From: kiramt <k.mourao@dundee.ac.uk>
Date: Fri, 3 Mar 2017 09:46:08 +0000 (+0000)
Subject: JAL-2388 Initial removal of hidden cols/seqs out of overview
X-Git-Tag: Release_2_10_2~3^2~92^2~56
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=571d15a897c11bdc2dda76ce03686604596f220d;p=jalview.git

JAL-2388 Initial removal of hidden cols/seqs out of overview
---

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 0d3f058..0e22af9 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -123,22 +123,23 @@ public class OverviewPanel extends Panel implements Runnable,
   @Override
   public void mousePressed(MouseEvent evt)
   {
-    od.setBoxPositionByMouse(evt.getX(), evt.getY());
-    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
-    ap.paintAlignment(false);
+    mouseAction(evt);
   }
 
   @Override
   public void mouseReleased(MouseEvent evt)
   {
-    od.setBoxPositionByMouse(evt.getX(), evt.getY());
-    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
-    ap.paintAlignment(false);
+    mouseAction(evt);
   }
 
   @Override
   public void mouseDragged(MouseEvent evt)
   {
+    mouseAction(evt);
+  }
+
+  private void mouseAction(MouseEvent evt)
+  {
     od.setBoxPositionByMouse(evt.getX(), evt.getY());
     ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
     ap.paintAlignment(false);
@@ -197,11 +198,10 @@ public class OverviewPanel extends Panel implements Runnable,
 
     Graphics mg = miniMe.getGraphics();
 
-    od.updateScales();
+    // od.updateScales();
 
     int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getHeight()
-            + av.getAlignment().getHiddenSequences().getSize();
+    int alheight = av.getAlignment().getAbsoluteHeight();
     float sampleCol = alwidth / (float) od.getWidth();
     float sampleRow = alheight / (float) od.getSequencesHeight();
 
@@ -244,7 +244,7 @@ public class OverviewPanel extends Panel implements Runnable,
     int sameCol = 0;
 
     jalview.datamodel.SequenceI seq = null;
-    final boolean hasHiddenRows = av.hasHiddenRows();
+
     final boolean hasHiddenCols = av.hasHiddenColumns();
     boolean hiddenRow = false;
 
@@ -256,33 +256,10 @@ public class OverviewPanel extends Panel implements Runnable,
       }
       else
       {
-        // this should largely be a method in Alignment
-        hiddenRow = false;
-        if (hasHiddenRows)
-        {
-          // look for sequence in hidden rows
-          seq = av.getAlignment().getHiddenSequences()
-                  .getHiddenSequence(lastrow);
-          if (seq == null)
-          {
-            // didn't find in hidden rows, adjust the index and retrieve from
-            // full row set
-            int index = av.getAlignment().getHiddenSequences()
-                    .findIndexWithoutHiddenSeqs(lastrow);
-
-            seq = av.getAlignment().getSequenceAt(index);
-          }
-          else
-          {
-            // found in hidden rows, ergo this row is hidden
-            hiddenRow = true;
-          }
-        }
-        else
-        {
-          seq = av.getAlignment().getSequenceAt(lastrow);
-        }
-        // end of Alignment method
+        // get the sequence which would be at alignment index 'lastrow' if no
+        // columns were hidden, and determine whether it is hidden or not
+        hiddenRow = av.getAlignment().isHidden(lastrow);
+        seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
 
         for (int col = 0; col < od.getWidth(); col++)
         {
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index a6f2bf4..2546d41 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -185,14 +185,7 @@ public class Alignment implements AlignmentI
     return AlignmentUtils.getSequencesByName(this);
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param i
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
+
   @Override
   public SequenceI getSequenceAt(int i)
   {
@@ -206,6 +199,28 @@ public class Alignment implements AlignmentI
     return null;
   }
 
+  @Override
+  public SequenceI getSequenceAtAbsoluteIndex(int i)
+  {
+    SequenceI seq = null;
+    if (getHiddenSequences().getSize() > 0)
+    {
+      seq = getHiddenSequences().getHiddenSequence(i);
+      if (seq == null)
+      {
+        // didn't find the sequence in the hidden sequences, get it from the
+        // alignment
+        int index = getHiddenSequences().findIndexWithoutHiddenSeqs(i);
+        seq = getSequenceAt(index);
+      }
+    }
+    else
+    {
+      seq = getSequenceAt(i);
+    }
+    return seq;
+  }
+
   /**
    * Adds a sequence to the alignment. Recalculates maxLength and size. Note
    * this currently does not recalculate whether or not the alignment is
@@ -668,22 +683,19 @@ public class Alignment implements AlignmentI
     return -1;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
+
   @Override
   public int getHeight()
   {
     return sequences.size();
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
+  @Override
+  public int getAbsoluteHeight()
+  {
+    return sequences.size() + getHiddenSequences().getSize();
+  }
+
   @Override
   public int getWidth()
   {
@@ -769,6 +781,12 @@ public class Alignment implements AlignmentI
     return true;
   }
 
+  @Override
+  public boolean isHidden(int alignmentIndex)
+  {
+    return (getHiddenSequences().getHiddenSequence(alignmentIndex) == null);
+  }
+
   /**
    * Delete all annotations, including auto-calculated if the flag is set true.
    * Returns true if at least one annotation was deleted, else false.
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 5d185cd..1ecff9a 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -31,13 +31,22 @@ import java.util.Set;
 public interface AlignmentI extends AnnotatedCollectionI
 {
   /**
-   * Calculates the number of sequences in an alignment
+   * Calculates the number of sequences in an alignment, excluding hidden
+   * sequences
    * 
    * @return Number of sequences in alignment
    */
   int getHeight();
 
