Beispiel #1
0
 /**
  * Returns the base 10 logarithm of a {@link BigInteger}.
  *
  * @param theValue
  * @return
  */
 public static double log10(final BigInteger theValue) {
   /*
    * log10(x) = (x / (10 ^ len(x))) + len(x)
    * http://ubuntuforums.org/showthread.php?t=1461903
    */
   final int length = theValue.toString().length();
   BigDecimal div = BigDecimal.TEN.pow(length);
   BigDecimal res = new BigDecimal(theValue).divide(div);
   return java.lang.Math.log10(res.doubleValue()) + length;
 }
Beispiel #2
0
  // ---------------------------------------------------------------------------
  private String Calculate1(String oper, String str1) throws Exception {
    double n1 = Values.StringToDouble(str1);
    double val = 0;

    if (oper.equalsIgnoreCase("SEN")) val = java.lang.Math.sin(n1);
    else if (oper.equalsIgnoreCase("COS")) val = java.lang.Math.cos(n1);
    else if (oper.equalsIgnoreCase("TAN")) val = java.lang.Math.tan(n1);
    else if (oper.equalsIgnoreCase("CTG")) val = 1.0 / java.lang.Math.tan(n1);
    else if (oper.equalsIgnoreCase("ASEN")) val = java.lang.Math.asin(n1);
    else if (oper.equalsIgnoreCase("ACOS")) val = java.lang.Math.acos(n1);
    else if (oper.equalsIgnoreCase("ATAN")) val = java.lang.Math.atan(n1);
    else if (oper.equalsIgnoreCase("ACTG")) val = 1.0 / java.lang.Math.atan(n1);
    else if (oper.equalsIgnoreCase("SENH")) val = java.lang.Math.sinh(n1);
    else if (oper.equalsIgnoreCase("COSH")) val = java.lang.Math.cosh(n1);
    else if (oper.equalsIgnoreCase("TANH")) val = java.lang.Math.tanh(n1);
    else if (oper.equalsIgnoreCase("CTGH")) val = 1.0 / java.lang.Math.tanh(n1);
    else if (oper.equalsIgnoreCase("EXP")) val = java.lang.Math.exp(n1);
    // valor absoluto de inteiros s�o inteiros
    else if (oper.equalsIgnoreCase("ABS")) {
      val = java.lang.Math.abs(n1);
      if (Values.IsInteger(str1)) return Values.IntegerToString(val);
    } else if (oper.equalsIgnoreCase("RAIZ")) val = java.lang.Math.sqrt(n1);
    else if (oper.equalsIgnoreCase("LOG")) val = java.lang.Math.log10(n1);
    else if (oper.equalsIgnoreCase("LN")) val = java.lang.Math.log(n1);
    // parte inteira do numeros
    else if (oper.equalsIgnoreCase("INT")) {
      return Values.IntegerToString(n1);
    }
    // parte real
    else if (oper.equalsIgnoreCase("FRAC")) {
      String num = Values.DoubleToString(n1);
      return num.substring(num.indexOf('.') + 1);
    }

    // parte real
    else if (oper.equalsIgnoreCase("ARRED")) {
      double vm = java.lang.Math.ceil(n1);
      if (n1 - vm >= 0.5) return Values.IntegerToString((int) n1 + 1);
      return Values.IntegerToString((int) n1);
    } else throw new Exception("ERRO fun��o Desconhecida 1 [" + oper + "]");
    return Values.DoubleToString(val);
  }
Beispiel #3
0
  public void start() {

    Connection connection = null; // manages connection
    Connection connection2 = null;
    Statement statement = null; // query statement
    Statement statement2 = null;
    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 {
      Class.forName(JDBC_DRIVER); // load database driver class
      for (windows_size = Data.windows_size; windows_size <= Data.windows_size; windows_size += 2) {
        shift = windows_size / 2;
        // establish connection to database
        connection = DriverManager.getConnection(DATABASE_URL, "", "");
        connection2 = DriverManager.getConnection(DATABASE_URL, "", "");
        // create Statement for querying database
        statement = connection.createStatement();
        statement2 = connection2.createStatement();
        String ACC = null;
        String SEQUENCE = null;
        String KINASES = null;
        String LIKE = "LIKE";
        // int POSITION = 0;
        // int index = 0;
        String temp = null;
        // 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;

