JAL-2446 merged to spike branch

[jalview.git] / src / jalview / renderer / ScaleRenderer.java

diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
index 164c7c7..9fec256 100644 (file)
--- a/src/jalview/renderer/ScaleRenderer.java
+++ b/src/jalview/renderer/ScaleRenderer.java
@@ -34,7 +34,7 @@ import java.util.List;
  */
 public class ScaleRenderer
 {
-  public class ScaleMark
+  public final class ScaleMark
   {
     public final boolean major;
 
@@ -62,8 +62,8 @@ public class ScaleRenderer
    *         marker position in alignment column coords, a String to be rendered
    *         at the position (or null)
    */
-  public List<ScaleMark> calculateMarks(AlignViewportI av,
-          int startx, int endx)
+  public List<ScaleMark> calculateMarks(AlignViewportI av, int startx,
+          int endx)
   {
     int scalestartx = (startx / 10) * 10;
 
@@ -73,7 +73,7 @@ public class ScaleRenderer
     {
       // find bounds and set origin appopriately
       // locate first visible position for this sequence
-      int[] refbounds = av.getColumnSelection()
+      int[] refbounds = av.getAlignment().getHiddenColumns()
               .locateVisibleBoundsOfSequence(refSeq);
 
       refSp = refbounds[0];
@@ -96,12 +96,14 @@ public class ScaleRenderer
       {
         if (refSeq == null)
         {
-          iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1) + 1;
+          iadj = av.getAlignment().getHiddenColumns()
+                  .adjustForHiddenColumns(i - 1) + 1;
           string = String.valueOf(iadj);
         }
         else
         {
-          iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1);
+          iadj = av.getAlignment().getHiddenColumns()
+                  .adjustForHiddenColumns(i - 1);
           refN = refSeq.findPosition(iadj);
           // TODO show bounds if position is a gap
           // - ie L--R -> "1L|2R" for