JAL-2629 add padding for .sto annotations to fix issues with hmmbuild

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index dbb33f3..ead653f 100644 (file)
--- 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);