@jbrowse/plugin-sequence 1.6.9 → 1.7.3

package/dist/index.js

@@ -1,8 +1,327 @@
+"use strict";
 
-'use strict'
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-if (process.env.NODE_ENV === 'production') {
-  module.exports = require('./plugin-sequence.cjs.production.min.js')
-} else {
-  module.exports = require('./plugin-sequence.cjs.development.js')
-}
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+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 _models = require("@jbrowse/core/pluggableElementTypes/models");
+
+var _FeatureRendererType2 = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType"));
+
+var _TrackType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
+
+var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
+
+var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
+
+var _tracks = require("@jbrowse/core/util/tracks");
+
+var _BgzipFastaAdapter = require("./BgzipFastaAdapter");
+
+var _ChromSizesAdapter = require("./ChromSizesAdapter");
+
+var _DivSequenceRenderer = require("./DivSequenceRenderer");
+
+var _IndexedFastaAdapter = require("./IndexedFastaAdapter");
+
+var _LinearReferenceSequenceDisplay = require("./LinearReferenceSequenceDisplay");
+
+var _TwoBitAdapter = require("./TwoBitAdapter");
+
+var _GCContentAdapter = _interopRequireDefault(require("./GCContentAdapter"));
+
+var _referenceSeqTrackConfig = require("./referenceSeqTrackConfig");
+
+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 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 _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; } }
+
+/* adjust in both directions */
+var DivSequenceRenderer = /*#__PURE__*/function (_FeatureRendererType) {
+  (0, _inherits2["default"])(DivSequenceRenderer, _FeatureRendererType);
+
+  var _super = _createSuper(DivSequenceRenderer);
+
+  function DivSequenceRenderer() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, DivSequenceRenderer);
+
+    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), "supportsSVG", true);
+    return _this;
+  }
+
+  (0, _createClass2["default"])(DivSequenceRenderer, [{
+    key: "getExpandedRegion",
+    value: function getExpandedRegion(region) {
+      return _objectSpread(_objectSpread({}, region), {}, {
+        start: Math.max(region.start - 3, 0),
+        end: region.end + 3
+      });
+    }
+  }]);
+  return DivSequenceRenderer;
+}(_FeatureRendererType2["default"]);
+
+var SequencePlugin = /*#__PURE__*/function (_Plugin) {
+  (0, _inherits2["default"])(SequencePlugin, _Plugin);
+
+  var _super2 = _createSuper(SequencePlugin);
+
+  function SequencePlugin() {
+    var _this2;
+
+    (0, _classCallCheck2["default"])(this, SequencePlugin);
+
+    for (var _len2 = arguments.length, args = new Array(_len2), _key2 = 0; _key2 < _len2; _key2++) {
+      args[_key2] = arguments[_key2];
+    }
+
+    _this2 = _super2.call.apply(_super2, [this].concat(args));
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this2), "name", 'SequencePlugin');
+    return _this2;
+  }
+
+  (0, _createClass2["default"])(SequencePlugin, [{
+    key: "install",
+    value: function install(pluginManager) {
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'TwoBitAdapter',
+          configSchema: _TwoBitAdapter.configSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
+          getAdapterClass: function getAdapterClass() {
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('./TwoBitAdapter/TwoBitAdapter'));
+            }).then(function (r) {
+              return r["default"];
+            });
+          }
+        });
+      });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.2bit$/i;
+          var adapterName = 'TwoBitAdapter';
+          var fileName = (0, _tracks.getFileName)(file);
+          var obj = {
+            type: adapterName,
+            twoBitLocation: file
+          };
+
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'TwoBitAdapter') {
+            return 'ReferenceSequenceTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'ChromSizesAdapter',
