[Biojava-dev] biojava / Security

[David Huen]

On Tuesday 19 Aug 2003 11:08 am, pjm wrote:

> /nfs/pathdb/prod/external/build/biojava-1.3-2003-08-19/ant-build/src/main
>/org/biojava/bio/seq/io/SeqIOTools.java:342: cannot resolve symbol
>     [javac] symbol  : class GenpeptFormat
>     [javac] location: class org.biojava.bio.seq.io.SeqIOTools
>     [javac]         SequenceFormat former = new GenpeptFormat();
>     [javac]                                     ^
>     [javac] Note: Some input files use or override a deprecated API.
>     [javac] Note: Recompile with -deprecation for details.
>     [javac] 3 errors
>

> The last problem is a one line change;
>
>           SequenceFormat former = new GenbankFormat();
> ---
>
> >         SequenceFormat former = new GenpeptFormat();
>
> "Schreiber, Mark" wrote:
> > I just made a bit of an effort to synchronize the bj-live and bj1.3 to
> > catch most of the recent bug fixes which was pretty tricky and I'm not
> > certain that I ported everything so something like this kind of daily
> > email would be even more useful than I thought.
> >

Mark, I don't know about the other two but for the last problem, you will 
need to port back to the 1.3 stable the GenpeptFormat class in biojava-live 
from org.biojava.bio.seq.io.  The change is required because of a prior 
change to the GenbankFormat class that removed direct Genpept support from 
it.

Regards,
David Huen

-- 

David Huen, Ph.D.              Email: smh1008 at cus.cam.ac.uk
Dept. of Genetics              Fax  : +44 1223 333992
University of Cambridge        Phone: +44 1223 333982/766748
Cambridge, CB2 3UH
U.K.