@jbrowse/plugin-linear-genome-view 1.7.9 → 2.0.0

package/dist/LinearBasicDisplay/model.js

@@ -1,162 +1,183 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _react = require("react");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _util = require("@jbrowse/core/util");
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _Visibility = _interopRequireDefault(require("@material-ui/icons/Visibility"));
-
-var _BaseLinearDisplay = require("../BaseLinearDisplay");
-
-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 _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; }
-
-var SetMaxHeightDlg = /*#__PURE__*/(0, _react.lazy)(function () {
-  return Promise.resolve().then(function () {
-    return _interopRequireWildcard(require('./components/SetMaxHeight'));
-  });
-});
-
-var stateModelFactory = function stateModelFactory(configSchema) {
-  return _mobxStateTree.types.compose('LinearBasicDisplay', _BaseLinearDisplay.BaseLinearDisplay, _mobxStateTree.types.model({
-    type: _mobxStateTree.types.literal('LinearBasicDisplay'),
-    trackShowLabels: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
-    trackShowDescriptions: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
-    trackDisplayMode: _mobxStateTree.types.maybe(_mobxStateTree.types.string),
-    trackMaxHeight: _mobxStateTree.types.maybe(_mobxStateTree.types.number),
-    configuration: (0, _configuration.ConfigurationReference)(configSchema)
-  })).views(function (self) {
-    return {
-      get rendererTypeName() {
-        return (0, _configuration.getConf)(self, ['renderer', 'type']);
-      },
-
-      get showLabels() {
-        var _self$trackShowLabels;
-
-        return (_self$trackShowLabels = self.trackShowLabels) !== null && _self$trackShowLabels !== void 0 ? _self$trackShowLabels : (0, _configuration.getConf)(self, ['renderer', 'showLabels']);
-      },
-
-      get showDescriptions() {
-        var _self$trackShowDescri;
-
-        return (_self$trackShowDescri = self.trackShowDescriptions) !== null && _self$trackShowDescri !== void 0 ? _self$trackShowDescri : (0, _configuration.getConf)(self, ['renderer', 'showLabels']);
-      },
-
-      get maxHeight() {
-        var _self$trackMaxHeight;
-
-        return (_self$trackMaxHeight = self.trackMaxHeight) !== null && _self$trackMaxHeight !== void 0 ? _self$trackMaxHeight : (0, _configuration.getConf)(self, ['renderer', 'maxHeight']);
-      },
-
-      get displayMode() {
-        var _self$trackDisplayMod;
-
-        var displayMode = (0, _configuration.getConf)(self, ['renderer', 'displayMode']);
-        return (_self$trackDisplayMod = self.trackDisplayMode) !== null && _self$trackDisplayMod !== void 0 ? _self$trackDisplayMod : displayMode;
-      },
-
-      get rendererConfig() {
-        var configBlob = (0, _configuration.getConf)(self, ['renderer']) || {};
-        return self.rendererType.configSchema.create(_objectSpread(_objectSpread({}, configBlob), {}, {
-          showLabels: this.showLabels,
-          showDescriptions: this.showDescriptions,
-          displayMode: this.displayMode,
-          maxHeight: this.maxHeight
-        }), (0, _mobxStateTree.getEnv)(self));
-      }
-
-    };
-  }).actions(function (self) {
-    return {
-      toggleShowLabels: function toggleShowLabels() {
-        self.trackShowLabels = !self.showLabels;
-      },
-      toggleShowDescriptions: function toggleShowDescriptions() {
-        self.trackShowDescriptions = !self.showDescriptions;
-      },
-      setDisplayMode: function setDisplayMode(val) {
-        self.trackDisplayMode = val;
-      },
-      setMaxHeight: function setMaxHeight(val) {
-        self.trackMaxHeight = val;
-      }
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
     };
-  }).views(function (self) {
-    var superTrackMenuItems = self.trackMenuItems,
-        superRenderProps = self.renderProps;
-    return {
-      renderProps: function renderProps() {
-        var config = self.rendererConfig;
-        return _objectSpread(_objectSpread({}, superRenderProps()), {}, {
-          config: config
-        });
-      },
-      trackMenuItems: function trackMenuItems() {
-        return [].concat((0, _toConsumableArray2.default)(superTrackMenuItems()), [{
-          label: 'Show labels',
-          icon: _Visibility.default,
-          type: 'checkbox',
-          checked: self.showLabels,
-          onClick: function onClick() {
-            self.toggleShowLabels();
-          }
-        }, {
-          label: 'Show descriptions',
-          icon: _Visibility.default,
-          type: 'checkbox',
-          checked: self.showDescriptions,
-          onClick: function onClick() {
-            self.toggleShowDescriptions();
-          }
-        }, {
-          label: 'Display mode',
-          icon: _Visibility.default,
-          subMenu: ['compact', 'reducedRepresentation', 'normal', 'collapse'].map(function (val) {
-            return {
-              label: val,
-              onClick: function onClick() {
-                self.setDisplayMode(val);
-              }
-            };
-          })
-        }, {
-          label: 'Set max height',
-          onClick: function onClick() {
-            (0, _util.getSession)(self).queueDialog(function (doneCallback) {
-              return [SetMaxHeightDlg, {
-                model: self,
-                handleClose: doneCallback
-              }];
-            });
-          }
-        }]);
-      }
-    };
-  });
+    return __assign.apply(this, arguments);
+};
+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;
+});
+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 __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];
+        }
+    }
+    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 });
+var react_1 = require("react");
