[Bioc-devel] recalling methods

[Michael Lawrence]

Cool. I see hypertext as being useful here, because the generics and
classes form an intricate and sometimes ambiguous web, especially when
multiple inheritance and dispatch are involved. I think we should first
build better tooling for introspecting S4 and for graph-based modeling and
analysis of S4 architecture. For example, could we statically detect
whether a dispatch ambiguity exists, knowing all of the methods and
classes? And based on that build one or more end-user UIs?



On Fri, Dec 5, 2014 at 11:05 AM, Michael Love <michaelisaiahlove at gmail.com>
wrote:

> On Thu, Dec 4, 2014 at 4:01 PM, Michael Lawrence
> <lawrence.michael at gene.com> wrote:
> >
> > I think this gets at the heart of at least one of the usability issues
> in Bioconductor: interface discoverability. Many simpler command line tools
> have a single-faceted interface for which it is easy to enumerate a list of
> features. There's definitely room for better ways to interrogate our
> object-oriented APIs, but it's challenging. Essentially we need a way for
> the user to ask "what can I do with this object?". Yes, we need better
> introspection utilities, but we also need to integrate the query with
> documentation. In other words, we need a more dynamic, more fluid help
> system, oriented around S4.
> >
>
> I would be interested in working on this. A minimal goal for me is a
> function that just returns a character vector of the names of the
> generics defined for the object. Filtering that down to give methods
> which are "likely relevant" using the documentation will definitely be
> a bigger challenge.
>
>
> >
> >
> >
> > On Thu, Dec 4, 2014 at 9:56 AM, Michael Love <
> michaelisaiahlove at gmail.com> wrote:
> >>
> >> I was thinking about a request from someone at Bioc2014 (I can't
> >> remember at the moment)
> >>
> >> As an end-user, if I have an object x, how can I *quickly* recall the
> >> main methods for that? As in, without breaking my flow and going to
> >> ?myClass or help("myClass-class"). Suppose x is a GRanges, how can I
> >> remember that there is a method called narrow() which works on x?
> >>
> >> showMethods(classes=class(x)) will print out a huge list for many
> >> complex Bioc classes. And printTo=FALSE turns this huge list into an
> >> unhelpful character vector, e.g.:
> >>
> >> head(showMethods(classes="GRanges",printTo=FALSE),8)
> >> [1] ""                                    "Function \".asSpace\":"
> >>   [3] " <not an S4 generic function>"       ""
> >>   [5] "Function \".linkToCachedObject<-\":" " <not an S4 generic
> function>"
> >>   [7] ""                                    "Function \".replaceSEW\":"
> >>
> >> any ideas?
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
>

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