From a30d9ff391d01301e9733d386d2346bfc3e953d3 Mon Sep 17 00:00:00 2001
From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Mon, 14 Aug 2017 14:58:19 +0100
Subject: [PATCH] JAL-2629 add padding for .sto annotations to fix issues with
 hmmbuild

---
 src/jalview/io/StockholmFile.java |    7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index dbb33f3..ead653f 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1027,7 +1027,12 @@ public class StockholmFile extends AlignFile
           String seq = "";
           for (int k = 0; k < ann.length; k++)
           {
-            seq += outputCharacter(key, k, isrna, ann, s[i]);
+            char character = outputCharacter(key, k, isrna, ann, s[i]);
+            if (character == ' ')
+            {
+              character = '.';
+            }
+            seq += character;
           }
           out.append(seq);
           out.append(newline);
-- 
1.7.10.2