").append("Built: ")
+ .append(Cache.getDefault("BUILD_DATE", "unknown")).append(" from ")
+ .append(Cache.getBuildDetailsForSplash()).append("");
String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking");
- if (latestVersion.equals("Checking"))
- {
+ if (latestVersion.equals("Checking")) {
// JBP removed this message for 2.11: May be reinstated in future version
// message.append(" ...Checking latest version...");
- }
- else if (!latestVersion.equals(Cache.getProperty("VERSION")))
- {
+ } else if (!latestVersion.equals(Cache.getProperty("VERSION"))) {
boolean red = false;
- if (Cache.getProperty("VERSION").toLowerCase()
- .indexOf("automated build") == -1)
- {
+ if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT).indexOf("automated build") == -1) {
red = true;
// Displayed when code version and jnlp version do not match and code
// version is not a development build
message.append("
");
}
- message.append(" !! Version ")
- .append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
- .append(" is available for download from ")
- .append(Cache.getDefault("www.jalview.org",
- "http://www.jalview.org"))
- .append(" !!");
- if (red)
- {
+ message.append(" !! Version ").append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
+ .append(" is available for download from ")
+ .append(Cache.getDefault("www.jalview.org", "https://www.jalview.org")).append(" !!");
+ if (red) {
message.append("
");
}
}
@@ -1403,6 +1460,8 @@ public class Desktop extends jalview.jbgui.GDesktop
message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS));
message.append(CITATION);
+ message.append("
");
+
return message.toString();
}
@@ -1410,15 +1469,11 @@ public class Desktop extends jalview.jbgui.GDesktop
* Action on requesting Help documentation
*/
@Override
- public void documentationMenuItem_actionPerformed()
- {
- try
- {
- if (Platform.isJS())
- {
- BrowserLauncher.openURL("http://www.jalview.org/help.html");
- }
- else
+ public void documentationMenuItem_actionPerformed() {
+ try {
+ if (Platform.isJS()) {
+ BrowserLauncher.openURL("https://www.jalview.org/help.html");
+ } else
/**
* Java only
*
@@ -1427,8 +1482,7 @@ public class Desktop extends jalview.jbgui.GDesktop
{
Help.showHelpWindow();
}
- } catch (Exception ex)
- {
+ } catch (Exception ex) {
System.err.println("Error opening help: " + ex.getMessage());
}
}
@@ -1437,7 +1491,7 @@ public class Desktop extends jalview.jbgui.GDesktop
public void closeAll_actionPerformed(ActionEvent e)
{
// TODO show a progress bar while closing?
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
for (int i = 0; i < frames.length; i++)
{
try
@@ -1489,9 +1543,9 @@ public class Desktop extends jalview.jbgui.GDesktop
protected void garbageCollect_actionPerformed(ActionEvent e)
{
// We simply collect the garbage
- Cache.log.debug("Collecting garbage...");
+ jalview.bin.Console.debug("Collecting garbage...");
System.gc();
- Cache.log.debug("Finished garbage collection.");
+ jalview.bin.Console.debug("Finished garbage collection.");
}
/*
@@ -1504,7 +1558,7 @@ public class Desktop extends jalview.jbgui.GDesktop
@Override
protected void showMemusage_actionPerformed(ActionEvent e)
{
- desktop.showMemoryUsage(showMemusage.isSelected());
+ desktopPane.showMemoryUsage(showMemusage.isSelected());
}
/*
@@ -1541,13 +1595,14 @@ public class Desktop extends jalview.jbgui.GDesktop
void reorderAssociatedWindows(boolean minimize, boolean close)
{
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
if (frames == null || frames.length < 1)
{
return;
}
- AlignmentViewport source = null, target = null;
+ AlignViewportI source = null;
+ AlignViewportI target = null;
if (frames[0] instanceof AlignFrame)
{
source = ((AlignFrame) frames[0]).getCurrentView();
@@ -1623,9 +1678,8 @@ public class Desktop extends jalview.jbgui.GDesktop
* DOCUMENT ME!
