"calc.all.pms" <-
function(ont="BP",organism="yeast")
  {    
    if(!(ont %in% c("BP","MF","CC")))
      stop("Invalid ontology (must be one of 'BP','MF', or 'CC')")
    if(!(organism %in% c("yeast","human","mouse","rat")))
      stop("Invalid organism (must be one of 'yeast','human','mouse', or 'rat')")

    MAT.name <- paste("go",ont,"aMAT",sep="")
    if(is.null(tryCatch(data(list=MAT.name,package="mBison"),warning=function(w) NULL)) && !exists(MAT.name) && is.null(tryCatch(load(paste(MAT.name,".RData",sep="")),error=function(e) NULL)))
      stop("Accessibility matrix ",MAT.name," not found")
    expr <- paste("goAmat <- ",MAT.name,sep="")
    eval(parse(text=expr))

    ooc.name <- paste("go",ont,"ooc.",organism,sep="")
    if(is.null(tryCatch(data(list=ooc.name,package="mBison"),warning=function(w) NULL)) && !exists(ooc.name) && is.null(tryCatch(load(paste(ooc.name,".RData",sep="")),error=function(e) NULL)))
      stop("Object-ontology complex ",ooc.name," not found")
    expr <- paste("goOOC <- ",ooc.name,sep="")
    eval(parse(text=expr))

    pc.name <- paste("go",ont,"pc.",organism,sep="")
    if(is.null(tryCatch(data(list=pc.name,package="mBison"),warning=function(w) NULL)) && !exists(pc.name) && is.null(tryCatch(load(paste(pc.name,".RData",sep="")),error=function(e) NULL)))
      stop("Concept probability list ",pc.name," not found")
    expr <- paste("goPC <- ",pc.name,sep="")
    eval(parse(text=expr))

    go.names <- nodes(DAG(rDAG(ontology(goOOC))))
    goPMS <- matrix(1,length(go.names),length(go.names))
	if(length(go.names)==0)
		return(goPMS)
    cat("Starting PMS calculations (may take a WHILE)...\n")
    ncomps <- length(go.names)*(length(go.names)-1)/2
    n <- 0
    cat(paste("Progress (out of ",ncomps," comparisons):\n",sep=""))
    for(i in 1:length(go.names)) {
      for(j in i:length(go.names)) {
        if(go.names[i]==go.names[j])
          goPMS[i,j] <- goPC[[go.names[i]]]
		else if(any(c(go.names[i],go.names[j]) %in% c("GO:0008150","GO:0005575","GO:0003674")))
			goPMS[i,j] <- 1
        else
          goPMS[i,j] <- pms(go.names[i],go.names[j],goOOC,acc=goAmat,pc=goPC)
        n <- n+1
        if((n %% 5)==0) {
          cat(paste(n," ",sep=""))
          if((n %% 200)==0)
            cat("\n")
        }
      }
    }
    tPMS <- t(goPMS)
    goPMS[lower.tri(goPMS)] <- tPMS[lower.tri(tPMS)]
    rownames(goPMS) <- colnames(goPMS) <- go.names
    return(goPMS)
  }