[Biojava-dev] BioJava 3 status

[Ambikesh Jayal]

Hi,

I could get it working with the alpha5 version of all the jars. Following
was the error with the  alpha6-SNAPSHOT version while running the
DemoCE.main(). There are no classpath errors as I am using eclipse to import
the jar files.

Exception in thread "main" java.lang.NoSuchMethodError:
org.biojava.bio.structure.io.PDBFileReader.setPdbDirectorySplit(Z)V
at
org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:307)
at demo.DemoCE.main(DemoCE.java:69)
at T6.main(T6.java:11)



Kind Regards,
Ambi.



On Thu, Nov 18, 2010 at 5:06 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi Ambikesh,
>
> you already got the latest version, if you are on alpha6-SNAPSHOT.
> However it could be that you have a CLASSPATH configuration error and
> your code can't find some of the jars?
> Can you send the full exception ?
>
> Andreas
>
>
>
>
>
> On Thu, Nov 18, 2010 at 5:40 AM, Ambikesh Jayal <ambi1999 at gmail.com>
> wrote:
> > Hi Andreas,
> > Thanks.  Can you send me the link to download the latest version of
> > biojava3? Is there some place where all the latest jars are bundled into
> a
> > single biojava3.jar? I tried to run the DemoCE java file after
> downloading
> > the various jar from the link but it gives me some errors.
> > http://www.biojava.org/download/maven/org/biojava/
> >
> > Error:
> > Exception in thread "main" java.lang.NoSuchMethodError:
> > org.biojava.bio.structure.io.PDBFileReader.setPdbDirectorySplit(Z)V
> >
> > Jars I downloaded
> > biojava3-structure-gui-3.0-alpha6-SNAPSHOT
> > biojava3-structure-3.0-alpha6-SNAPSHOT
> > biojava3-alignment-3.0-alpha6-SNAPSHOT
> > biojava3-core-3.0-alpha6-SNAPSHOT
> > biojava3-genome-3.0-alpha6-SNAPSHOT
> > Kind Regards,
> > Ambi.
> >
> > On Tue, Nov 2, 2010 at 2:23 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> >>
> >> Hi Ambikesh,
> >>
> >> BioJava 3 will be released around Dec 12th. In the meanwhile, the
> >> features that you are interested in are already available from our
> >> code repository (git, svn, maven) for download.
> >>
> >> Andreas
> >>
> >> On Mon, Nov 1, 2010 at 10:01 AM, Ambikesh Jayal <ambi1999 at gmail.com>
> >> wrote:
> >> > Hi,
> >> >
> >> > When will BioJava3 (any release, even if it is developmental) be
> >> > available
> >> > for download? I have read at the following link that BioJava 3 will
> have
> >> > enhanced facilities for protein structure alignment and so it would be
> >> > exciting.
> >> >
> >> > http://biojava.org/wiki/BioJava:CookBook:PDB:align
> >> >
> >> >
> >> > Kind Regards,
> >> > Ambi.
> >> > _______________________________________________
> >> > biojava-dev mailing list
> >> > biojava-dev at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >> >
> >
> >
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>