@jbrowse/plugin-variants 2.1.0 → 2.1.2

package/dist/ChordVariantDisplay/index.js

@@ -3,19 +3,19 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var plugin_circular_view_1 = require("@jbrowse/plugin-circular-view");
-var ChordVariantDisplay_1 = __importDefault(require("./models/ChordVariantDisplay"));
-var DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-exports.default = (function (pluginManager) {
-    var load = pluginManager.load;
-    var _a = load(ChordVariantDisplay_1.default), stateModel = _a.stateModel, configSchema = _a.configSchema;
+const plugin_circular_view_1 = require("@jbrowse/plugin-circular-view");
+const ChordVariantDisplay_1 = __importDefault(require("./models/ChordVariantDisplay"));
+const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+exports.default = (pluginManager) => {
+    const { load } = pluginManager;
+    const { stateModel, configSchema } = load(ChordVariantDisplay_1.default);
     return new DisplayType_1.default({
         name: 'ChordVariantDisplay',
-        configSchema: configSchema,
-        stateModel: stateModel,
+        configSchema,
+        stateModel,
         trackType: 'VariantTrack',
         viewType: 'CircularView',
         ReactComponent: plugin_circular_view_1.BaseChordDisplayComponent,
     });
-});
+};
 //# sourceMappingURL=index.js.map

package/dist/ChordVariantDisplay/index.js.map

@@ -1 +1 @@
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package/dist/ChordVariantDisplay/models/ChordVariantDisplay.js

@@ -1,40 +1,38 @@
 "use strict";
-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);
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-var plugin_circular_view_1 = require("@jbrowse/plugin-circular-view");
-var configuration_1 = require("@jbrowse/core/configuration");
-var mobx_state_tree_1 = require("mobx-state-tree");
-var util_1 = require("@jbrowse/core/util");
-var tracks_1 = require("@jbrowse/core/util/tracks");
-var ChordVariantDisplayF = function (pluginManager) {
-    var configSchema = (0, configuration_1.ConfigurationSchema)('ChordVariantDisplay', {
+const plugin_circular_view_1 = require("@jbrowse/plugin-circular-view");
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const ChordVariantDisplayF = pluginManager => {
+    const configSchema = (0, configuration_1.ConfigurationSchema)('ChordVariantDisplay', {
         renderer: mobx_state_tree_1.types.optional(pluginManager.pluggableConfigSchemaType('renderer'), { type: 'StructuralVariantChordRenderer' }),
     }, { baseConfiguration: plugin_circular_view_1.baseChordDisplayConfig, explicitlyTyped: true });
-    var stateModel = mobx_state_tree_1.types
+    const stateModel = mobx_state_tree_1.types
         .compose('ChordVariantDisplay', plugin_circular_view_1.BaseChordDisplayModel, mobx_state_tree_1.types.model({
         type: mobx_state_tree_1.types.literal('ChordVariantDisplay'),
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
     }))
-        .views(function (self) { return ({
+        .views(self => ({
         get rendererTypeName() {
             return self.configuration.renderer.type;
         },
-        renderProps: function () {
-            var view = (0, util_1.getContainingView)(self);
-            return __assign(__assign({}, (0, tracks_1.getParentRenderProps)(self)), { rpcDriverName: self.rpcDriverName, displayModel: self, bezierRadius: view.radiusPx * self.bezierRadiusRatio, radius: view.radiusPx, blockDefinitions: this.blockDefinitions, config: self.configuration.renderer, onChordClick: self.onChordClick });
+        renderProps() {
+            const view = (0, util_1.getContainingView)(self);
+            return {
+                ...(0, tracks_1.getParentRenderProps)(self),
+                rpcDriverName: self.rpcDriverName,
+                displayModel: self,
+                bezierRadius: view.radiusPx * self.bezierRadiusRatio,
+                radius: view.radiusPx,
+                blockDefinitions: this.blockDefinitions,
+                config: self.configuration.renderer,
+                onChordClick: self.onChordClick,
+            };
         },
-    }); });
-    return { stateModel: stateModel, configSchema: configSchema };
+    }));
+    return { stateModel, configSchema };
 };
 // http://localhost:3000/test_data/hs37d5.HG002-SequelII-CCS.sv.vcf.gz.tbi
 // render request is for 1.5x the current viewing window

