Output jvsuffix, dbref

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