[Biojava-dev] Biojava3 structure

[trevor paterson (RI)]

Andreas

I am trying to do an anoymous checkout of the whole bio-java 3 trunk  and it is failing on the structure module

I cant even do a copy command

the src/main tree seems corrupted - throwing an error
Error: Decompression of svndiff data failed  

Trevor Paterson PhD
new email trevor.paterson at roslin.ed.ac.uk

Bioinformatics 
The Roslin Institute
The Royal (Dick) School of Veterinary Studies
University of Edinburgh
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> -----Original Message-----
> From: biojava-dev-bounces at lists.open-bio.org 
> [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of 
> Andreas Prlic
> Sent: 29 March 2010 03:03
> To: Scooter Willis
> Cc: biojava-dev
> Subject: Re: [Biojava-dev] Biojava3 structure
> 
> Hi Scooter,
> 
> at the present the structure modules depend on the alignment 
> module and on the (old) core module.  This is for aligning 
> ATOM and SEQRES residues in the PDB files, and for the Smith 
> Waterman alignment based 3D structure superposition. If we 
> target a release of biojava 3 in about a month, I don't think 
> it will be possible to break this out, mainly because the 
> alignment module is still based on the biojava 1 code base. 
> Overall I think that the core module probably should still be 
> part of the BioJava 3 release. Any opinions on that?
> 
> Andreas
> 
> On Sun, Mar 28, 2010 at 3:06 PM, Scooter Willis 
> <HWillis at scripps.edu> wrote:
> 
> > Andreas
> >
> > I needed to do some work with a PDB file so started to use the 
> > structure library. It looks like it depends on all the old biojava 
> > code. Mainly the structure exceptions that extend 
> bioexception is the 
> > first thing tripping me up. Should the biojava3-structure 
> module have 
> > any external dependencies or am I working with the wrong package?
> >
> > Thanks
> >
> > Scooter
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