action.save_project = Save Project
action.save_project_as = Save Project as...
action.quit = Quit
-label.quit_jalview = Quit Jalview?
+action.force_quit = Force quit
+label.quit_jalview = Are you sure you want to quit Jalview?
+label.wait_for_save = Wait for save
+label.unsaved_changes = There are unsaved changes.
+label.save_in_progress = Some files are still saving:
+label.unknown = Unknown
+label.quit_after_saving = Jalview will quit after saving.
+label.all_saved = All files saved.
+label.quitting_bye = Quitting, bye!
+action.wait = Wait
+action.cancel_quit = Cancel quit
action.expand_views = Expand Views
action.gather_views = Gather Views
action.page_setup = Page Setup...
action.save_project = Guardar proyecto
action.save_project_as = Guardar proyecto como...
action.quit = Salir
-label.quit_jalview = Salir de Jalview?
+action.force_quit = Forzar la salida
+label.quit_jalview = ¿Estás seguro de que quieres salir de Jalview?
+label.wait_for_save = Esperar a guardar
+label.unsaved_changes = Hay cambios sin guardar.
+label.save_in_progress = Algunos archivos aún se están guardando:
+label.unknown = desconocido
+label.quit_after_saving = Jalview se cerrará después de guardar.
+label.all_saved = Todos los archivos guardados.
+label.quitting_bye = Saliendo ¡chao!
+action.wait = Espere
+action.cancel_quit = Cancelar la salida
action.expand_views = Expandir vistas
action.gather_views = Capturar vistas
action.page_setup = Configuración de la página
sb.append("Java version: ");
sb.append(System.getProperty("java.version"));
sb.append("\n");
+ sb.append("Java platform: ");
sb.append(System.getProperty("os.arch"));
sb.append(" ");
sb.append(System.getProperty("os.name"));
sb.append(" (");
sb.append(lafClass);
sb.append(")\n");
+ appendIfNotNull(sb, "Channel: ",
+ ChannelProperties.getProperty("channel"), "\n", null);
if (Console.isDebugEnabled()
|| !"release".equals(ChannelProperties.getProperty("channel")))
{
- appendIfNotNull(sb, "Channel: ",
- ChannelProperties.getProperty("channel"), "\n", null);
appendIfNotNull(sb, "Getdown appdir: ",
System.getProperty("getdowninstanceappdir"), "\n", null);
appendIfNotNull(sb, "Getdown appbase: ",
System.getProperty("getdowninstanceappbase"), "\n", null);
appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
"\n", "unknown");
+ appendIfNotNull(sb, "Preferences file: ", propertiesFile, "\n",
+ "unknown");
}
return sb.toString();
}
if (customProxySet &&
// we have a username but no password for the scheme being
// requested
- (protocol.equalsIgnoreCase("http")
- && (httpUser != null && httpUser.length() > 0
- && (httpPassword == null
- || httpPassword.length == 0)))
+ (protocol.equalsIgnoreCase("http")
+ && (httpUser != null
+ && httpUser.length() > 0
+ && (httpPassword == null
+ || httpPassword.length == 0)))
|| (protocol.equalsIgnoreCase("https")
&& (httpsUser != null
&& httpsUser.length() > 0
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.PromptUserConfig;
+import jalview.gui.QuitHandler;
+import jalview.gui.QuitHandler.QResponse;
import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
if (!Platform.isJS())
{
System.setSecurityManager(null);
+
+ Runtime.getRuntime().addShutdownHook(new Thread()
+ {
+ public void run()
+ {
+ Console.debug("Running shutdown hook");
+ if (QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT)
+ {
+ // Got to here by a SIGTERM signal.
+ // Note we will not actually cancel the quit from here -- it's too
+ // late -- but we can wait for saving files.
+ Console.debug("Checking for saving files");
+ QuitHandler.getQuitResponse(false);
+ }
+ else
+ {
+ Console.debug("Nothing more to do");
+ }
+ Console.debug("Exiting, bye!");
+ // shutdownHook cannot be cancelled, JVM will now halt
+ }
+ });
}
System.out
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
+
String val = System.getProperty("sys.install4jVersion");
if (val != null)
{
Cache.loadBuildProperties(true);
ArgsParser aparser = new ArgsParser(args);
+
boolean headless = false;
String usrPropsFile = aparser.getValue("props");
- Cache.loadProperties(usrPropsFile); // must do this before
+ Cache.loadProperties(usrPropsFile); // must do this
+ // before
if (usrPropsFile != null)
{
System.out.println(
try
{
Console.initLogger();
- } catch (NoClassDefFoundError error)
+ } catch (
+
+ NoClassDefFoundError error)
{
error.printStackTrace();
System.out.println("\nEssential logging libraries not found."
}
String file = null, data = null;
+
FileFormatI format = null;
+
DataSourceType protocol = null;
+
FileLoader fileLoader = new FileLoader(!headless);
String groovyscript = null; // script to execute after all loading is
System.out.println("No files to open!");
System.exit(1);
}
+
long progress = -1;
// Finally, deal with the remaining input data.
if (file != null)
}
}
}
+
AlignFrame startUpAlframe = null;
// We'll only open the default file if the desktop is visible.
// And the user
}
/**
- * Quit method delegates to Desktop.quit - unless running in headless mode
- * when it just ends the JVM
+ * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
*/
public void quit()
{
- if (desktop != null)
- {
- desktop.quit();
- }
- else
- {
- System.exit(0);
- }
+ // System.exit will run the shutdownHook first
+ System.exit(0);
}
public static AlignFrame getCurrentAlignFrame()
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.jbgui;
-
-import javax.swing.JFrame;
-import javax.swing.JOptionPane;
+package jalview.gui;
import com.formdev.flatlaf.extras.FlatDesktop;
import com.formdev.flatlaf.extras.FlatDesktop.Action;
-import jalview.util.MessageManager;
import jalview.util.Platform;
public class APQHandlers
public static boolean setQuit = false;
- public static boolean setAPQHandlers(GDesktop desktop)
+ public static boolean setAPQHandlers(Desktop desktop)
{
if (Platform.isJS())
{
}
if (FlatDesktop.isSupported(Action.APP_QUIT_HANDLER))
{
- FlatDesktop.setQuitHandler(response -> {
- boolean confirmQuit = jalview.bin.Cache.getDefault(
- jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT, true);
- boolean canQuit = !confirmQuit;
- int n;
- if (confirmQuit)
- {
- // ensure Jalview window is brought to front for Quit confirmation
- // window to be visible
-
- // this method of raising the Jalview window is broken in java
- // jalviewDesktop.setVisible(true);
- // jalviewDesktop.toFront();
-
- // a better hack which works instead
- JFrame dialogParent = new JFrame();
- dialogParent.setAlwaysOnTop(true);
-
- n = JOptionPane.showConfirmDialog(dialogParent,
- MessageManager.getString("label.quit_jalview"),
- MessageManager.getString("action.quit"),
- JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE,
- null);
-
- dialogParent.setAlwaysOnTop(false);
- dialogParent.dispose();
- }
- else
- {
- n = JOptionPane.OK_OPTION;
- }
- canQuit = (n == JOptionPane.OK_OPTION);
- if (canQuit)
- {
- response.performQuit();
- }
- else
- {
- response.cancelQuit();
- }
- });
+ QuitHandler.setQuitHandler();
setQuit = true;
}
// if we got to here, no exceptions occurred when we set the handlers.
