SequenceServer

https://github.com/wurmlab/sequenceserver
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SequenceServer is a graphical user interface for setting up BLAST+ servers with an intuitive...
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### Run SequenceServer from Source

Source: https://github.com/wurmlab/sequenceserver/blob/master/README.md

Execute SequenceServer using bundler after installing dependencies. This command starts the application.

```bash
bundle exec bin/sequenceserver
```

--------------------------------

### String.includes, String.startsWith, and String.endsWith Examples

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Demonstrates using String.includes, String.startsWith, and String.endsWith for substring checks with optional starting positions.

```javascript
'foobarbaz'.includes('bar');      // => true
'foobarbaz'.includes('bar', 4);   // => false
'foobarbaz'.startsWith('foo');    // => true
'foobarbaz'.startsWith('bar', 3); // => true
'foobarbaz'.endsWith('baz');      // => true
'foobarbaz'.endsWith('bar', 6);   // => true
```

--------------------------------

### Install isarray using component

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/isarray@0.0.1/README.md

Install the isarray package using component for use in your component.io projects.

```bash
$ component install juliangruber/isarray
```

--------------------------------

### String.codePointAt and String.fromCodePoint Examples

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Illustrates using String.codePointAt to get the code point of a character and String.fromCodePoint to create a string from code points.

```javascript
'𠮷'.codePointAt(0); // => 134071
String.fromCodePoint(97, 134071, 98); // => 'a𠮷b'
```

--------------------------------

### Live Configuration Options Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/demos/cfgs/input-datetime-local.html

Illustrates how to dynamically set configuration properties for the datetime-local widget using JavaScript. This example shows setting min, max, and step attributes.

```javascript
// Example for setting min/max/step via $.prop/$.attr
$("#my-input").prop("min", "2014-01-01");
$("#my-input").prop("max", "2014-12-31");
$("#my-input").prop("step", "1800"); // 30 minutes in seconds
```

--------------------------------

### Install core-js using npm or bower

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Instructions for installing core-js using package managers.

```bash
npm i core-js
bower install core.js
```

--------------------------------

### Install isarray using npm

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/isarray@0.0.1/README.md

Install the isarray package using npm for use in your Node.js projects.

```bash
$ npm install isarray
```

--------------------------------

### Install Frontend Dependencies

Source: https://github.com/wurmlab/sequenceserver/blob/master/README.md

Install Node.js and npm dependencies required for building and managing frontend code.

```bash
npm install
```

--------------------------------

### Install Buffer Module

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/buffer@5.7.1/README.md

Install the buffer module using npm for direct use.

```bash
npm install buffer
```

--------------------------------

### core-js Map Usage Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Demonstrates the basic usage of the core-js Map polyfill, including initialization, setting and getting values, checking for keys, iterating, and deleting entries. Note that object keys are compared by reference.

```javascript
var a = [1];

var map = new Map([['a', 1], [42, 2]]);
map.set(a, 3).set(true, 4);

log(map.size);        // => 4
log(map.has(a));      // => true
log(map.has([1]));    // => false
log(map.get(a));      // => 3
map.forEach(function(val, key){
  log(val);           // => 1, 2, 3, 4
  log(key);           // => 'a', 42, [1], true
});
map.delete(a);
log(map.size);        // => 3
log(map.get(a));      // => undefined
log(Array.from(map)); // => [['a', 1], [42, 2], [true, 4]]
```

--------------------------------

### Install vm-browserify with npm

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/vm-browserify@0.0.4/readme.markdown

Install the vm-browserify module directly using npm if you need to use it independently of browserify.

```bash
npm install vm-browserify
```

--------------------------------

### Array.of Examples

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Shows how to use Array.of to create arrays with the provided arguments.

```javascript
Array.of(1);       // => [1]
Array.of(1, 2, 3); // => [1, 2, 3]
```

--------------------------------

### Install util module via npm

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/util@0.10.3/README.md

Use this command to install the util module from npm.

```shell
npm install util
```

--------------------------------

### Install Development Dependencies

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/font-awesome@4.4.0/README.md

Install the necessary tools for developing Font Awesome, including Ruby gems and Node.js packages.

```bash
$ bundle install
$ npm install
```

