# function writes a modified "phylo" object to a simmap Newick string
# written by Liam Revell 2011

write.simmap<-function(tree,file=NULL,append=FALSE,map.order=NULL){
	if(class(tree)!="phylo") stop("tree is not an object of class 'phylo.'")
	if(is.null(tree$maps)) stop("tree is does not contain a stochastic character map.")
	if(is.null(map.order)){
		if(!is.null(attr(tree,"map.order")))
			map.order<-attr(tree,"map.order")
		else {
			message("map order should be specified in function call or by tree attribute \"map.order\".\nAssuming right-to-left order.")
			map.order<-"R"
		}
	}
	map.order<-toupper(unlist(strsplit(map.order,NULL))[1])
	if(map.order!="R"&&map.order!="L"){
		message("do not recognize map order. Assuming right-to-left order.")
		map.order<-"R"
	}
	tree<-reorderSimmap(tree,"cladewise")
	n<-length(tree$tip)
	string<-vector(); string[1]<-"("; j<-2
	for(i in 1:nrow(tree$edge)){
		if(tree$edge[i,2]<=n){ 
			string[j]<-tree$tip.label[tree$edge[i,2]]; j<-j+1
			string[j]<-":{"; j<-j+1
			if(map.order=="L"){
				for(l in 1:length(tree$maps[[i]])){
					string[j]<-paste(c(names(tree$maps[[i]])[l],",",round(tree$maps[[i]][l],8)),collapse="")
					string[j+1]<-":"; j<-j+2
				}
			} else {
				for(l in length(tree$maps[[i]]):1){
					string[j]<-paste(c(names(tree$maps[[i]])[l],",",round(tree$maps[[i]][l],8)),collapse="")
					string[j+1]<-":"; j<-j+2
				}
			}					
			string[j-1]<-"}"
			v<-which(tree$edge[,1]==tree$edge[i,1]); k<-i
			while(length(v)>0&&k==v[length(v)]){
				string[j]<-")"; j<-j+1
				w<-which(tree$edge[,2]==tree$edge[k,1])
				if(length(w)>0){
					string[j]<-":{"; j<-j+1
					if(map.order=="L"){
						for(l in 1:length(tree$maps[[w]])){
							string[j]<-paste(c(names(tree$maps[[w]])[l],",",round(tree$maps[[w]][l],8)),collapse="")
							string[j+1]<-":"; j<-j+2
						}
					} else {
						for(l in length(tree$maps[[w]]):1){
							string[j]<-paste(c(names(tree$maps[[w]])[l],",",round(tree$maps[[w]][l],8)),collapse="")
							string[j+1]<-":"; j<-j+2
						}
					}					
					string[j-1]<-"}"
				}
				v<-which(tree$edge[,1]==tree$edge[w,1]); k<-w
			} 
			string[j]<-","; j<-j+1
		} else if(tree$edge[i,2]>=n){
			string[j]<-"("; j<-j+1
		}
	}
	string<-c(string[1:(length(string)-1)],";")
	string<-paste(string,collapse="")
	if(is.null(file)) return(string)
	else write(string,file=file,append=append)
}

# function reorders simmap tree
# written Liam Revell 2011

reorderSimmap<-function(tree,order="cladewise"){
	ntree<-reorder(tree,order)
	o<-whichorder(ntree$edge[,2],tree$edge[,2])
	ntree$mapped.edge<-tree$mapped.edge[o,]
	ntree$maps<-tree$maps[o]
	return(ntree)
}