*/
@Override
- protected void preferences_actionPerformed(ActionEvent e)
- {
- new Preferences();
+ protected void preferences_actionPerformed(ActionEvent e) {
+ Preferences.openPreferences();
}
/**
@@ -1668,8 +1722,7 @@ public class Desktop extends jalview.jbgui.GDesktop
}
}
- if (approveSave || autoSave)
- {
+ if (approveSave || autoSave) {
final Desktop me = this;
final java.io.File chosenFile = projectFile;
new Thread(new Runnable()
@@ -1681,16 +1734,17 @@ public class Desktop extends jalview.jbgui.GDesktop
setProgressBar(MessageManager.formatMessage(
"label.saving_jalview_project", new Object[]
{ chosenFile.getName() }), chosenFile.hashCode());
- Cache.setProperty("LAST_DIRECTORY",
- chosenFile.getParent());
+ Cache.setProperty("LAST_DIRECTORY", chosenFile.getParent());
// TODO catch and handle errors for savestate
// TODO prevent user from messing with the Desktop whilst we're saving
try
{
- boolean doBackup = BackupFiles.getEnabled();
- BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null;
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile)
+ : null;
- new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile);
+ new Jalview2XML().saveState(
+ doBackup ? backupfiles.getTempFile() : chosenFile);
if (doBackup)
{
@@ -1703,7 +1757,7 @@ public class Desktop extends jalview.jbgui.GDesktop
+ chosenFile.getName(), oom);
} catch (Exception ex)
{
- Cache.log.error("Problems whilst trying to save to "
+ jalview.bin.Console.error("Problems whilst trying to save to "
+ chosenFile.getName(), ex);
JvOptionPane.showMessageDialog(me,
MessageManager.formatMessage(
@@ -1716,7 +1770,7 @@ public class Desktop extends jalview.jbgui.GDesktop
setProgressBar(null, chosenFile.hashCode());
}
}).start();
- }
+ }
}
@Override
@@ -1747,8 +1801,10 @@ public class Desktop extends jalview.jbgui.GDesktop
"Jalview Project (old)" };
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
- "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles,
- // allowBackupFiles
+ "Jalview Project", true, BackupFiles.getEnabled()); // last two
+ // booleans:
+ // allFiles,
+ // allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
chooser.setResponseHandler(0, new Runnable()
@@ -1765,29 +1821,30 @@ public class Desktop extends jalview.jbgui.GDesktop
@Override
public void run()
{
- try
+ try
{
new Jalview2XML().loadJalviewAlign(selectedFile);
} catch (OutOfMemoryError oom)
- {
- new OOMWarning("Whilst loading project from " + choice, oom);
- } catch (Exception ex)
- {
- Cache.log.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 OOMWarning("Whilst loading project from " + choice, oom);
+ } catch (Exception ex)
+ {
+ jalview.bin.Console.error(
+ "Problems whilst loading project from " + choice, ex);
+ JvOptionPane.showMessageDialog(getDesktopPane(),
+ MessageManager.formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[]
+ { choice }),
+ MessageManager
+ .getString("label.couldnt_load_project"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
}
}, "Project Loader").start();
}
});
-
+
chooser.showOpenDialog(this);
}
@@ -1818,7 +1875,7 @@ public class Desktop extends jalview.jbgui.GDesktop
{
progressPanel = new JPanel(new GridLayout(1, 1));
totalProgressCount = 0;
- instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+ getContentPane().add(progressPanel, BorderLayout.SOUTH);
}
JPanel thisprogress = new JPanel(new BorderLayout(10, 5));
JProgressBar progressBar = new JProgressBar();
@@ -1831,7 +1888,7 @@ public class Desktop extends jalview.jbgui.GDesktop
