[Pipet Devel] Getting rid of modification of xml definition files

[J.W. Bizzaro]

I recall the IRC conversation Brad and Jean-Marc first had about this a couple
months ago.  Basically, Overflow keeps class definitions in C++, which are
then inherited by the XML-based .n files.  The .n files also describe node
connectivity/linkage.  Jean-Marc asked during the conversation if the .def
files were class definitions or instances.  Brad replied that they were both.

Brad also mentioned that the advantages of .def and the use of the filesystem
hierarchy were (1) better access to class definitions (XML is used rather than
C++), (2) crash recovery (the DL is always writing to the filesystem), and (3)
the manipulation of networks (requiring a great deal of node and link
shuffling).  It seemed to me that Jean-Marc agreed about the advantages of
.def.

The advantages to .n that I can see are (1) clear distinction between class
definition and instance, and (2) the use of /less/ files (perhaps a network
can always be described in a single XML file).

Brad, if you want to switch to the use of .n files and Overflow's overall
approach, can you explain (1) how class definitions will be stored and
accessed, and if they'll be distinguished any better from class instances, (2)
how crash recovery will take place (will .n always reflect the state of the
networks?), and (3) if writing to .n all the time is any better or quicker
than writing to .def's all the time.

Cheers.
Jeff
-- 
J.W. Bizzaro                                           jeff at bioinformatics.org
Director, Bioinformatics.org: The Open Lab     http://bioinformatics.org/~jeff
"Let the machine do the dirty work." -- Kernighan and Ritchie
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