@jbrowse/plugin-legacy-jbrowse 1.7.11 → 2.1.0

package/dist/NCListAdapter/configSchema.js

@@ -1,27 +1,18 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = (0, _configuration.ConfigurationSchema)('NCListAdapter', {
-  rootUrlTemplate: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/my/{refseq}/trackData.json',
-      locationType: 'UriLocation'
-    }
-  },
-  refNames: {
-    type: 'stringArray',
-    defaultValue: [],
-    description: 'List of refNames used by the NCList used for aliasing'
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('NCListAdapter', {
+    rootUrlTemplate: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my/{refseq}/trackData.json',
+            locationType: 'UriLocation',
+        },
+    },
+    refNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'List of refNames used by the NCList used for aliasing',
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/NCListAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/NCListAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,eAAe,EACf;IACE,eAAe,EAAE;QACf,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,qCAAqC;YAC1C,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,QAAQ,EAAE;QACR,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,uDAAuD;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/NCListAdapter/index.js

@@ -1,15 +1,9 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-Object.defineProperty(exports, "configSchema", {
-  enumerable: true,
-  get: function get() {
-    return _configSchema.default;
-  }
-});
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.configSchema = void 0;
+var configSchema_1 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+//# sourceMappingURL=index.js.map

package/dist/NCListAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/NCListAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}