((GridLayout) progressPanel.getLayout()).setRows(
((GridLayout) progressPanel.getLayout()).getRows() + 1);
++totalProgressCount;
- instance.validate();
+ validate();
return thisprogress;
}
@@ -1885,7 +1942,7 @@ public class Desktop extends jalview.jbgui.GDesktop
*/
public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
{
- if (Desktop.desktop == null)
+ if (getDesktopPane() == null)
{
// no frames created and in headless mode
// TODO: verify that frames are recoverable when in headless mode
@@ -1927,9 +1984,9 @@ public class Desktop extends jalview.jbgui.GDesktop
public static AlignmentViewport[] getViewports(String sequenceSetId)
{
List viewp = new ArrayList<>();
- if (desktop != null)
+ if (getDesktopPane() != null)
{
- AlignFrame[] frames = Desktop.getAlignFrames();
+ AlignFrame[] frames = getAlignFrames();
for (AlignFrame afr : frames)
{
@@ -1976,9 +2033,7 @@ public class Desktop extends jalview.jbgui.GDesktop
// FIXME: ideally should use UI interface API
FeatureSettings viewFeatureSettings = (af.featureSettings != null
- && af.featureSettings.isOpen())
- ? af.featureSettings
- : null;
+ && af.featureSettings.isOpen()) ? af.featureSettings : null;
Rectangle fsBounds = af.getFeatureSettingsGeometry();
for (int i = 0; i < size; i++)
{
@@ -2011,7 +2066,8 @@ public class Desktop extends jalview.jbgui.GDesktop
addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- // and materialise a new feature settings dialog instance for the new alignframe
+ // 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()
@@ -2029,9 +2085,9 @@ public class Desktop extends jalview.jbgui.GDesktop
/**
* Gather expanded views (separate AlignFrame's) with the same sequence set
- * identifier back in to this frame as additional views, and close the expanded
- * views. Note the expanded frames may themselves have multiple views. We take
- * the lot.
+ * identifier back in to this frame as additional views, and close the
+ * expanded views. Note the expanded frames may themselves have multiple
+ * views. We take the lot.
*
* @param source
*/
@@ -2039,7 +2095,7 @@ public class Desktop extends jalview.jbgui.GDesktop
{
source.viewport.setGatherViewsHere(true);
source.viewport.setExplodedGeometry(source.getBounds());
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
String viewId = source.viewport.getSequenceSetId();
for (int t = 0; t < frames.length; t++)
{
@@ -2083,16 +2139,16 @@ public class Desktop extends jalview.jbgui.GDesktop
}
// refresh the feature setting UI for the source frame if it exists
- if (source.featureSettings != null
- && source.featureSettings.isOpen())
+ if (source.featureSettings != null && source.featureSettings.isOpen())
{
source.showFeatureSettingsUI();
}
+
}
public JInternalFrame[] getAllFrames()
{
- return desktop.getAllFrames();
+ return desktopPane.getAllFrames();
}
/**
@@ -2178,7 +2234,7 @@ public class Desktop extends jalview.jbgui.GDesktop
});
msgPanel.add(jcb);
- JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
+ JvOptionPane.showMessageDialog(desktopPane, msgPanel,
MessageManager
.getString("label.SEQUENCE_ID_no_longer_used"),
JvOptionPane.WARNING_MESSAGE);
@@ -2189,12 +2245,12 @@ public class Desktop extends jalview.jbgui.GDesktop
/**
* Proxy class for JDesktopPane which optionally displays the current memory
- * usage and highlights the desktop area with a red bar if free memory runs low.
+ * usage and highlights the desktop area with a red bar if free memory runs
+ * low.
