JAL-2491 Tidies to Overview panel calls in light of new code

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index c3458f9..308a550 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -745,6 +745,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
+    // Note that this event is NOT fired by the AWT scrollbar when setValues is
+    // called. Instead manually call adjustHorizontal and adjustVertical
+    // directly.
     if (evt == null || evt.getSource() == apvscroll)
     {
       annotationPanel.setScrollOffset(apvscroll.getValue(), false);
@@ -896,8 +899,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
      * Scroll to position but centring the target residue. Also set a state flag
      * to prevent adjustmentValueChanged performing this recursively.
      */
-    // setFollowingComplementScroll(true);
-    // this should be scrollToPosition(sr,verticalOffset,
     scrollToPosition(sr, seqOffset, true, true);
   }
 

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 0f37544..c1b5f9c 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -151,7 +151,6 @@ public class OverviewPanel extends Panel implements Runnable,
     od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment()
             .getHiddenSequences(), av.getColumnSelection(), av
             .getRanges());
-    // ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
     ap.paintAlignment(false);
   }
 

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 1b047a3..095a573 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -108,6 +108,7 @@ public class OverviewPanel extends JPanel implements Runnable,
                 || (getHeight() != (od.getHeight())))
         {
           updateOverviewImage();
+          setBoxPosition();
         }
       }
     });
@@ -124,7 +125,6 @@ public class OverviewPanel extends JPanel implements Runnable,
                   .getColumnSelection(), av.getRanges());
           // TODO set via ViewportRanges in overview dimensions once JAL-2388 is
           // merged
-          // ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
     });
@@ -141,13 +141,12 @@ public class OverviewPanel extends JPanel implements Runnable,
                   .getColumnSelection(), av.getRanges());
           // TODO set via ViewportRanges in overview dimensions once JAL-2388 is
           // merged
-
-          // ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
     });
 
     updateOverviewImage();
+    setBoxPosition();
   }
 
   /**
@@ -243,7 +242,7 @@ public class OverviewPanel extends JPanel implements Runnable,
       lastMiniMe = miniMe;
     }
 
-    setBoxPosition();
+    // setBoxPosition();
   }
 
   /*

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index e4c24e1..1abc93b 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -60,12 +60,6 @@ public class OverviewDimensions
   // height of box
   private int boxHeight = -1;
 
-  // scroll position in viewport corresponding to boxX
-  private int scrollCol = -1;
-
-  // scroll position in viewport corresponding to boxY
-  private int scrollRow = -1;
-
   /**
    * Create an OverviewDimensions object
    * 
@@ -171,14 +165,14 @@ public class OverviewDimensions
       // went past the end of the alignment, adjust backwards
 
       // if last position was before the end of the alignment, need to update
-      if ((scrollCol + vpwidth - 1) < visAlignWidth)
+      if ((ranges.getStartRes() + vpwidth - 1) < visAlignWidth)
       {
         visXAsRes = hiddenCols.findColumnPosition(hiddenCols
                 .subtractVisibleColumns(vpwidth - 1, alwidth - 1));
       }
       else
       {
-        visXAsRes = scrollCol;
+        visXAsRes = ranges.getStartRes();
       }
     }
 
@@ -205,22 +199,19 @@ public class OverviewDimensions
     if (visYAsRes + vpheight - 1 > visAlignHeight)
     {
       // went past the end of the alignment, adjust backwards
-      if ((scrollRow + vpheight - 1) < visAlignHeight)
+      if ((ranges.getEndRes() + vpheight - 1) < visAlignHeight)
       {
         visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
                 .subtractVisibleRows(vpheight - 1, alheight - 1));
       }
       else
       {
-        visYAsRes = scrollRow;
+        visYAsRes = ranges.getEndRes();
       }
     }
 
-    // update scroll values
-    // scrollCol = visXAsRes;
-    // scrollRow = visYAsRes;
+    // update viewport
     ranges.setStartRes(visXAsRes);
-
     ranges.setStartSeq(visYAsRes);
   }
 
@@ -272,20 +263,12 @@ public class OverviewDimensions
    */
   public void drawBox(Graphics g)
   {
+    System.out.println("Drawbox: " + boxX + " " + boxY + " " + boxWidth
+            + " " + boxHeight);
     g.drawRect(boxX, boxY, boxWidth, boxHeight);
     g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
   }
 
-  /*public int getScrollCol()
-  {
-    return scrollCol;
-  }
-
-  public int getScrollRow()
-  {
-    return scrollRow;
-  }*/
-
   // TODO should be removed, when unit test has mock Graphics object available
   // to check boxX/boxY
   public int getBoxX()

diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index 267b50e..ac310cc 100644 (file)
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -145,27 +145,38 @@ public class ViewportRanges extends ViewportProperties
    */
   public void setEndRes(int res)
   {
+    int startres = res;
     int width = getViewportWidth();
-    setStartEndRes(res - width + 1, res);
+    if (startres + width - 1 > al.getWidth() - 1)
+    {
+      startres = al.getWidth() - width;
+    }
+    setStartEndRes(startres - width + 1, startres);
   }
 