package/dist/ChordVariantDisplay/models/ChordVariantDisplay.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ChordVariantDisplay.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/ChordVariantDisplay.js"],"names":[],"mappings":";;AAAA,wEAGsC;AACtC,+DAGoC;AACpC,qDAAuC;AACvC,6CAAsD;AACtD,sDAAgE;AAEhE,MAAM,oBAAoB,GAAG,aAAa,CAAC,EAAE;IAC3C,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,qBAAqB,EACrB;QACE,QAAQ,EAAE,uBAAK,CAAC,QAAQ,CACtB,aAAa,CAAC,yBAAyB,CAAC,UAAU,CAAC,EACnD,EAAE,IAAI,EAAE,gCAAgC,EAAE,CAC3C;KACF,EACD,EAAE,iBAAiB,EAAE,6CAAsB,EAAE,eAAe,EAAE,IAAI,EAAE,CACrE,CAAA;IAED,MAAM,UAAU,GAAG,uBAAK;SACrB,OAAO,CACN,qBAAqB,EACrB,4CAAqB,EACrB,uBAAK,CAAC,KAAK,CAAC;QACV,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,qBAAqB,CAAC;QAC1C,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;QAED,WAAW;YACT,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;YACpC,OAAO;gBACL,GAAG,IAAA,6BAAoB,EAAC,IAAI,CAAC;gBAC7B,aAAa,EAAE,IAAI,CAAC,aAAa;gBACjC,YAAY,EAAE,IAAI;gBAClB,YAAY,EAAE,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,iBAAiB;gBACpD,MAAM,EAAE,IAAI,CAAC,QAAQ;gBACrB,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;gBACnC,YAAY,EAAE,IAAI,CAAC,YAAY;aAChC,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;IAEL,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,CAAA;AACrC,CAAC,CAAA;AAED,0EAA0E;AAE1E,wDAAwD;AAExD,2BAA2B;AAC3B,EAAE;AACF,kBAAe,oBAAoB,CAAA"}

package/dist/LinearVariantDisplay/configSchema.js

@@ -1,10 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.LinearVariantDisplayConfigFactory = void 0;
-var configuration_1 = require("@jbrowse/core/configuration");
-var plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const configuration_1 = require("@jbrowse/core/configuration");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 function LinearVariantDisplayConfigFactory(pluginManager) {
-    var configSchema = (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager);
+    const configSchema = (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager);
     return (0, configuration_1.ConfigurationSchema)('LinearVariantDisplay', {}, { baseConfiguration: configSchema, explicitlyTyped: true });
 }
 exports.LinearVariantDisplayConfigFactory = LinearVariantDisplayConfigFactory;

package/dist/LinearVariantDisplay/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/configSchema.ts"],"names":[],"mappings":";;;AAAA,+DAAiE;AAGjE,kFAA0F;AAE1F,SAAgB,iCAAiC,CAC/C,aAA4B;IAE5B,MAAM,YAAY,GAAG,IAAA,iEAAqC,EAAC,aAAa,CAAC,CAAA;IAEzE,OAAO,IAAA,mCAAmB,EACxB,sBAAsB,EACtB,EAAE,EACF,EAAE,iBAAiB,EAAE,YAAY,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA;AACH,CAAC;AAVD,8EAUC"}

package/dist/LinearVariantDisplay/index.d.ts

@@ -1,2 +1,3 @@
-export { LinearVariantDisplayConfigFactory as configSchemaFactory } from './configSchema';
-export { default as modelFactory } from './model';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/LinearVariantDisplay/index.js

