@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/dist/LinearSNPCoverageDisplay/models/model.js

@@ -1,237 +1,264 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _mobx = require("mobx");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _pluginWiggle = require("@jbrowse/plugin-wiggle");
-
-var _util = require("@jbrowse/core/util");
-
-var _Tooltip = _interopRequireDefault(require("../components/Tooltip"));
-
-var _shared = require("../../shared");
-
-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; }
-
+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;
+    };
+    return __assign.apply(this, arguments);
+};
+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());
+    });
+};
+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;
+            }
+            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];
+        }
+    }
+    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 mobx_state_tree_1 = require("mobx-state-tree");
+var mobx_1 = require("mobx");
+var configuration_1 = require("@jbrowse/core/configuration");
+var plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
+var util_1 = require("@jbrowse/core/util");
+var Tooltip_1 = __importDefault(require("../components/Tooltip"));
+var shared_1 = require("../../shared");
 // using a map because it preserves order
 var rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
-
-var stateModelFactory = function stateModelFactory(pluginManager, configSchema) {
-  return _mobxStateTree.types.compose('LinearSNPCoverageDisplay', (0, _pluginWiggle.linearWiggleDisplayModelFactory)(pluginManager, configSchema), _mobxStateTree.types.model({
-    type: _mobxStateTree.types.literal('LinearSNPCoverageDisplay'),
-    drawInterbaseCounts: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
-    drawIndicators: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
-    drawArcs: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
-    filterBy: _mobxStateTree.types.optional(_mobxStateTree.types.model({
-      flagInclude: _mobxStateTree.types.optional(_mobxStateTree.types.number, 0),
-      flagExclude: _mobxStateTree.types.optional(_mobxStateTree.types.number, 1540),
-      readName: _mobxStateTree.types.maybe(_mobxStateTree.types.string),
-      tagFilter: _mobxStateTree.types.maybe(_mobxStateTree.types.model({
-        tag: _mobxStateTree.types.string,
-        value: _mobxStateTree.types.string
-      }))
-    }), {}),
-    colorBy: _mobxStateTree.types.maybe(_mobxStateTree.types.model({
-      type: _mobxStateTree.types.string,
-      tag: _mobxStateTree.types.maybe(_mobxStateTree.types.string)
+var stateModelFactory = function (pluginManager, configSchema) {
+    return mobx_state_tree_1.types
+        .compose('LinearSNPCoverageDisplay', (0, plugin_wiggle_1.linearWiggleDisplayModelFactory)(pluginManager, configSchema), mobx_state_tree_1.types.model({
+        type: mobx_state_tree_1.types.literal('LinearSNPCoverageDisplay'),
+        drawInterbaseCounts: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
+        drawIndicators: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
+        drawArcs: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
+        filterBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.model({
+            flagInclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
+            flagExclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1540),
+            readName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+            tagFilter: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({ tag: mobx_state_tree_1.types.string, value: mobx_state_tree_1.types.string })),
+        }), {}),
+        colorBy: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({
+            type: mobx_state_tree_1.types.string,
+            tag: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+        })),
     }))
-  })).volatile(function () {
-    return {
-      modificationTagMap: _mobx.observable.map({})
-    };
-  }).actions(function (self) {
-    return {
-      setConfig: function setConfig(configuration) {
-        self.configuration = configuration;
-      },
-      setFilterBy: function setFilterBy(filter) {
-        self.filterBy = (0, _mobxStateTree.cast)(filter);
-      },
-      setColorBy: function setColorBy(colorBy) {
-        self.colorBy = (0, _mobxStateTree.cast)(colorBy);
-      },
-      updateModificationColorMap: function updateModificationColorMap(uniqueModifications) {
-        var colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
-        var i = 0;
-        uniqueModifications.forEach(function (value) {
