@Override
public void actionPerformed(ActionEvent e) {
Object[] options = {"Cancel", "No!", "Ok"};
int n =
JOptionPane.showOptionDialog(
Application.get(),
"<html>Would you like to <b>delete</b> the selected data layer?",
"Delete values from heatmap",
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE,
null,
options,
options[2]);
if (n == 1 | n == 0) {
return;
}
AbstractCommand cmd =
new AbstractCommand() {
@Override
public void execute(IProgressMonitor monitor) throws CommandException {
getHeatmap().removeLayer(layer);
}
};
JobThread.execute(Application.get(), cmd);
Application.get().showNotification("Data layer deleted");
}
public void show(boolean forceShow) {
Properties tipProperties = Tips.get().getTips();
TipOfTheDayModel loadedTips = TipLoader.load(tipProperties);
final boolean settingsShowDialog = Settings.get().isShowTipsAtStartup();
JXTipOfTheDay tipOfTheDay = new JXTipOfTheDay(loadedTips);
Random generator = new Random();
int i = generator.nextInt(loadedTips.getTipCount());
tipOfTheDay.setCurrentTip(i);
tipOfTheDay.showDialog(
Application.get(),
new JXTipOfTheDay.ShowOnStartupChoice() {
@Override
public void setShowingOnStartup(boolean showOnStartup) {
Settings.get().setShowTipsAtStartup(showOnStartup);
}
@Override
public boolean isShowingOnStartup() {
return settingsShowDialog && !Settings.get().isProxyEnabled();
}
},
forceShow);
}
@Override
public void execute(IProgressMonitor monitor) throws CommandException {
super.execute(monitor);
if (Application.get().getEditorsPanel().getSelectedEditor() instanceof HeatmapEditor) {
final HeatmapEditor currentEditor =
(HeatmapEditor) Application.get().getEditorsPanel().getSelectedEditor();
if (saveAsFile != null) {
currentEditor.doSaveAsNoUI(monitor, saveAsFile, discardHidden, optimize, false);
} else if (save) {
currentEditor.doSave(heatmap.getLocator(), monitor, false);
}
if (currentEditor.doClose(false)) {
Application.get().getEditorsPanel().removeEditorNoUI(currentEditor);
}
}
}
@Override
public void actionPerformed(ActionEvent e) {
final EnsemblKeggModulesImporter importer = getImporter();
final ModulesImportWizard wz = getWizard(importer);
WizardDialog dlg = new WizardDialog(Application.get(), wz);
dlg.open();
if (dlg.isCancelled()) {
return;
}
JobThread.execute(
Application.get(),
new JobRunnable() {
@Override
public void run(IProgressMonitor monitor) {
try {
Map<String, String> descriptions = new HashMap<>();
IModuleMap mmap = importer.importMap(monitor, descriptions);
if (!monitor.isCancelled()) {
String extension = wz.getSaveFilePage().getFormat().getExtension();
File file = wz.getSaveFilePage().getPathAsFile();
IResourceLocator resourceLocator = new UrlResourceLocator(file);
if (GmxModuleMapFormat.EXTENSION.equals(extension)
|| GmtModuleMapFormat.EXTENSION.equals(extension)) {
IMatrix mat = MatrixUtils.moduleMapToMatrix(mmap);
IResourceFormat format =
ApplicationContext.getPersistenceManager()
.getFormat(extension, mat.getClass());
ApplicationContext.getPersistenceManager()
.store(resourceLocator, mat, format, monitor);
} else {
IResourceFormat format =
ApplicationContext.getPersistenceManager()
.getFormat(extension, mmap.getClass());
ApplicationContext.getPersistenceManager()
.store(resourceLocator, mmap, format, monitor);
}
// TODO Use PersistenceManager
String prefix = FilenameUtils.getName(file.getName());
file = new File(file.getParentFile(), prefix + "_annotations.tsv");
monitor.begin("Saving module annotations ...", mmap.getModules().size());
PrintWriter pw = new PrintWriter(file);
pw.println("id\tname");
for (String module : mmap.getModules()) {
pw.print(module);
pw.print('\t');
pw.println(descriptions.get(module));
monitor.worked(1);
}
pw.close();
} else {
setStatus("Operation cancelled");
}
} catch (Throwable ex) {
monitor.exception(ex);
}
}
});
}