   /**
+   * Calculates the number of sequences in an alignment, including hidden
+   * sequences
+   * 
+   * @return Number of sequences in alignment
+   */
+  int getAbsoluteHeight();
+
+  /**
    * 
    * Calculates the maximum width of the alignment, including gaps.
    * 
@@ -65,6 +74,15 @@ public interface AlignmentI extends AnnotatedCollectionI
   boolean isAligned(boolean includeHidden);
 
   /**
+   * Answers if the sequence at alignmentIndex is hidden
+   * 
+   * @param alignmentIndex
+   *          the index to check
+   * @return true if the sequence is hidden
+   */
+  boolean isHidden(int alignmentIndex);
+
+  /**
    * Gets sequences as a Synchronized collection
    * 
    * @return All sequences in alignment.
@@ -90,6 +108,17 @@ public interface AlignmentI extends AnnotatedCollectionI
   SequenceI getSequenceAt(int i);
 
   /**
+   * Find a specific sequence in this alignment.
+   * 
+   * @param i
+   *          Index of required sequence in full alignment, i.e. if all columns
+   *          were visible
+   * 
+   * @return SequenceI at given index.
+   */
+  SequenceI getSequenceAtAbsoluteIndex(int i);
+
+  /**
    * Returns a map of lists of sequences keyed by sequence name.
    * 
    * @return
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7bebfa9..5c264c0 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -310,7 +310,7 @@ public class AlignViewport extends AlignmentViewport implements
       residueShading.setConsensus(hconsensus);
     }
 
-    posProps = new ViewportPositionProps(this.alignment, this.viewStyle);
+    posProps = new ViewportPositionProps(this.alignment, this);
   }
 
   /**
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index d87285c..e553657 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -181,15 +181,11 @@ public class OverviewPanel extends JPanel implements Runnable
     mg.setColor(Color.orange);
     mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
 
-    // calculate scale based on current alignment width and height
-    od.updateScales();
-
     // calculate sampleCol and sampleRow
     // alignment width is max number of residues/bases
     // alignment height is number of sequences
     int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getHeight()
-            + av.getAlignment().getHiddenSequences().getSize();
+    int alheight = av.getAlignment().getAbsoluteHeight();
 
     // sampleCol or sampleRow is the width/height allocated to each residue
     // in particular, sometimes we may need more than one row/col of the
@@ -239,7 +235,7 @@ public class OverviewPanel extends JPanel implements Runnable
     int color = Color.white.getRGB();
 
     jalview.datamodel.SequenceI seq = null;
-    final boolean hasHiddenRows = av.hasHiddenRows();
+
     final boolean hasHiddenCols = av.hasHiddenColumns();
     boolean hiddenRow = false;
     // get hidden row and hidden column map once at beginning.
@@ -255,29 +251,10 @@ public class OverviewPanel extends JPanel implements Runnable
 
         lastrow = currentrow;
 
-        hiddenRow = false;
-        // should be method(s) in Alignment
-        if (hasHiddenRows)
-        {
-          seq = av.getAlignment().getHiddenSequences()
-                  .getHiddenSequence(lastrow);
-          if (seq == null)
-          {
-            int index = av.getAlignment().getHiddenSequences()
-                    .findIndexWithoutHiddenSeqs(lastrow);
-
-            seq = av.getAlignment().getSequenceAt(index);
-          }
-          else
-          {
-            hiddenRow = true;
-          }
-        }
-        else
-        {
-          seq = av.getAlignment().getSequenceAt(lastrow);
-        }
-        // end of Alignment method(s)
+        // get the sequence which would be at alignment index 'lastrow' if no
+        // columns were hidden, and determine whether it is hidden or not
+        hiddenRow = av.getAlignment().isHidden(lastrow);
+        seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
       }
 
       if (seq == null)
diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index b4c7c6d..fe9f4db 100644
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -77,8 +77,8 @@ public class OverviewDimensions
     this.posProps = av.getPosProps();
 
     // scale the initial size of overviewpanel to shape of alignment
-    float initialScale = (float) av.getAlignment().getWidth()
-            / (float) av.getAlignment().getHeight();
+    float initialScale = (float) posProps.getAlignmentWidthInCols()
+            / (float) posProps.getAlignmentHeightInRows();
 
     // TODO: in applet this was getSequenceConsensusHash()
     // check if it makes any functional difference
@@ -116,6 +116,9 @@ public class OverviewDimensions
    */
   public void setBoxPositionByMouse(int x, int y)
   {
+    int alwidth = av.getAlignment().getWidth();
+    int alheight = av.getAlignment().getAbsoluteHeight();
+
     boxX = x;
     boxY = y;
     if (boxY < 0)
@@ -124,7 +127,7 @@ public class OverviewDimensions
     }
     else if (boxY > (sequencesHeight - boxHeight))
     {
-      boxY = sequencesHeight - boxHeight + 1;
+      boxY = sequencesHeight - boxHeight;
     }
 
     if (boxX < 0)
@@ -136,28 +139,23 @@ public class OverviewDimensions
       if (av.hasHiddenColumns())
       {
         // Try smallest possible box
-        boxWidth = (int) (posProps.convertResiduesToPixels(posProps
-                .getEndRes() - posProps.getStartRes() + 1) * scalew);
-
-        // boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1)
-        // * av.getCharWidth() * scalew);
+        boxWidth = Math.round((float) (posProps.getEndRes()
+                - posProps.getStartRes() + 1)
+                * width / alwidth);
       }
       boxX = width - boxWidth;
     }
 