-          if (!self.modificationTagMap.has(value)) {
-            var newColor = colorPalette[i++];
-            self.modificationTagMap.set(value, newColor);
-          }
-        });
-      }
-    };
-  }).views(function (self) {
-    var superRenderProps = self.renderProps;
-    return {
-      get rendererConfig() {
-        var configBlob = (0, _configuration.getConf)(self, ['renderers', self.rendererTypeName]) || {};
-        return self.rendererType.configSchema.create(_objectSpread(_objectSpread({}, configBlob), {}, {
-          drawInterbaseCounts: self.drawInterbaseCounts === undefined ? configBlob.drawInterbaseCounts : self.drawInterbaseCounts,
-          drawIndicators: self.drawIndicators === undefined ? configBlob.drawIndicators : self.drawIndicators,
-          drawArcs: self.drawArcs === undefined ? configBlob.drawArcs : self.drawArcs
-        }), (0, _mobxStateTree.getEnv)(self));
-      },
-
-      get drawArcsSetting() {
-        return self.drawArcs !== undefined ? self.drawArcs : (0, _configuration.readConfObject)(this.rendererConfig, 'drawArcs');
-      },
-
-      get drawInterbaseCountsSetting() {
-        return self.drawInterbaseCounts !== undefined ? self.drawInterbaseCounts : (0, _configuration.readConfObject)(this.rendererConfig, 'drawInterbaseCounts');
-      },
-
-      get drawIndicatorsSetting() {
-        return self.drawIndicators !== undefined ? self.drawIndicators : (0, _configuration.readConfObject)(this.rendererConfig, 'drawIndicators');
-      },
-
-      get modificationsReady() {
-        var _self$colorBy;
-
-        return ((_self$colorBy = self.colorBy) === null || _self$colorBy === void 0 ? void 0 : _self$colorBy.type) === 'modifications' ? Object.keys(JSON.parse(JSON.stringify(self.modificationTagMap))).length > 0 : true;
-      },
-
-      renderProps: function renderProps() {
-        var superProps = superRenderProps();
-        return _objectSpread(_objectSpread({}, superProps), {}, {
-          notReady: superProps.notReady || !this.modificationsReady,
-          modificationTagMap: JSON.parse(JSON.stringify(self.modificationTagMap)),
-          // must use getSnapshot because otherwise changes to e.g. just the
-          // colorBy.type are not read
-          colorBy: self.colorBy ? (0, _mobxStateTree.getSnapshot)(self.colorBy) : undefined,
-          filterBy: self.filterBy ? (0, _mobxStateTree.getSnapshot)(self.filterBy) : undefined
-        });
-      }
-    };
-  }).actions(function (self) {
-    return {
-      toggleDrawIndicators: function toggleDrawIndicators() {
-        self.drawIndicators = !self.drawIndicatorsSetting;
-      },
-      toggleDrawInterbaseCounts: function toggleDrawInterbaseCounts() {
-        self.drawInterbaseCounts = !self.drawInterbaseCountsSetting;
-      },
-      toggleDrawArcs: function toggleDrawArcs() {
-        self.drawArcs = !self.drawArcsSetting;
-      },
-      afterAttach: function afterAttach() {
-        (0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)( /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-          var colorBy, _ref2, staticBlocks, vals;
-
-          return _regenerator.default.wrap(function _callee$(_context) {
-            while (1) {
-              switch (_context.prev = _context.next) {
-                case 0:
-                  _context.prev = 0;
-                  colorBy = self.colorBy;
-                  _ref2 = (0, _util.getContainingView)(self), staticBlocks = _ref2.staticBlocks;
-
-                  if (!((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications')) {
-                    _context.next = 8;
-                    break;
-                  }
-
-                  _context.next = 6;
-                  return (0, _shared.getUniqueModificationValues)(self, (0, _configuration.getConf)(self.parentTrack, 'adapter'), colorBy, staticBlocks);
-
-                case 6:
-                  vals = _context.sent;
-                  self.updateModificationColorMap(vals);
-
-                case 8:
-                  _context.next = 14;
-                  break;
-
-                case 10:
-                  _context.prev = 10;
-                  _context.t0 = _context["catch"](0);
-                  console.error(_context.t0);
-                  self.setError(_context.t0);
-
-                case 14:
-                case "end":
-                  return _context.stop();
-              }
-            }
-          }, _callee, null, [[0, 10]]);
-        })), {
-          delay: 1000
-        }));
-      }
-    };
-  }).views(function (self) {
-    var superTrackMenuItems = self.trackMenuItems;
-    return {
-      get TooltipComponent() {
