Merge branch 'improvement/JAL-4206_improve_JalviewFileChooser_for_flatlaf' into merge...

[jalview.git] / src / jalview / gui / Desktop.java

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 6fd70a9..66055a4 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -439,7 +439,7 @@ public class Desktop extends jalview.jbgui.GDesktop
          * 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";
@@ -536,6 +536,9 @@ public class Desktop extends jalview.jbgui.GDesktop
       setBounds(xPos, yPos, 900, 650);
     }
 
+    // start dialogue queue for single dialogues
+    startDialogQueue();
+
     if (!Platform.isJS())
     /**
      * Java only
@@ -871,7 +874,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         }
       } catch (Exception ex)
       {
-        System.out.println(
+        jalview.bin.Console.outPrintln(
                 "Unable to paste alignment from system clipboard:\n" + ex);
       }
     }
@@ -1076,7 +1079,36 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     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);
 
@@ -1601,7 +1633,7 @@ 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());
     }
   }
 
@@ -1832,7 +1864,7 @@ 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"));
 
@@ -3060,7 +3092,7 @@ 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;
 
@@ -3078,12 +3110,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       {
         if (dialogPause)
         {
-          try
-          {
-            block.acquire();
-          } catch (InterruptedException x)
-          {
-          }
+          acquireDialogQueue();
         }
         if (instance == null)
         {
@@ -3101,12 +3128,41 @@ public class Desktop extends jalview.jbgui.GDesktop
     });
   }
 
+  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;
   }
 
   /**
@@ -3357,7 +3413,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         {
           if (Platform.isAMacAndNotJS())
           {
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "Please ignore plist error - occurs due to problem with java 8 on OSX");
           }
         }
@@ -3599,8 +3655,42 @@ public class Desktop extends jalview.jbgui.GDesktop
     {
       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
+   * @return
+   */
+  public boolean operationsAreInProgress()
+  {
+    JInternalFrame[] frames = getAllFrames();
+    for (JInternalFrame frame:frames)
+    {
+      if (frame instanceof IProgressIndicator)
+      {
+        if (((IProgressIndicator)frame).operationInProgress())
+        {
+          return true;
+        }
+      }
     }
+    return operationInProgress();
   }
 }