public static void main(String args[]) {
wmatrix wmatrix = new wmatrix();
wmatrix.start();
try {
PrintWriter profilefout =
new PrintWriter(
new BufferedWriter(
new FileWriter(
"profile_"
+ Data.kinease
+ "_"
+ Data.code
+ "_"
+ Data.windows_size
+ ".csv")));
profilefout.print("Position=");
for (int j = 0; j < Data.windows_size; j++) {
profilefout.print("," + (j - Data.windows_size / 2));
}
profilefout.println();
for (int i = 0; i < 20; i++) {
for (int j = 0; j < Data.windows_size; j++) {
profilefout.print("," + wm[i][j]);
}
profilefout.println();
}
profilefout.close();
} catch (IOException ex) {
}
}
/**
* It draws the population to a file. A character allele is drawn as 1 o 0. Otherwise, a real
* allele is drawn in ten points, that represent the interval [0..1] divided in ten fragments. In
* each fragment, three types of symbol are possible: . --> The fragment is not covered by the
* classifier. o --> The fragment is partially covered by the classifier. O --> The fragment is
* totally covered by the classifier.
*
* <p>This notation has been obtained from Wilson2000 XCSR
*
* @param fout is the file where the population has to be drawn.
*/
public void draw(PrintWriter fout) {
double lower = 0, upper = 0;
if (Config.ternaryRep) {
fout.print(" " + ((char) rep[0].getAllele()) + " ");
for (int i = 1; i < rep.length; i++) {
fout.print("| " + ((char) rep[i].getAllele()) + " ");
}
} else {
if (Config.typeOfAttributes[0].equals("character")) {
fout.print(" " + ((char) rep[0].getAllele()) + " ");
} else {
printInterval(fout, rep[0].getLowerAllele(), rep[0].getUpperAllele());
}
for (int i = 1; i < rep.length; i++) {
if (Config.typeOfAttributes[i].equals("character")) {
fout.print("| " + ((char) rep[i].getAllele()) + " ");
} else if (Config.typeOfAttributes[i].equals("integer")) {
printInterval(i, fout, ((int) rep[i].getLowerAllele()), ((int) rep[i].getUpperAllele()));
} else {
printInterval(fout, rep[i].getLowerAllele(), rep[i].getUpperAllele());
}
}
}
fout.print("\t " + action);
} // end draw
/**
* Prints the classifier to the specified file.
*
* @param fout is the file output where the classifier has to be printed.
*/
public void print(PrintWriter fout) {
fout.print(" ");
for (int i = 0; i < rep.length; i++) {
rep[i].print(fout);
}
fout.print(" " + action + " ");
if (parameters != null) parameters.print(fout);
}
/**
* Prints the classifier to the specified file.
*
* @param fout is the output file.
*/
public void print(PrintWriter fout) {
fout.print(" ");
for (int i = 0; i < rep.length; i++) {
rep[i].print(fout);
}
fout.print("\t " + action);
} // end print
/**
* It draws an integer interval
*
* @param fout is a reference to the file where the classifier has to be drawn.
* @param numInterval is the position of the interval in the classifier.
* @param lower is the lower value of the interval
* @param upper is the upper value of the interval.
*/
private void printInterval(int numInterval, PrintWriter fout, int lower, int upper) {
double aux = 0.0;
int points = Config.realDrawnPrecision;
int inc =
((int) Config.attBounds[numInterval][1] - (int) Config.attBounds[numInterval][0] + 1)
/ points;
for (int i = 0; i < points; i++) {
if (i * inc >= lower && i * inc <= upper) {
fout.print("O");
} else {
fout.print(".");
}
}
fout.print(" | ");
}
/**
* Prints the classifier to the specified file.
*
* @param fout is the output file.
*/
public void printNotNorm(PrintWriter fout) {
int i = 0;
fout.print(" ");
try {
for (i = 0; i < rep.length; i++) {
if (Config.typeOfAttributes[i].equals("enumerate")) {
rep[i].printNotNorm(fout, Config.enumConv[i]);
} else if (Config.typeOfAttributes[i].equals("integer")) {
if (Config.enumConv[i].size() > 0) rep[i].printNotNorm(fout, Config.enumConv[i]);
else rep[i].printNotNorm(fout, (int) Config.attBounds[i][0]);
} else if (Config.typeOfAttributes[i].equals("real")) {
rep[i].printNotNorm(fout, Config.attBounds[i][0], Config.attBounds[i][1]);
}
}
} catch (Exception e) {
System.out.println("Exception when printing the attribute: " + i);
e.printStackTrace();
}
fout.print("\t " + (String) Config.classConv.elementAt(action));
} // end print
/**
* Prints the desnormalized classifier to the specified file.
