## read.dna.R (2012-05-03)

##   Read DNA Sequences in a File

## Copyright 2003-2012 Emmanuel Paradis

## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.

read.dna <- function(file, format = "interleaved", skip = 0,
                     nlines = 0, comment.char = "#",
                     as.character = FALSE, as.matrix = NULL)
{
    findFirstNucleotide <- function(x) {
        ## actually find the 1st non-blank character
        ## just in case: pat.base <- "[-AaCcGgTtUuMmRrWwSsYyKkVvHhDdBbNn?]{10}"
        tmp <- regexpr("[[:blank:]]+", x[1]) # consider only a single string
        tmp[1] + attr(tmp, "match.length")
    }
    getTaxaNames <- function(x) {
        x <- sub("^['\" ]+", "", x) # remove the leading quotes and spaces
        x <- sub("['\" ]+$", "", x) #   "     "  trailing  "     "    "
        x
    }
    getNucleotide <- function(x) {
        x <- gsub(" ", "", x)
        x <- strsplit(x, NULL)
        tolower(unlist(x))
    }
    formats <- c("interleaved", "sequential", "fasta", "clustal")
    format <- match.arg(format, formats)
    phylip <- if (format %in% formats[1:2]) TRUE else FALSE
    X <- scan(file = file, what = "", sep = "\n", quiet = TRUE,
              skip = skip, nlines = nlines, comment.char = comment.char)

    if (phylip) {
        ## need to remove the possible leading spaces and/or tabs in the first line
        fl <- gsub("^[[:blank:]]+", "", X[1])
        fl <- as.numeric(unlist(strsplit(fl, "[[:blank:]]+")))
        if (length(fl) != 2 || any(is.na(fl)))
            stop("the first line of the file must contain the dimensions of the data")
        n <- fl[1]
        s <- fl[2]
        obj <- matrix("", n, s)
        X <- X[-1]
    }
    switch(format,
    "interleaved" = {
        start.seq <- findFirstNucleotide(X[1])
        one2n <- 1:n
        taxa <- getTaxaNames(substr(X[one2n], 1, start.seq - 1))
        X[one2n] <- substr(X[one2n], start.seq, nchar(X[one2n]))
        nl <- length(X)
        for (i in one2n)
            obj[i, ] <- getNucleotide(X[seq(i, nl, n)])
    },
    "sequential" = {
        taxa <- character(n)
        j <- 1L # line number
        for (i in 1:n) {
            start.seq <- findFirstNucleotide(X[j])
            taxa[i] <- getTaxaNames(substr(X[j], 1, start.seq - 1))
            sequ <- getNucleotide(substr(X[j], start.seq, nchar(X[j])))
            j <- j + 1L
            while (length(sequ) < s) {
                sequ <- c(sequ, getNucleotide(X[j]))
                j <- j + 1L
            }
            obj[i, ] <- sequ
        }
        taxa <- getTaxaNames(taxa)
    },
    "fasta" = {
        start <- grep("^ {0,}>", X)
        taxa <- X[start]
        taxa <- sub("^ {0,}>", "", taxa) # remove the hook and the spaces before
        taxa <- getTaxaNames(taxa)
        n <- length(taxa)
        obj <- vector("list", n)
        start <- c(start, length(X) + 1) # this avoids the following to crash when `i = n'
        for (i in 1:n)
            obj[[i]] <- getNucleotide(X[(start[i] + 1):(start[i + 1] - 1)])
    },
    "clustal" = {
        X <- X[-1] # drop the line with "Clustal bla bla..."
        ## find where the 1st sequence starts
        start.seq <- findFirstNucleotide(X[1])
        ## find the lines with *********....
        nspaces <- paste("^ {", start.seq - 1, "}", sep = "", collapse = "")
        stars <- grep(nspaces, X)
        ## we now know how many sequences in the file:
        n <- stars[1] - 1
        taxa <- getTaxaNames(substr(X[1:n], 1, start.seq - 1))
        ## need to remove the sequence names before getting the sequences:
        X <- substr(X, start.seq, nchar(X))
        nl <- length(X)
        ## find the length of the 1st sequence:
        tmp <- getNucleotide(X[seq(1, nl, n + 1)])
        s <- length(tmp)
        obj <- matrix("", n, s)
        obj[1, ] <- tmp
        for (i in 2:n)
            obj[i, ] <- getNucleotide(X[seq(i, nl, n + 1)])
    })

    if (format != "fasta") {
        rownames(obj) <- taxa
    } else {
        names(obj) <- taxa
        LENGTHS <- unique(unlist(lapply(obj, length)))
        allSameLength <- length(LENGTHS) == 1
        if (is.logical(as.matrix)) {
            if (as.matrix && !allSameLength)
                stop("sequences in FASTA file not of the same length")
        } else {
            as.matrix <- allSameLength
        }
        if (as.matrix) {
            obj <- matrix(unlist(obj), ncol = LENGTHS, byrow = TRUE)
            rownames(obj) <- taxa
        }
    }
    if (!as.character) obj <- as.DNAbin(obj)
    obj
}