*/
package jalview.gui;
-import jalview.api.AlignExportSettingsI;
-import jalview.api.AlignViewportI;
-import jalview.io.FileFormatI;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.FlowLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+import java.util.concurrent.Callable;
import javax.swing.JCheckBox;
import javax.swing.JPanel;
+import jalview.api.AlignExportSettingsI;
+import jalview.api.AlignViewportI;
+import jalview.io.FileFormatI;
+import jalview.util.MessageManager;
+
/**
* A dialog that allows the user to specify whether to include hidden columns or
* sequences in an alignment export, and possibly features, annotations and
*
* @param action
*/
- public void setResponseAction(Object response, Runnable action)
+ public void setResponseAction(Object response, Callable action)
{
dialog.setResponseHandler(response, action);
}
import java.util.List;
import java.util.Locale;
import java.util.Vector;
+import java.util.concurrent.Callable;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
shortName);
+ Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
+ if (lastSaveSuccessful)
+ {
+ this.getViewport().setSavedUpToDate(true);
+ }
+
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
{ file, format }));
}
AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
- Runnable cancelAction = new Runnable()
- {
- @Override
- public void run()
+ Callable<Void> cancelAction = () -> {
+ lastSaveSuccessful = false;
+ return null;
+ };
+ Callable<Void> outputAction = () -> {
+ // todo defer this to inside formatSequences (or later)
+ AlignmentExportData exportData = viewport.getAlignExportData(options);
+ String output = new FormatAdapter(alignPanel, options)
+ .formatSequences(format, exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ viewport.getAlignment().getHiddenColumns());
+ if (output == null)
{
lastSaveSuccessful = false;
}
- };
- Runnable outputAction = new Runnable()
- {
- @Override
- public void run()
+ else
{
- // todo defer this to inside formatSequences (or later)
- AlignmentExportData exportData = viewport
- .getAlignExportData(options);
- String output = new FormatAdapter(alignPanel, options)
- .formatSequences(format, exportData.getAlignment(),
- exportData.getOmitHidden(),
- exportData.getStartEndPostions(),
- viewport.getAlignment().getHiddenColumns());
- if (output == null)
+ // create backupfiles object and get new temp filename destination
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = null;
+ if (doBackup)
{
- lastSaveSuccessful = false;
+ Console.trace("ALIGNFRAME making backupfiles object for " + file);
+ backupfiles = new BackupFiles(file);
}
- else
+ try
{
- // create backupfiles object and get new temp filename destination
- boolean doBackup = BackupFiles.getEnabled();
- BackupFiles backupfiles = null;
- if (doBackup)
+ String tempFilePath = doBackup ? backupfiles.getTempFilePath()
+ : file;
+ Console.trace("ALIGNFRAME setting PrintWriter");
+ PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
+
+ if (backupfiles != null)
{
- Console.trace(
- "ALIGNFRAME making backupfiles object for " + file);
- backupfiles = new BackupFiles(file);
+ Console.trace("ALIGNFRAME about to write to temp file "
+ + backupfiles.getTempFilePath());
}
- try
- {
- String tempFilePath = doBackup ? backupfiles.getTempFilePath()
- : file;
- Console.trace("ALIGNFRAME setting PrintWriter");
- PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
- if (backupfiles != null)
- {
- Console.trace("ALIGNFRAME about to write to temp file "
- + backupfiles.getTempFilePath());
- }
+ 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() }));
+ lastSaveSuccessful = true;
+ } catch (IOException e)
+ {
+ lastSaveSuccessful = false;
+ Console.error(
+ "ALIGNFRAME Something happened writing the temp file");
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
+ } catch (Exception ex)
+ {
+ lastSaveSuccessful = false;
+ Console.error(
+ "ALIGNFRAME Something unexpected happened writing the temp file");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
+ }
- 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() }));
- lastSaveSuccessful = true;
- } catch (IOException e)
- {
- lastSaveSuccessful = false;
- Console.error(
- "ALIGNFRAME Something happened writing the temp file");
- Console.error(e.getMessage());
- Console.debug(Cache.getStackTraceString(e));
- } catch (Exception ex)
- {
- lastSaveSuccessful = false;
- Console.error(
- "ALIGNFRAME Something unexpected happened writing the temp file");
- Console.error(ex.getMessage());
- Console.debug(Cache.getStackTraceString(ex));
- }
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(lastSaveSuccessful);
+ Console.debug("ALIGNFRAME writing temp file was "
+ + (lastSaveSuccessful ? "" : "NOT ") + "successful");
+ // do the backup file roll and rename the temp file to actual file
+ Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
+ lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
+ + (lastSaveSuccessful ? "" : "un") + "successfully");
+ }
- if (doBackup)
- {
- backupfiles.setWriteSuccess(lastSaveSuccessful);
- Console.debug("ALIGNFRAME writing temp file was "
- + (lastSaveSuccessful ? "" : "NOT ") + "successful");
- // do the backup file roll and rename the temp file to actual file
- Console.trace(
- "ALIGNFRAME about to rollBackupsAndRenameTempFile");
- lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
- Console.debug(
- "ALIGNFRAME performed rollBackupsAndRenameTempFile "
- + (lastSaveSuccessful ? "" : "un")
- + "successfully");
- }
+ Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
+ if (lastSaveSuccessful)
+ {
+ AlignFrame.this.getViewport().setSavedUpToDate(true);
}
}
+ return null;
};
/*
}
else
{
- outputAction.run();
+ try
+ {
+ outputAction.call();
+ } catch (Exception e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
}
}
FileFormatI fileFormat = FileFormats.getInstance()
.forName(fileFormatName);
AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
- Runnable outputAction = new Runnable()
- {
- @Override
- public void run()
+ Callable<Void> outputAction = () -> {
+ // todo defer this to inside formatSequences (or later)
+ AlignmentExportData exportData = viewport.getAlignExportData(options);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
+ try
{
- // todo defer this to inside formatSequences (or later)
- AlignmentExportData exportData = viewport
- .getAlignExportData(options);
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput(null);
- try
- {
- FileFormatI format = fileFormat;
- cap.setText(new FormatAdapter(alignPanel, options)
- .formatSequences(format, exportData.getAlignment(),
- exportData.getOmitHidden(),
- exportData.getStartEndPostions(),
- viewport.getAlignment().getHiddenColumns()));
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.alignment_output_command", new Object[]
- { fileFormat.getName() }), 600, 500);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Outputting alignment as " + fileFormat.getName(),
- oom);
- cap.dispose();
- }
+ FileFormatI format = fileFormat;
+ cap.setText(new FormatAdapter(alignPanel, options).formatSequences(
+ format, exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ viewport.getAlignment().getHiddenColumns()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new Object[]
+ { fileFormat.getName() }), 600, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Outputting alignment as " + fileFormat.getName(),
+ oom);
+ cap.dispose();
}
+ return null;
};
/*
}
else
{
- outputAction.run();
+ try
+ {
+ outputAction.call();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
}
}
.getString("label.load_jalview_annotations");
chooser.setDialogTitle(tooltip);
chooser.setToolTipText(tooltip);
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
- {
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", choice);
- loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
- }
+ chooser.setResponseHandler(0, () -> {
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
+ return null;
});
chooser.showOpenDialog(this);
return;
}
- Runnable okAction = new Runnable()
- {
- @Override
- public void run()
- {
- SequenceI[] cut = sg.getSequences()
- .toArray(new SequenceI[sg.getSize()]);
+ Callable okAction = () -> {
+ SequenceI[] cut = sg.getSequences()
+ .toArray(new SequenceI[sg.getSize()]);
- addHistoryItem(new EditCommand(
- MessageManager.getString("label.cut_sequences"), Action.CUT,
- cut, sg.getStartRes(),
- sg.getEndRes() - sg.getStartRes() + 1,
- viewport.getAlignment()));
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
- viewport.setSelectionGroup(null);
- viewport.sendSelection();
- viewport.getAlignment().deleteGroup(sg);
+ viewport.setSelectionGroup(null);
+ viewport.sendSelection();
+ viewport.getAlignment().deleteGroup(sg);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
- if (viewport.getAlignment().getHeight() < 1)
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ if (viewport.getAlignment().getHeight() < 1)
+ {
+ try
+ {
+ AlignFrame.this.setClosed(true);
+ } catch (Exception ex)
{
- try
- {
- AlignFrame.this.setClosed(true);
- } catch (Exception ex)
- {
- }
}
}
+ return null;
};
/*
}
else
{
- okAction.run();
+ try
+ {
+ okAction.call();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
}
}
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
+ chooser.setResponseHandler(0, () -> {
+ String filePath = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", filePath);
+ NewickFile fin = null;
+ try
{
- String filePath = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", filePath);
- NewickFile fin = null;
- try
- {
- fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
- DataSourceType.FILE));
- viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
- } catch (Exception ex)
- {
- JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
- MessageManager
- .getString("label.problem_reading_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
- ex.printStackTrace();
- }
- if (fin != null && fin.hasWarningMessage())
- {
- JvOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(),
- MessageManager.getString(
- "label.possible_problem_with_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
- }
+ fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
+ DataSourceType.FILE));
+ viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
+ } catch (Exception ex)
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+ MessageManager.getString("label.problem_reading_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ ex.printStackTrace();
}
+ if (fin != null && fin.hasWarningMessage())
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ fin.getWarningMessage(),
+ MessageManager
+ .getString("label.possible_problem_with_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ return null;
});
chooser.showOpenDialog(this);
}
chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
final AlignFrame us = this;
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
- {
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", choice);
- SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
- new VCFLoader(choice).loadVCF(seqs, us);
- }
+ chooser.setResponseHandler(0, () -> {
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+ new VCFLoader(choice).loadVCF(seqs, us);
+ return null;
});
chooser.showOpenDialog(null);
*/
package jalview.gui;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+
+import javax.swing.JInternalFrame;
+
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.AlignViewportI;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-
-import javax.swing.JInternalFrame;
-
/**
* DOCUMENT ME!
*
* in reverse order)
*/
JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
- .setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
- {
- addDataToAlignment(al);
- }
- }).setResponseHandler(1, new Runnable()
- {
- @Override
- public void run()
- {
- us.openLinkedAlignmentAs(al, title, true);
- }
- }).setResponseHandler(2, new Runnable()
- {
- @Override
- public void run()
- {
- us.openLinkedAlignmentAs(al, title, false);
- }
+ .setResponseHandler(0, () -> {
+ addDataToAlignment(al);
+ return null;
+ }).setResponseHandler(1, () -> {
+ us.openLinkedAlignmentAs(al, title, true);
+ return null;
+ }).setResponseHandler(2, () -> {
+ us.openLinkedAlignmentAs(al, title, false);
+ return null;
});
dialog.showDialog(question,
MessageManager.getString("label.open_split_window"),
*/
package jalview.gui;
-import java.util.Locale;
-
-import jalview.analysis.AlignSeq;
-import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.FileFormat;
-import jalview.io.FormatAdapter;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
import java.awt.Color;
import java.awt.Cursor;
import java.awt.Dimension;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
+import java.util.Locale;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JMenuItem;
import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
/**
* The panel that holds the labels for alignment annotations, providing
* tooltips, context menus, drag to reorder rows, and drag to adjust panel
EditNameDialog dialog = new EditNameDialog(annotation.label,
annotation.description, name, description);
- dialog.showDialog(ap.alignFrame, title, new Runnable()
- {
- @Override
- public void run()
+ dialog.showDialog(ap.alignFrame, title, () -> {
+ annotation.label = dialog.getName();
+ String text = dialog.getDescription();
+ if (text != null && text.length() == 0)
{
- annotation.label = dialog.getName();
- String text = dialog.getDescription();
- if (text != null && text.length() == 0)
- {
- text = null;
- }
- annotation.description = text;
- if (addNew)
- {
- ap.av.getAlignment().addAnnotation(annotation);
- ap.av.getAlignment().setAnnotationIndex(annotation, 0);
- }
- ap.refresh(true);
+ text = null;
}
+ annotation.description = text;
+ if (addNew)
+ {
+ ap.av.getAlignment().addAnnotation(annotation);
+ ap.av.getAlignment().setAnnotationIndex(annotation, 0);
+ }
+ ap.refresh(true);
+ return null;
});
}
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
frame = initFrame("Java Console", screenSize.width / 2,
screenSize.height / 2, -1, -1);
+ frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
initConsole(true);
}
{
}
}
+ /*
if (!frame.isVisible())
{
frame.dispose();
}
+ */
// System.exit(0);
}
import java.util.ListIterator;
import java.util.Locale;
import java.util.Vector;
+import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Semaphore;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JDesktopPane;
+import javax.swing.JFrame;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
import javax.swing.JTextField;
import javax.swing.KeyStroke;
import javax.swing.SwingUtilities;
+import javax.swing.WindowConstants;
import javax.swing.event.HyperlinkEvent;
import javax.swing.event.HyperlinkEvent.EventType;
import javax.swing.event.InternalFrameAdapter;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.gui.QuitHandler.QResponse;
import jalview.io.BackupFiles;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
setIconImages(ChannelProperties.getIconList());
+ // override quit handling when GUI OS close [X] button pressed
+ this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
addWindowListener(new WindowAdapter()
{
-
@Override
public void windowClosing(WindowEvent ev)
{
- quit();
+ QuitHandler.QResponse ret = desktopQuit(true, true); // ui, disposeFlag
}
});
this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
- this.addWindowListener(new WindowAdapter()
- {
- @Override
- public void windowClosing(WindowEvent evt)
- {
- quit();
- }
- });
-
MouseAdapter ma;
this.addMouseListener(ma = new MouseAdapter()
{
MessageManager.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
- {
- File selectedFile = chooser.getSelectedFile();
- Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
+ chooser.setResponseHandler(0, () -> {
+ File selectedFile = chooser.getSelectedFile();
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
- FileFormatI format = chooser.getSelectedFormat();
+ FileFormatI format = chooser.getSelectedFormat();
- /*
- * Call IdentifyFile to verify the file contains what its extension implies.