*
* @param fout is the file output where the classifier has to be printed.
*/
public void printNotNorm(PrintWriter fout) {
int i = 0;
fout.print(" ");
try {
for (i = 0; i < rep.length; i++) {
if (Config.typeOfAttributes[i].equals("ternary")) {
rep[i].print(fout);
} else if (Config.typeOfAttributes[i].equals("integer")) {
rep[i].printNotNorm(fout, Config.attBounds[i][0]);
} else if (Config.typeOfAttributes[i].equals("real")) {
rep[i].printNotNorm(fout, Config.attBounds[i][0], Config.attBounds[i][1]);
}
}
} catch (Exception e) {
System.out.println("Exception when printing the attribute: " + i);
e.printStackTrace();
}
fout.print("\t " + (String) Config.classConv.elementAt(action));
if (parameters != null) parameters.print(fout);
}
/**
* It draws a real interval
*
* @param fout is a reference to the file where the classifier has to be drawn.
* @param lower is the lower value of the interval
* @param upper is the upper value of the interval.
*/
private void printInterval(PrintWriter fout, double lower, double upper) {
double aux = 0.0;
int points = Config.realDrawnPrecision;
double inc = 1. / (double) points;
for (double i = 0.; i < (double) points; i++) {
if (i * inc < lower && (i * inc + inc) <= lower) {
fout.print(".");
} else if (i * inc < lower && (i * inc + inc) > lower) {
fout.print("o");
} // In the next if, the value is bigger than the lower
else if (i * inc < upper && (i * inc + inc) <= upper) {
fout.print("O");
} else if (i * inc < upper && (i * inc + inc) > upper) {
fout.print("o");
} else if (i * inc >= lower) {
fout.print(".");
} else {
fout.print("ERR. Case not covered!!");
}
}
fout.print(" | ");
}
/**
* Remove a quiz from a course. Also deletes all the quiz visualization files from the students'
* folder who is registered in the course. Caution: vizualisation file will be deleted eventhough
* it also relates to anther course if the student is also registered to that course. (FIX ME!)
* Throws InvalidDBRequestException if the quiz is not registered in the course, error occured
* during deletion, or other exception occured.
*
* @param quizName quiz name
* @param courseID course id (course number + instructor name)
* @throws InvalidDBRequestException
*/
public void deleteQuiz(String quizName, String courseID)
throws InvalidDBRequestException, FileFailureException {
try {
Class.forName(GaigsServer.DBDRIVER);
db =
DriverManager.getConnection(GaigsServer.DBURL, GaigsServer.DBLOGIN, GaigsServer.DBPASSWD);
Statement stmt = db.createStatement();
ResultSet rs;
int count = 0;
// check if quiz is used in the course
rs =
stmt.executeQuery(
"select test_name from courseTest where test_name = '"
+ quizName
+ "' and course_id = '"
+ courseID
+ "'");
if (!rs.next()) throw new InvalidDBRequestException("Quiz is not registered for the course");
else {
// remove quiz from course
count =
stmt.executeUpdate(
"delete from courseTest where course_id = '"
+ courseID
+ "' and test_name = '"
+ quizName
+ "'");
if (count != 1) throw new InvalidDBRequestException("Error occured during deletion");
else {
// delete quiz visualization files
rs =
stmt.executeQuery(
"select distinct unique_id, scores.user_login from scores, courseRoster "
+ "where courseRoster.user_login = scores.user_login "
+ "and course_id = '"
+ courseID
+ "' "
+ "and test_name = '"
+ quizName
+ "'");
while (rs.next()) {
deleteVisualization(rs.getString(1), rs.getString(2), quizName);
count =
stmt.executeUpdate(
"delete from scores where unique_id = " + rs.getString(1).trim());
}
// rewrite the menu for the course
rs =
stmt.executeQuery(
"select distinct menu_text, name, script_type, visual_type from test t, courseTest c "
+ "where t.name = c.test_name "
