optimclass2<-function (comm, stride, pval = 0.01, counts = 2) 
{
  if (!inherits(stride, "stride")) 
    stop("The second argument must be of class 'stride'")
  strides <- ncol(stride$clustering)
  mondo.fisher <- function(comm, clust) {
    rows <- ncol(comm)
    cols <- length(table(clust))
    res <- matrix(NA, nrow = rows, ncol = cols)
    for (i in 1:rows) {
      for (j in 1:cols) {
        if(length(unique(comm[, i]>0))==2) res[i, j] <- fisher.test(comm[, i] > 0, clust == j)$p.val
        else (res[i, j]<-1)
      }
    }
    res
  }
  vals <- rep(NA, strides)
  cts <- rep(NA, strides)
  for (i in 1:strides) {
    tmp <- mondo.fisher(comm = comm, clust = stride$clustering[, 
      i])
    vals[i] <- sum(tmp <= pval)
    cts[i] <- sum(apply(tmp <= pval, 2, sum) >= counts)
  }
  out <- data.frame(stride$seq, vals, cts)
  names(out) <- c("clusters", "sig.spc", "sig.clust")
  attr(out, "call") <- match.call()
  attr(out, "timestamp") <- date()
  out
}