X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=28f062f8d48478811156f9e212f4fedf1aa56b3a;hb=fecbdab721ea3f701b9c8107a5aac5371617943d;hp=cff328b040d35d7cb99db90779b53cc1c3c30928;hpb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index cff328b..28f062f 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -90,7 +90,7 @@ public class StockholmFile extends AlignFile
   // use the following regex to decide an annotations (whole) line is NOT an RNA
   // SS (it contains only E,H,e,h and other non-brace/non-alpha chars)
   private static final Regex NOT_RNASS = new Regex(
-          "^[^<>[\\](){}A-DF-Za-df-z]*$");
+          "^[^<>[\\](){}ADFJ-RUVWYZadfj-ruvwyz]*$");
 
   StringBuffer out; // output buffer
 
@@ -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)
       {