#' transprob
#'
#' \code{transprob} creats the transition matrix for the hidden markov chain.
#'
#' @export
#' @param trans c(rho_u, rho, delta)
#' @param stp 1 if next codon is stop codon
#' @param stp2 In \code{generate_uORF}, stp = theta_u, stp2 = theta
#' @return The transition matrix \code{A}
#'
#' @examples
#' trans <- c(0.1, 0.2, 0.3)
#' stp <- 0.4; stp2 <- 0.45
#' A <- transprob(trans, stp, stp2)
#' colnames(A) <- seq(1,21)
#' View(A)
transprob <- function(trans, stp, stp2){
A <- diag(21)
A <- cbind(0, A[,-21])
A[1,1] <- 1 - trans[1] - trans[2]
A[1,2] <- trans[1]
A[1,12] <- trans[2]
A[11, 12] <- trans[3]
A[11, 11] <- 1-trans[3]
A[4,8] <- A[7,8] <- stp
A[4,5] <- A[7,5] <- 1-stp
A[14,18] <- A[17,18] <- stp2
A[14,15] <- A[17,15] <- 1-stp2
A[21,21] <- 1
return(A)
}
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