├── public
    ├── robots.txt
    ├── favicon.ico
    ├── logo192.png
    ├── logo512.png
    ├── manifest.json
    └── index.html
├── src
    ├── setupTests.js
    ├── App.test.js
    ├── reportWebVitals.js
    ├── index.css
    ├── index.js
    ├── App.css
    ├── logo.svg
    └── App.js
├── README.md
├── .gitignore
├── package.json
└── LICENSE


/public/robots.txt:
--------------------------------------------------------------------------------
1 | # https://www.robotstxt.org/robotstxt.html
2 | User-agent: *
3 | Disallow:
4 | 


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/public/favicon.ico:
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https://raw.githubusercontent.com/theosanderson/Codon2Nucleotide/HEAD/public/favicon.ico


--------------------------------------------------------------------------------
/public/logo192.png:
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https://raw.githubusercontent.com/theosanderson/Codon2Nucleotide/HEAD/public/logo192.png


--------------------------------------------------------------------------------
/public/logo512.png:
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https://raw.githubusercontent.com/theosanderson/Codon2Nucleotide/HEAD/public/logo512.png


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/src/setupTests.js:
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1 | // jest-dom adds custom jest matchers for asserting on DOM nodes.
2 | // allows you to do things like:
3 | // expect(element).toHaveTextContent(/react/i)
4 | // learn more: https://github.com/testing-library/jest-dom
5 | import '@testing-library/jest-dom';
6 | 


--------------------------------------------------------------------------------
/src/App.test.js:
--------------------------------------------------------------------------------
1 | import { render, screen } from '@testing-library/react';
2 | import App from './App';
3 | 
4 | test('renders learn react link', () => {
5 |   render(<App />);
6 |   const linkElement = screen.getByText(/learn react/i);
7 |   expect(linkElement).toBeInTheDocument();
8 | });
9 | 


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/README.md:
--------------------------------------------------------------------------------
1 | # Codon2Nucleotide
2 | 
3 | ## http://codon2nucleotide.theo.io/
4 | 
5 | 
6 | ## Development
7 | 
8 | This tool was originally developed by Theo Sanderson. [Zach Hensel](https://www.itqb.unl.pt/research/biology/single-molecule-microbiology/zach-hensel-lab) provided additional functionality for conversion from coordinates in ORF1ab to coordinates in indidual NSP proteins.


--------------------------------------------------------------------------------
/.gitignore:
--------------------------------------------------------------------------------
 1 | # See https://help.github.com/articles/ignoring-files/ for more about ignoring files.
 2 | 
 3 | # dependencies
 4 | /node_modules
 5 | /.pnp
 6 | .pnp.js
 7 | 
 8 | # testing
 9 | /coverage
10 | 
11 | # production
12 | /build
13 | 
14 | # misc
15 | .DS_Store
16 | .env.local
17 | .env.development.local
18 | .env.test.local
19 | .env.production.local
20 | 
21 | npm-debug.log*
22 | yarn-debug.log*
23 | yarn-error.log*
24 | 


--------------------------------------------------------------------------------
/src/reportWebVitals.js:
--------------------------------------------------------------------------------
 1 | const reportWebVitals = onPerfEntry => {
 2 |   if (onPerfEntry && onPerfEntry instanceof Function) {
 3 |     import('web-vitals').then(({ getCLS, getFID, getFCP, getLCP, getTTFB }) => {
 4 |       getCLS(onPerfEntry);
 5 |       getFID(onPerfEntry);
 6 |       getFCP(onPerfEntry);
 7 |       getLCP(onPerfEntry);
 8 |       getTTFB(onPerfEntry);
 9 |     });
10 |   }
11 | };
12 | 
13 | export default reportWebVitals;
14 | 


--------------------------------------------------------------------------------
/src/index.css:
--------------------------------------------------------------------------------
 1 | body {
 2 |   margin: 0;
 3 |   font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', 'Roboto', 'Oxygen',
 4 |     'Ubuntu', 'Cantarell', 'Fira Sans', 'Droid Sans', 'Helvetica Neue',
 5 |     sans-serif;
 6 |   -webkit-font-smoothing: antialiased;
 7 |   -moz-osx-font-smoothing: grayscale;
 8 |   font-size:1em;
 9 |   color:#333
10 | }
11 | 
12 | code {
13 |   font-family: source-code-pro, Menlo, Monaco, Consolas, 'Courier New',
14 |     monospace;
15 | }
16 | 
17 | input{width:5em}
18 | 
19 | 
20 | 


