label.successfully_loaded_file = Successfully loaded file {0}
label.successfully_loaded_matrix = Successfully loaded score matrix {0}
label.successfully_saved_to_file_in_format = Successfully saved to file: {0} in {1} format.
+label.successfully_printed_to_stdout_in_format = Successfully printed to STDOUT in {0} format.
label.copied_sequences_to_clipboard = Copied {0} sequences to clipboard.
label.check_file_matches_sequence_ids_alignment = Check that the file matches sequence IDs in the alignment.
label.problem_reading_tcoffee_score_file = Problem reading T-COFFEE score file
label.interpret_tempfac_as = Interpret Temperature Factor as
label.add_pae_matrix_file = Add PAE matrix file
label.nothing_selected = Nothing selected
-prompt.google_analytics_title = Jalview Usage Statistics
-prompt.google_analytics = Do you want to help make Jalview better by enabling the collection of usage statistics with Google Analytics?\nYou can enable or disable usage tracking in the preferences.
+prompt.analytics_title = Jalview Usage Statistics
+prompt.analytics = Do you want to help make Jalview better by enabling the collection of usage statistics with Plausible analytics?\nYou can enable or disable usage tracking in the preferences.
label.working_ellipsis = Working ...
action.show_groups_on_matrix = Show groups on matrix
action.show_groups_on_matrix_tooltip = When enabled, clusters defined on the matrix's associated tree or below the assigned threshold are shown as different colours on the matrix annotation row
action.cluster_matrix = Cluster matrix
action.clustering_matrix_for = Calculating tree for matrix {0} and clustering at {1}
action.cluster_matrix_tooltip = Computes an average distance tree for the matrix and displays it
-
+ label.all_known_alignment_files = All known alignment files
label.successfully_loaded_file = Fichero cargado exitosamente {0}
label.successfully_loaded_matrix = Matriz cargada exitosamente {0}
label.successfully_saved_to_file_in_format = Guardado exitosamente en el fichero: {0} en formato {1}.
+label.successfully_printed_to_stdout_in_format = Impresso exitosamente al STDOUT en formato {0}.
label.copied_sequences_to_clipboard = Copiadas {0} secuencias en el portapapeles.
label.check_file_matches_sequence_ids_alignment = Comprobar que el fichero coincide con el ID de la secuencia en el alineamiento.
label.problem_reading_tcoffee_score_file = Problema de lectura del fichero de puntuaciones T-COFFEE
label.tftype_plddt = pLDDT
label.add_pae_matrix_file = Añadir un fichero de matriz PAE
label.nothing_selected = Nada seleccionado
-prompt.google_analytics_title = Jalview Estadísticas de Uso
-prompt.google_analytics = ¿Quiere ayudar a mejorar Jalview habilitando la recopilación de estadísticas de uso con Google Analytics?\nPuede habilitar o deshabilitar el seguimiento de uso en las preferencias.
+prompt.analytics_title = Jalview Estadísticas de Uso
+prompt.analytics = ¿Quiere ayudar a mejorar Jalview habilitando la recopilación de estadísticas de uso con análisis Plausible?\nPuede habilitar o deshabilitar el seguimiento de uso en las preferencias.
