[BioC] formal methods and classes and capitalization conventions
Gordon Smyth
smyth at wehi.edu.au
Tue Mar 25 17:25:51 MET 2003
I'd like to raise the issue of a capitalization convention for naming
objects in R. Almost everything in R used to be lowercase but recently
there is increasing use of mixed upper/lower case to define names. There is
potential for using the capitalizations to make code more self explanatory,
but only if a consistent system is used.
In Java, capitalization is used to indicate the type of object. Names of
methods are capitalized except for the first word (e.g., geneNames), names
of classes are fully capitalized (e.g., ExprSet), names of data objects are
all lowercase, and names of libraries have their own conventions but
normally with lowercase letters. A programmer can recognize the type of
object in many cases simply from the name.
In R, Java capitalization has started to be used for formal generic
functions, but the point of the convention is being lost because the same
capitalization is being used for classes, non-generic functions, package
names and even function arguments. Naming is not always done consistently
and different conventions seem to be used by different people, so within
Bioconductor we have classes, functions, arguments, and packages with lots
of different capitalization styles. One cannot predict what capitalization
style will be used for a given object, so capitalization is on the way to
being a complication rather than a clarification.
Here is a suggestion for a convention, which people can shoot down if they
like:
Classes: full capitalization, e.g., ExprSet, AffyBatch, MarrayNorm
Generic functions: lower case first word, e.g., maNorm, normalize, rma,
geneNames
Non-generic functions: lowercase, possibly with dot separaters
Members of data classes: lowercase, possibly with dot separaters
Function arguments: lowercase, possibly with dot separaters
Packages: lowercase, e.g., affy, marraynorm
Cheers
Gordon
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