X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=eeadcbf60401a71b499e915b6216f9c329a77ede;hb=49ff0aa506eb0b2e031fa3e8d16337e0c8cf2508;hp=5d645cafe30874f85fe0b58a06619da2571c91c8;hpb=0ae965fc73680bdc69b06986c060ff17342c4787;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 5d645ca..eeadcbf 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -219,7 +219,7 @@ public class StockholmFile extends AlignFile
     if (!r.search(nextLine()))
     {
       throw new IOException(MessageManager
-              .getString("exception.stockholm_invalid_format"));
+			    .getString("exception.stockholm_invalid_format") +" ("+r+")");
     }
     else
     {
@@ -1048,9 +1048,18 @@ 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)
       {