@jbrowse/plugin-wiggle 1.7.11 → 2.0.0

package/dist/BigWigAdapter/BigWigAdapter.test.js

@@ -1,157 +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 _BigWigAdapter = _interopRequireDefault(require("./BigWigAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-describe('adapter can fetch features from volvox.bw', function () {
-  var adapter;
-  beforeEach(function () {
-    adapter = new _BigWigAdapter.default(_configSchema.default.create({
-      bigWigLocation: {
-        localPath: require.resolve('./test_data/volvox.bw'),
-        locationType: 'LocalPathLocation'
-      }
-    }));
-  });
-  it('test basic aspects of getfeatures', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-    var features, featuresArray, featuresJsonArray;
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            features = adapter.getFeatures({
-              refName: 'ctgA',
-              start: 0,
-              end: 20000,
-              assemblyName: 'volvox'
-            });
-            _context.t0 = expect;
-            _context.next = 4;
-            return adapter.refIdToName(0);
-
-          case 4:
-            _context.t1 = _context.sent;
-            (0, _context.t0)(_context.t1).toBe('ctgA');
-            _context.t2 = expect;
-            _context.next = 9;
-            return adapter.refIdToName(1);
-
-          case 9:
-            _context.t3 = _context.sent;
-            (0, _context.t2)(_context.t3).toBe(undefined);
-            _context.t4 = expect;
-            _context.next = 14;
-            return adapter.hasDataForRefName('ctgA');
-
-          case 14:
-            _context.t5 = _context.sent;
-            (0, _context.t4)(_context.t5).toBe(true);
-            _context.t6 = expect;
-            _context.next = 19;
-            return adapter.hasDataForRefName('ctgB');
-
-          case 19:
-            _context.t7 = _context.sent;
-            (0, _context.t6)(_context.t7).toBe(false);
-            _context.next = 23;
-            return features.pipe((0, _operators.toArray)()).toPromise();
-
-          case 23:
-            featuresArray = _context.sent;
-            featuresJsonArray = featuresArray.map(function (f) {
-              return f.toJSON();
-            });
-            expect(featuresJsonArray.slice(1000, 1010)).toMatchSnapshot();
-
-          case 26:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee);
-  })));
-  it('adapter can fetch stats from volvox.bw', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-    return _regenerator.default.wrap(function _callee2$(_context2) {
-      while (1) {
-        switch (_context2.prev = _context2.next) {
-          case 0:
-            _context2.t0 = expect;
-            _context2.next = 3;
-            return adapter.getGlobalStats();
-
-          case 3:
-            _context2.t1 = _context2.sent;
-            (0, _context2.t0)(_context2.t1).toMatchSnapshot();
-
-          case 5:
-          case "end":
-            return _context2.stop();
-        }
-      }
-    }, _callee2);
-  })));
-  it('get region stats', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-    return _regenerator.default.wrap(function _callee3$(_context3) {
-      while (1) {
-        switch (_context3.prev = _context3.next) {
-          case 0:
-            _context3.t0 = expect;
-            _context3.next = 3;
-            return adapter.getRegionStats({
-              refName: 'ctgA',
-              start: 10000,
-              end: 40000,
-              assemblyName: 'volvox'
-            });
-
-          case 3:
-            _context3.t1 = _context3.sent;
-            (0, _context3.t0)(_context3.t1).toMatchSnapshot();
-
-          case 5:
-          case "end":
-            return _context3.stop();
-        }
-      }
-    }, _callee3);
-  })));
-  it('get local stats', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
-    return _regenerator.default.wrap(function _callee4$(_context4) {
-      while (1) {
-        switch (_context4.prev = _context4.next) {
-          case 0:
-            _context4.t0 = expect;
-            _context4.next = 3;
-            return adapter.getMultiRegionStats([{
-              refName: 'ctgA',
-              start: 10000,
-              end: 39999,
-              assemblyName: 'volvox'
-            }, {
-              refName: 'ctgB',
-              start: 0,
-              end: 99,
-              assemblyName: 'volvox'
-            }]);
-
-          case 3:
-            _context4.t1 = _context4.sent;
-            (0, _context4.t0)(_context4.t1).toMatchSnapshot();
-
-          case 5:
-          case "end":
-            return _context4.stop();
-        }
-      }
-    }, _callee4);
-  })));
-});

