")
.append("Built: ")
.append(Cache.getDefault("BUILD_DATE", "unknown"))
@@ -1381,7 +1639,7 @@ public class Desktop extends jalview.jbgui.GDesktop
else if (!latestVersion.equals(Cache.getProperty("VERSION")))
{
boolean red = false;
- if (Cache.getProperty("VERSION").toLowerCase()
+ if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT)
.indexOf("automated build") == -1)
{
red = true;
@@ -1394,7 +1652,7 @@ public class Desktop extends jalview.jbgui.GDesktop
.append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
.append(" is available for download from ")
.append(Cache.getDefault("www.jalview.org",
- "http://www.jalview.org"))
+ "https://www.jalview.org"))
.append(" !!");
if (red)
{
@@ -1405,6 +1663,8 @@ public class Desktop extends jalview.jbgui.GDesktop
message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS));
message.append(CITATION);
+ message.append("
");
+
return message.toString();
}
@@ -1418,7 +1678,7 @@ public class Desktop extends jalview.jbgui.GDesktop
{
if (Platform.isJS())
{
- BrowserLauncher.openURL("http://www.jalview.org/help.html");
+ BrowserLauncher.openURL("https://www.jalview.org/help.html");
}
else
/**
@@ -1431,7 +1691,8 @@ public class Desktop extends jalview.jbgui.GDesktop
}
} catch (Exception ex)
{
- System.err.println("Error opening help: " + ex.getMessage());
+ jalview.bin.Console
+ .errPrintln("Error opening help: " + ex.getMessage());
}
}
@@ -1449,8 +1710,8 @@ public class Desktop extends jalview.jbgui.GDesktop
{
}
}
- Jalview.setCurrentAlignFrame(null);
- System.out.println("ALL CLOSED");
+ Jalview.getInstance().setCurrentAlignFrame(null);
+ jalview.bin.Console.info("ALL CLOSED");
/*
* reset state of singleton objects as appropriate (clear down session state
@@ -1464,6 +1725,22 @@ public class Desktop extends jalview.jbgui.GDesktop
}
}
+ public int structureViewersStillRunningCount()
+ {
+ int count = 0;
+ JInternalFrame[] frames = desktop.getAllFrames();
+ for (int i = 0; i < frames.length; i++)
+ {
+ if (frames[i] != null
+ && frames[i] instanceof JalviewStructureDisplayI)
+ {
+ if (((JalviewStructureDisplayI) frames[i]).stillRunning())
+ count++;
+ }
+ }
+ return count;
+ }
+
@Override
public void raiseRelated_actionPerformed(ActionEvent e)
{
@@ -1491,17 +1768,16 @@ 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.");
}
/*
* (non-Javadoc)
*
- * @see
- * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
- * )
+ * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.
+ * ActionEvent )
*/
@Override
protected void showMemusage_actionPerformed(ActionEvent e)
@@ -1647,7 +1923,8 @@ public class Desktop extends jalview.jbgui.GDesktop
boolean autoSave = projectFile != null && !saveAs
&& BackupFiles.getEnabled();
- // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
+ // jalview.bin.Console.outPrintln("autoSave="+autoSave+",
+ // projectFile='"+projectFile+"',
// saveAs="+saveAs+", Backups
// "+(BackupFiles.getEnabled()?"enabled":"disabled"));
@@ -1682,7 +1959,8 @@ public class Desktop extends jalview.jbgui.GDesktop
// TODO: refactor to Jalview desktop session controller action.
