private static void createBrokenMarkerFile(@Nullable Throwable reason) {
final File brokenMarker = getCorruptionMarkerFile();
try {
final ByteArrayOutputStream out = new ByteArrayOutputStream();
final PrintStream stream = new PrintStream(out);
try {
new Exception().printStackTrace(stream);
if (reason != null) {
stream.print("\nReason:\n");
reason.printStackTrace(stream);
}
} finally {
stream.close();
}
LOG.info("Creating VFS corruption marker; Trace=\n" + out.toString());
final FileWriter writer = new FileWriter(brokenMarker);
try {
writer.write(
"These files are corrupted and must be rebuilt from the scratch on next startup");
} finally {
writer.close();
}
} catch (IOException e) {
// No luck.
}
}
private void saveSrc() {
fileChooser.resetChoosableFileFilters();
fileChooser.addChoosableFileFilter(asmFilter);
fileChooser.setFileFilter(asmFilter);
if (fileChooser.showSaveDialog(frame) == JFileChooser.APPROVE_OPTION) {
try {
File file = fileChooser.getSelectedFile();
if (fileChooser.getFileFilter() == asmFilter && !asmFilter.accept(file)) {
file = new File(file.getAbsolutePath() + asmFilter.getExtensions()[0]);
}
if (file.exists()) {
if (JOptionPane.showConfirmDialog(
frame, "File exists. Overwrite?", "Confirm", JOptionPane.YES_NO_OPTION)
!= JOptionPane.YES_OPTION) {
return;
}
}
PrintStream output = new PrintStream(file);
output.print(sourceTextarea.getText());
output.close();
} catch (IOException e1) {
JOptionPane.showMessageDialog(
frame, "Unable to open file", "Error", JOptionPane.ERROR_MESSAGE);
e1.printStackTrace();
}
}
}
// --------------------------------------------------
public void close() {
try {
is.close();
os.close();
socket.close();
responseArea.appendText("***Connection closed" + "\n");
} catch (IOException e) {
responseArea.appendText("IO Exception" + "\n");
}
}
private void saveDataToFile(File file) {
try {
PrintStream out = new PrintStream(new FileOutputStream(file));
// Print header line
out.print("Time");
for (Sequence seq : seqs) {
out.print("," + seq.name);
}
out.println();
// Print data lines
if (seqs.size() > 0 && seqs.get(0).size > 0) {
for (int i = 0; i < seqs.get(0).size; i++) {
double excelTime = toExcelTime(times.time(i));
out.print(String.format(Locale.ENGLISH, "%.6f", excelTime));
for (Sequence seq : seqs) {
out.print("," + getFormattedValue(seq.value(i), false));
}
out.println();
}
}
out.close();
JOptionPane.showMessageDialog(
this,
Resources.format(
Messages.FILE_CHOOSER_SAVED_FILE, file.getAbsolutePath(), file.length()));
} catch (IOException ex) {
String msg = ex.getLocalizedMessage();
String path = file.getAbsolutePath();
if (msg.startsWith(path)) {
msg = msg.substring(path.length()).trim();
}
JOptionPane.showMessageDialog(
this,
Resources.format(Messages.FILE_CHOOSER_SAVE_FAILED_MESSAGE, path, msg),
Messages.FILE_CHOOSER_SAVE_FAILED_TITLE,
JOptionPane.ERROR_MESSAGE);
}
}
private void doExportTimeTree() {
FileDialog dialog = new FileDialog(this, "Export Time Tree File...", FileDialog.SAVE);
dialog.setVisible(true);
if (dialog.getFile() != null) {
File file = new File(dialog.getDirectory(), dialog.getFile());
PrintStream ps = null;
try {
ps = new PrintStream(file);
writeTimeTreeFile(ps);
ps.close();
} catch (IOException ioe) {
JOptionPane.showMessageDialog(
this,
"Error writing tree file: " + ioe.getMessage(),
"Export Error",
JOptionPane.ERROR_MESSAGE);
}
}
}
public void applyAction(ActionEvent evt) {
String fileStr = getArg("file");
System.out.println("Output string " + fileStr);
if (FormatProperties.contains(getArg("format"))) {
if (parent instanceof AlignFrame) {
AlignFrame af = (AlignFrame) parent;
String outStr =
FormatAdapter.get(getArg("format").toUpperCase(), av.getAlignment().getSequences());
System.out.println(outStr + " " + fileStr);
try {
PrintStream ps =
new PrintStream(new BufferedOutputStream(new FileOutputStream(fileStr)));
fireStatusEvent("Saving file");
try {
Thread.sleep(500);
} catch (Exception ex2) {
}
ps.print(outStr);
ps.close();
fireStatusEvent("done");
fireJalActionEvent(new JalActionEvent(this, this, JalActionEvent.DONE));