--------------------------------

### Install React and React DOM

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/react-dom@18.0.0/README.md

Installs the necessary packages for React development, including the core React library and the DOM renderer.

```sh
npm install react react-dom
```

--------------------------------

### Install Ruby Dependencies

Source: https://github.com/wurmlab/sequenceserver/blob/master/README.md

Use bundler to install all necessary Ruby dependencies for running SequenceServer from source.

```bash
bundle install
```

--------------------------------

### Install CodeClimate engines

Source: https://github.com/wurmlab/sequenceserver/blob/master/README.md

Install the necessary CodeClimate engines for static code analysis.

```bash
codeclimate engines:install
```

--------------------------------

### Map and Set toJSON Examples

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Shows how Map#toJSON and Set#toJSON are serialized by JSON.stringify, converting them into arrays.

```javascript
JSON.stringify(new Map([['a', 'b'], ['c', 'd']])); // => '[["a","b"],["c","d"]]
JSON.stringify(new Set([1, 2, 3, 2, 1]));          // => '[1,2,3]'
```

--------------------------------

### Install Font Awesome as a Component

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/font-awesome@4.4.0/README.md

Include Font Awesome as a component in your project by running the installation command or adding it to your component.json dependencies.

```bash
$ component install FortAwesome/Font-Awesome
```

```json
{
  "FortAwesome/Font-Awesome": "*"
}
```

--------------------------------

### Customizing Mediaelement Controls with CSS and JavaScript

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/index.html

Provides an example of how to apply custom styles to media elements and use Webshim's 'replaceUI' option to enable custom, styleable controls. This setup is useful for creating a consistent player appearance across different browsers.

```html
<style>
						/* add basic styles */
						.mediaplayer {
							position: relative;
							height: 0;
							width: 100%;
							padding-bottom: 56.25%; /* 16/9 */
						}

						.mediaplayer video,
						.mediaplayer .polyfill-video {
							position: absolute;
							top: 0;
							left: 0;
							height: 100%;
							width: 100%;
						}
					</style>
					
					<script>
						webshim.setOptions('mediaelement', {replaceUI: 'auto'});
						webshim.polyfill('mediaelement');
					</script>
					
					<div class="mediaplayer">
						<video poster="poster.jpg" src="http://www.youtube.com/watch?v=siOHh0uzcuY&vq=large">
						</video>
					</div>
```

--------------------------------

### Install and Load Webshim with jQuery

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/index.html

Shows how to include jQuery, the Webshim polyfiller, and request specific features. It's recommended to use this within a DOM-ready callback.

```html
<script src="js/jquery.js"></script>
<script src="js-webshim/minified/polyfiller.js"></script>
  
<script>
  //webshim.setOptions('basePath', '/js-webshim/minified/shims/');

  //request the features you need:
  webshim.polyfill('es5 mediaelement forms');
  
  $(function(){
    // use all implemented API-features on DOM-ready
  });
</script>
```

--------------------------------

### String Padding Examples

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Illustrates String.prototype.padLeft and String.prototype.padRight for adding padding to strings with specified lengths and fill characters.

```javascript
'hello'.padLeft(10);          // => '     hello'
'hello'.padLeft(10, '1234');  // => '41234hello'
'hello'.padRight(10);         // => 'hello     '
'hello'.padRight(10, '1234'); // => 'hello12341'
```

--------------------------------

### URL Polyfill Usage Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/index.html

Demonstrates how to use the URL polyfill for parsing and manipulating URL components and search parameters.

```javascript
var link = new URL('http://afarkas.github.io/webshim/demos/index.html?param1=value1');
link.protocol; // returns 'http:'
link.searchParams.get('param1'); // returns 'value1'
link.searchParams.append('param2', 'value2');
link.href // returns 'http://afarkas.github.io/webshim/demos/index.html?param1=value1&param2=value2'
```

--------------------------------

### Install Bundler Gem

Source: https://github.com/wurmlab/sequenceserver/blob/master/README.md

Install the bundler gem, which is required to manage Ruby dependencies for SequenceServer.

```bash
gem install bundler
```

