Nothing
# modification on git from copied files
setMethod("[", "alignmentData", function(x, i, j, ..., drop = FALSE) {
x <- callNextMethod(x, i, j, ..., drop = FALSE)
if(!missing(i))
{
i <- as.vector(i)
x@data <- x@data[i,, drop = FALSE]
}
if(!missing(j))
{
j <- as.vector(j)
x@libsizes <- x@libsizes[j]
x@data <- x@data[,j,drop = FALSE]
}
x
})
setMethod("libsizes<-", signature = "alignmentData", function(x, value) {
if(!is.numeric(value)) stop("All members of libsizes for an alignmentData object must be numeric.")
if(length(value) != ncol(x)) stop("Length of libsizes must be identical to the number of columns of the alignmentData object.")
if(any(value <= 0)) stop("Library sizes less than or equal to zero make no sense to me!")
x@libsizes <- value
x
})
setMethod("libsizes", signature = "alignmentData", function(x) {
x@libsizes
})
setValidity("alignmentData", function(object) {
# message("mark0")
# acValid <- callNextMethod(object)
# if(class(acValid) == "character") valid <- FALSE else valid = TRUE
# if(class(acValid) == "character") valid <- acValid else valid = ""
valid <- TRUE
validmess <- c()
if(length(object@replicates) != length(object@libnames))
{
valid <- FALSE
validmess <- c(validmess, "The length of the '@replicates' slot must equal the length of the '@libnames' slot.")
}
if(nrow(object@data) != length(object@alignments))
{
valid <- FALSE
validmess <- c(validmess, "The number of rows in the '@data' slot must equal the number of rows in the '@alignments' slot.")
}
if(length(object@libsizes) != length(object@libnames))
{
valid <- FALSE
validmess <- c(validmess, "The number of library names defined in the '@libnames' slot must equal the length of the '@libsizes' slot.")
}
if(any(as.integer(object@data) != object@data))
{
valid <- FALSE
validmess <- c(validmess, "All members of the '@data' matrix must be castable as integers.")
}
if(valid) return(valid) else validmess
})
setMethod("show", "alignmentData", function(object) {
callNextMethod(object)
cat('\nSlot "data":\n')
.printIRangesMatrix(object@data)
cat('\nSlot "libsizes":\n')
print(object@libsizes)
})
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