Added a flag to control if the "/<seq_start>-<seq_end>" field of

[jalview.git] / src / jalview / ws / Jemboss.java

diff --git a/src/jalview/ws/Jemboss.java b/src/jalview/ws/Jemboss.java
index 336be27..a8bf163 100755 (executable)
--- a/src/jalview/ws/Jemboss.java
+++ b/src/jalview/ws/Jemboss.java
@@ -134,12 +134,12 @@ public class Jemboss
     for (int i=0; i<sequences.length; i++) {
         myseq[i] = new Sequence(sequences[i]);
     }
-    // Uniqueify, and 
+    // Uniqueify, and
     Hashtable namemap = uniquify(myseq);
     // Load sequence file into hash
-    
+
     filesToMove.put("jalseqs.fasta",
-                    jalview.io.FastaFile.print(myseq,124,false).getBytes());
+                    jalview.io.FastaFile.print(myseq,124,false, false).getBytes());
 
     if(vamsas_server.getUseAuth() == true)
       if(vamsas_server.getServiceUserName() == null)
@@ -163,7 +163,7 @@ public class Jemboss
           String alfile = h.get(thiskey).toString();
           String format = IdentifyFile.Identify(alfile, "Paste");
           SequenceI[] alignment = null;
-          
+
           if (FormatProperties.contains(format))
             alignment = FormatAdapter.read(alfile, "Paste", format);
           else