[Biojava-dev] default AtomCache constructor

[Spencer Bliven]

Great! AtomCache and ScopInstallation now have default constructors.

On my system (OS X) the java.io.tmpdir location is ugly and
randomized, and it changes with every program instance. I suggest
setting the PDB_DIR environmental variable to something sensible, like
/tmp or ~/pdb. This will cache pdb files (and the large SCOP database)
between program runs.

-Spencer

PS Setting environmental variables in eclipse on OSX is a bit tricky.
I recommend adding it to your ~/.launchd.conf, as suggested at
http://stackoverflow.com/questions/603785/environment-variables-in-mac-os-x


On Mon, Aug 29, 2011 at 22:26, Andreas Prlic <andreas at sdsc.edu> wrote:
>
> yea, that makes more sense like you propose..
>
> A
>
> On Mon, Aug 29, 2011 at 7:03 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:
> > I've noticed a lot of hard-coded paths in the structure module from creating
> > AtomCaches. For instance, very common in main() functions:
> >
> >    AtomCache cache = new AtomCache("/tmp",true);
> >
> > This is not cross-platform compatible. I believe the proper way of doing
> > this is
> >
> >    AtomCache cache = new AtomCache(new UserConfiguration());
> >
> > which chooses the save location intelligently (java.io.tmpdir or PDB_DIR
> > system properties). Would anyone object if I made this the default AtomCache
> > constructor and removed all the existing hard paths?
> >
> > -Spencer
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> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >