@jbrowse/plugin-sequence 1.6.7 → 1.7.0

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": "1.6.7",
+  "version": "1.7.0",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -18,15 +18,12 @@
   "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",
@@ -55,5 +52,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "02012ec299c36647f755316571775d36b0fee5ec"
+  "gitHead": "cc13844074d11881d211342a6a7eea113561b70b"
 }

package/src/IndexedFastaAdapter/IndexedFastaAdapter.ts

@@ -57,11 +57,6 @@ export default class extends BaseSequenceAdapter {
     }))
   }
 
-  /**
-   * Fetch features for a certain region
-   * @param param -
-   * @returns Observable of Feature objects in the region
-   */
   public getFeatures(region: NoAssemblyRegion, opts?: BaseOptions) {
     const { refName, start, end } = region
     return ObservableCreate<Feature>(async observer => {

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 {