-    scrollCol = posProps.convertPixelsToResidues(Math.round(boxX / scalew));
-    scrollRow = posProps
-            .convertPixelsToSequences(Math.round(boxY / scaleh));
-
-    // scrollCol = (int) (boxX / scalew / av.getCharWidth());
-    // scrollRow = (int) (boxY / scaleh / av.getCharHeight());
+    scrollCol = Math.round((float) boxX * alwidth / width);
+    scrollRow = Math.round((float) boxY * alheight / sequencesHeight);
 
     if (av.hasHiddenColumns())
     {
-      if (!av.getColumnSelection().isVisible(scrollCol))
+      // doesn't seem to do anything useful
+      /*if (!av.getColumnSelection().isVisible(scrollCol))
       {
         return;
-      }
+      }*/
 
       scrollCol = av.getColumnSelection().findColumnPosition(scrollCol);
     }
@@ -176,60 +174,22 @@ public class OverviewDimensions
    */
   public void setBoxPosition()
   {
-    updateScales();
-
-    int startRes = av.getStartRes();
-    int endRes = av.getEndRes();
-
-    if (av.hasHiddenColumns())
-    {
-      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
-    }
-
-    int startSeq = av.getStartSeq();
-    int endSeq = av.getEndSeq();
-
-    if (av.hasHiddenRows())
-    {
-      startSeq = av.getAlignment().getHiddenSequences()
-              .adjustForHiddenSeqs(startSeq);
-
-      endSeq = av.getAlignment().getHiddenSequences()
-              .adjustForHiddenSeqs(endSeq);
-    }
+    int alwidth = av.getAlignment().getWidth();
+    int alheight = av.getAlignment().getAbsoluteHeight();
 
-    boxX = Math.round(posProps.convertResiduesToPixels(startRes) * scalew);
-    boxY = Math.round(posProps.convertSequencesToPixels(startSeq) * scaleh);
+    int startRes = av.getPosProps().getAbsoluteStartRes();
+    int endRes = av.getPosProps().getAbsoluteEndRes();
 
-    // boxX = (int) (startRes * av.getCharWidth() * scalew);
-    // boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+    int startSeq = av.getPosProps().getAbsoluteStartSeq();
+    int endSeq = av.getPosProps().getAbsoluteEndSeq();
 
-    boxWidth = Math.round(posProps.convertResiduesToPixels(endRes
-            - startRes
-            + 1) * scalew);
-    boxHeight = Math.round(posProps.convertSequencesToPixels(endSeq
-            - startSeq)
-            * scaleh);
+    boxX = Math.round((float) startRes * width / alwidth);
+    boxY = Math.round((float) startSeq * sequencesHeight / alheight);
 
-    // boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
-    // boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
-  }
-
-  /**
-   * Update width and height scales in terms of the alignment width and height
-   */
-  public void updateScales()
-  {
-    int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getHeight()
-            + av.getAlignment().getHiddenSequences().getSize();
-
-    int fullsizeWidth = alwidth * av.getCharWidth();
-    int fullsizeHeight = alheight * av.getCharHeight();
-
-    scalew = (float) width / fullsizeWidth;
-    scaleh = (float) sequencesHeight / fullsizeHeight;
+    boxWidth = Math
+            .round((float) (endRes - startRes + 1) * width / alwidth);
+    boxHeight = Math.round((float) (endSeq - startSeq) * sequencesHeight
+            / alheight);
   }
 
   /**
@@ -269,11 +229,13 @@ public class OverviewDimensions
     return boxY;
   }
 
+  // TODO should be removed, when unit test has mock Graphics object available
   public int getBoxWidth()
   {
     return boxWidth;
   }
 
+  // TODO should be removed, when unit test has mock Graphics object available
   public int getBoxHeight()
   {
     return boxHeight;
diff --git a/src/jalview/viewmodel/ViewportPositionProps.java b/src/jalview/viewmodel/ViewportPositionProps.java
index 1bb49af..f00d69f 100644
--- a/src/jalview/viewmodel/ViewportPositionProps.java
+++ b/src/jalview/viewmodel/ViewportPositionProps.java
@@ -20,7 +20,7 @@
  */
 package jalview.viewmodel;
 
-import jalview.api.ViewStyleI;
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentI;
 
 /**
@@ -42,23 +42,18 @@ public class ViewportPositionProps extends ViewportProperties
   // end sequence of viewport
   private int endSeq;
 
-  // character height
-  private int charHeight;
-
-  // character width
-  private int charWidth;
-
   // alignment
   private AlignmentI al;
 
-  // viewstyle
-  private ViewStyleI viewstyle;
+  // viewport
+  private AlignViewportI av; // this is a bad dependency, viewmodel should not
+                             // depend on api
 
   /**
    * Constructor
    * @param alignment TODO
    */
-  public ViewportPositionProps(AlignmentI alignment, ViewStyleI vstyle)
+  public ViewportPositionProps(AlignmentI alignment, AlignViewportI viewport)
   {
     // initial values of viewport settings
     this.startRes = 0;
@@ -66,17 +61,7 @@ public class ViewportPositionProps extends ViewportProperties
     this.startSeq = 0;
     this.endSeq = alignment.getHeight() - 1;
     this.al = alignment;
-    this.viewstyle = vstyle;
-  }
-
-  public void setCharHeight(int h)
-  {
-    viewstyle.setCharHeight(h);
-  }
-
-  public void setCharWidth(int w)
-  {
-    viewstyle.setCharWidth(w);
+    this.av = viewport;
   }
 
   // ways to update values
@@ -116,22 +101,22 @@ public class ViewportPositionProps extends ViewportProperties
 
   public void setEndRes(int res)
   {
-    if (res > al.getWidth() - 1)
+    if (res > al.getWidth())
     {
-      res = al.getWidth() - 1;
+      res = al.getWidth();
     }
-    else if (res < 0)
+    else if (res < 1)
     {
-      res = 0;
+      res = 1;
     }
     this.endRes = res;
   }
 
   public void setStartSeq(int seq)
   {
-    if (seq > al.getHeight())
+    if (seq > al.getHeight() - 1)
     {
-      seq = al.getHeight();
+      seq = al.getHeight() - 1;
     }
     else if (seq < 0)
     {
@@ -146,9 +131,9 @@ public class ViewportPositionProps extends ViewportProperties
     {
       seq = al.getHeight();
     }
-    else if (seq < 0)
+    else if (seq < 1)
     {
-      seq = 0;
+      seq = 1;
     }
     this.endSeq = seq;
   }
@@ -184,68 +169,62 @@ public class ViewportPositionProps extends ViewportProperties
   {
     return endSeq;
   }
+
   /**
-   * Get start residue of viewport
+   * Get absolute start residue of viewport
    */
-  public int getStartRes(boolean countHidden)
+  public int getAbsoluteStartRes()
   {
-    if (countHidden)
-    {
-      return 0; // av.getColumnSelection().adjustForHiddenColumns(startRes);
-    }
-    else
+    int start = startRes;
+
+    if (av.hasHiddenColumns())
     {
-      return startRes;
+      start = av.getColumnSelection().adjustForHiddenColumns(start);
     }
+    return start;
   }
 
