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 806bfc1..0aa4878 100644 (file)
--- 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;
@@ -46,6 +47,7 @@ import jalview.datamodel.StructureViewerModel;
 import jalview.datamodel.StructureViewerModel.StructureData;
 import jalview.gui.ImageExporter.ImageWriterI;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.exceptions.ImageOutputException;
 import jalview.structure.StructureCommand;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.BrowserLauncher;
@@ -262,6 +264,8 @@ public class AppJmol extends StructureViewerBase
     }
     jmb.executeCommand(new StructureCommand(command), false);
     jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false);
+    jmb.executeCommand(new StructureCommand("set antialiasdisplay on"),
+            false);
     jmb.setFinishedInit(true);
   }
 
@@ -363,9 +367,10 @@ 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();
@@ -426,21 +431,28 @@ public class AppJmol extends StructureViewerBase
   @Override
   public void makePDBImage(ImageMaker.TYPE type)
   {
-    makePDBImage(null, type, null,
-            BitmapImageSizing.nullBitmapImageSizing());
+    try
+    {
+      makePDBImage(null, type, null,
+              BitmapImageSizing.defaultBitmapImageSizing());
+    } catch (ImageOutputException ioex)
+    {
+      Console.error("Unexpected error whilst writing " + type.toString(),
+              ioex);
+    }
   }
 
   public void makePDBImage(File file, ImageMaker.TYPE type, String renderer,
-          BitmapImageSizing userBis)
+          BitmapImageSizing userBis) throws ImageOutputException
   {
     int width = getWidth();
     int height = getHeight();
 
     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()
     {
@@ -452,22 +464,73 @@ public class AppJmol extends StructureViewerBase
                 RenderingHints.VALUE_ANTIALIAS_ON);
         if (type == TYPE.PNG && usescale > 0.0f)
         {
-          // for a scaled image, this scales down a bigger image to increase
-          // resolution
-
-          ig2.scale(1 / usescale, 1 / usescale);
+          // for a scaled image, this scales down a bigger image to give the
+          // right resolution
+          if (usescale > 0.0f)
+          {
+            ig2.scale(1 / usescale, 1 / usescale);
+          }
         }
 
-        jmb.jmolViewer.antialiased = true;
         jmb.jmolViewer.requestRepaintAndWait("image export");
         jmb.jmolViewer.renderScreenImage(ig2, usewidth, useheight);
       }
     };
     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();
+      long time = 0;
+      do
+      {
+        Thread.sleep(25);
+      } 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(
+              "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
@@ -479,7 +542,8 @@ 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());
     }
   }