import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.bin.Jalview;
+import jalview.io.BackupFiles;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.JalviewFileView;
import jalview.jbgui.GSplitFrame;
import jalview.jbgui.GStructureViewer;
+import jalview.project.Jalview2XML;
import jalview.structure.StructureSelectionManager;
import jalview.urls.IdOrgSettings;
import jalview.util.ImageMaker;
import java.awt.datatransfer.ClipboardOwner;
import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.Transferable;
-import java.awt.desktop.AboutEvent;
-import java.awt.desktop.AboutHandler;
-import java.awt.desktop.PreferencesEvent;
-import java.awt.desktop.PreferencesHandler;
-import java.awt.desktop.QuitEvent;
-import java.awt.desktop.QuitHandler;
-import java.awt.desktop.QuitResponse;
import java.awt.dnd.DnDConstants;
import java.awt.dnd.DropTargetDragEvent;
import java.awt.dnd.DropTargetDropEvent;
import java.awt.event.WindowEvent;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
-import java.io.BufferedInputStream;
import java.io.File;
-import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.net.URL;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JProgressBar;
import javax.swing.event.HyperlinkEvent.EventType;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
import org.stackoverflowusers.file.WindowsShortcut;
private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
- public static HashMap<String, FileWriter> savingFiles = new HashMap<>();
+ protected static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
+
+ public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>();
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
* constructor.
*/
instance = this;
- doVamsasClientCheck();
doConfigureStructurePrefs();
setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
- // setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- /* comments
- * galore
- * to
- * change the line numbers
- */
-
+ /*
if (!Platform.isAMac())
{
// this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
}
else
{
- // this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
- java.awt.Desktop desktop = java.awt.Desktop.getDesktop();
+ this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
+ }
+ */
- desktop.setAboutHandler(new AboutHandler()
- {
- @Override
- public void handleAbout(AboutEvent e)
- {
- aboutMenuItem_actionPerformed(null);
- }
- });
- desktop.setPreferencesHandler(new PreferencesHandler()
- {
- @Override
- public void handlePreferences(PreferencesEvent e)
- {
- preferences_actionPerformed(null);
- }
- });
- desktop.setQuitHandler(new QuitHandler()
- {
- @Override
- public void handleQuitRequestWith(QuitEvent e, QuitResponse r)
- {
- int n = JOptionPane.showConfirmDialog(null,
- MessageManager.getString("label.quit_jalview"),
- MessageManager.getString("action.quit"),
- JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE,
- null);
- if (n == JOptionPane.OK_OPTION)
- {
- System.out.println("Shortcut Quit confirmed by user");
- quit();
- }
- else
- {
- System.out.println("Shortcut Quit cancelled by user");
- }
- }
- });
+ try
+ {
+ APQHandlers.setAPQHandlers(this);
+ } catch (Exception e)
+ {
+ System.out.println("Cannot set APQHandlers");
+ // e.printStackTrace();
+ } catch (Throwable t)
+ {
+ System.out.println("Cannot set APQHandlers");
+ // t.printStackTrace();
+ }
- addWindowListener(new WindowAdapter()
- {
- @Override
- public void windowClosing(WindowEvent ev)
- {
- quit();
- }
- });
- }
+ addWindowListener(new WindowAdapter()
+ {
+
+ @Override
+ public void windowClosing(WindowEvent ev)
+ {
+ quit();
+ }
+ });
boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
false);
}
jconsole = new Console(this, showjconsole);
// add essential build information
- jconsole.setHeader(
- "Jalview Version: " + jalview.bin.Cache.getProperty("VERSION")
- + "\n" + "Jalview Installation: "
- + jalview.bin.Cache.getDefault("INSTALLATION",
- "unknown")
- + "\n" + "Build Date: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
- + "\n" + "Java version: "
- + System.getProperty("java.version") + "\n"
- + System.getProperty("os.arch") + " "
- + System.getProperty("os.name") + " "
- + System.getProperty("os.version"));
+ jconsole.setHeader(jalview.bin.Cache.getVersionDetailsForConsole());
showConsole(showjconsole);
return null;
}
- private void doVamsasClientCheck()
- {
- if (jalview.bin.Cache.vamsasJarsPresent())
- {
- setupVamsasDisconnectedGui();
- VamsasMenu.setVisible(true);
- final Desktop us = this;
- VamsasMenu.addMenuListener(new MenuListener()
- {
- // this listener remembers when the menu was first selected, and
- // doesn't rebuild the session list until it has been cleared and
- // reselected again.
