JAL-1551 spotless

[jalview.git] / src / jalview / io / StockholmFile.java

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index cff328b..28f062f 100644 (file)
--- 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)
       {