X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=a9763d3ae34dd7a69b1e98cf98171bc876434f84;hb=2e699d341f8e64868e3c279f9c02af617c4e9b44;hp=8a4c6696602c51e14cc171654727336f09ce378d;hpb=bc77e2f0f477053147a4e56b681131c710eb3ec8;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 8a4c669..a9763d3 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -142,7 +142,7 @@ public class Jalview2XML
     }
 
     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
-    public void SaveAlignment(AlignFrame af, String jarFile,
+    public boolean SaveAlignment(AlignFrame af, String jarFile,
         String fileName)
     {
         try
@@ -163,10 +163,12 @@ public class Jalview2XML
 
           out.close();
           jout.close();
+          return true;
         }
         catch (Exception ex)
         {
           ex.printStackTrace();
+          return false;
         }
     }
 
@@ -230,7 +232,7 @@ public class Jalview2XML
               vamsasSeq = new Sequence();
               vamsasSeq.setId(id + "");
               vamsasSeq.setName(jds.getName());
-              vamsasSeq.setSequence(jds.getSequence());
+              vamsasSeq.setSequence(jds.getSequenceAsString());
               vamsasSeq.setDescription(jds.getDescription());
 
               if (jds.getDatasetSequence().getDBRef() != null)
@@ -1005,7 +1007,6 @@ public class Jalview2XML
 
         BufferedReader in = new BufferedReader(new InputStreamReader(jin));
         File outFile = File.createTempFile("jalview_pdb", ".txt");
-        System.out.println("CREATE "+outFile);
         outFile.deleteOnExit();
         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
         String data;