        String statementquery1 =
            "SELECT Mid(sequence,(position-"
                + shift
                + "),"
                + windows_size
                + ") AS TARGET, index,code,length,position,sequence FROM Dataset_041106 WHERE ((position-"
                + shift
                + ")>1) AND ((position +"
                + shift
                + ")<length) AND kinases "
                + LIKE
                + " '"
                + QueryKinasesName
                + "' AND (code LIKE '"
                + QueryCodeName
                + "')";
        System.out.println("#" + statementquery1);
        /// fout.println("#"+statementquery1);
        ResultSet resultSet1 = statement.executeQuery(statementquery1);
        int seqsize = 0;
        while ((resultSet1.next())) {
          String posseq = resultSet1.getString("TARGET");
          seqsize = posseq.length();
          if (posseq.charAt(0) != 'X' && posseq.charAt(seqsize - 1) != 'X') { // �h����t

            for (int i = 0; i < seqsize; i++) {

              weightmatrix[i][posseq.charAt(i)]++;
            }
            // 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[] expmatrix = {
          0.0701313443873091,
          0.0582393695201718,
          0.0359362961736045,
          0.0520743144385134,
          0.0172010453343506,
          0.0498574962335004,
          0.0796465136978452,
          0.0624720283551962,
          0.0241405228512130,
          0.0416989778376737,
          0.0934441156861220,
          0.0632334844952389,
          0.0213293464067050,
          0.0324554733241482,
          0.0651181982370858,
          0.0881672518230193,
          0.0524630941595624,
          0.0101093184162382,
          0.0244701177088640,
          0.0578116909136386
        };
        // double[] aaMapfreq = new double[windows_size];
        double freq = 0;
        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++) {

            freq = ((weightmatrix[j][aaMap[i]]) / (totalAAcount[j])) + 1;

            wm[i][j] = Math.log10((freq / expmatrix[i])) / Math.log10(2.0);

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

          }
          // profilefout.println();
        }

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

        resultSet1.close();
        connection.close();
      }

    } // end try
    catch (ClassNotFoundException classNotFound) {
      classNotFound.printStackTrace();
      System.exit(1);
    } catch (NullPointerException nullpointerException) {
      nullpointerException.printStackTrace();
      System.exit(1);

    } catch (SQLException ex) {
      /** @todo Handle this exception */
      /*        } catch (IOException ex) {
       */
      /** @todo Handle this exception */
    } catch (NoClassDefFoundError ex) {

    } finally { // ensure statement and connection are closed properly
      try {
        statement.close();
        statement2.close();

        connection.close();

        connection2.close();
      } catch (Exception exception) { // end try
        exception.printStackTrace();
        System.exit(1);
      } // end catch
    } // end finally
  } // end main
Beispiel #4
0
  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 ACC = null;
        String SEQUENCE = null;
        String KINASES = null;
        String LIKE = "LIKE";
        // int POSITION = 0;
        // int index = 0;
        String temp = null;
        // 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[] expmatrix = {
          0.0701313443873091,
          0.0582393695201718,
          0.0359362961736045,
          0.0520743144385134,
          0.0172010453343506,
          0.0498574962335004,
          0.0796465136978452,
          0.0624720283551962,
          0.0241405228512130,
          0.0416989778376737,
          0.0934441156861220,
          0.0632334844952389,
          0.0213293464067050,
          0.0324554733241482,
          0.0651181982370858,
          0.0881672518230193,
          0.0524630941595624,
          0.0101093184162382,
          0.0244701177088640,
          0.0578116909136386
        };
        // double[] aaMapfreq = new double[windows_size];
        double freq = 0;
        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++) {

            freq = ((weightmatrix[j][aaMap[i]] + 0.05) / (totalAAcount[j] + 1));

            wm[i][j] = Math.log10((freq / expmatrix[i])) / Math.log10(2.0);

            //  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
  private Object interpretFunction(Functions function, Sprite sprite) {
    Object left = null;
    Object right = null;

    Double doubleValueOfLeftChild = null;
    Double doubleValueOfRightChild = null;

    if (leftChild != null) {
      left = leftChild.interpretRecursive(sprite);
      if (left instanceof String) {
        try {
          doubleValueOfLeftChild = Double.valueOf((String) left);
        } catch (NumberFormatException numberFormatException) {
          Log.d(getClass().getSimpleName(), "Couldn't parse String", numberFormatException);
        }
      } else {
        doubleValueOfLeftChild = (Double) left;
      }
    }

    if (rightChild != null) {
      right = rightChild.interpretRecursive(sprite);
      if (right instanceof String) {
        try {
          doubleValueOfRightChild = Double.valueOf((String) right);
        } catch (NumberFormatException numberFormatException) {
          Log.d(getClass().getSimpleName(), "Couldn't parse String", numberFormatException);
        }
      } else {
        doubleValueOfRightChild = (Double) right;
      }
    }