- * Skip this step for dynamically added file formats, because IdentifyFile does
- * not know how to recognise them.
- */
- if (FileFormats.getInstance().isIdentifiable(format))
+ /*
+ * Call IdentifyFile to verify the file contains what its extension implies.
+ * Skip this step for dynamically added file formats, because IdentifyFile does
+ * not know how to recognise them.
+ */
+ if (FileFormats.getInstance().isIdentifiable(format))
+ {
+ try
{
- try
- {
- format = new IdentifyFile().identify(selectedFile,
- DataSourceType.FILE);
- } catch (FileFormatException e)
- {
- // format = null; //??
- }
+ format = new IdentifyFile().identify(selectedFile,
+ DataSourceType.FILE);
+ } catch (FileFormatException e)
+ {
+ // format = null; //??
}
-
- new FileLoader().LoadFile(viewport, selectedFile,
- DataSourceType.FILE, format);
}
+
+ new FileLoader().LoadFile(viewport, selectedFile, DataSourceType.FILE,
+ format);
+ return null;
});
chooser.showOpenDialog(this);
}
Object[] options = new Object[] { MessageManager.getString("action.ok"),
MessageManager.getString("action.cancel") };
- Runnable action = new Runnable()
- {
- @Override
- public void run()
- {
- @SuppressWarnings("unchecked")
- String url = (history instanceof JTextField
- ? ((JTextField) history).getText()
- : ((JComboBox<String>) history).getEditor().getItem()
- .toString().trim());
+ Callable<Void> action = () -> {
+ @SuppressWarnings("unchecked")
+ String url = (history instanceof JTextField
+ ? ((JTextField) history).getText()
+ : ((JComboBox<String>) history).getEditor().getItem()
+ .toString().trim());
- if (url.toLowerCase(Locale.ROOT).endsWith(".jar"))
+ if (url.toLowerCase(Locale.ROOT).endsWith(".jar"))
+ {
+ if (viewport != null)
{
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- FileFormat.Jalview);
- }
- else
- {
- new FileLoader().LoadFile(url, DataSourceType.URL,
- FileFormat.Jalview);
- }
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ FileFormat.Jalview);
}
else
{
- FileFormatI format = null;
- try
- {
- format = new IdentifyFile().identify(url, DataSourceType.URL);
- } catch (FileFormatException e)
- {
- // TODO revise error handling, distinguish between
- // URL not found and response not valid
- }
+ new FileLoader().LoadFile(url, DataSourceType.URL,
+ FileFormat.Jalview);
+ }
+ }
+ else
+ {
+ FileFormatI format = null;
+ try
+ {
+ format = new IdentifyFile().identify(url, DataSourceType.URL);
+ } catch (FileFormatException e)
+ {
+ // TODO revise error handling, distinguish between
+ // URL not found and response not valid
+ }
- if (format == null)
- {
- String msg = MessageManager
- .formatMessage("label.couldnt_locate", url);
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
- MessageManager.getString("label.url_not_found"),
- JvOptionPane.WARNING_MESSAGE);
+ if (format == null)
+ {
+ String msg = MessageManager.formatMessage("label.couldnt_locate",
+ url);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
+ MessageManager.getString("label.url_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
- return;
- }
+ return null; // Void
+ }
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- format);
- }
- else
- {
- new FileLoader().LoadFile(url, DataSourceType.URL, format);
- }
+ if (viewport != null)
+ {
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ format);
+ }
+ else
+ {
+ new FileLoader().LoadFile(url, DataSourceType.URL, format);
}
}
+ return null; // Void
};
String dialogOption = MessageManager
.getString("label.input_alignment_from_url");
}
/*
- * Exit the program
+ * Check with user and saving files before actually quitting
*/
- @Override
- public void quit()
+ public void desktopQuit()
{
- Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
- Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
- Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
- storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
- getWidth(), getHeight()));
+ desktopQuit(true, false);
+ }
- if (jconsole != null)
- {
- storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
- jconsole.stopConsole();
- }
- if (jvnews != null)
- {
- storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
+ public QuitHandler.QResponse desktopQuit(boolean ui, boolean disposeFlag)
+ {
+ final Callable<Void> doDesktopQuit = () -> {
+ Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+ Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
+ Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
+ storeLastKnownDimensions("", new Rectangle(getBounds().x,
+ getBounds().y, getWidth(), getHeight()));
- }
- if (dialogExecutor != null)
- {
- dialogExecutor.shutdownNow();
- }
- closeAll_actionPerformed(null);
+ if (jconsole != null)
+ {
+ storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
+ jconsole.stopConsole();
+ }
- if (groovyConsole != null)
- {
- // suppress a possible repeat prompt to save script
- groovyConsole.setDirty(false);
- groovyConsole.exit();
- }
+ if (jvnews != null)
+ {
+ storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
+
+ }
+
+ if (dialogExecutor != null)
+ {
+ dialogExecutor.shutdownNow();
+ }
+
+ closeAll_actionPerformed(null);
+
+ if (groovyConsole != null)
+ {
+ // suppress a possible repeat prompt to save script
+ groovyConsole.setDirty(false);
+ groovyConsole.exit();
+ }
+
+ if (QuitHandler.gotQuitResponse() == QResponse.FORCE_QUIT)
+ {
+ // note that shutdown hook will not be run
+ jalview.bin.Console.debug("Force Quit selected by user");
+ Runtime.getRuntime().halt(0);
+ }
+
+ jalview.bin.Console.debug("Quit selected by user");
+ if (disposeFlag)
+ {
+ instance.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+ // instance.dispose();
+ }
+ instance.quit();
+
+ return null; // Void
+ };
+
+ return QuitHandler.getQuitResponse(ui, doDesktopQuit, doDesktopQuit,
+ QuitHandler.defaultCancelQuit);
+ }
+
+ /**
+ * Don't call this directly, use desktopQuit() above. Exits the program.
+ */
+ @Override
+ public void quit()
+ {
+ // this will run the shutdownHook but QuitHandler.getQuitResponse() should
+ // not run a second time if gotQuitResponse flag has been set (i.e. user
+ // confirmed quit of some kind).
System.exit(0);
}
// allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
+ chooser.setResponseHandler(0, () -> {
+ File selectedFile = chooser.getSelectedFile();
+ setProjectFile(selectedFile);
+ String choice = selectedFile.getAbsolutePath();
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
+ new Thread(new Runnable()
{
- File selectedFile = chooser.getSelectedFile();
- setProjectFile(selectedFile);
- String choice = selectedFile.getAbsolutePath();
- Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
- new Thread(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
+ try
{
- try
- {
- new Jalview2XML().loadJalviewAlign(selectedFile);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Whilst loading project from " + choice, oom);
- } catch (Exception ex)
- {
- jalview.bin.Console.error(
- "Problems whilst loading project from " + choice, ex);
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.error_whilst_loading_project_from",
- new Object[]
- { choice }),
- MessageManager
- .getString("label.couldnt_load_project"),
- JvOptionPane.WARNING_MESSAGE);
- }
+ new Jalview2XML().loadJalviewAlign(selectedFile);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Whilst loading project from " + choice, oom);
+ } catch (Exception ex)
+ {
+ jalview.bin.Console.error(
+ "Problems whilst loading project from " + choice, ex);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[]
+ { choice }),
+ MessageManager.getString("label.couldnt_load_project"),
+ JvOptionPane.WARNING_MESSAGE);
}
- }, "Project Loader").start();
- }
+ }
+ }, "Project Loader").start();
+ return null;
});
chooser.showOpenDialog(this);
@Override
public void actionPerformed(ActionEvent e)
{
- quit();
+ desktopQuit();
}
});
}
import java.awt.FlowLayout;
import java.awt.Font;
+import java.util.concurrent.Callable;
import javax.swing.BoxLayout;
import javax.swing.JButton;
*
* @param action
*/
- public void showDialog(JComponent parent, String title, Runnable action)
+ public void showDialog(JComponent parent, String title, Callable action)
{
Object[] options = new Object[] { MessageManager.getString("action.ok"),
MessageManager.getString("action.cancel") };
import java.awt.event.MouseEvent;
import java.util.ArrayList;
import java.util.List;
+import java.util.concurrent.Callable;
import javax.swing.JComboBox;
import javax.swing.JLabel;
*/
public void showDialog()
{
- Runnable okAction = forCreate ? getCreateAction() : getAmendAction();
- Runnable cancelAction = getCancelAction();
+ Callable<Void> okAction = forCreate ? getCreateAction()
+ : getAmendAction();
+ Callable<Void> cancelAction = getCancelAction();
/*
* set dialog action handlers for OK (create/Amend) and Cancel options
*
* @return
*/
- protected Runnable getCancelAction()
+ protected Callable getCancelAction()
{
- Runnable okAction = new Runnable()
- {
- @Override
- public void run()
- {
- ap.highlightSearchResults(null);
- ap.paintAlignment(false, false);
- }
+ Callable<Void> okAction = () -> {
+ ap.highlightSearchResults(null);
+ ap.paintAlignment(false, false);
+ return null;
};
return okAction;
}
*
* @return
*/
- protected Runnable getCreateAction()
+ protected Callable getCreateAction()
{
- Runnable okAction = new Runnable()
+ Callable<Void> okAction = new Callable()
{
boolean useLastDefaults = features.get(0).getType() == null;
@Override
- public void run()
+ public Void call()
{
final String enteredType = name.getText().trim();
final String enteredGroup = group.getText().trim();
repaintPanel();
}
+ return null;
}
};
return okAction;
*
* @return
*/
- protected Runnable getDeleteAction()
+ protected Callable getDeleteAction()
{
- Runnable deleteAction = new Runnable()
- {
- @Override
- public void run()
- {
- SequenceFeature sf = features.get(featureIndex);
- sequences.get(0).getDatasetSequence().deleteFeature(sf);
- fr.featuresAdded();
- ap.getSeqPanel().seqCanvas.highlightSearchResults(null);
- ap.paintAlignment(true, true);
- }
+ Callable<Void> deleteAction = () -> {
+ SequenceFeature sf = features.get(featureIndex);
+ sequences.get(0).getDatasetSequence().deleteFeature(sf);
