, {
-    className: classes.slider,
-    value: value,
-    min: -Math.log2(maxBpPerPx) * 100,
-    max: -Math.log2(minBpPerPx) * 100,
-    onChange: function onChange(_, val) {
-      return setValue(val);
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
+    }
+    return ar;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var react_1 = __importStar(require("react"));
+var mobx_react_1 = require("mobx-react");
+var material_1 = require("@mui/material");
+var mui_1 = require("tss-react/mui");
+var ZoomIn_1 = __importDefault(require("@mui/icons-material/ZoomIn"));
+var ZoomOut_1 = __importDefault(require("@mui/icons-material/ZoomOut"));
+var useStyles = (0, mui_1.makeStyles)()({
+    container: {
+        display: 'flex',
+        flexDirection: 'row',
+        alignItems: 'center',
     },
-    onChangeCommitted: function onChangeCommitted() {
-      return model.zoomTo(Math.pow(2, -value / 100));
+    slider: {
+        width: 70,
     },
-    disabled: scaleFactor !== 1
-  }), /*#__PURE__*/_react.default.createElement(_IconButton.default, {
-    "data-testid": "zoom_in",
-    onClick: function onClick() {
-      model.zoom(model.bpPerPx / 2);
-    },
-    disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1,
-    color: "secondary"
-  }, /*#__PURE__*/_react.default.createElement(_ZoomIn.default, null)));
+});
+function ZoomControls(_a) {
+    var model = _a.model;
+    var classes = useStyles().classes;
+    var maxBpPerPx = model.maxBpPerPx, minBpPerPx = model.minBpPerPx, bpPerPx = model.bpPerPx, scaleFactor = model.scaleFactor;
+    var _b = __read((0, react_1.useState)(-Math.log2(bpPerPx) * 100), 2), value = _b[0], setValue = _b[1];
+    (0, react_1.useEffect)(function () {
+        setValue(-Math.log2(bpPerPx) * 100);
+    }, [setValue, bpPerPx]);
+    return (react_1.default.createElement("div", { className: classes.container },
+        react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_out", onClick: function () { return model.zoom(bpPerPx * 2); }, disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1, color: "secondary", size: "large" },
+            react_1.default.createElement(ZoomOut_1.default, null)),
+        react_1.default.createElement(material_1.Slider, { size: "small", className: classes.slider, value: value, min: -Math.log2(maxBpPerPx) * 100, max: -Math.log2(minBpPerPx) * 100, onChange: function (_, val) { return setValue(val); }, onChangeCommitted: function () { return model.zoomTo(Math.pow(2, (-value / 100))); }, disabled: scaleFactor !== 1 }),
+        react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_in", onClick: function () { return model.zoom(model.bpPerPx / 2); }, disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1, color: "secondary", size: "large" },
+            react_1.default.createElement(ZoomIn_1.default, null))));
 }
-
-var _default = (0, _mobxReact.observer)(ZoomControls);
-
-exports.default = _default;
+exports.default = (0, mobx_react_1.observer)(ZoomControls);
+//# sourceMappingURL=ZoomControls.js.map

package/dist/LinearGenomeView/components/ZoomControls.js.map

@@ -0,0 +1 @@
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package/dist/LinearGenomeView/components/util.js

@@ -1,75 +1,98 @@
 "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] : [];
-  var cb = arguments.length > 1 ? arguments[1] : undefined;
-  return results.filter(function (elt, idx, self) {
-    return idx === self.findIndex(function (t) {
-      return cb(t) === cb(elt);
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
-  });
-}
-
-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');
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
             }
-
-            _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();
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+var __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
+    }
+    return ar;
+};
+var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
         }
-      }
-    }, _callee);
-  }));
-  return _fetchResults.apply(this, arguments);
-}
+    }
+    return to.concat(ar || Array.prototype.slice.call(from));
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.fetchResults = exports.dedupe = void 0;
+var BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
+function dedupe(results, cb) {
+    if (results === void 0) { results = []; }
+    return results.filter(function (elt, idx, self) { return idx === self.findIndex(function (t) { return cb(t) === cb(elt); }); });
+}
+exports.dedupe = dedupe;
+function fetchResults(_a) {
+    var _b;
+    var queryString = _a.queryString, searchType = _a.searchType, searchScope = _a.searchScope, rankSearchResults = _a.rankSearchResults, textSearchManager = _a.textSearchManager, assembly = _a.assembly;
+    return __awaiter(this, void 0, void 0, function () {
+        var textSearchResults, refNameResults;
+        return __generator(this, function (_c) {
+            switch (_c.label) {
+                case 0:
+                    if (!textSearchManager) {
+                        console.warn('No text search manager');
+                    }
+                    return [4 /*yield*/, (textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
+                            queryString: queryString,
+                            searchType: searchType,
+                        }, searchScope, rankSearchResults))];
+                case 1:
+                    textSearchResults = _c.sent();
+                    refNameResults = (_b = assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) === null || _b === void 0 ? void 0 : _b.filter(function (ref) { return ref.toLowerCase().startsWith(queryString.toLowerCase()); }).slice(0, 10).map(function (r) { return new BaseResults_1.default({ label: r }); });
+                    return [2 /*return*/, dedupe(__spreadArray(__spreadArray([], __read((refNameResults || [])), false), __read((textSearchResults || [])), false), function (elt) { return elt.getId(); })];
+            }
+        });
+    });
+}
+exports.fetchResults = fetchResults;
+//# sourceMappingURL=util.js.map