@@ -3,9 +3,21 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.modelFactory = exports.configSchemaFactory = void 0;
-var configSchema_1 = require("./configSchema");
-Object.defineProperty(exports, "configSchemaFactory", { enumerable: true, get: function () { return configSchema_1.LinearVariantDisplayConfigFactory; } });
-var model_1 = require("./model");
-Object.defineProperty(exports, "modelFactory", { enumerable: true, get: function () { return __importDefault(model_1).default; } });
+const configSchema_1 = require("./configSchema");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+const model_1 = __importDefault(require("./model"));
+exports.default = (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const configSchema = (0, configSchema_1.LinearVariantDisplayConfigFactory)(pluginManager);
+        return new DisplayType_1.default({
+            name: 'LinearVariantDisplay',
+            configSchema,
+            stateModel: (0, model_1.default)(configSchema),
+            trackType: 'VariantTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
+        });
+    });
+};
 //# sourceMappingURL=index.js.map

package/dist/LinearVariantDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,iDAAkE;AAClE,kFAA+E;AAC/E,kGAAyE;AACzE,oDAAuC;AAEvC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,gDAAiC,EAAC,aAAa,CAAC,CAAA;QACrE,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,sBAAsB;YAC5B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAiB,EAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/LinearVariantDisplay/model.js

@@ -1,85 +1,37 @@
 "use strict";
-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 };
-    }
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-var configuration_1 = require("@jbrowse/core/configuration");
-var tracks_1 = require("@jbrowse/core/util/tracks");
-var util_1 = require("@jbrowse/core/util");
-var plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-var mobx_state_tree_1 = require("mobx-state-tree");
+const configuration_1 = require("@jbrowse/core/configuration");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const util_1 = require("@jbrowse/core/util");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const mobx_state_tree_1 = require("mobx-state-tree");
 function default_1(configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearVariantDisplay', (0, plugin_linear_genome_view_1.linearBasicDisplayModelFactory)(configSchema), mobx_state_tree_1.types.model({
         type: mobx_state_tree_1.types.literal('LinearVariantDisplay'),
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
     }))
-        .actions(function (self) { return ({
-        selectFeature: function (feature) {
-            return __awaiter(this, void 0, void 0, function () {
-                var session, rpcManager, sessionId, track, adapterConfig, header, featureWidget;
-                return __generator(this, function (_a) {
-                    switch (_a.label) {
-                        case 0:
-                            session = (0, util_1.getSession)(self);
-                            if (!(0, util_1.isSessionModelWithWidgets)(session)) return [3 /*break*/, 2];
-                            rpcManager = session.rpcManager;
-                            sessionId = (0, tracks_1.getRpcSessionId)(self);
-                            track = (0, util_1.getContainingTrack)(self);
-                            adapterConfig = (0, configuration_1.getConf)(track, 'adapter');
-                            return [4 /*yield*/, rpcManager.call(sessionId, 'CoreGetMetadata', {
-                                    adapterConfig: adapterConfig,
-                                })];
-                        case 1:
-                            header = _a.sent();
-                            featureWidget = session.addWidget('VariantFeatureWidget', 'variantFeature', {
-                                featureData: feature.toJSON(),
-                                view: (0, util_1.getContainingView)(self),
-                                descriptions: header,
-                            });
-                            session.showWidget(featureWidget);
-                            _a.label = 2;
-                        case 2:
-                            session.setSelection(feature);
-                            return [2 /*return*/];
-                    }
+        .actions(self => ({
+        async selectFeature(feature) {
+            const session = (0, util_1.getSession)(self);
+            if ((0, util_1.isSessionModelWithWidgets)(session)) {
+                const { rpcManager } = session;
+                const sessionId = (0, tracks_1.getRpcSessionId)(self);
+                const track = (0, util_1.getContainingTrack)(self);
+                const adapterConfig = (0, configuration_1.getConf)(track, 'adapter');
+                const header = await rpcManager.call(sessionId, 'CoreGetMetadata', {
+                    adapterConfig,
+                });
+                const featureWidget = session.addWidget('VariantFeatureWidget', 'variantFeature', {
+                    featureData: feature.toJSON(),
+                    view: (0, util_1.getContainingView)(self),
+                    descriptions: header,
                 });
-            });
+                session.showWidget(featureWidget);
+            }
+            session.setSelection(feature);
         },
-    }); });
+    }));
 }
 exports.default = default_1;
 //# sourceMappingURL=model.js.map

