X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FScaleRenderer.java;h=6d4edd94b3bb811f690ae0fe232dd21968ccde15;hb=02bdd4e842db62a0c9c3a36bbddd2b4f7249df92;hp=d310705bb905705fee0b6465f52a4b75c0caebca;hpb=1e263f063aeb478185020687227ea688be7d0847;p=jalview.git

diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
index d310705..6d4edd9 100644
--- a/src/jalview/renderer/ScaleRenderer.java
+++ b/src/jalview/renderer/ScaleRenderer.java
@@ -68,17 +68,23 @@ public class ScaleRenderer
     int scalestartx = (startx / 10) * 10;
 
     SequenceI refSeq = av.getAlignment().getSeqrep();
-    int refSp = 0, refStartI = 0, refEndI = -1;
+    int refSp = 0;
+    int refStartI = 0;
+    int refEndI = -1;
     if (refSeq != null)
     {
-      // find bounds and set origin appopriately
+      // find bounds and set origin appropriately
       // locate first visible position for this sequence
-      int[] refbounds = av.getAlignment().getHiddenColumns()
+      refSp = av.getAlignment().getHiddenColumns()
               .locateVisibleBoundsOfSequence(refSeq);
 
-      refSp = refbounds[0];
-      refStartI = refbounds[1];
-      refEndI = refbounds[2];
+      refStartI = refSeq.findIndex(refSeq.getStart()) - 1;
+
+      int seqlength = refSeq.getLength();
+      // get sequence position past the end of the sequence
+      int pastEndPos = refSeq.findPosition(seqlength + 1);
+      refEndI = refSeq.findIndex(pastEndPos - 1) - 1;
+
       scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
     }