- // ii = 0;
- // while ((ii < s.length) && (s[ii] != null))
- // {
- // bs2[ii] = new BinarySequence(s[ii], nucleotides);
- // if (scoreMatrix != null)
- // {
- // try
- // {
- // bs2[ii].matrixEncode(scoreMatrix);
- // } catch (InvalidSequenceTypeException x)
- // {
- // details.append("Unexpected mismatch of sequence type and score matrix. Calculation will not be valid!\n\n");
- // }
- // }
- // ii++;
- // }
- //
- // int count = 0;
- // while ((count < bs.length) && (bs[count] != null))
- // {
- // count++;
- // }
- //
- // double[][] seqmat = new double[count][];
- // double[][] seqmat2 = new double[count][];
- //
- // int i = 0;
- // while (i < count)
- // {
- // seqmat[i] = bs[i].getDBinary();
- // seqmat2[i] = bs2[i].getDBinary();
- // i++;
- // }
- //
- // /*
- // * using a SparseMatrix to hold the encoded sequences matrix
- // * greatly speeds up matrix multiplication as these are mostly zero
- // */
- // m = new SparseMatrix(seqmat);
- // m2 = new Matrix(seqmat2);
-