+ fr.featuresAdded();
+ ap.getSeqPanel().seqCanvas.highlightSearchResults(null);
+ ap.paintAlignment(true, true);
+ return null;
};
return deleteAction;
}
*
* @return
*/
- protected Runnable getAmendAction()
+ protected Callable getAmendAction()
{
- Runnable okAction = new Runnable()
+ Callable<Void> okAction = new Callable()
{
boolean useLastDefaults = features.get(0).getType() == null;
String featureGroup = group.getText();
@Override
- public void run()
+ public Void call()
{
final String enteredType = name.getText().trim();
final String enteredGroup = group.getText().trim();
fr.featuresAdded();
}
repaintPanel();
+ return null;
}
};
return okAction;
chooser.setDialogTitle(
MessageManager.getString("label.load_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.load"));
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
- {
- File file = chooser.getSelectedFile();
- load(file);
- }
+ chooser.setResponseHandler(0, () -> {
+ File file = chooser.getSelectedFile();
+ load(file);
+ return null;
});
chooser.showOpenDialog(this);
}
*/
package jalview.gui;
+import java.awt.Component;
+import java.awt.Graphics;
+import java.io.File;
+import java.util.concurrent.Callable;
+import java.util.concurrent.atomic.AtomicBoolean;
+
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.io.JalviewFileChooser;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import java.awt.Component;
-import java.awt.Graphics;
-import java.io.File;
-import java.util.concurrent.atomic.AtomicBoolean;
-
/**
* A class that marshals steps in exporting a view in image graphics format
* <ul>
&& !Jalview.isHeadlessMode())
{
final File chosenFile = file;
- Runnable okAction = new Runnable()
- {
- @Override
- public void run()
- {
- exportImage(chosenFile, !textSelected.get(), width, height,
- messageId);
- }
+ Callable<Void> okAction = () -> {
+ exportImage(chosenFile, !textSelected.get(), width, height,
+ messageId);
+ return null;
};
LineartOptions epsOption = new LineartOptions(TYPE.EPS.getName(),
textSelected);
- epsOption.setResponseAction(1, new Runnable()
+ epsOption.setResponseAction(1, new Callable<Void>()
{
@Override
- public void run()
+ public Void call()
{
setStatus(MessageManager.formatMessage(
"status.cancelled_image_export_operation",
imageType.getName()), messageId);
+ return null;
}
});
epsOption.setResponseAction(0, okAction);
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.concurrent.Callable;
import java.util.concurrent.Executors;
import javax.swing.Icon;
import javax.swing.JButton;
import javax.swing.JDialog;
+import javax.swing.JFrame;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
import javax.swing.UIManager;
import javax.swing.event.InternalFrameEvent;
import javax.swing.event.InternalFrameListener;
private Component parentComponent;
- private Map<Object, Runnable> callbacks = new HashMap<>();
+ private Map<Object, Callable<Void>> callbacks = new HashMap<>();
/*
* JalviewJS reports user choice in the dialog as the selected
public JvOptionPane(final Component parent)
{
this.parentComponent = Platform.isJS() ? this : parent;
- this.setIcon(WindowIcons.logoIcon);
}
public static int showConfirmDialog(Component parentComponent,
* @param string2
* @return
*/
+ public static JvOptionPane newOptionDialog()
+ {
+ return new JvOptionPane(null);
+ }
+
public static JvOptionPane newOptionDialog(Component parentComponent)
{
return new JvOptionPane(parentComponent);
initialValue, true);
}
- public void showDialog(String message, String title, int optionType,
+ public void showDialog(Object message, String title, int optionType,
int messageType, Icon icon, Object[] options, Object initialValue,
boolean modal)
{
+ showDialog(message, title, optionType, messageType, icon, options,
+ initialValue, modal, null);
+ }
+
+ public void showDialog(Object message, String title, int optionType,
+ int messageType, Icon icon, Object[] options, Object initialValue,
+ boolean modal, JButton[] buttons)
+ {
if (!isInteractiveMode())
{
handleResponse(getMockResponse());
if (modal)
{
+ boolean useButtons = false;
+ Object initialValueButton = null;
+ NOTNULL: if (buttons != null)
+ {
+ if (buttons.length != options.length)
+ {
+ jalview.bin.Console.error(
+ "Supplied buttons array not the same length as supplied options array.");
+ break NOTNULL;
+ }
+ int[] buttonActions = { JOptionPane.YES_OPTION,
+ JOptionPane.NO_OPTION, JOptionPane.CANCEL_OPTION };
+ for (int i = 0; i < options.length; i++)
+ {
+ Object o = options[i];
+ jalview.bin.Console.debug(
+ "Setting button " + i + " to '" + o.toString() + "'");
+ JButton jb = buttons[i];
+
+ if (o.equals(initialValue))
+ initialValueButton = jb;
+
+ int buttonAction = buttonActions[i];
+ Callable<Void> action = callbacks.get(buttonAction);
+ jb.setText((String) o);
+ jb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+
+ Object obj = e.getSource();
+ if (obj == null || !(obj instanceof Component))
+ {
+ jalview.bin.Console.debug(
+ "Could not find Component source of event object "
+ + obj);
+ return;
+ }
+ Object joptionpaneObject = SwingUtilities.getAncestorOfClass(
+ JOptionPane.class, (Component) obj);
+ if (joptionpaneObject == null
+ || !(joptionpaneObject instanceof JOptionPane))
+ {
+ jalview.bin.Console.debug(
+ "Could not find JOptionPane ancestor of event object "
+ + obj);
+ return;
+ }
+ JOptionPane joptionpane = (JOptionPane) joptionpaneObject;
+ joptionpane.setValue(buttonAction);
+ if (action != null)
+ Executors.newSingleThreadExecutor().submit(action);
+ joptionpane.transferFocusBackward();
+ joptionpane.setVisible(false);
+ // put focus and raise parent window if possible, unless cancel or
+ // no button pressed
+ boolean raiseParent = (parentComponent != null);
+ if (buttonAction == JOptionPane.CANCEL_OPTION)
+ raiseParent = false;
+ if (optionType == JOptionPane.YES_NO_OPTION
+ && buttonAction == JOptionPane.NO_OPTION)
+ raiseParent = false;
+ if (raiseParent)
+ {
+ parentComponent.requestFocus();
+ if (parentComponent instanceof JInternalFrame)
+ {
+ JInternalFrame jif = (JInternalFrame) parentComponent;
+ jif.show();
+ jif.moveToFront();
+ jif.grabFocus();
+ }
+ else if (parentComponent instanceof Window)
+ {
+ Window w = (Window) parentComponent;
+ w.toFront();
+ w.requestFocus();
+ }
+ }
+ joptionpane.setVisible(false);
+ }
+ });
+
+ }
+ useButtons = true;
+ }
// use a JOptionPane as usual
int response = JOptionPane.showOptionDialog(parentComponent, message,
- title, optionType, messageType, icon, options, initialValue);
+ title, optionType, messageType, icon,
+ useButtons ? buttons : options,
+ useButtons ? initialValueButton : initialValue);
/*
* In Java, the response is returned to this thread and handled here;
ArrayList<JButton> options_btns = new ArrayList<>();
Object initialValue_btn = null;
- if (!Platform.isJS()) // JalviewJS already uses callback, don't need to
- // add them here
+ if (!Platform.isJS()) // JalviewJS already uses callback, don't need to add them here
{
for (int i = 0; i < options.length && i < 3; i++)
{
this.setMessage(mainPanel);
ourOptions = Arrays.asList(options);
+ int response;
if (parentComponent != this)
{
JInternalFrame jif = this.createInternalFrame(parentComponent, title);
}
}
+ /*
@Override
public JvOptionPane setResponseHandler(Object response, Runnable action)
{
+ callbacks.put(response, new Callable<Void>()
+ {
+ @Override
+ public Void call()
+ {
+ action.run();
+ return null;
+ }
+ });
+ return this;
+ }
+ */
+ @Override
+ public JvOptionPane setResponseHandler(Object response,
+ Callable<Void> action)
+ {
callbacks.put(response, action);
return this;
}
/**
+ * showDialogOnTop will create a dialog that (attempts to) come to top of OS
+ * desktop windows
+ */
+ public static int showDialogOnTop(String label, String actionString,
+ int JOPTIONPANE_OPTION, int JOPTIONPANE_MESSAGETYPE)
+ {
+ // Ensure Jalview window is brought to front (primarily for Quit
+ // confirmation window to be visible)
+
+ // This method of raising the Jalview window is broken in java
+ // jalviewDesktop.setVisible(true);
+ // jalviewDesktop.toFront();
+
+ // A better hack which works is to create a new JFrame parent with
+ // setAlwaysOnTop(true)
+ JFrame dialogParent = new JFrame();
+ dialogParent.setAlwaysOnTop(true);
+
+ int answer = JOptionPane.showConfirmDialog(dialogParent, label,
+ actionString, JOPTIONPANE_OPTION, JOPTIONPANE_MESSAGETYPE);
+
+ dialogParent.setAlwaysOnTop(false);
+ dialogParent.dispose();
+
+ return answer;
+ }
+
+ public void showDialogOnTopAsync(String label, String actionString,
+ int JOPTIONPANE_OPTION, int JOPTIONPANE_MESSAGETYPE, Icon icon,
+ Object[] options, Object initialValue, boolean modal)
+ {
+ showDialogOnTopAsync(new JFrame(), label, actionString,
+ JOPTIONPANE_OPTION, JOPTIONPANE_MESSAGETYPE, icon, options,
+ initialValue, modal);
+ }
+
+ public void showDialogOnTopAsync(JFrame dialogParent, Object label,
+ String actionString, int JOPTIONPANE_OPTION,
+ int JOPTIONPANE_MESSAGETYPE, Icon icon, Object[] options,
+ Object initialValue, boolean modal)
+ {
+ showDialogOnTopAsync(dialogParent, label, actionString,
+ JOPTIONPANE_OPTION, JOPTIONPANE_MESSAGETYPE, icon, options,
+ initialValue, modal, null);
+ }
+
+ public void showDialogOnTopAsync(JFrame dialogParent, Object label,
+ String actionString, int JOPTIONPANE_OPTION,
+ int JOPTIONPANE_MESSAGETYPE, Icon icon, Object[] options,
+ Object initialValue, boolean modal, JButton[] buttons)
+ {
+ // Ensure Jalview window is brought to front (primarily for Quit
+ // confirmation window to be visible)
+
+ // This method of raising the Jalview window is broken in java
+ // jalviewDesktop.setVisible(true);
+ // jalviewDesktop.toFront();
+
+ // A better hack which works is to create a new JFrame parent with
+ // setAlwaysOnTop(true)
+ dialogParent.setAlwaysOnTop(true);
+ parentComponent = dialogParent;
+
+ showDialog(label, actionString, JOPTIONPANE_OPTION,
+ JOPTIONPANE_MESSAGETYPE, icon, options, initialValue, modal,
+ buttons);
+
+ dialogParent.setAlwaysOnTop(false);
+ dialogParent.dispose();
+ }
+
+ /**
* JalviewJS signals option selection by a property change event for the
* option e.g. "OK". This methods responds to that by running the response
* action that corresponds to that option.
