JAL-2388 Unit tests and tidies

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index f927e63..f5d6ce7 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -39,6 +39,7 @@ import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportPositionProps;
 
 import java.awt.Font;
 
@@ -74,6 +75,7 @@ public class AlignViewport extends AlignmentViewport implements
     calculator = new jalview.workers.AlignCalcManager();
     this.applet = applet;
     alignment = al;
+    posProps = new ViewportPositionProps(this.alignment);
     // we always pad gaps
     this.setPadGaps(true);
     this.setStartRes(0);

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 836a800..f0dd524 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.appletgui;
 
+import jalview.datamodel.SequenceI;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
@@ -61,10 +62,10 @@ public class OverviewPanel extends Panel implements Runnable,
 
   private Frame nullFrame;
 
-  public OverviewPanel(AlignmentPanel ap)
+  public OverviewPanel(AlignmentPanel alPanel)
   {
-    this.av = ap.av;
-    this.ap = ap;
+    this.av = alPanel.av;
+    this.ap = alPanel;
     setLayout(null);
     nullFrame = new Frame();
     nullFrame.addNotify();
@@ -75,15 +76,7 @@ public class OverviewPanel extends Panel implements Runnable,
     sr.forOverview = true;
     fr = new FeatureRenderer(av);
 
-    boolean showAnnotation = true;
-    // TODO: in applet this was getSequenceConsensusHash()
-    // check if it makes any functional difference: hconsensus or conservation
-    if (av.getAlignmentConservationAnnotation() == null)
-    {
-      showAnnotation = false;
-    }
-
-    od = new OverviewDimensions(av.getPosProps(), showAnnotation);
+    od = new OverviewDimensions(av.getPosProps(), av.isShowAnnotation());
 
     setSize(new Dimension(od.getWidth(), od.getHeight()));
     addComponentListener(new ComponentAdapter()
@@ -156,7 +149,7 @@ public class OverviewPanel extends Panel implements Runnable,
   }
 
   /**
-   * DOCUMENT ME!
+   * Updates the overview image when the related alignment panel is updated
    */
   public void updateOverviewImage()
   {
@@ -175,8 +168,8 @@ public class OverviewPanel extends Panel implements Runnable,
 
     if ((getWidth() > 0) && (getHeight() > 0))
     {
-      od.setWidth(getWidth()); // width = getWidth();
-      od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight;
+      od.setWidth(getWidth());
+      od.setHeight(getHeight());
     }
     setSize(new Dimension(od.getWidth(), od.getHeight()));
 
@@ -208,8 +201,6 @@ public class OverviewPanel extends Panel implements Runnable,
 
     Graphics mg = miniMe.getGraphics();
 
-    // od.updateScales();
-
     int alwidth = av.getAlignment().getWidth();
     int alheight = av.getAlignment().getAbsoluteHeight();
     float sampleCol = alwidth / (float) od.getWidth();
@@ -217,7 +208,7 @@ public class OverviewPanel extends Panel implements Runnable,
 
     buildImage(sampleRow, sampleCol, mg);
 
-    if (av.getAlignmentConservationAnnotation() != null)
+    if (av.isShowAnnotation())
     {
       for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
       {
@@ -243,6 +234,9 @@ public class OverviewPanel extends Panel implements Runnable,
     }
   }
 
+  /*
+   * Build the overview panel image
+   */
   private void buildImage(float sampleRow, float sampleCol, Graphics mg)
   {
     int lastcol = 0;
@@ -253,7 +247,7 @@ public class OverviewPanel extends Panel implements Runnable,
     int sameRow = 0;
     int sameCol = 0;
 
-    jalview.datamodel.SequenceI seq = null;
+    SequenceI seq = null;
 
     final boolean hasHiddenCols = av.hasHiddenColumns();
     boolean hiddenRow = false;
@@ -304,7 +298,6 @@ public class OverviewPanel extends Panel implements Runnable,
         sameRow = 1;
       }
     }
-
   }
 
   /*
@@ -326,7 +319,7 @@ public class OverviewPanel extends Panel implements Runnable,
     }
     else
     {
-      color = Color.white; // White
+      color = Color.white;
     }
 
     if (hiddenRow

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 9c02f29..d3aa01a 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -260,8 +260,14 @@ public class HiddenSequences
     }
     int index = 0;
     int hiddenSeqs = 0;
+    int diff = 0;
     if (hiddenSequences.length <= alignmentIndex)
     {
+      // if the alignmentIndex runs past the end of hidden sequences
+      // and therefore actually past the end of the alignment
+      // store the difference to add back on at the end, so that behaviour
+      // is consistent with hidden columns behaviour (used by overview panel)
+      diff = alignmentIndex - hiddenSequences.length + 1;
       alignmentIndex = hiddenSequences.length - 1;
     }
 