    switch (function) {
      case SIN:
        return doubleValueOfLeftChild == null
            ? 0d
            : java.lang.Math.sin(Math.toRadians(doubleValueOfLeftChild));
      case COS:
        return doubleValueOfLeftChild == null
            ? 0d
            : java.lang.Math.cos(Math.toRadians(doubleValueOfLeftChild));
      case TAN:
        return doubleValueOfLeftChild == null
            ? 0d
            : java.lang.Math.tan(Math.toRadians(doubleValueOfLeftChild));
      case LN:
        return doubleValueOfLeftChild == null ? 0d : java.lang.Math.log(doubleValueOfLeftChild);
      case LOG:
        return doubleValueOfLeftChild == null ? 0d : java.lang.Math.log10(doubleValueOfLeftChild);
      case SQRT:
        return doubleValueOfLeftChild == null ? 0d : java.lang.Math.sqrt(doubleValueOfLeftChild);
      case RAND:
        return (doubleValueOfLeftChild == null || doubleValueOfRightChild == null)
            ? 0d
            : interpretFunctionRand(doubleValueOfLeftChild, doubleValueOfRightChild);
      case ABS:
        return doubleValueOfLeftChild == null ? 0d : java.lang.Math.abs(doubleValueOfLeftChild);
      case ROUND:
        return doubleValueOfLeftChild == null
            ? 0d
            : (double) java.lang.Math.round(doubleValueOfLeftChild);
      case PI:
        return java.lang.Math.PI;
      case MOD:
        return (doubleValueOfLeftChild == null || doubleValueOfRightChild == null)
            ? 0d
            : interpretFunctionMod(doubleValueOfLeftChild, doubleValueOfRightChild);
      case ARCSIN:
        return doubleValueOfLeftChild == null
            ? 0d
            : java.lang.Math.toDegrees(Math.asin(doubleValueOfLeftChild));
      case ARCCOS:
        return doubleValueOfLeftChild == null
            ? 0d
            : java.lang.Math.toDegrees(Math.acos(doubleValueOfLeftChild));
      case ARCTAN:
        return doubleValueOfLeftChild == null
            ? 0d
            : java.lang.Math.toDegrees(Math.atan(doubleValueOfLeftChild));
      case EXP:
        return doubleValueOfLeftChild == null ? 0d : java.lang.Math.exp(doubleValueOfLeftChild);
      case POWER:
        return (doubleValueOfLeftChild == null || doubleValueOfRightChild == null)
            ? 0d
            : java.lang.Math.pow(doubleValueOfLeftChild, doubleValueOfRightChild);
      case FLOOR:
        return doubleValueOfLeftChild == null ? 0d : java.lang.Math.floor(doubleValueOfLeftChild);
      case CEIL:
        return doubleValueOfLeftChild == null ? 0d : java.lang.Math.ceil(doubleValueOfLeftChild);
      case MAX:
        return (doubleValueOfLeftChild == null || doubleValueOfRightChild == null)
            ? 0d
            : java.lang.Math.max(doubleValueOfLeftChild, doubleValueOfRightChild);
      case MIN:
        return (doubleValueOfLeftChild == null || doubleValueOfRightChild == null)
            ? 0d
            : java.lang.Math.min(doubleValueOfLeftChild, doubleValueOfRightChild);
      case TRUE:
        return 1d;
      case FALSE:
        return 0d;
      case LETTER:
        return interpretFunctionLetter(right, left);
      case LENGTH:
        return interpretFunctionLength(left, sprite);
      case JOIN:
        return interpretFunctionJoin(sprite);
      case ARDUINODIGITAL:
        Arduino arduinoDigital =
            ServiceProvider.getService(CatroidService.BLUETOOTH_DEVICE_SERVICE)
                .getDevice(BluetoothDevice.ARDUINO);
        if (arduinoDigital != null && left != null) {
          if (doubleValueOfLeftChild < 0 || doubleValueOfLeftChild > 13) {
            return 0d;
          }
          return arduinoDigital.getDigitalArduinoPin(doubleValueOfLeftChild.intValue());
        }
        break;
      case ARDUINOANALOG:
        Arduino arduinoAnalog =
            ServiceProvider.getService(CatroidService.BLUETOOTH_DEVICE_SERVICE)
                .getDevice(BluetoothDevice.ARDUINO);
        if (arduinoAnalog != null && left != null) {
          if (doubleValueOfLeftChild < 0 || doubleValueOfLeftChild > 5) {
            return 0d;
          }
          return arduinoAnalog.getAnalogArduinoPin(doubleValueOfLeftChild.intValue());
        }
        break;
      case RASPIDIGITAL:
        RPiSocketConnection connection = RaspberryPiService.getInstance().connection;
        int pin = doubleValueOfLeftChild.intValue();
        try {
          return connection.getPin(pin) ? 1d : 0d;
        } catch (Exception e) {
          Log.e(getClass().getSimpleName(), "RPi: exception during getPin: " + e);
        }
        break;
      case MULTI_FINGER_TOUCHED:
        return TouchUtil.isFingerTouching(doubleValueOfLeftChild.intValue()) ? 1d : 0d;
      case MULTI_FINGER_X:
        return Double.valueOf(TouchUtil.getX(doubleValueOfLeftChild.intValue()));
      case MULTI_FINGER_Y:
        return Double.valueOf(TouchUtil.getY(doubleValueOfLeftChild.intValue()));
      case LIST_ITEM:
        return interpretFunctionListItem(left, sprite);
      case CONTAINS:
        return interpretFunctionContains(right, sprite);
      case NUMBER_OF_ITEMS:
        return interpretFunctionNumberOfItems(left, sprite);
    }
    return 0d;
  }
Beispiel #6
0
 @Override
 public double getLogValue(final double nonLogValue) {
   return Math.log10(nonLogValue);
 }
Beispiel #7
0
 @Override
 public double LOG(double x) {
   result = Math.log10(x);
   return result;
 }