--------------------------------------------------------------------------------
/src/index.js:
--------------------------------------------------------------------------------
 1 | import React from 'react';
 2 | import ReactDOM from 'react-dom';
 3 | import './index.css';
 4 | import App from './App';
 5 | import reportWebVitals from './reportWebVitals';
 6 | 
 7 | ReactDOM.render(
 8 |   <React.StrictMode>
 9 |     <App />
10 |   </React.StrictMode>,
11 |   document.getElementById('root')
12 | );
13 | 
14 | // If you want to start measuring performance in your app, pass a function
15 | // to log results (for example: reportWebVitals(console.log))
16 | // or send to an analytics endpoint. Learn more: https://bit.ly/CRA-vitals
17 | reportWebVitals();
18 | 


--------------------------------------------------------------------------------
/public/manifest.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "short_name": "React App",
 3 |   "name": "Create React App Sample",
 4 |   "icons": [
 5 |     {
 6 |       "src": "favicon.ico",
 7 |       "sizes": "64x64 32x32 24x24 16x16",
 8 |       "type": "image/x-icon"
 9 |     },
10 |     {
11 |       "src": "logo192.png",
12 |       "type": "image/png",
13 |       "sizes": "192x192"
14 |     },
15 |     {
16 |       "src": "logo512.png",
17 |       "type": "image/png",
18 |       "sizes": "512x512"
19 |     }
20 |   ],
21 |   "start_url": ".",
22 |   "display": "standalone",
23 |   "theme_color": "#000000",
24 |   "background_color": "#ffffff"
25 | }
26 | 


--------------------------------------------------------------------------------
/package.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "name": "codon2nucleotide",
 3 |   "version": "0.1.0",
 4 |   "private": true,
 5 |   "dependencies": {
 6 |     "@testing-library/jest-dom": "^5.11.4",
 7 |     "@testing-library/react": "^11.1.0",
 8 |     "@testing-library/user-event": "^12.1.10",
 9 |     "react": "^17.0.2",
10 |     "react-dom": "^17.0.2",
11 |     "react-scripts": "4.0.3",
12 |     "web-vitals": "^1.0.1"
13 |   },
14 |   "scripts": {
15 |     "start": "react-scripts start",
16 |     "build": "react-scripts build",
17 |     "test": "react-scripts test",
18 |     "eject": "react-scripts eject"
19 |   },
20 |   "eslintConfig": {
21 |     "extends": [
22 |       "react-app",
23 |       "react-app/jest"
24 |     ]
25 |   },
26 |   "browserslist": {
27 |     "production": [
28 |       ">0.2%",
29 |       "not dead",
30 |       "not op_mini all"
31 |     ],
32 |     "development": [
33 |       "last 1 chrome version",
34 |       "last 1 firefox version",
35 |       "last 1 safari version"
36 |     ]
37 |   }
38 | }
39 | 


--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
 1 | MIT License
 2 | 
 3 | Copyright (c) 2021 Theo Sanderson
 4 | 
 5 | Permission is hereby granted, free of charge, to any person obtaining a copy
 6 | of this software and associated documentation files (the "Software"), to deal
 7 | in the Software without restriction, including without limitation the rights
 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 | 
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 | 
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 | 


