X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFileLoader.java;h=90c509ec0ac529e401ebf7dbb22f99d7fe2df4b1;hb=81c9c8d460d5e2261111f7bdced2a75f1af64f9a;hp=73fbc884f48c72994357a6900c441dc6842bfe85;hpb=cc04412e8052d7c2546e8e7ffdcdcf8dc579f10a;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 73fbc88..90c509e 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -26,6 +26,7 @@ import jalview.api.FeaturesDisplayedI;
 import jalview.api.FeaturesSourceI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
@@ -426,6 +427,17 @@ public class FileLoader implements Runnable
               SequenceI seq = alignment
                       .getSequenceAt(alignment.getAbsoluteHeight() - 1);
               seq.setIsHMMConsensusSequence(true);
+              AlignmentAnnotation[] annots = viewport.getAlignment()
+                      .getAlignmentAnnotation();
+              for (AlignmentAnnotation annot : annots)
+              {
+                if ("RF".equals(annot.label)
+                        || annot.label.contains("Reference"))
+                {
+                  seq.mapToReference(annot);
+                  break;
+                }
+              }
               alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
               alignment.insertSequenceAt(0, seq);
               viewport.getAlignPanel().adjustAnnotationHeight();