--------------------------------

### Array.from Examples

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Demonstrates using Array.from with iterables, array-like objects, and a mapping function.

```javascript
Array.from(new Set([1, 2, 3, 2, 1]));      // => [1, 2, 3]
Array.from({0: 1, 1: 2, 2: 3, length: 3}); // => [1, 2, 3]
Array.from('123', Number);                 // => [1, 2, 3]
Array.from('123', function(it){
  return it * it;
});                                        // => [1, 4, 9]
```

--------------------------------

### String Trimming Examples

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Demonstrates String.prototype.trimLeft and String.prototype.trimRight for removing whitespace from the beginning and end of strings.

```javascript
'   hello   '.trimLeft();  // => 'hello   '
'   hello   '.trimRight(); // => '   hello'
```

--------------------------------

### Install base64-js with npm

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/base64-js@1.5.1/README.md

Install the base64-js package using npm and require it in your Node.js project.

```bash
npm install base64-js
```

```javascript
var base64js = require('base64-js')
```

--------------------------------

### Initialize Webshims with 'html5shiv'

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/tests/test-ext/base-tag-loading.html

Initializes Webshims and waits for the 'html5shiv' module to be ready before proceeding. This is a basic setup for testing polyfill functionality.

```javascript
$.webshims.ready('html5shiv', function(){ QUnit.reset = function(){ $("#main, #qunit-fixture").htmlPolyfill( QUnit.config.fixture ); }; });
```

--------------------------------

### Promise.all Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Shows how Promise.all can be used to run multiple Promises concurrently and wait for all of them to resolve, returning an array of their results.

```javascript
Promise.all([
  'foo',
  sleepRandom(5),
  sleepRandom(15),
  sleepRandom(10)  // after 15 sec:
]).then(log);      // => ['foo', 956, 85, 382]
```

--------------------------------

### String.repeat Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Shows how to use String.repeat to concatenate a string multiple times.

```javascript
'string'.repeat(3); // => 'stringstringstring'
```

--------------------------------

### Symbol.for and Symbol.keyFor Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Illustrates how Symbol.for() creates or retrieves a global symbol registry entry, and Symbol.keyFor() retrieves the key for a given symbol.

```javascript
var symbol = Symbol.for('key');
symbol === Symbol.for('key'); // true
Symbol.keyFor(symbol);        // 'key'
```

--------------------------------

### Install stream-browserify with npm

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/stream-browserify@1.0.0/readme.markdown

Install the stream-browserify package using npm. If using browserify, this module is automatically available when requiring 'stream'.

```bash
npm install stream-browserify
```

--------------------------------

### Array.find and Array.findIndex Examples

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Illustrates using Array.find and Array.findIndex with callback functions to search for elements.

```javascript
function isOdd(val){
  return val % 2;
}
[4, 8, 15, 16, 23, 42].find(isOdd);      // => 15
[4, 8, 15, 16, 23, 42].findIndex(isOdd); // => 2
[4, 8, 15, 16, 23, 42].find(isNaN);      // => undefined
[4, 8, 15, 16, 23, 42].findIndex(isNaN); // => -1
```

--------------------------------

### Install Jest for Javascript testing

Source: https://github.com/wurmlab/sequenceserver/blob/master/README.md

Add Jest as a development dependency for frontend unit tests.

```bash
npm install --save-dev jest
```

--------------------------------

### Core-js Examples Without Global Namespace

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Shows how to use core-js polyfills without polluting the global namespace by requiring the 'core-js/library' module.

```javascript
var core = require('core-js/library'); // With a modular system, otherwise use global `core`
core.Array.from(new core.Set([1, 2, 3, 2, 1])); // => [1, 2, 3]
core.String.repeat('*', 10);                    // => '**********'
core.Promise.resolve(32).then(core.log);        // => 32
core.setImmediate(core.log, 42);                // => 42
```

--------------------------------

### Array.fill Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Demonstrates using Array.fill to populate an array with a static value.

```javascript
Array(5).fill(42); // => [42, 42, 42, 42, 42]
```

--------------------------------

### Core-js Examples with Global Namespace

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Demonstrates common core-js polyfills like Array.from, String.repeat, Promise, and setImmediate when used with global namespace pollution.

```javascript
Array.from(new Set([1, 2, 3, 2, 1])); // => [1, 2, 3]
'*'.repeat(10);                       // => '**********'
Promise.resolve(32).then(log);        // => 32
setImmediate(log, 42);                // => 42
```

