Nothing
"pairwise" <-
function(N) {
# deternine the indices for pairwise
# comparison of N things (where N = 'number.of.things')
# Used in function 'identity'
#
# A <- read.fasta(system.file("examples/kinesin.fa",
# package = "bio3d"))
#
# N<-nrow(A$ali)
# # comparison indices
# inds<-pairwise(N)
# # store score in 's'
# s<-rep(NA,nrow(inds))
# # go through all comparisons
# for(i in 1:nrow(inds)) {
# s[i]<-ide(A$ALI[ inds[i,1], ], A[ inds[i,2], ])
# }
# # reformat 's' as a NxN matrix
# mat<-matrix(NA,ncol=N,nrow=N)
# mat[inds]<-s; mat[inds[,c(2,1)]]<-s
if (!is.numeric(N) || N<0 || length(N)>1) {
stop("pairwise: N must be positve numeric and of length 1")
}
pair <- matrix(NA, ncol=2,
nrow= ( ((N*N)/2)-(N/2) ))
start<-1
for(i in 1:(N-1)) {
end = N-i
inds = start:( (start-1)+end )
pair[inds,1] = rep(i, end)
pair[inds,2] = (i+1):N
start = start+end
}
return(pair)
}
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