@jbrowse/plugin-sequence 1.6.9 → 1.7.3

package/dist/DivSequenceRenderer/components/DivSequenceRendering.js

@@ -0,0 +1,239 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _extends2 = _interopRequireDefault(require("@babel/runtime/helpers/extends"));
+
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _react = _interopRequireDefault(require("react"));
+
+var _color = require("@jbrowse/core/util/color");
+
+var _ui = require("@jbrowse/core/ui");
+
+var _mobxReact = require("mobx-react");
+
+var _util = require("@jbrowse/core/util");
+
+/* eslint-disable @typescript-eslint/no-explicit-any */
+function Translation(props) {
+  var codonTable = props.codonTable,
+      seq = props.seq,
+      frame = props.frame,
+      bpPerPx = props.bpPerPx,
+      region = props.region,
+      height = props.height,
+      y = props.y,
+      _props$reverse = props.reverse,
+      reverse = _props$reverse === void 0 ? false : _props$reverse,
+      theme = props.theme;
+  var scale = bpPerPx; // the tilt variable normalizes the frame to where we are starting from,
+  // which increases consistency across blocks
+
+  var tilt = 3 - region.start % 3; // the effectiveFrame incorporates tilt and the frame to say what the
+  // effective frame that is plotted. The +3 is for when frame is -2 and this
+  // can otherwise result in effectiveFrame -1
+
+  var effectiveFrame = (frame + tilt + 3) % 3;
+  var seqSliced = seq.slice(effectiveFrame);
+  var translated = [];
+
+  for (var i = 0; i < seqSliced.length; i += 3) {
+    var codon = seqSliced.slice(i, i + 3);
+    var normalizedCodon = reverse ? (0, _util.revcom)(codon) : codon;
+    var aminoAcid = codonTable[normalizedCodon] || '';
+    translated.push({
+      letter: aminoAcid,
+      codon: normalizedCodon.toUpperCase()
+    });
+  }
+
+  var w = 1 / scale * 3;
+  var drop = region.start === 0 ? 0 : w;
+  var render = 1 / bpPerPx >= 12;
+  var width = (region.end - region.start) / bpPerPx;
+  var map = ['#d8d8d8', '#adadad', '#8f8f8f'].reverse();
+  return /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, translated.map(function (element, index) {
+    var x = region.reversed ? width - (w * (index + 1) + effectiveFrame / scale - drop) : w * index + effectiveFrame / scale - drop;
+    var letter = element.letter,
+        codon = element.codon;
+    return /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, {
+      key: "".concat(index, "-").concat(letter)
+    }, /*#__PURE__*/_react["default"].createElement("rect", {
+      x: x,
+      y: y,
+      width: render ? w : w + 0.7
+      /* small fudge factor when zoomed out*/
+      ,
+      height: height,
+      stroke: render ? '#555' : 'none',
+      fill: _util.defaultStarts.includes(codon) ? theme.palette.startCodon : _util.defaultStops.includes(codon) ? theme.palette.stopCodon : map[Math.abs(frame)]
+    }), render ? /*#__PURE__*/_react["default"].createElement("text", {
+      x: x + w / 2,
+      y: y + height / 2,
+      dominantBaseline: "middle",
+      textAnchor: "middle"
+    }, letter) : null);
+  }));
+}
+
+function DNA(props) {
+  var bpPerPx = props.bpPerPx,
+      region = props.region,
+      feature = props.feature,
+      theme = props.theme,
+      height = props.height,
+      seq = props.seq,
+      y = props.y;
+  var render = 1 / bpPerPx >= 12;
+
+  var _bpSpanPx = (0, _util.bpSpanPx)(feature.get('start'), feature.get('end'), region, bpPerPx),
+      _bpSpanPx2 = (0, _slicedToArray2["default"])(_bpSpanPx, 2),
+      leftPx = _bpSpanPx2[0],
+      rightPx = _bpSpanPx2[1];
+
+  var reverse = region.reversed;
+  var len = feature.get('end') - feature.get('start');
+  var w = Math.max((rightPx - leftPx) / len, 0.8);
+  return /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, seq.split('').map(function (letter, index) {
+    var color = theme.palette.bases[letter.toUpperCase()];
+    var x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
+    return /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, {
+      key: index
+    }, /*#__PURE__*/_react["default"].createElement("rect", {
