Jay, The AtomCache also gives a performance boost when re-reading PDB files by using a cached IO mode. I believe you can manually activate this mode for your PDBFileReader; see line 115 of AtomCache<http://www.biojava.org/docs/api/src-html/org/biojava/bio/structure/align/util/AtomCache.html#line.115> class for the example.
I'm not completely sure on this, but I think any time you are re-reading the same structure within the same JVM instance there is an advantage. -da On Fri, Sep 16, 2011 at 17:15, JAX <[email protected]> wrote: > Ok cool... Maybe it we be good to make the atom cache java doc should > explicitly state that it is only for PDB files, and not any other > structures. > > Jay Vyas > MMSB > UCHC > > On Sep 16, 2011, at 6:57 PM, Andreas Prlic <[email protected]> wrote: > > > Hi, > > > > had a quick offline discussion with Spencer about this: The AtomCache > > provides a local mirror for public data, expects a specific > > organisation of files and only supports one toplevel-path under which > > all data is stored. If we would add support for private files to it, > > public and personal files would end mixed up in the same location, > > which in all likelihood would cause confusion. As such it makes more > > sense to access your personal files with the PDBFileReader and manage > > private files yourself. It is a one-liner in both classes anyways... > > > > Andreas > > > > > > > > > > On Fri, Sep 16, 2011 at 11:13 AM, Spencer Bliven <[email protected]> > wrote: > >> I think that AtomCache is the wrong tool for this job. If you have > private > >> PDB files you should just use a PDBFileReader to get each one (see > >> > http://biojava.org/wiki/BioJava:CookBook:PDB:read3.0#Getting_more_control > ). > >> I don't think AtomCache should be modified to support this. > >> > >> -Spencer > >> > >> On Fri, Sep 16, 2011 at 07:43, Andreas Prlic <[email protected]> wrote: > >>> > >>> If you > >>> think it is useful we can add something like a pre-fix which would > >>> tell the cache to load local files with a nonstandard name. Something > >>> like : private:a1 could be the name to describe your own file. > >> > >> > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
