[Biojava-dev] biojava / Security

[Schreiber, Mark]

Thanks for this. I forgot the CVS add command before the CVS commit command :(
 
I have now back ported two files that should allow for a compile. Can someone check this has worked before I proceed with some more patches?
 
Thanks
 
Mark
 

	-----Original Message----- 
	From: David Huen [mailto:smh1008 at cus.cam.ac.uk] 
	Sent: Tue 19/08/2003 11:33 p.m. 
	To: pjm at sanger.ac.uk; Schreiber, Mark 
	Cc: biojava-dev at biojava.org 
	Subject: Re: [Biojava-dev] biojava / Security
	
	

	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.
	


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