{
return;
}
- Runnable action = callbacks.get(response);
+ Callable<Void> action = callbacks.get(response);
if (action != null)
{
- action.run();
- parentComponent.requestFocus();
+ try
+ {
+ action.call();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ if (parentComponent != null)
+ parentComponent.requestFocus();
}
}
/**
+ * Create a non-modal confirm dialog
+ */
+ public JDialog createDialog(Component parentComponent, Object message,
+ String title, int optionType, int messageType, Icon icon,
+ Object[] options, Object initialValue, boolean modal)
+ {
+ return createDialog(parentComponent, message, title, optionType,
+ messageType, icon, options, initialValue, modal, null);
+ }
+
+ public JDialog createDialog(Component parentComponent, Object message,
+ String title, int optionType, int messageType, Icon icon,
+ Object[] options, Object initialValue, boolean modal,
+ JButton[] buttons)
+ {
+ JButton[] optionsButtons = null;
+ Object initialValueButton = null;
+ JOptionPane joptionpane = new JOptionPane();
+ // Make button options
+ int[] buttonActions = { JOptionPane.YES_OPTION, JOptionPane.NO_OPTION,
+ JOptionPane.CANCEL_OPTION };
+
+ // we need the strings to make the buttons with actionEventListener
+ if (options == null)
+ {
+ ArrayList<String> options_default = new ArrayList<>();
+ options_default.add(UIManager.getString("OptionPane.yesButtonText"));
+ if (optionType == JOptionPane.YES_NO_OPTION
+ || optionType == JOptionPane.YES_NO_CANCEL_OPTION)
+ {
+ options_default.add(UIManager.getString("OptionPane.noButtonText"));
+ }
+ if (optionType == JOptionPane.YES_NO_CANCEL_OPTION)
+ {
+ options_default
+ .add(UIManager.getString("OptionPane.cancelButtonText"));
+ }
+ options = options_default.toArray();
+ }
+ if (!Platform.isJS()) // JalviewJS already uses callback, don't need to
+ // add them here
+ {
+ if (((optionType == JOptionPane.YES_OPTION
+ || optionType == JOptionPane.NO_OPTION
+ || optionType == JOptionPane.CANCEL_OPTION
+ || optionType == JOptionPane.OK_OPTION
+ || optionType == JOptionPane.DEFAULT_OPTION)
+ && options.length < 1)
+ || ((optionType == JOptionPane.YES_NO_OPTION
+ || optionType == JOptionPane.OK_CANCEL_OPTION)
+ && options.length < 2)
+ || (optionType == JOptionPane.YES_NO_CANCEL_OPTION
+ && options.length < 3))
+ {
+ jalview.bin.Console
+ .debug("JvOptionPane: not enough options for dialog type");
+ }
+ optionsButtons = new JButton[options.length];
+ for (int i = 0; i < options.length && i < 3; i++)
+ {
+ Object o = options[i];
+ int buttonAction = buttonActions[i];
+ Callable<Void> action = callbacks.get(buttonAction);
+ JButton jb;
+ if (buttons != null && buttons.length > i && buttons[i] != null)
+ {
+ jb = buttons[i];
+ }
+ else
+ {
+ jb = new JButton();
+ }
+ jb.setText((String) o);
+ jb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ joptionpane.setValue(buttonAction);
+ if (action != null)
+ Executors.newSingleThreadExecutor().submit(action);
+ // joptionpane.transferFocusBackward();
+ joptionpane.transferFocusBackward();
+ joptionpane.setVisible(false);
+ // put focus and raise parent window if possible, unless cancel
+ // button pressed
+ boolean raiseParent = (parentComponent != null);
+ if (buttonAction == JOptionPane.CANCEL_OPTION)
+ raiseParent = false;
+ if (optionType == JOptionPane.YES_NO_OPTION
+ && buttonAction == JOptionPane.NO_OPTION)
+ raiseParent = false;
+ if (raiseParent)
+ {
+ parentComponent.requestFocus();
+ if (parentComponent instanceof JInternalFrame)
+ {
+ JInternalFrame jif = (JInternalFrame) parentComponent;
+ jif.show();
+ jif.moveToFront();
+ jif.grabFocus();
+ }
+ else if (parentComponent instanceof Window)
+ {
+ Window w = (Window) parentComponent;
+ w.toFront();
+ w.requestFocus();
+ }
+ }
+ joptionpane.setVisible(false);
+ }
+ });
+ optionsButtons[i] = jb;
+ if (o.equals(initialValue))
+ initialValueButton = jb;
+ }
+ }
+ joptionpane.setMessage(message);
+ joptionpane.setMessageType(messageType);
+ joptionpane.setOptionType(optionType);
+ joptionpane.setIcon(icon);
+ joptionpane.setOptions(Platform.isJS() ? options : optionsButtons);
+ joptionpane.setInitialValue(
+ Platform.isJS() ? initialValue : initialValueButton);
+
+ JDialog dialog = joptionpane.createDialog(parentComponent, title);
+ dialog.setModalityType(
+ modal ? ModalityType.APPLICATION_MODAL : ModalityType.MODELESS);
+ dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+ return dialog;
+ }
+
+ /**
+ * Utility to programmatically click a button on a JOptionPane (as a JFrame)
+ *
+ * returns true if button was found
+ */
+ public static boolean clickButton(JFrame frame, int buttonType)
+ {
+
+ return false;
+ }
+
+ /**
* This helper method makes the JInternalFrame wait until it is notified by an
* InternalFrameClosing event. This method also adds the given JOptionPane to
* the JInternalFrame and sizes it according to the JInternalFrame's preferred
*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.util.MessageManager;
-
import java.awt.FlowLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.util.concurrent.Callable;
import java.util.concurrent.atomic.AtomicBoolean;
import javax.swing.BorderFactory;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
+import jalview.bin.Cache;
+import jalview.util.MessageManager;
+
/**
* A dialog where the user may choose Text or Lineart rendering, and optionally
* save this as a preference ("Don't ask me again")
*
* @param action
*/
- public void setResponseAction(Object response, Runnable action)
+ public void setResponseAction(Object response, Callable action)
{
dialog.setResponseHandler(response, action);
}
MessageManager.getString("label.group_description"));
dialog.showDialog(ap.alignFrame,
MessageManager.getString("label.edit_group_name_description"),
- new Runnable()
- {
- @Override
- public void run()
- {
- sg.setName(dialog.getName());
- sg.setDescription(dialog.getDescription());
- refresh();
- }
+ () -> {
+ sg.setName(dialog.getName());
+ sg.setDescription(dialog.getDescription());
+ refresh();
+ return null;
});
}
sequence.getDescription(),
MessageManager.getString("label.sequence_name"),
MessageManager.getString("label.sequence_description"));
- dialog.showDialog(ap.alignFrame, MessageManager.getString(
- "label.edit_sequence_name_description"), new Runnable()
- {
- @Override
- public void run()
+ dialog.showDialog(ap.alignFrame, MessageManager
+ .getString("label.edit_sequence_name_description"), () -> {
+ if (dialog.getName() != null)
{
- if (dialog.getName() != null)
+ if (dialog.getName().indexOf(" ") > -1)
{
- if (dialog.getName().indexOf(" ") > -1)
- {
- JvOptionPane.showMessageDialog(ap,
- MessageManager.getString(
- "label.spaces_converted_to_underscores"),
- MessageManager.getString(
- "label.no_spaces_allowed_sequence_name"),
- JvOptionPane.WARNING_MESSAGE);
- }
- sequence.setName(dialog.getName().replace(' ', '_'));
- ap.paintAlignment(false, false);
+ JvOptionPane.showMessageDialog(ap,
+ MessageManager.getString(
+ "label.spaces_converted_to_underscores"),
+ MessageManager.getString(
+ "label.no_spaces_allowed_sequence_name"),
+ JvOptionPane.WARNING_MESSAGE);
}
- sequence.setDescription(dialog.getDescription());
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ sequence.setName(dialog.getName().replace(' ', '_'));
+ ap.paintAlignment(false, false);
}
+ sequence.setDescription(dialog.getDescription());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ return null;
});
}
seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
null, MessageManager.getString("label.edit_sequence"), null);
dialog.showDialog(ap.alignFrame,
- MessageManager.getString("label.edit_sequence"),
- new Runnable()
- {
- @Override
- public void run()
- {
- EditCommand editCommand = new EditCommand(
- MessageManager.getString("label.edit_sequences"),
- Action.REPLACE,
- dialog.getName().replace(' ',
- ap.av.getGapCharacter()),
- sg.getSequencesAsArray(
- ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1,
- ap.av.getAlignment());
- ap.alignFrame.addHistoryItem(editCommand);
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
- }
+ MessageManager.getString("label.edit_sequence"), () -> {
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
+ Action.REPLACE,
+ dialog.getName().replace(' ',
+ ap.av.getGapCharacter()),
+ sg.getSequencesAsArray(
+ ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1,
+ ap.av.getAlignment());
+ ap.alignFrame.addHistoryItem(editCommand);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ return null;
});
}
}
--- /dev/null
+package jalview.gui;
+
+import java.io.File;
+import java.util.List;
+import java.util.concurrent.Callable;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.TimeoutException;
+
+import javax.swing.JButton;
+import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+import javax.swing.JTextPane;
+
+import com.formdev.flatlaf.extras.FlatDesktop;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.BackupFiles;
+import jalview.project.Jalview2XML;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+public class QuitHandler
+{
+ private static final int MIN_WAIT_FOR_SAVE = 3000;
+
+ private static final int MAX_WAIT_FOR_SAVE = 20000;
+
+ public static enum QResponse
+ {
+ NULL, QUIT, CANCEL_QUIT, FORCE_QUIT
+ };
+
+ private static ExecutorService executor = Executors.newFixedThreadPool(3);
+
+ public static QResponse setQuitHandler()
+ {
+ FlatDesktop.setQuitHandler(response -> {
+ Callable<Void> performQuit = () -> {
+ response.performQuit();
+ setResponse(QResponse.QUIT);
+ return null;
+ };
+ Callable<Void> performForceQuit = () -> {
+ response.performQuit();
+ setResponse(QResponse.FORCE_QUIT);
+ return null;
+ };
+ Callable<Void> cancelQuit = () -> {
+ response.cancelQuit();
+ // reset
+ setResponse(QResponse.NULL);
+ return null;
+ };
+ getQuitResponse(true, performQuit, performForceQuit, cancelQuit);
+ });
+
+ return gotQuitResponse();
+ }
+
+ private static QResponse gotQuitResponse = QResponse.NULL;
+
+ private static QResponse setResponse(QResponse qresponse)
+ {
+ gotQuitResponse = qresponse;
+ return qresponse;
+ }
+
+ public static QResponse gotQuitResponse()
+ {
+ return gotQuitResponse;
+ }
+
+ public static final Callable<Void> defaultCancelQuit = () -> {
+ Console.debug("QuitHandler: (default) Quit action CANCELLED by user");
+ // reset
+ setResponse(QResponse.NULL);
+ return null;
+ };
+
+ public static final Callable<Void> defaultOkQuit = () -> {
+ Console.debug("QuitHandler: (default) Quit action CONFIRMED by user");
+ setResponse(QResponse.QUIT);
+ return null;
+ };
+
+ public static final Callable<Void> defaultForceQuit = () -> {
+ Console.debug("QuitHandler: (default) Quit action FORCED by user");
+ // note that shutdown hook will not be run
+ Runtime.getRuntime().halt(0);
+ setResponse(QResponse.FORCE_QUIT); // this line never reached!