package/dist/LinearGenomeView/components/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/util.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAEA,qFAA6D;AAI7D,SAAgB,MAAM,CACpB,OAA0B,EAC1B,EAAkC;IADlC,wBAAA,EAAA,YAA0B;IAG1B,OAAO,OAAO,CAAC,MAAM,CACnB,UAAC,GAAG,EAAE,GAAG,EAAE,IAAI,IAAK,OAAA,GAAG,KAAK,IAAI,CAAC,SAAS,CAAC,UAAA,CAAC,IAAI,OAAA,EAAE,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC,EAAjB,CAAiB,CAAC,EAA9C,CAA8C,CACnE,CAAA;AACH,CAAC;AAPD,wBAOC;AAED,SAAsB,YAAY,CAAC,EAclC;;QAbC,WAAW,iBAAA,EACX,UAAU,gBAAA,EACV,WAAW,iBAAA,EACX,iBAAiB,uBAAA,EACjB,iBAAiB,uBAAA,EACjB,QAAQ,cAAA;;;;;;oBASR,IAAI,CAAC,iBAAiB,EAAE;wBACtB,OAAO,CAAC,IAAI,CAAC,wBAAwB,CAAC,CAAA;qBACvC;oBAEyB,qBAAM,CAAA,iBAAiB,aAAjB,iBAAiB,uBAAjB,iBAAiB,CAAE,MAAM,CACvD;4BACE,WAAW,aAAA;4BACX,UAAU,YAAA;yBACX,EACD,WAAW,EACX,iBAAiB,CAClB,CAAA,EAAA;;oBAPK,iBAAiB,GAAG,SAOzB;oBAEK,cAAc,GAAG,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,0CACxC,MAAM,CAAC,UAAA,GAAG,IAAI,OAAA,GAAG,CAAC,WAAW,EAAE,CAAC,UAAU,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,EAAvD,CAAuD,EACtE,KAAK,CAAC,CAAC,EAAE,EAAE,EACX,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,IAAI,qBAAU,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,EAA5B,CAA4B,CAAC,CAAA;oBAEzC,sBAAO,MAAM,wCACP,CAAC,cAAc,IAAI,EAAE,CAAC,kBAAK,CAAC,iBAAiB,IAAI,EAAE,CAAC,WACxD,UAAA,GAAG,IAAI,OAAA,GAAG,CAAC,KAAK,EAAE,EAAX,CAAW,CACnB,EAAA;;;;CACF;AArCD,oCAqCC"}

package/dist/LinearGenomeView/index.d.ts

@@ -131,10 +131,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         coord: number;
         offset: number;
         index: number;
-        refName: string;
         start: number;
         end: number;
         reversed: boolean;
+        refName: string;
         assemblyName: string;
     };
     getTrack(id: string): any;
@@ -146,10 +146,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         coord: number;
         offset: number;
         index: number;
-        refName: string;
         start: number;
         end: number;
         reversed: boolean;
+        refName: string;
         assemblyName: string;
     } | undefined;
 } & {
@@ -169,7 +169,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
     hideTrack(trackId: string): number;
 } & {
-    moveTrack(movingTrackId: string, targetTrackId: string): void;
+    moveTrack(movingId: string, targetId: string): void;
     closeView(): void;
     toggleTrack(trackId: string): void;
     setTrackLabels(setting: 'overlapping' | 'offset' | 'hidden'): void;