JAL-1835 added UI for BioJSON embbeding preference

[jalview.git] / src / jalview / io / AppletFormatAdapter.java

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index d3d4d6e..7dc263b 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -29,6 +29,7 @@ import jalview.datamodel.AlignmentView;
 import jalview.util.MessageManager;
 
 import java.io.File;
+import java.io.IOException;
 import java.io.InputStream;
 import java.util.List;
 
@@ -205,6 +206,10 @@ public class AppletFormatAdapter
   public static final boolean isValidFormat(String format,
           boolean forwriting)
   {
+    if (format == null)
+    {
+      return false;
+    }
     boolean valid = false;
     String[] format_list = (forwriting) ? WRITEABLE_FORMATS
             : READABLE_FORMATS;
@@ -339,7 +344,10 @@ public class AppletFormatAdapter
           ex.printStackTrace();
         }
       }
-
+      if (format.equalsIgnoreCase("HTML"))
+      {
+        throw new IOException(e.getMessage());
+      }
       // If we get to this stage, the format was not supported
       throw new java.io.IOException(SUPPORTED_FORMATS);
     }
@@ -483,7 +491,7 @@ public class AppletFormatAdapter
   private AlignmentI buildAlignmentFrom(AlignFile alignFile2)
   {
     // Standard boilerplate for creating alignment from parser
-    alignFile.configureForView(viewpanel);
+    // alignFile.configureForView(viewpanel);
 
     AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
 
@@ -519,7 +527,7 @@ public class AppletFormatAdapter
         aselview.addAnnotation(aa);
       }
     }
-
+    viewpanel = ap;
     return formatSequences(format, aselview, jvsuffix);
   }
 
@@ -597,11 +605,10 @@ public class AppletFormatAdapter
       {
         throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
       }
+
       afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);
-
       afile.setExportSettings(exportSettings);
-
       afile.configureForView(viewpanel);
 
       // check whether we were given a specific alignment to export, rather than