X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FScalePanel.java;h=aedb15790680f89c891aa79e49da177313936e54;hb=2303177fbc4c86e4a63c1e8efa8c8bc50516b6a5;hp=e595e6554eb05ff6f17e9e7ff44ba5a59cd2b96f;hpb=e224b72118c12cd77ae96f0f8d86c123e0416dc7;p=jalview.git

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index e595e65..aedb157 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -494,7 +494,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     int scalestartx = (startx / 10) * 10;
 
     SequenceI refSeq = av.getAlignment().getSeqrep();
-    int refSp = 0, refEp = -1;
+    int refSp = 0, refEp = -1, refStart = 0, refEnd = -1, refStartI = 0, refEndI = -1;
     if (refSeq != null)
     {
       // find bounds and set origin appopriately
@@ -502,8 +502,12 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       int[] refbounds = av.getColumnSelection()
               .locateVisibleBoundsOfSequence(refSeq);
 
-      refSp = refbounds[0] - 1;
-      refEp = refbounds[1] - 1;
+      refSp = refbounds[0];
+      refEp = refbounds[1];
+      refStart = refbounds[2];
+      refEnd = refbounds[3];
+      refStartI = refbounds[4];
+      refEndI = refbounds[5];
       scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
     }
 
@@ -536,13 +540,13 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
           // TODO show bounds if position is a gap
           // - ie L--R -> "1L|2R" for
           // marker
-          if (iadj < refSp)
+          if (iadj < refStartI)
           {
-            string = String.valueOf(iadj - refSp);
+            string = String.valueOf(iadj - refStartI);
           }
-          else if (iadj > refEp)
+          else if (iadj > refEndI)
           {
-            string = "+" + String.valueOf(iadj - refEp);
+            string = "+" + String.valueOf(iadj - refEndI);
           }
           else
           {