sequence-viewer/README.md

A protein sequence viewer written in javascript

# neXtProt - The knowledge resource on human proteins

This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project

See: http://www.nextprot.org/

# neXtProt sequence viewer

[![Build Status](https://travis-ci.org/calipho-sib/sequence-viewer.svg?branch=master)](https://travis-ci.org/calipho-sib/sequence-viewer)

> The sequence viewer is a super easy javascript library to use in order to draw a protein sequence in a readable way.

![Sequence viewer1](/assets/sequence-viewer-complete.png)

Live demo: https://cdn.rawgit.com/calipho-sib/sequence-viewer/master/examples/index.html

Simple example: https://cdn.rawgit.com/calipho-sib/sequence-viewer/master/examples/simple.html

## Getting Started

1) Include the library using bower or npm or simply by including the javascript sequence-viewer.js
```
//BOWER//
bower install sequence-viewer

//NODE//
npm install sequence-viewer
```

2) Specify a div in your html
```
<div id="sequence-viewer"></div>
```
3) Create an instance of Sequence in javascript and apply the render method
```javascript
//For Node add before : var Sequence = require("sequence-viewer"); //


var seq = new Sequence('MALWMRLLPLLALLALWGPGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN');
// Render the sequence with or without rendering options
// (Check the interactive documentation)
seq.render('#sequence-viewer');

```
4) Et voila!

![Sequence viewer2](/assets/sequence-viewer-simple.png)


Note: if you choose the later approach with only the main javascript you should also include the dependencies, jquery,handlebars and bootstrap.min.css

## Documentation

Check out this interactive page for a better understanding of how to use the sequence viewer and its possibilities :
* https://cdn.rawgit.com/calipho-sib/sequence-viewer/master/examples/index.html


## Options
* Show chars per line
* Wrap lines
* Highlight
* Coverage
* Labels
* Toolbar (chars per line)
* Search
* Title
* sequenceMaxHeight
* Events
* Badge

## Examples 

[https://search.nextprot.org/entry/NX_P01308/view/proteomics](https://search.nextprot.org/entry/NX_P01308/view/proteomics)

## Support

If you have any problem or suggestion please open an issue [here](https://github.com/calipho-sib/sequence-viewer/issues).

## Development

`git clone https://github.com/calipho-sib/sequence-viewer.git` 

`npm install`  (will install the development dependencies)

`bower install`  (will install the browser dependencies)

...make your changes and modifications...

`npm run dist` (will create the min & bundle versions in dist/)

`npm run build` (will create the bundle js & css in build/ for node)

`grunt bump` (will push and add a new release)

`npm publish` (will publish in npm)



## License 
This software is licensed under the GNU GPL v2 license, quoted below.

Copyright (c) 2015, SIB Swiss Institute of Bioinformatics