alignment.js
Version:
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/
236 lines (189 loc) • 10.9 kB
JavaScript
;
Object.defineProperty(exports, "__esModule", {
value: true
});
exports.Immunology = Immunology;
exports.HIV = HIV;
Object.defineProperty(exports, "BaseSVGTreeInstance", {
enumerable: true,
get: function get() {
return _Components.BaseSVGTreeInstance;
}
});
exports.FNAViewer = void 0;
var _react = _interopRequireWildcard(require("react"));
var _d3Fetch = require("d3-fetch");
var _fileSaver = require("file-saver");
var _TreeAlignment = _interopRequireDefault(require("../TreeAlignment.js"));
var _fasta = require("../helpers/fasta");
var _Components = require("./Components.js");
var _Button = _interopRequireDefault(require("../components/Button.js"));
var _FileUploadButton = _interopRequireDefault(require("./FileUploadButton.js"));
var _Modal = _interopRequireDefault(require("./Modal.js"));
var _colors = require("../helpers/colors");
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 _extends() { _extends = Object.assign || function (target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i]; for (var key in source) { if (Object.prototype.hasOwnProperty.call(source, key)) { target[key] = source[key]; } } } return target; }; return _extends.apply(this, arguments); }
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; }
function Immunology(props) {
return /*#__PURE__*/_react["default"].createElement("h1", null, "Immunology example will go here.");
}
function HIV(props) {
return /*#__PURE__*/_react["default"].createElement("h1", null, "HIV example will go here.");
}
var FNAViewer = /*#__PURE__*/function (_Component) {
_inherits(FNAViewer, _Component);
var _super = _createSuper(FNAViewer);
function FNAViewer(props) {
var _this;
_classCallCheck(this, FNAViewer);
_this = _super.call(this, props);
_defineProperty(_assertThisInitialized(_this), "handleFileChange", function (e) {
var files = e.target.files;
if (files.length == 1) {
var file = files[0],
reader = new FileReader();
reader.onload = function (e) {
_this.loadFNA(e.target.result);
};
reader.readAsText(file);
}
document.body.click();
});
_this.state = {
data: null,
site_size: 20,
show_differences: ""
};
return _this;
}
_createClass(FNAViewer, [{
key: "componentDidMount",
value: function componentDidMount() {
var _this2 = this;
(0, _d3Fetch.text)("data/CD2.fna").then(function (data) {
return _this2.loadFNA(data);
});
}
}, {
key: "loadFNA",
value: function loadFNA(text) {
this.setState({
data: (0, _fasta.fnaParser)(text, true),
show_differences: ""
});
}
}, {
key: "saveFNA",
value: function saveFNA() {
var blob = new Blob([(0, _fasta.fnaToText)(this.state.data)], {
type: "text/plain:charset=utf-8;"
});
(0, _fileSaver.saveAs)(blob, "sequences.fna");
}
}, {
key: "siteColor",
value: function siteColor() {
var _this3 = this;
if (!this.state.show_differences) return _colors.nucleotide_color;
var desired_record = this.state.data.sequence_data.filter(function (datum) {
return datum.header == _this3.state.show_differences;
})[0];
return (0, _colors.nucleotide_difference)(desired_record);
}
}, {
key: "molecule",
value: function molecule() {
var _this4 = this;
if (!this.state.show_differences) return function (molecule) {
return molecule;
};
var desired_record = this.state.data.sequence_data.filter(function (datum) {
return datum.header == _this4.state.show_differences;
})[0];
return function (mol, site, header) {
if (mol == "-") return "-";
if (header == desired_record.header) return mol;
return mol == desired_record.seq[site - 1] ? "." : mol;
};
}
}, {
key: "render",
value: function render() {
var _this5 = this;
var toolbar_style = {
display: "flex",
justifyContent: "space-between",
width: 960
};
var options = this.state.data ? this.state.data.sequence_data.map(function (datum) {
return /*#__PURE__*/_react["default"].createElement("option", {
key: datum.header,
value: datum.header
}, datum.header);
}) : null;
return /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement("h1", null, "FNA Viewer Application"), /*#__PURE__*/_react["default"].createElement("div", {
style: toolbar_style
}, /*#__PURE__*/_react["default"].createElement(_FileUploadButton["default"], {
label: "Import",
onChange: this.handleFileChange
}), /*#__PURE__*/_react["default"].createElement(_Button["default"], {
label: "Export",
onClick: function onClick() {
return $("#modal").modal("show");
}
}), /*#__PURE__*/_react["default"].createElement("span", null, /*#__PURE__*/_react["default"].createElement("label", null, "Site size:"), /*#__PURE__*/_react["default"].createElement("input", {
type: "number",
value: this.state.site_size,
min: 15,
max: 100,
step: 5,
onChange: function onChange(e) {
return _this5.setState({
site_size: e.target.value
});
}
})), /*#__PURE__*/_react["default"].createElement("span", null, /*#__PURE__*/_react["default"].createElement("label", null, "Highlight difference from:"), /*#__PURE__*/_react["default"].createElement("select", {
value: this.state.show_differences,
onChange: function onChange(e) {
return _this5.setState({
show_differences: e.target.value
});
}
}, /*#__PURE__*/_react["default"].createElement("option", {
value: ""
}, "None"), options))), /*#__PURE__*/_react["default"].createElement(_TreeAlignment["default"], _extends({}, this.state.data, {
site_size: this.state.site_size,
molecule: this.molecule(),
site_color: this.siteColor()
})), /*#__PURE__*/_react["default"].createElement(_Modal["default"], {
title: "Export fasta"
}, /*#__PURE__*/_react["default"].createElement(_Button["default"], {
label: "Download",
onClick: function onClick() {
return _this5.saveFNA();
}
}), /*#__PURE__*/_react["default"].createElement("div", {
style: {
overflowY: "scroll",
width: 400,
height: 400
}
}, /*#__PURE__*/_react["default"].createElement("p", null, this.state.data ? (0, _fasta.fnaToText)(this.state.data) : null))));
}
}]);
return FNAViewer;
}(_react.Component);
exports.FNAViewer = FNAViewer;