/**
* Fills the structure (str) string with the predicted structure according to running the CYK
* algorithm and traceback on the provided sequence string (seq). The parameters should be
* double[3] including the following probabilities:
*
* <p>params[0] = p(S->L) params[1] = p(L->s) params[2] = p(F->LS)
*
* @param seq - The sequence to predict from.
* @param str - The string to fill with the predicted value.
* @param params - The Knudson-Hein Grammar parameters as described above.
* @param verbose - Display output to command line if true.
*/
public static String predictFromGrammar(String seq, Grammar grammar) {
int size = seq.length();
BigDecimal[][][] parr = new BigDecimal[size][size][3];
int[][][] tau = new int[size][size][3];
String pred = null;
if (size < 1) {
return pred;
}
for (int i = 0; i < size; i++) {
for (int j = 0; j < size; j++) {
for (int k = 0; k < 3; k++) {
tau[i][j][k] = -1;
parr[i][j][k] = new BigDecimal(0);
}
}
}
if (grammar instanceof PfoldGrammar) {
PfoldGrammar pfold = (PfoldGrammar) grammar;
// BigDouble[] kh_params = new BigDouble[pfold.get_kh_params().length];
// for(int i=0;i<kh_params.length;i++)
// kh_params[i] = new BigDouble(pfold.get_kh_params()[i].doubleValue());
// BigDouble[] Pfold_paramsUnmatched = new
// BigDouble[pfold.getPfold_paramsUnmatched().length];
// for(int i=0;i<Pfold_paramsUnmatched.length;i++)
// Pfold_paramsUnmatched[i] = new
// BigDouble(pfold.getPfold_paramsUnmatched()[i].doubleValue());
// BigDouble[][] Pfold_paramsBasePairs = new
// BigDouble[pfold.getPfold_paramsBasePairs().length][pfold.getPfold_paramsBasePairs()[0].length];
// for(int i=0;i<Pfold_paramsBasePairs.length;i++)
// for(int j=0;j<Pfold_paramsBasePairs[i].length;j++)
// Pfold_paramsBasePairs[i][j] = new
// BigDouble(pfold.getPfold_paramsBasePairs()[i][j].doubleValue());
BigDecimal[] kh_params = new BigDecimal[pfold.get_kh_params().length];
for (int i = 0; i < kh_params.length; i++)
kh_params[i] = new BigDecimal(pfold.get_kh_params()[i].doubleValue());
BigDecimal[] Pfold_paramsUnmatched = new BigDecimal[pfold.getPfold_paramsUnmatched().length];
for (int i = 0; i < Pfold_paramsUnmatched.length; i++)
Pfold_paramsUnmatched[i] =
new BigDecimal(pfold.getPfold_paramsUnmatched()[i].doubleValue());
BigDecimal[][] Pfold_paramsBasePairs =
new BigDecimal[pfold.getPfold_paramsBasePairs().length]
[pfold.getPfold_paramsBasePairs()[0].length];
for (int i = 0; i < Pfold_paramsBasePairs.length; i++)
for (int j = 0; j < Pfold_paramsBasePairs[i].length; j++)
Pfold_paramsBasePairs[i][j] =
new BigDecimal(pfold.getPfold_paramsBasePairs()[i][j].doubleValue());
Pfold_CYK(seq, kh_params, Pfold_paramsUnmatched, Pfold_paramsBasePairs, parr, tau);
}
// BigDouble prob = parr[0][size - 1][0];
BigDecimal prob = parr[0][size - 1][0];
int compVal = prob.compareTo(BigDecimal.ZERO);
if (compVal > 0) pred = kh_trace_back(tau);
else
output.out(
"Probability of highest probability parse is <= 0. ("
+ prob.toString()
+ " :: "
+ compVal
+ ")");
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();
}