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#
# Pairwise Distances from Aligned Protein or DNA/RNA Sequences
#
dist.alignment <- function(x, matrix = c("similarity", "identity"),gap )
{
#
# Check arguments:
#
if (!inherits(x, "alignment")) stop("Object of class 'alignment' expected")
#
# Match arguments:
#
matrix <- match.arg(matrix)
#
# Compute arguments for the C distance function:
#
sequences <- toupper(x$seq)
nbseq <- x$nb
matNumber <-ifelse(matrix == "similarity", 1, 2)
#
# The following shouldn't be hard encoded, an argument for full
# user control should be added.
#
seqtype <- as.numeric(.Call("is_a_protein_seq", sequences[1], PACKAGE = "seqinr") >= 0.8)
#
# Call the C distance function:
#
if (missing(gap)) {
dist <- .Call("distance", sequences, nbseq, matNumber, seqtype,0, PACKAGE = "seqinr")
}
else {
dist <- .Call("distance", sequences, nbseq, matNumber, seqtype,gap, PACKAGE = "seqinr")
}
#
# Convert the result in a object of class dist:
#
mat <- matrix(dist, nbseq, nbseq, byrow = TRUE)
dimnames(mat) <- list(x$nam, x$nam)
return( as.dist(mat) )
}
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