/**
* Output the specified character to the output stream without manipulating the current buffer.
*/
private final void printCharacter(final int c) throws IOException {
if (c == '\t') {
char cbuf[] = new char[TAB_WIDTH];
Arrays.fill(cbuf, ' ');
out.write(cbuf);
return;
}
out.write(c);
}
/**
* Move the cursor <i>where</i> characters, withough checking the current buffer.
*
* @see #where
* @param where the number of characters to move to the right or left.
*/
private final void moveInternal(final int where) throws IOException {
// debug ("move cursor " + where + " ("
// + buf.cursor + " => " + (buf.cursor + where) + ")");
buf.cursor += where;
char c;
if (where < 0) {
int len = 0;
for (int i = buf.cursor; i < buf.cursor - where; i++) {
if (buf.getBuffer().charAt(i) == '\t') len += TAB_WIDTH;
else len++;
}
char cbuf[] = new char[len];
Arrays.fill(cbuf, BACKSPACE);
out.write(cbuf);
return;
} else if (buf.cursor == 0) {
return;
} else if (mask != null) {
c = mask.charValue();
} else {
printCharacters(buf.buffer.substring(buf.cursor - where, buf.cursor).toCharArray());
return;
}
// null character mask: don't output anything
if (NULL_MASK.equals(mask)) {
return;
}
printCharacters(c, Math.abs(where));
}
/** The listener method. */
public void actionPerformed(ActionEvent event) {
Object source = event.getSource();
if (source == b1) // click button
{
try {
String message = tf.getText();
server.sendPrivateMessage(parent, selfIdentity, message);
ta.append("<" + parent.getUserName() + ">: " + message + lineSeparator);
ta.setCaretPosition(ta.getText().length());
tf.setText("");
} catch (RemoteException ex) {
System.out.print("Exception encountered while sending" + " private message.");
}
}
if (source == tf) // press return
{
try {
String message = tf.getText();
server.sendPrivateMessage(parent, selfIdentity, message);
ta.append("<" + parent.getUserName() + ">: " + message + lineSeparator);
ta.setCaretPosition(ta.getText().length());
tf.setText("");
} catch (RemoteException ex) {
System.out.print("Exception encountered while sending" + " private message.");
}
}
if (source == jMenuItem3) {
JFileChooser fileChooser = new JFileChooser();
fileChooser.setDialogTitle("Choose or create a new file to store the conversation");
fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
fileChooser.setDoubleBuffered(true);
fileChooser.showOpenDialog(this);
File file = fileChooser.getSelectedFile();
try {
if (file != null) {
Writer writer = new BufferedWriter(new FileWriter(file));
writer.write(ta.getText());
writer.flush();
writer.close();
}
} catch (IOException ex) {
System.out.println("Can't write to file. " + ex);
}
}
if (source == jMenuItem4) {
selfRemove();
this.dispose();
}
}
private void writeWeights(
String orig, GeneBranch from, GeneBranch to, String edgeType, Writer writer)
throws IOException {
Set<String> dwstr = to.getAllGenes();
dwstr.retainAll(downstream.get(orig));
assert !dwstr.isEmpty();
double cumPval = calcPVal(orig, dwstr);
boolean upreg = calcChangeDirection(orig, to.gene);
String key = from.gene + " " + edgeType + " " + to.gene;
writer.write("edge\t" + key + "\tcolor\t" + val2Color(cumPval, 0) + "\n");
writer.write("edge\t" + key + "\twidth\t2\n");
if (affectedDw.get(orig).contains(to.gene)) {
double pval = calcPVal(orig, Collections.singleton(to.gene));
writer.write("node\t" + to.gene + "\tcolor\t" + val2Color(pval, upreg ? 1 : -1) + "\n");
} else {
writer.write("node\t" + to.gene + "\tcolor\t255 255 255\n");
}
}
@Override
@SuppressWarnings("SleepWhileHoldingLock")
public void run() {
try {
// initialize the statusbar
status.removeAll();
JProgressBar progress = new JProgressBar();
progress.setMinimum(0);
progress.setMaximum(doc.getLength());
status.add(progress);
status.revalidate();
// start writing
Writer out = new FileWriter(f);
Segment text = new Segment();
text.setPartialReturn(true);
int charsLeft = doc.getLength();
int offset = 0;
while (charsLeft > 0) {
doc.getText(offset, Math.min(4096, charsLeft), text);
out.write(text.array, text.offset, text.count);
charsLeft -= text.count;
offset += text.count;
progress.setValue(offset);
try {