+ "and course_id = '"
+ courseID
+ "'");
PrintWriter fileOStream =
new PrintWriter(new FileOutputStream("./html_root/cat/" + courseID + ".list"));
while (rs.next()) {
if (debug)
System.out.println(
rs.getString(1).trim()
+ "\n"
+ rs.getString(2).trim()
+ " "
+ rs.getString(3).trim()
+ " "
+ rs.getString(4).trim().toLowerCase()
+ "\n****\n");
fileOStream.print(
rs.getString(1).trim()
+ "\n"
+ rs.getString(2).trim()
+ " "
+ rs.getString(3).trim()
+ " "
+ rs.getString(4).trim().toLowerCase()
+ "\n****\n");
}
fileOStream.flush();
fileOStream.close();
}
}
rs.close();
stmt.close();
db.close();
} catch (SQLException e) {
System.err.println("Invalid SQL in addQuiz: " + e.getMessage());
throw new InvalidDBRequestException("??? ");
} catch (ClassNotFoundException e) {
System.err.println("Driver Not Loaded");
throw new InvalidDBRequestException("Internal Server Error");
} catch (Exception e) {
System.err.println("Error in recreating menu for course: " + courseID);
System.err.println(e.getMessage());
throw new FileFailureException();
}
}
/**
* Add a quiz to a course if not already so. Also write the menu file for the course. Throws
* InvalidDBRequestException if quiz already in the course, error occured during insertion, or
* other exception occured. Throws FileFailureException if fail to append quiz to the menu.
*
* @param quizname the quiz name
* @param courseID the course id (course number + instructor name)
* @throws InvalidDBRequestException
*/
public void addQuiz(String quizName, String courseID)
throws InvalidDBRequestException, FileFailureException {
try {
Class.forName(GaigsServer.DBDRIVER);
db =
DriverManager.getConnection(GaigsServer.DBURL, GaigsServer.DBLOGIN, GaigsServer.DBPASSWD);
Statement stmt = db.createStatement();
Statement cstmt = db.createStatement();
ResultSet rs, courseRS;
int count = 0;
// get quiz info
courseRS =
cstmt.executeQuery(
"select menu_text, script_type, visual_type from test where name = '"
+ quizName
+ "'");
// check if quiz in the database
if (!courseRS.next())
throw new InvalidDBRequestException("Quiz is not registered in the database");
else {
// check if quiz already in the course
rs =
stmt.executeQuery(
"select test_name from courseTest where test_name = '"
+ quizName
+ "' and course_id = '"
+ courseID
+ "'");
if (rs.next()) throw new InvalidDBRequestException("Quiz is already added for the course");
else {
count =
stmt.executeUpdate(
"insert into courseTest (course_id, test_name) values ('"
+ courseID
+ "', '"
+ quizName
+ "')");
if (count != 1) throw new InvalidDBRequestException("Error occured during insertion");
else {
// append quiz info to the course menu
try {
PrintWriter fileOStream =
new PrintWriter(
new FileOutputStream("./html_root/cat/" + courseID + ".list", true));
if (debug)
System.out.println(
courseRS.getString(1).trim()
+ "\n"
+ quizName
+ " "
+ courseRS.getString(2).trim()
+ " "
+ courseRS.getString(3).trim().toLowerCase()
+ "\n****\n");
fileOStream.print(
courseRS.getString(1).trim()
+ "\n"
+ quizName
+ " "
+ courseRS.getString(2).trim()
+ " "
+ courseRS.getString(3).trim().toLowerCase()
+ "\n****\n");
fileOStream.flush();
fileOStream.close();
} catch (Exception e) {
System.err.println("Error in creating the menu: " + e.getMessage());
throw new FileFailureException("Error in creating the menu: " + e.getMessage());
}
}
}
}
courseRS.close();
rs.close();
stmt.close();
cstmt.close();
db.close();
} catch (SQLException e) {
System.err.println("Invalid SQL in addQuiz: " + e.getMessage());
throw new InvalidDBRequestException("??? ");
} catch (ClassNotFoundException e) {
System.err.println("Driver Not Loaded");
throw new InvalidDBRequestException("Internal Server Error");
}
}