} catch (IOException ex) {
fireStatusEvent("Can't open file", StatusEvent.ERROR);
System.out.println("Exception : " + ex);
}
} else {
fireStatusEvent("(Internal Error) Parent isn't Alignment Frame", StatusEvent.ERROR);
}
} else {
fireStatusEvent("Format not yet supported", StatusEvent.ERROR);
}
}
void setPassword() throws IOException {
PrintStream ps = new PrintStream(new FileOutputStream("password.txt"));
ps.println(password);
ps.close();
}
public void saveUnsaved() throws SaveAbortedException {
if (!saved) {
int option = 0;
if (loadedFile == null)
option =
JOptionPane.showConfirmDialog(
this,
new JLabel("Save changes to UNTITLED?"),
"Warning",
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.WARNING_MESSAGE);
else
option =
JOptionPane.showConfirmDialog(
this,
new JLabel("Save changes to " + loadedFile.getName() + "?"),
"Warning",
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.WARNING_MESSAGE);
if (option == JOptionPane.YES_OPTION) {
if (loadedFile == null) // SAVE NEW FILE
{
if (nameTF.getText().equals("")) {
JOptionPane.showMessageDialog(
this,
new JLabel("Please type in the Scale Name"),
"Warning",
JOptionPane.WARNING_MESSAGE);
throw new SaveAbortedException();
}
fileChooser.setFileFilter(filter);
int option2 = fileChooser.showSaveDialog(this);
if (option2 == JFileChooser.APPROVE_OPTION) {
File target = fileChooser.getSelectedFile();
try {
PrintStream stream = new PrintStream(new FileOutputStream(target), true);
save(stream);
stream.close();
} catch (Exception ex) {
JOptionPane.showMessageDialog(
this,
new JLabel("Error: " + ex.getMessage()),
"Error",
JOptionPane.ERROR_MESSAGE);
}
} else throw new SaveAbortedException();
;
} else // save LOADED FILE
{
try {
PrintStream stream = new PrintStream(new FileOutputStream(loadedFile), true);
save(stream);
stream.close();
} catch (Exception ex) {
JOptionPane.showMessageDialog(
this, new JLabel("Error: " + ex.getMessage()), "Error", JOptionPane.ERROR_MESSAGE);
}
}
} else if (option == JOptionPane.CANCEL_OPTION) throw new SaveAbortedException();
;
}
}
public void actionPerformed(ActionEvent e) {
JButton b = (JButton) e.getSource();
if (b.getText() == "PLAY") {
if (scoreP != null) scoreP.playScale(sp.getScale(), tempoP.getValue());
} else if (b.getText() == "New") {
try {
saveUnsaved();
} catch (SaveAbortedException ex) {
return;
}
sp.notes.removeAllElements();
sp.repaint();
nameTF.setText("");
loadedFile = null;
} else if (b.getText() == "Save") {
if (nameTF.getText().equals("")) {
JOptionPane.showMessageDialog(
this,
new JLabel("Please type in the Scale Name"),
"Warning",
JOptionPane.WARNING_MESSAGE);
return;
}
fileChooser.setFileFilter(filter);
int option = fileChooser.showSaveDialog(this);
if (option == JFileChooser.APPROVE_OPTION) {
File target = fileChooser.getSelectedFile();
if (target.getName().indexOf(".scl") == -1) target = new File(target.getPath() + ".scl");
try {
PrintStream stream = new PrintStream(new FileOutputStream(target), true);
save(stream);
stream.close();
} catch (Exception ex) {
JOptionPane.showMessageDialog(
this, new JLabel("Error: " + ex.getMessage()), "Error", JOptionPane.ERROR_MESSAGE);
}
}
} else if (b.getText() == "Load") {
try {
saveUnsaved();
} catch (SaveAbortedException ex) {
return;
}
fileChooser.setFileFilter(filter);
int option = fileChooser.showOpenDialog(this);
if (option == JFileChooser.APPROVE_OPTION) {
loadedFile = fileChooser.getSelectedFile();
SAXParserFactory factory = SAXParserFactory.newInstance();
ScaleParser handler = new ScaleParser(false);
try {
SAXParser parser = factory.newSAXParser();
parser.parse(loadedFile, handler);
// System.out.println("success");
} catch (Exception ex) {
// System.out.println("no!!!!!! exception: "+e);
// System.out.println(ex.getMessage());
ex.printStackTrace();
}
// -----now :P:P---------------
System.out.println("name: " + handler.getName());
nameTF.setText(handler.getName());
sp.notes.removeAllElements();
int[] scale = handler.getScale();
for (int i = 0; i < scale.length; i++) {
sp.addNote(scale[i]);
}
sp.repaint();
} else loadedFile = null;
}
}
