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);
}
}
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);
}
}