@@ -274,7 +280,7 @@ public class HiddenSequences
       index++;
     }
 
-    return (alignmentIndex - hiddenSeqs);
+    return (alignmentIndex - hiddenSeqs + diff);
   }
 
   /**

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 923616f..2c77942 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 import jalview.viewmodel.OverviewDimensions;
 
@@ -88,14 +89,7 @@ public class OverviewPanel extends JPanel implements Runnable
     sr.forOverview = true;
     fr = new FeatureRenderer(alPanel);
 
-    boolean showAnnotation = true;
-    // TODO: in applet this was getSequenceConsensusHash()
-    // check if it makes any functional difference: hconsensus or conservation
-    if (av.getAlignmentConservationAnnotation() == null)
-    {
-      showAnnotation = false;
-    }
-    od = new OverviewDimensions(av.getPosProps(), showAnnotation);
+    od = new OverviewDimensions(av.getPosProps(), av.isShowAnnotation());
 
     addComponentListener(new ComponentAdapter()
     {
@@ -117,8 +111,6 @@ public class OverviewPanel extends JPanel implements Runnable
       {
         if (!av.getWrapAlignment())
         {
-          // TODO: feature: jv2.5 detect shift drag and update selection from
-          // it.
           od.updateViewportFromMouse(evt.getX(), evt.getY(), av
                   .getAlignment().getHiddenSequences(), av
                   .getColumnSelection(), av.getPosProps());
@@ -160,8 +152,8 @@ public class OverviewPanel extends JPanel implements Runnable
 
     if ((getWidth() > 0) && (getHeight() > 0))
     {
-      od.setWidth(getWidth()); // width = getWidth();
-      od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight;
+      od.setWidth(getWidth());
+      od.setHeight(getHeight());
     }
 
     setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
@@ -208,7 +200,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     buildImage(sampleRow, sampleCol);
 
-    if (av.getAlignmentConservationAnnotation() != null)
+    if (av.isShowAnnotation())
     {
       renderer.updateFromAlignViewport(av);
       for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
@@ -239,13 +231,16 @@ public class OverviewPanel extends JPanel implements Runnable
     setBoxPosition();
   }
 
+  /*
+   * Build the overview panel image
+   */
   private void buildImage(float sampleRow, float sampleCol)
   {
     int lastcol = -1;
     int lastrow = -1;
     int color = Color.white.getRGB();
 
-    jalview.datamodel.SequenceI seq = null;
+    SequenceI seq = null;
 
     final boolean hasHiddenCols = av.hasHiddenColumns();
     boolean hiddenRow = false;
@@ -268,12 +263,6 @@ public class OverviewPanel extends JPanel implements Runnable
         seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
       }
 
-      if (seq == null)
-      {
-        System.out.println(lastrow + " null");
-        continue;
-      }
-
       for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
       {
         if (doCopy)
@@ -287,9 +276,7 @@ public class OverviewPanel extends JPanel implements Runnable
           color = getColumnColourFromSequence(seq, hiddenRow, hasHiddenCols,
                   lastcol);
         }
-        // else if ((int) (col * sampleCol) == lastcol && (int) (row *
-        // sampleRow) == lastrow))
-        // we just use the color we already have , so don't need to set it
+        // else we just use the color we already have , so don't need to set it
 
         miniMe.setRGB(col, row, color);
       }
@@ -304,7 +291,11 @@ public class OverviewPanel extends JPanel implements Runnable
   {
     int color;
 
-    if (seq.getLength() > lastcol)
+    if (seq == null)
+    {
+      color = Color.white.getRGB();
+    }
+    else if (seq.getLength() > lastcol)
     {
       color = sr.getResidueBoxColour(seq, lastcol).getRGB();
 
@@ -315,7 +306,7 @@ public class OverviewPanel extends JPanel implements Runnable
     }
     else
     {
-      color = Color.white.getRGB(); // White
+      color = Color.white.getRGB();
     }
 
     if (hiddenRow
@@ -367,7 +358,7 @@ public class OverviewPanel extends JPanel implements Runnable
         g.fillRect(0, 0, getWidth(), getHeight());
       }
     }
-    // TODO: render selected regions
+
     g.setColor(Color.red);
     od.drawBox(g);
   }

