Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 5b935b7..4d0de1b 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -421,6 +421,14 @@ public class AppJmol extends StructureViewerBase
 
   }
 
 
   }
 

+  public boolean isRepainting()
+  {
+    if (renderPanel!=null && renderPanel.isVisible())
+    {
+      return renderPanel.repainting;
+    }
+    return false;
+  }

   /**
    * Outputs the Jmol viewer image as an image file, after prompting the user to
    * choose a file and (for EPS) choice of Text or Lineart character rendering
   /**
    * Outputs the Jmol viewer image as an image file, after prompting the user to
    * choose a file and (for EPS) choice of Text or Lineart character rendering

@@ -431,10 +439,17 @@ public class AppJmol extends StructureViewerBase
   @Override
   public void makePDBImage(ImageMaker.TYPE type)
   {
   @Override
   public void makePDBImage(ImageMaker.TYPE type)
   {

+    while (!isRepainting())
+    {
+      try {
+        Thread.sleep(2);
+      } catch (Exception q)
+      {}
+    }

     try
     {
       makePDBImage(null, type, null,
     try
     {
       makePDBImage(null, type, null,

-              BitmapImageSizing.defaultBitmapImageSizing(), null);
+              BitmapImageSizing.defaultBitmapImageSizing());

     } catch (ImageOutputException ioex)
     {
       Console.error("Unexpected error whilst writing " + type.toString(),
     } catch (ImageOutputException ioex)
     {
       Console.error("Unexpected error whilst writing " + type.toString(),

@@ -443,8 +458,7 @@ public class AppJmol extends StructureViewerBase
   }
 
   public void makePDBImage(File file, ImageMaker.TYPE type, String renderer,
   }
 
   public void makePDBImage(File file, ImageMaker.TYPE type, String renderer,

-          BitmapImageSizing userBis, List<String> extraCommands)
-          throws ImageOutputException
+          BitmapImageSizing userBis) throws ImageOutputException

   {
     int width = getWidth();
     int height = getHeight();
   {
     int width = getWidth();
     int height = getHeight();

@@ -473,24 +487,8 @@ public class AppJmol extends StructureViewerBase
           }
         }
 
           }
         }
 

-        String saveStateNameTemp = "JalviewSaveStateTemp";
-        jmb.executeCommand(
-                new StructureCommand("save STATE " + saveStateNameTemp),
-                false);
-
-        if (extraCommands != null)
-        {
-          for (String cmd : extraCommands)
-          {
-            jmb.executeCommand(new StructureCommand(cmd), false);
-          }
-        }
-

         jmb.jmolViewer.requestRepaintAndWait("image export");
         jmb.jmolViewer.renderScreenImage(ig2, usewidth, useheight);
         jmb.jmolViewer.requestRepaintAndWait("image export");
         jmb.jmolViewer.renderScreenImage(ig2, usewidth, useheight);

-        jmb.executeCommand(
-                new StructureCommand("restore STATE " + saveStateNameTemp),
-                false);

       }
     };
     String view = MessageManager.getString("action.view")
       }
     };
     String view = MessageManager.getString("action.view")

@@ -520,10 +518,17 @@ public class AppJmol extends StructureViewerBase
                 }
               });
       runner.start();
                 }
               });
       runner.start();

+      long time = 0;

       do
       {
         Thread.sleep(25);
       do
       {
         Thread.sleep(25);

-      } while (runner.isAlive());
+      } while (runner.isAlive() && time++ < 4000);
+      if (time >= 4000)
+      {
+        runner.interrupt();
+        throw new ImageOutputException(
+                "Jmol took too long to export. Waited for 100 seconds.");
+      }

     } catch (Throwable e)
     {
       throw new ImageOutputException(
     } catch (Throwable e)
     {
       throw new ImageOutputException(

@@ -637,10 +642,17 @@ public class AppJmol extends StructureViewerBase
       }
       else
       {
       }
       else
       {

-        jmb.jmolViewer.renderScreenImage(g, currentSize.width,
-                currentSize.height);
+        repainting=true;
+        synchronized (jmb)
+        {
+          jmb.jmolViewer.renderScreenImage(g, currentSize.width,
+                  currentSize.height);
+          
+        }
+        repainting=false;

       }
     }
       }
     }

+    volatile boolean repainting=false;

   }
 
   @Override
   }
 
   @Override