"Csim.go" <-
function(sim,assoc,ont="BP",organism="yeast",sim.method="lin",thresh=0)
{
  if(!(is.matrix.csr(sim) || is.matrix(sim)) || (nrow(sim) != ncol(sim)) || (nrow(sim)==0))
    stop("Invalid sim matrix")
  if(!is.list(assoc) || (length(assoc) != nrow(sim)) || !is.character(unlist(assoc)))
    stop("Invalid assoc list")
  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')")
  if(!(sim.method %in% c("lin","resnik","jiang")))
    stop("Invalid similarity method (must be one of 'lin','resnik', or 'jiang')")
  if(!is.numeric(thresh) || is.null(thresh) || is.na(thresh) || (thresh<0))
    stop("Threshold similarity must be a numeric >= 0")

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

  if(nrow(sim)==1)
	return(as.matrix.csr(0,nrow(sim),ncol(sim)))

  sim <- .Call("Csim_go",assoc,goPC,goPMS,sim.method,thresh,PACKAGE="mBison")

  rm(goPC,goPMS)
  gc(FALSE)
  sim <- as.matrix.csr(sim)
  gc(FALSE)
  sim <- sim+t(sim)
  gc(FALSE)
  return(sim)
}