Merge branch 'bug/JAL-2421overviewboxflicker' into

features/JAL-2388OverviewWindow

Conflicts:
	src/jalview/gui/AlignmentPanel.java

diff --combined src/jalview/gui/AlignmentPanel.java
index 3e24b94,d793e6a..146df38
--- 1/src/jalview/gui/AlignmentPanel.java
--- 2/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@@ -91,9 -91,9 +91,9 @@@ public class AlignmentPanel extends GAl
    // this value is set false when selection area being dragged
    boolean fastPaint = true;
  
-   int hextent = 0;
+   private int hextent = 0;
  
-   int vextent = 0;
+   private int vextent = 0;
  
    /*
     * Flag set while scrolling to follow complementary cDNA/protein scroll. When
@@@ -688,7 -688,6 +688,6 @@@
     */
    public void setScrollValues(int x, int y)
    {
-     // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
      if (av == null || av.getAlignment() == null)
      {
        return;
@@@ -698,6 -697,7 +697,7 @@@
  
      if (av.hasHiddenColumns())
      {
+       // reset the width to exclude hidden columns
        width = av.getColumnSelection().findColumnPosition(width);
      }
  
@@@ -734,6 -734,7 +734,8 @@@
        x = 0;
      }
  
++
+     // update endRes after x has (possibly) been adjusted
      av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
              .getCharWidth())) - 1);