X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=28f062f8d48478811156f9e212f4fedf1aa56b3a;hb=d4271d32477e99e9fbbfa5db3e11f1b79324e60d;hp=5d645cafe30874f85fe0b58a06619da2571c91c8;hpb=0ae965fc73680bdc69b06986c060ff17342c4787;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 5d645ca..28f062f 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -218,8 +218,9 @@ public class StockholmFile extends AlignFile
     r = new Regex("# STOCKHOLM ([\\d\\.]+)");
     if (!r.search(nextLine()))
     {
-      throw new IOException(MessageManager
-              .getString("exception.stockholm_invalid_format"));
+      throw new IOException(
+              MessageManager.getString("exception.stockholm_invalid_format")
+                      + " (" + r + ")");
     }
     else
     {
@@ -1048,9 +1049,18 @@ public class StockholmFile extends AlignFile
       }
     }
 
-    // output annotations
+    // output description and annotations
+
     while (i < slen && (seq = s[i]) != null)
     {
+      if (seq.getDescription() != null)
+      {
+        // out.append("#=GR ");
+        out.append(new Format("%-" + maxid + "s").form("#=GS "
+                + printId(seq, jvSuffix) + " DE " + seq.getDescription()));
+        out.append(newline);
+      }
+
       AlignmentAnnotation[] alAnot = seq.getAnnotation();
       if (alAnot != null)
       {