+      x: x,
+      y: y,
+      width: w,
+      height: height,
+      fill: color ? color.main : '#aaa',
+      stroke: render ? '#555' : 'none'
+    }), render ? /*#__PURE__*/_react["default"].createElement("text", {
+      x: x + w / 2,
+      y: y + height / 2,
+      dominantBaseline: "middle",
+      textAnchor: "middle",
+      fill: color ? (0, _color.contrastingTextColor)(color.main) : 'black'
+    }, letter) : null);
+  }));
+}
+
+var SequenceSVG = function SequenceSVG(_ref) {
+  var regions = _ref.regions,
+      configTheme = _ref.theme,
+      _ref$features = _ref.features,
+      features = _ref$features === void 0 ? new Map() : _ref$features,
+      showReverse = _ref.showReverse,
+      showForward = _ref.showForward,
+      showTranslation = _ref.showTranslation,
+      bpPerPx = _ref.bpPerPx;
+
+  var _regions = (0, _slicedToArray2["default"])(regions, 1),
+      region = _regions[0];
+
+  var theme = (0, _ui.createJBrowseTheme)(configTheme);
+  var codonTable = (0, _util.generateCodonTable)(_util.defaultCodonTable);
+  var height = 20;
+
+  var _ref2 = (0, _toConsumableArray2["default"])(features.values()),
+      feature = _ref2[0];
+
+  if (!feature) {
+    return null;
+  }
+
+  var seq = feature.get('seq');
+
+  if (!seq) {
+    return null;
+  } // incrementer for the y-position of the current sequence being rendered
+  // (applies to both translation rows and dna rows)
+
+
+  var currY = -20;
+  return /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, showTranslation && (region.reversed ? showReverse : showForward) ? [2, 1, 0].map(function (index) {
+    return /*#__PURE__*/_react["default"].createElement(Translation, {
+      key: "translation-".concat(index),
+      seq: seq,
+      y: currY += 20,
+      codonTable: codonTable,
+      frame: index,
+      bpPerPx: bpPerPx,
+      region: region,
+      theme: theme,
+      height: height,
+      reverse: region.reversed
+    });
+  }) : null, showForward ? /*#__PURE__*/_react["default"].createElement(DNA, {
+    height: height,
+    y: currY += 20,
+    feature: feature,
+    region: region,
+    seq: region.reversed ? (0, _util.complement)(seq) : seq,
+    bpPerPx: bpPerPx,
+    theme: theme
+  }) : null, showReverse ? /*#__PURE__*/_react["default"].createElement(DNA, {
+    height: height,
+    y: currY += 20,
+    feature: feature,
+    region: region,
+    seq: region.reversed ? seq : (0, _util.complement)(seq),
+    bpPerPx: bpPerPx,
+    theme: theme
+  }) : null, showTranslation && (region.reversed ? showForward : showReverse) ? [0, -1, -2].map(function (index) {
+    return /*#__PURE__*/_react["default"].createElement(Translation, {
+      key: "rev-translation-".concat(index),
+      seq: seq,
+      y: currY += 20,
+      codonTable: codonTable,
+      frame: index,
+      bpPerPx: bpPerPx,
+      region: region,
+      theme: theme,
+      height: height,
+      reverse: !region.reversed
+    });
+  }) : null);
+};
+
+var Wrapper = function Wrapper(_ref3) {
+  var exportSVG = _ref3.exportSVG,
+      width = _ref3.width,
+      totalHeight = _ref3.totalHeight,
+      children = _ref3.children;
+  return exportSVG ? /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, children) : /*#__PURE__*/_react["default"].createElement("svg", {
+    "data-testid": "sequence_track",
+    width: width,
+    height: totalHeight,
+    style: {
+      width: width,
+      height: totalHeight
+    }
+  }, children);
+};
+
+function Sequence(props) {
+  var regions = props.regions,
+      bpPerPx = props.bpPerPx;
+
+  var _regions2 = (0, _slicedToArray2["default"])(regions, 1),
+      region = _regions2[0];
+
+  var width = (region.end - region.start) / bpPerPx;
+  var totalHeight = 200;
+  return /*#__PURE__*/_react["default"].createElement(Wrapper, (0, _extends2["default"])({}, props, {
+    totalHeight: totalHeight,
+    width: width
+  }), /*#__PURE__*/_react["default"].createElement(SequenceSVG, props));
+}
+
+var _default = (0, _mobxReact.observer)(Sequence);
+
+exports["default"] = _default;