setProgressBar(MessageManager.formatMessage(
"label.saving_jalview_project", new Object[]
- { chosenFile.getName() }), chosenFile.hashCode());
+ { chosenFile.getName() }),
+ IdUtils.newId(IdType.PROGRESS, chosenFile));
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
@@ -1706,7 +1984,7 @@ 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 +1994,7 @@ public class Desktop extends jalview.jbgui.GDesktop
MessageManager.getString("label.couldnt_save_project"),
JvOptionPane.WARNING_MESSAGE);
}
- setProgressBar(null, chosenFile.hashCode());
+ setProgressBar(null, IdUtils.newId(IdType.PROGRESS, chosenFile));
}
}).start();
}
@@ -1728,7 +2006,7 @@ public class Desktop extends jalview.jbgui.GDesktop
saveState_actionPerformed(true);
}
- private void setProjectFile(File choice)
+ protected void setProjectFile(File choice)
{
this.projectFile = choice;
}
@@ -1756,42 +2034,36 @@ public class Desktop extends jalview.jbgui.GDesktop
// 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)
- {
- 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 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();
});
chooser.showOpenDialog(this);
@@ -1898,7 +2170,7 @@ public class Desktop extends jalview.jbgui.GDesktop
return null;
}
List aps = new ArrayList<>();
- AlignFrame[] frames = getAlignFrames();
+ AlignFrame[] frames = Desktop.getDesktopAlignFrames();
if (frames == null)
{
return null;
@@ -1935,7 +2207,7 @@ public class Desktop extends jalview.jbgui.GDesktop
List viewp = new ArrayList<>();
if (desktop != null)
{
- AlignFrame[] frames = Desktop.getAlignFrames();
+ AlignFrame[] frames = Desktop.getDesktopAlignFrames();
for (AlignFrame afr : frames)
{
@@ -2001,9 +2273,8 @@ public class Desktop extends jalview.jbgui.GDesktop
}
/*
- * Restore the view's last exploded frame geometry if known. Multiple
- * views from one exploded frame share and restore the same (frame)
- * position and size.
+ * Restore the view's last exploded frame geometry if known. Multiple views from
+ * one exploded frame share and restore the same (frame) position and size.
*/
Rectangle geometry = ap.av.getExplodedGeometry();
if (geometry != null)
@@ -2092,6 +2363,7 @@ public class Desktop extends jalview.jbgui.GDesktop
{
source.showFeatureSettingsUI();
}
+
}
public JInternalFrame[] getAllFrames()
@@ -2296,12 +2568,12 @@ public class Desktop extends jalview.jbgui.GDesktop
*
* @return an array of AlignFrame, or null if none found
*/
- public static AlignFrame[] getAlignFrames()
+ @Override
+ public AlignFrame[] getAlignFrames()
{
- if (Jalview.isHeadlessMode())
+ if (desktop == null)
{
- // Desktop.desktop is null in headless mode
- return new AlignFrame[] { Jalview.currentAlignFrame };
+ return null;
}
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -2343,6 +2615,25 @@ public class Desktop extends jalview.jbgui.GDesktop
}
/**
+ * static version
+ */
+ public static AlignFrame[] getDesktopAlignFrames()
+ {
+ if (Jalview.isHeadlessMode())
+ {
+ // Desktop.desktop is null in headless mode
+ return Jalview.getInstance().getAlignFrames();
+ }
+
+ if (instance != null && desktop != null)
+ {
+ return instance.getAlignFrames();
+ }
+
+ return null;
+ }
+
+ /**
* Returns an array of any AppJmol frames in the Desktop (or null if none).
*
* @return
@@ -2384,7 +2675,7 @@ public class Desktop extends jalview.jbgui.GDesktop
openGroovyConsole();
} catch (Exception ex)
{
- Cache.log.error("Groovy Shell Creation failed.", ex);
+ jalview.bin.Console.error("Groovy Console creation failed.", ex);
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_create_groovy_shell"),
@@ -2400,15 +2691,18 @@ public class Desktop extends jalview.jbgui.GDesktop
{
if (groovyConsole == null)
{
- groovyConsole = new groovy.ui.Console();
- groovyConsole.setVariable("Jalview", this);
+ JalviewObjectI j = new JalviewObject(this);
+ groovyConsole = new groovy.console.ui.Console();
+ groovyConsole.setVariable(JalviewObjectI.jalviewObjectName, j);
+ groovyConsole.setVariable(JalviewObjectI.currentAlFrameName,
+ getCurrentAlignFrame());
groovyConsole.run();
/*
* We allow only one console at a time, so that AlignFrame menu option
- * 'Calculate | Run Groovy script' is unambiguous.