+ return null;
+ };
+
+ public static QResponse getQuitResponse(boolean ui)
+ {
+ return getQuitResponse(ui, defaultOkQuit, defaultForceQuit,
+ defaultCancelQuit);
+ }
+
+ private static boolean interactive = true;
+
+ public static QResponse getQuitResponse(boolean ui, Callable<Void> okQuit,
+ Callable<Void> forceQuit, Callable<Void> cancelQuit)
+ {
+ QResponse got = gotQuitResponse();
+ if (got != QResponse.NULL && got != QResponse.CANCEL_QUIT)
+ {
+ // quit has already been selected, continue with calling quit method
+ return got;
+ }
+
+ interactive = ui && !Platform.isHeadless();
+ // confirm quit if needed and wanted
+ boolean confirmQuit = true;
+
+ if (!interactive)
+ {
+ Console.debug("Non interactive quit -- not confirming");
+ confirmQuit = false;
+ }
+ else if (Jalview2XML.allSavedUpToDate())
+ {
+ Console.debug("Nothing changed -- not confirming quit");
+ confirmQuit = false;
+ }
+ else
+ {
+ confirmQuit = jalview.bin.Cache
+ .getDefault(jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT, true);
+ Console.debug("Jalview property '"
+ + jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT
+ + "' is/defaults to " + confirmQuit + " -- "
+ + (confirmQuit ? "" : "not ") + "confirming quit");
+ }
+ got = confirmQuit ? QResponse.NULL : QResponse.QUIT;
+ setResponse(got);
+
+ if (confirmQuit)
+ {
+ JvOptionPane.newOptionDialog()
+ .setResponseHandler(JOptionPane.YES_OPTION, defaultOkQuit)
+ .setResponseHandler(JOptionPane.NO_OPTION, defaultCancelQuit)
+ .showDialogOnTopAsync(
+ new StringBuilder(MessageManager
+ .getString("label.quit_jalview"))
+ .append("\n")
+ .append(MessageManager.getString(
+ "label.unsaved_changes"))
+ .toString(),
+ MessageManager.getString("action.quit"),
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.QUESTION_MESSAGE, null, new Object[]
+ { MessageManager.getString("action.quit"),
+ MessageManager.getString("action.cancel") },
+ MessageManager.getString("action.quit"), true);
+ }
+
+ got = gotQuitResponse();
+ boolean wait = false;
+ if (got == QResponse.CANCEL_QUIT)
+ {
+ // reset
+ setResponse(QResponse.NULL);
+ // but return cancel
+ return QResponse.CANCEL_QUIT;
+ }
+ else if (got == QResponse.QUIT)
+ {
+ if (Cache.getDefault("WAIT_FOR_SAVE", true)
+ && BackupFiles.hasSavesInProgress())
+ {
+ waitQuit(interactive, okQuit, forceQuit, cancelQuit);
+ QResponse waitResponse = gotQuitResponse();
+ wait = waitResponse == QResponse.QUIT;
+ }
+ }
+
+ Callable<Void> next = null;
+ switch (gotQuitResponse())
+ {
+ case QUIT:
+ next = okQuit;
+ break;
+ case FORCE_QUIT: // not actually an option at this stage
+ next = forceQuit;
+ break;
+ default:
+ next = cancelQuit;
+ break;
+ }
+ try
+ {
+ executor.submit(next).get();
+ got = gotQuitResponse();
+ } catch (InterruptedException | ExecutionException e)
+ {
+ jalview.bin.Console
+ .debug("Exception during quit handling (final choice)", e);
+ }
+ setResponse(got);
+
+ if (gotQuitResponse() == QResponse.CANCEL_QUIT)
+ {
+ // reset if cancelled
+ setResponse(QResponse.NULL);
+ return QResponse.CANCEL_QUIT;
+ }
+ return gotQuitResponse();
+ }
+
+ private static QResponse waitQuit(boolean interactive,
+ Callable<Void> okQuit, Callable<Void> forceQuit,
+ Callable<Void> cancelQuit)
+ {
+ // check for saves in progress
+ if (!BackupFiles.hasSavesInProgress())
+ return QResponse.QUIT;
+
+ int size = 0;
+ AlignFrame[] afArray = Desktop.getAlignFrames();
+ if (!(afArray == null || afArray.length == 0))
+ {
+ for (int i = 0; i < afArray.length; i++)
+ {
+ AlignFrame af = afArray[i];
+ List<? extends AlignmentViewPanel> avpList = af.getAlignPanels();
+ for (AlignmentViewPanel avp : avpList)
+ {
+ AlignmentI a = avp.getAlignment();
+ List<SequenceI> sList = a.getSequences();
+ for (SequenceI s : sList)
+ {
+ size += s.getLength();
+ }
+ }
+ }
+ }
+ int waitTime = Math.min(MAX_WAIT_FOR_SAVE,
+ Math.max(MIN_WAIT_FOR_SAVE, size / 2));
+ Console.debug("Set waitForSave to " + waitTime);
+
+ int iteration = 0;
+ boolean doIterations = true; // note iterations not used in the gui now,
+ // only one pass without the "Wait" button
+ while (doIterations && BackupFiles.hasSavesInProgress()
+ && iteration++ < (interactive ? 100 : 5))
+ {
+ // future that returns a Boolean when all files are saved
+ CompletableFuture<Boolean> filesAllSaved = new CompletableFuture<>();
+
+ // callback as each file finishes saving
+ for (CompletableFuture<Boolean> cf : BackupFiles
+ .savesInProgressCompletableFutures(false))
+ {
+ // if this is the last one then complete filesAllSaved
+ cf.whenComplete((ret, e) -> {
+ if (!BackupFiles.hasSavesInProgress())
+ {
+ filesAllSaved.complete(true);
+ }
+ });
+ }
+ try
+ {
+ filesAllSaved.get(waitTime, TimeUnit.MILLISECONDS);
+ } catch (InterruptedException | ExecutionException e1)
+ {
+ Console.debug(
+ "Exception whilst waiting for files to save before quit",
+ e1);
+ } catch (TimeoutException e2)
+ {
+ // this Exception to be expected
+ }
+
+ if (interactive && BackupFiles.hasSavesInProgress())
+ {
+ boolean showForceQuit = iteration > 0; // iteration > 1 to not show
+ // force quit the first time
+ JFrame parent = new JFrame();
+ JButton[] buttons = { new JButton(), new JButton() };
+ JvOptionPane waitDialog = JvOptionPane.newOptionDialog();
+ JTextPane messagePane = new JTextPane();
+ messagePane.setBackground(waitDialog.getBackground());
+ messagePane.setBorder(null);
+ messagePane.setText(waitingForSaveMessage());
+ // callback as each file finishes saving
+ for (CompletableFuture<Boolean> cf : BackupFiles
+ .savesInProgressCompletableFutures(false))
+ {
+ cf.whenComplete((ret, e) -> {
+ if (BackupFiles.hasSavesInProgress())
+ {
+ // update the list of saving files as they save too
+ messagePane.setText(waitingForSaveMessage());
+ }
+ else
+ {
+ if (!(QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT
+ || QuitHandler.gotQuitResponse() == QResponse.NULL))
+ {
+ for (int i = 0; i < buttons.length; i++)
+ {
+ Console.debug("DISABLING BUTTON " + buttons[i].getText());
+ buttons[i].setEnabled(false);
+ buttons[i].setVisible(false);
+ }
+ // if this is the last one then close the dialog
+ messagePane.setText(new StringBuilder()
+ .append(MessageManager.getString("label.all_saved"))
+ .append("\n")
+ .append(MessageManager
+ .getString("label.quitting_bye"))
+ .toString());
+ messagePane.setEditable(false);
+ try
+ {
+ Thread.sleep(1500);
+ } catch (InterruptedException e1)
+ {
+ }
+ parent.dispose();
+ }
+ }
+ });
+ }
+
+ String[] options;
+ int dialogType = -1;
+ if (showForceQuit)
+ {
+ options = new String[2];
+ options[0] = MessageManager.getString("action.force_quit");
+ options[1] = MessageManager.getString("action.cancel_quit");
+ dialogType = JOptionPane.YES_NO_OPTION;
+ waitDialog.setResponseHandler(JOptionPane.YES_OPTION, forceQuit)
+ .setResponseHandler(JOptionPane.NO_OPTION, cancelQuit);
+ }
+ else
+ {
+ options = new String[1];
+ options[0] = MessageManager.getString("action.cancel_quit");
+ dialogType = JOptionPane.YES_OPTION;
+ waitDialog.setResponseHandler(JOptionPane.YES_OPTION, cancelQuit);
+ }
+ waitDialog.showDialogOnTopAsync(parent, messagePane,
+ MessageManager.getString("label.wait_for_save"), dialogType,
+ JOptionPane.WARNING_MESSAGE, null, options,
+ MessageManager.getString("action.cancel_quit"), true,
+ buttons);
+
+ parent.dispose();
+ final QResponse thisWaitResponse = gotQuitResponse();
+ switch (thisWaitResponse)
+ {
+ case QUIT: // wait -- do another iteration
+ break;
+ case FORCE_QUIT:
+ doIterations = false;
+ break;
+ case CANCEL_QUIT:
+ doIterations = false;
+ break;
+ case NULL: // already cancelled
+ doIterations = false;
+ break;
+ default:
+ }
+ } // end if interactive
+
+ } // end while wait iteration loop
+ return gotQuitResponse();
+ };
+
+ private static String waitingForSaveMessage()
+ {
+ StringBuilder messageSB = new StringBuilder();
+
+ messageSB.append(MessageManager.getString("label.save_in_progress"));
+ List<File> files = BackupFiles.savesInProgressFiles(false);
+ boolean any = files.size() > 0;
+ if (any)
+ {
+ for (File file : files)
+ {
+ messageSB.append("\n\u2022 ").append(file.getName());
+ }
+ }
+ else
+ {
+ messageSB.append(MessageManager.getString("label.unknown"));
+ }
+ messageSB.append("\n\n")
+ .append(MessageManager.getString("label.quit_after_saving"));
+ return messageSB.toString();
+ }
+
+ public static void abortQuit()
+ {
+ setResponse(QResponse.CANCEL_QUIT);
+ }
+}
\ No newline at end of file
