X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=3a647169a8eb2ead5c32b31e7536cee61c0703d2;hb=4f77328104498504339216829abf5ea87e2791ec;hp=aad4a96ac52a0cb5858990ceb21c11bd2f81d88b;hpb=2bfa6fa77d4ad322d566bd52851c6981fb08509c;p=jalview.git

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index aad4a96..3a64716 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -428,15 +428,28 @@ public class AppVarna extends JInternalFrame
     {
       return;
     }
-    if (seqsel != null && seqsel.getSize() > 0)
+
+    RnaModel rnaModel = models.get(rna);
+
+    if (seqsel != null && seqsel.getSize() > 0
+            && seqsel.contains(rnaModel.seq))
     {
       int start = seqsel.getStartRes(), end = seqsel.getEndRes();
-      ShiftList shift = offsets.get(rna);
-      if (shift != null)
+      if (rnaModel.gapped)
+      {
+        ShiftList shift = offsets.get(rna);
+        if (shift != null)
+        {
+          start = shift.shift(start);
+          end = shift.shift(end);
+        }
+      }
+      else
       {
-        start = shift.shift(start);
-        end = shift.shift(end);
+        start = rnaModel.seq.findPosition(start) - rnaModel.seq.getStart();
+        end = rnaModel.seq.findPosition(end) - rnaModel.seq.getStart();
       }
+
       selectionHighlighter.highlightRegion(rna, start, end);
       selectionHighlighter.getLastHighlight()
               .setOutlineColor(seqsel.getOutlineColour());