From b809a0696ac3ac626b4abf98bad1efad33ad2112 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 2 Nov 2005 16:05:11 +0000
Subject: [PATCH] Output jvsuffix, dbref

---
 src/jalview/io/AppletFormatAdapter.java |    8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 80a624d..fa2373e 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -110,7 +110,10 @@
          *
          * @return DOCUMENT ME!
          */
-        public String formatSequences(String format, Vector seqs)
+        public String formatSequences(String format,
+                                      Vector seqs,
+                                      boolean dbref,
+                                      boolean jvsuffix)
         {
             SequenceI[] s = new SequenceI[seqs.size()];
 
@@ -150,6 +153,9 @@
                     afile = new PfamFile();
                 }
 
+                afile.addDBPrefix(dbref);
+                afile.addJVSuffix(jvsuffix);
+
                 afile.setSeqs(s);
 
                 return afile.print();
-- 
1.7.10.2