--------------------------------

### Canvas Drawing Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/index.html

Demonstrates how to use the getContext method to draw on a canvas element and apply styles.

```javascript
var ctx = $('#my-canvas').getContext('2d');
ctx.clearRect(10, 10, 100, 100);
ctx.fillStyle = "rgb(200,0,0)";  
ctx.fillRect(10, 10, 55, 50);

ctx.fillStyle = "rgba(0, 0, 200, 0.5)";  
ctx.fillRect(30, 30, 55, 50);
```

--------------------------------

### Run Frontend Watch Server

Source: https://github.com/wurmlab/sequenceserver/blob/master/README.md

Start a watch server that automatically rebuilds frontend code upon detecting changes. This streamlines frontend development.

```bash
npm run-script watch
```

--------------------------------

### Basic Promise Chaining Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Demonstrates creating a Promise that resolves after a random delay and chaining .then() calls to handle sequential asynchronous operations.

```javascript
function sleepRandom(time){
  return new Promise(function(resolve, reject){
    setTimeout(resolve, time * 1e3, 0 | Math.random() * 1e3);
  });
}

log('Run');                    // => Run
sleepRandom(5).then(function(result){
  log(result);                 // => 869, after 5 sec.
  return sleepRandom(10);
}).then(function(result){
  log(result);                 // => 202, after 10 sec.
}).then(function(){
  log('immediately after');    // => immediately after
  throw Error('Irror!');
}).then(function(){
  log('will not be displayed');
}).catch(log);                 // => => Error: Irror!
```

--------------------------------

### Initialize jTree with HTML

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/github/vakata/jstree@3.3.8/demo/basic/index.html

Initializes jTree on an existing HTML element. This is the simplest way to get started.

```javascript
$('#html').jstree();
```

--------------------------------

### Object.values and Object.entries Examples

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Shows how to use Object.values to get an array of an object's own enumerable property values and Object.entries to get an array of an object's own enumerable string-keyed property [key, value] pairs.

```javascript
Object.values({a: 1, b: 2, c: 3});  // => [1, 2, 3]
Object.entries({a: 1, b: 2, c: 3}); // => [['a', 1], ['b', 2], ['c', 3]]
```

--------------------------------

### Initialize Webshim with Form Polyfills

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/demos/cfgs/input-time.html

Initializes Webshim with specific options for forms and loads the necessary polyfills. This is typically done once at the start of your application.

```javascript
webshim.setOptions('forms', { lazyCustomMessages: true, replaceValidationUI: true, addValidators: true, customDatalist: true });
webshim.setOptions('forms-ext', { replaceUI: true });
// load the forms polyfill
webshim.polyfill('forms forms-ext');
```

--------------------------------

### Webshim Configuration and Initialization

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/tests/test-ext/require-loading-6.html

Sets up the Webshim configuration for testing, including test data and polyfill modules. It then waits for the 'forms-ext' and 'geolocation' polyfills to be ready before signaling completion to the opener or parent window.

```javascript
window.asyncWebshims = {
  cfg: {
    testData: 'test6',
    waitReady: false,
    forms: {
      customMessages: true
    }
  },
  polyfill: "forms forms-ext geolocation"
};
(function(){
  var webshimsReady = false;
  webshimsReady = !!($.webshims);
  webshims.ready('forms-ext geolocation', function(){
    setTimeout(function(){
      (window.opener || window.parent).loadingTest($.webshims.cfg.testData, $.webshims.cfg.extendNative);
    }, 1);
  });
})();
```

--------------------------------

### Enable Lazy Custom Messages and Replace Validation UI

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/demos/forms.html

Configures the forms polyfill to load custom validation messages lazily and to replace the default validation UI with custom, styleable elements. This setup is then applied by starting the polyfill.

```javascript
webshim.setOptions('forms', {
	//set lazyCustomMessages to true
	lazyCustomMessages: true,
	//show custom styleable validation bubble
	replaceValidationUI: true
});

//start polyfilling
webshim.polyfill('forms');
```

