// private static void Pfold_CYK(String seq, BigDouble[] p, BigDouble[] p_u,
// BigDouble[][] p_bp, BigDouble[][][] arr, int[][][] tau) {
private static void Pfold_CYK(
String seq,
BigDecimal[] p,
BigDecimal[] p_u,
BigDecimal[][] p_bp,
BigDecimal[][][] arr,
int[][][] tau) {
int S = 0, L = 1, F = 2;
int[] seq2 = PfoldGrammar.getNucleotideIndexArray(seq);
BigDecimal temp, tempProd, one = new BigDecimal(1);
BigDecimal S_LS, L_dFd, F_dFd;
S_LS = one.subtract(p[S]);
L_dFd = one.subtract(p[L]);
F_dFd = one.subtract(p[F]);
MathContext precision = MathContext.DECIMAL128;
for (int i = 0; i < seq.length(); i++) {
temp = p[L].multiply(p_u[seq2[i]]);
arr[i][i][L] = p[L].multiply(p_u[seq2[i]]);
tau[i][i][S] = 0;
tau[i][i][L] = 0;
tau[i][i][F] = 0;
}
System.out.println();
long start = System.currentTimeMillis();
for (int j = 0; j < seq.length(); j++) {
// Progress Bar
CommandLine.DisplayBar(seq.length(), j, ((long) (System.currentTimeMillis() - start) / 1000));
for (int i = 0; i + j < seq.length(); i++) {
int ij = i + j;
if (j > 2) {
tempProd = p_bp[seq2[i]][seq2[ij]].multiply(arr[i + 1][ij - 1][F], precision);
// ///////
// L->dFd
temp = L_dFd.multiply(tempProd, precision);
if (arr[i][ij][L].compareTo(temp) <= 0) {
arr[i][ij][L] = new BigDecimal(temp.toPlainString());
tau[i][ij][L] = (F << 8) | 0xff;
}
// ///////
// F->dFd
temp = F_dFd.multiply(tempProd, precision);
if (arr[i][ij][F].compareTo(temp) <= 0) {
arr[i][ij][F] = new BigDecimal(temp.toPlainString());
tau[i][ij][F] = (F << 8) | 0xff;
}
}
// /////
// S->L
temp = p[S].multiply(arr[i][ij][L], precision);
if (arr[i][ij][S].compareTo(temp) <= 0) {
arr[i][ij][S] = new BigDecimal(temp.toPlainString());
tau[i][ij][S] = (L << 8) | 0xff;
}
for (int k = i; k < ij; k++) {
tempProd = arr[i][k][L].multiply(arr[k + 1][ij][S], precision);
// //////
// S->LS
temp = S_LS.multiply(tempProd, precision);
if (arr[i][ij][S].compareTo(temp) <= 0) {
arr[i][ij][S] = new BigDecimal(temp.toPlainString());
tau[i][ij][S] = (k << 16) | (L << 8) | (S);
}
// //////
// F->LS
temp = p[F].multiply(tempProd, precision);
if (arr[i][ij][F].compareTo(temp) <= 0) {
arr[i][ij][F] = new BigDecimal(temp.toPlainString());
tau[i][ij][F] = (k << 16) | (L << 8) | (S);
}
}
}
}
CommandLine.DisplayBarFinish();
}
