Nothing
traceBack <- function(D, global = TRUE){
stopifnot("stringDist" %in% class(D) | "stringSim" %in% class(D))
TB <- attr(D, "TraceBackMatrix")
SM <- attr(D, "ScoringMatrix")
if(global){
m <- nrow(TB)
n <- ncol(TB)
}else{
wmax <- which.max(SM)
if(wmax %% nrow(SM) == 0){
m <- nrow(SM)
n <- wmax %/% nrow(SM)
}else{
m <- wmax %% nrow(SM)
n <- wmax %/% nrow(SM) + 1
}
}
x <- NULL
y <- NULL
local <- FALSE
while(m > 1 | n > 1){
if(length(grep("stop", TB[m,n])) > 0){
local <- TRUE
break
}
if(length(grep("m", TB[m,n])) > 0){
x <- c(rownames(TB)[m], x)
y <- c(colnames(TB)[n], y)
m <- m-1
n <- n-1
next
}
if(length(grep("d", TB[m,n]))){
x <- c(rownames(TB)[m], x)
y <- c("-", y)
m <- m-1
next
}
if(length(grep("i", TB[m,n]))){
y <- c(colnames(TB)[n], y)
x <- c("-", x)
n <- n-1
next
}
}
res <- rbind(paste(x, collapse = ""), paste(y, collapse = ""))
rownames(res) <- c("x'", "y'")
if(global)
colnames(res) <- c("pairwise global alignment")
else
colnames(res) <- c("pairwise local alignment")
res
}
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