alignment.js/app/FASTA/highlight.js

A suite of reusable [React](http://reactjs.org/) components for creating a variety of visualizations involving [multiple sequence alignments](https://en.wikipedia.org/wiki/Multiple_sequence_alignment). [View the live demo here](http://alignment.hyphy.org/

"use strict";

Object.defineProperty(exports, "__esModule", {
  value: true
});
exports["default"] = void 0;

var _react = _interopRequireWildcard(require("react"));

var _d = require("d3");

var _Alignment = _interopRequireDefault(require("../../Alignment.js"));

var _fasta = _interopRequireDefault(require("../../helpers/fasta.js"));

var _colors = require("../../helpers/colors.js");

function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { "default": obj }; }

function _getRequireWildcardCache() { if (typeof WeakMap !== "function") return null; var cache = new WeakMap(); _getRequireWildcardCache = function _getRequireWildcardCache() { return cache; }; return cache; }

function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (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; }

function _typeof(obj) { "@babel/helpers - typeof"; if (typeof Symbol === "function" && typeof Symbol.iterator === "symbol") { _typeof = function _typeof(obj) { return typeof obj; }; } else { _typeof = function _typeof(obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; } return _typeof(obj); }

function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }

function _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }

function _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); return Constructor; }

function _createSuper(Derived) { return function () { var Super = _getPrototypeOf(Derived), result; if (_isNativeReflectConstruct()) { var NewTarget = _getPrototypeOf(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return _possibleConstructorReturn(this, result); }; }

function _possibleConstructorReturn(self, call) { if (call && (_typeof(call) === "object" || typeof call === "function")) { return call; } return _assertThisInitialized(self); }

function _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError("this hasn't been initialised - super() hasn't been called"); } return self; }

function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Date.prototype.toString.call(Reflect.construct(Date, [], function () {})); return true; } catch (e) { return false; } }

function _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }

function _inherits(subClass, superClass) { if (typeof superClass !== "function" && superClass !== null) { throw new TypeError("Super expression must either be null or a function"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); if (superClass) _setPrototypeOf(subClass, superClass); }

function _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }

function highlight_codon_color(character, position, header) {
  if (header == "DUCK_VIETNAM_272_2005" && Math.floor((position - 1) / 3) == 3) return "red";
  return character == "-" ? "white" : "GhostWhite";
}

function highlight_codon_text_color(character, position, header) {
  return character == "G" ? "Gold" : (0, _colors.nucleotide_color)(character);
}

var Highlight = /*#__PURE__*/function (_Component) {
  _inherits(Highlight, _Component);

  var _super = _createSuper(Highlight);

  function Highlight(props) {
    var _this;

    _classCallCheck(this, Highlight);

    _this = _super.call(this, props);
    _this.state = {
      sequence_data: null
    };
    return _this;
  }

  _createClass(Highlight, [{
    key: "componentDidMount",
    value: function componentDidMount() {
      var _this2 = this;

      (0, _d.text)("data/Flu.fasta").then(function (data) {
        var sequence_data = (0, _fasta["default"])(data);

        _this2.setState({
          sequence_data: sequence_data
        });
      });
    }
  }, {
    key: "render",
    value: function render() {
      return /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement("h1", null, "Highlighting specific sites")), /*#__PURE__*/_react["default"].createElement(_Alignment["default"], {
        fasta: this.state.sequence_data,
        site_color: highlight_codon_color,
        text_color: highlight_codon_text_color
      }));
    }
  }]);

  return Highlight;
}(_react.Component);

var _default = Highlight;
exports["default"] = _default;