From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 9 May 2017 15:55:14 +0000 (+0100)
Subject: JAL-2507 unpaired RNA marked as ‘ ‘ in Stockholm SS line
X-Git-Tag: Release_2_10_2~3^2~88^2~13
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=938156d64565a0dc49af81eaf62743aeb03d8435;p=jalview.git

JAL-2507 unpaired RNA marked as ‘ ‘ in Stockholm SS line
---

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 32e6ff7..c2726a7 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1084,8 +1084,8 @@ public class StockholmFile extends AlignFile
     {
       if (annot == null)
       {
-        // sensible gap character if one is available or make one up
-        return sequenceI == null ? '-' : sequenceI.getCharAt(k);
+        // sensible gap character
+        return ' ';
       }
       else
       {