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=1758b5bb105dbdd29aa2b2f3384a6bf82682529b;hpb=b78a8a809f8ffbda3ca79e83d3df1c89064ef202;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 1758b5b..cfbac04 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -31,6 +31,7 @@ import java.io.File;
 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;
@@ -364,9 +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();
@@ -427,11 +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);
     }
   }
 
@@ -443,9 +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()
     {
@@ -472,11 +477,52 @@ public class AppJmol extends StructureViewerBase
     };
     String view = MessageManager.getString("action.view")
             .toLowerCase(Locale.ROOT);
-    ImageExporter exporter = new ImageExporter(writer,
+    final ImageExporter exporter = new ImageExporter(writer,
             getProgressIndicator(), type, getTitle());
-    
-    exporter.doExport(file, this, width, height, view, renderer, userBis);
-    
+
+    final Throwable[] exceptions = new Throwable[1];
+    exceptions[0] = null;
+    final AppJmol us = this;
+    try
+    {
+      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
+      {
+        Thread.sleep(25);
+      } while (runner.isAlive());
+    } catch (Throwable e)
+    {
+      throw new ImageOutputException(
+              "Unexpected error when generating image", e);
+    }
+    if (exceptions[0] != null)
+    {
+      if (exceptions[0] instanceof ImageOutputException)
+      {
+        throw ((ImageOutputException) exceptions[0]);
+      }
+      else
+      {
+        throw new ImageOutputException(
+                "Unexpected error when generating image", exceptions[0]);
+      }
+    }
   }
 
   @Override
@@ -488,7 +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());
     }
   }