Hi Vince,
On 04/17/2014 04:19 AM, Vincent Carey wrote:
On Thu, Apr 17, 2014 at 2:37 AM, Hervé Pagès <hpa...@fhcrc.org
<mailto:hpa...@fhcrc.org>> wrote:
Hi Vince,
On 04/10/2014 08:16 AM, Vincent Carey wrote:
seems like something we should use more routinely, and it was not
straightforward for me to find it in IRanges
I could do that but...
Good object design would be that if a developer wants its class to
support the metadata() getter and setter, s/he should extend the
Annotated class defined in IRanges. This class has only 1 slot, the
metadata slot, and a very simple API: just metadata(). So by extending
it, metadata() will work out-of-the-box on his/her objects. This avoids
code duplication and ensures that the metadata() getter and setter
behave consistently on all objects.
I can see that a developer could be reluctant to depend on IRanges just
to inherit the Annotated class though. But maybe this means that the
Annotated class and the metadata() generic are in the wrong package?
thanks for the comment; i can deal with the situation as is.
An update on this: the Annotated class and metadata() accessor are now
in S4Vectors. Note that, as Michael pointed out, the Annotated class
is only an implementation for metadata(). It's really straightforward
(and very convenient) to have your class extend it. However if, for
whatever reason, you cannot or don't want to do this, you still need
to depend on S4Vectors to get the metadata() generic getter and setter,
which is not as light as BiocGenerics but is lower-level and lighter
than IRanges. The hope is that developers will be less reluctant to
depend on S4Vectors than on IRanges.
Cheers,
H.
Cheers,
H.
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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
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Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org <mailto:hpa...@fhcrc.org>
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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: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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