[Bioperl-l] Other object oddities

Kevin Brown Kevin.M.Brown at asu.edu
Thu Apr 30 17:56:16 EDT 2009

So, I'm using quite a bit of bioperl code in my own stuff and have been
seeing some oddities with the naming of methods. A good example would be
in the Bio::Seq and Bio::SeqFeature::Generic. Both have a method called
"seq" but in the latter case it returns an object (and expects an object
when doing a Set) and in the former it returns a string and expects a
string when doing a Set.

This makes for a bit of brain freeze on my part when the return from
another object might be a Bio::Seq or Bio::SeqFeature::Generic and now
calling the ->seq returns different things.

Guess I'm just curious if anyone has done an audit of the methods of the
various objects and their return types to see how consistent they are
across even a subsection of the codebase?

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