[Bioc-devel] recalling methods

[Michael Love]

nice. I will play around with this. thanks Gabe!

On Fri, Dec 5, 2014 at 6:37 PM, Gabe Becker <becker.gabe at gene.com> wrote:
> Hey guys,
>
> Surgically removed from promptClass:
>
>   classInSig <- function(g, where, cl) {
>         cl %in% unique(unlist(findMethods(g, where)@signatures))
>     }
>     genWithClass <- function(cl, where) {
>         allgen <- getGenerics(where = where)
>         ok <- as.logical(unlist(lapply(allgen, classInSig, cl = cl,
>             where = where)))
>         allgen[ok]
>     }
>
>> genWithClass("IRanges", find(classMetaName("IRanges")))
>  [1] "c"            "coerce"       "end<-"        "gaps"         "intersect"
>  [6] "isNormal"     "names<-"      "names"        "pgap"
> "pintersect"
> [11] "psetdiff"     "punion"       "reduce"       "reverse"      "setdiff"
> [16] "start<-"      "start"        "threebands"   "union"
> "updateObject"
> [21] "update"       "width<-"      "width"
>
>
> For semantic guessing of which ones will be useful, I've got nothing (for
> now).
>
> ~G
>
> On Fri, Dec 5, 2014 at 11:28 AM, Michael Lawrence
> <lawrence.michael at gene.com> wrote:
>>
>> 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
>> > >
>> > >
>> >
>>
>>         [[alternative HTML version deleted]]
>>
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>
>
>
>
> --
> Computational Biologist
> Genentech Research