Thread.sleep(10);
} catch (InterruptedException e) {
Logger.getLogger(FileSaver.class.getName()).log(Level.SEVERE, null, e);
}
}
out.flush();
out.close();
} catch (IOException e) {
final String msg = e.getMessage();
SwingUtilities.invokeLater(
new Runnable() {
public void run() {
JOptionPane.showMessageDialog(
getFrame(),
"Could not save file: " + msg,
"Error saving file",
JOptionPane.ERROR_MESSAGE);
}
});
} catch (BadLocationException e) {
System.err.println(e.getMessage());
}
// we are done... get rid of progressbar
status.removeAll();
status.revalidate();
}
/**
* Create a file that contains the specified message
*
* @param root a git repository root
* @param message a message to write
* @return a file reference
* @throws IOException if file cannot be created
*/
private File createMessageFile(VirtualFile root, final String message) throws IOException {
// filter comment lines
File file = FileUtil.createTempFile(GIT_COMMIT_MSG_FILE_PREFIX, GIT_COMMIT_MSG_FILE_EXT);
file.deleteOnExit();
@NonNls String encoding = GitConfigUtil.getCommitEncoding(myProject, root);
Writer out = new OutputStreamWriter(new FileOutputStream(file), encoding);
try {
out.write(message);
} finally {
out.close();
}
return file;
}
public void write(Writer out, Document doc, int pos, int len, Map<String, String> copiedImgs)
throws IOException, BadLocationException {
Debug.log(9, "SikuliEditorKit.write %d %d", pos, len);
DefaultStyledDocument sdoc = (DefaultStyledDocument) doc;
int i = pos;
String absPath;
while (i < pos + len) {
Element e = sdoc.getCharacterElement(i);
int start = e.getStartOffset(), end = e.getEndOffset();
if (e.getName().equals(StyleConstants.ComponentElementName)) {
// A image argument to be filled
AttributeSet attr = e.getAttributes();
Component com = StyleConstants.getComponent(attr);
out.write(com.toString());
if (copiedImgs != null
&& (com instanceof EditorPatternButton || com instanceof EditorPatternLabel)) {
if (com instanceof EditorPatternButton) {
absPath = ((EditorPatternButton) com).getFilename();
} else {
absPath = ((EditorPatternLabel) com).getFile();
}
String fname = (new File(absPath)).getName();
copiedImgs.put(fname, absPath);
Debug.log(3, "save image for copy&paste: " + fname + " -> " + absPath);
}
} else {
if (start < pos) {
start = pos;
}
if (end > pos + len) {
end = pos + len;
}
out.write(doc.getText(start, end - start));
}
i = end;
}
out.close();
}
public boolean continueShellProcess(Process proc) {
if (progIndicator.isAborted()) {
try {
Writer stream;
stream = new OutputStreamWriter((BufferedOutputStream) proc.getOutputStream());
stream.write((char) 3);
stream.flush();
stream.close();
} catch (IOException e) {
}
return false;
}
return true;
}
private void writeSelf(
String origTarget, GeneBranch currentParent, GeneBranch down, Writer writer1, Writer writer2)
throws IOException {
if (!down.isSelected()) return;
String edgeTag;
if (down.isLeaf() || travExp.getUpstream(down.gene).contains(currentParent)) {
edgeTag = SIFEnum.CONTROLS_EXPRESSION_OF.getTag();
} else edgeTag = SIFEnum.CONTROLS_STATE_CHANGE_OF.getTag();
writer1.write(currentParent.gene + "\t" + edgeTag + "\t" + down.gene + "\n");
writeWeights(origTarget, currentParent, down, edgeTag, writer2);
writeBranches(origTarget, down, writer1, writer2);
}
/**
* Output the specified characters to the output stream without manipulating the current buffer.
*/
private final void printCharacters(final char[] c) throws IOException {
int len = 0;
for (int i = 0; i < c.length; i++)
if (c[i] == '\t') len += TAB_WIDTH;
else len++;
char cbuf[];
if (len == c.length) cbuf = c;
else {
cbuf = new char[len];
int pos = 0;
for (int i = 0; i < c.length; i++) {
if (c[i] == '\t') {
Arrays.fill(cbuf, pos, pos + TAB_WIDTH, ' ');
pos += TAB_WIDTH;
} else {
cbuf[pos] = c[i];
pos++;
}
}
}
out.write(cbuf);
}
/**
* Read a line from the <i>in</i> {@link InputStream}, and return the line (without any trailing
* newlines).
*
* @param prompt the prompt to issue to the console, may be null.
* @return a line that is read from the terminal, or null if there was null input (e.g.,
* <i>CTRL-D</i> was pressed).
