[Biojava-dev] default AtomCache constructor

[Steve Darnell]

Hi Spencer,

As a BioJava user, I would applaud your efforts to create and maintain
cross-platform code -- especially since the coded capability already
exists for this instance.

Regards,
Steve

-----Original Message-----
From: biojava-dev-bounces at lists.open-bio.org
[mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of Spencer
Bliven
Sent: Monday, August 29, 2011 9:03 PM
To: biojava-dev
Subject: [Biojava-dev] default AtomCache constructor

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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