--------------------------------------------------------------------------------
/src/App.css:
--------------------------------------------------------------------------------
  1 | .App {
  2 |   text-align: center;
  3 | }
  4 | 
  5 | .bolded{font-weight: bold;}
  6 | .App-logo {
  7 |   height: 40vmin;
  8 |   pointer-events: none;
  9 | }
 10 | 
 11 | @media (prefers-reduced-motion: no-preference) {
 12 |   .App-logo {
 13 |     animation: App-logo-spin infinite 20s linear;
 14 |   }
 15 | }
 16 | 
 17 | .App-header {
 18 |   background-color: #282c34;
 19 |   min-height: 100vh;
 20 |   display: flex;
 21 |   flex-direction: column;
 22 |   align-items: center;
 23 |   justify-content: center;
 24 |   font-size: calc(10px + 2vmin);
 25 |   color: white;
 26 | }
 27 | 
 28 | .App-link {
 29 |   color: #61dafb;
 30 | }
 31 | 
 32 | @keyframes App-logo-spin {
 33 |   from {
 34 |     transform: rotate(0deg);
 35 |   }
 36 |   to {
 37 |     transform: rotate(360deg);
 38 |   }
 39 | }
 40 | 
 41 | .flex-container {
 42 |   display: flex;
 43 |   max-width: 800px;
 44 |   margin: 0 auto;
 45 | }
 46 | 
 47 | .flex-child {
 48 |   flex: 1;
 49 |   border: 2px solid #eee;
 50 |   padding: 10px;
 51 |   padding-bottom: 50px;
 52 |   margin-top: 20px;
 53 |   padding-top: 0px;
 54 | }
 55 | 
 56 | .flex-child:first-child {
 57 |   margin-right: 20px;
 58 | }
 59 | 
 60 | .flex-child:nth-child(2) {
 61 |   margin-right: 20px;
 62 | }
 63 | 
 64 | * {
 65 |   font-size: 18px;
 66 | }
 67 | h3 {
 68 |   font-size: 24px;
 69 | }
 70 | input {
 71 |   padding: 3px;
 72 |   width: 150px;
 73 | }
 74 | select {
 75 |   padding: 3px;
 76 | }
 77 | 
 78 | h1 {
 79 |   font-size: 30px;
 80 | }
 81 | .to_sec {
 82 |   min-width: 5em;
 83 |   display: inline-block;
 84 | }
 85 | 
 86 | button {
 87 |   font-size: 40%;
 88 |   /* remove all style and format as link*/
 89 |   border: none;
 90 |   background: none;
 91 |   cursor: pointer;
 92 |   padding: 0;
 93 |   font-size: inherit;
 94 |   color: rgb(167, 167, 167);
 95 |   text-decoration: underline;
 96 | }
 97 | 
 98 | .margined{
 99 |   margin-top:50px;
100 | }


--------------------------------------------------------------------------------
/public/index.html:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html>
 2 | <html lang="en">
 3 | 
 4 | <head>
 5 |   
 6 |   <!-- Global site tag (gtag.js) - Google Analytics -->
 7 | <script async src="https://www.googletagmanager.com/gtag/js?id=G-W3TJTHDBX3"></script>
 8 | <script>
 9 |   window.dataLayer = window.dataLayer || [];
10 |   function gtag(){dataLayer.push(arguments);}
11 |   gtag('js', new Date());
12 | 
13 |   gtag('config', 'G-W3TJTHDBX3');
14 | </script>
15 |   
16 |   <meta charset="utf-8" />
17 |   <link rel="icon" href="%PUBLIC_URL%/favicon.ico" />
18 |   <meta name="viewport" content="width=device-width, initial-scale=1" />
19 |   <meta name="theme-color" content="#000000" />
20 |   <meta name="description" content="Converson tool to find the position in the SARS-CoV-2 genome in nucleotide coordinates from a codon position within a protein, or vice versa. Also converts between NSPs and ORF1a/b." />
21 |   <link rel="apple-touch-icon" href="%PUBLIC_URL%/logo192.png" />
22 |   <!--
23 |       manifest.json provides metadata used when your web app is installed on a
24 |       user's mobile device or desktop. See https://developers.google.com/web/fundamentals/web-app-manifest/
25 |     -->
26 |   <link rel="manifest" href="%PUBLIC_URL%/manifest.json" />
27 |   <!--
28 |       Notice the use of %PUBLIC_URL% in the tags above.
29 |       It will be replaced with the URL of the `public` folder during the build.
30 |       Only files inside the `public` folder can be referenced from the HTML.
31 | 
32 |       Unlike "/favicon.ico" or "favicon.ico", "%PUBLIC_URL%/favicon.ico" will
33 |       work correctly both with client-side routing and a non-root public URL.
34 |       Learn how to configure a non-root public URL by running `npm run build`.
35 |     -->
36 |   <title>Codon2Nucleotide</title>
37 | </head>
38 | 
39 | <body>
40 |   <noscript>You need to enable JavaScript to run this app.</noscript>
41 |   <div id="root"></div>
42 |   <!--
43 |       This HTML file is a template.
44 |       If you open it directly in the browser, you will see an empty page.
45 | 
46 |       You can add webfonts, meta tags, or analytics to this file.
47 |       The build step will place the bundled scripts into the <body> tag.
48 | 
49 |       To begin the development, run `npm start` or `yarn start`.
50 |       To create a production bundle, use `npm run build` or `yarn build`.
51 |     -->
52 | </body>
53 | 
54 | </html>
55 | 


--------------------------------------------------------------------------------
/src/logo.svg:
--------------------------------------------------------------------------------
1 | <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 841.9 595.3"><g fill="#61DAFB"><path d="M666.3 296.5c0-32.5-40.7-63.3-103.1-82.4 14.4-63.6 8-114.2-20.2-130.4-6.5-3.8-14.1-5.6-22.4-5.6v22.3c4.6 0 8.3.9 11.4 2.6 13.6 7.8 19.5 37.5 14.9 75.7-1.1 9.4-2.9 19.3-5.1 29.4-19.6-4.8-41-8.5-63.5-10.9-13.5-18.5-27.5-35.3-41.6-50 32.6-30.3 63.2-46.9 84-46.9V78c-27.5 0-63.5 19.6-99.9 53.6-36.4-33.8-72.4-53.2-99.9-53.2v22.3c20.7 0 51.4 16.5 84 46.6-14 14.7-28 31.4-41.3 49.9-22.6 2.4-44 6.1-63.6 11-2.3-10-4-19.7-5.2-29-4.7-38.2 1.1-67.9 14.6-75.8 3-1.8 6.9-2.6 11.5-2.6V78.5c-8.4 0-16 1.8-22.6 5.6-28.1 16.2-34.4 66.7-19.9 130.1-62.2 19.2-102.7 49.9-102.7 82.3 0 32.5 40.7 63.3 103.1 82.4-14.4 63.6-8 114.2 20.2 130.4 6.5 3.8 14.1 5.6 22.5 5.6 27.5 0 63.5-19.6 99.9-53.6 36.4 33.8 72.4 53.2 99.9 53.2 8.4 0 16-1.8 22.6-5.6 28.1-16.2 34.4-66.7 19.9-130.1 62-19.1 102.5-49.9 102.5-82.3zm-130.2-66.7c-3.7 12.9-8.3 26.2-13.5 39.5-4.1-8-8.4-16-13.1-24-4.6-8-9.5-15.8-14.4-23.4 14.2 2.1 27.9 4.7 41 7.9zm-45.8 106.5c-7.8 13.5-15.8 26.3-24.1 38.2-14.9 1.3-30 2-45.2 2-15.1 0-30.2-.7-45-1.9-8.3-11.9-16.4-24.6-24.2-38-7.6-13.1-14.5-26.4-20.8-39.8 6.2-13.4 13.2-26.8 20.7-39.9 7.8-13.5 15.8-26.3 24.1-38.2 14.9-1.3 30-2 45.2-2 15.1 0 30.2.7 45 1.9 8.3 11.9 16.4 24.6 24.2 38 7.6 13.1 14.5 26.4 20.8 39.8-6.3 13.4-13.2 26.8-20.7 39.9zm32.3-13c5.4 13.4 10 26.8 13.8 39.8-13.1 3.2-26.9 5.9-41.2 8 4.9-7.7 9.8-15.6 14.4-23.7 4.6-8 8.9-16.1 13-24.1zM421.2 430c-9.3-9.6-18.6-20.3-27.8-32 9 .4 18.2.7 27.5.7 9.4 0 18.7-.2 27.8-.7-9 11.7-18.3 22.4-27.5 32zm-74.4-58.9c-14.2-2.1-27.9-4.7-41-7.9 3.7-12.9 8.3-26.2 13.5-39.5 4.1 8 8.4 16 13.1 24 4.7 8 9.5 15.8 14.4 23.4zM420.7 163c9.3 9.6 18.6 20.3 27.8 32-9-.4-18.2-.7-27.5-.7-9.4 0-18.7.2-27.8.7 9-11.7 18.3-22.4 27.5-32zm-74 58.9c-4.9 7.7-9.8 15.6-14.4 23.7-4.6 8-8.9 16-13 24-5.4-13.4-10-26.8-13.8-39.8 13.1-3.1 26.9-5.8 41.2-7.9zm-90.5 125.2c-35.4-15.1-58.3-34.9-58.3-50.6 0-15.7 22.9-35.6 58.3-50.6 8.6-3.7 18-7 27.7-10.1 5.7 19.6 13.2 40 22.5 60.9-9.2 20.8-16.6 41.1-22.2 60.6-9.9-3.1-19.3-6.5-28-10.2zM310 490c-13.6-7.8-19.5-37.5-14.9-75.7 1.1-9.4 2.9-19.3 5.1-29.4 19.6 4.8 41 8.5 63.5 10.9 13.5 18.5 27.5 35.3 41.6 50-32.6 30.3-63.2 46.9-84 46.9-4.5-.1-8.3-1-11.3-2.7zm237.2-76.2c4.7 38.2-1.1 67.9-14.6 75.8-3 1.8-6.9 2.6-11.5 2.6-20.7 0-51.4-16.5-84-46.6 14-14.7 28-31.4 41.3-49.9 22.6-2.4 44-6.1 63.6-11 2.3 10.1 4.1 19.8 5.2 29.1zm38.5-66.7c-8.6 3.7-18 7-27.7 10.1-5.7-19.6-13.2-40-22.5-60.9 9.2-20.8 16.6-41.1 22.2-60.6 9.9 3.1 19.3 6.5 28.1 10.2 35.4 15.1 58.3 34.9 58.3 50.6-.1 15.7-23 35.6-58.4 50.6zM320.8 78.4z"/><circle cx="420.9" cy="296.5" r="45.7"/><path d="M520.5 78.1z"/></g></svg>