- boolean refresh = true;
-
- @Override
- public void menuCanceled(MenuEvent e)
- {
- refresh = true;
- }
-
- @Override
- public void menuDeselected(MenuEvent e)
- {
- refresh = true;
- }
-
- @Override
- public void menuSelected(MenuEvent e)
- {
- if (refresh)
- {
- us.buildVamsasStMenu();
- refresh = false;
- }
- }
- });
- vamsasStart.setVisible(true);
- }
- }
-
void showPasteMenu(int x, int y)
{
JPopupMenu popup = new JPopupMenu();
} catch (java.lang.ClassCastException cex)
{
Cache.log.warn(
- "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
+ "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
cex);
}
}
KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
InputEvent.CTRL_DOWN_MASK);
KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask());
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
InputMap inputMap = frame
.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser chooser = JalviewFileChooser
- .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+ .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, BackupFiles.getEnabled());
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
panel.add(history);
history.setPreferredSize(new Dimension(400, 20));
history.setEditable(true);
- history.addItem("http://www.");
+ history.addItem("https://www.");
String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
@Override
public void quit()
{
- System.out.println("********** Desktop.quit()");
- System.out.println(savingFiles.toString());
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
screen.width + "");
message.append("<h1><strong>Version: "
+ jalview.bin.Cache.getProperty("VERSION")
+ "</strong></h1>");
- message.append("<strong>Last Updated: <em>"
+ message.append("<strong>Built: <em>"
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
- + "</em></strong>");
+ + "</em> from " + jalview.bin.Cache.getBuildDetailsForSplash()
+ + "</strong>");
}
else
if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
.equals("Checking"))
{
- message.append("<br>...Checking latest version...</br>");
+ // JBP removed this message for 2.11: May be reinstated in future version
+ // message.append("<br>...Checking latest version...</br>");
}
else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
.equals(jalview.bin.Cache.getProperty("VERSION")))
"..Checking..")
+ " is available for download from "
+ jalview.bin.Cache.getDefault("www.jalview.org",
- "http://www.jalview.org")
+ "https://www.jalview.org")
+ " !!");
if (red)
{
"AUTHORFNAMES",
"The Jalview Authors (See AUTHORS file for current list)")
+ "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
- + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+ + "<br><br>For help, see the FAQ at <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+ "<br><br>If you use Jalview, please cite:"
+ "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
}
Jalview.setCurrentAlignFrame(null);
System.out.println("ALL CLOSED");
- if (v_client != null)
- {
- // TODO clear binding to vamsas document objects on close_all
- }
/*
* reset state of singleton objects as appropriate (clear down session state
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Shows a file chooser dialog and writes out the current session as a Jalview
+ * project file
*/
@Override
- public void saveState_actionPerformed(ActionEvent e)
+ public void saveState_actionPerformed()
{
- JalviewFileChooser chooser = new JalviewFileChooser("jvp",
- "Jalview Project");
+ saveState_actionPerformed(false);
+ }
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_state"));
+ public void saveState_actionPerformed(boolean saveAs)
+ {
+ java.io.File projectFile = getProjectFile();
+ // autoSave indicates we already have a file and don't need to ask
+ boolean autoSave = projectFile != null && !saveAs
+ && BackupFiles.getEnabled();
- int value = chooser.showSaveDialog(this);
+ // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
+ // saveAs="+saveAs+", Backups
+ // "+(BackupFiles.getEnabled()?"enabled":"disabled"));
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ boolean approveSave = false;
+ if (!autoSave)
{
- final Desktop me = this;
- final java.io.File choice = chooser.getSelectedFile();
- setProjectFile(choice);
+ JalviewFileChooser chooser = new JalviewFileChooser("jvp",
+ "Jalview Project");
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager.getString("label.save_state"));
+
+ int value = chooser.showSaveDialog(this);
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ projectFile = chooser.getSelectedFile();
+ setProjectFile(projectFile);
+ approveSave = true;
+ }
+ }
+
+ if (approveSave || autoSave)
+ {
+ final Desktop me = this;
+ final java.io.File chosenFile = projectFile;
new Thread(new Runnable()
{
@Override
// TODO: refactor to Jalview desktop session controller action.
