genind2df <- function (x, pop = NULL, sep = "", usepop = TRUE, oneColPerAll = FALSE, rm.incompleteGeno=F) 
{
    if (!is.genind(x)) 
        stop("x is not a valid genind object")
    if (is.null(pop)) {
        pop <- x@pop
    }
    if (x@type == "PA") {
        res <- tab(x)
        if (usepop && !is.null(pop)) 
            res <- cbind.data.frame(pop = pop(x), res)
        return(res)
    }
    kX <- seploc(x, res.type = "matrix")
    if (oneColPerAll & all(x@ploidy == x@ploidy[1])) {
        sep <- "/"
    }
    recod <- function(vec, lab) {
        if (any(is.na(vec))) 
            return(NA)
        res <- paste(rep(lab, vec), collapse = sep)
        return(res)
    }
    kGen <- lapply(1:length(kX), function(i) apply(kX[[i]], 1, 
        recod, x@all.names[[i]]))
    names(kGen) <- locNames(x)
    if (oneColPerAll) {
        if (all(x@ploidy == x@ploidy[1])) {
            f1 <- function(vec) {
                vec[is.na(vec)] <- paste(rep("NA", x@ploidy[1]), 
                  collapse = sep)
                return(vec)
            }
            temp <- lapply(kGen, f1)
            temp <- lapply(temp, strsplit, sep)

    ### added by Naoki to deal with genotypes when there are missing alleles            
            if(! rm.incompleteGeno) {
                ## incomplete genotype is retained, and NA is used for the missing allleles
                adjustVectLength <- function(vect, fill, min.len) {
                    return(c(vect,rep(fill, max(0, min.len - length(vect)))))
                }
                temp <- lapply(temp, function(l) lapply(l, adjustVectLength, fill="NA", min.len=x@ploidy[1]))
            } else  {
                ## alleles of incomplete genotypes are replaced with NA
                checkVectLength <- function(vect, fill, len) {
                    if (length(vect) != len) {
                        return(rep(fill,len))
                    } else {
                        return(vect)
                    }
                }
                temp <- lapply(temp, function(l) lapply(l, checkVectLength, fill="NA", len=x@ploidy[1]))
            }
    ### end of addition
            
            res <- lapply(temp, function(e) matrix(unlist(e), 
                ncol = x@ploidy[1], byrow = TRUE))
            res <- data.frame(res, stringsAsFactors = FALSE)
            
    ### Naoki added this to replace character string "NA" with NA            
            res[res == "NA"] <- NA
    ### end of addition            
            
            names(res) <- paste(rep(locNames(x), each = x@ploidy[1]), 
                1:x@ploidy[1], sep = ".")
            if (!is.null(pop) & usepop) 
                res <- cbind.data.frame(pop, res, stringsAsFactors = FALSE)
            rownames(res) <- indNames(x)
            return(res)
        }
        else {
            warning("All ploidies must be equal in order to separate the alleles.\nReturning one column per locus")
        }
    }
    res <- as.data.frame(do.call(cbind, kGen), stringsAsFactors = FALSE)
    rownames(res) <- indNames(x)
    colnames(res) <- locNames(x)
    if (!is.null(pop) & usepop) 
        res <- cbind.data.frame(pop, res, stringsAsFactors = FALSE)
    return(res)
}