*
* @author AMW
*/
- public class MyDesktopPane extends JDesktopPane
- implements Runnable
+ public class MyDesktopPane extends JDesktopPane implements Runnable
{
private static final float ONE_MB = 1048576f;
@@ -2281,6 +2337,9 @@ public class Desktop extends jalview.jbgui.GDesktop
10, getHeight() - fm.getHeight());
}
}
+
+ // output debug scale message. Important for jalview.bin.HiDPISettingTest2
+ Desktop.debugScaleMessage(Desktop.getDesktopPane().getGraphics());
}
}
@@ -2293,11 +2352,10 @@ public class Desktop extends jalview.jbgui.GDesktop
{
if (Jalview.isHeadlessMode())
{
- // Desktop.desktop is null in headless mode
- return new AlignFrame[] { Jalview.currentAlignFrame };
+ return new AlignFrame[] { Jalview.getInstance().currentAlignFrame };
}
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = getDesktopPane().getAllFrames();
if (frames == null)
{
@@ -2342,7 +2400,7 @@ public class Desktop extends jalview.jbgui.GDesktop
*/
public GStructureViewer[] getJmols()
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
if (frames == null)
{
@@ -2377,8 +2435,8 @@ public class Desktop extends jalview.jbgui.GDesktop
openGroovyConsole();
} catch (Exception ex)
{
- Cache.log.error("Groovy Shell Creation failed.", ex);
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ jalview.bin.Console.error("Groovy Shell Creation failed.", ex);
+ JvOptionPane.showInternalMessageDialog(desktopPane,
MessageManager.getString("label.couldnt_create_groovy_shell"),
MessageManager.getString("label.groovy_support_failed"),
@@ -2431,14 +2489,15 @@ public class Desktop extends jalview.jbgui.GDesktop
}
/**
- * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this binding
- * when opened
+ * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
+ * binding when opened
*/
protected void addQuitHandler()
{
+
getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
.put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
+ Platform.SHORTCUT_KEY_MASK),
"Quit");
getRootPane().getActionMap().put("Quit", new AbstractAction()
{
@@ -2511,6 +2570,13 @@ public class Desktop extends jalview.jbgui.GDesktop
progressBars.put(Long.valueOf(id), addProgressPanel(message));
}
}
+
+ @Override
+ public void removeProgressBar(long id)
+ {
+ //TODO
+ throw new UnsupportedOperationException("not implemented");
+ }
/*
* (non-Javadoc)
@@ -2567,15 +2633,16 @@ public class Desktop extends jalview.jbgui.GDesktop
}
/**
- * This will return the first AlignFrame holding the given viewport instance. It
- * will break if there are more than one AlignFrames viewing a particular av.
+ * This will return the first AlignFrame holding the given viewport instance.
+ * It will break if there are more than one AlignFrames viewing a particular
+ * av.
*
* @param viewport
* @return alignFrame for viewport
*/
public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
{
- if (desktop != null)
+ if (getDesktopPane() != null)
{
AlignmentPanel[] aps = getAlignmentPanels(
viewport.getSequenceSetId());
@@ -2622,52 +2689,63 @@ public class Desktop extends jalview.jbgui.GDesktop
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)
{
- boolean alive = true;
- Thread t0 = null, t1 = null, t2 = null;
+ jalview.bin.Console.debug("Starting service discovery");
+
+ var tasks = new ArrayList>();
// JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
- if (true)
+
+ System.out.println("loading services");
+
+ /** @j2sIgnore */
{
// todo: changesupport handlers need to be transferred
if (discoverer == null)
{
- discoverer = new jalview.ws.jws1.Discoverer();
+ discoverer = jalview.ws.jws1.Discoverer.getInstance();
// register PCS handler for desktop.
discoverer.addPropertyChangeListener(changeSupport);
}
// JAL-940 - disabled JWS1 service configuration - always start discoverer
// until we phase out completely
- (t0 = new Thread(discoverer)).start();
+ var f = new FutureTask(discoverer, null);
+ new Thread(f).start();
+ tasks.add(f);
}
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .startDiscoverer(changeSupport);
+ tasks.add(jalview.ws.jws2.Jws2Discoverer.getInstance().startDiscoverer());
}
- Thread t3 = null;
+ if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
{
- // TODO: do rest service discovery
+ tasks.add(jalview.ws.slivkaws.SlivkaWSDiscoverer.getInstance().startDiscoverer());
}
if (blocking)
{
- while (alive)
- {