package/dist/index.js

@@ -1,124 +1,105 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
+var __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+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 _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
-
-var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
-
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
-
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-
-var _TextSearchAdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/TextSearchAdapterType"));
-
-var _ConnectionType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/ConnectionType"));
-
-var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
-
-var _NCListAdapter = require("./NCListAdapter");
-
-var _JBrowse1TextSeachAdapter = require("./JBrowse1TextSeachAdapter");
-
-var _tracks = require("@jbrowse/core/util/tracks");
-
-var _JBrowse1Connection = require("./JBrowse1Connection");
-
-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; }
-
-function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
-
-function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
-
-var LegacyJBrowsePlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2.default)(LegacyJBrowsePlugin, _Plugin);
-
-  var _super = _createSuper(LegacyJBrowsePlugin);
-
-  function LegacyJBrowsePlugin() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, LegacyJBrowsePlugin);
-
-    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-      args[_key] = arguments[_key];
+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 __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+var TextSearchAdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TextSearchAdapterType"));
+var ConnectionType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ConnectionType"));
+var Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+var NCListAdapter_1 = require("./NCListAdapter");
+var JBrowse1TextSeachAdapter_1 = require("./JBrowse1TextSeachAdapter");
+var tracks_1 = require("@jbrowse/core/util/tracks");
+var JBrowse1Connection_1 = require("./JBrowse1Connection");
+var LegacyJBrowsePlugin = /** @class */ (function (_super) {
+    __extends(LegacyJBrowsePlugin, _super);
+    function LegacyJBrowsePlugin() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
+        _this.name = 'LegacyJBrowsePlugin';
+        return _this;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'LegacyJBrowsePlugin');
-    return _this;
-  }
-
-  (0, _createClass2.default)(LegacyJBrowsePlugin, [{
-    key: "install",
-    value: function install(pluginManager) {
-      pluginManager.addAdapterType(function () {
-        return new _AdapterType.default({
-          name: 'NCListAdapter',
-          configSchema: _NCListAdapter.configSchema,
-          getAdapterClass: function getAdapterClass() {
-            return Promise.resolve().then(function () {
-              return _interopRequireWildcard(require('./NCListAdapter/NCListAdapter'));
-            }).then(function (r) {
-              return r.default;
+    LegacyJBrowsePlugin.prototype.install = function (pluginManager) {
+        pluginManager.addAdapterType(function () {
+            return new AdapterType_1.default({
+                name: 'NCListAdapter',
+                configSchema: NCListAdapter_1.configSchema,
+                getAdapterClass: function () {
+                    return Promise.resolve().then(function () { return __importStar(require('./NCListAdapter/NCListAdapter')); }).then(function (r) { return r.default; });
+                },
             });
-          }
         });
-      });
-      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-        return function (file, index, adapterHint) {
-          var regexGuess = /trackData.jsonz?$/i;
-          var adapterName = 'NCListAdapter';
-          var fileName = (0, _tracks.getFileName)(file);
-
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              rootUrlTemplate: file
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+            return function (file, index, adapterHint) {
+                var regexGuess = /trackData.jsonz?$/i;
+                var adapterName = 'NCListAdapter';
+                var fileName = (0, tracks_1.getFileName)(file);
+                if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                    return {
+                        type: adapterName,
+                        rootUrlTemplate: file,
+                    };
+                }
+                return adapterGuesser(file, index, adapterHint);
             };
-          }
-
-          return adapterGuesser(file, index, adapterHint);
-        };
-      });
-      pluginManager.addTextSearchAdapterType(function () {
-        return new _TextSearchAdapterType.default({
-          name: 'JBrowse1TextSearchAdapter',
-          configSchema: _JBrowse1TextSeachAdapter.configSchema,
-          AdapterClass: _JBrowse1TextSeachAdapter.AdapterClass,
-          description: 'A JBrowse 1 text search adapter'
         });
-      });
-      pluginManager.addConnectionType(function () {
-        return new _ConnectionType.default({
-          name: 'JBrowse1Connection',
-          configSchema: _JBrowse1Connection.configSchema,
-          stateModel: (0, _JBrowse1Connection.modelFactory)(pluginManager),
-          displayName: 'JBrowse 1 Data',
-          description: 'A JBrowse 1 data directory',
-          url: '//jbrowse.org/'
+        pluginManager.addTextSearchAdapterType(function () {
+            return new TextSearchAdapterType_1.default({
+                name: 'JBrowse1TextSearchAdapter',
+                configSchema: JBrowse1TextSeachAdapter_1.configSchema,
+                AdapterClass: JBrowse1TextSeachAdapter_1.AdapterClass,
+                description: 'A JBrowse 1 text search adapter',
+            });
         });
-      });
-    }
-  }]);
-  return LegacyJBrowsePlugin;
-}(_Plugin2.default);
-
-exports.default = LegacyJBrowsePlugin;
+        pluginManager.addConnectionType(function () {
+            return new ConnectionType_1.default({
+                name: 'JBrowse1Connection',
+                configSchema: JBrowse1Connection_1.configSchema,
+                stateModel: (0, JBrowse1Connection_1.modelFactory)(pluginManager),
+                displayName: 'JBrowse 1 Data',
+                description: 'A JBrowse 1 data directory',
+                url: '//jbrowse.org/',
+            });
+        });
+    };
+    return LegacyJBrowsePlugin;
+}(Plugin_1.default));
+exports.default = LegacyJBrowsePlugin;
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,gGAAyE;AACzE,oHAA6F;AAC7F,sGAA+E;AAC/E,gEAAyC;AAGzC,iDAA2E;AAC3E,uEAGmC;AACnC,oDAAuE;AAEvE,2DAG6B;AAE7B;IAAiD,uCAAM;IAAvD;QAAA,qEAyDC;QAxDC,UAAI,GAAG,qBAAqB,CAAA;;IAwD9B,CAAC;IAtDC,qCAAO,GAAP,UAAQ,aAA4B;QAClC,aAAa,CAAC,cAAc,CAC1B;YACE,OAAA,IAAI,qBAAW,CAAC;gBACd,IAAI,EAAE,eAAe;gBACrB,YAAY,EAAE,4BAAyB;gBACvC,eAAe,EAAE;oBACf,OAAA,iEAAO,+BAA+B,OAAE,IAAI,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,OAAO,EAAT,CAAS,CAAC;gBAA5D,CAA4D;aAC/D,CAAC;QALF,CAKE,CACL,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,UAAC,cAA8B;YAC7B,OAAO,UACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB;gBAEpB,IAAM,UAAU,GAAG,oBAAoB,CAAA;gBACvC,IAAM,WAAW,GAAG,eAAe,CAAA;gBACnC,IAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;gBAClC,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,eAAe,EAAE,IAAI;qBACtB,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,wBAAwB,CACpC;YACE,OAAA,IAAI,+BAAqB,CAAC;gBACxB,IAAI,EAAE,2BAA2B;gBACjC,YAAY,EAAE,uCAA2B;gBACzC,YAAY,EAAE,uCAA8B;gBAC5C,WAAW,EAAE,iCAAiC;aAC/C,CAAC;QALF,CAKE,CACL,CAAA;QAED,aAAa,CAAC,iBAAiB,CAC7B;YACE,OAAA,IAAI,wBAAc,CAAC;gBACjB,IAAI,EAAE,oBAAoB;gBAC1B,YAAY,EAAE,iCAAoB;gBAClC,UAAU,EAAE,IAAA,iCAAoB,EAAC,aAAa,CAAC;gBAC/C,WAAW,EAAE,gBAAgB;gBAC7B,WAAW,EAAE,4BAA4B;gBACzC,GAAG,EAAE,gBAAgB;aACtB,CAAC;QAPF,CAOE,CACL,CAAA;IACH,CAAC;IACH,0BAAC;AAAD,CAAC,AAzDD,CAAiD,gBAAM,GAyDtD"}