package/dist/LinearVariantDisplay/model.js.map

@@ -1 +1 @@
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+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":";;AAAA,+DAA6E;AAC7E,sDAA2D;AAC3D,6CAK2B;AAG3B,kFAAmF;AACnF,qDAAuC;AAGvC,mBAAyB,YAA6C;IACpE,OAAO,uBAAK;SACT,OAAO,CACN,sBAAsB,EACtB,IAAA,0DAA8B,EAAC,YAAY,CAAC,EAC5C,uBAAK,CAAC,KAAK,CAAC;QACV,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,KAAK,CAAC,aAAa,CAAC,OAAgB;YAClC,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAI,IAAA,gCAAyB,EAAC,OAAO,CAAC,EAAE;gBACtC,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAC9B,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,IAAI,CAAC,CAAA;gBACvC,MAAM,KAAK,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,CAAA;gBACtC,MAAM,aAAa,GAAG,IAAA,uBAAO,EAAC,KAAK,EAAE,SAAS,CAAC,CAAA;gBAC/C,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,iBAAiB,EAAE;oBACjE,aAAa;iBACd,CAAC,CAAA;gBACF,MAAM,aAAa,GAAG,OAAO,CAAC,SAAS,CACrC,sBAAsB,EACtB,gBAAgB,EAChB;oBACE,WAAW,EAAE,OAAO,CAAC,MAAM,EAAE;oBAC7B,IAAI,EAAE,IAAA,wBAAiB,EAAC,IAAI,CAAC;oBAC7B,YAAY,EAAE,MAAM;iBACrB,CACF,CAAA;gBACD,OAAO,CAAC,UAAU,CAAC,aAAa,CAAC,CAAA;aAClC;YAED,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;QAC/B,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AApCD,4BAoCC"}

