public static String predictFromGrammar23S(
String seq, String nat, Grammar grammar, boolean verbose) {
int size = seq.length();
Map<String, BigDouble> parr = new HashMap<String, BigDouble>();
int[][][] tau = new int[size][size][3];
output.out("\t\tTau allocated");
String pred = null;
if (size < 1) {
output.out("\nInvalid sequence provided: \n\t[ " + seq + " ]");
return pred;
}
output.out("\nPredicting secondary structure for \n\t\t[ " + seq + " ]");
long start = System.currentTimeMillis();
for (int i = 0; i < size; i++) {
// Progress Bar
CommandLine.DisplayBar(seq.length(), i, ((long) (System.currentTimeMillis() - start) / 1000));
for (int j = i; j < size; j++) {
String ij = i + ":" + (i + j);
for (int k = 0; k < 3; k++) {
tau[i][j][k] = -1;
parr.put(ij + ":" + k, new BigDouble(0));
}
}
}
CommandLine.DisplayBarFinish();
// Fill Array
if (grammar instanceof PfoldGrammar) {
PfoldGrammar pfold = (PfoldGrammar) grammar;
// _23S_CYK(seq, pfold.getKH_params(), pfold
// .getPfold_paramsUnmatched(), pfold
// .getPfold_paramsBasePairs(), parr, tau);
}
BigDouble prob = parr.get("0:" + (size - 1) + ":" + 0);
output.out("\t-Probability of highest probability parse for sequence is \n\t\t" + prob);
if (prob != null) {
// grammar.recordProbability(prob);
// Trace Back
if (prob.compareTo(0) > 0) {
pred = kh_trace_back(tau);
{
output.out("\t-Highest probability parse generates structure\n\t\t[ " + pred + " ]");
if (nat != null)
output.out(
"\t-FMeasure for predicted structure is\n\t\t" + Compare.getFMeasureBD(nat, pred));
}
}
}
return pred;
}
// 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();
}