+          configSchema: _ChromSizesAdapter.configSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
+          getAdapterClass: function getAdapterClass() {
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('./ChromSizesAdapter/ChromSizesAdapter'));
+            }).then(function (r) {
+              return r["default"];
+            });
+          }
+        });
+      });
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'IndexedFastaAdapter',
+          configSchema: _IndexedFastaAdapter.configSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
+          getAdapterClass: function getAdapterClass() {
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('./IndexedFastaAdapter/IndexedFastaAdapter'));
+            }).then(function (r) {
+              return r["default"];
+            });
+          }
+        });
+      });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.(fa|fasta|fas|fna|mfa)$/i;
+          var adapterName = 'IndexedFastaAdapter';
+          var fileName = (0, _tracks.getFileName)(file);
+          var obj = {
+            type: adapterName,
+            fastaLocation: file,
+            faiLocation: index || (0, _tracks.makeIndex)(file, '.fai')
+          };
+
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'IndexedFastaAdapter') {
+            return 'ReferenceSequenceTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'BgzipFastaAdapter',
+          configSchema: _BgzipFastaAdapter.configSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
+          getAdapterClass: function getAdapterClass() {
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('./BgzipFastaAdapter/BgzipFastaAdapter'));
+            }).then(function (r) {
+              return r["default"];
+            });
+          }
+        });
+      });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.(fa|fasta|fas|fna|mfa)\.b?gz$/i;
+          var adapterName = 'BgzipFastaAdapter';
+          var fileName = (0, _tracks.getFileName)(file);
+          var obj = {
+            type: adapterName,
+            faiLocation: (0, _tracks.makeIndex)(file, '.fai'),
+            gziLocation: (0, _tracks.makeIndex)(file, '.gzi')
+          };
+
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'BgzipFastaAdapter') {
+            return 'ReferenceSequenceTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"](_objectSpread({
+          name: 'GCContentAdapter',
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          }
+        }, pluginManager.load(_GCContentAdapter["default"])));
+      });
+      pluginManager.addTrackType(function () {
+        var configSchema = (0, _referenceSeqTrackConfig.createReferenceSeqTrackConfig)(pluginManager);
+        return new _TrackType["default"]({
+          name: 'ReferenceSequenceTrack',
+          configSchema: configSchema,
+          stateModel: (0, _models.createBaseTrackModel)(pluginManager, 'ReferenceSequenceTrack', configSchema)
+        });
+      });
+      pluginManager.addDisplayType(function () {
+        var stateModel = (0, _LinearReferenceSequenceDisplay.modelFactory)(_LinearReferenceSequenceDisplay.configSchema);
+        return {
+          name: 'LinearReferenceSequenceDisplay',
+          configSchema: _LinearReferenceSequenceDisplay.configSchema,
+          stateModel: stateModel,
+          trackType: 'ReferenceSequenceTrack',
+          viewType: 'LinearGenomeView',
+          ReactComponent: _pluginLinearGenomeView.BaseLinearDisplayComponent
+        };
+      });
+      pluginManager.addRendererType(function () {
+        return new DivSequenceRenderer({
+          name: 'DivSequenceRenderer',
+          ReactComponent: _DivSequenceRenderer.ReactComponent,
+          configSchema: _DivSequenceRenderer.configSchema,
+          pluginManager: pluginManager
+        });
+      });
+    }
+  }]);
+  return SequencePlugin;
+}(_Plugin2["default"]);
+
+exports["default"] = SequencePlugin;