package/dist/StructuralVariantChordRenderer/ReactComponent.js

@@ -22,124 +22,84 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __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 __values = (this && this.__values) || function(o) {
-    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
-    if (m) return m.call(o);
-    if (o && typeof o.length === "number") return {
-        next: function () {
-            if (o && i >= o.length) o = void 0;
-            return { value: o && o[i++], done: !o };
-        }
-    };
-    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
-};
 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 util_1 = require("@jbrowse/core/util");
-var configuration_1 = require("@jbrowse/core/configuration");
-var mst_1 = require("@jbrowse/core/util/types/mst");
-var vcf_1 = require("@gmod/vcf");
-var prop_types_1 = __importDefault(require("prop-types"));
+const react_1 = __importStar(require("react"));
+const mobx_react_1 = require("mobx-react");
+const util_1 = require("@jbrowse/core/util");
+const configuration_1 = require("@jbrowse/core/configuration");
+const mst_1 = require("@jbrowse/core/util/types/mst");
+const vcf_1 = require("@gmod/vcf");
+const prop_types_1 = __importDefault(require("prop-types"));
 function bpToRadians(block, pos) {
-    var blockStart = block.region.elided ? 0 : block.region.start;
-    var blockEnd = block.region.elided ? 0 : block.region.end;
-    var bpOffset = block.flipped ? blockEnd - pos : pos - blockStart;
-    var radians = bpOffset / block.bpPerRadian + block.startRadians;
+    const blockStart = block.region.elided ? 0 : block.region.start;
+    const blockEnd = block.region.elided ? 0 : block.region.end;
+    const bpOffset = block.flipped ? blockEnd - pos : pos - blockStart;
+    const radians = bpOffset / block.bpPerRadian + block.startRadians;
     return radians;
 }
-var Chord = (0, mobx_react_1.observer)(function Chord(_a) {
-    var _b;
-    var _c, _d, _e, _f, _g;
-    var feature = _a.feature, blocksForRefs = _a.blocksForRefs, radius = _a.radius, config = _a.config, bezierRadius = _a.bezierRadius, selected = _a.selected, onClick = _a.onClick;
+const Chord = (0, mobx_react_1.observer)(function Chord({ feature, blocksForRefs, radius, config, bezierRadius, selected, onClick, }) {
+    var _a, _b, _c, _d, _e;
     // find the blocks that our start and end points belong to
-    var startBlock = blocksForRefs[feature.get('refName')];
+    const startBlock = blocksForRefs[feature.get('refName')];
     if (!startBlock) {
         return null;
     }
-    var svType;
+    let svType;
     if (feature.get('INFO')) {
         ;
-        _b = __read(feature.get('INFO').SVTYPE || [], 1), svType = _b[0];
+        [svType] = feature.get('INFO').SVTYPE || [];
     }
     else if (feature.get('mate')) {
         svType = 'mate';
     }
-    var endPosition;
-    var endBlock;
-    var alt = (_c = feature.get('ALT')) === null || _c === void 0 ? void 0 : _c[0];
-    var bnd = alt && (0, vcf_1.parseBreakend)(alt);
+    let endPosition;
+    let endBlock;
+    const alt = (_a = feature.get('ALT')) === null || _a === void 0 ? void 0 : _a[0];
+    const bnd = alt && (0, vcf_1.parseBreakend)(alt);
     if (bnd) {
         // VCF BND
-        var matePosition = bnd.MatePosition.split(':');
+        const matePosition = bnd.MatePosition.split(':');
         endPosition = +matePosition[1];
         endBlock = blocksForRefs[matePosition[0]];
     }
     else if (alt === '<TRA>') {
         // VCF TRA
-        var chr2 = (_e = (_d = feature.get('INFO')) === null || _d === void 0 ? void 0 : _d.CHR2) === null || _e === void 0 ? void 0 : _e[0];
-        var end = (_g = (_f = feature.get('INFO')) === null || _f === void 0 ? void 0 : _f.END) === null || _g === void 0 ? void 0 : _g[0];
+        const chr2 = (_c = (_b = feature.get('INFO')) === null || _b === void 0 ? void 0 : _b.CHR2) === null || _c === void 0 ? void 0 : _c[0];
+        const end = (_e = (_d = feature.get('INFO')) === null || _d === void 0 ? void 0 : _d.END) === null || _e === void 0 ? void 0 : _e[0];
         endPosition = parseInt(end, 10);
         endBlock = blocksForRefs[chr2];
     }
     else if (svType === 'mate') {
         // generic simplefeatures arcs
-        var mate = feature.get('mate');
-        var chr2 = mate.refName;
+        const mate = feature.get('mate');
+        const chr2 = mate.refName;
         endPosition = mate.start;
         endBlock = blocksForRefs[chr2];
     }
     if (endBlock) {
-        var startPos = feature.get('start');
-        var startRadians = bpToRadians(startBlock, startPos);
-        var endRadians = bpToRadians(endBlock, endPosition);
-        var startXY = (0, util_1.polarToCartesian)(radius, startRadians);
-        var endXY = (0, util_1.polarToCartesian)(radius, endRadians);
-        var controlXY = (0, util_1.polarToCartesian)(bezierRadius, (endRadians + startRadians) / 2);
-        var strokeColor_1 = selected
-            ? (0, configuration_1.readConfObject)(config, 'strokeColorSelected', { feature: feature })
-            : (0, configuration_1.readConfObject)(config, 'strokeColor', { feature: feature });
-        var hoverStrokeColor_1 = (0, configuration_1.readConfObject)(config, 'strokeColorHover', {
-            feature: feature,
