#SOSCC algorithm
#George M. Garrity and Timothy G. Lilburn
#Copyright Michigan State University 2004, all rights reserved


"step12" = function(taxon.subset, genus.order)
{
	#print("inside step12")
	all.genus <- substring(as.character(taxon.subset[, 4]), 1, regexpr("[^a-zA-Z]", as.character(taxon.subset[, 4])) - 1)
	reorder <- as.data.frame(cbind(as.character(taxon.subset[, 5]), all.genus))
	dimnames(reorder)[[1]] <- as.factor(dimnames(taxon.subset)[[1]])
	x <- NULL
	for(i in 1:length(all.genus)) {
		x <- c(x, dimnames(reorder)[[1]][reorder[, 2] == genus.order[i]])
		#x <- c(x, dimnames(reorder)[[1]][reorder[, 1] == genus.order[i]])
	}
	taxon.subset <- taxon.subset[x,  ]
	family.order <- taxon.subset[1, 5]
	j <- length(family.order)
	for(i in 1:nrow(taxon.subset)) {
		if(taxon.subset[i, 5] == family.order[j])
			next
		if(taxon.subset[i, 5] != family.order[j]) {
			family.order <- c(as.character(family.order), as.character(taxon.subset[i, 5]))
			j <- j + 1
		}
	}
	return(x, family.order)
}