-        return _Tooltip.default;
-      },
-
-      get adapterConfig() {
-        var subadapter = (0, _configuration.getConf)(self.parentTrack, 'adapter');
+        .volatile(function () { return ({
+        modificationTagMap: mobx_1.observable.map({}),
+    }); })
+        .actions(function (self) { return ({
+        setConfig: function (configuration) {
+            self.configuration = configuration;
+        },
+        setFilterBy: function (filter) {
+            self.filterBy = (0, mobx_state_tree_1.cast)(filter);
+        },
+        setColorBy: function (colorBy) {
+            self.colorBy = (0, mobx_state_tree_1.cast)(colorBy);
+        },
+        updateModificationColorMap: function (uniqueModifications) {
+            var colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
+            var i = 0;
+            uniqueModifications.forEach(function (value) {
+                if (!self.modificationTagMap.has(value)) {
+                    var newColor = colorPalette[i++];
+                    self.modificationTagMap.set(value, newColor);
+                }
+            });
+        },
+    }); })
+        .views(function (self) {
+        var superRenderProps = self.renderProps;
         return {
-          type: 'SNPCoverageAdapter',
-          subadapter: subadapter
+            get rendererConfig() {
+                var _a, _b, _c;
+                var configBlob = (0, configuration_1.getConf)(self, ['renderers', self.rendererTypeName]) || {};
+                return self.rendererType.configSchema.create(__assign(__assign({}, configBlob), { drawInterbaseCounts: (_a = self.drawInterbaseCounts) !== null && _a !== void 0 ? _a : configBlob.drawInterbaseCounts, drawIndicators: (_b = self.drawIndicators) !== null && _b !== void 0 ? _b : configBlob.drawIndicators, drawArcs: (_c = self.drawArcs) !== null && _c !== void 0 ? _c : configBlob.drawArcs }), (0, mobx_state_tree_1.getEnv)(self));
+            },
+            get drawArcsSetting() {
+                var _a;
+                return ((_a = self.drawArcs) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawArcs'));
+            },
+            get drawInterbaseCountsSetting() {
+                var _a;
+                return ((_a = self.drawInterbaseCounts) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawInterbaseCounts'));
+            },
+            get drawIndicatorsSetting() {
+                var _a;
+                return ((_a = self.drawIndicators) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawIndicators'));
+            },
+            get modificationsReady() {
+                var _a;
+                return ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) === 'modifications'
+                    ? Object.keys(JSON.parse(JSON.stringify(self.modificationTagMap)))
+                        .length > 0
+                    : true;
+            },
+            renderProps: function () {
+                var superProps = superRenderProps();
+                var colorBy = self.colorBy, filterBy = self.filterBy, modificationTagMap = self.modificationTagMap;
+                return __assign(__assign({}, superProps), { notReady: superProps.notReady || !this.modificationsReady, modificationTagMap: Object.fromEntries(modificationTagMap.toJSON()), 
+                    // must use getSnapshot because otherwise changes to e.g. just the
+                    // colorBy.type are not read
+                    colorBy: colorBy ? (0, mobx_state_tree_1.getSnapshot)(colorBy) : undefined, filterBy: filterBy ? (0, mobx_state_tree_1.getSnapshot)(filterBy) : undefined });
+            },
         };
-      },
-
-      get rendererTypeName() {
-        return rendererTypes.get('snpcoverage');
-      },
-
-      get needsScalebar() {
-        return true;
-      },
-
-      contextMenuItems: function contextMenuItems() {
-        return [];
-      },
-      trackMenuItems: function trackMenuItems() {
-        return [].concat((0, _toConsumableArray2.default)(superTrackMenuItems()), [{
-          label: 'Draw insertion/clipping indicators',
-          type: 'checkbox',
-          checked: self.drawIndicatorsSetting,
-          onClick: function onClick() {
-            self.toggleDrawIndicators();
-          }
-        }, {
-          label: 'Draw insertion/clipping counts',
-          type: 'checkbox',
-          checked: self.drawInterbaseCountsSetting,
-          onClick: function onClick() {
-            self.toggleDrawInterbaseCounts();
-          }
-        }, {
-          label: 'Draw arcs',
-          type: 'checkbox',
-          checked: self.drawArcsSetting,
