alignment.js/components/SiteBarPlotExample.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 _fasta = _interopRequireDefault(require("../helpers/fasta"));

var _computeLabelWidth = _interopRequireDefault(require("../helpers/computeLabelWidth"));

var _BaseAlignment = _interopRequireDefault(require("./BaseAlignment.js"));

var _SiteAxis = _interopRequireDefault(require("./SiteAxis.js"));

var _Placeholder = _interopRequireDefault(require("./Placeholder.js"));

var _SequenceAxis = _interopRequireDefault(require("./SequenceAxis.js"));

var _ScrollBroadcaster = _interopRequireDefault(require("./../helpers/ScrollBroadcaster"));

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

var _nucleotideComposition = require("./../helpers/nucleotideComposition");

var _BaseSiteBarPlot = _interopRequireDefault(require("./BaseSiteBarPlot.js"));

var _SitePlotAxis = _interopRequireDefault(require("./SitePlotAxis.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 _defineProperty(obj, key, value) { if (key in obj) { Object.defineProperty(obj, key, { value: value, enumerable: true, configurable: true, writable: true }); } else { obj[key] = value; } return obj; }

var $ = require("jquery");

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

  var _super = _createSuper(SiteBarPlotExample);

  function SiteBarPlotExample(props) {
    var _this;

    _classCallCheck(this, SiteBarPlotExample);

    _this = _super.call(this, props);

    _defineProperty(_assertThisInitialized(_this), "getSiteNucleotideData", function (sequence_data) {
      (0, _nucleotideComposition.siteComposition)(sequence_data, _this.setSiteNucleotideDataToState);
    });

    _defineProperty(_assertThisInitialized(_this), "setSiteNucleotideDataToState", function (siteNucleotideData) {
      _this.setState({
        siteNucleotideData: siteNucleotideData
      });
    });

    _defineProperty(_assertThisInitialized(_this), "switchNucleotide", function (nucleotide) {
      _this.setState({
        nucleotideInView: nucleotide
      });
    });

    _this.label_width = 200;
    _this.state = {
      nucleotideInView: "A",
      siteNucleotideData: null
    };

    _this.initialize(_this.props);

    return _this;
  }

  _createClass(SiteBarPlotExample, [{
    key: "componentDidMount",
    value: function componentDidMount() {
      this.getSiteNucleotideData(this.sequence_data);
    }
  }, {
    key: "componentWillUpdate",
    value: function componentWillUpdate(nextProps, prevState) {
      //TODO: replace componentWillUpdate as this is deprecated in future versions of react.
      this.setScrollingEvents(nextProps);
    }
  }, {
    key: "componentDidUpdate",
    value: function componentDidUpdate(prevProps, prevState) {
      if (this.state.siteNucleotideData == null) {
        this.getSiteNucleotideData(this.sequence_data);
      }
    }
  }, {
    key: "setScrollingEvents",
    value: function setScrollingEvents(props) {
      var _this2 = this;

      if (props.fasta) {
        var width = props.width,
            height = props.height,
            axis_height = props.axis_height;
        this.scroll_broadcaster = new _ScrollBroadcaster["default"]({
          width: this.full_pixel_width,
          height: this.full_pixel_height,
          x_pad: width - this.label_width,
          y_pad: height - axis_height,
          x_pixel: this.x_pixel,
          y_pixel: this.y_pixel,
          bidirectional: ["alignmentjs-siteBarPlot-div", "alignmentjs-alignment", "alignmentjs-axis-div", "alignmentjs-labels-div"]
        }); // Update this.x_pixel on scroll events so that the alignment and plots will render to the correct scroll location on re-renders.

        document.getElementById("alignmentjs-alignment").addEventListener("alignmentjs_wheel_event", function (e) {
          _this2.x_pixel = e.detail.x_pixel;
        });
      }
    }
  }, {
    key: "initialize",
    value: function initialize(props) {
      if (props.fasta) {
        var fasta = props.fasta,
            site_size = props.site_size,
            width = props.width,
            height = props.height;
        this.sequence_data = (0, _fasta["default"])(props.fasta);
        var sequence_data = this.sequence_data;
        var label_padding = this.props.label_padding;
        this.label_width = (0, _computeLabelWidth["default"])(sequence_data, label_padding);
        this.full_pixel_width = site_size * sequence_data.number_of_sites;
        this.full_pixel_height = site_size * sequence_data.number_of_sequences;
        var centerOnSite = props.centerOnSite,
            centerOnHeader = props.centerOnHeader;
        this.x_pixel = site_size * centerOnSite - width / 2 || 0;
        this.y_pixel = centerOnHeader ? site_size * this.sequence_data.map(function (record) {
          return record.header;
        }).indexOf(centerOnHeader) - height / 2 : 0;
      }

