# neXtProt - The knowledge resource on human proteins
This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project
See: https://www.nextprot.org/
# neXtProt feature viewer
[](https://zenodo.org/badge/latestdoi/36719341)
> The feature viewer is a super easy javascript library to use in order to draw the different features covering a sequence for a better visualization.
**Full documentation and live demo** : http://calipho-sib.github.io/feature-viewer/examples/
This version is made in Javascript using the D3 library. For the TypeScript version, see : https://github.com/Lisanna/feature-viewer-typescript
## Getting Started
**1.** You can get the library in your project using NPM/Yarn
```
//NPM//
npm install feature-viewer
//Yarn//
yarn add feature-viewer
```
Or Include the feature-viewer from jsDelivr CDN in the header of your html
```html
```
**NOTE** : If you already got the dependencies (D3, Bootstrap & Jquery) in your project, use the simple minified version instead of the bundle :
```html
```
**2.** Specify a div in your html
```
```
**3.** Create an instance of FeatureViewer in JavaScript with the sequence (or a length), the div in which it will be display and the rendering options of your choice.
```javascript
var ft = new FeatureViewer.createFeature('MALWMRLLPLLALLALWGPGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLE',
'#fv1',
{
showAxis: true,
showSequence: true,
brushActive: true, //zoom
toolbar:true, //current zoom & mouse position
bubbleHelp:true,
zoomMax:50 //define the maximum range of the zoom
});
//Instead of a sequence, you can also initialize the feature viewer with a length (integer) :
var ft = new FeatureViewer.createFeature(213,'#fv1');
```
To import Feature Viewer into an ES2015 application, you can import specific symbols from specific Feature Viewer modules:
```javascript
import { createFeature } from "feature-viewer";
```
In Node:
```javascript
const { createFeature } = require("feature-viewer");
```
**4.** Finally, add the features
```javascript
ft.addFeature({
data: [{x:20,y:32},{x:46,y:100},{x:123,y:167}],
name: "test feature 1",
className: "test1", //can be used for styling
color: "#0F8292",
type: "rect" // ['rect', 'path', 'line']
});
```
**5.** Et voila!
## Functionalities
* Zoom into the Feature-viewer by selecting a part of the sequence with your mouse. Zoom out with a right-click.
You can also zoom programmatically with the methods **```zoom(start,end)```** and **```resetZoom()```**
* A tooltip appears when the mouse is over a feature, giving its exact positions, and optionally, a description.
* beside the positions for each element, you can also give a description & an ID, allowing you to link click event on the feature to the rest of your project.
## Options
* Show axis
* Show sequence
* Brush active (zoom)
* Toolbar (current zoom & position)
* Bubble help
* Zoom max
* Features height
* Offset
## ClearInstance()
You may sometimes want to reload your feature-viewer with new parameters. To avoid memory leaks, the method **```clearInstance()```** will clear each element & listener for you before you delete the feature-viewer instance.
## Documentation
Check out this page for a better understanding of how to use the feature viewer and its possibilities :
* http://calipho-sib.github.io/feature-viewer/examples/
## Use it with NeXtProt API
It is possible to fill the feature viewer with protein features from [NeXtProt](https://www.nextprot.org/), the human protein database.
- First, find your protein of interest in NeXtProt and get the neXtProt accession (NX_...). (You can find your protein by entering an accession number of another database, like UniProt or Ensembl)
- Then, check the type of feature in the [NeXtProt API](https://api.nextprot.org/) that you would like to add to your viewer. For example, "propeptide" or "mature-protein".
- Include the feature viewer bundle with nextprot to your html : feature-viewer.nextprot.js
- Finally, create your feature-viewer like this :
```javascript
//initalize nextprot Client
var applicationName = 'demo app'; //please provide a name for your application
var clientInfo='calipho group at sib'; //please provide some information about you
const { nxFeatureViewer, Nextprot } = FeatureViewer;
var nx = new Nextprot.Client(applicationName, clientInfo);
//var entry = "NX_P01308";
var isoform = "NX_P01308-1";
// feature viewer options
var options = {showAxis: true, showSequence: true,
brushActive: true, toolbar:true,
bubbleHelp: true, zoomMax:20 };
// Create nextprot feature viewer
nxFeatureViewer(nx, isoform, "#div2", options).then(function(ff){
// Add first custom feature
ff.addFeature({
data: [{x:20,y:32},{x:46,y:100},{x:123,y:167}],
name: "test feature 1",
className: "test1",
color: "#0F8292",
type: "rect",
filter: "type1"
});
// Add second feature from nextprot
var styles = [
{name: "Propeptide",className: "pro",color: "#B3B3B3",type: "rect",filter:"Processing"},
{name: "Mature protein",className: "mat",color: "#B3B3C2",type: "rect",filter:"Processing"}
];
ff.addNxFeature(["propeptide","mature-protein"], styles);
```
## Examples
https://api.nextprot.org/entry/NX_P01308/proteomics
## Support
If you have any problem or suggestion please open an issue [here](https://github.com/calipho-sib/feature-viewer/issues).
## Development
`git clone https://github.com/calipho-sib/feature-viewer.git`
`npm install` (will install the development dependencies)
`npm start` (will start the development server on localhost:8080)
...make your changes and modifications...
`npm run build` (will create the bundle js & css in build/)
`npm publish` (will publish in npm)
## License
Copyright (c) 2015, SIB Swiss Institute of Bioinformatics
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.