X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMERCommands.java;fp=src%2Fjalview%2Fhmmer%2FHMMERCommands.java;h=4c1748b3aa2ca383a886f66875f122add3fa64b0;hb=dbdc8807d9059dacf65a087b7bcb8363be53fb8f;hp=ba4c57b58ef8d7b3e8141fb9c015ab917c2dfe02;hpb=14a3623b86376f7f896667d5268123b5feb45a3c;p=jalview.git

diff --git a/src/jalview/hmmer/HMMERCommands.java b/src/jalview/hmmer/HMMERCommands.java
index ba4c57b..4c1748b 100644
--- a/src/jalview/hmmer/HMMERCommands.java
+++ b/src/jalview/hmmer/HMMERCommands.java
@@ -1,7 +1,9 @@
 package jalview.hmmer;
 
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -128,12 +130,24 @@ public class HMMERCommands
    * @throws IOException
    */
   public void exportData(SequenceI[] seqs,
-          File stoLocation, HiddenMarkovModel hmm, File hmmLocation)
+          File stoLocation, HiddenMarkovModel hmm, File hmmLocation,
+          AnnotatedCollectionI al)
           throws IOException
   {
     if (seqs != null)
     {
-      StockholmFile file = new StockholmFile(new Alignment(seqs));
+      AlignmentI newAl = new Alignment(seqs);
+      if (stoLocation != null)
+      {
+        for (AlignmentAnnotation annot : al.getAlignmentAnnotation())
+        {
+          if (annot.label.contains("Reference") || "RF".equals(annot.label))
+          {
+            newAl.addAnnotation(annot);
+          }
+        }
+      }
+      StockholmFile file = new StockholmFile(newAl);
       String output = file.print(seqs, false);
       PrintWriter writer = new PrintWriter(stoLocation);
       writer.println(output);