R/AAA.R

In Bioconductor/GSEABase: Gene set enrichment data structures and methods

mkScalar <- function(x) {
    if (length(x) != 1L)
        stop("expected length 1, object has length ", length(x), ": ",
             "\n  ", paste(head(x), collapse=", "))
    x[1]
}

.checkRequired <- function(required, provided) {
    idx <- which(!(required %in% provided))
    if (length(idx) > 0)
        stop("missing required argument(s): '",
             paste(required[idx], collapse="', '"), "'")
}

## for a vector c(CONSTRUCTOR=CLASS, ...) create a
## functionCONSTRUCTOR(...) calling new(CLASS, ...). Missing
## CONSTRUCTOR are filled with CLASS
.constructors_Simple <- function(klasses,
                                 required=NULL, optional=NULL,
                                 where=topenv()) {
    klassnames <- names(.nameAll(klasses))
    args <- .nameAll(c(required, optional, "...")) # convenience of automatic matching
    iargs <- sapply(args, function(y) alist(y=)$y) # input args as pairlist
    oargs <- sapply(args, as.symbol)    # output args
    for (cl in seq_along(klasses))
        eval(substitute({
            f <- function() {
                args <- names(match.call())[-1]
                .checkRequired(REQUIRED, args)
                miss <- OPTIONAL[!OPTIONAL %in% args]
                test <- !is.null(optional) && optional == "annotation" &&
                    !missing(annotation)
                if (test)
                    annotation <- orgPackageName(annotation)
                oargs <- OARGS[!names(OARGS) %in% miss]
                do.call(new, c(CLASS, oargs))
            }
            formals(f) <- IARGS
            assign(CONSTRUCTOR, f, envir=WHERE)
        }, list(CONSTRUCTOR = klassnames[[cl]],
                CLASS = klasses[[cl]],
                IARGS=iargs,
                OARGS=oargs,
                REQUIRED=required,
                OPTIONAL=optional,
                WHERE=where)))
}

setMethod("orgPackageName", "character", function(x) {x})

## constructors for GeneSet and derived classes, with required fields.
.constructors_GeneSet<- function(klass, required) {
    ## construct the arg list of symbols with no defaults
    ## constructor input arguments: type, name, ...
    args <- .nameAll(c("type", required, "...", "setIdentifier"))
    iargs <- sapply(args, function(y) alist(y=)$y) # input args as pairlist
    iargs[["setIdentifier"]] <- quote(.uniqueIdentifier())
    oargs <- sapply(args[-1], as.symbol) # output args
    eval(substitute({
        if (!isGeneric(CLASS))
            setGeneric(CLASS,
                       function(type, ...,
                                setIdentifier=.uniqueIdentifier()) {
                           standardGeneric(CLASS)
                       },
                       signature=c("type"))

        ## missing
        f <- function() {
            .checkRequired(REQUIRED, names(match.call()))
            do.call(new, c(CLASS, OARGS))
        }
        formals(f) <- IARGS
        setMethod(CLASS, signature = signature(type = "missing"), f)

        ## character
        f <- function() {
            .checkRequired(REQUIRED, names(match.call()))
            do.call(new, c(CLASS, list(geneIds=type), OARGS))
        }
        formals(f) <- IARGS
        setMethod(CLASS, signature = signature(type = "character"), f)

        ## GeneIdentifierType
        f <- function() {
            .checkRequired(REQUIRED, names(match.call()))
            do.call(new, c(CLASS, geneIdType=type, OARGS))
        }
        formals(f) <- IARGS
        setMethod(CLASS,
                  signature=signature(type="GeneIdentifierType"), f)

        ## GOCollection
        f <- function() {
            .checkRequired(c(REQUIRED, "geneIdType"), names(match.call()))
            if (!nzchar(annotation(geneIdType)))
                .stopf("'annotation(geneIdType)' must have non-zero number of characters")
            map <- getAnnMap("GO", annotation(geneIdType))
            ids <- mget(ids(type), map, ifnotfound=NA_character_)
            ids <- lapply(ids,
                          function(x, codes) x[names(x) %in% codes],
                          evidenceCode(type))
            geneIds <- unique(unlist(ids, use.names=FALSE))
            do.call(new,
                    c(CLASS,
                      geneIdType=geneIdType,
                      collectionType=type,
                      list(geneIds=geneIds),
                      OARGS))
        }
        formals(f) <- c(IARGS[-length(IARGS)],
                        alist(geneIdType=),
                        IARGS[length(IARGS)])
        setMethod(CLASS,
                  signature=signature(type="GOCollection"), f)