   /**
-   * Convert distance x in viewport pixels to a distance in number of residues
-   * 
-   * @param x
-   *          number of pixels
-   * @return number of residues
+   * Get absolute start residue of viewport
    */
-  public int convertPixelsToResidues(int x)
+  public int getAbsoluteEndRes()
   {
-    return Math.round((float) x / viewstyle.getCharWidth());
-    // return (int) ((float) x / viewstyle.getCharWidth());
-  }
+    int end = endRes;
 
-  /**
-   * Convert distance y in viewport pixels to a distance in number of sequences
-   * 
-   * @param y
-   *          number of pixels
-   * @return number of sequences
-   */
-  public int convertPixelsToSequences(int y)
-  {
-    return Math.round((float) y / viewstyle.getCharHeight());
-    // return (int) ((float) y / viewstyle.getCharHeight());
+    if (av.hasHiddenColumns())
+    {
+      end = av.getColumnSelection().adjustForHiddenColumns(end);
+    }
+    return end;
   }
-  
+
   /**
-   * Convert number of sequences s to a height in viewport pixels
-   * 
-   * @param s
-   *          number of sequences
-   * @return number of pixels
+   * Get absolute start sequence of viewport
    */
-  public int convertSequencesToPixels(int s)
+  public int getAbsoluteStartSeq()
   {
-    return (s * viewstyle.getCharHeight());
+    int start = startSeq;
+
+    if (av.hasHiddenRows())
+    {
+      start = av.getAlignment().getHiddenSequences()
+              .adjustForHiddenSeqs(start);
+    }
+    return start;
   }
 
   /**
-   * Convert number of residues r to a width in viewport pixels
-   * 
-   * @param r
-   *          number of residues
-   * @return number of pixels
+   * Get absolute end sequence of viewport
    */
-  public int convertResiduesToPixels(int r)
+  public int getAbsoluteEndSeq()
   {
-    return (r * viewstyle.getCharWidth());
+    int end = endSeq;
+
+    if (av.hasHiddenRows())
+    {
+      end = av.getAlignment().getHiddenSequences().adjustForHiddenSeqs(end);
+    }
+    return end;
   }
+
 }
diff --git a/test/jalview/viewmodel/OverviewDimensionsTest.java b/test/jalview/viewmodel/OverviewDimensionsTest.java
index 94fb83f..cc808d6 100644
--- a/test/jalview/viewmodel/OverviewDimensionsTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsTest.java
@@ -78,6 +78,12 @@ public class OverviewDimensionsTest {
 
   int viewHeight;
 
+  int viewWidth;
+
+  int alheight;
+
+  int alwidth;
+
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
@@ -135,11 +141,6 @@ public class OverviewDimensionsTest {
     
     av = af.getViewport();
 
-    if (av.isCalcInProgress())
-    {
-
-    }
-
     od = new OverviewDimensions(av);
 
     while (av.isCalcInProgress())
@@ -149,24 +150,13 @@ public class OverviewDimensionsTest {
         Thread.sleep(50);
       } catch (InterruptedException e)
       {
-        System.out.println("Hiding cols interruption");
+
       }
     }
 
     // Initial box sizing - default path through code
     od.setBoxPosition();
 
-    scalew = (float) od.getWidth()
-            / (av.getAlignment().getWidth() * av.getCharWidth());
-    scaleh = (float) od.getSequencesHeight()
-            / (av.getAlignment().getHeight() * av.getCharHeight());
-    boxWidth = Math.round((av.getEndRes() - av.getStartRes() + 1)
-            * av.getCharWidth() * scalew);
-    boxHeight = Math.round((av.getEndSeq() - av.getStartSeq())
-            * av.getCharHeight() * scaleh);
-
-    viewHeight = av.getEndSeq() - av.getStartSeq();
-
     init();
   }
 
@@ -192,6 +182,34 @@ public class OverviewDimensionsTest {
 
     mouseClick(od, 0, 0);
     moveViewport(0, 0);
+
+    viewHeight = av.getEndSeq() - av.getStartSeq();
+    viewWidth = av.getEndRes() - av.getStartRes();
+
+    // wait for gui to get set up
+    while (viewHeight != 17 || viewWidth != 59)
+    {
+      try
+      {
+        Thread.sleep(50);
+        viewHeight = av.getEndSeq() - av.getStartSeq();
+        viewWidth = av.getEndRes() - av.getStartRes();
+      } catch (InterruptedException e)
+      {
+
+      }
+    }
+
+    // calculate before hidden columns so we get absolute values
+    alheight = av.getAlignment().getHeight();
+    alwidth = av.getAlignment().getWidth();
+
+    boxWidth = Math.round((float) (av.getEndRes() - av.getStartRes() + 1)
+            / alwidth * od.getWidth());
+    boxHeight = Math.round((float) (av.getEndSeq() - av.getStartSeq())
+            / alheight * od.getHeight());
+    System.out.println(boxHeight);
+
   }
 
