@jbrowse/plugin-alignments 1.6.9 → 1.7.3

package/dist/LinearPileupDisplay/configSchema.js

@@ -0,0 +1,47 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
+
+var _mobxStateTree = require("mobx-state-tree");
+
+function PileupConfigFactory(pluginManager) {
+  var PileupRendererConfigSchema = pluginManager.getRendererType('PileupRenderer').configSchema;
+  var SvgFeatureRendererConfigSchema = pluginManager.getRendererType('SvgFeatureRenderer').configSchema; // modify config schema to take in a sub coverage display
+
+  return (0, _configuration.ConfigurationSchema)('LinearPileupDisplay', {
+    defaultRendering: {
+      type: 'stringEnum',
+      model: _mobxStateTree.types.enumeration('Rendering', ['pileup', 'svg']),
+      defaultValue: 'pileup'
+    },
+    renderers: (0, _configuration.ConfigurationSchema)('RenderersConfiguration', {
+      PileupRenderer: PileupRendererConfigSchema,
+      SvgFeatureRenderer: SvgFeatureRendererConfigSchema
+    }),
+    renderer: '',
+    maxFeatureScreenDensity: {
+      type: 'number',
+      description: 'maximum features per pixel that is displayed in the view',
+      defaultValue: 5
+    },
+    colorScheme: {
+      type: 'stringEnum',
+      model: _mobxStateTree.types.enumeration('colorScheme', ['strand', 'normal', 'insertSize', 'insertSizeAndOrientation', 'mappingQuality', 'tag']),
+      description: 'color scheme to use',
+      defaultValue: 'normal'
+    }
+  }, {
+    baseConfiguration: (0, _pluginLinearGenomeView.linearBasicDisplayConfigSchemaFactory)(pluginManager),
+    explicitlyTyped: true
+  });
+}
+
+var _default = PileupConfigFactory;
+exports["default"] = _default;

package/dist/LinearPileupDisplay/configSchema.test.js

@@ -0,0 +1,92 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+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 _Plugin3 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
+
+var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
+
+var _BoxRendererType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType"));
+
+var _pluginSvg = require("@jbrowse/plugin-svg");
+
+var _PileupRenderer = _interopRequireDefault(require("../PileupRenderer"));
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+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; } }
+
+// mock warnings to avoid unnecessary outputs
+beforeEach(function () {
+  jest.spyOn(console, 'warn').mockImplementation(function () {});
+});
+afterEach(function () {
+  console.warn.mockRestore();
+});
+
+var PileupRendererPlugin = /*#__PURE__*/function (_Plugin) {
+  (0, _inherits2["default"])(PileupRendererPlugin, _Plugin);
+
+  var _super = _createSuper(PileupRendererPlugin);
+
+  function PileupRendererPlugin() {
+    (0, _classCallCheck2["default"])(this, PileupRendererPlugin);
+    return _super.apply(this, arguments);
+  }
+
+  (0, _createClass2["default"])(PileupRendererPlugin, [{
+    key: "install",
+    value: function install(pluginManager) {
+      (0, _PileupRenderer["default"])(pluginManager);
+    }
+  }]);
+  return PileupRendererPlugin;
+}(_Plugin3["default"]);
+
+var SvgFeatureRendererPlugin = /*#__PURE__*/function (_Plugin2) {
+  (0, _inherits2["default"])(SvgFeatureRendererPlugin, _Plugin2);
+
+  var _super2 = _createSuper(SvgFeatureRendererPlugin);
+
+  function SvgFeatureRendererPlugin() {
+    (0, _classCallCheck2["default"])(this, SvgFeatureRendererPlugin);
+    return _super2.apply(this, arguments);
+  }
+
+  (0, _createClass2["default"])(SvgFeatureRendererPlugin, [{
+    key: "install",
+    value: function install(pluginManager) {
+      pluginManager.addRendererType(function () {
+        return new _BoxRendererType["default"]({
+          name: 'SvgFeatureRenderer',
+          ReactComponent: _pluginSvg.SvgFeatureRendererReactComponent,
+          configSchema: _pluginSvg.svgFeatureRendererConfigSchema,
+          pluginManager: pluginManager
+        });
+      });
+    }
+  }]);
+  return SvgFeatureRendererPlugin;
+}(_Plugin3["default"]);
+
+test('has a type attr', function () {
+  var configSchema = (0, _configSchema["default"])(new _PluginManager["default"]([new PileupRendererPlugin(), new SvgFeatureRendererPlugin()]).createPluggableElements().configure());
+  var config = configSchema.create({
+    type: 'LinearPileupDisplay',
+    displayId: 'display0',
+    name: 'Zonker Display'
+  });
+  expect(config.type).toEqual('LinearPileupDisplay');
+});

package/dist/LinearPileupDisplay/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-export default function register(pluginManager: PluginManager): void;
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function register(pluginManager: PluginManager): void;

package/dist/LinearPileupDisplay/index.js

@@ -0,0 +1,30 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = register;
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+var _model = _interopRequireDefault(require("./model"));
+
+var _DisplayType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+
+var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
+
+function register(pluginManager) {
+  pluginManager.addDisplayType(function () {
+    var configSchema = (0, _configSchema["default"])(pluginManager);
+    return new _DisplayType["default"]({
+      name: 'LinearPileupDisplay',
+      configSchema: configSchema,
+      stateModel: (0, _model["default"])(configSchema),
+      trackType: 'AlignmentsTrack',
+      viewType: 'LinearGenomeView',
+      ReactComponent: _pluginLinearGenomeView.BaseLinearDisplayComponent
+    });
+  });
+}