+ label.all_known_alignment_files = Todos los archivos de alineación conocidos
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
+import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
// if (viewport.cursorMode)
// {
// alignPanel.seqPanel.insertNucAtCursor(false,"A");
- // //System.out.println("A");
+ // //jalview.bin.Console.outPrintln("A");
// }
// break;
/*
* case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
- * System.out.println("closing bracket"); } break;
+ * jalview.bin.Console.outPrintln("closing bracket"); } break;
*/
case KeyEvent.VK_DELETE:
case KeyEvent.VK_BACK_SPACE:
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- // // System.out.println("Discoverer property change.");
+ // // jalview.bin.Console.outPrintln("Discoverer property
+ // change.");
// if (evt.getPropertyName().equals("services"))
{
SwingUtilities.invokeLater(new Runnable()
@Override
public void run()
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Rebuild WS Menu for service change");
BuildWebServiceMenu();
}
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
- // System.out.println("deregistering discoverer listener");
+ // jalview.bin.Console.outPrintln("deregistering discoverer listener");
Desktop.instance.removeJalviewPropertyChangeListener("services",
thisListener);
closeMenuItem_actionPerformed(true);
*/
public void saveAlignment(String file, FileFormatI format)
{
+ saveAlignment(file, format, false);
+ }
+
+ public void saveAlignment(String file, FileFormatI format, boolean stdout)
+ {
lastSaveSuccessful = true;
- lastFilenameSaved = file;
+ if (!stdout)
+ {
+ lastFilenameSaved = file;
+ }
lastFormatSaved = format;
if (FileFormat.Jalview.equals(format))
shortName = shortName
.substring(shortName.lastIndexOf(File.separatorChar) + 1);
}
+ // TODO deal with stdout=true
lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
shortName);
else
{
// create backupfiles object and get new temp filename destination
- boolean doBackup = BackupFiles.getEnabled();
+ boolean doBackup = BackupFiles.getEnabled() && !stdout;
BackupFiles backupfiles = null;
if (doBackup)
{
String tempFilePath = doBackup ? backupfiles.getTempFilePath()
: file;
Console.trace("ALIGNFRAME setting PrintWriter");
- PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
+ PrintWriter out = stdout
+ ? new PrintWriter(new OutputStreamWriter(System.out))
+ : new PrintWriter(new FileWriter(tempFilePath));
if (backupfiles != null)
{
}
out.print(output);
- Console.trace("ALIGNFRAME about to close file");
- out.close();
- Console.trace("ALIGNFRAME closed file");
- AlignFrame.this.setTitle(file);
- statusBar.setText(MessageManager.formatMessage(
- "label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format.getName() }));
+ out.flush();
+ if (!stdout)
+ {
+ Console.trace("ALIGNFRAME about to close file");
+ out.close();
+ Console.trace("ALIGNFRAME closed file");
+ }
+ AlignFrame.this.setTitle(stdout ? "STDOUT" : file);
+ if (stdout)
+ {
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_printed_to_stdout_in_format",
+ new Object[]
+ { format.getName() }));
+ }
+ else
+ {
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format",
+ new Object[]
+ { fileName, format.getName() }));
+ }
lastSaveSuccessful = true;
} catch (IOException e)
{
} catch (Exception ex)
{
ex.printStackTrace();
- System.out.println("Exception whilst pasting: " + ex);
+ jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex);
// could be anything being pasted in here
}
} catch (Exception ex)
{
ex.printStackTrace();
- System.out.println("Exception whilst pasting: " + ex);
+ jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex);
// could be anything being pasted in here
} catch (OutOfMemoryError oom)
{
@Override
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
- scaleAbove.setVisible(wrapMenuItem.isSelected());
- scaleLeft.setVisible(wrapMenuItem.isSelected());
- scaleRight.setVisible(wrapMenuItem.isSelected());
- viewport.setWrapAlignment(wrapMenuItem.isSelected());
+ setWrapFormat(wrapMenuItem.isSelected(), false);
+ }
+
+ public void setWrapFormat(boolean b, boolean setMenuItem)
+ {
+ scaleAbove.setVisible(b);
+ scaleLeft.setVisible(b);
+ scaleRight.setVisible(b);