   @AfterMethod(alwaysRun = true)
@@ -318,7 +336,7 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollRow(),
-            Math.round(10 / scaleh / av.getCharHeight()));
+            Math.round((float) 10 * alheight / od.getSequencesHeight()));
     assertEquals(od.getScrollCol(), 0);
 
     // negative boxY value reset to 0
@@ -327,41 +345,43 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            Math.round(6 / scalew / av.getCharWidth()));
+            Math.round((float) 6 * alwidth / od.getWidth()));
     assertEquals(od.getScrollRow(), 0);
 
     // overly large boxX value reset to width-boxWidth
     mouseClick(od, 100, 6);
-    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth(), 1.5);
-    assertEquals(od.getBoxY(), 6, 1.5);
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
+    assertEquals(od.getBoxY(), 6);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
     assertEquals(od.getScrollRow(),
-            (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()));
 
     // overly large boxY value reset to sequenceHeight - boxHeight
     mouseClick(od, 10, 520);
-    assertEquals(od.getBoxX(), 10, 1.5);
-    assertEquals(od.getBoxY(), od.getSequencesHeight() - od.getBoxHeight(),
-            1.5);
+    assertEquals(od.getBoxX(), 10);
+    assertEquals(od.getBoxY(), od.getSequencesHeight() - od.getBoxHeight());
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
     assertEquals(od.getScrollRow(),
-            (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()));
 
     // click past end of alignment, as above
     mouseClick(od, 3000, 5);
-    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth(), 1.5);
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
     assertEquals(od.getScrollRow(),
-            (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()));
 
     // move viewport so startRes non-zero and then mouseclick
     moveViewportH(50);
@@ -370,14 +390,15 @@ public class OverviewDimensionsTest {
     int oldboxx = od.getBoxX();
     int oldboxy = od.getBoxY();
     mouseClick(od, od.getBoxX() + 5, od.getBoxY() + 2);
-    assertEquals(od.getBoxX(), oldboxx + 5, 1.5);
+    assertEquals(od.getBoxX(), oldboxx + 5);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
-    assertEquals(od.getBoxY(), oldboxy + 2, 1.5);
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+    assertEquals(od.getBoxY(), oldboxy + 2);
     assertEquals(od.getScrollRow(),
-            (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()));
 
     // click at top corner
     mouseClick(od, 0, 0);
@@ -386,7 +407,7 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getScrollRow(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxHeight(), boxHeight);
   }
 
   /**
@@ -410,7 +431,8 @@ public class OverviewDimensionsTest {
 
     od.setBoxPosition();
     assertEquals(od.getBoxX(),
-            Math.round((lastHiddenCol + 1) * scalew * av.getCharWidth()));
+            Math.round((float) (lastHiddenCol + 1) * od.getWidth()
+                    / alwidth));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
@@ -419,21 +441,20 @@ public class OverviewDimensionsTest {
     /*    int xpos = 10;
         mouseClick(od, xpos, 0);
         assertEquals(od.getBoxX(),
-                Math.round ((lastHiddenCol + 1) * scalew * av.getCharWidth()));
+                Math.round ((lastHiddenCol + 1) * od.getWidth() / alwidth));
         assertEquals(od.getBoxY(), 0);
         assertEquals(od.getBoxWidth(), boxWidth);
         assertEquals(od.getBoxHeight(), boxHeight);
         assertEquals(od.getScrollRow(), 0);
         assertEquals(od.getScrollCol(),
-                Math.round (xpos / scalew / av.getCharWidth()));
+                Math.round (xpos * alwidth / od.getWidth()));
     */
     // click to right of hidden columns, box moves to click point
     testBoxIsAtClickPoint(40, 0);
     assertEquals(od.getScrollRow(), 0);
     assertEquals(od.getScrollCol(),
-            Math.round(40 / scalew / av.getCharWidth())
- - lastHiddenCol,
-            1.5);
+            Math.round((float) 40 * alwidth / od.getWidth())
+                    - (lastHiddenCol + 1));
 
     // click to right of hidden columns such that box runs over right hand side
     // of alignment
@@ -441,16 +462,16 @@ public class OverviewDimensionsTest {
     // overly large boxX value reset to width-boxWidth
     int xpos = 100;
     mouseClick(od, xpos, 5);
-    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth(), 1.5);
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
     assertEquals(od.getBoxY(), 5);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            Math.round(od.getBoxX() / scalew / av.getCharWidth())
-                    - lastHiddenCol, 1.5);
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth())
+                    - (lastHiddenCol + 1));
     assertEquals(od.getScrollRow(),
-            Math.round(od.getBoxY() / scaleh / av.getCharHeight()));
-
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()));
   }
 
   /**
@@ -478,7 +499,7 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getScrollCol(), 0);
     assertEquals(od.getScrollRow(), 0);
-    
+
     // move box so that it overlaps with hidden cols on one side
     // box width changes, boxX and scrollCol as for unhidden case
     int xpos = 50 - boxWidth; // 50 is position in overview halfway between cols
@@ -488,11 +509,11 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxY(), 0);
     assertEquals(
             od.getBoxWidth(),
-            Math.round(boxWidth + (lastHidden - firstHidden + 1) * scalew
-                    * av.getCharWidth()));
+            Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
+                    * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            Math.round(xpos / scalew / av.getCharWidth()));
+            Math.round(xpos * alwidth / od.getWidth()));
     assertEquals(od.getScrollRow(), 0);
 
     // move box so that it completely covers hidden cols
@@ -503,11 +524,11 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxY(), 0);
     assertEquals(
             od.getBoxWidth(),
-            Math.round(boxWidth + (lastHidden - firstHidden + 1) * scalew
-                    * av.getCharWidth()));
+            Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
+                    * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            Math.round(xpos / scalew / av.getCharWidth()), 1.5);
+            Math.round(xpos * alwidth / od.getWidth()));
     assertEquals(od.getScrollRow(), 0);
 