package/dist/DivSequenceRenderer/components/DivSequenceRendering.test.js

@@ -0,0 +1,245 @@
+"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 _react = _interopRequireDefault(require("react"));
+
+var _propTypes = _interopRequireDefault(require("prop-types"));
+
+var _react2 = require("@testing-library/react");
+
+var _ui = require("@jbrowse/core/ui");
+
+var _PrecomputedLayout = _interopRequireDefault(require("@jbrowse/core/util/layouts/PrecomputedLayout"));
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+var _core = require("@material-ui/core");
+
+var _DivSequenceRendering = _interopRequireDefault(require("./DivSequenceRendering"));
+
+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; } }
+
+function Rendering(props) {
+  return /*#__PURE__*/_react["default"].createElement(_core.ThemeProvider, {
+    theme: (0, _ui.createJBrowseTheme)()
+  }, /*#__PURE__*/_react["default"].createElement(_DivSequenceRendering["default"], props));
+}
+
+var ErrorCatcher = /*#__PURE__*/function (_React$Component) {
+  (0, _inherits2["default"])(ErrorCatcher, _React$Component);
+
+  var _super = _createSuper(ErrorCatcher);
+
+  function ErrorCatcher(props) {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, ErrorCatcher);
+    _this = _super.call(this, props);
+    _this.state = {
+      hasError: false,
+      errorText: ''
+    };
+    return _this;
+  }
+
+  (0, _createClass2["default"])(ErrorCatcher, [{
+    key: "render",
+    value: function render() {
+      var _this$state = this.state,
+          hasError = _this$state.hasError,
+          errorText = _this$state.errorText;
+
+      if (hasError) {
+        // You can render any custom fallback UI
+        return /*#__PURE__*/_react["default"].createElement("h1", {
+          className: "error"
+        }, errorText);
+      }
+
+      var children = this.props.children;
+      return children;
+    }
+  }], [{
+    key: "getDerivedStateFromError",
+    value: function getDerivedStateFromError(error) {
+      // Update state so the next render will show the fallback UI.
+      return {
+        hasError: true,
+        errorText: String(error)
+      };
+    }
+  }]);
+  return ErrorCatcher;
+}(_react["default"].Component);
+
+ErrorCatcher.propTypes = {
+  children: _propTypes["default"].node.isRequired
+};
+describe('<DivSequenceRendering />', function () {
+  // This just keeps our testing logs clean by not displaying `console.error`s
+  // from errors we intentionally throw in our tests. Hopefully React will
+  // someday provide a way for error boundaries to prevent error logging so we
+  // won't have to do this: https://github.com/facebook/react/issues/15069
+  var originalError = console.error;
+  beforeAll(function () {
+    console.error = function () {
+      for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
+        args[_key] = arguments[_key];
+      }
+
+      if (args[0].includes('feature one did not contain a valid `seq` attribute') || args[0].includes('The above error occurred in the <SequenceDivs> component')) {
+        return;
+      }
+
+      originalError.call.apply(originalError, [console].concat(args));
+    };
+  });
+  afterAll(function () {
+    console.error = originalError;
+  });
+  it('renders with no features', function () {
+    var _render = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(Rendering, {
+      width: 500,
+      height: 500,
+      regions: [{
+        refName: 'zonk',
+        start: 0,
+        end: 300
+      }],
+      layout: new _PrecomputedLayout["default"]({
+        rectangles: {},
+        totalHeight: 20
+      }),
+      config: _configSchema["default"].create(),
+      bpPerPx: 3
+    })),
+        container = _render.container;
+
+    expect(container).toMatchSnapshot();
+  });
+  it('renders with one, zoomed way out', function () {
+    var _render2 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(Rendering, {
+      width: 500,
+      height: 500,
+      regions: [{
+        refName: 'zonk',
+        start: 0,
+        end: 1000
+      }],
+      features: new Map([['one', new _simpleFeature["default"]({
+        uniqueId: 'one',
+        start: 1,
+        end: 3,
+        seq: 'AB'
+      })]]),
+      config: _configSchema["default"].create({}),
+      bpPerPx: 3
+    })),
+        container = _render2.container;
+
+    expect(container).toMatchSnapshot();
+  });
+  it('renders with one feature with no seq, zoomed in, should throw', function () {
+    var _render3 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(ErrorCatcher, null, /*#__PURE__*/_react["default"].createElement(Rendering, {
+      width: 500,
+      height: 500,
+      regions: [{
+        refName: 'zonk',
+        start: 0,
+        end: 1000
+      }],
+      features: new Map([['one', new _simpleFeature["default"]({
+        uniqueId: 'one',
+        start: 1,
+        end: 3
+      })]]),
+      config: _configSchema["default"].create({}),
+      bpPerPx: 0.05
+    }))),
+        container = _render3.container;
+
+    expect(container).toMatchSnapshot();
+  });
+  it('renders with one feature with an incorrect seq, zoomed in, should throw', function () {
+    var _render4 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(ErrorCatcher, null, /*#__PURE__*/_react["default"].createElement(Rendering, {
+      width: 500,
+      height: 500,
+      regions: [{
+        refName: 'zonk',
+        start: 0,
+        end: 1000
+      }],
+      features: new Map([['one', new _simpleFeature["default"]({
+        uniqueId: 'one',
+        start: 1,
+        end: 3,
+        seq: 'ABC'
+      })]]),
+      config: _configSchema["default"].create({}),
+      bpPerPx: 0.05
+    }))),
+        container = _render4.container;
+
+    expect(container).toMatchSnapshot();
+  });
+  it('renders with one feature with a correct seq, zoomed in, should render nicely', function () {
+    var _render5 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(Rendering, {
+      width: 500,
+      height: 500,
+      regions: [{
+        refName: 'zonk',
+        start: 0,
+        end: 1000
+      }],
+      features: new Map([['one', new _simpleFeature["default"]({
+        uniqueId: 'one',
+        start: 1,
+        end: 10,
+        seq: 'ABCDEFGHI'
+      })]]),
+      config: _configSchema["default"].create({}),
+      bpPerPx: 0.05
+    })),
+        container = _render5.container;
+
+    expect(container).toMatchSnapshot();
+  });
+  it('renders with one feature reversed with a correct seq, zoomed in, should render nicely', function () {
+    var _render6 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(Rendering, {
+      width: 500,
+      height: 500,
+      regions: [{
+        refName: 'zonk',
+        start: 0,
+        end: 1000,
+        reversed: true
+      }],
+      features: new Map([['one', new _simpleFeature["default"]({
+        uniqueId: 'one',
+        start: 1,
+        end: 10,
+        seq: 'ABCDEFGHI'
+      })]]),
+      config: _configSchema["default"].create({}),
+      bpPerPx: 0.05
+    })),
+        container = _render6.container;
+
+    expect(container).toMatchSnapshot();
+  });
+});

