[Bioc-devel] Generic for write to BiocGenerics

[Laurent Gatto]

Out of curiosity, do you also have an import() function?

On 18 September 2017 22:22, Michael Lawrence wrote:

> 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
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>>
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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
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>>
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>
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-- 
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/