*/
public String readLine(final String prompt, final Character mask) throws IOException {
this.mask = mask;
if (prompt != null) this.prompt = prompt;
try {
terminal.beforeReadLine(this, this.prompt, mask);
if ((this.prompt != null) && (this.prompt.length() > 0)) {
out.write(this.prompt);
out.flush();
}
// if the terminal is unsupported, just use plain-java reading
if (!terminal.isSupported()) {
return readLine(in);
}
while (true) {
int[] next = readBinding();
if (next == null) {
return null;
}
int c = next[0];
int code = next[1];
if (c == -1) {
return null;
}
boolean success = true;
switch (code) {
case EXIT: // ctrl-d
if (buf.buffer.length() == 0) {
return null;
}
case COMPLETE: // tab
success = complete();
break;
case MOVE_TO_BEG:
success = setCursorPosition(0);
break;
case KILL_LINE: // CTRL-K
success = killLine();
break;
case CLEAR_SCREEN: // CTRL-L
success = clearScreen();
break;
case KILL_LINE_PREV: // CTRL-U
success = resetLine();
break;
case NEWLINE: // enter
moveToEnd();
printNewline(); // output newline
return finishBuffer();
case DELETE_PREV_CHAR: // backspace
success = backspace();
break;
case DELETE_NEXT_CHAR: // delete
success = deleteCurrentCharacter();
break;
case MOVE_TO_END:
success = moveToEnd();
break;
case PREV_CHAR:
success = moveCursor(-1) != 0;
break;
case NEXT_CHAR:
success = moveCursor(1) != 0;
break;
case NEXT_HISTORY:
success = moveHistory(true);
break;
case PREV_HISTORY:
success = moveHistory(false);
break;
case REDISPLAY:
break;
case PASTE:
success = paste();
break;
case DELETE_PREV_WORD:
success = deletePreviousWord();
break;
case PREV_WORD:
success = previousWord();
break;
case NEXT_WORD:
success = nextWord();
break;
case START_OF_HISTORY:
success = history.moveToFirstEntry();
if (success) setBuffer(history.current());
break;
case END_OF_HISTORY:
success = history.moveToLastEntry();
if (success) setBuffer(history.current());
break;
case CLEAR_LINE:
moveInternal(-(buf.buffer.length()));
killLine();
break;
case INSERT:
buf.setOvertyping(!buf.isOvertyping());
break;
case UNKNOWN:
default:
if (c != 0) { // ignore null chars
ActionListener action =
(ActionListener) triggeredActions.get(new Character((char) c));
if (action != null) action.actionPerformed(null);
else putChar(c, true);
} else success = false;
}
if (!(success)) {
beep();
}
flushConsole();
}
} finally {
terminal.afterReadLine(this, this.prompt, mask);
}
}
public NewUser() {
super("Registration");
create = new JButton("Create");
newUserPanel = new JPanel();
txuserer = new JTextField(15);
passer = new JPasswordField(15);
setSize(300, 200);
setLocation(500, 280);
newUserPanel.setLayout(null);
txuserer.setBounds(70, 30, 150, 20);
passer.setBounds(70, 65, 150, 20);
create.setBounds(110, 100, 80, 20);
newUserPanel.add(create);
newUserPanel.add(txuserer);
newUserPanel.add(passer);
getContentPane().add(newUserPanel);
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
setVisible(true);
Writer writer = null;
File check = new File("userPass.txt");
if (check.exists()) {
// Checks if the file exists. will not add anything if the file does exist.
} else {
try {
File texting = new File("userPass.txt");
writer = new BufferedWriter(new FileWriter(texting));
writer.write("message");
} catch (IOException e) {
e.printStackTrace();
}
}
create.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
try {
File file = new File("userPass.txt");
Scanner scan = new Scanner(file);
;
FileWriter filewrite = new FileWriter(file, true);
String usertxter = " ";
String passtxter = " ";
String punamer = txuserer.getText();
String ppaswder = passer.getText();
while (scan.hasNext()) {
usertxter = scan.nextLine();
passtxter = scan.nextLine();
}
if (punamer.equals(usertxter) && ppaswder.equals(passtxter)) {
JOptionPane.showMessageDialog(null, "Username is already in use");
txuserer.setText("");
passer.setText("");
txuserer.requestFocus();
} else if (punamer.equals("") && ppaswder.equals("")) {
JOptionPane.showMessageDialog(null, "Please insert Username and Password");
} else {
filewrite.write(punamer + "\r\n" + ppaswder + "\r\n");
filewrite.close();
JOptionPane.showMessageDialog(null, "Account has been created.");
dispose();
login log = new login();
}
} catch (IOException d) {
d.printStackTrace();
}
}
});
}