R/readCCModel.R

In procoil: Prediction of Oligomerization of Coiled Coil Proteins

readCCModel <- function(file)
{
    datatable <- read.table(file, header=FALSE, sep=",",
                            stringsAsFactors=FALSE)

    if (ncol(datatable) != 2) stop("file is in invalid format")

    lst <- as.list(datatable[, 2])
    names(lst) <- datatable[, 1]

    model <- new("CCModel")

    if (is.null(lst[["_b"]]) || !is.numeric(lst[["_b"]]) ||
        length(lst[["_b"]]) != 1)
        stop("file is in invalid format")
    else
    {
        model@b <- lst[["_b"]]
        lst[["_b"]] <- NULL
    }

    if (is.null(lst[["_m"]]) || !is.numeric(lst[["_m"]]) ||
        length(lst[["_m"]]) != 1 || lst[["_m"]] < 0)
        stop("file is in invalid format")
    else
    {
        model@m <- as.integer(lst[["_m"]])
        lst[["_m"]] <- NULL
    }

    if (is.null(lst[["_scaling"]]))
        stop("file is in invalid format")
    else
    {
        model@scaling <- ifelse(lst[["_scaling"]], TRUE, FALSE)
        lst[["_scaling"]] <- NULL
    }

    weights <- sort(unlist(lst), decreasing=TRUE)

    model@weights <- matrix(weights, nrow=1)
    colnames(model@weights) <- names(weights)

    model
}