[Biopython-dev] _Switch and _Option questions

[Vincent Davis]

I am just getting started with class AbstractCommandline(object): The first
set of questions is more about questions I had after reading the
documentation.

First questions/comment mostly about documentation:
It appears that not all attributes need to be set in _Options and _Switch,
for example
    _Switch: o is_set -- if the parameter has been set, I don't see and
example of this being specified in a  _Switch self.parameter statement. I
see that it defaults to False, Is there a case that this is set in a
self.parameters statement? I think I understand this. It is just documented
as though it should be specified.

If I don't need a checker_function in _Options then I must use an None, I
guess as a place holder?

Not clear if equate should be used as  "equate" or 0,1, by this I mean it is
not documented well
   same goes for is_required

Looks like Value is similar to is_set in that it is not ever specified in a
self.Parameters statement

I don't think the example using Bio.Emboss.Applications import
WaterCommandline includes the use of a _switch

---------
Second set of questions
For both of the next questions I am mostly asking if the
feature/functionality is part of the class AbstractCommandline(object):

If two _Switches are mutually exclusive in there use is there a way to make
sure that they not both specified? Example anywhere?

Basically same question for _Option, How do I refer to the value of another
_option.


Thanks

  *Vincent Davis
720-301-3003 *
vincent at vincentdavis.net
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