     // move box so boxX is in hidden cols, box overhangs at right
@@ -517,12 +538,12 @@ public class OverviewDimensionsTest {
     /*    xpos = 50;
         mouseClick(od, xpos, 0);
         assertEquals(od.getBoxX(),
-                (lastHidden + 1) * scalew * av.getCharWidth(), 1.5);
+                (lastHidden + 1) * scalew * av.getCharWidth());
         assertEquals(od.getBoxY(), 0);
-        assertEquals(od.getBoxWidth(), boxWidth, 1.5);
+        assertEquals(od.getBoxWidth(), boxWidth);
         assertEquals(od.getBoxHeight(), boxHeight);
         assertEquals(od.getScrollCol(),
-                Math.round(xpos / scalew / av.getCharWidth()), 1.5);
+                Math.round(xpos * alwidth / od.getWidth()));
         assertEquals(od.getScrollRow(), 0);*/
 
     // move box so boxX is to right of hidden cols, but does not go beyond full
@@ -538,22 +559,23 @@ public class OverviewDimensionsTest {
        testBoxIsAtClickPoint(xpos, 0);
        assertEquals(od.getScrollRow(), 0);
        assertEquals(od.getScrollCol(),
-               Math.round(xpos / scalew / av.getCharWidth())
-               - lastHidden, 1.5);*/
+               Math.round(xpos * alwidth / od.getWidth())
+               - lastHidden);*/
     
     // move box so it goes beyond full width of alignment
     // boxX, scrollCol adjusted back, box width normal
     xpos = 3000;
     mouseClick(od, xpos, 5);
-    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth(), 1.5);
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
     assertEquals(od.getBoxY(), 5);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            Math.round((od.getBoxX() / scalew / av.getCharWidth())
+            Math.round(((float) od.getBoxX() * alwidth / od.getWidth())
                     - (lastHidden - firstHidden + 1)));
     assertEquals(od.getScrollRow(),
-            Math.round(od.getBoxY() / scaleh / av.getCharHeight()));
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()));
 
   }
 
@@ -588,7 +610,7 @@ public class OverviewDimensionsTest {
     testBoxIsAtClickPoint(xpos, 0);
     assertEquals(od.getScrollRow(), 0);
     assertEquals(od.getScrollCol(),
-            Math.round(xpos / scalew / av.getCharWidth()), 1.5);
+            Math.round((float) xpos * alwidth / od.getWidth()));
 
     // click to left of hidden cols, with overlap
     // boxX and scrollCol adjusted for hidden cols, width normal
@@ -599,12 +621,12 @@ public class OverviewDimensionsTest {
     assertEquals(
             od.getBoxX(),
             Math.round((firstHidden - 1) * scalew * av.getCharWidth())
-                    - od.getBoxWidth(), 1.5);
+                    - od.getBoxWidth());
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            Math.round(od.getBoxX() / scalew / av.getCharWidth()), 1.5);
+            Math.round(od.getBoxX() * alwidth / od.getWidth()));
     assertEquals(od.getScrollRow(), 0);*/
 
     // click in hidden cols
@@ -614,12 +636,12 @@ public class OverviewDimensionsTest {
     assertEquals(
             od.getBoxX(),
             Math.round((firstHidden - 1) * scalew * av.getCharWidth())
-                    - od.getBoxWidth(), 1.5);
+                    - od.getBoxWidth());
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            Math.round(od.getBoxX() / scalew / av.getCharWidth()), 1.5);
+            Math.round(od.getBoxX() * alwidth / od.getWidth()));
     assertEquals(od.getScrollRow(), 0);*/
 
     // click off end of alignment
@@ -629,12 +651,12 @@ public class OverviewDimensionsTest {
         assertEquals(
                 od.getBoxX(),
                 Math.round((firstHidden - 1) * scalew * av.getCharWidth())
-                        - od.getBoxWidth(), 1.5);
+                        - od.getBoxWidth());
         assertEquals(od.getBoxY(), 0);
-        assertEquals(od.getBoxWidth(), boxWidth, 1.5);
+        assertEquals(od.getBoxWidth(), boxWidth);
         assertEquals(od.getBoxHeight(), boxHeight);
         assertEquals(od.getScrollCol(),
-                Math.round(od.getBoxX() / scalew / av.getCharWidth()), 1.5);
+                Math.round(od.getBoxX() * alwidth / od.getWidth()));
         assertEquals(od.getScrollRow(), 0);*/
   }
 
@@ -654,25 +676,28 @@ public class OverviewDimensionsTest {
 
     // move viewport to right
     moveViewportH(70);
-    assertEquals(od.getBoxX(), Math.round(70 * scalew * av.getCharWidth()));
+    assertEquals(od.getBoxX(),
+            Math.round((float) 70 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport down
     moveViewportV(100);
-    assertEquals(od.getBoxX(), Math.round(70 * scalew * av.getCharWidth()));
+    assertEquals(od.getBoxX(),
+            Math.round((float) 70 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(),
-            Math.round(100 * scaleh * av.getCharHeight()));
+            Math.round(100 * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to bottom right
     moveViewport(98, 508);
-    assertEquals(od.getBoxX(), Math.round(98 * scalew * av.getCharWidth()));
+    assertEquals(od.getBoxX(),
+            Math.round((float) 98 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(),
-            Math.round(508 * scaleh * av.getCharHeight()));
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
+            Math.round((float) 508 * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
   }
 
@@ -690,7 +715,7 @@ public class OverviewDimensionsTest {
     // move viewport to start of alignment
     moveViewport(0, 0);
     assertEquals(od.getBoxX(),
-            Math.round((lastHidden + 1) * scalew * av.getCharWidth()));
+            Math.round((float) (lastHidden + 1) * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
@@ -698,7 +723,8 @@ public class OverviewDimensionsTest {
     // move viewport to end of alignment - need to make startRes by removing
     // hidden cols because of how viewport/overview are implemented
     moveViewport(98 - lastHidden - 1, 0);
-    assertEquals(od.getBoxX(), Math.round(98 * scalew * av.getCharWidth()));
+    assertEquals(od.getBoxX(),
+            Math.round((float) 98 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
@@ -718,7 +744,8 @@ public class OverviewDimensionsTest {
     // move viewport before hidden columns
     moveViewport(3, 0);
 
