[gmx-developers] changes in filename option handling

[Jan Henning Peters]

Hi,

I'm currently working on an analysis module based on the trajectory
analysis framework of the master git branch.

Since my last rebase, I noticed a change in the handling of default
filenames that I believe might be unintended.

As far as I can see, the FileNameOption class only has a method
defaultBasename (attempting to call defaultValue results in a compiler
error), which does not allow supplying a file extension - if a
"filename.ext" is given, this is taken as the basename, and a standard
file extension is appended. The default file extension is then appended
by the framework based on the filetype set. Unfortunately,
eftTrajectory for example this limits the default filetype to .xtc -
setting a .trr or .pdb file as default output is not possible any more
for the developer.

There seems to be a similar problem even with the older modules, I
noticed that gmx covar now by default produces a file named average.pdb.gro.

Jan