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/src/App.js:
--------------------------------------------------------------------------------
  1 | import React, { useState } from 'react';
  2 | 
  3 | import './App.css';
  4 | 
  5 | const genes = {
  6 |   'ORF1a': [266, 13467],
  7 |   'ORF1b': [13468, 21556],
  8 |   'S': [21563, 25385],
  9 |   'ORF3a': [25393, 26221],
 10 |   'E': [26245, 26473],
 11 |   'M': [26523, 27192],
 12 |   'ORF6': [27202, 27388],
 13 |   'ORF7a': [27394, 27760],
 14 |   'ORF7b': [27756, 27888],
 15 |   'ORF8': [27894, 28260],
 16 |   'N': [28274, 29534],
 17 |   'ORF10': [29558, 29675]
 18 | }
 19 | 
 20 | // const nsps = { // from uniprot P0DTD1 orf1ab numbering of nsps
 21 | //   'nsp1': [1, 180],
 22 | //   'nsp2': [181, 818],
 23 | //   'nsp3': [819, 2763],
 24 | //   'nsp4': [2764, 3263],
 25 | //   'nsp5 (Mpro)': [3264, 3569],
 26 | //   'nsp6': [3570, 3859],
 27 | //   'nsp7': [3860, 3942],
 28 | //   'nsp8': [3943, 4140],
 29 | //   'nsp9': [4141, 4253],
 30 | //   'nsp10': [4254, 4392],
 31 | //   'nsp12 (RdRp)': [4393, 5324],
 32 | //   'nsp13': [5325, 5925],
 33 | //   'nsp14': [5926, 6452],
 34 | //   'nsp15': [6453, 6798],
 35 | //   'nsp16': [6799, 7096]
 36 | // }
 37 | 
 38 | const nsps = { // from uniprot P0DTD1 orf1ab numbering of nsps
 39 |   'nsp1': 1,
 40 |   'nsp2': 181,
 41 |   'nsp3': 819,
 42 |   'nsp4': 2764,
 43 |   'nsp5 (Mpro)': 3264,
 44 |   'nsp6': 3570,
 45 |   'nsp7': 3860,
 46 |   'nsp8': 3943,
 47 |   'nsp9': 4141,
 48 |   'nsp10': 4254,
 49 |   'nsp12 (RdRp)': 4393,
 50 |   'nsp13': 5325,
 51 |   'nsp14': 5926,
 52 |   'nsp15': 6453,
 53 |   'nsp16': 6799
 54 | }
 55 | 
 56 | function App() {
 57 | 
 58 |   let [codon, setCodon] = useState(484);
 59 |   let [nucleotide, setNucleotide] = useState(null);
 60 |   let [gene, setGene] = useState("S")
 61 |   let [nsp, setNsp] = useState("nsp6")
 62 |   let [themode,setthemode] = useState("nucleotide")
 63 |   let end_nucleotide = ""
 64 | 
 65 |   if (nucleotide == null) {
 66 |     const start_nucleotide = genes[gene][0] + (codon - 1) * 3
 67 |     end_nucleotide = start_nucleotide + 2
 68 |     nucleotide = start_nucleotide
 69 |   }
 70 | 
 71 |   if (codon == null) {
 72 |     const matches = Object.keys(genes).filter(x => genes[x][0] <= nucleotide & genes[x][1] >= nucleotide)
 73 |     if (matches.length === 1) {
 74 |       console.log(matches)
 75 | 
 76 |       gene = matches[0]
 77 |       const the_start = genes[gene][0]
 78 |       codon = Math.floor((nucleotide - the_start) / 3) + 1
 79 |     }
 80 |     else {
 81 |       codon = "!!"
 82 |     }
 83 |   }
 84 | 
 85 |   let [orf1aorb, setOrf1aOrb] = useState(null);
 86 |   let [orf1aorbcodon, setORF1aorBCodon] = useState(null);
 87 |   let [nspCodon, setNspCodon] = useState(null);
 88 |   let [combinedCodon,setCombinedCodon] = useState(3646);
 89 | 
 90 |   if (combinedCodon == null) {
 91 |     if (orf1aorbcodon == null) {
 92 | 
 93 |       combinedCodon = nsps[nsp] + nspCodon - 1;
 94 |       
 95 |       if(combinedCodon > 4401) {
 96 |         orf1aorbcodon = nsps[nsp]+nspCodon-1-4401;
 97 |         orf1aorb = "ORF1b";
 98 |       }
 99 |       else {
100 |         orf1aorbcodon = nsps[nsp]+nspCodon-1;
101 |         orf1aorb = "ORF1a";
102 |       }
103 | 
104 |     }
105 |     combinedCodon = orf1aorbcodon + (orf1aorb === "ORF1b" ? 4401 : 0)
106 |   }
107 |   else{
108 |     if(combinedCodon > 4401){
109 |       orf1aorbcodon = combinedCodon - 4401
110 |       orf1aorb = "ORF1b"
111 |     }
112 |     else{
113 |       orf1aorb = "ORF1a"
114 |       orf1aorbcodon = combinedCodon
115 |       
116 |     }
117 |   }
118 | 
119 |   if (nspCodon == null) {
120 | 
121 |     nsp="nsp1"
122 |     nspCodon=combinedCodon - nsps[nsp] + 1
123 | 
124 |     for (const [key, value] of Object.entries(nsps)) {
125 |       if (combinedCodon > value && combinedCodon - value < combinedCodon - nsps[nsp]) {
126 |         nsp = key;
127 |         nspCodon = combinedCodon - value + 1;
128 |       }
129 |     }
130 |   }
131 | 
132 |   if (themode === "nucleotide") {
133 |     if( ["ORF1a","ORF1b"].includes(gene)){
134 |       if (orf1aorb !== gene){
135 |       setOrf1aOrb(gene)
136 |       setCombinedCodon(null)
137 |       console.log("b")
138 |     }
139 |     if(orf1aorbcodon !== codon && !(isNaN(codon)&& isNaN(orf1aorb))) {
140 |         console.log("c",codon,orf1aorbcodon)
141 | 
142 |       setORF1aorBCodon(codon)
143 |       setCombinedCodon(null)
144 |       }
145 |     }
146 | 
147 |   }
148 |   else{
149 |     if(gene!==orf1aorb){
150 |       console.log("d")
151 |       setGene(orf1aorb)
152 |       setNucleotide(null)
153 |     }
154 |     if (codon !== orf1aorbcodon && !(isNaN(codon)&& isNaN(orf1aorbcodon))){
155 |       console.log("e")
156 |       setCodon(orf1aorbcodon)
157 |       setNucleotide(null)
158 |     }
159 |     
160 |   }
161 | 
162 |   return (
163 |     <div className="App">
164 |       <h1>Codon2Nucelotide</h1>
165 |       {themode==="nucleotide"&&
166 |       <>
167 |       <p class="bolded margined">Convert from SARS-CoV-2 codon position to genomic coordinates or vice versa</p>
168 |       <p><button onClick={()=> {
169 |   setthemode("orf1ab")
170 | }}>Convert between ORF1a/b, ORF1ab, and polyprotein nsps</button></p></>
171 | }
172 | 
173 | {themode==="orf1ab"&&
174 |       <>
175 |     
176 |       <p class=" margined"><button onClick={()=> {
177 |   setthemode("nucleotide")
178 | }}>Convert from SARS-CoV-2 codon position to genomic coordinates or vice versa</button></p>
179 |   <p class="bolded">Convert between ORF1a/b, ORF1ab, and polyprotein nsps</p>
180 |   </>
181 | }
182 |       
183 |      
184 |       
185 |     
186 |       {themode==="nucleotide"&&
187 |         <div className="flex-container">
188 | 
189 |         <div className="flex-child magenta">
190 | 
191 |           <h3>Codon </h3>
192 |           <div style={{ marginBottom: "5px" }}> Gene: <select value={gene} onChange={e => { setGene(e.target.value); setCodon(codon); setNucleotide(null) }}>
