R/methods-SRSet.R

In Bioconductor/ShortRead: FASTQ input and manipulation

.SRSet_validity <- function(object) {
    msg <- NULL
    len <- length(readIndex(object))
    rlen <- c(readData = nrow(readData(object)))
    if (!all(rlen==len)) {
        bad <- rlen!=len
        msg <- c(msg,
                 sprintf("read length mismatch: expected %d, found:\n  %s",
                         rlen, paste(names(rlen)[bad], rlen[bad],
                                     sep="=", collapse=", ")))
    }
    snames <- sampleNames(sourcePath(object))
    slen <- length(snames)
    oslen <- c(phenoData = nrow(phenoData(object)),
               readCount = length(readCount(object)))
    if (!all(oslen==slen)) {
        bad <- oslen!=slen
        msg <- c(msg,
                 sprintf("sample length mismatch: expected %d, found:\n  %s",
                         slen, paste(names(oslen)[bad], oslen[bad],
                                     sep="=", collapse=", ")))
    }
    osnames <- sampleNames(object)
    stest <- snames == osnames
    if (!all(stest))
        msg <- c(msg,
                 sprintf("sample names mismatch:\n  %s",
                         slen, paste(snames[!stest], osnames[!stest],
                                     sep = "!=", collapse = ", ")))
    rind <- readIndex(object)
    if (!all(rind > 0 & rind <= len))
        msg <- c(msg, "values in 'readIndex' must be > 0 and <= number of reads")
    rcount <- readCount(object)
    if (!all(rcount >= 0))
        msg <- c(msg, "values in 'readCount' must be non-negative")
    if (sum(rcount) != len)
        msg <- c(msg,
                 sprintf("'sum(readCount)', %d, must equal the number of reads, %d",
                         sum(rcount), len))
    if (is.null(msg)) TRUE else msg
}

setMethod(.srValidity, "SRSet", .SRSet_validity)

.make_getter(c("readData", "sourcePath", "readIndex", "readCount"))

setMethod(experimentPath, "SRSet", function(object, ...) {
    callGeneric(sourcePath(object), ...)
})

setMethod(sampleNames, "SRSet", function(object) {
    sampleNames(phenoData(object))
})
          
setMethod(show, "SRSet", function(object) {
    callNextMethod()
    cat("experimentPath(object): ", experimentPath(object), "\n",
        sep="")
})

setMethod(detail, "SRSet", function(x, ...) {
    callNextMethod()
    cat("\nsourcePath\n")
    detail(sourcePath(x), ...)
    cat("\nphenoData\n")
    pd <- phenoData(x)
    cat("pData:\n")
    print(pData(pd))
    cat("varMetadata:\n")
    print(varMetadata(pd))
})

setMethod(phenoData, "SRSet", function(object) object@phenoData)


## proposed
##setMethod(readSRQ, "SRSet", function(object) readSRQ(sourcePath(object)))