--------------------------------

### core-js WeakMap Usage Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Demonstrates the use of the core-js WeakMap polyfill for storing key-value pairs where keys are objects. It shows basic operations like setting, getting, checking for keys, and deleting. WeakMaps do not prevent garbage collection of their keys.

```javascript
var a = [1]
  , b = [2]
  , c = [3];

var wmap = new WeakMap([[a, 1], [b, 2]]);
wmap.set(c, 3).set(b, 4);
log(wmap.has(a));   // => true
log(wmap.has([1])); // => false
log(wmap.get(a));   // => 1
wmap.delete(a);
log(wmap.get(a));   // => undefined

// Private properties store:
var Person = (function(){
  var names = new WeakMap;
  function Person(name){
    names.set(this, name);
  }
  Person.prototype.getName = function(){
    return names.get(this);
  };
  return Person;
})();

var person = new Person('Vasya');
log(person.getName());          // => 'Vasya'
for(var key in person)log(key); // => only 'getName'
```

--------------------------------

### Creating and Using Dict Objects

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Demonstrates how to create Dict objects from various inputs like objects, Maps, and iterables. Also shows instance properties and checks.

```javascript
var map = new Map([['a', 1], ['b', 2], ['c', 3]]);

Dict();                    // => {__proto__: null}
Dict({a: 1, b: 2, c: 3});  // => {__proto__: null, a: 1, b: 2, c: 3}
Dict(map);                 // => {__proto__: null, a: 1, b: 2, c: 3}
Dict([1, 2, 3].entries()); // => {__proto__: null, 0: 1, 1: 2, 2: 3}

var dict = Dict({a: 42});
dict instanceof Object;   // => false
dict.a;                   // => 42
dict.toString;            // => undefined
'a' in dict;              // => true
'hasOwnProperty' in dict; // => false

Dict.isDict({});     // => false
Dict.isDict(Dict()); // => true
```

--------------------------------

### Install ieee754 package

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/ieee754@1.2.1/README.md

Install the ieee754 package using npm. This command downloads and installs the package and its dependencies.

```bash
npm install ieee754
```

--------------------------------

### Setup Image Upload Module

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/demos/filereader/index.html

Sets up the image upload functionality for elements with the 'show-upload' class. It handles file selection, image preview, and applies the filereader polyfill.

```javascript
function showUpload(){
    var $image, reader;
    var displaySel = '.upload-display';
    var $module = $(this);
    var $input = $(this).find('input[type="file"]');
    var $display = $(displaySel, $module);
    var showSelectedFile = function () {
        var file = ($(this).prop('files') || [])[0];
        //if there is no file or first file is not an image abort
        if(!file || file.type.indexOf('image/')){
            return;
        }
        if(!reader){
            reader = new FileReader();
        }
        reader.onload = function (evt) {
            var fileData = evt.target.result;
            if(!$image){
                $image = $("<img />").appendTo($display);
            }
            $image.attr('src', fileData);
        };
        //use $.prop to access files property
        reader.readAsDataURL(file);
    };
    $input.on('change', showSelectedFile);
    //polyfill if not already in markup
    if(!$input.is('.ws-filereader')){
        $input.addClass('ws-filereader').updatePolyfill();
    }
    showSelectedFile();
}
```

--------------------------------

### Install events module

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/events@1.0.2/Readme.md

Install the events module using npm. This command should be run in your project's terminal.

```bash
npm install events
```

--------------------------------

### Install CircosJS using Bower

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/github/nicgirault/circosJs@1.7.0/readme.md

Use this command to install the CircosJS library via the Bower package manager.

```bash
bower install circosjs
```

--------------------------------

### Build Docker Image

Source: https://github.com/wurmlab/sequenceserver/blob/master/README.md

Build the Docker image for SequenceServer. Ensure the Dockerfile is configured correctly for building.

```bash
docker build -t sequenceserver .
```

--------------------------------

### Load All Webshim Polyfills

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/index.html

This snippet demonstrates the basic initialization of Webshim to load all available polyfills.

```javascript
webshim.polyfill(); // load all available polyfills
```

