Modularization of jmztab

[GoogleCodeExporter]

I have created a fork of the currently latest svn respository version of jmztab 
in order to 
make it more modular and to cut down the dependencies to the absolute necessary 
ones. This may be especially useful for developers who do not need the 
peptide/proteomics parts of jmztab, but rather only the small molecules part, 
as in my case. 

I therefore separated the model from the utils packages, as well as providing 
separate modules for the pride-converter, the cli, and the gui. 
Building the cli or the gui distributions can now be triggered by using maven 
profiles.
Would be great if someone else found this useful.

You can find the git repository here:

github.com/nilshoffmann/jmztab

Original issue reported on code.google.com by nils.hof...@web.de on 21 Feb 2014 at 4:48

[GoogleCodeExporter]

Modularization of jmztab is good idea to cover different requirements of users. 
We will think about it in the coming version. 

You would like to separate small molecules part from jmztab, however, I thought 
your modularization way not support it. Because of, there exists many 
relationships among different sections in mzTab file. In jmztab project, we 
create a separate module 
(https://code.google.com/p/mztab/source/browse/#svn%2Fjmztab%2Ftrunk%2Fsrc%2Fmai
n%2Fjava%2Fuk%2Fac%2Febi%2Fpride%2Fjmztab%2Fmodel) to maintain five sections 
(metadata, protein, peptide, PSM, small molecule) as a whole target.

In the next stage, we will think about separating parse, validate and gui/cli 
utils from jmztab core module, and create a couple of dependences projects. 
Hopefully new solution will archive your requirement. 

I looked your work in git repository, it looked very nice. We will reference 
your modularization way and hopefully keep communication in the future.

Original comment by xuqing...@gmail.com on 22 Feb 2014 at 2:38

[GoogleCodeExporter]

I changed the groupId in the github project to net.sf.maltcms.mztab for now to 
avoid any artifact clashes between your main-line and the fork. I will be happy 
to help with a reintegration in the future. I am not planning to add any major 
changes, so that should be manageable.

The modularization seemed necessary for Maltcms due to the large number of 
dependencies that were pulled in transitively through the ion-generator 
dependency. The reorganization helped me to understand the interdependencies 
within jmztab much better. Maybe the (transitive) dependencies that are not 
required for jmztab's functionality could be removed in the future? 

Original comment by nils.hof...@web.de on 4 Mar 2014 at 7:55