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 41248b1..47f7d9d 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -2679,44 +2679,22 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void setStartSeq(int seq)
   {
     posProps.setStartSeq(seq);
-    // this.startSeq = seq;
   }
 
   public void setEndRes(int res)
   {
     posProps.setEndRes(res);
-    /*if (res > alignment.getWidth() - 1)
-    {
-      // log.System.out.println(" Corrected res from " + res + " to maximum " +
-      // (alignment.getWidth()-1));
-      res = alignment.getWidth() - 1;
-    }
-    if (res < 0)
-    {
-      res = 0;
-    }
-    this.endRes = res;*/
   }
 
   public void setEndSeq(int seq)
   {
     posProps.setEndSeq(seq);
-    /*if (seq > alignment.getHeight())
-    {
-      seq = alignment.getHeight();
-    }
-    if (seq < 0)
-    {
-      seq = 0;
-    }
-    this.endSeq = seq;*/
   }
 
   @Override
   public int getEndSeq()
   {
     return posProps.getEndSeq();
-    // return endSeq;
   }
 
   /**

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index 60b4ee9..b34c85d 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -91,7 +91,7 @@ public class OverviewDimensions
     {
       // wider
       width = MAX_WIDTH;
-      sequencesHeight = (int) (MAX_WIDTH / initialScale);
+      sequencesHeight = Math.round(MAX_WIDTH / initialScale);
       if (sequencesHeight < MIN_SEQ_HEIGHT)
       {
         sequencesHeight = MIN_SEQ_HEIGHT;
@@ -100,7 +100,7 @@ public class OverviewDimensions
     else
     {
       // taller
-      width = (int) (MAX_WIDTH * initialScale);
+      width = Math.round(MAX_WIDTH * initialScale);
       sequencesHeight = MAX_SEQ_HEIGHT;
 
       if (width < MIN_WIDTH)
@@ -173,7 +173,8 @@ public class OverviewDimensions
       // if last position was before the end of the alignment, need to update
       if ((scrollCol + vpwidth - 1) < visAlignWidth)
       {
-        visXAsRes = hiddenCols.findColumnNToLeft(vpwidth - 1, alwidth - 1);
+        visXAsRes = hiddenCols.findColumnPosition(hiddenCols
+                .findColumnNToLeft(vpwidth - 1, alwidth - 1));
       }
       else
       {
@@ -199,19 +200,16 @@ public class OverviewDimensions
     yAsSeq = hiddenSeqs.adjustForHiddenSeqs(hiddenSeqs
             .findIndexWithoutHiddenSeqs(yAsSeq));
 
-    // get where end seq should be by adding the viewport height on
-    int endSeq = yAsSeq + vpheight - 1;
-
     // check in case we went off the edge of the alignment
     int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
     int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
-    if (hiddenSeqs.findIndexWithoutHiddenSeqs(endSeq) > visAlignHeight)
+    if (visYAsRes + vpheight - 1 > visAlignHeight)
     {
       // went past the end of the alignment, adjust backwards
       if ((scrollRow + vpheight - 1) < visAlignHeight)
       {
-        visYAsRes = hiddenSeqs
-                .findIndexNAboveRow(vpheight - 1, alheight - 1);
+        visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
+                .findIndexNAboveRow(vpheight - 1, alheight - 1));
       }
       else
       {
@@ -219,10 +217,9 @@ public class OverviewDimensions
       }
     }
 
-    // convert absolute positions back to visible alignment positions for
-    // viewport scrolling
+    // update scroll values
     scrollCol = visXAsRes;
-    scrollRow = visYAsRes; // hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
+    scrollRow = visYAsRes;
 
   }
 
@@ -278,7 +275,6 @@ public class OverviewDimensions
     g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
   }
 
-  // don't like this, scroll vals are separate from setting code
   public int getScrollCol()
   {
     return scrollCol;

diff --git a/src/jalview/viewmodel/ViewportPositionProps.java b/src/jalview/viewmodel/ViewportPositionProps.java
index 69a60f5..d143130 100644 (file)
--- a/src/jalview/viewmodel/ViewportPositionProps.java
+++ b/src/jalview/viewmodel/ViewportPositionProps.java
@@ -24,7 +24,7 @@ import jalview.datamodel.AlignmentI;
 
 /**
  * Supplies and updates viewport properties relating to position such as: start
- * and end residues and sequences, hidden column/row adjustments, etc
+ * and end residues and sequences
  */
 public class ViewportPositionProps extends ViewportProperties
 {
@@ -45,7 +45,9 @@ public class ViewportPositionProps extends ViewportProperties
 