--------------------------------

### Include Webshim Polyfiller and Initialize

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/readme.md

Include the jQuery library, the Webshim polyfiller script, and then call `webshims.polyfill()` to load all unsupported features. Alternatively, you can specify individual features to polyfill.

```html
<script src="js/jquery.js"></script>

<script src="js-webshim/minified/polyfiller.js"></script> 

<script> 
	webshims.polyfill();
	
	// or only load a specific feature
	//webshims.polyfill('forms es5');
</script>
```

--------------------------------

### Build Docker Image with Minified Frontend

Source: https://github.com/wurmlab/sequenceserver/blob/master/README.md

Build a Docker image that includes minified frontend code. Use the --target=minify flag for this purpose.

```bash
docker build . -t seqserv-with-customisations --target=minify
```

--------------------------------

### Geolocation API - Get Current Position

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/index.html

Implements the navigator.geolocation API to get the user's current position. Supports success and error callbacks, as well as timeout options.

```javascript
navigator.getCurrentPosition: successCallback, errorCallback and options ({timeout: number}) are supported
```

--------------------------------

### jQuery to Get Background Color and Check Support

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/tests/jquery/data/support/bodyBackground.html

Uses jQuery to get the body's background color and check support properties, then calls a parent iframe callback.

```javascript
jQuery(function() { window.parent.iframeCallback( jQuery( "body" ).css( "backgroundColor" ), jQuery.support ); });
```

--------------------------------

### Get Current Locale

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/demos/forms.html

Retrieves the currently set language locale for Webshim.

```javascript
webshim.activeLang();
```

--------------------------------

### Serve Font Awesome Locally

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/font-awesome@4.4.0/README.md

Serve the Font Awesome project on a local server for development and testing.

```bash
$ bundle exec jekyll -w serve
```

--------------------------------

### Build Font Awesome Project

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/font-awesome@4.4.0/README.md

Build the Font Awesome project and its documentation using Jekyll.

```bash
$ bundle exec jekyll build
```

--------------------------------

### Webshim Initialization and Configuration

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/demos/cfgs/input-month.html

Initializes webshim with specific options for forms and forms-extended, then loads the forms polyfill. It also sets up event listeners for jQuery and loads demo/configuration scripts.

```javascript
webshim.setOptions('forms', { lazyCustomMessages: true, replaceValidationUI: true, addValidators: true, customDatalist: true });
webshim.setOptions('forms-ext', { replaceUI: true, "types": "month number" });
webshim.setOptions('debug', 'noCombo');
// load the forms polyfill
webshim.polyfill('forms forms-ext');
webshim.ready('jquery', function(){
    webshim.loader.loadScript("../../demo-js/demo.js", false, false, true);
    webshim.loader.loadScript("assets/cfg.js", false, false, true);
});
```

--------------------------------

### String.raw Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Demonstrates using String.raw with template literals and with an object containing a 'raw' property.

```javascript
var name = 'Bob';
String.raw`Hi\n${name}!`;           // => 'Hi\\nBob!' (ES6 template string syntax)
String.raw({raw: 'test'}, 0, 1, 2); // => 't0e1s2t'
```

--------------------------------

### Initialize Webshim Forms and Forms-Ext Polyfills

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/demos/cfgs/input-date.html

Initializes the Webshim forms and forms-ext polyfills. This is a core setup step for enabling enhanced form element functionalities.

```javascript
webshim.polyfill('forms forms-ext');
```

--------------------------------

### Array.copyWithin Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Shows how Array.copyWithin can be used to copy a sequence of array elements within the array.

```javascript
[1, 2, 3, 4, 5].copyWithin(0, 3); // => [4, 5, 3, 4, 5]
```

--------------------------------

### Basic Polyfill Initialization

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/index.html

Call the polyfill method with a whitespace-separated list of features to enable. This should be done as early as possible in your application.

```javascript
webshim.polyfill( "canvas geolocation" );
```

--------------------------------

### Array.prototype.includes Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Demonstrates the usage of Array.prototype.includes for checking element existence, including cases with NaN and undefined.

```javascript
[1, 2, 3].includes(2);        // => true
[1, 2, 3].includes(4);        // => false
[1, 2, 3].includes(2, 2);     // => false

[NaN].indexOf(NaN);           // => -1
[NaN].includes(NaN);          // => true
Array(1).indexOf(undefined);  // => -1
Array(1).includes(undefined); // => true
```

