Tracking my work on myFavouriteProtein - a webpage to use BioJS components Part 2 - getting all the other required stuff...

Checking out the websites, I need to gather the following dependencies...

Protein Portfolio
https://www.ebi.ac.uk/Tools/biojs/registry/Biojs.ProteinPortafolio.html

Clicking on Installation Tab:

Biojs scripts

1 2 3 4 5 6

<script language="JavaScript" type="text/javascript" src="src/Biojs.js"> <script language="JavaScript" type="text/javascript" src="../biojs/Biojs.PDBLogos.js"></script> <script language="JavaScript" type="text/javascript" src="../biojs/Biojs.Sequence.js"></script> <script language="JavaScript" type="text/javascript" src="../biojs/Biojs.Protein3D.js"></script> <script language="JavaScript" type="text/javascript" src="../biojs/Biojs.Protein3DWS.js"></script> <script language="JavaScript" type="text/javascript" src="src/Biojs.ProteinPortafolio.js"></script>

External script(s)

1 2 3

<script language="JavaScript" type="text/javascript" src="../biojs/dependencies/jquery/jquery-1.6.4.js"> <script language="JavaScript" type="text/javascript" src="../biojs/dependencies/graphics/raphael-2.1.0.js"></script> <script language="JavaScript" type="text/javascript" src="../biojs/dependencies/jmol-12.0.48/Jmol.js"></script>

CSS stylesheet(s)

1 2	<link href="../biojs/css/biojs.Protein3D.css" rel="stylesheet" type="text/css" /> <link href="../biojs/css/biojs.ProteinPortafolio.css" rel="stylesheet" type="text/css">

Probably the easiest thing is just to download all of the Biojs scripts and put them in a folder.
Where do I get these from?
Github, of course. But where exactly?

To get something secure and stable, it's probably best to go to the release page on Github:
https://github.com/biojs/biojs/releases

Press the source code button to download the zip file.

Then open it on your computer. 

Sadly this doesn't have everything or maybe it does. I down loaded other stuff too so I'm a bit confused. 

Let's assume, this did download everything. I will check again on a different computer to ensure. 

I am going to create a separate biojs folder in my dist folder. 

In my biojs folder, I am creating a css and a js folder. 

Then I am going to put all the necessary bits in there. 

I didn't need to create the folders. Just copy them in paste them into the Aptana folder structure.

Copy dependencies folder into the dist. 

Copy the js folder into biojs.

I think everything is there. 

Some testing required to be sure. 

First, have a look. 

Yes, everything seems to be in place although slightly differently organised. 

Let's cut and paste in the code and organise the files and that will be a good start. 

I added the code in a script box and tried to get it to work but it hasn't. 

Error messages include:

"

Consider using 'dppx' units, as in CSS 'dpi' means dots-per-CSS-inch, not dots-per-physical-inch, so does not correspond to the actual 'dpi' of a screen. In media query expression: (-webkit-min-device-pixel-ratio: 1.5), (min-resolution: 144dpi) tweet_button.1409007440.html:1

Requesting features for 'P99999' Biojs.js:181

Failed to load resource: net::ERR_FILE_NOT_FOUND file:///Users/paulbrennan/Documents/Aptana%20Studio%203%20Workspace/biojs/d…%2Fdas-srv%2Funiprot%2Fdas%2Funiprot-summary%2Ffeatures%3Fsegment%3DP99999

Error requesting features for P99999 Biojs.js:181

SUCCESS: data received Biojs.js:181

_createOptions: <option value="3NWV.D (2..105)">3NWV.D (2..105)</option><option value="3ZOO.D (2..105)">3ZOO.D (2..105)</option><option value="3ZOO.A (2..105)">3ZOO.A (2..105)</option><option value="3NWV.A (2..105)">3NWV.A (2..105)</option><option value="3NWV.B (2..105)">3NWV.B (2..105)</option><option value="3NWV.C (2..105)">3NWV.C (2..105)</option><option value="3ZCF.D (2..105)">3ZCF.D (2..105)</option><option value="3ZOO.C (2..105)">3ZOO.C (2..105)</option><option value="3ZCF.A (2..105)">3ZCF.A (2..105)</option><option value="3ZCF.B (2..105)">3ZCF.B (2..105)</option><option value="3ZCF.C (2..105)">3ZCF.C (2..105)</option><option value="1J3S.A (2..105)">1J3S.A (2..105)</option><option value="3ZOO.B (2..105)">3ZOO.B (2..105)</option> Biojs.js:181

Alignments for pdb 3NWV.D Biojs.js:181

Object Biojs.js:181

Current alignment Biojs.js:181

Object Biojs.js:181

Uncaught TypeError: undefined is not a function Biojs.ProteinPortafolio.js:294"

UGGHH!