   /**
-   * Set the first sequence visible in the viewport. Fires a property change
-   * event.
+   * Set the first sequence visible in the viewport, maintaining the height. If
+   * the viewport would extend past the last sequence, sets the viewport so it
+   * sits at the bottom of the alignment. Fires a property change event.
    * 
    * @param seq
    *          sequence position
    */
   public void setStartSeq(int seq)
   {
+    int startseq = seq;
     int height = getViewportHeight();
-    setStartEndSeq(seq, seq + height - 1);
+    if (startseq + height - 1 > al.getHeight() - 1)
+    {
+      startseq = al.getHeight() - height;
+    }
+    setStartEndSeq(startseq, startseq + height - 1);
   }
 
   /**
-   * Set start and end sequences at the same time. This method only fires one
-   * event for the two changes, and should be used in preference to separate
-   * calls to setStartSeq and setEndSeq.
+   * Set start and end sequences at the same time. The viewport height may
+   * change. This method only fires one event for the two changes, and should be
+   * used in preference to separate calls to setStartSeq and setEndSeq.
    * 
    * @param start
    *          the start sequence

diff --git a/test/jalview/viewmodel/OverviewDimensionsTest.java b/test/jalview/viewmodel/OverviewDimensionsTest.java
index 42b9289..7aa665f 100644 (file)
--- a/test/jalview/viewmodel/OverviewDimensionsTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsTest.java
@@ -76,10 +76,8 @@ public class OverviewDimensionsTest
     hiddenCols.revealAllHiddenColumns();
     
     vpranges = new ViewportRanges(al);
-    vpranges.setStartRes(0);
-    vpranges.setEndRes(62);
-    vpranges.setStartSeq(0);
-    vpranges.setEndSeq(17);
+    vpranges.setViewportStartAndHeight(0, 18);
+    vpranges.setViewportStartAndWidth(0, 63);
 
     viewHeight = vpranges.getEndSeq() - vpranges.getStartSeq() + 1;
     viewWidth = vpranges.getEndRes() - vpranges.getStartRes() + 1;
@@ -202,26 +200,26 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // negative boxX value reset to 0
     mouseClick(od, -5, 10);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollRow(),
+    assertEquals(vpranges.getStartSeq(),
             Math.round((float) 10 * alheight / od.getSequencesHeight()));
-    assertEquals(od.getScrollCol(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
 
     // negative boxY value reset to 0
     mouseClick(od, 6, -2);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) 6 * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // overly large boxX value reset to width-boxWidth
     mouseClick(od, 100, 6);
@@ -229,9 +227,10 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxY(), 6);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(),
+    assertEquals(
+            vpranges.getStartSeq(),
             Math.round((float) od.getBoxY() * alheight
                     / od.getSequencesHeight()));
 
@@ -241,13 +240,14 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxY(), od.getSequencesHeight() - od.getBoxHeight());
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
 
     // here (float) od.getBoxY() * alheight / od.getSequencesHeight() = 507.5
     // and round rounds to 508; however we get 507 working with row values
     // hence the subtraction of 1
-    assertEquals(od.getScrollRow(),
+    assertEquals(
+            vpranges.getStartSeq(),
             Math.round((float) od.getBoxY() * alheight
                     / od.getSequencesHeight()) - 1);
 
@@ -256,9 +256,10 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(),
+    assertEquals(
+            vpranges.getStartSeq(),
             Math.round((float) od.getBoxY() * alheight
                     / od.getSequencesHeight()));
 
@@ -272,19 +273,20 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxX(), oldboxx + 5);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
     assertEquals(od.getBoxY(), oldboxy + 2);
-    assertEquals(od.getScrollRow(),
+    assertEquals(
+            vpranges.getStartSeq(),
             Math.round((float) od.getBoxY() * alheight
                     / od.getSequencesHeight()));
 
     // click at top corner
     mouseClick(od, 0, 0);
     assertEquals(od.getBoxX(), 0);
-    assertEquals(od.getScrollCol(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
   }
@@ -301,8 +303,8 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // hide cols at start and check updated box position is correct
     // changes boxX but not boxwidth
@@ -326,13 +328,13 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollRow(), 0);
-    assertEquals(od.getScrollCol(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
 
     // click to right of hidden columns, box moves to click point
     testBoxIsAtClickPoint(40, 0);
-    assertEquals(od.getScrollRow(), 0);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartSeq(), 0);
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) 40 * alwidth / od.getWidth())
                     - (lastHiddenCol + 1));
 
