").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("
");
}
}
@@ -1398,6 +1460,8 @@ public class Desktop extends jalview.jbgui.GDesktop
message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS));
message.append(CITATION);
+ message.append("
");
+
return message.toString();
}
@@ -1405,15 +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
*
@@ -1422,8 +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());
}
}
@@ -1432,7 +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
@@ -1484,9 +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.");
}
/*
@@ -1499,7 +1558,7 @@ public class Desktop extends jalview.jbgui.GDesktop
@Override
protected void showMemusage_actionPerformed(ActionEvent e)
{
- desktop.showMemoryUsage(showMemusage.isSelected());
+ desktopPane.showMemoryUsage(showMemusage.isSelected());
}
/*
@@ -1536,13 +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();
@@ -1618,8 +1678,7 @@ public class Desktop extends jalview.jbgui.GDesktop
* DOCUMENT ME!
*/
@Override
- protected void preferences_actionPerformed(ActionEvent e)
- {
+ protected void preferences_actionPerformed(ActionEvent e) {
Preferences.openPreferences();
}
@@ -1663,8 +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()
@@ -1699,7 +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(
@@ -1771,9 +1829,9 @@ public class Desktop extends jalview.jbgui.GDesktop
new OOMWarning("Whilst loading project from " + choice, oom);
} catch (Exception ex)
{
- Cache.log.error(
+ jalview.bin.Console.error(
"Problems whilst loading project from " + choice, ex);
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(getDesktopPane(),
MessageManager.formatMessage(
"label.error_whilst_loading_project_from",
new Object[]
@@ -1817,7 +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();
@@ -1830,7 +1888,7 @@ public class Desktop extends jalview.jbgui.GDesktop
((GridLayout) progressPanel.getLayout()).setRows(
((GridLayout) progressPanel.getLayout()).getRows() + 1);
++totalProgressCount;
- instance.validate();
+ validate();
return thisprogress;
}
@@ -1884,7 +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
@@ -1926,9 +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)
{
@@ -2037,7 +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++)
{
@@ -2085,11 +2143,12 @@ public class Desktop extends jalview.jbgui.GDesktop
{
source.showFeatureSettingsUI();
}
+
}
public JInternalFrame[] getAllFrames()
{
- return desktop.getAllFrames();
+ return desktopPane.getAllFrames();
}
/**
@@ -2175,7 +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);
@@ -2278,6 +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());
}
}
@@ -2290,11 +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)
{
@@ -2339,7 +2400,7 @@ public class Desktop extends jalview.jbgui.GDesktop
*/
public GStructureViewer[] getJmols()
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
if (frames == null)
{
@@ -2374,8 +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"),
@@ -2433,12 +2494,10 @@ public class Desktop extends jalview.jbgui.GDesktop
*/
protected void addQuitHandler()
{
- getRootPane()
- .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
- KeyStroke
- .getKeyStroke(KeyEvent.VK_Q,
- jalview.util.ShortcutKeyMaskExWrapper
- .getMenuShortcutKeyMaskEx()),
+
+ getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
+ .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
+ Platform.SHORTCUT_KEY_MASK),
"Quit");
getRootPane().getActionMap().put("Quit", new AbstractAction()
{
@@ -2511,6 +2570,20 @@ public class Desktop extends jalview.jbgui.GDesktop
progressBars.put(Long.valueOf(id), addProgressPanel(message));
}
}
+
+ @Override
+ public void addProgressBar(long id, String message)
+ {
+ // TODO
+ throw new UnsupportedOperationException("not implemented");
+ }
+
+ @Override
+ public void removeProgressBar(long id)
+ {
+ //TODO
+ throw new UnsupportedOperationException("not implemented");
+ }
/*
* (non-Javadoc)
@@ -2576,7 +2649,7 @@ public class Desktop extends jalview.jbgui.GDesktop
*/
public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
{
- if (desktop != null)
+ if (getDesktopPane() != null)
{
AlignmentPanel[] aps = getAlignmentPanels(
viewport.getSequenceSetId());
@@ -2623,52 +2696,64 @@ 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.ws2.client.slivka.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());
}
}
}
@@ -2682,8 +2767,10 @@ 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))
@@ -2721,7 +2808,7 @@ 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,"
@@ -2739,7 +2826,7 @@ 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);
}
@@ -2758,7 +2845,7 @@ public class Desktop extends jalview.jbgui.GDesktop
*/
public static void showUrl(final String url)
{
- showUrl(url, Desktop.instance);
+ showUrl(url, getInstance());
}
/**
@@ -2787,7 +2874,7 @@ 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"),
@@ -2827,20 +2914,13 @@ 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.
}
@@ -2886,7 +2966,7 @@ public class Desktop extends jalview.jbgui.GDesktop
{
}
}
- if (instance == null)
+ if (Jalview.isHeadlessMode())
{
return;
}
@@ -2895,7 +2975,7 @@ 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);
}
}
});
@@ -2934,7 +3014,7 @@ 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());
}
};
@@ -3012,7 +3092,7 @@ public class Desktop extends jalview.jbgui.GDesktop
{
splitFrame.setLocation(geometry.getLocation());
}
- Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
+ addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
}
/*
@@ -3050,7 +3130,7 @@ 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)
@@ -3113,6 +3193,7 @@ public class Desktop extends jalview.jbgui.GDesktop
* - the payload from the drop event
* @throws Exception
*/
+ @SuppressWarnings("unchecked")
public static void transferFromDropTarget(List