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rformassspectrometry / unimod

Amino acid modifications for mass spectrometry
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Depending on Biobase #4

Closed lgatto closed 7 years ago

lgatto commented 7 years ago

The current version of unimod imports 3 symbols from Biobase:

I think that the trend in Bioc core is to drop the class version slot. Although it can be handy to update object from one class to another (rather than inspecting the slots one by one to figure out the old class definition), it can also be a substantial overhead when many object are created. I am wondering if it is really necessary to have a class version and if yes, then I think it is probably easier to have a plain character and from importing the two first symbols above.

I am unsure if we thus still need to depend on Biobase for the description generic. The slot and/or accessor could simply be renamed unimodName.

@sgibb, what do you think?

sgibb commented 7 years ago

I am not sure that we need a version slot. I thought it is code standard of Bioc S4 classes. But I am happy to drop that slot (and the dependency on Biobase).