-    assertEquals(od.getBoxX(), Math.round(3 * scalew * av.getCharWidth()));
+    assertEquals(od.getBoxX(),
+            Math.round((float) 3 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
     System.out.println(od.getBoxWidth());
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -727,30 +754,32 @@ public class OverviewDimensionsTest {
 
     // move viewport to left of hidden columns with overlap
     moveViewport(10, 0);
-    assertEquals(od.getBoxX(), Math.round(10 * scalew * av.getCharWidth()));
+    assertEquals(od.getBoxX(),
+            Math.round((float) 10 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
     assertEquals(
             od.getBoxWidth(),
             boxWidth
-                    + Math.round((lastHidden - firstHidden + 1) * scalew
-                            * av.getCharWidth()));
+                    + Math.round((float) (lastHidden - firstHidden + 1)
+                            * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to straddle hidden columns
     moveViewport(60, 0);
-    assertEquals(od.getBoxX(), Math.round(60 * scalew * av.getCharWidth()));
+    assertEquals(od.getBoxX(),
+            Math.round((float) 60 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
     assertEquals(
             od.getBoxWidth(),
             boxWidth
-                    + Math.round((lastHidden - firstHidden + 1) * scalew
-                            * av
-.getCharWidth()));
+                    + Math.round((lastHidden - firstHidden + 1)
+                            * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to right of hidden columns, no overlap
     moveViewport(80 - (lastHidden - firstHidden + 1), 0);
-    assertEquals(od.getBoxX(), Math.round(80 * scalew * av.getCharWidth()));
+    assertEquals(od.getBoxX(),
+            Math.round((float) 80 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
@@ -770,8 +799,8 @@ public class OverviewDimensionsTest {
 
     // move viewport before hidden columns
     moveViewport(3, 0);
-    assertEquals(od.getBoxX(), Math.round(3 * scalew * av.getCharWidth()),
-            1.5);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 3 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
@@ -779,14 +808,14 @@ public class OverviewDimensionsTest {
     // move viewport to hidden columns
     // TODO boxwidth includes hidden in overview panel (why?)
     moveViewport(98, 0);
-    assertEquals(od.getBoxX(), Math.round(98 * scalew * av.getCharWidth()),
-            1.5);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 98 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
     assertEquals(
             od.getBoxWidth(),
             boxWidth
-                    + Math.round((lastHidden - firstHidden + 1) * scalew
-                            * av.getCharWidth()), 1.5);
+                    + Math.round((float) (lastHidden - firstHidden + 1)
+                            * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
   }
 
@@ -806,7 +835,8 @@ public class OverviewDimensionsTest {
     moveViewport(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(),
-            Math.round((lastHidden + 1) * scaleh * av.getCharHeight()));
+            Math.round((float) (lastHidden + 1) * od.getSequencesHeight()
+                    / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
@@ -823,9 +853,9 @@ public class OverviewDimensionsTest {
         assertEquals(od.getBoxX(), 0);
         assertEquals(od.getBoxY(),
                 (525 - viewHeight) * scaleh
-                * av.getCharHeight(), 1.5);
-        assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-        assertEquals(od.getBoxHeight(), boxHeight, 1.5);*/
+                * av.getCharHeight());
+        assertEquals(od.getBoxWidth(), boxWidth);
+        assertEquals(od.getBoxHeight(), boxHeight);*/
   }
 
   /**
@@ -845,8 +875,8 @@ public class OverviewDimensionsTest {
     /*moveViewport(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);*/
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);*/
 
     // move viewport to straddle hidden rows
     // TODO also fails with boxY out by 12
@@ -854,7 +884,7 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), Math.round (198 * scaleh * av.getCharHeight()),
             1.5);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight
             + ((lastHidden - firstHidden) * scaleh * av.getCharHeight()),
             1.5);*/
@@ -885,13 +915,13 @@ public class OverviewDimensionsTest {
         assertEquals(od.getBoxX(), 0);
         assertEquals(od.getBoxY(),
      Math.round ((firstHidden - viewHeight - 1)
-                * scaleh * av.getCharHeight()), 1.5);
-        assertEquals(od.getBoxWidth(), boxWidth, 1.5);
+                * scaleh * av.getCharHeight()));
+        assertEquals(od.getBoxWidth(), boxWidth);
         assertEquals(
                 od.getBoxHeight(),
                 boxHeight
                         + Math.round ((lastHidden - firstHidden + 1) * scaleh * av
-                                .getCharHeight()), 1.5);*/
+                                .getCharHeight()));*/
 
   }
 
@@ -918,7 +948,8 @@ public class OverviewDimensionsTest {
     od.setBoxPosition();
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(),
-            Math.round((lastHiddenRow + 1) * scaleh * av.getCharHeight()));
+            Math.round((float) (lastHiddenRow + 1)
+                    * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
@@ -927,7 +958,7 @@ public class OverviewDimensionsTest {
     /*    mouseClick(od, 0, 0);
         assertEquals(od.getBoxX(), 0);
         assertEquals(od.getBoxY(), 0);
-        assertEquals(od.getBoxWidth(), boxWidth, 1.5);
+        assertEquals(od.getBoxWidth(), boxWidth);
         assertEquals(od.getBoxHeight(), boxHeight
                 + Math.round ((lastHiddenRow + 1) * scaleh * av.getCharHeight()),
                 1.5);*/
@@ -935,7 +966,7 @@ public class OverviewDimensionsTest {
     // click below hidden rows
     mouseClick(od, 0, 150);
     assertEquals(od.getBoxX(), 0);
-    assertEquals(od.getBoxY(), 150, 1.5);
+    assertEquals(od.getBoxY(), 150);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
   }
@@ -947,12 +978,8 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenRowsInMiddle()
   {
-    assertEquals(od.getBoxHeight(), 10);
-
     od.setBoxPositionByMouse(0, 0);
 
