X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=cfbac044734f01e2f4148197c233682516ea2d08;hb=refs%2Fheads%2Ffeature%2FJAL-4274_configurable_bitmap_export_preferences;hp=a14fabbf4d7e52c12e2e35e245268965b1de0dec;hpb=4e0bf08fc16e9388bb76cdd3eac84d767d102690;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index a14fabb..cfbac04 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -28,10 +28,10 @@ import java.awt.Graphics;
 import java.awt.Graphics2D;
 import java.awt.RenderingHints;
 import java.io.File;
-import java.lang.reflect.InvocationTargetException;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
+import java.util.concurrent.Executors;
 
 import javax.swing.JPanel;
 import javax.swing.JSplitPane;
@@ -365,9 +365,10 @@ public class AppJmol extends StructureViewerBase
       }
       if (waitTotal > waitMax)
       {
-        System.err.println("Timed out waiting for Jmol to load files after "
-                + waitTotal + "ms");
-        // System.err.println("finished: " + jmb.isFinishedInit()
+        jalview.bin.Console.errPrintln(
+                "Timed out waiting for Jmol to load files after "
+                        + waitTotal + "ms");
+        // jalview.bin.Console.errPrintln("finished: " + jmb.isFinishedInit()
         // + "; loaded: " + Arrays.toString(jmb.getPdbFile())
         // + "; files: " + files.toString());
         jmb.getStructureFiles();
@@ -428,11 +429,14 @@ public class AppJmol extends StructureViewerBase
   @Override
   public void makePDBImage(ImageMaker.TYPE type)
   {
-    try {
-    makePDBImage(null, type, null,
-            BitmapImageSizing.nullBitmapImageSizing());
-    } catch (ImageOutputException ioex) {
-      Console.error("Unexpected error whilst writing "+type.toString(),ioex);
+    try
+    {
+      makePDBImage(null, type, null,
+              BitmapImageSizing.defaultBitmapImageSizing());
+    } catch (ImageOutputException ioex)
+    {
+      Console.error("Unexpected error whilst writing " + type.toString(),
+              ioex);
     }
   }
 
@@ -444,9 +448,9 @@ public class AppJmol extends StructureViewerBase
 
     BitmapImageSizing bis = ImageMaker.getScaleWidthHeight(width, height,
             userBis);
-    float usescale = bis.scale;
-    int usewidth = bis.width;
-    int useheight = bis.height;
+    float usescale = bis.scale();
+    int usewidth = bis.width();
+    int useheight = bis.height();
 
     ImageWriterI writer = new ImageWriterI()
     {
@@ -475,34 +479,37 @@ public class AppJmol extends StructureViewerBase
             .toLowerCase(Locale.ROOT);
     final ImageExporter exporter = new ImageExporter(writer,
             getProgressIndicator(), type, getTitle());
-    // hack to pass back and throw to caller
+
     final Throwable[] exceptions = new Throwable[1];
     exceptions[0] = null;
     final AppJmol us = this;
     try
     {
-      SwingUtilities.invokeAndWait(new Runnable()
+      Thread runner = Executors.defaultThreadFactory()
+              .newThread(new Runnable()
+              {
+                @Override
+                public void run()
+                {
+                  try
+                  {
+                    exporter.doExport(file, us, width, height, view,
+                            renderer, userBis);
+                  } catch (Throwable t)
+                  {
+                    exceptions[0] = t;
+                  }
+                }
+              });
+      runner.start();
+      do
       {
-        @Override
-        public void run()
-        {
-          try
-          {
-            exporter.doExport(file, us, width, height, view, renderer,
-                    userBis);
-          } catch (Throwable t)
-          {
-            exceptions[0] = t;
-          }
-        }
-      });
-    } catch (InvocationTargetException e)
+        Thread.sleep(25);
+      } while (runner.isAlive());
+    } catch (Throwable e)
     {
       throw new ImageOutputException(
               "Unexpected error when generating image", e);
-    } catch (InterruptedException e)
-    {
-      Console.debug("Interrupted whilst waiting for image export", e);
     }
     if (exceptions[0] != null)
     {
@@ -527,7 +534,8 @@ public class AppJmol extends StructureViewerBase
               .openURL("http://wiki.jmol.org");// http://jmol.sourceforge.net/docs/JmolUserGuide/");
     } catch (Exception ex)
     {
-      System.err.println("Show Jmol help failed with: " + ex.getMessage());
+      jalview.bin.Console
+              .errPrintln("Show Jmol help failed with: " + ex.getMessage());
     }
   }