- * Disable 'Groovy Console', and enable 'Run script', when the console is
- * opened, and the reverse when it is closed
+ * 'Calculate | Run Groovy script' is unambiguous. Disable 'Groovy Console', and
+ * enable 'Run script', when the console is opened, and the reverse when it is
+ * closed
*/
Window window = (Window) groovyConsole.getFrame();
window.addWindowListener(new WindowAdapter()
@@ -2431,8 +2725,8 @@ public class Desktop extends jalview.jbgui.GDesktop
((Window) groovyConsole.getFrame()).setVisible(true);
/*
- * if we got this far, enable 'Run Groovy' in AlignFrame menus
- * and disable opening a second console
+ * if we got this far, enable 'Run Groovy' in AlignFrame menus and disable
+ * opening a second console
*/
enableExecuteGroovy(true);
}
@@ -2455,7 +2749,7 @@ public class Desktop extends jalview.jbgui.GDesktop
@Override
public void actionPerformed(ActionEvent e)
{
- quit();
+ desktopQuit();
}
});
}
@@ -2469,12 +2763,12 @@ public class Desktop extends jalview.jbgui.GDesktop
public void enableExecuteGroovy(boolean enabled)
{
/*
- * disable opening a second Groovy console
- * (or re-enable when the console is closed)
+ * disable opening a second Groovy console (or re-enable when the console is
+ * closed)
*/
groovyShell.setEnabled(!enabled);
- AlignFrame[] alignFrames = getAlignFrames();
+ AlignFrame[] alignFrames = getDesktopAlignFrames();
if (alignFrames != null)
{
for (AlignFrame af : alignFrames)
@@ -2499,8 +2793,6 @@ public class Desktop extends jalview.jbgui.GDesktop
@Override
public void setProgressBar(String message, long id)
{
- // Platform.timeCheck("Desktop " + message, Platform.TIME_MARK);
-
if (progressBars == null)
{
progressBars = new Hashtable<>();
@@ -2633,13 +2925,36 @@ 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)
{
+ 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
@@ -2657,7 +2972,8 @@ public class Desktop extends jalview.jbgui.GDesktop
(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);
@@ -2710,24 +3026,19 @@ public class Desktop extends jalview.jbgui.GDesktop
/*
* JalviewDialog jd =new JalviewDialog() {
*
- * @Override protected void cancelPressed() { // TODO
- * Auto-generated method stub
+ * @Override protected void cancelPressed() { // TODO Auto-generated method stub
*
- * }@Override protected void okPressed() { // TODO
- * Auto-generated method stub
+ * }@Override protected void okPressed() { // TODO Auto-generated method stub
*
- * }@Override protected void raiseClosed() { // TODO
- * Auto-generated method stub
+ * }@Override protected void raiseClosed() { // TODO Auto-generated method stub
*
- * } }; jd.initDialogFrame(new
- * JLabel("
" +
+ * ermsg +
* " It may be that you have invalid JABA URLs in your web service preferences,"
* + " or mis-configured HTTP proxy settings. " +
- * "Check the Connections and Web services tab of the"
- * +
- * " Tools->Preferences dialog box to change them.
"
- * ), true, true, "Web Service Configuration Problem", 450,
- * 400);
+ * "Check the Connections and Web services tab of the" +
+ * " Tools->Preferences dialog box to change them.
" ),
+ * true, true, "Web Service Configuration Problem", 450, 400);
*
* jd.waitForInput();
*/
@@ -2749,7 +3060,7 @@ 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);
}
@@ -2768,7 +3079,16 @@ public class Desktop extends jalview.jbgui.GDesktop
*/
public static void showUrl(final String url)
{
- showUrl(url, Desktop.instance);
+ if (url != null && !url.trim().equals(""))
+ {
+ jalview.bin.Console.info("Opening URL: " + url);
+ showUrl(url, Desktop.instance);
+ }
+ else
+ {
+ jalview.bin.Console.warn("Ignoring attempt to show an empty URL.");
+ }
+
}
/**
@@ -2792,7 +3112,7 @@ public class Desktop extends jalview.jbgui.GDesktop
{
progress.setProgressBar(MessageManager
.formatMessage("status.opening_params", new Object[]
- { url }), this.hashCode());
+ { url }), IdUtils.newId(IdType.PROGRESS, this));
}
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
@@ -2807,7 +3127,8 @@ public class Desktop extends jalview.jbgui.GDesktop
}
if (progress != null)
{
- progress.setProgressBar(null, this.hashCode());
+ progress.setProgressBar(null,
+ IdUtils.newId(IdType.PROGRESS, this));
}
}
}).start();
@@ -2842,15 +3163,8 @@ public class Desktop extends jalview.jbgui.GDesktop
{
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.");
- }
+ jalview.bin.Console
+ .error("Couldn't handle string " + url + " as a URL.");
}
// ignore any exceptions due to dud links.
