#' boundEntropy function
#'
#' This function is one of the functions that makes EntropyMSA works.
#' @param H The is the calculated H, entropy value, to be bounded by the maximum entropy
#' and minimum entropy possible.
#' @param n By default, n = 1, which means only a single character per alignment
#' column per sequence. For example, users may change to n = 9 for nonamer
#' scoring instead of monomer.
#' @param totalCharacters This depends on whether the standard 20 amino acids plus
#' a gap scoring is used or not. Users may set this to 20 if they wish to ignore
#' gap character.
#' @keywords entropy
#' @export
#' @examples
#' #see EntropyMSA function
boundEntropy <- function(H,n,totalCharacters = 21){
#assume 21 characters as the default
max <- log2(totalCharacters^n)
for (i in length(H)){
if (H[i] > max) H[i] <- max
if (H[i] < 0) H[i] <- 0
}
H
}
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