/**
* 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;
}
// ---------------------------------------------------------------------------
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);
}
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
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;
}
@Override
public double getLogValue(final double nonLogValue) {
return Math.log10(nonLogValue);
}
@Override
public double LOG(double x) {
result = Math.log10(x);
return result;
}
