Re: [Scaffoldhunter-devel] GSoC 2014 participation and Command Line Support project

[<nl...@us...>]

Hi Nyah,

thanks for your interest. A good starting point is to look at the tutorial [1] 
to make yourself familiar with the software and the analysis methods supported 
by Scaffold Hunter. You can check out the source code from the SVN repository 
(trunk). The packages edu.udo.scaffoldhunter.model.clustering and 
edu.udo.scaffoldhunter.model.treegen are most important for the project idea 
since they contain the code for clustering and the scaffold tree generation, 
which should be supported by a CLI. We have recently added a very basic 
command line tool for a specific task that can be found in the package 
edu.udo.scaffoldhunter.cli. It uses the library JCommander [2] for argument 
parsing. Of course, you are free to use a different library. However, you may 
want to have a look at the code to get an idea how command line support for 
Scaffold Hunter can be implemented.


Regards,
  Nils

[1] http://scaffoldhunter.sourceforge.net/tutorials.html
[2] http://jcommander.org/


On Thursday 27 February 2014 13:46:16 Check Nyah wrote:
> Hi,
> I am Nyah Check, a sophomore computer engineering student at the
> University of Buea(Cameroon), a 3 year Biochemistry student at my
> University where I did some deep study of nucleotides and cheminformatics
> which is this project's application domain and a GSoC participant for 2013
> where I worked with BRL-CAD on implementing a pull routine to reverse
> the effects
> of a push on Geometry. I wish to implement the command line interface for
> this great software and would love to get some guidance on where to look in
> the software, online tutorials I could look at in addition to the Scaffold
> preprint document which would assist me in implementing this project and
> alsothe priority of this project in relation to the organization's vision
> for this year's GSoC. I see this project as both an intellectual challenge
> and a forum to exercise my Java and also interact with the cutting edge
> researchers
> in this domain. Can't wait to work with you guys this year :-). Thanks for
> the assistance.
> 
> Cheers!
> Nyah