setConstructorS3("PairedPSCBSFileSet", function(...) {
extend(GenericDataFileSet(...), "PairedPSCBSFileSet")
})
# setMethodS3("byPath", "PairedPSCBSFileSet", function(static, ..., pattern=".*(,PairedPSCBS[.]xdr|[.]RData)$") {
# # Drop argument 'chipType'
# args <- list(static=static, ..., pattern=pattern)
# excl <- which("chipType" == names(args))
# if (length(excl) > 0) {
# args <- args[-excl]
# }
#
# # Call the "next" method
# args <- c(list("byPath"), args)
# do.call("NextMethod", args)
# }, static=TRUE)
#setMethodS3("findByName", "PairedPSCBSFileSet", function(static, ..., chipType=NULL, paths="pscbsData/") {
# # Argument 'chipType':
# if (!is.null(chipType)) {
# chipType <- Arguments$getCharacter(chipType)
# }
#
# # Argument 'paths':
# if (is.null(paths)) {
# paths <- eval(formals(findByName.PairedPSCBSFileSet)[["paths"]])
# }
#
# # Drop argument 'subdirs'
# args <- list(...)
# excl <- which("subdirs" == names(args))
# if (length(excl) > 0) {
# args <- args[-excl]
# }
# args <- c(list(static=static), args, subdirs=chipType, paths=paths)
#
# # Call the "next" method
# args <- c(list("findByName"), args)
# do.call("NextMethod", args)
#}, static=TRUE, protected=TRUE)
setMethodS3("byPath", "PairedPSCBSFileSet", function(static, ..., pattern=".*(,PairedPSCBS[.]xdr|[.]RData)$") {
NextMethod("byPath")
}, static=TRUE)
setMethodS3("findByName", "PairedPSCBSFileSet", function(static, ..., chipType, paths="pscbsData/") {
# Argument 'chipType':
chipType <- Arguments$getCharacter(chipType)
# Argument 'paths':
if (!is.null(paths)) paths <- Arguments$getCharacters(paths)
NextMethod("findByName", subdirs=chipType, paths=paths)
}, static=TRUE, protected=TRUE)
setMethodS3("byName", "PairedPSCBSFileSet", function(static, name, ...) {
path <- findByName(static, name=name, ...)
if (is.null(path)) {
throw("Failed to locate ", class(static)[1L])
}
# Call byPath without argument 'chipType'
args <- list(static, path=path, ...)
excl <- which("chipType" == names(args))
if (length(excl) > 0) args <- args[-excl]
do.call(byPath, args=args)
})
setMethodS3("getPlatform", "PairedPSCBSFileSet", function(this, ...) {
res <- this$platform
if (is.null(res)) {
res <- NA
}
res
})
setMethodS3("getDefaultFullName", "PairedPSCBSFileSet", function(this, ...) {
res <- getPath(this)
res <- getParent(res)
res <- basename(res)
res
}, protected=TRUE)
setMethodS3("getChipType", "PairedPSCBSFileSet", function(this, ...) {
res <- this$chipType
if (is.null(res)) {
path <- getPath(this)
res <- basename(path)
}
res
})
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