package/dist/index.test.js

@@ -0,0 +1,29 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _ = _interopRequireDefault(require("."));
+
+test('plugin in a stock JBrowse', function () {
+  console.warn = jest.fn();
+  var pluginManager = new _PluginManager["default"]([new _["default"]()]);
+  pluginManager.createPluggableElements();
+  pluginManager.configure();
+  expect(function () {
+    return pluginManager.addPlugin(new _["default"]());
+  }).toThrow(/JBrowse already configured, cannot add plugins/);
+  var TwoBitAdapter = pluginManager.getAdapterType('TwoBitAdapter');
+  var config = TwoBitAdapter.configSchema.create({
+    type: 'TwoBitAdapter'
+  });
+  expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
+  var IndexedFastaAdapter = pluginManager.getAdapterType('IndexedFastaAdapter');
+  var config2 = IndexedFastaAdapter.configSchema.create({
+    type: 'IndexedFastaAdapter'
+  });
+  expect((0, _mobxStateTree.getSnapshot)(config2)).toMatchSnapshot();
+});

package/dist/referenceSeqTrackConfig.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+import PluginManager from '@jbrowse/core/PluginManager';
+export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/dist/referenceSeqTrackConfig.js

@@ -0,0 +1,88 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.createReferenceSeqTrackConfig = createReferenceSeqTrackConfig;
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+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; }
+
+/*
+Note: this is primarily a copy of createBaseTrackConfig, except with a subset
+of the config slots, to avoid including fields that don't make sense for the
+ReferenceSequenceTrack
+*/
+function createReferenceSeqTrackConfig(pluginManager) {
+  return (0, _configuration.ConfigurationSchema)('ReferenceSequenceTrack', {
+    adapter: pluginManager.pluggableConfigSchemaType('adapter'),
+    displays: _mobxStateTree.types.array(pluginManager.pluggableConfigSchemaType('display')),
+    metadata: {
+      type: 'frozen',
+      description: 'anything to add about this track',
+      defaultValue: {}
+    }
+  }, {
+    preProcessSnapshot: function preProcessSnapshot(s) {
+      var snap = JSON.parse(JSON.stringify(s));
+      var displayTypes = new Set();
+      var _snap$displays = snap.displays,
+          displays = _snap$displays === void 0 ? [] : _snap$displays;
+
+      if (snap.trackId !== 'placeholderId') {
+        // Gets the displays on the track snapshot and the possible displays
+        // from the track type and adds any missing possible displays to the
+        // snapshot
+        displays.forEach(function (d) {
+          return d && displayTypes.add(d.type);
+        });
+        var trackType = pluginManager.getTrackType(snap.type);
+        trackType.displayTypes.forEach(function (displayType) {
+          if (!displayTypes.has(displayType.name)) {
+            displays.push({
+              displayId: "".concat(snap.trackId, "-").concat(displayType.name),
+              type: displayType.name
+            });
+          }
+        });
+      }
+
+      return _objectSpread(_objectSpread({}, snap), {}, {
+        displays: displays
+      });
+    },
+    explicitIdentifier: 'trackId',
+    explicitlyTyped: true,
+    actions: function actions(self) {
+      return {
+        addDisplayConf: function addDisplayConf(displayConf) {
+          var type = displayConf.type;
+
+          if (!type) {
+            throw new Error("unknown display type ".concat(type));
+          }
+
+          var display = self.displays.find(function (d) {
+            return d && d.displayId === displayConf.displayId;
+          });
+
+          if (display) {
+            return display;
+          }
+
+          var length = self.displays.push(displayConf);
+          return self.displays[length - 1];
+        }
+      };
+    }
+  });
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "1.6.9",
+  "version": "1.7.3",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -18,21 +18,19 @@
   "distMain": "dist/index.js",
   "srcMain": "src/index.ts",
   "main": "dist/index.js",
-  "distModule": "dist/plugin-sequence.esm.js",
-  "module": "dist/plugin-sequence.esm.js",
   "files": [
     "dist",
     "src"
   ],
   "scripts": {
-    "start": "tsdx watch --verbose --noClean",
-    "build": "tsdx build",
+    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
     "test": "cd ../..; jest plugins/sequence",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js"
+    "useSrc": "node ../../scripts/useSrc.js",
+    "postbuild": "tsc --build tsconfig.build.json"
   },
   "dependencies": {
     "@gmod/indexedfasta": "^2.0.2",
@@ -55,5 +53,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "f6c3d4edfadc26f7ac635a2fa7259f50f0c7e5e3"
+  "gitHead": "09b13c85acf4ac68dd71ab23af87656c7552fdaf"
 }

package/src/index.ts

@@ -1,13 +1,17 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import { Region } from '@jbrowse/core/util/types'
+import { Region, FileLocation } from '@jbrowse/core/util/types'
 import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
 import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
-import { FileLocation } from '@jbrowse/core/util/types'
-import { makeIndex } from '@jbrowse/core/util/tracks'
+import {
+  makeIndex,
+  AdapterGuesser,
+  getFileName,
+  TrackTypeGuesser,
+} from '@jbrowse/core/util/tracks'
 import { configSchema as bgzipFastaAdapterConfigSchema } from './BgzipFastaAdapter'
 import { configSchema as chromSizesAdapterConfigSchema } from './ChromSizesAdapter'
 import {
@@ -22,11 +26,6 @@ import {
 import { configSchema as twoBitAdapterConfigSchema } from './TwoBitAdapter'
 import GCContentAdapterF from './GCContentAdapter'
 import { createReferenceSeqTrackConfig } from './referenceSeqTrackConfig'
-import {
-  AdapterGuesser,
-  getFileName,
-  TrackTypeGuesser,
-} from '@jbrowse/core/util/tracks'
 
 /* adjust in both directions */
 class DivSequenceRenderer extends FeatureRendererType {

package/dist/DivSequenceRenderer/components/DivSequenceRendering.test.d.ts

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

package/dist/index.test.d.ts

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