Nothing
div <- function
(file=NULL, sequence=NULL, sqs=NULL, method="LWL85", pairwise=TRUE, max.lim=3)
{
stopifnot(
!(is.null(file) && is.null(sequence)),
method[1] %in% c("LWL85"),
requireNamespace("gtools", quietly=TRUE))
if (!is.null(file)) {
if (!requireNamespace("seqinr", quietly=TRUE)) {
stop("Reading FASTA files require package seqinr")
}
sequence <- seqinr::read.fasta(file)
}
sequence <- .checkseq(sequence, gene.name=if (is.null(file)) "" else file)
if (is.null(sqs)) {
sqs <- names(sequence)
}
if (length(sqs) < 2)
stop("Less than 2 sequences in ", file)
combn <- gtools::combinations(n=length(sqs), r=2, v=sqs)
if (method[1]=="LWL85") {
return(data.frame(div=.LWL85(sequence, combn[,1], combn[,2], pairwise=pairwise, max.lim=max.lim), sp1=combn[,1], sp2=combn[,2]))
}
stop("Method ", method, " unknown.") # This should never happen
}
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