setProgressBar(MessageManager.formatMessage(
"label.saving_jalview_project", new Object[]
- { choice.getName() }), choice.hashCode());
+ { chosenFile.getName() }), chosenFile.hashCode());
jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- choice.getParent());
+ chosenFile.getParent());
// TODO catch and handle errors for savestate
// TODO prevent user from messing with the Desktop whilst we're saving
try
{
- new Jalview2XML().saveState(choice);
+ BackupFiles backupfiles = new BackupFiles(chosenFile);
+
+ new Jalview2XML().saveState(backupfiles.getTempFile());
+
+ backupfiles.setWriteSuccess(true);
+ backupfiles.rollBackupsAndRenameTempFile();
} catch (OutOfMemoryError oom)
{
- new OOMWarning(
- "Whilst saving current state to " + choice.getName(),
- oom);
+ new OOMWarning("Whilst saving current state to "
+ + chosenFile.getName(), oom);
} catch (Exception ex)
{
- Cache.log.error(
- "Problems whilst trying to save to " + choice.getName(),
- ex);
+ Cache.log.error("Problems whilst trying to save to "
+ + chosenFile.getName(), ex);
JvOptionPane.showMessageDialog(me,
MessageManager.formatMessage(
"label.error_whilst_saving_current_state_to",
new Object[]
- { choice.getName() }),
+ { chosenFile.getName() }),
MessageManager.getString("label.couldnt_save_project"),
JvOptionPane.WARNING_MESSAGE);
}
- setProgressBar(null, choice.hashCode());
+ setProgressBar(null, chosenFile.hashCode());
}
}).start();
}
}
+ @Override
+ public void saveAsState_actionPerformed(ActionEvent e)
+ {
+ saveState_actionPerformed(true);
+ }
+
private void setProjectFile(File choice)
{
this.projectFile = choice;
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Shows a file chooser dialog and tries to read in the selected file as a
+ * Jalview project
*/
@Override
- public void loadState_actionPerformed(ActionEvent e)
+ public void loadState_actionPerformed()
{
+ final String[] suffix = new String[] { "jvp", "jar" };
+ final String[] desc = new String[] { "Jalview Project",
+ "Jalview Project (old)" };
JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jvp", "jar" },
- new String[]
- { "Jalview Project", "Jalview Project (old)" },
- "Jalview Project");
+ Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
+ "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles,
+ // allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
return;
}
+ // FIXME: ideally should use UI interface API
+ FeatureSettings viewFeatureSettings = (af.featureSettings != null
+ && af.featureSettings.isOpen())
+ ? af.featureSettings
+ : null;
+ Rectangle fsBounds = af.getFeatureSettingsGeometry();
for (int i = 0; i < size; i++)
{
AlignmentPanel ap = af.alignPanels.get(i);
+
AlignFrame newaf = new AlignFrame(ap);
+ // transfer reference for existing feature settings to new alignFrame
+ if (ap == af.alignPanel)
+ {
+ if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap)
+ {
+ newaf.featureSettings = viewFeatureSettings;
+ }
+ newaf.setFeatureSettingsGeometry(fsBounds);
+ }
+
/*
* Restore the view's last exploded frame geometry if known. Multiple
* views from one exploded frame share and restore the same (frame)
addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
+ // and materialise a new feature settings dialog instance for the new alignframe
+ // (closes the old as if 'OK' was pressed)
+ if (ap == af.alignPanel && newaf.featureSettings != null
+ && newaf.featureSettings.isOpen()
+ && af.alignPanel.getAlignViewport().isShowSequenceFeatures())
+ {
+ newaf.showFeatureSettingsUI();
+ }
}
+ af.featureSettings = null;
af.alignPanels.clear();
af.closeMenuItem_actionPerformed(true);
source.viewport.setExplodedGeometry(source.getBounds());
JInternalFrame[] frames = desktop.getAllFrames();
String viewId = source.viewport.getSequenceSetId();
-
for (int t = 0; t < frames.length; t++)
{
if (frames[t] instanceof AlignFrame && frames[t] != source)
if (gatherThis)
{
- af.alignPanels.clear();
- af.closeMenuItem_actionPerformed(true);
- }
- }
- }
-
- }
-
- jalview.gui.VamsasApplication v_client = null;
-
- @Override
- public void vamsasImport_actionPerformed(ActionEvent e)
- {
- if (v_client == null)
- {
- // Load and try to start a session.
