Ejemplo n.º 1
0
  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;
  }
Ejemplo n.º 2
0
 //	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();
 }