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();
}
}
}
/**
* Set current pen color. Default to black if null.
*
* @param c new pen color.
*/
public void setColor(Color c) {
if (c != null) {
m_localGraphicsState.setColor(c);
if (m_psGraphicsState.getColor().equals(c)) {
return;
}
m_psGraphicsState.setColor(c);
} else {
m_localGraphicsState.setColor(Color.black);
m_psGraphicsState.setColor(getColor());
}
m_printstream.print(getColor().getRed() / 255.0);
m_printstream.print(" ");
m_printstream.print(getColor().getGreen() / 255.0);
m_printstream.print(" ");
m_printstream.print(getColor().getBlue() / 255.0);
m_printstream.println(" setrgbcolor");
}
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);
}
}
/**
* PS see http://astronomy.swin.edu.au/~pbourke/geomformats/postscript/ Java
* http://show.docjava.com:8086/book/cgij/doc/ip/graphics/SimpleImageFrame.java.html
*/
public boolean drawImage(
Image img, int x, int y, int width, int height, Color bgcolor, ImageObserver observer) {
try {
// get data from image
int[] pixels = new int[width * height];
PixelGrabber grabber = new PixelGrabber(img, 0, 0, width, height, pixels, 0, width);
grabber.grabPixels();
ColorModel model = ColorModel.getRGBdefault();
// print data to ps
m_printstream.println("gsave");
m_printstream.println(
xTransform(xScale(x)) + " " + (yTransform(yScale(y)) - yScale(height)) + " translate");
m_printstream.println(xScale(width) + " " + yScale(height) + " scale");
m_printstream.println(
width + " " + height + " " + "8" + " [" + width + " 0 0 " + (-height) + " 0 " + height
+ "]");
m_printstream.println("{<");
int index;
for (int i = 0; i < height; i++) {
for (int j = 0; j < width; j++) {
index = i * width + j;
m_printstream.print(toHex(model.getRed(pixels[index])));
m_printstream.print(toHex(model.getGreen(pixels[index])));
m_printstream.print(toHex(model.getBlue(pixels[index])));
}
m_printstream.println();
}
m_printstream.println(">}");
m_printstream.println("false 3 colorimage");
m_printstream.println("grestore");
return true;
} catch (Exception e) {
e.printStackTrace();
return false;
}
}
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);
}
}
private void dumpEditorMarkupAndSelection(PrintStream dumpStream) {
dumpStream.println(mySearchResults.getFindModel());
if (myReplacementPreviewText != null) {
dumpStream.println("--");
dumpStream.println("Replacement Preview: " + myReplacementPreviewText);
}
dumpStream.println("--");
Editor editor = mySearchResults.getEditor();
RangeHighlighter[] highlighters = editor.getMarkupModel().getAllHighlighters();
List<Pair<Integer, Character>> ranges = new ArrayList<Pair<Integer, Character>>();
for (RangeHighlighter highlighter : highlighters) {
ranges.add(new Pair<Integer, Character>(highlighter.getStartOffset(), '['));
ranges.add(new Pair<Integer, Character>(highlighter.getEndOffset(), ']'));
}
SelectionModel selectionModel = editor.getSelectionModel();
if (selectionModel.getSelectionStart() != selectionModel.getSelectionEnd()) {
ranges.add(new Pair<Integer, Character>(selectionModel.getSelectionStart(), '<'));
ranges.add(new Pair<Integer, Character>(selectionModel.getSelectionEnd(), '>'));
}
ranges.add(new Pair<Integer, Character>(-1, '\n'));
ranges.add(new Pair<Integer, Character>(editor.getDocument().getTextLength() + 1, '\n'));
ContainerUtil.sort(
ranges,
new Comparator<Pair<Integer, Character>>() {
@Override
public int compare(Pair<Integer, Character> pair, Pair<Integer, Character> pair2) {
int res = pair.first - pair2.first;
if (res == 0) {
Character c1 = pair.second;
Character c2 = pair2.second;
if (c1 == '<' && c2 == '[') {
return 1;
} else if (c1 == '[' && c2 == '<') {
return -1;
}
return c1.compareTo(c2);
}
return res;
}
});
Document document = editor.getDocument();
for (int i = 0; i < ranges.size() - 1; ++i) {
Pair<Integer, Character> pair = ranges.get(i);
Pair<Integer, Character> pair1 = ranges.get(i + 1);
dumpStream.print(
pair.second
+ document.getText(
TextRange.create(
Math.max(pair.first, 0), Math.min(pair1.first, document.getTextLength()))));
}
dumpStream.println("\n--");
if (NotFound) {
dumpStream.println("Not Found");
dumpStream.println("--");
NotFound = false;
}
for (RangeHighlighter highlighter : highlighters) {
dumpStream.println(highlighter + " : " + highlighter.getTextAttributes());
}
dumpStream.println("------------");
}
private static void indent(PrintStream ps, int n) {
for (int i = 0; i < n; i++) ps.print(" ");
}
