@jbrowse/plugin-alignments 1.7.0 → 1.7.4

package/dist/index.js

@@ -7,7 +7,7 @@ var _typeof = require("@babel/runtime/helpers/typeof");
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = exports.MismatchParser = void 0;
+exports.default = exports.MismatchParser = void 0;
 
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
@@ -57,36 +57,36 @@ var _tracks = require("@jbrowse/core/util/tracks");
 
 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 _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 _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 AlignmentsPlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2["default"])(AlignmentsPlugin, _Plugin);
+  (0, _inherits2.default)(AlignmentsPlugin, _Plugin);
 
   var _super = _createSuper(AlignmentsPlugin);
 
   function AlignmentsPlugin() {
     var _this;
 
-    (0, _classCallCheck2["default"])(this, AlignmentsPlugin);
+    (0, _classCallCheck2.default)(this, AlignmentsPlugin);
 
     for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
       args[_key] = arguments[_key];
     }
 
     _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "name", 'AlignmentsPlugin');
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'AlignmentsPlugin');
     return _this;
   }
 
-  (0, _createClass2["default"])(AlignmentsPlugin, [{
+  (0, _createClass2.default)(AlignmentsPlugin, [{
     key: "install",
     value: function install(pluginManager) {
       ;
-      [_BamAdapter["default"], _CramAdapter["default"], _LinearPileupDisplay["default"], _LinearSNPCoverageDisplay["default"], _AlignmentsTrack["default"], _SNPCoverageAdapter["default"], _HtsgetBamAdapter["default"], _PileupRenderer["default"], _SNPCoverageRenderer["default"], _LinearAlignmentsDisplay["default"], _AlignmentsFeatureDetail["default"]].map(function (f) {
+      [_BamAdapter.default, _CramAdapter.default, _LinearPileupDisplay.default, _LinearSNPCoverageDisplay.default, _AlignmentsTrack.default, _SNPCoverageAdapter.default, _HtsgetBamAdapter.default, _PileupRenderer.default, _SNPCoverageRenderer.default, _LinearAlignmentsDisplay.default, _AlignmentsFeatureDetail.default].map(function (f) {
         return f(pluginManager);
       });
       pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
@@ -151,6 +151,6 @@ var AlignmentsPlugin = /*#__PURE__*/function (_Plugin) {
     }
   }]);
   return AlignmentsPlugin;
-}(_Plugin2["default"]);
+}(_Plugin2.default);
 
-exports["default"] = AlignmentsPlugin;
+exports.default = AlignmentsPlugin;

package/dist/index.test.js

@@ -12,11 +12,11 @@ var _ = _interopRequireDefault(require("."));
 
 test('plugin in a stock JBrowse', function () {
   console.warn = jest.fn();
-  var pluginManager = new _PluginManager["default"]([new _["default"](), new _pluginSvg["default"]()]);
+  var pluginManager = new _PluginManager.default([new _.default(), new _pluginSvg.default()]);
   pluginManager.createPluggableElements();
   pluginManager.configure();
   expect(function () {
-    return pluginManager.addPlugin(new _["default"]());
+    return pluginManager.addPlugin(new _.default());
   }).toThrow(/JBrowse already configured, cannot add plugins/);
   var BamAdapter = pluginManager.getAdapterType('BamAdapter');
   var config = BamAdapter.configSchema.create({

package/dist/shared.d.ts

@@ -1,25 +1,25 @@
-import { BlockSet } from '@jbrowse/core/util/blockTypes';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-export declare function getUniqueTagValues(self: IAnyStateTreeNode & {
-    adapterConfig: AnyConfigurationModel;
-}, colorScheme: {
-    type: string;
-    tag?: string;
-}, blocks: BlockSet, opts?: {
-    headers?: Record<string, string>;
-    signal?: AbortSignal;
-    filters?: string[];
-}): Promise<string[]>;
-export declare function getUniqueModificationValues(self: IAnyStateTreeNode & {
-    parentTrack: IAnyStateTreeNode & {
-        configuration: AnyConfigurationModel;
-    };
-}, adapterConfig: AnyConfigurationModel, colorScheme: {
-    type: string;
-    tag?: string;
-}, blocks: BlockSet, opts?: {
-    headers?: Record<string, string>;
-    signal?: AbortSignal;
-    filters?: string[];
-}): Promise<string[]>;
+import { BlockSet } from '@jbrowse/core/util/blockTypes';
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+export declare function getUniqueTagValues(self: IAnyStateTreeNode & {
+    adapterConfig: AnyConfigurationModel;
+}, colorScheme: {
+    type: string;
+    tag?: string;
+}, blocks: BlockSet, opts?: {
+    headers?: Record<string, string>;
+    signal?: AbortSignal;
+    filters?: string[];
+}): Promise<string[]>;
+export declare function getUniqueModificationValues(self: IAnyStateTreeNode & {
+    parentTrack: IAnyStateTreeNode & {
+        configuration: AnyConfigurationModel;
+    };
+}, adapterConfig: AnyConfigurationModel, colorScheme: {
+    type: string;
+    tag?: string;
+}, blocks: BlockSet, opts?: {
+    headers?: Record<string, string>;
+    signal?: AbortSignal;
+    filters?: string[];
+}): Promise<string[]>;

package/dist/shared.js

@@ -20,17 +20,17 @@ var _tracks = require("@jbrowse/core/util/tracks");
 
