[Bioc-devel] recalling methods

[Gabe Becker]

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
> > >
> > >
> >
>
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>
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-- 
Computational Biologist
Genentech Research

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