      this.setScrollingEvents(props);
    }
  }, {
    key: "render",
    value: function render() {
      var full_pixel_width = this.full_pixel_width,
          full_pixel_height = this.full_pixel_height,
          label_width = this.label_width,
          width = full_pixel_width ? Math.min(label_width + full_pixel_width, this.props.width) : this.props.width,
          height = full_pixel_height ? Math.min(full_pixel_height + this.props.axis_height, this.props.height) : this.props.height;
      var barPlotHeight = 120;
      var bar_plot_data = this.state.siteNucleotideData == null ? null : this.state.siteNucleotideData[this.state.nucleotideInView];
      return /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement(SwitchNucleotideButtons, {
        switchNucleotide: this.switchNucleotide
      }), /*#__PURE__*/_react["default"].createElement("div", {
        id: "alignmentjs-main-div",
        style: {
          width: width,
          height: height
        }
      }, /*#__PURE__*/_react["default"].createElement(_SitePlotAxis["default"], {
        label_width: this.label_width,
        data: bar_plot_data,
        height: barPlotHeight,
        max_value: 1,
        axis_label: "Nucleotide %",
        scroll_broadcaster: this.scroll_broadcaster
      }), /*#__PURE__*/_react["default"].createElement(_BaseSiteBarPlot["default"], {
        data: bar_plot_data,
        siteSize: this.props.site_size,
        width: full_pixel_width,
        height: barPlotHeight,
        fillColor: this.props.site_color(this.state.nucleotideInView),
        outlineColor: this.props.text_color(this.state.nucleotideInView),
        x_pixel: this.x_pixel,
        max_value: 1,
        scroll_broadcaster: this.scroll_broadcaster
      }), /*#__PURE__*/_react["default"].createElement(_Placeholder["default"], {
        width: this.label_width,
        height: this.props.axis_height
      }), /*#__PURE__*/_react["default"].createElement(_SiteAxis["default"], {
        height: this.props.axis_height,
        site_size: this.props.site_size,
        sequence_data: this.sequence_data,
        x_pixel: this.x_pixel,
        scroll_broadcaster: this.scroll_broadcaster
      }), /*#__PURE__*/_react["default"].createElement(_SequenceAxis["default"], {
        width: this.label_width,
        height: height - this.props.axis_height,
        sequence_data: this.sequence_data,
        site_size: this.props.site_size,
        y_pixel: this.y_pixel,
        scroll_broadcaster: this.scroll_broadcaster
      }), /*#__PURE__*/_react["default"].createElement(_BaseAlignment["default"], {
        width: width - this.label_width,
        height: height - this.props.axis_height,
        sequence_data: this.sequence_data,
        site_color: this.props.site_color,
        text_color: this.props.text_color,
        site_size: this.props.site_size,
        x_pixel: this.x_pixel,
        y_pixel: this.y_pixel,
        scroll_broadcaster: this.scroll_broadcaster
      })));
    }
  }]);

  return SiteBarPlotExample;
}(_react.Component);

SiteBarPlotExample.defaultProps = {
  site_color: _colors.nucleotide_color,
  text_color: _colors.nucleotide_text_color,
  label_padding: 10,
  site_size: 20,
  axis_height: 20,
  sender: "main"
};

var SwitchNucleotideButtons = /*#__PURE__*/function (_React$Component) {
  _inherits(SwitchNucleotideButtons, _React$Component);

  var _super2 = _createSuper(SwitchNucleotideButtons);

  function SwitchNucleotideButtons(props) {
    _classCallCheck(this, SwitchNucleotideButtons);

    return _super2.call(this, props);
  }

  _createClass(SwitchNucleotideButtons, [{
    key: "render",
    value: function render() {
      var _this3 = this;

      return /*#__PURE__*/_react["default"].createElement("div", {
        className: "btn-group btn-group-toggle",
        "data-toggle": "buttons"
      }, /*#__PURE__*/_react["default"].createElement("label", {
        className: "btn btn-light active",
        onClick: function onClick() {
          return _this3.props.switchNucleotide("A");
        }
      }, /*#__PURE__*/_react["default"].createElement("input", {
        type: "radio"
      }), "A"), /*#__PURE__*/_react["default"].createElement("label", {
        className: "btn btn-light",
        onClick: function onClick() {
          return _this3.props.switchNucleotide("C");
        }
      }, /*#__PURE__*/_react["default"].createElement("input", {
        type: "radio"
      }), "C"), /*#__PURE__*/_react["default"].createElement("label", {
        className: "btn btn-light",
        onClick: function onClick() {
          return _this3.props.switchNucleotide("G");
        }
      }, /*#__PURE__*/_react["default"].createElement("input", {
        type: "radio"
      }), "G"), /*#__PURE__*/_react["default"].createElement("label", {
        className: "btn btn-light",
        onClick: function onClick() {
          return _this3.props.switchNucleotide("T");
        }
      }, /*#__PURE__*/_react["default"].createElement("input", {
        type: "radio"
      }), "T"));
    }
  }]);

  return SwitchNucleotideButtons;
}(_react["default"].Component);

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