        ## ExpressionSet
        f <- function() {
            .checkRequired(REQUIRED, names(match.call()))
            organism <- 
                tryCatch({
                    pkg <- annotation(type)
                    if (length(pkg) == 1 && nchar(pkg) > 0)
                        getAnnMap("ORGANISM", pkg)
                    else
                        ""
                }, error=function(err) "")
            do.call(new,
                    c(CLASS,
                      geneIdType = AnnoOrEntrezIdentifier(annotation(type)),
                      list(geneIds = featureNames(type)),
                      shortDescription = experimentData(type)@title,
                      longDescription = abstract(type),
                      organism = organism,
                      pubMedIds = pubMedIds(experimentData(type)),
                      urls = experimentData(type)@url,
                      contributor = experimentData(type)@name,
                      collectionType = ExpressionSetCollection(),
                      OARGS))
        }
        formals(f) <- IARGS
        setMethod(CLASS, signature = signature(type="ExpressionSet"), f)
        ## BroadCollection
        f <- function() {
            .checkRequired(c("urls", REQUIRED), names(match.call()))
            gss <- getBroadSets(urls)
            if (length(gss) != 1)
              .stopf("'BroadCollection' at url '%s'\n  must have 1 gene set, but has %d",
                     urls, length(gss))
            gss[[1]]
        }
        formals(f) <- c(IARGS[-length(IARGS)],
                        urls=quote(character(0)),
                        IARGS[length(IARGS)])
        setMethod(CLASS, signature=signature(type="BroadCollection"), f)
    }, list(CLASS = klass, REQUIRED=required, IARGS=iargs, OARGS=oargs)))
}

.getters <- function(klass, slots, where=topenv(parent.frame()), ...) {
    slots <- .nameAll(slots)
    for (i in seq_along(slots)) {
        eval(substitute({
            if (!isGeneric(GENERIC))
                setGeneric(GENERIC,
                           function(object) standardGeneric(GENERIC),
                           where=WHERE)
            setMethod(GENERIC,
                      signature=signature(object=CLASS),
                      function(object) slot(object, SLOT),
                      where=WHERE)
        }, list(CLASS = klass,
                GENERIC = names(slots)[[i]],
                SLOT = slots[[i]],
                WHERE = where)))
    }
}

.setters <- function(klass, slots, where=topenv(parent.frame()), ...) {
    slots <- .nameAll(slots)
    for (i in seq(along=slots)) {
        eval(substitute({
            if (!isGeneric(SETTER))
                setGeneric(SETTER, function(object, value)
                           standardGeneric(SETTER),
                           where = WHERE)
            setReplaceMethod(GENERIC,
                             signature=signature(
                                 object=CLASS, value=getSlots(CLASS)[[SLOT]]),
                             function(object, value) {
                slot(object, SLOT) <- value
                validObject(object)
                object
            },
            where = WHERE)
        }, list(CLASS=klass,
                GENERIC=names(slots)[[i]],
                SETTER=paste(names(slots)[[i]], "<-", sep=""),
                SLOT=slots[[i]],
                WHERE=where)))
    }
}

## setters that also assign a new unique identifier
.GeneSet_setters <- function(klass, slots,
                             where=topenv(parent.frame()), ...) {
    slots <- .nameAll(slots)
    for (i in seq(along=slots)) {
        vtype <- getSlots(klass)[[ slots[[i]] ]]
        value <- quote(value)
        eval(substitute({
            if (!isGeneric(SETTER))
                setGeneric(SETTER, function(object, value)
                           standardGeneric(SETTER),
                           where = WHERE)
            ## Ugly hack for "organism<-" (whose generic is defined in
            ## BiocGenerics but not with the signature expected by the
            ## code below). There must be a better way to deal with this.
            ## Sorry for that! -- Herv\'e -- March 18, 2015
            if (identical(SETTER, "organism<-"))
                signature <- signature(object=CLASS)
            else
                signature <- signature(object=CLASS, value=VTYPE)
            setReplaceMethod(GENERIC,
                             signature=signature,
                             function(object, value) {
                                 slot(object, SLOT) <- VALUE
                                 `slot<-`(object, "setIdentifier",
                                          check=FALSE,
                                          mkScalar(.uniqueIdentifier()))
                                 validObject(object)
                                 object
                             },
                             where = WHERE)
        }, list(CLASS=klass,
                GENERIC=names(slots)[[i]],
                SETTER=paste(names(slots)[[i]], "<-", sep=""),
                SLOT=slots[[i]],
                VTYPE=vtype,
                VALUE=value,
                WHERE=where)))
    }
}