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Locale;
+import java.util.concurrent.Callable;
import java.util.concurrent.Executors;
import javax.swing.JCheckBox;
};
// fetch db refs if OK pressed
- final Runnable discoverCanonicalDBrefs = new Runnable()
- {
- @Override
- public void run()
+ final Callable discoverCanonicalDBrefs = () -> {
+ btn_queryTDB.setEnabled(false);
+ populateSeqsWithoutSourceDBRef();
+
+ final int y = seqsWithoutSourceDBRef.size();
+ if (y > 0)
{
- btn_queryTDB.setEnabled(false);
- populateSeqsWithoutSourceDBRef();
+ final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
+ .toArray(new SequenceI[y]);
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
+ progressBar, new DbSourceProxy[]
+ { new jalview.ws.dbsources.Uniprot() }, null, false);
+ dbRefFetcher.addListener(afterDbRefFetch);
+ // ideally this would also gracefully run with callbacks
- final int y = seqsWithoutSourceDBRef.size();
- if (y > 0)
- {
- final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
- .toArray(new SequenceI[y]);
- DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
- progressBar, new DbSourceProxy[]
- { new jalview.ws.dbsources.Uniprot() }, null, false);
- dbRefFetcher.addListener(afterDbRefFetch);
- // ideally this would also gracefully run with callbacks
-
- dbRefFetcher.fetchDBRefs(true);
- }
- else
- {
- // call finished action directly
- afterDbRefFetch.finished();
- }
+ dbRefFetcher.fetchDBRefs(true);
}
-
+ else
+ {
+ // call finished action directly
+ afterDbRefFetch.finished();
+ }
+ return null;
};
- final Runnable revertview = new Runnable()
- {
- @Override
- public void run()
+ final Callable revertview = () -> {
+ if (lastSelected != null)
{
- if (lastSelected != null)
- {
- cmb_filterOption.setSelectedItem(lastSelected);
- }
- };
+ cmb_filterOption.setSelectedItem(lastSelected);
+ }
+ return null;
};
int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
Console.debug("Using Uniprot fetch threshold of " + threshold);
if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold)
{
- Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs)
- .start();
+ Executors.newSingleThreadExecutor().submit(discoverCanonicalDBrefs);
return;
}
// need cancel and no to result in the discoverPDB action - mocked is
if (confirm == JvOptionPane.CANCEL_OPTION
|| confirm == JvOptionPane.CLOSED_OPTION)
{
+ // abort possible quit handling if CANCEL chosen
+ if (confirm == JvOptionPane.CANCEL_OPTION)
+ QuitHandler.abortQuit();
return;
}
forceClose = confirm == JvOptionPane.YES_OPTION;
import java.awt.event.MouseEvent;
import java.util.HashMap;
import java.util.Map;
+import java.util.concurrent.Callable;
import javax.swing.BorderFactory;
import javax.swing.JLabel;
MessageManager.getString("action.cancel") };
String title = MessageManager
.getString("label.adjust_foreground_text_colour_threshold");
- Runnable action = new Runnable() // response for 1 = Cancel
+ Callable<Void> action = () -> // response for 1 = Cancel
{
- @Override
- public void run()
- {
- restoreInitialSettings();
- }
+ restoreInitialSettings();
+ return null;
};
JvOptionPane.newOptionDialog(alignPanel.alignFrame)
.setResponseHandler(1, action).showInternalDialog(bigpanel,
chooser.setDialogTitle(
MessageManager.getString("label.load_colour_scheme"));
chooser.setToolTipText(MessageManager.getString("action.load"));
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
- {
- File choice = chooser.getSelectedFile();
- Cache.setProperty(LAST_DIRECTORY, choice.getParent());
-
- UserColourScheme ucs = ColourSchemeLoader
- .loadColourScheme(choice.getAbsolutePath());
- Color[] colors = ucs.getColours();
- schemeName.setText(ucs.getSchemeName());
+ chooser.setResponseHandler(0, () -> {
+ File choice = chooser.getSelectedFile();
+ Cache.setProperty(LAST_DIRECTORY, choice.getParent());
- if (ucs.getLowerCaseColours() != null)
- {
- caseSensitive.setSelected(true);
- lcaseColour.setEnabled(true);
- resetButtonPanel(true);
- for (int i = 0; i < lowerCaseButtons.size(); i++)
- {
- JButton button = lowerCaseButtons.get(i);
- button.setBackground(ucs.getLowerCaseColours()[i]);
- }
- }
- else
- {
- caseSensitive.setSelected(false);
- lcaseColour.setEnabled(false);
- resetButtonPanel(false);
- }
+ UserColourScheme ucs = ColourSchemeLoader
+ .loadColourScheme(choice.getAbsolutePath());
+ Color[] colors = ucs.getColours();
+ schemeName.setText(ucs.getSchemeName());
- for (int i = 0; i < upperCaseButtons.size(); i++)
+ if (ucs.getLowerCaseColours() != null)
+ {
+ caseSensitive.setSelected(true);
+ lcaseColour.setEnabled(true);
+ resetButtonPanel(true);
+ for (int i = 0; i < lowerCaseButtons.size(); i++)
{
- JButton button = upperCaseButtons.get(i);
- button.setBackground(colors[i]);
+ JButton button = lowerCaseButtons.get(i);
+ button.setBackground(ucs.getLowerCaseColours()[i]);
}
+ }
+ else
+ {
+ caseSensitive.setSelected(false);
+ lcaseColour.setEnabled(false);
+ resetButtonPanel(false);
+ }
- addNewColourScheme(choice.getPath());
+ for (int i = 0; i < upperCaseButtons.size(); i++)
+ {
+ JButton button = upperCaseButtons.get(i);
+ button.setBackground(colors[i]);
}
+
+ addNewColourScheme(choice.getPath());
+ return null;
});
chooser.showOpenDialog(this);
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import java.util.TreeMap;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
import jalview.bin.Cache;
import jalview.bin.Console;
private static final String oldTempFileSuffix = "_oldfile_tobedeleted";
+ // thread pool used for completablefutures
+ private static final ExecutorService executorService = Executors
+ .newFixedThreadPool(3);
+
+ private static List<BackupFiles> savesInProgress = new ArrayList<>();
+
+ private CompletableFuture<Boolean> myFuture = null;
+
+ private boolean addSaveInProgress()
+ {
+ if (savesInProgress.contains(this))
+ {
+ return false;
+ }
+ else
+ {
+ this.setMyFuture();
+ savesInProgress.add(this);
+ return true;
+ }
+ }
+
+ private boolean removeSaveInProgress(boolean ret)
+ {
+ if (savesInProgress.contains(this))
+ {
+ this.getMyFuture().complete(ret);
+ // remove all occurrences
+ while (savesInProgress.remove(this))
+ {
+ }
+ return true;
+ }
+ return false;
+ }
+
+ private static CompletableFuture<Boolean> getNewFuture()
+ {
+ return new CompletableFuture<Boolean>()
+ {
+ };
+ }
+
+ private CompletableFuture<Boolean> getMyFuture()
+ {
+ return this.myFuture;
+ }
+
+ private void setMyFuture()
+ {
+ this.myFuture = getNewFuture();
+ }
+
+ public static boolean hasSavesInProgress()
+ {
+ boolean has = false;
+ for (CompletableFuture cf : savesInProgressCompletableFutures(true))
+ {
+ has |= !cf.isDone();
+ }
+ return has;
+ }
+
+ public static List<File> savesInProgressFiles(boolean all)
+ {
+ List<File> files = new ArrayList<>();
+ for (BackupFiles bfile : savesInProgress)
+ {
+ if (all || !bfile.getMyFuture().isDone())
+ files.add(bfile.getFile());
+ }
+ return files;
+ }
+
+ public static List<CompletableFuture<Boolean>> savesInProgressCompletableFutures(
+ boolean all)
+ {
+ List<CompletableFuture<Boolean>> cfs = new ArrayList<>();
+ for (BackupFiles bfile : savesInProgress)
+ {
+ if (all || !bfile.getMyFuture().isDone())
+ cfs.add(bfile.getMyFuture());
+ }
+ return cfs;
+ }
+
+ public static Future<Boolean> allSaved()
+ {
+ CompletableFuture<Boolean> f = new CompletableFuture<>();
+
+ executorService.submit(() -> {
+ for (BackupFiles buf : savesInProgress)
+ {
+ boolean allSaved = true;
+ try
+ {
+ allSaved &= buf.getMyFuture().get();
+ } catch (InterruptedException e)
+ {
+ Console.debug("InterruptedException waiting for files to save",
+ e);
+ } catch (ExecutionException e)
+ {
+ Console.debug("ExecutionException waiting for files to save", e);
+ }
+ f.complete(allSaved);
+ }
+ });
+ return f;
+ }
+
public BackupFiles(String filename)
{
this(new File(filename));
{
classInit();
this.file = file;
+
+ // add this file from the save in progress stack
+ addSaveInProgress();
+
BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
.getSavedBackupEntry();
this.suffix = bfpe.suffix;
tidyUpFiles();
}
+ // remove this file from the save in progress stack
+ removeSaveInProgress(rename);
+
return rename;
}
return ret;
}
+ public File getFile()
+ {
+ return file;
+ }
+
public static boolean moveFileToFile(File oldFile, File newFile)
{
Console.initLogger();
{
alignFrame.setFileName(file, format);
alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
+ alignFrame.getViewport().setSavedUpToDate(true);
