Nothing
## class definitions
## class unions
setClassUnion("MefaMatrix", c("matrix","dgCMatrix"))
setClassUnion("MefaDataFrame", c("data.frame","NULL"))
## virtual classes to old mefa classes
setClass("stcs", representation("VIRTUAL"))
setClass("mefa", representation("VIRTUAL"))
## main Mefa class
setClass("Mefa",
representation(
xtab = "MefaMatrix",
samp = "MefaDataFrame",
taxa = "MefaDataFrame",
join = "character"),
prototype = list(
# xtab = as(matrix(0,0,0), "dgCMatrix"),
xtab = as(as(as(matrix(0,0,0), "dMatrix"), "generalMatrix"), "CsparseMatrix"),
samp = NULL,
taxa = NULL,
join = "left"),
validity = function(object) {
if (is.null(dim(object@xtab)))
return("'xtab' must have a 'dim' attribute")
if (length(dim(object@xtab)) != 2)
return("'xtab' dimension must be 2")
if (!is.null(object@samp) &&
!identical(rownames(object@xtab), rownames(object@samp)))
return("Inconsistent 'xtab' and 'samp' dimnames")
if (!is.null(object@taxa) &&
!identical(colnames(object@xtab), rownames(object@taxa)))
return("Inconsistent 'xtab' and 'taxa' dimnames")
if (!(object@join %in% c("left", "inner")))
return("'join' must be in c(\"left\", \"inner\")")
# if (is.null(object@samp) &&
# is.null(object@taxa) &&
# object@join != "left")
# return("'join' must be \"left\" if both 'samp' and 'taxa' slots are 'NULL'")
TRUE
})
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