[Bioc-devel] Generic for write to BiocGenerics

Michael Lawrence lawrence.michael at gene.com
Tue Sep 19 00:22:34 CEST 2017

I was also about to suggest that we converge on export() but held back
because I was obviously biased. I also agree with making the target
explicit in the function name. It makes the intent of the code way
more obvious.

On Mon, Sep 18, 2017 at 3:15 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> Hi jo,
> At the moment probably not much to be gained unless you ran into
> some conflicts with other "write" methods defined in Bioconductor?
> Note that the arguments/signature of base::write() don't really
> help making it a clean generic functions (e.g. weird 'file' default,
> 'ncolumns' and 'sep' args that lack generality, no ellipsis). It seems
> to me that instead of trying to force write() into a generic, it might
> be easier/cleaner to define a method for the export() generic defined
> in rtracklayer. Maybe the discussion would be whether we should consider
> moving rtracklayer::export() to BiocGenerics?
> Finally, IMO there is nothing wrong in using specific write* names like
> writeMgfData, writeMSData, writeMzTabData, etc... It plays nicely with
> tab-completion, the user can use args() to quickly see all the args and
> their defaults, tab-completion also works on the arguments, and the user
> does not struggle in finding the man page (like s/he does sometimes
> with generic and methods, especially when those are defined in
> different packages).
> H.
> On 09/18/2017 10:21 AM, Rainer Johannes wrote:
>> Dear all!
>> We are currently implementing mzML write support in `MSnbase` and did
>> implement a `write` method for the S4 objects in `MSnbase`. Now, the
>> question is whether it might not be better to define a `write` S4
>> generic in `BiocGenerics`?
>> cheers, jo
>> _______________________________________________
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> --
> Hervé Pagès
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> E-mail: hpages at fredhutch.org
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