From: Jim Procter <j.procter@dundee.ac.uk>
Date: Thu, 22 Jul 2021 17:02:19 +0000 (+0100)
Subject: JAL-3848 don’t include sequence limits in sequence id as it confuses slivka-0.8’s... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=65c32aa39e51d66319b48f0783ef152b07cd5d8e;p=jalview.git

JAL-3848 don’t include sequence limits in sequence id as it confuses slivka-0.8’s jalview-feature-file creation script
---

diff --git a/src/jalview/ws/slivkaws/SlivkaWSInstance.java b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
index 658d99e..0c71c35 100644
--- a/src/jalview/ws/slivkaws/SlivkaWSInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
@@ -95,8 +95,11 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
           format = FileFormat.Fasta;
           break;
         }
-        InputStream stream = new ByteArrayInputStream(
-            fa.formatSequences(format, sequences.toArray(new SequenceI[0]))
+        
+        // we avoid any use of Jalview's user facing export routines here
+        
+        InputStream stream = new ByteArrayInputStream(format.getWriter(null)
+                .print(sequences.toArray(new SequenceI[0]), false)
                 .getBytes());
         request.addFile(param.getId(), stream);
       }