private static void saveBookmarks(JTable table) {
BookmarksTableModel btm = (BookmarksTableModel) table.getModel();
List<Bookmark> bookmarks = btm.getData();
// get the path (null if none selected)
File selectedFile = DialogUtils.chooseFileForSave("Save Bookmarks", "Bookmarks.txt");
// set the genome
if (selectedFile != null) {
try {
saveBookmarks(selectedFile.getAbsolutePath(), bookmarks);
} catch (IOException ex) {
DialogUtils.displayError("Error", "Unable to save bookmarks: " + ex.getMessage());
}
}
}
private void loadBookmarks(JTable table) {
final BookmarksTableModel btm = (BookmarksTableModel) table.getModel();
List<Bookmark> bookmarks = btm.getData();
if (bookmarks.size() > 0) {
String message = "Clear existing bookmarks?";
String title = "Clear Bookmarks";
// display the JOptionPane showConfirmDialog
int reply = JOptionPane.showConfirmDialog(null, message, title, JOptionPane.YES_NO_OPTION);
if (reply == JOptionPane.YES_OPTION) {
btm.clearData();
BookmarkController.getInstance().clearBookmarks();
}
}
final File selectedFile = DialogUtils.chooseFileForOpen("Load Bookmarks", null, null);
// set the genome
if (selectedFile != null) {
int result =
JOptionPane.showOptionDialog(
null,
"Would you like to add padding to each bookmark range?",
"Add a margin?",
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE,
null,
null,
null);
final boolean addMargin = (result == JOptionPane.YES_OPTION);
Window w = SwingUtilities.getWindowAncestor(BookmarkSheet.this);
JOptionPane optionPane =
new JOptionPane(
"<html>Loading bookmarks from file.<br>This may take a moment.</html>",
JOptionPane.INFORMATION_MESSAGE,
JOptionPane.CANCEL_OPTION);
final JDialog dialog = new JDialog(w, "Loading Bookmarks", Dialog.ModalityType.MODELESS);
dialog.setContentPane(optionPane);
dialog.pack();
dialog.setLocationRelativeTo(w);
dialog.setVisible(true);
new Thread("BookmarkSheet.loadBookmarks") {
@Override
public void run() {
try {
BookmarkController.getInstance().addBookmarksFromFile(selectedFile, addMargin);
btm.fireTableDataChanged();
} catch (Exception ex) {
DialogUtils.displayError("Error", "Unable to load bookmarks: " + ex.getMessage());
} finally {
dialog.setVisible(false);
dialog.dispose();
}
}
}.start();
}
}
private void cancelButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_cancelButtonActionPerformed
if (DialogUtils.askYesNo("Confirm Cancel", "Are you sure you want to cancel?")
== DialogUtils.YES) {
formatter.cancel();
dispose();
}
} // GEN-LAST:event_cancelButtonActionPerformed
@Override
public void handleEvent(FormatEvent event) {
switch (event.getType()) {
case PROGRESS:
progressBar.setValue((int) (event.getProgress() * 100.0));
if (event.getSubTask() != null) {
statusLabel.setText(event.getSubTask());
}
break;
case COMPLETED:
setVisible(false);
if (GenomeController.getInstance().isGenomeLoaded()) {
if (formatter instanceof BAMToCoverage) {
// For coverage tracks, we report success, but don't offer to open the track.
DialogUtils.displayMessage(
"Format Successful",
String.format(
"<HTML>Format successful.<BR>Coverage will be available the next time you open <i>%s</i>.</HTML>",
formatter.getInputFile().getName()));
} else {
if (toLoadTrack
|| DialogUtils.askYesNo("Format Successful", "Format successful. Open track now?")
== DialogUtils.YES) {
try {
FrameController.getInstance()
.addTrackFromPath(formatter.getOutputFile().getAbsolutePath(), null, null);
} catch (Exception ex) {
}
}
}
} else {
DialogUtils.displayMessage(
"Format Successful",
"<HTML>Format successful. <BR>A genome must be loaded before you can open this track.</HTML>");
}
break;
case FAILED:
setVisible(false);
SavantFileFormatter.reportFormattingError(event.getError(), formatter.getInputFile());
break;
}
}