 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 _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 getUniqueTagValues(_x, _x2, _x3, _x4) {
   return _getUniqueTagValues.apply(this, arguments);
 }
 
 function _getUniqueTagValues() {
-  _getUniqueTagValues = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(self, colorScheme, blocks, opts) {
+  _getUniqueTagValues = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(self, colorScheme, blocks, opts) {
     var _getSession, rpcManager, adapterConfig, sessionId, values;
 
-    return _regenerator["default"].wrap(function _callee$(_context) {
+    return _regenerator.default.wrap(function _callee$(_context) {
       while (1) {
         switch (_context.prev = _context.next) {
           case 0:
@@ -64,10 +64,10 @@ function getUniqueModificationValues(_x5, _x6, _x7, _x8, _x9) {
 }
 
 function _getUniqueModificationValues() {
-  _getUniqueModificationValues = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(self, adapterConfig, colorScheme, blocks, opts) {
+  _getUniqueModificationValues = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(self, adapterConfig, colorScheme, blocks, opts) {
     var _getSession2, rpcManager, sessionId, values;
 
-    return _regenerator["default"].wrap(function _callee2$(_context2) {
+    return _regenerator.default.wrap(function _callee2$(_context2) {
       while (1) {
         switch (_context2.prev = _context2.next) {
           case 0:

package/dist/util.d.ts

@@ -1,19 +1,19 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AugmentedRegion } from '@jbrowse/core/util';
-export declare function getTag(feature: Feature, tag: string): any;
-export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
-export declare const orientationTypes: {
-    fr: {
-        [key: string]: string;
-    };
-    rf: {
-        [key: string]: string;
-    };
-    ff: {
-        [key: string]: string;
-    };
-};
-export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
-export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
-export declare function shouldFetchReferenceSequence(type?: string): boolean;
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { AugmentedRegion } from '@jbrowse/core/util';
+export declare function getTag(feature: Feature, tag: string): any;
+export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
+export declare const orientationTypes: {
+    fr: {
+        [key: string]: string;
+    };
+    rf: {
+        [key: string]: string;
+    };
+    ff: {
+        [key: string]: string;
+    };
+};
+export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
+export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
+export declare function shouldFetchReferenceSequence(type?: string): boolean;

package/dist/util.js

@@ -22,7 +22,7 @@ var _operators = require("rxjs/operators");
 
 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 _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; }
 
 // get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
 // BAM does not
@@ -101,11 +101,11 @@ function fetchSequence(_x, _x2) {
 
 
 function _fetchSequence() {
-  _fetchSequence = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(region, adapter) {
+  _fetchSequence = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(region, adapter) {
     var _feats$;
 
     var end, originalRefName, refName, feats;
-    return _regenerator["default"].wrap(function _callee$(_context) {
+    return _regenerator.default.wrap(function _callee$(_context) {
       while (1) {
         switch (_context.prev = _context.next) {
           case 0:

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "1.7.0",
+  "version": "1.7.4",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -24,6 +24,7 @@
   ],
   "scripts": {
     "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
+    "postbuild": "tsc --build tsconfig.build.json",
     "test": "cd ../..; jest plugins/alignments",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
@@ -32,15 +33,14 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
+    "@babel/runtime": "^7.17.9",
     "@gmod/bam": "^1.1.15",
     "@gmod/cram": "^1.6.1",
     "@material-ui/icons": "^4.9.1",
-    "abortable-promise-cache": "^1.5.0",
     "color": "^3.1.2",
     "copy-to-clipboard": "^3.3.1",
     "fast-deep-equal": "^3.1.3",
-    "generic-filehandle": "^2.2.2",
-    "json-stable-stringify": "^1.0.1"
+    "generic-filehandle": "^2.2.2"
   },
   "peerDependencies": {
     "@jbrowse/core": "^1.0.0",
@@ -57,5 +57,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "cc13844074d11881d211342a6a7eea113561b70b"
+  "gitHead": "0a3e0c58055bbab8e3ab0270c139291b96eff403"
 }

package/dist/AlignmentsFeatureDetail/index.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/LinearAlignmentsDisplay/models/configSchema.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/LinearPileupDisplay/configSchema.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/LinearSNPCoverageDisplay/models/configSchema.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/PileupRenderer/components/PileupRendering.test.d.ts

@@ -1 +0,0 @@
-export {};