--------------------------------

### Core-JS Function.name Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Demonstrates how to access the name property of a function, which returns the function's identifier.

```javascript
(function foo(){}).name // => 'foo'
```

--------------------------------

### Initialize Webshims Configuration

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/tests/test-ext/markup-loading-2.html

Sets up the configuration for Webshims, including disabling native extension and specifying test data for markup loading tests.

```javascript
window.asyncWebshims = window.asyncWebshims || {};
window.asyncWebshims.cfg = window.asyncWebshims.cfg || [];
window.asyncWebshims.cfg.push([{"extendNative": false, "testData": "markup2"}]);
```

--------------------------------

### Load Demo and Configuration Scripts

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/demos/cfgs/input-color.html

Loads additional JavaScript files for the demo and configuration using Webshim's loader.

```javascript
webshim.ready('jquery', function() {
  webshim.loader.loadScript("../../demo-js/demo.js", false, false, true);
  webshim.loader.loadScript("assets/cfg.js", false, false, true);
});
```

--------------------------------

### RegExp.escape Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Demonstrates RegExp.escape for escaping special characters in a string to be used safely within a regular expression.

```javascript
RegExp.escape('Hello, []{}()*+?.\^$|!'); // => 'Hello, \[\{\}\]\(\)\*\+\?\.\\\^\$\|!'
```

--------------------------------

### Initialize Webshims and Mediaelement Support

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/tests/mediaelement-test.html

Initializes Webshims and waits for 'DOM mediaelement swfobject' to be ready. This is typically used to set up the testing environment.

```javascript
(function($){ $.webshims.ready('dom-support', function(){ QUnit.reset = function(){ $("#main, #qunit-fixture").htmlPolyfill( QUnit.config.fixture ); }; }); module("init"); asyncTest("init", function(){ $.webshims.ready('DOM mediaelement swfobject', start); }); })(jQuery); jQuery.noConflict();
```

--------------------------------

### Creating Objects with webshim.objectCreate

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/index.html

Illustrates how to create a new object 'myCar' using webshim.objectCreate, inheriting from 'carProto' and defining its own properties and methods, including a custom '_create' initialization method.

```javascript
var carProto = {
    options: {
        foo: 'bar',
        baz: 'boom'
    },
    wheels: 4, 
    drive: function(){
        this.isDriving = true;
    }
};

var myCar = Object.create(carProto, {
    _create: {
        value: function(){
            this.drive();
        }
    },
    jumps: {
        value: function(){
            //implements jumping
        }
    },
    {baz: 'jo'}
});

// myCar will look like this:

{
    // own property:
    options: { 
        foo: 'bar',
        baz: 'jo'
    },
    
    // prototype:
    wheels: 4, 
    
    // prototype
    drive: function(){
        this.isDriving = true;
    },
    
    // own property:
    _create: function(){
        this.drive();
    },
    
    // own property:
    jumps: function(){
        //implements jumping
    },
    
    // own property:
    isDriving: true
}
```

--------------------------------

### String.prototype.at Example

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/core-js@1.1.2/README.md

Shows how to use String.prototype.at to access characters, including those outside the Basic Multilingual Plane (BMP).

```javascript
'a𠮷b'.at(1);        // => '𠮷'
'a𠮷b'.at(1).length; // => 2
```

--------------------------------

### AJAX Validation Response (Invalid)

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/demos/forms.html

Example of an invalid JSON response from an AJAX validation service, indicating an issue.

```json
{"valid": false}
```

--------------------------------

### Configure and Polyfill Mediaelement

Source: https://github.com/wurmlab/sequenceserver/blob/master/public/vendor/npm/webshim@1.15.8/demos/demos/mediaelement.html

Configures the mediaelement polyfill with custom options and then activates it. This is a foundational step before using mediaelement features.

```javascript
webshim.setOptions('mediaelement', {
		replaceUI: 'auto',
		plugins: ['plugin-name']
	});
    
    //start loading mediaelement including plugins
    webshim.polyfill('mediaelement');
    
    //wait until plugin-name is ready
    webshim.ready('plugin-name', function(){
    	//call ``pluginMethod``
    	$('.mediaplayer').jmeFn('pluginMethod');
    });
```
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