   /**
    * Constructor
-   * @param alignment TODO
+   * 
+   * @param alignment
+   *          the viewport's alignment
    */
   public ViewportPositionProps(AlignmentI alignment)
   {
@@ -79,6 +81,12 @@ public class ViewportPositionProps extends ViewportProperties
     return al.getHeight() + al.getHiddenSequences().getSize();
   }
 
+  /**
+   * Set first residue visible in the viewport
+   * 
+   * @param res
+   *          residue position
+   */
   public void setStartRes(int res)
   {
     if (res > al.getWidth() - 1)
@@ -92,6 +100,12 @@ public class ViewportPositionProps extends ViewportProperties
     this.startRes = res;
   }
 
+  /**
+   * Set last residue visible in the viewport
+   * 
+   * @param res
+   *          residue position
+   */
   public void setEndRes(int res)
   {
     if (res > al.getWidth())
@@ -105,6 +119,12 @@ public class ViewportPositionProps extends ViewportProperties
     this.endRes = res;
   }
 
+  /**
+   * Set the first sequence visible in the viewport
+   * 
+   * @param seq
+   *          sequence position
+   */
   public void setStartSeq(int seq)
   {
     if (seq > al.getHeight() - 1)
@@ -118,6 +138,12 @@ public class ViewportPositionProps extends ViewportProperties
     this.startSeq = seq;
   }
 
+  /**
+   * Set the last sequence visible in the viewport
+   * 
+   * @param seq
+   *          sequence position
+   */
   public void setEndSeq(int seq)
   {
     if (seq > al.getHeight())

diff --git a/test/jalview/viewmodel/OverviewDimensionsTest.java b/test/jalview/viewmodel/OverviewDimensionsTest.java
index 8ceadba..1ea07ea 100644 (file)
--- a/test/jalview/viewmodel/OverviewDimensionsTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsTest.java
@@ -137,7 +137,7 @@ public class OverviewDimensionsTest
     ViewportPositionProps props = new ViewportPositionProps(al1);
 
     OverviewDimensions od = new OverviewDimensions(props, true);
-    int scaledHeight = 266;
+    int scaledHeight = 267;
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), scaledHeight);
     assertEquals(od.getWidth(), maxWidth);
@@ -225,7 +225,7 @@ public class OverviewDimensionsTest
 
     // overly large boxX value reset to width-boxWidth
     mouseClick(od, 100, 6);
-    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth() + 1);
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
     assertEquals(od.getBoxY(), 6);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
@@ -243,13 +243,17 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
             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(),
             Math.round((float) od.getBoxY() * alheight
-                    / od.getSequencesHeight()));
+                    / od.getSequencesHeight()) - 1);
 
     // click past end of alignment, as above
     mouseClick(od, 3000, 5);
-    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth() + 1);
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
@@ -313,7 +317,6 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // try to click in hidden cols, check box does not move
-    // this test currently fails as the overview box does not behave like this!
     int xpos = 10;
     mouseClick(od, xpos, 0);
     assertEquals(
@@ -339,7 +342,7 @@ public class OverviewDimensionsTest
     // overly large boxX value reset to width-boxWidth
     xpos = 100;
     mouseClick(od, xpos, 5);
-    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth() + 1);
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
     assertEquals(od.getBoxY(), 5);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
@@ -440,7 +443,7 @@ public class OverviewDimensionsTest
     // boxX, scrollCol adjusted back, box width normal
     xpos = 3000;
     mouseClick(od, xpos, 5);
-    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth() + 1);
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
     assertEquals(od.getBoxY(), 5);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
@@ -492,44 +495,40 @@ public class OverviewDimensionsTest
     xpos = Math.round((float) 145 * od.getWidth() / alwidth) - boxWidth;
     mouseClick(od, xpos, 0);
     assertEquals(od.getBoxX(),
-            Math.round((firstHidden - 1) * od.getWidth() / alwidth)
-                    - boxWidth);
+            Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
+                    - boxWidth + 1);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            Math.round(od.getBoxX() * alwidth / od.getWidth()));
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
     assertEquals(od.getScrollRow(), 0);
 
     // click in hidden cols
     // boxX and scrollCol adjusted for hidden cols, width normal
-    // TODO breaks as above test
-    /*xpos = 115;
-    assertEquals(
-            od.getBoxX(),
-            Math.round((firstHidden - 1) * scalew * av.getCharWidth())
-                    - od.getBoxWidth());
+    xpos = 115;
+    assertEquals(od.getBoxX(),
+            Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
+                    - boxWidth + 1);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            Math.round(od.getBoxX() * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(), 0);*/
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+    assertEquals(od.getScrollRow(), 0);
 