}
if (proxyColourScheme != null)
{
*/
package jalview.io;
-import jalview.bin.Cache;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.LineartOptions;
-import jalview.gui.OOMWarning;
-import jalview.math.AlignmentDimension;
-import jalview.util.MessageManager;
-
import java.awt.Graphics;
import java.awt.print.PrinterException;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
+import java.util.concurrent.Callable;
import java.util.concurrent.atomic.AtomicBoolean;
import org.jfree.graphics2d.svg.SVGGraphics2D;
import org.jfree.graphics2d.svg.SVGHints;
+import jalview.bin.Cache;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.LineartOptions;
+import jalview.gui.OOMWarning;
+import jalview.math.AlignmentDimension;
+import jalview.util.MessageManager;
+
public class HtmlSvgOutput extends HTMLOutput
{
public HtmlSvgOutput(AlignmentPanel ap)
/*
* configure the action to run on OK in the dialog
*/
- Runnable okAction = new Runnable()
- {
- @Override
- public void run()
- {
- doOutput(textOption.get());
- }
+ Callable<Void> okAction = () -> {
+ doOutput(textOption.get());
+ return null;
};
/*
if (renderStyle.equalsIgnoreCase("Prompt each time") && !isHeadless())
{
LineartOptions svgOption = new LineartOptions("HTML", textOption);
- svgOption.setResponseAction(1, new Runnable()
- {
- @Override
- public void run()
- {
- setProgressMessage(MessageManager.formatMessage(
- "status.cancelled_image_export_operation",
- getDescription()));
- }
+ svgOption.setResponseAction(1, () -> {
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation",
+ getDescription()));
+ return null;
});
svgOption.setResponseAction(0, okAction);
svgOption.showDialog();
//////////////////////////////////////////////////////////////////
package jalview.io;
+import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.dialogrunner.DialogRunnerI;
+
import java.awt.Component;
import java.awt.Dimension;
import java.awt.EventQueue;
import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
+import java.util.concurrent.Callable;
import javax.swing.BoxLayout;
import javax.swing.DefaultListCellRenderer;
import javax.swing.JDialog;
import javax.swing.JFileChooser;
import javax.swing.JList;
+import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.SpringLayout;
{
private static final long serialVersionUID = 1L;
- private Map<Object, Runnable> callbacks = new HashMap<>();
+ private Map<Object, Callable> callbacks = new HashMap<>();
File selectedFile = null;
if (selectedFile.exists())
{
- int confirm = JvOptionPane.showConfirmDialog(this,
- MessageManager.getString("label.overwrite_existing_file"),
- MessageManager.getString("label.file_already_exists"),
- JvOptionPane.YES_NO_OPTION);
+ int confirm = Cache.getDefault("CONFIRM_OVERWRITE_FILE", true)
+ ? JvOptionPane.showConfirmDialog(this,
+ MessageManager
+ .getString("label.overwrite_existing_file"),
+ MessageManager.getString("label.file_already_exists"),
+ JvOptionPane.YES_NO_OPTION)
+ : JOptionPane.YES_OPTION;
if (confirm != JvOptionPane.YES_OPTION)
{
}
+ /*
+ @Override
+ public JalviewFileChooser setResponseHandler(Object response,
+ Runnable action)
+ {
+ callbacks.put(response, new Callable<Void>()
+ {
+ @Override
+ public Void call()
+ {
+ action.run();
+ return null;
+ }
+ });
+ return this;
+ }
+ */
+
@Override
- public DialogRunnerI setResponseHandler(Object response, Runnable action)
+ public DialogRunnerI setResponseHandler(Object response, Callable action)
{
callbacks.put(response, action);
return this;
{
return;
}
- Runnable action = callbacks.get(response);
+ Callable action = callbacks.get(response);
if (action != null)
{
- action.run();
+ try
+ {
+ action.call();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
}
}
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
+import jalview.gui.APQHandlers;
+import jalview.gui.Desktop;
import jalview.io.FileFormatException;
import jalview.util.MessageManager;
import jalview.util.Platform;
*/
private void jbInit() throws Exception
{
- boolean apqHandlersSet = false;
/**
* APQHandlers sets handlers for About, Preferences and Quit actions
* peculiar to macOS's application menu. APQHandlers will check to see if a
*/
try
{
- apqHandlersSet = APQHandlers.setAPQHandlers(this);
+ APQHandlers.setAPQHandlers((Desktop) this);
} catch (Exception e)
{
System.out.println("Cannot set APQHandlers");
@Override
public void actionPerformed(ActionEvent e)
{
- quit();
+ if (Desktop.instance != null)
+ Desktop.instance.desktopQuit();
}
});
aboutMenuItem.setText(MessageManager.getString("label.about"));
private static final String UTF_8 = "UTF-8";
/**
+ * used in decision if quit confirmation should be issued
+ */
+ private static boolean stateSavedUpToDate = false;
+
+ /**
* prefix for recovering datasets for alignments with multiple views where
* non-existent dataset IDs were written for some views
*/
{
AlignFrame[] frames = Desktop.getAlignFrames();
+ setStateSavedUpToDate(true);
+
+ if (Cache.getDefault("DEBUG_DELAY_SAVE", false))
+ {
+ int n = 20;
+ int i = 0;
+ while (i < n)
+ {
+ Console.debug("***** debugging save sleep " + i + "/" + n);
+ try
+ {
+ Thread.sleep(1000);
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ i++;
+ }
+ }
+
if (frames == null)
{
return;
FileOutputStream fos = new FileOutputStream(
doBackup ? backupfiles.getTempFilePath() : jarFile);
+ if (Cache.getDefault("DEBUG_DELAY_SAVE", false))
+ {
+ int n = 20;
+ int i = 0;
+ while (i < n)
+ {
+ Console.debug("***** debugging save sleep " + i + "/" + n);
+ try
+ {
+ Thread.sleep(1000);
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ i++;
+ }
+ }
+
JarOutputStream jout = new JarOutputStream(fos);
List<AlignFrame> frames = new ArrayList<>();
return colour;
}
+
+ public static void setStateSavedUpToDate(boolean s)
+ {
+ Console.debug("Setting overall stateSavedUpToDate to " + s);
+ stateSavedUpToDate = s;
+ }
+
+ public static boolean stateSavedUpToDate()
+ {
+ Console.debug("Returning overall stateSavedUpToDate value: "
+ + stateSavedUpToDate);
+ return stateSavedUpToDate;
+ }
+
+ public static boolean allSavedUpToDate()
+ {
+ if (stateSavedUpToDate()) // nothing happened since last project save
+ return true;
+
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames != null)
+ {
+ for (int i = 0; i < frames.length; i++)
+ {
+ if (frames[i] == null)
+ continue;
+ if (!frames[i].getViewport().savedUpToDate())
+ return false; // at least one alignment is not individually saved
+ }
+ }
+ return true;
+ }
}
*/
package jalview.util.dialogrunner;
+import java.util.concurrent.Callable;
+
/**
* An interface for blocking dialog response handling. This is motivated by
* JalviewJS - when running as Javascript, there is only a single thread, and
* @param action
* @return
*/
- DialogRunnerI setResponseHandler(Object response, Runnable action);
+ DialogRunnerI setResponseHandler(Object response, Callable<Void> action);
+
+ // DialogRunnerI setResponseHandler(Object response, Runnable action);
/**
* Runs the registered handler (if any) for the given response. The default
*/
package jalview.viewmodel;
+import java.awt.Color;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeaturesDisplayedI;
import jalview.api.ViewStyleI;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.project.Jalview2XML;
import jalview.renderer.ResidueShader;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
-import java.awt.Color;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
/**
* base class holding visualization and analysis attributes and common logic for
* an active alignment view displayed in the GUI
protected Deque<CommandI> redoList = new ArrayDeque<>();
/**
+ * used to determine if quit should be confirmed
+ */
+ private boolean savedUpToDate = false;
+
+ /**
* alignment displayed in the viewport. Please use get/setter
*/
protected AlignmentI alignment;
{
this.historyList.push(command);
broadcastCommand(command, false);
+ setSavedUpToDate(false);
+ Jalview2XML.setStateSavedUpToDate(false);
}
}
return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
false));
}
+
+ public void setSavedUpToDate(boolean s)
+ {
+ Console.debug(
+ "Setting " + this.getViewId() + " setSavedUpToDate to " + s);
+ savedUpToDate = s;
+ }
+
+ public boolean savedUpToDate()
+ {
+ Console.debug("Returning " + this.getViewId() + " savedUpToDate value: "
+ + savedUpToDate);
+ return savedUpToDate;
+ }
}
git://source.jalview.org / jalview.git / commitdiff