@@ -346,10 +348,11 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxY(), 5);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth())
                     - (lastHiddenCol + 1));
-    assertEquals(od.getScrollRow(),
+    assertEquals(
+            vpranges.getStartSeq(),
             Math.round((float) od.getBoxY() * alheight
                     / od.getSequencesHeight()));
   }
@@ -366,8 +369,8 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
     
     // hide columns 63-73, no change to box position or dimensions
     int firstHidden = 63;
@@ -378,8 +381,8 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // move box so that it overlaps with hidden cols on one side
     // box width changes, boxX and scrollCol as for unhidden case
@@ -393,9 +396,9 @@ public class OverviewDimensionsTest
             Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
                     * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round(xpos * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // move box so that it completely covers hidden cols
     // box width changes, boxX and scrollCol as for hidden case
@@ -408,9 +411,9 @@ public class OverviewDimensionsTest
             Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
                     * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) xpos * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // move box so boxX is in hidden cols, box overhangs at right
     // boxX and scrollCol at left of hidden area, box width extends across
@@ -426,16 +429,16 @@ public class OverviewDimensionsTest
                     + Math.round((float) (lastHidden - firstHidden + 1)
                             * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(), firstHidden - 1);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), firstHidden - 1);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // move box so boxX is to right of hidden cols, but does not go beyond full
     // width of alignment
     // box width, boxX and scrollCol all as for non-hidden case
     xpos = 75;
     testBoxIsAtClickPoint(xpos, 0);
-    assertEquals(od.getScrollRow(), 0);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartSeq(), 0);
+    assertEquals(vpranges.getStartRes(),
             Math.round(xpos * alwidth / od.getWidth())
                     - (lastHidden - firstHidden + 1));
     
@@ -447,10 +450,12 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxY(), 5);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(
+            vpranges.getStartRes(),
             Math.round(((float) od.getBoxX() * alwidth / od.getWidth())
                     - (lastHidden - firstHidden + 1)));
-    assertEquals(od.getScrollRow(),
+    assertEquals(
+            vpranges.getStartSeq(),
             Math.round((float) od.getBoxY() * alheight
                     / od.getSequencesHeight()));
 
@@ -468,8 +473,8 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // hide columns 140-164, no change to box position or dimensions
     int firstHidden = 140;
@@ -479,15 +484,15 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // click to left of hidden cols, without overlapping
     // boxX, scrollCol and width as normal
     int xpos = 5;
     testBoxIsAtClickPoint(xpos, 0);
-    assertEquals(od.getScrollRow(), 0);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartSeq(), 0);
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) xpos * alwidth / od.getWidth()));
 
     // click to left of hidden cols, with overlap
@@ -500,9 +505,9 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // click in hidden cols
     // boxX and scrollCol adjusted for hidden cols, width normal
@@ -513,9 +518,9 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // click off end of alignment
     // boxX and scrollCol adjusted for hidden cols, width normal
@@ -526,9 +531,9 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
   }
 
   /**
@@ -796,8 +801,8 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // hide rows at start and check updated box position is correct
     // changes boxY but not boxheight
@@ -844,8 +849,8 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // hide rows in middle and check updated box position is correct
     // no changes
@@ -902,8 +907,8 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // hide rows at end and check updated box position is correct
     // no changes
@@ -958,8 +963,7 @@ public class OverviewDimensionsTest
    */
   private void moveViewportH(int startRes)
   {
-    vpranges.setStartRes(startRes);
-    vpranges.setEndRes(startRes + viewWidth - 1);
+    vpranges.setViewportStartAndWidth(startRes, viewWidth);
     od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
   }
 
@@ -968,8 +972,7 @@ public class OverviewDimensionsTest
    */
   private void moveViewportV(int startSeq)
   {
-    vpranges.setStartSeq(startSeq);
-    vpranges.setEndSeq(startSeq + viewHeight - 1);
+    vpranges.setViewportStartAndHeight(startSeq, viewHeight);
     od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
   }
 
@@ -978,10 +981,8 @@ public class OverviewDimensionsTest
    */
   private void moveViewport(int startRes, int startSeq)
   {
-    vpranges.setStartRes(startRes);
-    vpranges.setEndRes(startRes + viewWidth - 1);
-    vpranges.setStartSeq(startSeq);
-    vpranges.setEndSeq(startSeq + viewHeight - 1);
+    vpranges.setViewportStartAndWidth(startRes, viewWidth);
+    vpranges.setViewportStartAndHeight(startSeq, viewHeight);
     od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
   }
 
@@ -996,9 +997,6 @@ public class OverviewDimensionsTest
     // updates require an OverviewPanel to exist which it doesn't here
     // so call setBoxPosition() as it would be called by the AlignmentPanel
     // normally
-
-    vpranges.setStartRes(od.getScrollCol());
-    vpranges.setStartSeq(od.getScrollRow());
     od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
   }