+var configuration_1 = require("@jbrowse/core/configuration");
+var util_1 = require("@jbrowse/core/util");
+var mobx_state_tree_1 = require("mobx-state-tree");
+// icons
+var Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
+// locals
+var BaseLinearDisplay_1 = require("../BaseLinearDisplay");
+var SetMaxHeightDlg = (0, react_1.lazy)(function () { return Promise.resolve().then(function () { return __importStar(require('./components/SetMaxHeight')); }); });
+var stateModelFactory = function (configSchema) {
+    return mobx_state_tree_1.types
+        .compose('LinearBasicDisplay', BaseLinearDisplay_1.BaseLinearDisplay, mobx_state_tree_1.types.model({
+        type: mobx_state_tree_1.types.literal('LinearBasicDisplay'),
+        trackShowLabels: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
+        trackShowDescriptions: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
+        trackDisplayMode: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+        trackMaxHeight: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
+        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
+    }))
+        .views(function (self) { return ({
+        get rendererTypeName() {
+            return (0, configuration_1.getConf)(self, ['renderer', 'type']);
+        },
+        get showLabels() {
+            var _a;
+            return (_a = self.trackShowLabels) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, ['renderer', 'showLabels']);
+        },
+        get showDescriptions() {
+            var _a;
+            return ((_a = self.trackShowDescriptions) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, ['renderer', 'showDescriptions']));
+        },
+        get maxHeight() {
+            var _a;
+            return (_a = self.trackMaxHeight) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, ['renderer', 'maxHeight']);
+        },
+        get displayMode() {
+            var _a;
+            return ((_a = self.trackDisplayMode) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, ['renderer', 'displayMode']));
+        },
+    }); })
+        .views(function (self) { return ({
+        get rendererConfig() {
+            var configBlob = (0, configuration_1.getConf)(self, ['renderer']) || {};
+            var config = configBlob;
+            return self.rendererType.configSchema.create(__assign(__assign({}, config), { showLabels: self.showLabels, showDescriptions: self.showDescriptions, displayMode: self.displayMode, maxHeight: self.maxHeight }), (0, mobx_state_tree_1.getEnv)(self));
+        },
+    }); })
+        .actions(function (self) { return ({
+        toggleShowLabels: function () {
+            self.trackShowLabels = !self.showLabels;
+        },
+        toggleShowDescriptions: function () {
+            self.trackShowDescriptions = !self.showDescriptions;
+        },
+        setDisplayMode: function (val) {
+            self.trackDisplayMode = val;
+        },
+        setMaxHeight: function (val) {
+            self.trackMaxHeight = val;
+        },
+    }); })
+        .views(function (self) {
+        var superTrackMenuItems = self.trackMenuItems, superRenderProps = self.renderProps;
+        return {
+            renderProps: function () {
+                var config = self.rendererConfig;
+                var superProps = superRenderProps();
+                var superPropsOmit = superProps;
+                return __assign(__assign({}, superPropsOmit), { config: config });
+            },
+            trackMenuItems: function () {
+                return __spreadArray(__spreadArray([], __read(superTrackMenuItems()), false), [
+                    {
+                        label: 'Show labels',
+                        icon: Visibility_1.default,
+                        type: 'checkbox',
+                        checked: self.showLabels,
+                        onClick: function () {
+                            self.toggleShowLabels();
+                        },
+                    },
+                    {
+                        label: 'Show descriptions',
+                        icon: Visibility_1.default,
+                        type: 'checkbox',
+                        checked: self.showDescriptions,
+                        onClick: function () { return self.toggleShowDescriptions(); },
+                    },
+                    {
+                        label: 'Display mode',
+                        icon: Visibility_1.default,
+                        subMenu: [
+                            'compact',
+                            'reducedRepresentation',
+                            'normal',
+                            'collapse',
+                        ].map(function (val) { return ({
+                            label: val,
+                            onClick: function () {
+                                self.setDisplayMode(val);
+                            },
+                        }); }),
+                    },
+                    {
+                        label: 'Set max height',
+                        onClick: function () {
+                            (0, util_1.getSession)(self).queueDialog(function (handleClose) { return [
+                                SetMaxHeightDlg,
+                                { model: self, handleClose: handleClose },
+                            ]; });
+                        },
+                    },
+                ], false);
+            },
+        };
+    });
 };
-
-var _default = stateModelFactory;
-exports.default = _default;
+exports.default = stateModelFactory;
+//# sourceMappingURL=model.js.map

package/dist/LinearBasicDisplay/model.js.map

@@ -0,0 +1 @@
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package/dist/LinearGenomeView/components/CenterLine.d.ts