193 |             {Object.keys(genes).sort().map(x =>
194 |               <option key={x} value={x}>{x}</option>
195 |             )}
196 |           </select></div>
197 | 
198 |           Codon: <input type="number" value={codon} onChange={e => { setCodon(parseInt(e.target.value)); setNucleotide(null) }}></input>
199 | 
200 |         </div>
201 | 
202 |         <div className="flex-child green">
203 |           <h3>Nucleotide </h3>
204 |           Nucleotide: <input type="number" value={nucleotide} onChange={e => { setNucleotide(parseInt(e.target.value)); setCodon(null); }}></input>
205 |           <div className="to_sec">{end_nucleotide && " to " + end_nucleotide}</div>
206 |           <div><a target="_blank" style={{color: "rgb(167, 167, 167)", marginTop:"10px", display:"block"}} href={"https://gensplore.theo.io/?gb=%2Fsequence.gb&search="+nucleotide}>View in Gensplore</a></div>
207 |         </div>
208 | 
209 |       </div>
210 |     }
211 | 
212 |     {themode==="orf1ab"&&
213 |       <div className="flex-container">
214 | 
215 |       <div className="flex-child magenta">
216 | 
217 |         <h3>ORF1a or B </h3>
218 |         <div style={{ marginBottom: "5px" }}> Gene: <select value={orf1aorb} onChange={e => { setOrf1aOrb(e.target.value); setORF1aorBCodon(orf1aorbcodon); setCombinedCodon(null); setNspCodon(null)}}>
219 |           {['ORF1a','ORF1b'].sort().map(x =>
220 |             <option key={x} value={x}>{x}</option>
221 |           )}
222 |         </select></div>
223 | 
224 |         Codon: <input type="number" value={orf1aorbcodon} onChange={e => {  setORF1aorBCodon(parseInt(e.target.value)); setOrf1aOrb(orf1aorb); setCombinedCodon(null); setNspCodon(null)}}></input>
225 | 
226 |       </div>
227 | 
228 |       <div className="flex-child green">
229 | 
230 |         <h3>ORF1ab </h3>
231 | 
232 |         Codon: <input type="number" value={combinedCodon} onChange={e => { setCombinedCodon(parseInt(e.target.value)); setORF1aorBCodon(null); setNspCodon(null)}}></input>
233 | 
234 |       </div>
235 | 
236 |       <div className="flex-child plaid">
237 |         
238 |         <h3>nsp </h3>
239 | 
240 |         <div style={{ marginBottom: "5px" }}> Gene: <select value={nsp} onChange={e => { setNsp(e.target.value); setNspCodon(nspCodon); setCombinedCodon(null); setORF1aorBCodon(null)}}>
241 |           {Object.keys(nsps).map(x =>
242 |             <option key={x} value={x}>{x}</option>
243 |           )}
244 |         </select></div>
245 | 
246 |         Codon: <input type="number" value={nspCodon} onChange={e => { setNspCodon(parseInt(e.target.value)); setNsp(nsp); setCombinedCodon(null); setORF1aorBCodon(null)}}></input>
247 | 
248 |       </div>
249 | 
250 |     </div>
251 | }
252 | 
253 | 
254 | <p class="margined"><a style={{color: "rgb(167, 167, 167)"}} href="https://github.com/theosanderson/codon2nucleotide">GitHub</a></p>
255 | 
256 |     </div >
257 |   );
258 | }
259 | 
260 | export default App;
261 | 


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