import java.awt.geom.AffineTransform;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
+import java.beans.PropertyVetoException;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.List;
import java.util.ListIterator;
import java.util.Locale;
+import java.util.Map;
import java.util.Vector;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
* Send this message to stderr as the warning that follows (due to
* reflection) also goes to stderr.
*/
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Linux platform only! You may have the following warning next: \"WARNING: An illegal reflective access operation has occurred\"\nThis is expected and cannot be avoided, sorry about that.");
}
final String awtAppClassName = "awtAppClassName";
}
} catch (Exception ex)
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"Unable to paste alignment from system clipboard:\n" + ex);
}
}
setKeyBindings(frame);
- desktop.add(frame);
+ // Since the latest FlatLaf patch, we occasionally have problems showing structureViewer frames...
+ int tries=3;
+ boolean shown=false;
+ Exception last=null;
+ do
+ {
+ try
+ {
+ desktop.add(frame);
+ shown=true;
+ } catch (IllegalArgumentException iaex)
+ {
+ last=iaex;
+ tries--;
+ jalview.bin.Console.info(
+ "Squashed IllegalArgument Exception (" + tries + " left) for "+frame.getTitle(),
+ iaex);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException iex)
+ {
+ }
+ ;
+ }
+ } while (!shown && tries > 0);
+ if (!shown)
+ {
+ jalview.bin.Console.error("Serious Problem whilst showing window "+frame.getTitle(),last);
+ }
windowMenu.add(menuItem);
}
} catch (Exception ex)
{
- System.err.println("Error opening help: " + ex.getMessage());
+ jalview.bin.Console.errPrintln("Error opening help: " + ex.getMessage());
}
}
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"));
{
if (Platform.isAMacAndNotJS())
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Please ignore plist error - occurs due to problem with java 8 on OSX");
}
}
{
Desktop.instance.closeAll_actionPerformed(null);
Desktop.instance.setVisible(false);
- Desktop.instance.dispose();
+ Desktop us = Desktop.instance;
Desktop.instance = null;
+ // call dispose in a separate thread - try to avoid indirect deadlocks
+ new Thread(new Runnable() {
+ @Override
+ public void run()
+ {
+ ExecutorService dex = us.dialogExecutor;
+ if (dex!=null) {
+ dex.shutdownNow();
+ us.dialogExecutor=null;
+ us.block.drainPermits();
+ }
+ us.dispose();
+ }
+ }).start();
}
}
/**
- * checks if any progress bars are being displayed in any of the windows managed by the desktop
+ * checks if any progress bars are being displayed in any of the windows
+ * managed by the desktop
+ *
* @return
*/
public boolean operationsAreInProgress()
{
JInternalFrame[] frames = getAllFrames();
- for (JInternalFrame frame:frames)
+ for (JInternalFrame frame : frames)
{
if (frame instanceof IProgressIndicator)
{
- if (((IProgressIndicator)frame).operationInProgress())
+ if (((IProgressIndicator) frame).operationInProgress())
{
return true;
}
}
return operationInProgress();
}
+
+ /**
+ * keep track of modal JvOptionPanes open as modal dialogs for AlignFrames.
+ * The way the modal JInternalFrame is made means it cannot be a child of an
+ * AlignFrame, so closing the AlignFrame might leave the modal open :(
+ */
+ private static Map<AlignFrame, JInternalFrame> alignFrameModalMap = new HashMap<>();
+
+ protected static void addModal(AlignFrame af, JInternalFrame jif)
+ {
+ alignFrameModalMap.put(af, jif);
+ }
+
+ protected static void closeModal(AlignFrame af)
+ {
+ if (!alignFrameModalMap.containsKey(af))
+ {
+ return;
+ }
+ JInternalFrame jif = alignFrameModalMap.get(af);
+ if (jif != null)
+ {
+ try
+ {
+ jif.setClosed(true);
+ } catch (PropertyVetoException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ alignFrameModalMap.remove(af);
+ }
+
}