package/dist/DivSequenceRenderer/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/DivSequenceRenderer/configSchema.js

@@ -0,0 +1,20 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _default = (0, _configuration.ConfigurationSchema)('DivSequenceRenderer', {
+  height: {
+    type: 'number',
+    description: 'height in pixels of each line of sequence',
+    defaultValue: 16
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/DivSequenceRenderer/index.d.ts

@@ -1,2 +1,2 @@
-export { default as ReactComponent } from './components/DivSequenceRendering';
-export { default as configSchema } from './configSchema';
+export { default as ReactComponent } from './components/DivSequenceRendering';
+export { default as configSchema } from './configSchema';

package/dist/DivSequenceRenderer/index.js

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

package/dist/GCContentAdapter/GCContentAdapter.d.ts

@@ -1,23 +1,23 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-export default class extends BaseFeatureDataAdapter {
-    private windowSize;
-    private windowDelta;
-    private gcMode;
-    static capabilities: string[];
-    configure(): Promise<BaseFeatureDataAdapter>;
-    getRefNames(): Promise<string[]>;
-    /**
-     * Fetch features for a certain region
-     * @param param -
-     * @returns Observable of Feature objects in the region
-     */
-    getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources(): void;
-}
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+export default class extends BaseFeatureDataAdapter {
+    private windowSize;
+    private windowDelta;
+    private gcMode;
+    static capabilities: string[];
+    configure(): Promise<BaseFeatureDataAdapter>;
+    getRefNames(): Promise<string[]>;
+    /**
+     * Fetch features for a certain region
+     * @param param -
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources(): void;
+}