package/esm/JBrowse1Connection/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/JBrowse1Connection/configSchema.js

@@ -0,0 +1,18 @@
+import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('JBrowse1Connection', {
+    dataDirLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: 'http://mysite.com/jbrowse/data/',
+            locationType: 'UriLocation',
+        },
+        description: 'the location of the JBrowse 1 data directory, often something like http://mysite.com/jbrowse/data/',
+    },
+    assemblyNames: {
+        description: 'name of the assembly the connection belongs to, should be a single entry',
+        type: 'stringArray',
+        defaultValue: [],
+    },
+}, { baseConfiguration: baseConnectionConfig });
+//# sourceMappingURL=configSchema.js.map

package/esm/JBrowse1Connection/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,oBAAoB,EAAE,MAAM,4CAA4C,CAAA;AACjF,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,oBAAoB,EACpB;IACE,eAAe,EAAE;QACf,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,iCAAiC;YACtC,YAAY,EAAE,aAAa;SAC5B;QACD,WAAW,EACT,oGAAoG;KACvG;IACD,aAAa,EAAE;QACb,WAAW,EACT,0EAA0E;QAC5E,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,iBAAiB,EAAE,oBAAoB,EAAE,CAC5C,CAAA"}

package/esm/JBrowse1Connection/index.d.ts

@@ -0,0 +1,2 @@
+export { default as modelFactory } from './model';
+export { default as configSchema } from './configSchema';

package/esm/JBrowse1Connection/index.js

@@ -0,0 +1,3 @@
+export { default as modelFactory } from './model';
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/JBrowse1Connection/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,SAAS,CAAA;AACjD,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/JBrowse1Connection/jb1ConfigLoad.d.ts

@@ -0,0 +1,36 @@
+import { JBLocation, Config } from './types';
+export declare function fetchJb1(dataRoot?: JBLocation, baseConfig?: Config, baseConfigRoot?: JBLocation): Promise<Config>;
+export declare function createFinalConfig(baseConfig: Config, defaults?: {
+    tracks: never[];
+    containerID: string;
+    dataRoot: string;
+    show_tracklist: boolean;
+    show_nav: boolean;
+    show_menu: boolean;
+    show_overview: boolean;
+    show_fullviewlink: boolean;
+    update_browser_title: boolean;
+    updateBrowserURL: boolean;
+    refSeqs: string;
+    include: string[];
+    nameUrl: string;
+    datasets: {
+        _DEFAULT_EXAMPLES: boolean;
+        volvox: {
+            url: string;
+            name: string;
+        };
+        modencode: {
+            url: string;
+            name: string;
+        };
+        yeast: {
+            url: string;
+            name: string;
+        };
+    };
+    highlightSearchedRegions: boolean;
+    highResolutionMode: string;
+}): Promise<Config>;
+export declare function fetchConfigFile(location: JBLocation): Promise<Config>;
+export declare function parseJb1(config: string, url?: string): Config;