# Function to export to STRUCTURE format from genind object.
# genind objects are created in the R package adegenet.  The function below is an R function.
# Lindsay V. Clark, 14 March 2013

# obj: genind object
# file: file name to write
# pops: whether to include population info in the file
# Function is flexible with regards to ploidy, although genotypes are
# considered to be unambiguous.
# Missing data must be recorded as NA in obj@tab.

# example use: 
# data(nancycats)
# genind2structure(nancycats, file="nancy_structure.txt", pops=TRUE)

genind2structure <- function(obj, file="", pops=FALSE){
    if(!"genind" %in% class(obj)){
        warning("Function was designed for genind objects.")
    }

    # get the ploidy of the dataset
    pl <- obj@ploidy
    # get the number of individuals
    S <- length(obj@ind.names)
    # column of individual names to write; set up data.frame
    tab <- data.frame(ind=rep(obj@ind.names, each=pl))
    # column of pop ids to write
    if(pops){
        popnums <- 1:length(obj@pop.names)
        names(popnums) <- obj@pop.names
        popcol <- rep(popnums[as.character(pop(obj))], each=pl)
        tab <- cbind(tab, data.frame(pop=popcol))
    }

    # begin going through loci
    gen <- obj@tab * pl # genotypes with allele counts
    loci <- names(obj@loc.names) # use the simplified names here, convert later
    for(L in loci){
        thesegen <- gen[,grep(L, dimnames(gen)[[2]])] # genotypes by locus
        al <- 1:dim(thesegen)[2] # numbered alleles
        loccol <- c() # column to add to table
        for(s in 1:S){
            if(!all(!is.na(thesegen[s,]))){
                loccol <- c(loccol, rep(-9, pl))
            } else {
                loccol <- c(loccol, rep(al, times=thesegen[s,]))
            }
        }
        if(length(loccol) != S*pl) stop("Missing data must be recorded as NA.")
        tab <- cbind(tab, data.frame(x=loccol))
        names(tab)[length(names(tab))] <- obj@loc.names[L]
    }

    # export table
    write.table(tab, file=file, sep="\t", quote=FALSE, row.names=FALSE)
}