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: [email protected] > To: [email protected] > CC: [email protected]; [email protected] > 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 > <[email protected]>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: [email protected] > > | > > > > > > > > > > > > _______________________________________________ > > Biojava-l mailing list - [email protected] > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > -- > ----------------------------------------------------------------------- > Dr. Andreas Prlic > Senior Scientist, RCSB PDB Protein Data Bank > University of California, San Diego > (+1) 858.246.0526 > ----------------------------------------------------------------------- > _______________________________________________ > biojava-dev mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-dev
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