R/read.tree.nodes.R

In bomeara/phybase: Basic functions for phylogenetic analysis

read.tree.nodes <-function(str,name="")
{
	#eliminate the content between []
	str<-gsub("\\[.*\\]","",str)
	nobrlens <- 0
	if(length(grep(":",str))==0)
	{
		nobrlens <- 1
		str<-gsub(",",":1.0,",str)
		str<-gsub(")",":1.0)",str)
		str<-gsub(";",":1.0;",str)
	}
    	string <- unlist(strsplit(str, NULL))
    	leftpar<-which(string=="(")  
    	rightpar<-which(string==")") 
    	if(length(leftpar) != length(leftpar))
     		stop("The number of left parenthesis is NOT equal to the number of right  parenthesis")

    	speciesname<-sort(species.name(str))
    	nspecies<-length(speciesname)

    	{if(length(leftpar) == (nspecies-1))
		rooted<-TRUE
    	else if(length(leftpar) == (nspecies-2))
		rooted<-FALSE
    	else
		stop("The number of comma in the tree string is wrong!")}
    
    	if(length(name)>1 & (nspecies != length(name)))
		stop("Wrong number of species names!")

    	if(length(name)>1)
		speciesname<-name
    	{if(rooted)
    		nNodes<-2*nspecies-1
    	else
		nNodes<-2*nspecies-2
    	nodes<-matrix(-9,nrow=nNodes,ncol=7)}

    	str1<-str
    	if(length(grep("[a-z]",speciesname,ignore.case=TRUE)))
    		str1<-name2node(str1,speciesname)
    	father<-nspecies+1

    while(father < (nNodes+1))
	{
        string <- unlist(strsplit(str1, NULL))   
        leftpar<-which(string=="(")  
        rightpar<-which(string==")") 
  		colon<-which(string==":") 
		
        {if(length(leftpar) == 1) substr <- paste(string[leftpar[sum(leftpar < rightpar[1])]:rightpar[1]], 
sep = "", collapse = "")
        else substr <- paste(string[leftpar[sum(leftpar < rightpar[1])]:(colon[which(colon>rightpar[1])[1]]-1)], 
sep = "", collapse = "")}
    		
        substring<-unlist(strsplit(substr, NULL)) 
        colon<-which(substring==":") 
        comma<-which(substring==",")
        pound<-which(substring=="#")
        percent<-which(substring=="%")
        combine<-which(substring=="," | substring==")" | substring=="#" | substring=="%")
 
  		node1<-as.integer(paste(substring[2:(colon[1]-1)],sep="",collapse=""))
        node2<-as.integer(paste(substring[(comma[1]+1):(colon[2]-1)],sep="",collapse=""))
 
		if(length(comma)>1)
			node3<-as.integer(paste(substring[(comma[2]+1):(colon[3]- 1)],sep="",collapse=""))
    
		#branch length
        if(length(colon)==0)
		{
     			node1Branch<--9;
        		node2Branch<--9;
        }
        if(length(colon)>0)
		{
			x1<-combine[sum(combine<colon[1])+1]-1
			x2<-combine[sum(combine<colon[2])+1]-1
			if(length(colon)==3)
			{
				x3<-combine[sum(combine<colon[3])+1]-1
				nodes[node3,4]<-as.double(paste(substring[(colon[3] +1):x3],sep="",collapse=""))
			}
            node1Branch<-as.double(paste(substring[(colon[1] +1):x1],sep="",collapse=""))
            node2Branch<-as.double(paste(substring[(colon[2] +1):x2],sep="",collapse=""))
        }

        #mutation rates
        if(length(percent)==0)
		{
     			node1mu<--9
        		node2mu<--9
        }
        if (length(percent)==1)
		{
			if(percent[1]<comma[1])
			{
				node1mu<-as.double(paste(substring[(percent[1]+1):(comma[1]- 1)],sep="",collapse=""))
				node2mu<--9
    			}
    			else
			{		
				node2mu<-as.double(paste(substring[(percent[1]+1):(length (substring)-1)],sep="",collapse=""))
				node1mu<--9
			}
        }
        if(length(percent)==2)
		{
			node1mu<-as.double(paste(substring[(percent[1]+1):(comma[1]- 1)],sep="",collapse=""))
			node2mu<-as.double(paste(substring[(percent[2]+1):(length(substring)- 1)],sep="",collapse=""))
        }
        if(length(percent)==3)
		{
			node1mu<-as.double(paste(substring[(percent[1]+1):(comma[1]- 1)],sep="",collapse=""))
			node2mu<-as.double(paste(substring[(percent[2]+1):(comma[2]- 1)],sep="",collapse=""))
			node3mu<-as.double(paste(substring[(percent[3]+1):(length(substring)- 1)],sep="",collapse=""))
			nodes[node3,5]<-node3mu
        }

