X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=eac7cf2d61228ebe5ff868d039f49917ae051a8e;hb=6235128370382f0fecdf3ba1cc683052c5aa11e7;hp=85ea8e059fa918ed0a890b5750fc19d95e84e0bb;hpb=51d41d5951ea5865488d3f163b14d297cddd27b4;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 85ea8e0..eac7cf2 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -52,14 +52,16 @@ public class AppletFormatAdapter
    * that are writable by the application.
    */
   public static final String[] WRITABLE_EXTENSIONS = new String[]
-  { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+  { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+      "sto,stk" };
 
   /**
    * List of writable formats by the application. Order must correspond with the
    * WRITABLE_EXTENSIONS list of formats.
    */
   public static final String[] WRITABLE_FNAMES = new String[]
-  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+      "STH" };
 
   /**
    * List of readable format file extensions by application in order
@@ -455,7 +457,7 @@ public class AppletFormatAdapter
       }
       else if (format.equalsIgnoreCase("STH"))
       {
-        afile = new StockholmFile();
+        afile = new StockholmFile(alignment);
       }
       else if (format.equalsIgnoreCase("AMSA"))
       {
@@ -549,7 +551,6 @@ public class AppletFormatAdapter
           System.out
                   .println("Difference between free memory now and before is "
                           + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
-
         } catch (Exception e)
         {
           System.err.println("Exception when dealing with " + i