@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/dist/CramAdapter/CramAdapter.test.js

@@ -1,138 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _operators = require("rxjs/operators");
-
-var _genericFilehandle = require("generic-filehandle");
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _CramAdapter = _interopRequireDefault(require("./CramAdapter"));
-
-var _CramTestAdapters = require("./CramTestAdapters");
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-var pluginManager = new _PluginManager.default();
-var configSchema = pluginManager.load(_configSchema.default);
-
-var getVolvoxSequenceSubAdapter = /*#__PURE__*/function () {
-  var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            return _context.abrupt("return", {
-              dataAdapter: new _CramTestAdapters.SequenceAdapter(new _genericFilehandle.LocalFile(require.resolve('../../test_data/volvox.fa'))),
-              sessionIds: new Set()
-            });
-
-          case 1:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee);
-  }));
-
-  return function getVolvoxSequenceSubAdapter() {
-    return _ref.apply(this, arguments);
-  };
-}();
-
-test('adapter can fetch features from volvox-sorted.cram', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-  var adapter, features, featuresArray, featuresJsonArray;
-  return _regenerator.default.wrap(function _callee2$(_context2) {
-    while (1) {
-      switch (_context2.prev = _context2.next) {
-        case 0:
-          adapter = new _CramAdapter.default(configSchema.create({
-            cramLocation: {
-              localPath: require.resolve('../../test_data/volvox-sorted.cram'),
-              locationType: 'LocalPathLocation'
-            },
-            craiLocation: {
-              localPath: require.resolve('../../test_data/volvox-sorted.cram.crai'),
-              locationType: 'LocalPathLocation'
-            }
-          }), getVolvoxSequenceSubAdapter, pluginManager);
-          features = adapter.getFeatures({
-            assemblyName: 'volvox',
-            refName: 'ctgA',
-            start: 0,
-            end: 20000
-          });
-          _context2.next = 4;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 4:
-          featuresArray = _context2.sent;
-          expect(featuresArray[0].get('refName')).toBe('ctgA');
-          featuresJsonArray = featuresArray.map(function (f) {
-            return f.toJSON();
-          });
-          expect(featuresJsonArray.length).toEqual(3809);
-          expect(featuresJsonArray.slice(1000, 1010)).toMatchSnapshot();
-          expect(adapter.refIdToName(0)).toBe('ctgA');
-          expect(adapter.refIdToName(1)).toBe(undefined);
-          _context2.t0 = expect;
-          _context2.next = 14;
-          return adapter.hasDataForRefName('ctgA');
-
-        case 14:
-          _context2.t1 = _context2.sent;
-          (0, _context2.t0)(_context2.t1).toBe(true);
-
-        case 16:
-        case "end":
-          return _context2.stop();
-      }
-    }
-  }, _callee2);
-})));
-test('test usage of cramSlightlyLazyFeature toJSON (used in the widget)', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-  var adapter, features, featuresArray, f;
-  return _regenerator.default.wrap(function _callee3$(_context3) {
-    while (1) {
-      switch (_context3.prev = _context3.next) {
-        case 0:
-          adapter = new _CramAdapter.default(configSchema.create({
-            cramLocation: {
-              localPath: require.resolve('../../test_data/volvox-sorted.cram'),
-              locationType: 'LocalPathLocation'
-            },
-            craiLocation: {
-              localPath: require.resolve('../../test_data/volvox-sorted.cram.crai'),
-              locationType: 'LocalPathLocation'
-            }
-          }), getVolvoxSequenceSubAdapter, pluginManager);
-          features = adapter.getFeatures({
-            assemblyName: 'volvox',
-            refName: 'ctgA',
-            start: 0,
-            end: 100
-          });
-          _context3.next = 4;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 4:
-          featuresArray = _context3.sent;
-          f = featuresArray[0].toJSON();
-          expect(f.refName).toBe('ctgA');
-          expect(f.start).toBe(2);
-          expect(f.end).toBe(102); // don't pass the mismatches to the frontend
-
-          expect(f.mismatches).toEqual(undefined);
-
-        case 10:
-        case "end":
-          return _context3.stop();
-      }
-    }
-  }, _callee3);
-})));

