public  void start2 () {


       wm = new double[20][Data.windows_size];
       String QueryKinasesName = "%" + Data.kinease + "%";
       //data.code = data.codenames[3];
       String QueryCodeName = Data.code;
       int windows_size = Data.windows_size;

       //int windows_size = 9;

       int shift = windows_size / 2;

       try {

          {
               shift = windows_size / 2;
               // establish connection to database

               String LIKE = "LIKE";
               //int POSITION = 0;
               //int index = 0;
               //int numtemp = 0;
               //int LENGTH = (int) 0;
               //int count = 0;
               double[] totalAAcount = new double[windows_size];

               double weightmatrix[][] = new double[windows_size][128]; //windowssize;aa;


               ///fout.println("#"+statementquery1);

               int seqsize = 0;

               for (int i = 0; i < pwmseq.size(); i++){
                   String posseq = pwmseq.elementAt(i).toString();
                   seqsize = posseq.length();
                  {
                       for (int j = 0; j < seqsize; j++) {

                           weightmatrix[j][posseq.charAt(j)]++;

                       }
                       //possequence.addElement(posseq);
                   }

               } // end while
               char[] aaMap = {'A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H',
                              'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y',
                              'V', 'X'};

               //double[] aaMapfreq = new double[windows_size];

               for (int j = 0 ; j < weightmatrix.length;j++){
                   for (int i = 0; i < aaMap.length - 1; i++) {
                       totalAAcount[j] += weightmatrix[j][aaMap[i]];
                   }
               }

               for (int i = 0; i < aaMap.length - 1; i++) {
                   //profilefout.print(aaMap[i]);
                   for (int j = 0 ; j < windows_size;j++){


                         wm[i][j]   = ((weightmatrix[j][aaMap[i]]) / (totalAAcount[j]));

                     //  profilefout.print(","+aaMapfreq[i]);


                   }
                   //profilefout.println();
               }

               //fout.close();
               //profilefout.close();


           }

       } // end try

       catch (NullPointerException nullpointerException) {
           nullpointerException.printStackTrace();
           System.exit(1);

       }  catch (NoClassDefFoundError ex) {

       }

       finally { // ensure statement and connection are closed properly
           try {

           } catch (Exception exception) { // end try
               exception.printStackTrace();
               System.exit(1);
           } // end catch
       } // end finally
   } // end main