JAL-2629 refactoring of Hmmer preferences

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 73fbc88..90c509e 100755 (executable)
--- 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();