+ for (Future task : tasks) {
try
{
- Thread.sleep(15);
+ // block until all discovery tasks are done
+ task.get();
} catch (Exception e)
{
+ e.printStackTrace();
}
- alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive())
- || (t3 != null && t3.isAlive())
- || (t0 != null && t0.isAlive());
}
}
}
@@ -2681,8 +2759,10 @@ public class Desktop extends jalview.jbgui.GDesktop
{
if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
{
- final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .getErrorMessages();
+ final WSDiscovererI discoverer = jalview.ws.jws2.Jws2Discoverer
+ .getInstance();
+ final String ermsg = discoverer.getErrorMessages();
+ // CONFLICT:ALT:? final String ermsg = jalview.ws.jws2.Jws2Discoverer.getInstance()
if (ermsg != null)
{
if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
@@ -2720,7 +2800,7 @@ public class Desktop extends jalview.jbgui.GDesktop
*
* jd.waitForInput();
*/
- JvOptionPane.showConfirmDialog(Desktop.desktop,
+ JvOptionPane.showConfirmDialog(desktopPane,
new JLabel("
"
+ ermsg + "
"
+ "
It may be that you have invalid JABA URLs in your web service preferences,"
@@ -2738,7 +2818,7 @@ public class Desktop extends jalview.jbgui.GDesktop
}
else
{
- Cache.log.error(
+ jalview.bin.Console.error(
"Errors reported by JABA discovery service. Check web services preferences.\n"
+ ermsg);
}
@@ -2757,7 +2837,7 @@ public class Desktop extends jalview.jbgui.GDesktop
*/
public static void showUrl(final String url)
{
- showUrl(url, Desktop.instance);
+ showUrl(url, getInstance());
}
/**
@@ -2786,7 +2866,7 @@ public class Desktop extends jalview.jbgui.GDesktop
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(getDesktopPane(),
MessageManager
.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
@@ -2826,20 +2906,13 @@ public class Desktop extends jalview.jbgui.GDesktop
try
{
url = e.getURL().toString();
- Desktop.showUrl(url);
+ showUrl(url);
} catch (Exception x)
{
if (url != null)
{
- if (Cache.log != null)
- {
- Cache.log.error("Couldn't handle string " + url + " as a URL.");
- }
- else
- {
- System.err.println(
- "Couldn't handle string " + url + " as a URL.");
- }
+ // TODO does error send to stderr if no log exists ?
+ jalview.bin.Console.error("Couldn't handle string " + url + " as a URL.");
}
// ignore any exceptions due to dud links.
}
@@ -2885,7 +2958,7 @@ public class Desktop extends jalview.jbgui.GDesktop
{
}
}
- if (instance == null)
+ if (Jalview.isHeadlessMode())
{
return;
}
@@ -2894,7 +2967,7 @@ public class Desktop extends jalview.jbgui.GDesktop
SwingUtilities.invokeAndWait(prompter);
} catch (Exception q)
{
- Cache.log.warn("Unexpected Exception in dialog thread.", q);
+ jalview.bin.Console.warn("Unexpected Exception in dialog thread.", q);
}
}
});
@@ -2933,7 +3006,7 @@ public class Desktop extends jalview.jbgui.GDesktop
public void exportImage(Graphics g) throws Exception
{
paintAll(g);
- Cache.log.info("Successfully written snapshot to file "
+ jalview.bin.Console.info("Successfully written snapshot to file "
+ of.getAbsolutePath());
}
};
@@ -2945,8 +3018,8 @@ public class Desktop extends jalview.jbgui.GDesktop
/**
* Explode the views in the given SplitFrame into separate SplitFrame windows.
- * This respects (remembers) any previous 'exploded geometry' i.e. the size and
- * location last time the view was expanded (if any). However it does not
+ * This respects (remembers) any previous 'exploded geometry' i.e. the size
+ * and location last time the view was expanded (if any). However it does not
* remember the split pane divider location - this is set to match the
* 'exploding' frame.
*
@@ -3011,7 +3084,7 @@ public class Desktop extends jalview.jbgui.GDesktop
{
splitFrame.setLocation(geometry.getLocation());
}
- Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
+ addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
}
/*
@@ -3049,7 +3122,7 @@ public class Desktop extends jalview.jbgui.GDesktop
String topViewId = myTopFrame.viewport.getSequenceSetId();
String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
for (JInternalFrame frame : frames)
{
if (frame instanceof SplitFrame && frame != source)
@@ -3112,12 +3185,14 @@ public class Desktop extends jalview.jbgui.GDesktop
* - the payload from the drop event
* @throws Exception
*/
+ @SuppressWarnings("unchecked")
public static void transferFromDropTarget(List