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/
277 lines (237 loc) • 13.3 kB
JavaScript
"use strict";
require("./styles.scss");
var _react = _interopRequireWildcard(require("react"));
var _reactDom = _interopRequireDefault(require("react-dom"));
var _reactRouterDom = require("react-router-dom");
var _home = _interopRequireDefault(require("./app/home.js"));
var FASTA = _interopRequireWildcard(require("./app/FASTA.js"));
var FNA = _interopRequireWildcard(require("./app/FNA.js"));
var BAM = _interopRequireWildcard(require("./app/BAM.js"));
var _prevent_default_patch = _interopRequireDefault(require("./prevent_default_patch"));
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 Divider(props) {
return [/*#__PURE__*/_react["default"].createElement("div", {
className: "dropdown-divider",
key: "divider-div"
}), props.header ? /*#__PURE__*/_react["default"].createElement("h6", {
className: "dropdown-header",
key: "divider-header"
}, props.header) : null];
}
function Link(props) {
return /*#__PURE__*/_react["default"].createElement(_reactRouterDom.NavLink, {
className: "dropdown-item link",
to: props.to
}, props.header);
}
function Dropdown(props) {
return /*#__PURE__*/_react["default"].createElement("ul", {
className: "navbar-nav "
}, /*#__PURE__*/_react["default"].createElement("li", {
className: "nav-item dropdown"
}, /*#__PURE__*/_react["default"].createElement("a", {
className: "nav-link dropdown-toggle",
href: "#",
id: "navbarDropdown",
role: "button",
"data-toggle": "dropdown",
"aria-haspopup": "true",
"aria-expanded": "false"
}, props.title), /*#__PURE__*/_react["default"].createElement("div", {
className: "dropdown-menu",
"aria-labelledby": "navbarDropdown"
}, props.children)));
}
function FASTALinks(props) {
return /*#__PURE__*/_react["default"].createElement(Dropdown, {
title: "FASTA"
}, /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fasta-viewer",
header: "Viewer"
}), /*#__PURE__*/_react["default"].createElement(Divider, {
header: "Examples"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fasta-aminoacid",
header: "Amino acid alignment"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fasta-highlight",
header: "Highlight individual sites"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fasta-start",
header: "Start at a given sequence and site"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fasta-lowercase",
header: "Lower case alignment"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fasta-svg",
header: "SVG alignment"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fasta-quasispecies",
header: "Quasispecies"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fasta-sequence-bar",
header: "Sequence Bar Chart"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fasta-site-stacked-bar",
header: "Site Stacked Bar Chart"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fasta-ar",
header: "Artificial Recombination"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fasta-click-and-hover",
header: "Click handler"
}));
}
function FNALinks(props) {
return /*#__PURE__*/_react["default"].createElement(Dropdown, {
title: "FNA"
}, /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fna-viewer",
header: "Viewer"
}), /*#__PURE__*/_react["default"].createElement(Divider, {
header: "Examples"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fna-immunology",
header: "Immunology - heavy chain regions"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fna-hiv",
header: "HIV - site annotations"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/fna-basesvgtree",
header: "BaseSVGTreeInstance"
}));
}
function BAMLinks(props) {
return /*#__PURE__*/_react["default"].createElement(Dropdown, {
title: "BAM"
}, /*#__PURE__*/_react["default"].createElement(Link, {
to: "/sam-viewer",
header: "Viewer"
}), /*#__PURE__*/_react["default"].createElement(Divider, {
header: "Examples"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/sam-variantcaller",
header: "Variant caller"
}), /*#__PURE__*/_react["default"].createElement(Link, {
to: "/sam-scaffold",
header: "Scaffold viewer"
}));
}
function NavBar(props) {
return /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement("nav", {
className: "navbar navbar-expand-lg navbar-light bg-light"
}, /*#__PURE__*/_react["default"].createElement(_reactRouterDom.NavLink, {
className: "navbar-brand",
to: "/"
}, "Javascript Alignment Viewer"), /*#__PURE__*/_react["default"].createElement("div", {
className: "collapse navbar-collapse"
}, /*#__PURE__*/_react["default"].createElement(FASTALinks, null), /*#__PURE__*/_react["default"].createElement(FNALinks, null), /*#__PURE__*/_react["default"].createElement(BAMLinks, null))));
}
var App = /*#__PURE__*/function (_Component) {
_inherits(App, _Component);
var _super = _createSuper(App);
function App(props) {
var _this;
_classCallCheck(this, App);
_this = _super.call(this, props);
_this.state = {
data: null
};
return _this;
}
_createClass(App, [{
key: "render",
value: function render() {
return /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement(NavBar, null), /*#__PURE__*/_react["default"].createElement("div", {
style: {
maxWidth: 1140
},
className: "container-fluid"
}, /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
exact: true,
path: "/",
render: function render(props) {
return /*#__PURE__*/_react["default"].createElement(_home["default"], null);
}
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fasta-viewer",
render: function render(props) {
return /*#__PURE__*/_react["default"].createElement(FASTA.FASTAViewer, null);
}
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fasta-aminoacid",
component: FASTA.AminoAcid
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fasta-highlight",
component: FASTA.Highlight
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fasta-start",
component: FASTA.StartAtSiteAndSequence
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fasta-lowercase",
component: FASTA.Lowercase
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fasta-svg",
component: FASTA.SVGAlignmentExample
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fasta-quasispecies",
component: FASTA.Quasispecies
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fasta-sequence-bar",
component: FASTA.SequenceBarChart
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fasta-site-stacked-bar",
component: FASTA.SiteStackedBarChart
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fasta-ar",
component: FASTA.ArtificialRecombination
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fasta-click-and-hover",
component: FASTA.ClickAndHover
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fasta-test",
component: FASTA.Test
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fna-viewer",
component: FNA.FNAViewer
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fna-immunology",
component: FNA.Immunology
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fna-hiv",
component: FNA.HIV
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/fna-basesvgtree",
component: FNA.BaseSVGTreeInstance
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/sam-viewer",
component: BAM.BAMViewer
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/sam-scaffold",
component: BAM.ScaffoldExample
}), /*#__PURE__*/_react["default"].createElement(_reactRouterDom.Route, {
path: "/sam-variantcaller",
component: BAM.VariantCaller
})));
}
}]);
return App;
}(_react.Component);
function Main(props) {
return /*#__PURE__*/_react["default"].createElement(_reactRouterDom.BrowserRouter, null, /*#__PURE__*/_react["default"].createElement(App, null));
}
(0, _prevent_default_patch["default"])(document);
_reactDom["default"].render( /*#__PURE__*/_react["default"].createElement(Main, null), document.body.appendChild(document.createElement("div")));