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(
- MessageManager.getString("label.open_saved_vamsas_session"));
- chooser.setToolTipText(MessageManager.getString(
- "label.select_vamsas_session_opened_as_new_vamsas_session"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String fle = chooser.getSelectedFile().toString();
- if (!vamsasImport(chooser.getSelectedFile()))
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.couldnt_import_as_vamsas_session",
- new Object[]
- { fle }),
- MessageManager
- .getString("label.vamsas_document_import_failed"),
- JvOptionPane.ERROR_MESSAGE);
- }
- }
- }
- else
- {
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- }
- }
-
- /**
- * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
- *
- * @param file
- * @return true if import was a success and a session was started.
- */
- public boolean vamsasImport(URL url)
- {
- // TODO: create progress bar
- if (v_client != null)
- {
-
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- return false;
- }
-
- try
- {
- // copy the URL content to a temporary local file
- // TODO: be a bit cleverer here with nio (?!)
- File file = File.createTempFile("vdocfromurl", ".vdj");
- FileOutputStream fos = new FileOutputStream(file);
- BufferedInputStream bis = new BufferedInputStream(url.openStream());
- byte[] buffer = new byte[2048];
- int ln;
- while ((ln = bis.read(buffer)) > -1)
- {
- fos.write(buffer, 0, ln);
- }
- bis.close();
- fos.close();
- v_client = new jalview.gui.VamsasApplication(this, file,
- url.toExternalForm());
- } catch (Exception ex)
- {
- jalview.bin.Cache.log.error(
- "Failed to create new vamsas session from contents of URL "
- + url,
- ex);
- return false;
- }
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- return v_client.inSession();
- }
-
- /**
- * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
- *
- * @param file
- * @return true if import was a success and a session was started.
- */
- public boolean vamsasImport(File file)
- {
- if (v_client != null)
- {
-
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- return false;
- }
-
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- try
- {
- v_client = new jalview.gui.VamsasApplication(this, file, null);
- } catch (Exception ex)
- {
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- jalview.bin.Cache.log.error(
- "New vamsas session from existing session file failed:", ex);
- return false;
- }
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- return v_client.inSession();
- }
-
- public boolean joinVamsasSession(String mysesid)
- {
- if (v_client != null)
- {
- throw new Error(MessageManager
- .getString("error.try_join_vamsas_session_another"));
- }
- if (mysesid == null)
- {
- throw new Error(
- MessageManager.getString("error.invalid_vamsas_session_id"));
- }
- v_client = new VamsasApplication(this, mysesid);
- setupVamsasConnectedGui();
- v_client.initial_update();
- return (v_client.inSession());
- }
-
- @Override
- public void vamsasStart_actionPerformed(ActionEvent e)
- {
- if (v_client == null)
- {
- // Start a session.
- // we just start a default session for moment.
- /*
- * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- * getProperty("LAST_DIRECTORY"));
- *
- * chooser.setFileView(new JalviewFileView());
- * chooser.setDialogTitle("Load Vamsas file");
- * chooser.setToolTipText("Import");
- *
- * int value = chooser.showOpenDialog(this);
- *
- * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
- * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
- */
- v_client = new VamsasApplication(this);
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- }
- else
- {
- // store current data in session.
