X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fviewmodel%2FOverviewDimensionsTest.java;h=1ea07ea0f8f0f6b89d46008e15036946789e3c17;hb=7f4da0a2b0c10f158a03dbfce8878e67e90c4a68;hp=d01eaa3cb614f68370af030809ee41e4f3339d79;hpb=41f78bdf2b0650fa7fde4959a7b9d58fd5c77c71;p=jalview.git

diff --git a/test/jalview/viewmodel/OverviewDimensionsTest.java b/test/jalview/viewmodel/OverviewDimensionsTest.java
index d01eaa3..1ea07ea 100644
--- a/test/jalview/viewmodel/OverviewDimensionsTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsTest.java
@@ -21,162 +21,94 @@
 package jalview.viewmodel;
 
 import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertTrue;
 
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
+import jalview.analysis.AlignmentGenerator;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
-import jalview.io.DataSourceType;
-import jalview.io.FileLoader;
+
+import java.util.Hashtable;
 
 import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
-public class OverviewDimensionsTest {
-
-  boolean showConservationSetting;
-
-  SequenceI seq1 = new Sequence(
-          "Seq1",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq2 = new Sequence(
-          "Seq2",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq3 = new Sequence(
-          "Seq3",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq4 = new Sequence(
-          "Seq4",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq5 = new Sequence(
-          "Seq5",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq6 = new Sequence(
-          "Seq6",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq7 = new Sequence(
-          "Seq7",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq8 = new Sequence(
-          "Seq8",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq9 = new Sequence(
-          "Seq9",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq10 = new Sequence(
-          "Seq10",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq11 = new Sequence(
-          "Seq11",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq12 = new Sequence(
-          "Seq12",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq13 = new Sequence(
-          "Seq13",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq14 = new Sequence(
-          "Seq14",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq15 = new Sequence(
-          "Seq15",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq16 = new Sequence(
-          "Seq16",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq17 = new Sequence(
-          "Seq17",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq18 = new Sequence(
-          "Seq18",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq19 = new Sequence(
-          "Seq19",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+@Test(singleThreaded = true)
+public class OverviewDimensionsTest
+{
+  AlignmentI al;
+  OverviewDimensions od;
 
-  SequenceI seq20 = new Sequence(
-          "Seq20",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+  // cached widths and heights
+  int boxWidth;
+  int boxHeight;
+  int viewHeight;
+  int viewWidth;
+  int alheight;
+  int alwidth;
 
-  SequenceI seq21 = new Sequence(
-          "Seq21",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+  ViewportPositionProps posProps;
 
-  SequenceI seq22 = new Sequence(
-          "Seq22",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
-                  + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
-                  + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
-                  + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
-                  + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+  Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
 
-  SequenceI seq23 = new Sequence(
-          "Seq23",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+  ColumnSelection hiddenCols = new ColumnSelection();
 
-  AlignFrame af;
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    al = gen.generate(157, 525, 123, 5, 5);
+  }
 
   @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
-    Jalview.main(new String[] { "-nonews", "-props",
-        "test/jalview/testProps.jvprops" });
-
-    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
-            Boolean.TRUE.toString());
-    af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/testdata/bigal.fa",
-            DataSourceType.FILE);
-
-    /*
-     * wait for Consensus thread to complete
-     */
-    synchronized (this)
+    if (!hiddenRepSequences.isEmpty())
     {
-      while (af.getViewport().getConsensusSeq() == null)
-      {
-        try
-        {
-          wait(50);
-        } catch (InterruptedException e)
-        {
-        }
-      }
+      al.getHiddenSequences().showAll(hiddenRepSequences);
     }
-    // get cached setting for showConservation
-    // reset it in AfterClass!
-    showConservationSetting = Cache.getDefault("SHOW_CONSERVATION", true);
-  }
+    hiddenCols.revealAllHiddenColumns();
+    
+    posProps = new ViewportPositionProps(al);
+    posProps.setStartRes(0);
+    posProps.setEndRes(62);
+    posProps.setStartSeq(0);
+    posProps.setEndSeq(17);
 
+    viewHeight = posProps.getEndSeq() - posProps.getStartSeq() + 1;
+    viewWidth = posProps.getEndRes() - posProps.getStartRes() + 1;
+
+    ColumnSelection hiddenCols = new ColumnSelection();
+
+    od = new OverviewDimensions(posProps, true);
+    // Initial box sizing - default path through code
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+
+    mouseClick(od, 0, 0);
+    moveViewport(0, 0);
+
+    // calculate before hidden columns so we get absolute values
+    alheight = posProps.getAbsoluteAlignmentHeight();
+    alwidth = posProps.getAbsoluteAlignmentWidth();
+
+    boxWidth = Math.round((float) (posProps.getEndRes()
+            - posProps.getStartRes() + 1)
+            * od.getWidth() / alwidth);
+    boxHeight = Math.round((float) (posProps.getEndSeq()
+            - posProps.getStartSeq() + 1)
+            * od.getSequencesHeight() / alheight);
+  }
 