		#population size
		if(length(percent) == 0)
		{
			if(length(pound)==0)
			{
     			node1theta<--9
        		node2theta<--9
    			}
    			if (length(pound)==1)
			{
			if(pound[1]<comma[1])
			{
				node1theta<-as.double(paste(substring[(pound[1]+1):(comma[1]- 1)],sep="",collapse=""))
				node2theta<--9
    			}
    			else
			{		
				node2theta<-as.double(paste(substring[(pound[1]+1):(length (substring)-1)],sep="",collapse=""))
				node1theta<--9
			}
    			}
    			if(length(pound)==2)
			{
			node1theta<-as.double(paste(substring[(pound[1]+1):(comma[1]- 1)],sep="",collapse=""))
			node2theta<-as.double(paste(substring[(pound[2]+1):(length(substring)- 1)],sep="",collapse=""))
    			}
    			if(length(pound)==3)
			{
			node1theta<-as.double(paste(substring[(pound[1]+1):(comma[1]- 1)],sep="",collapse=""))
			node2theta<-as.double(paste(substring[(pound[2]+1):(comma[2]- 1)],sep="",collapse=""))
			node3theta<-as.double(paste(substring[(pound[3]+1):(length(substring)- 1)],sep="",collapse=""))
			nodes[node3,5]<-node3theta
    			}
		}
		if(length(percent)>0)
		{
			if(length(pound)==0)
			{
     			node1theta<--9
        		node2theta<--9
    			}
    			if (length(pound)==1)
			{
			if(pound[1]<comma[1])
			{
				node1theta<-as.double(paste(substring[(pound[1]+1):(percent[1]- 1)],sep="",collapse=""))
				node2theta<--9
    			}
    			else
			{		
				node2theta<-as.double(paste(substring[(pound[1]+1):(percent[2]-1)],sep="",collapse=""))
				node1theta<--9
			}
    			}
    			if(length(pound)==2)
			{
			node1theta<-as.double(paste(substring[(pound[1]+1):(percent[1]- 1)],sep="",collapse=""))
			node2theta<-as.double(paste(substring[(pound[2]+1):(percent[2]- 1)],sep="",collapse=""))
    			}
    			if(length(pound)==3)
			{
			node1theta<-as.double(paste(substring[(pound[1]+1):(percent[1]- 1)],sep="",collapse=""))
			node2theta<-as.double(paste(substring[(pound[2]+1):(percent[2]- 1)],sep="",collapse=""))
			node3theta<-as.double(paste(substring[(pound[3]+1):(percent[3]- 1)],sep="",collapse=""))
			nodes[node3,5]<-node3theta
    			}
		}
    		nodes[node1,1]<-father
    		nodes[node1,4]<-node1Branch
		nodes[node1,5]<-node1theta
    		nodes[node1,6]<-node1mu

    		nodes[node2,1]<-father
    		nodes[node2,4]<-node2Branch
		nodes[node2,5]<-node2theta
    		nodes[node2,6]<-node2mu
   
        if(length(comma)>1)
		{
            nodes[node3,1]<-father
			nodes[father,4]<-node3
        }

        nodes[father,2]<-node1
        nodes[father,3]<-node2
		
        rightpar1 <- which(substring == ")")
        if (rightpar1 < length(substring)) 
        {
            postprob <- paste(substring[(rightpar1+1):length(substring)],sep = "", collapse = "")
            nodes[father, 7] <- as.numeric(postprob)
        }

        substr<-gsub("[(]","[(]",substr)
        substr<-gsub("[)]","[)]",substr)
		substr<-gsub("\\+","",substr)
		str1<-gsub("\\+","",str1)
        str1<-gsub(substr,father,str1)
        father<-father+1
    }

    if(length(grep("%",str1)))
		nodes[nNodes,6]<-as.double(gsub(";","",gsub(".*\\%","",str1)))
	if(length(grep("#",str1)))
	{
		if(length(grep("%",str1)))
			nodes[nNodes,5]<-as.double(gsub(".*\\#","",gsub("\\%.*","",str1)))
		else
			nodes[nNodes,5]<-as.double(gsub(";","",gsub(".*\\#","",str1)))
	}
    if(!rooted)
    nodes[nNodes,1]<--8
	if(nobrlens == 1) nodes[,4]<--9
            
    z <- list(nodes = matrix(0, nNodes, 5), names ="", root=TRUE)

    z$nodes<-nodes
    z$names<-speciesname
    z$root<-rooted
    z
}