- v_client.push_update(); // TODO: thread
- }
- }
-
- protected void setupVamsasConnectedGui()
- {
- vamsasStart.setText(MessageManager.getString("label.session_update"));
- vamsasSave.setVisible(true);
- vamsasStop.setVisible(true);
- vamsasImport.setVisible(false); // Document import to existing session is
- // not possible for vamsas-client-1.0.
- }
-
- protected void setupVamsasDisconnectedGui()
- {
- vamsasSave.setVisible(false);
- vamsasStop.setVisible(false);
- vamsasImport.setVisible(true);
- vamsasStart
- .setText(MessageManager.getString("label.new_vamsas_session"));
- }
-
- @Override
- public void vamsasStop_actionPerformed(ActionEvent e)
- {
- if (v_client != null)
- {
- v_client.end_session();
- v_client = null;
- setupVamsasDisconnectedGui();
- }
- }
-
- protected void buildVamsasStMenu()
- {
- if (v_client == null)
- {
- String[] sess = null;
- try
- {
- sess = VamsasApplication.getSessionList();
- } catch (Exception e)
- {
- jalview.bin.Cache.log.warn("Problem getting current sessions list.",
- e);
- sess = null;
- }
- if (sess != null)
- {
- jalview.bin.Cache.log.debug(
- "Got current sessions list: " + sess.length + " entries.");
- VamsasStMenu.removeAll();
- for (int i = 0; i < sess.length; i++)
- {
- JMenuItem sessit = new JMenuItem();
- sessit.setText(sess[i]);
- sessit.setToolTipText(MessageManager
- .formatMessage("label.connect_to_session", new Object[]
- { sess[i] }));
- final Desktop dsktp = this;
- final String mysesid = sess[i];
- sessit.addActionListener(new ActionListener()
+ if (af.featureSettings != null && af.featureSettings.isOpen())
{
-
- @Override
- public void actionPerformed(ActionEvent e)
+ if (source.featureSettings == null)
{
- if (dsktp.v_client == null)
- {
- Thread rthr = new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- dsktp.v_client = new VamsasApplication(dsktp, mysesid);
- dsktp.setupVamsasConnectedGui();
- dsktp.v_client.initial_update();
- }
-
- });
- rthr.start();
- }
- };
- });
- VamsasStMenu.add(sessit);
+ // preserve the feature settings geometry for this frame
+ source.featureSettings = af.featureSettings;
+ source.setFeatureSettingsGeometry(
+ af.getFeatureSettingsGeometry());
+ }
+ else
+ {
+ // close it and forget
+ af.featureSettings.close();
+ }
+ }
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
}
- // don't show an empty menu.
- VamsasStMenu.setVisible(sess.length > 0);
-
- }
- else
- {
- jalview.bin.Cache.log.debug("No current vamsas sessions.");
- VamsasStMenu.removeAll();
- VamsasStMenu.setVisible(false);
}
}
- else
+ // refresh the feature setting UI for the source frame if it exists
+ if (source.featureSettings != null
+ && source.featureSettings.isOpen())
{
- // Not interested in the content. Just hide ourselves.
- VamsasStMenu.setVisible(false);
+ source.showFeatureSettingsUI();
}
- }
-
- @Override
- public void vamsasSave_actionPerformed(ActionEvent e)
- {
- if (v_client != null)
- {
- // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
- JalviewFileChooser chooser = new JalviewFileChooser("vdj",
- "Vamsas Document");
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.save_vamsas_document_archive"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- java.io.File choice = chooser.getSelectedFile();
- JPanel progpanel = addProgressPanel(MessageManager
- .formatMessage("label.saving_vamsas_doc", new Object[]
- { choice.getName() }));
- Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- String warnmsg = null;
- String warnttl = null;
- try
- {
- v_client.vclient.storeDocument(choice);
- } catch (Error ex)
- {
- warnttl = "Serious Problem saving Vamsas Document";
- warnmsg = ex.toString();
- jalview.bin.Cache.log
- .error("Error Whilst saving document to " + choice, ex);
- } catch (Exception ex)
- {
- warnttl = "Problem saving Vamsas Document.";
- warnmsg = ex.toString();
- jalview.bin.Cache.log.warn(
- "Exception Whilst saving document to " + choice, ex);
-
- }
- removeProgressPanel(progpanel);
- if (warnmsg != null)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-
- warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
- }
- }
- }
- }
-
- JPanel vamUpdate = null;
-
- /**
- * hide vamsas user gui bits when a vamsas document event is being handled.
