Protein description not accessible in API

[GoogleCodeExporter]

In the X!Tandem output we have the protein "label" and the protein description 
presented separately. However the API only gives access to the "label" value 
(Protein.getLabel() method). Can you please also add Protein.getDescription() ? 

Example of X!Tandem output: 

<protein expect="-1.4" id="5736.1" uid="4657" label="tr|F1RRZ6|F1RRZ6_PIG 
Uncharacterized protein (Fragment) OS=Sus scrofa GN=SH3PXD2B..." sumI="3.78" >
<note label="description">tr|F1RRZ6|F1RRZ6_PIG Uncharacterized protein 
(Fragment) OS=Sus scrofa GN=SH3PXD2B PE=4 SV=1:reversed</note>

Motivation: sometimes relevant information like whether the match is a decoy 
match or not is only found in the protein description (see ":reversed" suffix 
in example above).

Thanks and regards,

Pieter.

Original issue reported on code.google.com by pieterlu...@gmail.com on 31 Dec 2012 at 11:41

[GoogleCodeExporter]

Thanks for pointing this out.

It seems like the label value is often a shortened version of the actual 
protein description found in the description note. I've now added a 
getDescription method to the Protein object and recommend that this is used 
when available.

X!Tandem Parser v1.5.10 has just been deployed with this fix. This should take 
care of the issue, but let me know if this is not the case.

Original comment by harald.b...@gmail.com on 31 Dec 2012 at 5:26

• Changed state: Fixed

[GoogleCodeExporter]

Thanks for the fix. I tested it and it is working fine.

Original comment by pieterlu...@gmail.com on 28 Jan 2013 at 3:51