+ viewport.setWrapAlignment(b);
alignPanel.updateLayout();
+ if (setMenuItem)
+ {
+ wrapMenuItem.setSelected(b);
+ }
}
@Override
}
JInternalFrame frame = new JInternalFrame();
-
+ frame.setFrameIcon(null);
frame.getContentPane().add(new JScrollPane(pane));
Desktop.addInternalFrame(frame, MessageManager
return alignPanel.overviewPanel;
}
JInternalFrame frame = new JInternalFrame();
+ frame.setFrameIcon(null);
final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
showHidden);
frame.setContentPane(overview);
Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
frame.getHeight(), true, true);
- frame.setFrameIcon(null);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
final AlignmentPanel thePanel = this.alignPanel;
else
{
JInternalFrame frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(new PairwiseAlignPanel(viewport));
Desktop.addInternalFrame(frame,
MessageManager.getString("action.pairwise_alignment"), 600,
{
NewickFile fin = new NewickFile(
new FileParse(cm.getNewick(), DataSourceType.PASTE));
- String title = cm.getAnnotLabel() + " " + cm.getTreeMethod() + " tree"
- + aa.sequenceRef != null
+ String title = aa.label + " " + cm.getTreeMethod() + " tree"
+ + (aa.sequenceRef != null
? (" for " + aa.sequenceRef.getDisplayId(false))
- : "";
+ : "");
showColumnWiseTree(fin, aa, title, w, h, x, y);
} catch (Throwable xx)
{
return null;
}
- TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
+ TreePanel tp = new TreePanel(alignPanel, nf, aa, treeTitle);
tp.setSize(w, h);
tp.setLocation(x, y);
}
- Desktop.addInternalFrame(tp, title, w, h);
+ Desktop.addInternalFrame(tp, treeTitle, w, h);
return tp;
} catch (Throwable xx)
{
{
try
{
- System.err.println("Waiting for building menu to finish.");
+ jalview.bin.Console
+ .errPrintln("Waiting for building menu to finish.");
Thread.sleep(10);
} catch (Exception e)
{
final List<JMenuItem> legacyItems = new ArrayList<>();
try
{
- // System.err.println("Building ws menu again "
+ // jalview.bin.Console.errPrintln("Building ws menu again "
// + Thread.currentThread());
// TODO: add support for context dependent disabling of services based
// on
Desktop.instance);
if (pe != null)
{
- System.err.println("Associated file : "
+ jalview.bin.Console.errPrintln("Associated file : "
+ (fm[0].toString()) + " with "
+ toassoc.getDisplayId(true));
assocfiles++;
viewport.getAlignment()));
} catch (Exception ex)
{
- System.err.println(ex.getMessage());
+ jalview.bin.Console.errPrintln(ex.getMessage());
return;
}
}
console.runScript();
} catch (Exception ex)
{
- System.err.println((ex.toString()));
+ jalview.bin.Console.errPrintln((ex.toString()));
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_run_groovy_script"),
MessageManager.getString("label.groovy_support_failed"),
}
else
{
- System.err.println("Can't run Groovy script as console not found");
+ jalview.bin.Console
+ .errPrintln("Can't run Groovy script as console not found");
}
}
* Send this message to stderr as the warning that follows (due to
* reflection) also goes to stderr.
*/
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Linux platform only! You may have the following warning next: \"WARNING: An illegal reflective access operation has occurred\"\nThis is expected and cannot be avoided, sorry about that.");
}
final String awtAppClassName = "awtAppClassName";
}
// Thread off a new instance of the file chooser - this reduces the time
- // it
- // takes to open it later on.
+ // it takes to open it later on.
new Thread(new Runnable()
{
@Override
public void run()
{
jalview.bin.Console.debug("Filechooser init thread started.");
- String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ String fileFormat = FileLoader.getUseDefaultFileFormat()
+ ? Cache.getProperty("DEFAULT_FILE_FORMAT")
+ : null;
JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
fileFormat);
jalview.bin.Console.debug("Filechooser init thread finished.");
}
} catch (Exception ex)
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"Unable to paste alignment from system clipboard:\n" + ex);
}
}
setKeyBindings(frame);
- desktop.add(frame);
+ // Since the latest FlatLaf patch, we occasionally have problems showing structureViewer frames...