+        const startPos = feature.get('start');
+        const startRadians = bpToRadians(startBlock, startPos);
+        const endRadians = bpToRadians(endBlock, endPosition);
+        const startXY = (0, util_1.polarToCartesian)(radius, startRadians);
+        const endXY = (0, util_1.polarToCartesian)(radius, endRadians);
+        const controlXY = (0, util_1.polarToCartesian)(bezierRadius, (endRadians + startRadians) / 2);
+        const strokeColor = selected
+            ? (0, configuration_1.readConfObject)(config, 'strokeColorSelected', { feature })
+            : (0, configuration_1.readConfObject)(config, 'strokeColor', { feature });
+        const hoverStrokeColor = (0, configuration_1.readConfObject)(config, 'strokeColorHover', {
+            feature,
         });
-        return (react_1.default.createElement("path", { "data-testid": "chord-".concat(feature.id()), d: __spreadArray(__spreadArray(__spreadArray(__spreadArray(['M'], __read(startXY), false), ['Q'], false), __read(controlXY), false), __read(endXY), false).join(' '), style: { stroke: strokeColor_1 }, onClick: function (evt) {
-                return onClick(feature, startBlock.region, endBlock.region, evt);
-            }, onMouseOver: function (evt) {
+        return (react_1.default.createElement("path", { "data-testid": `chord-${feature.id()}`, d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), style: { stroke: strokeColor }, onClick: evt => onClick(feature, startBlock.region, endBlock.region, evt), onMouseOver: evt => {
                 if (!selected) {
-                    evt.target.style.stroke = hoverStrokeColor_1;
+                    evt.target.style.stroke = hoverStrokeColor;
                     evt.target.style.strokeWidth = 3;
                 }
-            }, onMouseOut: function (evt) {
+            }, onMouseOut: evt => {
                 if (!selected) {
-                    evt.target.style.stroke = strokeColor_1;
+                    evt.target.style.stroke = strokeColor;
                     evt.target.style.strokeWidth = 1;
                 }
             } }));
@@ -147,43 +107,37 @@ var Chord = (0, mobx_react_1.observer)(function Chord(_a) {
     return null;
 });
 function StructuralVariantChords(props) {
-    var e_1, _a;
-    var features = props.features, config = props.config, displayModel = props.displayModel, blockDefinitions = props.blockDefinitions, radius = props.radius, bezierRadius = props.bezierRadius, selectedFeatureId = props.displayModel.selectedFeatureId, onChordClick = props.onChordClick;
+    const { features, config, displayModel, blockDefinitions, radius, bezierRadius, displayModel: { selectedFeatureId }, onChordClick, } = props;
     // make a map of refName -> blockDefinition
-    var blocksForRefsMemo = (0, react_1.useMemo)(function () {
-        var blocksForRefs = {};
-        blockDefinitions.forEach(function (block) {
-            var regions = block.region.elided
+    const blocksForRefsMemo = (0, react_1.useMemo)(() => {
+        const blocksForRefs = {};
+        blockDefinitions.forEach(block => {
+            const regions = block.region.elided
                 ? block.region.regions
                 : [block.region];
-            regions.forEach(function (region) {
+            regions.forEach(region => {
                 blocksForRefs[region.refName] = block;
             });
         });
         return blocksForRefs;
     }, [blockDefinitions]);
     // console.log(blocksForRefs)
-    var chords = [];
-    try {
-        for (var features_1 = __values(features), features_1_1 = features_1.next(); !features_1_1.done; features_1_1 = features_1.next()) {
-            var _b = __read(features_1_1.value, 2), id = _b[0], feature = _b[1];
-            var selected = String(selectedFeatureId) === String(feature.id());
-            chords.push(react_1.default.createElement(Chord, { key: id, feature: feature, config: config, displayModel: displayModel, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
-        }
-    }
-    catch (e_1_1) { e_1 = { error: e_1_1 }; }
-    finally {
-        try {
-            if (features_1_1 && !features_1_1.done && (_a = features_1.return)) _a.call(features_1);
-        }
-        finally { if (e_1) throw e_1.error; }
+    const chords = [];
+    for (const [id, feature] of features) {
+        const selected = String(selectedFeatureId) === String(feature.id());
+        chords.push(react_1.default.createElement(Chord, { key: id, feature: feature, config: config, displayModel: displayModel, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
     }
-    var trackStyleId = "chords-".concat(displayModel.id);
+    const trackStyleId = `chords-${displayModel.id}`;
     return (react_1.default.createElement("g", { id: trackStyleId, "data-testid": "structuralVariantChordRenderer" },
         react_1.default.createElement("style", { 
             // eslint-disable-next-line react/no-danger
             dangerouslySetInnerHTML: {
-                __html: "\n          #".concat(trackStyleId, " > path {\n            cursor: crosshair;\n            fill: none;\n          }\n"),
+                __html: `
+          #${trackStyleId} > path {
+            cursor: crosshair;
+            fill: none;
+          }
+`,
             } }),
         chords));
 }

