[Biojava-l] [Biojava-dev] Stockholm Parser is on Biojava 3.0.5 SNAPSHOT

[Amr AL-HOSSARY]

Yes.I have a cache of Pfam23 database. I tried it on the first 10 alignments in the database on 2 successive calls to parse(pathName, 5) and parseNext(5), and it worked well.
RegardsAmr

> Date: Tue, 6 Nov 2012 08:58:37 -0800
> From: andreas at sdsc.edu
> To: amr_alhossary at hotmail.com
> CC: biojava-dev at lists.open-bio.org; biojava-l at lists.open-bio.org
> Subject: Re: [Biojava-dev] [Biojava-l] Stockholm Parser is on Biojava 3.0.5	SNAPSHOT
> 
> Hi Amr,
> 
> This is great! Did you try to load a couple of  different files from the
> Pfam web site? That should be good for testing...
> 
> Andreas
> 
> 
> On Tue, Nov 6, 2012 at 3:11 AM, Amr AL-HOSSARY <amr_alhossary at hotmail.com>wrote:
> 
> > Dear all,
> > I added stockholm parser beta to the package "org.biojava3.alignment.io"
> > of "biojava3-alignment" project.It should be ready on on the latest Biojava
> > snapshot build after 20 mins.
> > As stockholm format structure is not well defined (at least in contrast to
> > PDB), Not all of the features are well implemented yet.Please test it
> > against different files you have, and feed me back; so that I start with
> > the most important/most used features first.
> > Thanks to Marko Vas for his code base. I built on his code  and that saved
> > a lot of unnecessary time.
> >
> >
> > Best Regards,
> >
> >
> > Amr AL-HOSSARY
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > Amr Ali AL-HOSSARY |
> > Ph.D. Student |
> > International PhD program in Computational Biology and Bioinformatics |
> >   School of Computer Engineering |
> >   Nanyang Technological University  |
> > Singapore |
> > Email:  amra0001 at e.ntu.edu.sg
> >   |
> >
> >
> >
> >
> >
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> 
> 
> -- 
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
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