package/dist/LinearAlignmentsDisplay/models/configSchema.test.js

@@ -1,83 +0,0 @@
-"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 _Plugin2 = _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 _SNPCoverageRenderer = _interopRequireDefault(require("../../SNPCoverageRenderer"));
-
-var _LinearPileupDisplay = _interopRequireDefault(require("../../LinearPileupDisplay"));
-
-var _LinearSNPCoverageDisplay = _interopRequireDefault(require("../../LinearSNPCoverageDisplay"));
-
-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 AlignmentsPlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2.default)(AlignmentsPlugin, _Plugin);
-
-  var _super = _createSuper(AlignmentsPlugin);
-
-  function AlignmentsPlugin() {
-    (0, _classCallCheck2.default)(this, AlignmentsPlugin);
-    return _super.apply(this, arguments);
-  }
-
-  (0, _createClass2.default)(AlignmentsPlugin, [{
-    key: "install",
-    value: function install(pluginManager) {
-      (0, _PileupRenderer.default)(pluginManager);
-      pluginManager.addRendererType(function () {
-        return new _BoxRendererType.default({
-          name: 'SvgFeatureRenderer',
-          ReactComponent: _pluginSvg.SvgFeatureRendererReactComponent,
-          configSchema: _pluginSvg.svgFeatureRendererConfigSchema,
-          pluginManager: pluginManager
-        });
-      });
-      (0, _SNPCoverageRenderer.default)(pluginManager);
-      (0, _LinearPileupDisplay.default)(pluginManager);
-      (0, _LinearSNPCoverageDisplay.default)(pluginManager);
-    }
-  }]);
-  return AlignmentsPlugin;
-}(_Plugin2.default);
-
-test('has a type attr', function () {
-  var configSchema = (0, _configSchema.default)(new _PluginManager.default([new AlignmentsPlugin()]).createPluggableElements().configure());
-  var config = configSchema.create({
-    type: 'LinearAlignmentsDisplay',
-    displayId: 'display0',
-    name: 'Zonker Display'
-  });
-  expect(config.type).toEqual('LinearAlignmentsDisplay');
-});

package/dist/LinearPileupDisplay/configSchema.test.js

@@ -1,92 +0,0 @@
-"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/LinearSNPCoverageDisplay/models/configSchema.test.js

@@ -1,62 +0,0 @@
-"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 _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _SNPCoverageRenderer = _interopRequireDefault(require("../../SNPCoverageRenderer"));
-
-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();
-}); // change renderer
-
-var SNPCoverageRendererPlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2.default)(SNPCoverageRendererPlugin, _Plugin);
-
-  var _super = _createSuper(SNPCoverageRendererPlugin);
-
-  function SNPCoverageRendererPlugin() {
-    (0, _classCallCheck2.default)(this, SNPCoverageRendererPlugin);
-    return _super.apply(this, arguments);
-  }
-
-  (0, _createClass2.default)(SNPCoverageRendererPlugin, [{
-    key: "install",
-    value: function install(pluginManager) {
-      (0, _SNPCoverageRenderer.default)(pluginManager);
-    }
-  }]);
-  return SNPCoverageRendererPlugin;
-}(_Plugin2.default);
-
-test('has a type attr', function () {
-  var configSchema = (0, _configSchema.default)(new _PluginManager.default([new SNPCoverageRendererPlugin()]).createPluggableElements().configure());
-  var config = configSchema.create({
-    type: 'LinearSNPCoverageDisplay',
-    displayId: 'display1',
-    name: 'SNPZonker Display'
-  });
-  expect(config.type).toEqual('LinearSNPCoverageDisplay');
-});

package/dist/PileupRenderer/components/PileupRendering.test.js

@@ -1,36 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _PrecomputedLayout = _interopRequireDefault(require("@jbrowse/core/util/layouts/PrecomputedLayout"));
-
-var _react = _interopRequireDefault(require("react"));
-
-var _react2 = require("@testing-library/react");
-
-var _PileupRendering = _interopRequireDefault(require("./PileupRendering"));
-
-// these tests do very little, let's try to expand them at some point
-test('one', function () {
-  var _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_PileupRendering.default, {
-    width: 500,
-    height: 500,
-    regions: [{
-      refName: 'zonk',
-      start: 1,
-      end: 3
-    }],
-    layout: new _PrecomputedLayout.default({
-      rectangles: {},
-      totalHeight: 20
-    }),
-    displayModel: {},
-    bpPerPx: 3,
-    config: {
-      type: 'DummyRenderer'
-    }
-  })),
-      container = _render.container;
-
-  expect(container.firstChild).toMatchSnapshot();
-});

package/dist/declare.d.js

@@ -1 +0,0 @@
-"use strict";

package/dist/index.test.js

@@ -1,26 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _pluginSvg = _interopRequireDefault(require("@jbrowse/plugin-svg"));
-
-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(), new _pluginSvg.default()]);
-  pluginManager.createPluggableElements();
-  pluginManager.configure();
-  expect(function () {
-    return pluginManager.addPlugin(new _.default());
-  }).toThrow(/JBrowse already configured, cannot add plugins/);
-  var BamAdapter = pluginManager.getAdapterType('BamAdapter');
-  var config = BamAdapter.configSchema.create({
-    type: 'BamAdapter'
-  });
-  expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
-});