     // click off end of alignment
     // boxX and scrollCol adjusted for hidden cols, width normal
-    // TODO breaks as above test
-    /*    xpos = 3000;
-        assertEquals(
-                od.getBoxX(),
-                Math.round((firstHidden - 1) * scalew * av.getCharWidth())
-                        - od.getBoxWidth());
-        assertEquals(od.getBoxY(), 0);
-        assertEquals(od.getBoxWidth(), boxWidth);
-        assertEquals(od.getBoxHeight(), boxHeight);
-        assertEquals(od.getScrollCol(),
-                Math.round(od.getBoxX() * alwidth / od.getWidth()));
-        assertEquals(od.getScrollRow(), 0);*/
+    xpos = 3000;
+    assertEquals(od.getBoxX(),
+            Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
+                    - boxWidth + 1);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+    assertEquals(od.getScrollRow(), 0);
   }
 
   /**
@@ -683,7 +682,7 @@ public class OverviewDimensionsTest
             Math.round((float) 102 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth
-                    + Math.round((float) (lastHidden - firstHidden)
+                    + Math.round((float) (lastHidden - firstHidden + 1)
                             * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
   }
@@ -850,7 +849,7 @@ public class OverviewDimensionsTest
     // hide rows in middle and check updated box position is correct
     // no changes
     int firstHiddenRow = 50;
-    int lastHiddenRow = 60;
+    int lastHiddenRow = 54;
     hideSequences(firstHiddenRow, lastHiddenRow);
 
     od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
@@ -861,34 +860,32 @@ public class OverviewDimensionsTest
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // click above hidden rows, so that box overlaps
-    int ypos = 40;
-    // TODO test fails because box does not change height - dealt with by scroll
-    // values
-    /*    mouseClick(od, 0, Math.round (ypos * alheight / od.getSequencesHeight()));
-        assertEquals(od.getBoxX(), 0);
-        assertEquals(od.getBoxY(), Math.round (ypos * alheight / od.getSequencesHeight()),
-                1.5);
-        assertEquals(od.getBoxWidth(), boxWidth);
-        assertEquals(
-                od.getBoxHeight(),
-                boxHeight
-                        + Math.round ((lastHiddenRow - firstHiddenRow + 1) / scaleh / av
-                                .getCharHeight()));
-    */
+    int ypos = 35; // column value in residues
+    mouseClick(od, 0,
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(),
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(
+            od.getBoxHeight(),
+            boxHeight
+                    + Math.round((float) (lastHiddenRow - firstHiddenRow + 1)
+                            * od.getSequencesHeight() / alheight));
+
     // 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 * alheight / od.getSequencesHeight()));
+    ypos = 44; // column value in residues
+    mouseClick(od, 0,
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxX(), 0);
-    assertEquals(od.getBoxY(), Math.round (ypos * alheight / od.getSequencesHeight()),
-            1.5);
+    assertEquals(od.getBoxY(),
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(
             od.getBoxHeight(),
             boxHeight
-                    + Math.round ((lastHiddenRow - firstHiddenRow + 1) / scaleh / av
-                            .getCharHeight()));*/
+                    + Math.round((float) (lastHiddenRow - firstHiddenRow + 1)
+                            * od.getSequencesHeight() / alheight));
   }
 
   /**
@@ -931,29 +928,28 @@ public class OverviewDimensionsTest
 
     // click above hidden rows so box overlaps
     // boxY moved upwards, boxHeight remains same
-    // TODO fails with boxY located at row 497 - correction done by
-    // setScrollValues
-    /*   ypos = 497; // row 497
-       mouseClick(od, 0, Math.round (ypos * scaleh * av.getCharHeight()));
-       assertEquals(od.getBoxX(), 0);
-       assertEquals(
-               od.getBoxY(),
-               Math.round ((firstHidden - viewHeight) * scaleh * av.getCharHeight()),
-               1.5);
-       assertEquals(od.getBoxWidth(), boxWidth);
-       assertEquals(od.getBoxHeight(), boxHeight);*/
+    ypos = 497; // row 497
+    mouseClick(od, 0,
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(
+            od.getBoxY(),
+            Math.round((float) (firstHidden - viewHeight)
+                    * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // click within hidden rows
     ypos = 505;
-    // TODO: fails with wrong boxHeight - correction done by setScrollValues(?)
-    /*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 ((firstHidden - viewHeight) * scaleh * av.getCharHeight()),
-            1.5);
+            Math.round((firstHidden - viewHeight) * od.getSequencesHeight()
+                    / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getBoxHeight(), boxHeight);*/
+    assertEquals(od.getBoxHeight(), boxHeight);
   }
 
   /*