+ int tries=3;
+ boolean shown=false;
+ Exception last=null;
+ do
+ {
+ try
+ {
+ desktop.add(frame);
+ shown=true;
+ } catch (IllegalArgumentException iaex)
+ {
+ last=iaex;
+ tries--;
+ jalview.bin.Console.info(
+ "Squashed IllegalArgument Exception (" + tries + " left) for "+frame.getTitle(),
+ iaex);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException iex)
+ {
+ }
+ ;
+ }
+ } while (!shown && tries > 0);
+ if (!shown)
+ {
+ jalview.bin.Console.error("Serious Problem whilst showing window "+frame.getTitle(),last);
+ }
windowMenu.add(menuItem);
@Override
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
- String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ String fileFormat = FileLoader.getUseDefaultFileFormat()
+ ? Cache.getProperty("DEFAULT_FILE_FORMAT")
+ : null;
JalviewFileChooser chooser = JalviewFileChooser.forRead(
Cache.getProperty("LAST_DIRECTORY"), fileFormat,
BackupFiles.getEnabled());
}
} catch (Exception ex)
{
- System.err.println("Error opening help: " + ex.getMessage());
+ jalview.bin.Console.errPrintln("Error opening help: " + ex.getMessage());
}
}
boolean autoSave = projectFile != null && !saveAs
&& BackupFiles.getEnabled();
- // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
+ // jalview.bin.Console.outPrintln("autoSave="+autoSave+", projectFile='"+projectFile+"',
// saveAs="+saveAs+", Backups
// "+(BackupFiles.getEnabled()?"enabled":"disabled"));
{
if (Platform.isAMacAndNotJS())
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Please ignore plist error - occurs due to problem with java 8 on OSX");
}
}
{
Desktop.instance.closeAll_actionPerformed(null);
Desktop.instance.setVisible(false);
- Desktop.instance.dispose();
+ Desktop us = Desktop.instance;
Desktop.instance = null;
+ // call dispose in a separate thread - try to avoid indirect deadlocks
+ new Thread(new Runnable() {
+ @Override
+ public void run()
+ {
+ ExecutorService dex = us.dialogExecutor;
+ if (dex!=null) {
+ dex.shutdownNow();
+ us.dialogExecutor=null;
+ us.block.drainPermits();
+ }
+ us.dispose();
+ }
+ }).start();
}
}
if (Platform.isJS())
{
details = new JInternalFrame();
+ details.setFrameIcon(null);
JPanel panel = new JPanel(new BorderLayout());
panel.setOpaque(true);
panel.setBackground(Color.white);
protected void addReferenceAnnotations_actionPerformed(
Map<SequenceI, List<AlignmentAnnotation>> candidates)
{
- final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
final AlignmentI alignment = this.ap.getAlignment();
AlignmentUtils.addReferenceAnnotations(candidates, alignment,
- selectionGroup);
+ null);
refresh();
}
pane.setBackground(Color.WHITE);
pane.add(textLabel, BorderLayout.NORTH);
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.getContentPane().add(new JScrollPane(pane));
}
else
String[] omitHidden = null;
- System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
+ jalview.bin.Console.outPrintln("PROMPT USER HERE"); // TODO: decide if a prompt happens
// or we simply trust the user wants
// wysiwig behaviour
private File selectedFile;
+ private static boolean useDefaultFileFormat = false;
+
/**
* default constructor always raised errors in GUI dialog boxes
*/
if (format == null)
{
Desktop.instance.stopLoading();
- System.err.println("The input file \"" + file
+ jalview.bin.Console.errPrintln("The input file \"" + file
+ "\" has null or unidentifiable data content!");
if (!Jalview.isHeadlessMode())
{
if (source != null)
{
// Tell the user (developer?) that this is going to cause a problem
- System.err.println(
+ jalview.bin.Console.errPrintln(
"IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
// We read the data anyway - it might make sense.