@@ -1,14 +1,8 @@
 /// <reference types="react" />
-import { Instance } from 'mobx-state-tree';
-import { LinearGenomeViewStateModel } from '..';
-declare type LGV = Instance<LinearGenomeViewStateModel>;
+import { LinearGenomeViewModel } from '..';
+declare type LGV = LinearGenomeViewModel;
 declare function CenterLine({ model }: {
     model: LGV;
 }): JSX.Element | null;
-declare namespace CenterLine {
-    var propTypes: {
-        model: import("prop-types").Validator<any>;
-    };
-}
 declare const _default: typeof CenterLine;
 export default _default;

package/dist/LinearGenomeView/components/CenterLine.js

@@ -1,80 +1,66 @@
 "use strict";
-
-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 _styles = require("@material-ui/core/styles");
-
-var _mobxReact = require("mobx-react");
-
-var _react = _interopRequireWildcard(require("react"));
-
-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)(function () {
-  return {
+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;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var react_1 = __importStar(require("react"));
+var mui_1 = require("tss-react/mui");
+var mobx_react_1 = require("mobx-react");
+var useStyles = (0, mui_1.makeStyles)()(function () { return ({
     centerLineContainer: {
-      background: 'transparent',
-      height: '100%',
-      zIndex: 5,
-      // above the track but under menu
-      position: 'absolute',
-      border: '1px black dashed',
-      borderTop: 'none',
-      borderBottom: 'none',
-      pointerEvents: 'none'
+        background: 'transparent',
+        height: '100%',
+        zIndex: 5,
+        position: 'absolute',
+        border: '1px black dashed',
+        borderTop: 'none',
+        borderBottom: 'none',
+        pointerEvents: 'none',
     },
     centerLineText: {
-      position: 'absolute',
-      pointerEvents: 'none',
-      whiteSpace: 'nowrap',
-      fontWeight: 'bold'
-    }
-  };
-});
-
-function CenterLine(_ref) {
-  var model = _ref.model;
-  var bpPerPx = model.bpPerPx,
-      centerLineInfo = model.centerLineInfo,
-      trackHeights = model.trackHeights,
-      tracks = model.tracks,
-      width = model.width;
-  var ref = (0, _react.useRef)(null);
-  var classes = useStyles();
-  var startingPosition = width / 2;
-  return tracks.length ? /*#__PURE__*/_react.default.createElement("div", {
-    "data-testid": "centerline_container",
-    className: classes.centerLineContainer,
-    role: "presentation",
-    ref: ref,
-    style: {
-      left: "".concat(startingPosition, "px"),
-      width: Math.max(1 / bpPerPx, 1)
-    }
-  }, centerLineInfo && /*#__PURE__*/_react.default.createElement("div", {
-    // text that indicates what bp is center, positioned
-    // at the bottom right of the center line
-    "data-testid": "centerline_text",
-    className: classes.centerLineText,
-    role: "presentation",
-    style: {
-      left: Math.max(1 / bpPerPx, 1) + 5,
-      top: trackHeights
-    }
-  }, centerLineInfo.refName, ":", ' ', Math.max(Math.round(centerLineInfo.offset) + 1, 0))) : null;
+        position: 'absolute',
+        pointerEvents: 'none',
+        whiteSpace: 'nowrap',
+        fontWeight: 'bold',
+    },
+}); });
+function CenterLine(_a) {
+    var model = _a.model;
+    var bpPerPx = model.bpPerPx, centerLineInfo = model.centerLineInfo, trackHeights = model.trackHeights, tracks = model.tracks, width = model.width;
+    var ref = (0, react_1.useRef)(null);
+    var classes = useStyles().classes;
+    var startingPosition = width / 2;
+    return tracks.length ? (react_1.default.createElement("div", { "data-testid": "centerline_container", className: classes.centerLineContainer, role: "presentation", ref: ref, style: {
+            left: "".concat(startingPosition, "px"),
+            width: Math.max(1 / bpPerPx, 1),
+        } }, centerLineInfo && (react_1.default.createElement("div", { "data-testid": "centerline_text", className: classes.centerLineText, role: "presentation", style: {
+            left: Math.max(1 / bpPerPx, 1) + 5,
+            top: trackHeights,
+        } },
+        centerLineInfo.refName,
+        ":",
+        ' ',
+        Math.max(Math.round(centerLineInfo.offset) + 1, 0))))) : null;
 }
-
-CenterLine.propTypes = {
-  model: _mobxReact.PropTypes.objectOrObservableObject.isRequired
-};
-
-var _default = (0, _mobxReact.observer)(CenterLine);
-
-exports.default = _default;
+exports.default = (0, mobx_react_1.observer)(CenterLine);
+//# sourceMappingURL=CenterLine.js.map

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

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