}
@@ -2861,7 +3175,7 @@ public class Desktop extends jalview.jbgui.GDesktop
/**
* single thread that handles display of dialogs to user.
*/
- ExecutorService dialogExecutor = Executors.newSingleThreadExecutor();
+ ExecutorService dialogExecutor = Executors.newFixedThreadPool(3);
/**
* flag indicating if dialogExecutor should try to acquire a permit
@@ -2871,9 +3185,9 @@ public class Desktop extends jalview.jbgui.GDesktop
/**
* pause the queue
*/
- private java.util.concurrent.Semaphore block = new Semaphore(0);
+ private Semaphore block = new Semaphore(0);
- private static groovy.ui.Console groovyConsole;
+ private static groovy.console.ui.Console groovyConsole;
/**
* add another dialog thread to the queue
@@ -2889,12 +3203,7 @@ public class Desktop extends jalview.jbgui.GDesktop
{
if (dialogPause)
{
- try
- {
- block.acquire();
- } catch (InterruptedException x)
- {
- }
+ acquireDialogQueue();
}
if (instance == null)
{
@@ -2905,18 +3214,48 @@ 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);
}
}
});
}
+ private boolean dialogQueueStarted = false;
+
public void startDialogQueue()
{
+ if (dialogQueueStarted)
+ {
+ return;
+ }
// set the flag so we don't pause waiting for another permit and semaphore
// the current task to begin
- dialogPause = false;
+ releaseDialogQueue();
+ dialogQueueStarted = true;
+ }
+
+ public void acquireDialogQueue()
+ {
+ try
+ {
+ block.acquire();
+ dialogPause = true;
+ } catch (InterruptedException e)
+ {
+ jalview.bin.Console.debug("Interruption when acquiring DialogueQueue",
+ e);
+ }
+ }
+
+ public void releaseDialogQueue()
+ {
+ if (!dialogPause)
+ {
+ return;
+ }
block.release();
+ dialogPause = false;
}
/**
@@ -2944,14 +3283,22 @@ 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());
}
};
String title = "View of desktop";
ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS,
title);
- exporter.doExport(of, this, width, height, title);
+ try
+ {
+ exporter.doExport(of, this, width, height, title);
+ } catch (ImageOutputException ioex)
+ {
+ jalview.bin.Console.error(
+ "Unexpected error whilst writing Jalview desktop snapshot as EPS",
+ ioex);
+ }
}
/**
@@ -2978,16 +3325,15 @@ public class Desktop extends jalview.jbgui.GDesktop
}
/*
- * Processing in reverse order works, forwards order leaves the first panels
- * not visible. I don't know why!
+ * Processing in reverse order works, forwards order leaves the first panels not
+ * visible. I don't know why!
*/
for (int i = viewCount - 1; i >= 0; i--)
{
/*
- * Make new top and bottom frames. These take over the respective
- * AlignmentPanel objects, including their AlignmentViewports, so the
- * cdna/protein relationships between the viewports is carried over to the
- * new split frames.
+ * Make new top and bottom frames. These take over the respective AlignmentPanel
+ * objects, including their AlignmentViewports, so the cdna/protein
+ * relationships between the viewports is carried over to the new split frames.
*
* explodedGeometry holds the (x, y) position of the previously exploded
* SplitFrame, and the (width, height) of the AlignFrame component
@@ -3026,8 +3372,8 @@ public class Desktop extends jalview.jbgui.GDesktop
}
/*
- * Clear references to the panels (now relocated in the new SplitFrames)
- * before closing the old SplitFrame.
+ * Clear references to the panels (now relocated in the new SplitFrames) before
+ * closing the old SplitFrame.
*/
topPanels.clear();
bottomPanels.clear();
@@ -3103,7 +3449,7 @@ public class Desktop extends jalview.jbgui.GDesktop
myTopFrame.setDisplayedView(myTopFrame.alignPanel);
}
- public static groovy.ui.Console getGroovyConsole()
+ public static groovy.console.ui.Console getGroovyConsole()
{
return groovyConsole;
}
@@ -3128,28 +3474,6 @@ public class Desktop extends jalview.jbgui.GDesktop
Transferable t) throws Exception
{
- // BH 2018 changed List to List