package/dist/DensityRenderer/DensityRenderer.test.js

@@ -1,88 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _offscreenCanvasUtils = require("@jbrowse/core/util/offscreenCanvasUtils");
-
-var _ = _interopRequireWildcard(require("."));
-
-var _canvas = require("canvas");
-
-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; }
-
-global.nodeImage = _canvas.Image;
-global.nodeCreateCanvas = _canvas.createCanvas;
-var pluginManager = {};
-var renderer = new _.default({
-  name: 'DensityRenderer',
-  ReactComponent: _.ReactComponent,
-  configSchema: _.configSchema,
-  pluginManager: pluginManager
-});
-test('inverted mode and reversed', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var renderProps, res;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          renderProps = {
-            features: [new _simpleFeature.default({
-              id: 't1',
-              data: {
-                start: 1,
-                end: 100,
-                score: 1
-              }
-            }), new _simpleFeature.default({
-              id: 't2',
-              data: {
-                start: 101,
-                end: 200,
-                score: 2
-              }
-            })],
-            regions: [{
-              end: 100,
-              start: 1,
-              reversed: true,
-              refName: 'ctgA',
-              assemblyName: 'volvox'
-            }],
-            scaleOpts: {
-              domain: [0, 100],
-              inverted: true,
-              scaleType: 'linear'
-            },
-            bpPerPx: 3,
-            highResolutionScaling: 1,
-            config: {},
-            height: 100
-          };
-          _context.next = 3;
-          return (0, _offscreenCanvasUtils.renderToAbstractCanvas)(1000, 200, renderProps, function (ctx) {
-            return renderer.draw(ctx, renderProps);
-          });
-
-        case 3:
-          res = _context.sent;
-          expect(res).toMatchSnapshot({
-            imageData: expect.any(Object)
-          });
-
-        case 5:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));

package/dist/LinePlotRenderer/configSchema.js

@@ -1,70 +0,0 @@
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _default = (0, _configuration.ConfigurationSchema)('WiggleRenderer', {
-  color: {
-    type: 'color',
-    description: 'the color of track, overrides posColor and negColor',
-    defaultValue: '#f0f'
-  },
-  posColor: {
-    type: 'color',
-    description: 'the color to use when the score is positive',
-    defaultValue: 'blue'
-  },
-  negColor: {
-    type: 'color',
-    description: 'the color to use when the score is negative',
-    defaultValue: 'red'
-  },
-  highlightColor: {
-    type: 'color',
-    description: 'the color of highlights over the wiggle track',
-    defaultValue: 'rgba(255,255,0,0.5)'
-  },
-  clipColor: {
-    type: 'color',
-    description: 'the color of the clipping marker',
-    defaultValue: 'red'
-  },
-  renderType: {
-    type: 'stringEnum',
-    model: _mobxStateTree.types.enumeration('Rendering type', ['xyplot', 'density', 'line']),
-    description: 'The type of rendering for wiggle data to use',
-    defaultValue: 'xyplot'
-  },
-  filled: {
-    type: 'boolean',
-    description: 'fill in histogram',
-    defaultValue: true
-  },
-  bicolorPivot: {
-    type: 'stringEnum',
-    model: _mobxStateTree.types.enumeration('Scale type', ['numeric', 'mean', 'z_score', 'none']),
-    description: 'type of bicolor pivot',
-    defaultValue: 'numeric'
-  },
-  bicolorPivotValue: {
-    type: 'number',
-    defaultValue: 0,
-    description: 'value to use for bicolor pivot'
-  },
-  summaryScoreMode: {
-    type: 'stringEnum',
-    model: _mobxStateTree.types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
-    description: 'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
-    defaultValue: 'whiskers'
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;

package/dist/WiggleRendering.test.js

@@ -1,52 +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 _react = _interopRequireDefault(require("react"));
-
-var _react2 = require("@testing-library/react");
-
-var _WiggleRendering = _interopRequireDefault(require("./WiggleRendering"));
-
-// these tests do very little, let's try to expand them at some point
-test('one', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var _render, container, getByTestId, test;
-
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_WiggleRendering.default, {
-            width: 500,
-            height: 500,
-            features: new Map(),
-            highResolutionScaling: 1,
-            regions: [{
-              refName: 'chr1',
-              start: 1,
-              end: 3
-            }],
-            bpPerPx: 3,
-            config: {
-              type: 'DummyRenderer'
-            }
-          })), container = _render.container, getByTestId = _render.getByTestId;
-          _context.next = 3;
-          return getByTestId('wiggle-rendering-test');
-
-        case 3:
-          test = _context.sent;
-          expect(_react2.fireEvent.click(test)).toBeTruthy();
-          expect(container.firstChild).toMatchSnapshot();
-
-        case 6:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));

package/dist/XYPlotRenderer/XYPlotRenderer.test.js

@@ -1,87 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _offscreenCanvasUtils = require("@jbrowse/core/util/offscreenCanvasUtils");
-
-var _ = _interopRequireWildcard(require("."));
-
-var _canvas = require("canvas");
-
-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; }
-
-global.nodeImage = _canvas.Image;
-global.nodeCreateCanvas = _canvas.createCanvas;
-test('several features', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var pluginManager, renderer, renderProps, res;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          pluginManager = {};
-          renderer = new _.default({
-            name: 'XYPlotRenderer',
-            ReactComponent: _.ReactComponent,
-            configSchema: _.configSchema,
-            pluginManager: pluginManager
-          });
-          renderProps = {
-            features: [new _simpleFeature.default({
-              id: 't1',
-              data: {
-                start: 1,
-                end: 100,
-                score: 1
-              }
-            }), new _simpleFeature.default({
-              id: 't2',
-              data: {
-                start: 101,
-                end: 200,
-                score: 2
-              }
-            })],
-            regions: [{
-              end: 100,
-              start: 1
-            }],
-            scaleOpts: {
-              domain: [0, 100],
-              scaleType: 'linear'
-            },
-            config: {},
-            bpPerPx: 3,
-            highResolutionScaling: 1,
-            height: 100,
-            ticks: {
-              values: [0, 100]
-            }
-          };
-          _context.next = 5;
-          return (0, _offscreenCanvasUtils.renderToAbstractCanvas)(1000, 200, renderProps, function (ctx) {
-            return renderer.draw(ctx, renderProps);
-          });
-
-        case 5:
-          res = _context.sent;
-          expect(res).toMatchSnapshot({
-            imageData: expect.any(Object)
-          });
-
-        case 7:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));