- *
- * @param b
- * true to hide gui, false to reveal gui
- */
- public void setVamsasUpdate(boolean b)
- {
- Cache.log.debug("Setting gui for Vamsas update "
- + (b ? "in progress" : "finished"));
-
- if (vamUpdate != null)
- {
- this.removeProgressPanel(vamUpdate);
- }
- if (b)
- {
- vamUpdate = this.addProgressPanel(
- MessageManager.getString("label.updating_vamsas_session"));
- }
- vamsasStart.setVisible(!b);
- vamsasStop.setVisible(!b);
- vamsasSave.setVisible(!b);
}
public JInternalFrame[] getAllFrames()
{
getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
.put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()),
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
"Quit");
getRootPane().getActionMap().put("Quit", new AbstractAction()
{
progressBarHandlers = new Hashtable<>();
}
- if (progressBars.get(new Long(id)) != null)
+ if (progressBars.get(Long.valueOf(id)) != null)
{
- JPanel panel = progressBars.remove(new Long(id));
- if (progressBarHandlers.contains(new Long(id)))
+ JPanel panel = progressBars.remove(Long.valueOf(id));
+ if (progressBarHandlers.contains(Long.valueOf(id)))
{
- progressBarHandlers.remove(new Long(id));
+ progressBarHandlers.remove(Long.valueOf(id));
}
removeProgressPanel(panel);
}
else
{
- progressBars.put(new Long(id), addProgressPanel(message));
+ progressBars.put(Long.valueOf(id), addProgressPanel(message));
}
}
final IProgressIndicatorHandler handler)
{
if (progressBarHandlers == null
- || !progressBars.containsKey(new Long(id)))
+ || !progressBars.containsKey(Long.valueOf(id)))
{
throw new Error(MessageManager.getString(
"error.call_setprogressbar_before_registering_handler"));
}
- progressBarHandlers.put(new Long(id), handler);
- final JPanel progressPanel = progressBars.get(new Long(id));
+ progressBarHandlers.put(Long.valueOf(id), handler);
+ final JPanel progressPanel = progressBars.get(Long.valueOf(id));
if (handler.canCancel())
{
JButton cancel = new JButton(
public VamsasApplication getVamsasApplication()
{
- return v_client;
+ // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS
+ return null;
}
this.inBatchMode = inBatchMode;
}
+ /**
+ * start service discovery and wait till it is done
+ */
public void startServiceDiscovery()
{
startServiceDiscovery(false);
}
+ /**
+ * start service discovery threads - blocking or non-blocking
+ *
+ * @param blocking
+ */
public void startServiceDiscovery(boolean blocking)
{
+ startServiceDiscovery(blocking,false);
+ }
+
+ /**
+ * start service discovery threads
+ *
+ * @param blocking
+ * - false means call returns immediately
+ * @param ignore_SHOW_JWS2_SERVICES_preference
+ * - when true JABA services are discovered regardless of user's JWS2
+ * discovery preference setting
+ */
+ public void startServiceDiscovery(boolean blocking,
+ boolean ignore_SHOW_JWS2_SERVICES_preference)
+ {
boolean alive = true;
Thread t0 = null, t1 = null, t2 = null;
// JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
(t0 = new Thread(discoverer)).start();
}
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ if (ignore_SHOW_JWS2_SERVICES_preference
+ || Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
.startDiscoverer(changeSupport);
git://source.jalview.org / jalview.git / blobdiff