[Bioc-devel] recalling methods

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?

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--
Computational Biologist
Genentech Research