package/dist/declare.d.js

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

package/dist/index.test.js

@@ -1,24 +0,0 @@
-"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 BigWigAdapter = pluginManager.getAdapterType('BigWigAdapter');
-  var config = BigWigAdapter.configSchema.create({
-    type: 'BigWigAdapter'
-  });
-  expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
-});

package/dist/util.test.js

@@ -1,66 +0,0 @@
-"use strict";
-
-var _util = require("./util");
-
-test('linear scale', function () {
-  var scaleType = 'linear';
-  var domain = [0, 100];
-  var range = [0, 100];
-  var scale = (0, _util.getScale)({
-    scaleType: scaleType,
-    domain: domain,
-    range: range
-  });
-  expect(scale.domain()).toEqual(domain);
-});
-test('log scale', function () {
-  var scaleType = 'log';
-  var domain = [1, 100];
-  var range = [0, 100];
-  var scale = (0, _util.getScale)({
-    scaleType: scaleType,
-    domain: domain,
-    range: range
-  });
-  expect(scale.domain()).toEqual([1, 128]);
-});
-test('test inverted', function () {
-  var scaleType = 'log';
-  var inverted = true;
-  var domain = [1, 100];
-  var range = [0, 100];
-  var scale = (0, _util.getScale)({
-    scaleType: scaleType,
-    domain: domain,
-    range: range,
-    inverted: inverted
-  });
-  expect(scale.domain()).toEqual([1, 128]);
-  expect(scale.range()).toEqual(range.reverse());
-});
-test('test minScore', function () {
-  var scaleType = 'linear';
-  var domain = [0, 100];
-  var range = [0, 100];
-  var bounds = [50, undefined];
-  var ret = (0, _util.getNiceDomain)({
-    scaleType: scaleType,
-    domain: domain,
-    range: range,
-    bounds: bounds
-  });
-  expect(ret).toEqual([50, 100]);
-});
-test('test min and max score', function () {
-  var scaleType = 'linear';
-  var domain = [1, 100];
-  var range = [0, 100];
-  var bounds = [undefined, 70];
-  var ret = (0, _util.getNiceDomain)({
-    scaleType: scaleType,
-    domain: domain,
-    range: range,
-    bounds: bounds
-  });
-  expect(ret).toEqual([0, 70]);
-});

package/src/LinePlotRenderer/configSchema.js

@@ -1,68 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { types } from 'mobx-state-tree'
-
-export default ConfigurationSchema(
-  'WiggleRenderer',
-  {
-    color: {
-      type: 'color',
-      description: 'the color of track, overrides posColor and negColor',
-      defaultValue: '#f0f',
-    },
-    posColor: {
-      type: 'color',
-      description: 'the color to use when the score is positive',
-      defaultValue: 'blue',
-    },
-    negColor: {
-      type: 'color',
-      description: 'the color to use when the score is negative',
-      defaultValue: 'red',
-    },
-    highlightColor: {
-      type: 'color',
-      description: 'the color of highlights over the wiggle track',
-      defaultValue: 'rgba(255,255,0,0.5)',
-    },
-    clipColor: {
-      type: 'color',
-      description: 'the color of the clipping marker',
-      defaultValue: 'red',
-    },
-    renderType: {
-      type: 'stringEnum',
-      model: types.enumeration('Rendering type', ['xyplot', 'density', 'line']),
-      description: 'The type of rendering for wiggle data to use',
-      defaultValue: 'xyplot',
-    },
-    filled: {
-      type: 'boolean',
-      description: 'fill in histogram',
-      defaultValue: true,
-    },
-    bicolorPivot: {
-      type: 'stringEnum',
-      model: types.enumeration('Scale type', [
-        'numeric',
-        'mean',
-        'z_score',
-        'none',
-      ]),
-      description: 'type of bicolor pivot',
-      defaultValue: 'numeric',
-    },
-    bicolorPivotValue: {
-      type: 'number',
-      defaultValue: 0,
-      description: 'value to use for bicolor pivot',
-    },
-    summaryScoreMode: {
-      type: 'stringEnum',
-      model: types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
-      description:
-        'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
-      defaultValue: 'whiskers',
-    },
-  },
-  { explicitlyTyped: true },
-)