-          onClick: function onClick() {
-            self.toggleDrawArcs();
-          }
-        }]);
-      }
-    };
-  });
+    })
+        .actions(function (self) { return ({
+        toggleDrawIndicators: function () {
+            self.drawIndicators = !self.drawIndicatorsSetting;
+        },
+        toggleDrawInterbaseCounts: function () {
+            self.drawInterbaseCounts = !self.drawInterbaseCountsSetting;
+        },
+        toggleDrawArcs: function () {
+            self.drawArcs = !self.drawArcsSetting;
+        },
+        afterAttach: function () {
+            var _this = this;
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(function () { return __awaiter(_this, void 0, void 0, function () {
+                var colorBy, staticBlocks, vals, error_1;
+                return __generator(this, function (_a) {
+                    switch (_a.label) {
+                        case 0:
+                            _a.trys.push([0, 3, , 4]);
+                            colorBy = self.colorBy;
+                            staticBlocks = (0, util_1.getContainingView)(self).staticBlocks;
+                            if (!self.estimatedStatsReady) {
+                                return [2 /*return*/];
+                            }
+                            if (self.regionTooLarge) {
+                                return [2 /*return*/];
+                            }
+                            if (!((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications')) return [3 /*break*/, 2];
+                            return [4 /*yield*/, (0, shared_1.getUniqueModificationValues)(self, (0, configuration_1.getConf)(self.parentTrack, 'adapter'), colorBy, staticBlocks)];
+                        case 1:
+                            vals = _a.sent();
+                            self.updateModificationColorMap(vals);
+                            _a.label = 2;
+                        case 2: return [3 /*break*/, 4];
+                        case 3:
+                            error_1 = _a.sent();
+                            console.error(error_1);
+                            self.setError(error_1);
+                            return [3 /*break*/, 4];
+                        case 4: return [2 /*return*/];
+                    }
+                });
+            }); }, { delay: 1000 }));
+        },
+    }); })
+        .views(function (self) {
+        var superTrackMenuItems = self.trackMenuItems;
+        return {
+            get TooltipComponent() {
+                return Tooltip_1.default;
+            },
+            get adapterConfig() {
+                var subadapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
+                return {
+                    type: 'SNPCoverageAdapter',
+                    subadapter: subadapter,
+                };
+            },
+            get rendererTypeName() {
+                return rendererTypes.get('snpcoverage');
+            },
+            get needsScalebar() {
+                return true;
+            },
+            contextMenuItems: function () {
+                return [];
+            },
+            trackMenuItems: function () {
+                return __spreadArray(__spreadArray([], __read(superTrackMenuItems()), false), [
+                    {
+                        label: 'Draw insertion/clipping indicators',
+                        type: 'checkbox',
+                        checked: self.drawIndicatorsSetting,
+                        onClick: function () {
+                            self.toggleDrawIndicators();
+                        },
+                    },
+                    {
+                        label: 'Draw insertion/clipping counts',
+                        type: 'checkbox',
+                        checked: self.drawInterbaseCountsSetting,
+                        onClick: function () {
+                            self.toggleDrawInterbaseCounts();
+                        },
+                    },
+                    {
+                        label: 'Draw arcs',
+                        type: 'checkbox',
+                        checked: self.drawArcsSetting,
+                        onClick: function () {
+                            self.toggleDrawArcs();
+                        },
+                    },
+                ], false);
+            },
+        };
+    });
 };
-
-var _default = stateModelFactory;
-exports.default = _default;
+exports.default = stateModelFactory;
+//# sourceMappingURL=model.js.map

package/dist/LinearSNPCoverageDisplay/models/model.js.map

@@ -0,0 +1 @@
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