package/dist/StructuralVariantChordRenderer/ReactComponent.js.map

@@ -1 +1 @@
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package/dist/StructuralVariantChordRenderer/index.js

@@ -3,11 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var CircularChordRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType"));
-var configuration_1 = require("@jbrowse/core/configuration");
-var ReactComponent_1 = __importDefault(require("./ReactComponent"));
-var ChordRendererConfigF = function (pluginManager) {
-    var configSchema = (0, configuration_1.ConfigurationSchema)('StructuralVariantChordRenderer', {
+const CircularChordRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType"));
+const configuration_1 = require("@jbrowse/core/configuration");
+const ReactComponent_1 = __importDefault(require("./ReactComponent"));
+const ChordRendererConfigF = pluginManager => {
+    const configSchema = (0, configuration_1.ConfigurationSchema)('StructuralVariantChordRenderer', {
         strokeColor: {
             type: 'color',
             description: 'the line color of each arc',
@@ -30,8 +30,8 @@ var ChordRendererConfigF = function (pluginManager) {
     return new CircularChordRendererType_1.default({
         name: 'StructuralVariantChordRenderer',
         ReactComponent: ReactComponent_1.default,
-        configSchema: configSchema,
-        pluginManager: pluginManager,
+        configSchema,
+        pluginManager,
     });
 };
 exports.default = ChordRendererConfigF;

package/dist/StructuralVariantChordRenderer/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/StructuralVariantChordRenderer/index.js"],"names":[],"mappings":";;;;;AAAA,wIAAuG;AACvG,+DAAiE;AACjE,sEAA6C;AAE7C,MAAM,oBAAoB,GAAG,aAAa,CAAC,EAAE;IAC3C,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,gCAAgC,EAChC;QACE,WAAW,EAAE;YACX,IAAI,EAAE,OAAO;YACb,WAAW,EAAE,4BAA4B;YACzC,YAAY,EAAE,sBAAsB;YACpC,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;QACD,mBAAmB,EAAE;YACnB,IAAI,EAAE,OAAO;YACb,WAAW,EAAE,iDAAiD;YAC9D,YAAY,EAAE,OAAO;YACrB,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;QACD,gBAAgB,EAAE;YAChB,IAAI,EAAE,OAAO;YACb,WAAW,EACT,oEAAoE;YACtE,YAAY,EAAE,MAAM;YACpB,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;KACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;IACD,OAAO,IAAI,mCAAiB,CAAC;QAC3B,IAAI,EAAE,gCAAgC;QACtC,cAAc,EAAd,wBAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,kBAAe,oBAAoB,CAAA"}

package/dist/VariantFeatureWidget/AnnotGrid.d.ts

@@ -0,0 +1,5 @@
+/// <reference types="react" />
+export default function VariantAnnotPanel({ rows, columns, }: {
+    rows: any;
+    columns: any[];
+}): JSX.Element | null;