@jbrowse/plugin-variants 1.6.8 → 1.7.1

package/dist/ChordVariantDisplay/index.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/pluggableElementTypes").DisplayType;
-export default _default;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/pluggableElementTypes").DisplayType;
+export default _default;

package/dist/ChordVariantDisplay/index.js

@@ -0,0 +1,33 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _pluginCircularView = require("@jbrowse/plugin-circular-view");
+
+var _ChordVariantDisplay = _interopRequireDefault(require("./models/ChordVariantDisplay"));
+
+var _default = function _default(pluginManager) {
+  var lib = pluginManager.lib,
+      load = pluginManager.load;
+  var DisplayType = lib['@jbrowse/core/pluggableElementTypes/DisplayType'];
+
+  var _load = load(_ChordVariantDisplay["default"]),
+      stateModel = _load.stateModel,
+      configSchema = _load.configSchema;
+
+  return new DisplayType({
+    name: 'ChordVariantDisplay',
+    configSchema: configSchema,
+    stateModel: stateModel,
+    trackType: 'VariantTrack',
+    viewType: 'CircularView',
+    ReactComponent: (0, _pluginCircularView.BaseChordDisplayComponentFactory)(pluginManager)
+  });
+};
+
+exports["default"] = _default;

package/dist/ChordVariantDisplay/models/ChordVariantDisplay.d.ts

@@ -1,5 +1,5 @@
-export default ChordVariantDisplayF;
-declare function ChordVariantDisplayF(pluginManager: any): {
-    stateModel: any;
-    configSchema: any;
-};
+export default ChordVariantDisplayF;
+declare function ChordVariantDisplayF(pluginManager: any): {
+    stateModel: any;
+    configSchema: any;
+};

package/dist/ChordVariantDisplay/models/ChordVariantDisplay.js

@@ -0,0 +1,76 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _pluginCircularView = require("@jbrowse/plugin-circular-view");
+
+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; }
+
+var ChordVariantDisplayF = function ChordVariantDisplayF(pluginManager) {
+  var jbrequire = pluginManager.jbrequire;
+
+  var _jbrequire = jbrequire('mobx-state-tree'),
+      types = _jbrequire.types;
+
+  var _jbrequire2 = jbrequire('@jbrowse/core/configuration'),
+      ConfigurationSchema = _jbrequire2.ConfigurationSchema,
+      ConfigurationReference = _jbrequire2.ConfigurationReference;
+
+  var _jbrequire3 = jbrequire('@jbrowse/core/util'),
+      getContainingView = _jbrequire3.getContainingView;
+
+  var _jbrequire4 = jbrequire('@jbrowse/core/util/tracks'),
+      getParentRenderProps = _jbrequire4.getParentRenderProps;
+
+  var configSchema = ConfigurationSchema('ChordVariantDisplay', {
+    renderer: types.optional(pluginManager.pluggableConfigSchemaType('renderer'), {
+      type: 'StructuralVariantChordRenderer'
+    })
+  }, {
+    baseConfiguration: _pluginCircularView.baseChordDisplayConfig,
+    explicitlyTyped: true
+  });
+  var stateModel = types.compose('ChordVariantDisplay', _pluginCircularView.BaseChordDisplayModel, types.model({
+    type: types.literal('ChordVariantDisplay'),
+    configuration: ConfigurationReference(configSchema)
+  })).views(function (self) {
+    return {
+      get rendererTypeName() {
+        return self.configuration.renderer.type;
+      },
+
+      renderProps: function renderProps() {
+        var view = getContainingView(self);
+        return _objectSpread(_objectSpread({}, getParentRenderProps(self)), {}, {
+          rpcDriverName: self.rpcDriverName,
+          displayModel: self,
+          bezierRadius: view.radiusPx * self.bezierRadiusRatio,
+          radius: view.radiusPx,
+          blockDefinitions: this.blockDefinitions,
+          config: self.configuration.renderer,
+          onChordClick: self.onChordClick
+        });
+      }
+    };
+  });
+  return {
+    stateModel: stateModel,
+    configSchema: configSchema
+  };
+}; // http://localhost:3000/test_data/hs37d5.HG002-SequelII-CCS.sv.vcf.gz.tbi
+// render request is for 1.5x the current viewing window
+// tracks all have a height
+//
+
+
+var _default = ChordVariantDisplayF;
+exports["default"] = _default;

package/dist/LinearVariantDisplay/configSchema.d.ts

@@ -1,5 +1,5 @@
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
-export declare function LinearVariantDisplayConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export declare type LinearVariantDisplayConfigModel = ReturnType<typeof LinearVariantDisplayConfigFactory>;
-export declare type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;
+import { Instance } from 'mobx-state-tree';
+import PluginManager from '@jbrowse/core/PluginManager';
+export declare function LinearVariantDisplayConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare type LinearVariantDisplayConfigModel = ReturnType<typeof LinearVariantDisplayConfigFactory>;
+export declare type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;

package/dist/LinearVariantDisplay/configSchema.js

@@ -0,0 +1,18 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.LinearVariantDisplayConfigFactory = LinearVariantDisplayConfigFactory;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
+
+function LinearVariantDisplayConfigFactory(pluginManager) {
+  var configSchema = (0, _pluginLinearGenomeView.linearBasicDisplayConfigSchemaFactory)(pluginManager);
+  return (0, _configuration.ConfigurationSchema)('LinearVariantDisplay', {}, {
+    baseConfiguration: configSchema,
+    explicitlyTyped: true
+  });
+}

package/dist/LinearVariantDisplay/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 _BoxRendererType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType"));
+
+var _Plugin3 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
+
+var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
+
+var _PileupRenderer = _interopRequireDefault(require("@jbrowse/plugin-alignments/src/PileupRenderer"));
+
+var _SvgFeatureRenderer = require("@jbrowse/plugin-svg/src/SvgFeatureRenderer");
+
+var _configSchema = 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: _SvgFeatureRenderer.ReactComponent,
+          configSchema: _SvgFeatureRenderer.configSchema,
+          pluginManager: pluginManager
+        });
+      });
+    }
+  }]);
+  return SvgFeatureRendererPlugin;
+}(_Plugin3["default"]);
+
+test('has a viewType attr', function () {
+  var configSchema = (0, _configSchema.LinearVariantDisplayConfigFactory)(new _PluginManager["default"]([new PileupRendererPlugin(), new SvgFeatureRendererPlugin()]).createPluggableElements().configure());
+  var config = configSchema.create({
+    type: 'LinearVariantDisplay',
+    displayId: 'diplayId0',
+    name: 'Zonker Display'
+  });
+  expect(config.type).toEqual('LinearVariantDisplay');
+});

package/dist/LinearVariantDisplay/index.d.ts

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

package/dist/LinearVariantDisplay/index.js

@@ -0,0 +1,23 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "configSchemaFactory", {
+  enumerable: true,
+  get: function get() {
+    return _configSchema.LinearVariantDisplayConfigFactory;
+  }
+});
+Object.defineProperty(exports, "modelFactory", {
+  enumerable: true,
+  get: function get() {
+    return _model["default"];
+  }
+});
+
+var _configSchema = require("./configSchema");
+
+var _model = _interopRequireDefault(require("./model"));