}
}
else
{
- System.err.println(errorMessage);
+ jalview.bin.Console.errPrintln(errorMessage);
}
}
}
} catch (Exception er)
{
- System.err.println("Exception whilst opening file '" + file);
+ jalview.bin.Console.errPrintln("Exception whilst opening file '" + file);
er.printStackTrace();
if (raiseGUI)
{
}
});
}
- System.err.println("Out of memory loading file " + file + "!!");
+ jalview.bin.Console.errPrintln("Out of memory loading file " + file + "!!");
}
loadtime += System.currentTimeMillis();
{
AlignmentI al = alignFrame.getViewport().getAlignment();
- System.out.println("Loaded '" + title + "' in "
+ jalview.bin.Console.outPrintln("Loaded '" + title + "' in "
+ (loadtime / 1000.0) + "s, took an additional "
+ (1.0 * memused / (1024.0 * 1024.0)) + " MB ("
+ al.getHeight() + " seqs by " + al.getWidth() + " cols)");
{
// report that we didn't load anything probably due to an out of memory
// error
- System.out.println("Failed to load '" + title + "' in "
+ jalview.bin.Console.outPrintln("Failed to load '" + title + "' in "
+ (loadtime / 1000.0) + "s, took an additional "
+ (1.0 * memused / (1024.0 * 1024.0))
+ " MB (alignment is null)");
}
this.setShouldBeSaved();
+ // after first file loaded we revert to assuming a default file format
+ useDefaultFileFormat = true;
}
/**
QuitHandler.Message.UNSAVED_ALIGNMENTS);
}
+ public static boolean getUseDefaultFileFormat()
+ {
+ return useDefaultFileFormat;
+ }
+
}
import java.util.Vector;
import javax.swing.BoxLayout;
import javax.swing.JCheckBox;
import javax.swing.JDialog;
import javax.swing.JFileChooser;
+ import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
+ import javax.swing.ListCellRenderer;
import javax.swing.SpringLayout;
+ import javax.swing.SwingConstants;
+ import javax.swing.SwingUtilities;
+ import javax.swing.border.TitledBorder;
import javax.swing.filechooser.FileFilter;
import javax.swing.plaf.basic.BasicFileChooserUI;
}
else
{
- System.err.println("JalviewFileChooser arguments mismatch: "
+ jalview.bin.Console.errPrintln("JalviewFileChooser arguments mismatch: "
+ extensions + ", " + descs);
}
}
// file filters to fix bug on Mac OSX
setAcceptAllFileFilterUsed(acceptAny);
+ // add a "All known alignment files" option
+ List<String> allExtensions = new ArrayList<>();
+ for (String[] format : formats)
+ {
+ String[] extensions = format[0].split(",");
+ for (String ext : extensions)
+ {
+ if (!allExtensions.contains(ext))
+ {
+ allExtensions.add(ext);
+ }
+ }
+ }
+ allExtensions.sort(null);
+ JalviewFileFilter alljvf = new JalviewFileFilter(
+ allExtensions.toArray(new String[] {}),
+ MessageManager.getString("label.all_known_alignment_files"));
+ alljvf.setExtensionListInDescription(false);
+ addChoosableFileFilter(alljvf);
+
+ if (selected == null)
+ {
+ chosen = alljvf;
+ }
+
for (String[] format : formats)
{
JalviewFileFilter jvf = new JalviewFileFilter(format[0], format[1]);
return FileFormats.getInstance().forName(format);
} catch (IllegalArgumentException e)
{
- System.err.println("Unexpected format: " + format);
+ jalview.bin.Console.errPrintln("Unexpected format: " + format);
}
}
return null;
}
} catch (Throwable x)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Unexpected exception when trying to get filename.");
x.printStackTrace();
}
}
}
+ if (!file.isAbsolute() && file.exists())
+ {
+ file = file.getAbsoluteFile();
+ }
+
setSelectedFile(file);
}
}
}
list = new JList<>(recent);
-
- DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
- dlcr.setHorizontalAlignment(DefaultListCellRenderer.RIGHT);
- list.setCellRenderer(dlcr);
+ list.setCellRenderer(new recentlyOpenedCellRenderer());
list.addMouseListener(new MouseAdapter()
{
}
});