-    assertEquals(od.getBoxHeight(), 10);
-
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -964,12 +991,9 @@ public class OverviewDimensionsTest {
     // no changes
     int firstHiddenRow = 50;
     int lastHiddenRow = 60;
-    assertEquals(od.getBoxHeight(), 10);
     hideSequences(firstHiddenRow, lastHiddenRow + 1, lastHiddenRow + 1);
-    assertEquals(od.getBoxHeight(), 10);
 
     od.setBoxPosition();
-    assertEquals(od.getBoxHeight(), 10);
 
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
@@ -980,31 +1004,31 @@ public class OverviewDimensionsTest {
     int ypos = 40;
     // TODO test fails because box does not change height - dealt with by scroll
     // values
-    /*    mouseClick(od, 0, Math.round (ypos / scaleh / av.getCharHeight()));
+    /*    mouseClick(od, 0, Math.round (ypos * alheight / od.getSequencesHeight()));
         assertEquals(od.getBoxX(), 0);
-        assertEquals(od.getBoxY(), Math.round (ypos / scaleh / av.getCharHeight()),
+        assertEquals(od.getBoxY(), Math.round (ypos * alheight / od.getSequencesHeight()),
                 1.5);
-        assertEquals(od.getBoxWidth(), boxWidth, 1.5);
+        assertEquals(od.getBoxWidth(), boxWidth);
         assertEquals(
                 od.getBoxHeight(),
                 boxHeight
                         + Math.round ((lastHiddenRow - firstHiddenRow + 1) / scaleh / av
-                                .getCharHeight()), 1.5);
+                                .getCharHeight()));
     */
     // click so that box straddles hidden rows
     ypos = 48;
     // TODO test fails because box does not change height - dealt with by scroll
     // values
-    /*mouseClick(od, 0, Math.round (ypos / scaleh / av.getCharHeight()));
+    /*mouseClick(od, 0, Math.round (ypos * alheight / od.getSequencesHeight()));
     assertEquals(od.getBoxX(), 0);
-    assertEquals(od.getBoxY(), Math.round (ypos / scaleh / av.getCharHeight()),
+    assertEquals(od.getBoxY(), Math.round (ypos * alheight / od.getSequencesHeight()),
             1.5);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(
             od.getBoxHeight(),
             boxHeight
                     + Math.round ((lastHiddenRow - firstHiddenRow + 1) / scaleh / av
-                            .getCharHeight()), 1.5);*/
+                            .getCharHeight()));*/
   }
 
   /**
@@ -1036,10 +1060,11 @@ public class OverviewDimensionsTest {
 
     // click above hidden rows
     int ypos = 40; // row 40
-    mouseClick(od, 0, Math.round(ypos * scaleh * av.getCharHeight()));
+    mouseClick(od, 0,
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(),
-            Math.round(ypos * scaleh * av.getCharHeight()));
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
@@ -1054,8 +1079,8 @@ public class OverviewDimensionsTest {
                od.getBoxY(),
                Math.round ((firstHidden - viewHeight) * scaleh * av.getCharHeight()),
                1.5);
-       assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-       assertEquals(od.getBoxHeight(), boxHeight, 1.5);*/
+       assertEquals(od.getBoxWidth(), boxWidth);
+       assertEquals(od.getBoxHeight(), boxHeight);*/
 
     // click within hidden rows
     ypos = 505;
@@ -1066,8 +1091,8 @@ public class OverviewDimensionsTest {
             od.getBoxY(),
             Math.round ((firstHidden - viewHeight) * scaleh * av.getCharHeight()),
             1.5);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);*/
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);*/
   }
 
   /*
@@ -1075,9 +1100,8 @@ public class OverviewDimensionsTest {
    */
   private void moveViewportH(int startRes)
   {
-    int width = av.getEndRes() - av.getStartRes();
     av.setStartRes(startRes);
-    av.setEndRes(startRes + width);
+    av.setEndRes(startRes + viewWidth);
     od.setBoxPosition();
   }
 
@@ -1096,10 +1120,8 @@ public class OverviewDimensionsTest {
    */
   private void moveViewport(int startRes, int startSeq)
   {
-    int width = av.getEndRes() - av.getStartRes();
-
     av.setStartRes(startRes);
-    av.setEndRes(startRes + width);
+    av.setEndRes(startRes + viewWidth);
     av.setStartSeq(startSeq);
     av.setEndSeq(startSeq + viewHeight);
     od.setBoxPosition();
@@ -1114,22 +1136,22 @@ 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
-    int width = av.getEndRes() - av.getStartRes();
-    int height = av.getEndSeq() - av.getStartSeq();
+    // int width = av.getEndRes() - av.getStartRes();
+    // int height = av.getEndSeq() - av.getStartSeq();
     av.setStartRes(od.getScrollCol());
-    av.setEndRes(od.getScrollCol() + width);
+    av.setEndRes(od.getScrollCol() + viewWidth);
     av.setStartSeq(od.getScrollRow());
-    av.setEndSeq(od.getScrollRow() + height);
+    av.setEndSeq(od.getScrollRow() + viewHeight);
     od.setBoxPosition();
   }
   
   private void testBoxIsAtClickPoint(int xpos, int ypos)
   {
     mouseClick(od, xpos, ypos);
-    assertEquals(od.getBoxX(), xpos, 1.5);
-    assertEquals(od.getBoxY(), ypos, 1.5);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxX(), xpos);
+    assertEquals(od.getBoxY(), ypos);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
   }