- this.setBorder(new javax.swing.border.TitledBorder(
- MessageManager.getString("label.recently_opened")));
+ TitledBorder recentlyOpenedBorder = new TitledBorder(
+ MessageManager.getString("label.recently_opened"));
+ recentlyOpenedBorder.setTitleFont(
+ recentlyOpenedBorder.getTitleFont().deriveFont(10f));
+ this.setBorder(recentlyOpenedBorder);
final JScrollPane scroller = new JScrollPane(list);
layout.putConstraint(SpringLayout.NORTH, scroller, 5,
SpringLayout.NORTH, this);
- if (Platform.isAMacAndNotJS())
- {
- scroller.setPreferredSize(new Dimension(500, 100));
- }
- else
- {
- scroller.setPreferredSize(new Dimension(530, 200));
- }
-
+ // one size okay for all
+ scroller.setPreferredSize(new Dimension(280, 105));
this.add(scroller);
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
}
+ class recentlyOpenedCellRenderer extends JLabel
+ implements ListCellRenderer<String>
+ {
+ private final static int maxChars = 46;
+
+ private final static String ellipsis = "...";
+
+ @Override
+ public Component getListCellRendererComponent(
+ JList<? extends String> list, String value, int index,
+ boolean isSelected, boolean cellHasFocus)
+ {
+ String filename = value.toString();
+ String displayFilename;
+ if (filename.length() > maxChars)
+ {
+ StringBuilder displayFileSB = new StringBuilder();
+ File file = new File(filename);
+ displayFileSB.append(file.getName());
+ if (file.getParent() != null)
+ {
+ File parent = file;
+ boolean spaceleft = true;
+ while (spaceleft && parent.getParent() != null)
+ {
+ parent = parent.getParentFile();
+ String name = parent.getName();
+ displayFileSB.insert(0, File.separator);
+ if (displayFileSB.length() + name.length() < maxChars - 1)
+ {
+ displayFileSB.insert(0, name);
+ }
+ else
+ {
+ displayFileSB.insert(0, ellipsis);
+ spaceleft = false;
+ }
+ }
+ if (spaceleft && filename.startsWith(File.separator)
+ && !(displayFileSB.charAt(0) == File.separatorChar))
+ {
+ displayFileSB.insert(0, File.separator);
+ }
+ }
+ displayFilename = displayFileSB.toString();
+ }
+ else
+ {
+ displayFilename = filename;
+ }
+ this.setText(displayFilename.toString());
+ this.setToolTipText(filename);
+ if (isSelected)
+ {
+ setBackground(list.getSelectionBackground());
+ setForeground(list.getSelectionForeground());
+ }
+ else
+ {
+ setBackground(list.getBackground());
+ setForeground(list.getForeground());
+ }
+ this.setHorizontalAlignment(SwingConstants.TRAILING);
+ this.setEnabled(list.isEnabled());
+ this.setFont(list.getFont().deriveFont(12f));
+ this.setOpaque(true);
+ return this;
+ }
+
+ }
+
/*
@Override
public JalviewFileChooser setResponseHandler(Object response,
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.io.FileFormats;
- import jalview.io.exceptions.ImageOutputException;
import jalview.schemes.ResidueColourScheme;
import jalview.util.MessageManager;
import jalview.util.Platform;
{
try
{
+ setFrameIcon(null);
// for Web-page embedding using id=align-frame-div
setName("jalview-alignment");
}
} catch (Exception e)
{
- System.err.println(e.toString());
+ jalview.bin.Console.errPrintln(e.toString());
}
if (Platform.allowMnemonics()) // was "not mac and not JS"
protected void createPNG_actionPerformed(ActionEvent object)
{
// TODO Auto-generated method stub
-
+
}
protected void createEPS_actionPerformed(ActionEvent object)
{
// TODO Auto-generated method stub
-
+
}
protected void createSVG_actionPerformed(ActionEvent object)
{
// TODO Auto-generated method stub
-
+
}
protected void copyHighlightedColumns_actionPerformed(
{
}
-
protected void font_actionPerformed(ActionEvent e)
{
}
}
-
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
git://source.jalview.org / jalview.git / commitdiff