   @AfterClass(alwaysRun = true)
-  public void tearDown()
+  public void cleanUp()
   {
-    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
-            Boolean.toString(showConservationSetting));
+    al = null;
   }
 
   /**
@@ -199,17 +131,13 @@ public class OverviewDimensionsTest {
     int maxSeqHeight = 300;
     int minSeqHeight = 40;
 
-    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
-            Boolean.toString(true));
-
     // test for alignment with width > height
     SequenceI[] seqs1 = new SequenceI[] { seqa, seqb };
     Alignment al1 = new Alignment(seqs1);
-    al1.setDataset(null);
-    AlignViewport av1 = new AlignViewport(al1);
+    ViewportPositionProps props = new ViewportPositionProps(al1);
 
-    OverviewDimensions od = new OverviewDimensions(av1);
-    int scaledHeight = 266;
+    OverviewDimensions od = new OverviewDimensions(props, true);
+    int scaledHeight = 267;
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), scaledHeight);
     assertEquals(od.getWidth(), maxWidth);
@@ -218,10 +146,9 @@ public class OverviewDimensionsTest {
     // test for alignment with width < height
     SequenceI[] seqs2 = new SequenceI[] { seqa, seqb, seqc, seqd };
     Alignment al2 = new Alignment(seqs2);
-    al2.setDataset(null);
-    AlignViewport av2 = new AlignViewport(al2);
+    props = new ViewportPositionProps(al2);
 
-    od = new OverviewDimensions(av2);
+    od = new OverviewDimensions(props, true);
     int scaledWidth = 300;
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), maxSeqHeight);
@@ -232,10 +159,9 @@ public class OverviewDimensionsTest {
     // min value
     SequenceI[] seqs3 = new SequenceI[] { seqe };
     Alignment al3 = new Alignment(seqs3);
-    al3.setDataset(null);
-    AlignViewport av3 = new AlignViewport(al3);
+    props = new ViewportPositionProps(al3);
 
-    od = new OverviewDimensions(av3);
+    od = new OverviewDimensions(props, true);
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), minSeqHeight);
     assertEquals(od.getWidth(), maxWidth);
@@ -245,24 +171,18 @@ public class OverviewDimensionsTest {
     SequenceI[] seqs4 = new SequenceI[] { seqa, seqb, seqc, seqd, seqa,
         seqb, seqc, seqd, seqa, seqb, seqc, seqd, seqa, seqb, seqc, seqd };
     Alignment al4 = new Alignment(seqs4);
-    al4.setDataset(null);
-    AlignViewport av4 = new AlignViewport(al4);
+    props = new ViewportPositionProps(al4);
 
-    od = new OverviewDimensions(av4);
+    od = new OverviewDimensions(props, true);
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), maxSeqHeight);
     assertEquals(od.getWidth(), minWidth);
     assertEquals(od.getHeight(), maxSeqHeight + defaultGraphHeight);
 
-    // test for alignment where no conservation annotation is shown
-    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
-            Boolean.toString(false));
-
     Alignment al5 = new Alignment(seqs4);
-    al5.setDataset(null);
-    AlignViewport av5 = new AlignViewport(al5);
+    props = new ViewportPositionProps(al5);
 
-    od = new OverviewDimensions(av5);
+    od = new OverviewDimensions(props, false);
     assertEquals(od.getGraphHeight(), 0);
     assertEquals(od.getSequencesHeight(), maxSeqHeight);
     assertEquals(od.getWidth(), minWidth);
@@ -273,30 +193,12 @@ public class OverviewDimensionsTest {
    * Test that validation after mouse adjustments to boxX and boxY sets box
    * dimensions and scroll values correctly, when there are no hidden rows or
    * columns.
-   * 
-   * The current implementation uses multiple transformations between coordinate
-   * systems which often involve casting to int, which causes values to be
-   * truncated. As a result we can lose accuracy. The tests below use
-   * approximate test values where appropriate.
    */
   @Test(groups = { "Functional" })
   public void testSetBoxFromMouseClick()
   {
-    AlignViewport av = af.getViewport();
-    OverviewDimensions od = new OverviewDimensions(av);
-
-    // Initial box sizing - default path through code
-    od.setBoxPosition();
-    float scalew = (float) od.getWidth()
-            / (av.getAlignment().getWidth() * av.getCharWidth());
-    float scaleh = (float) od.getSequencesHeight()
-            / (av.getAlignment().getHeight() * av.getCharHeight());
-    int boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1)
-            * av.getCharWidth() * scalew);
-    int boxHeight = (int) ((av.getEndSeq() - av.getStartSeq())
-            * av.getCharHeight() * scaleh);
-
-    od.checkValid();
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            posProps);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -309,7 +211,7 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollRow(),
-            (int) (10 / scaleh / av.getCharHeight()));
+            Math.round((float) 10 * alheight / od.getSequencesHeight()));
     assertEquals(od.getScrollCol(), 0);
 
     // negative boxY value reset to 0
@@ -317,57 +219,65 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(), (int) (6 / scalew / av.getCharWidth()));
+    assertEquals(od.getScrollCol(),
+            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()));
+
+    // 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(),
-            (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()) - 1);
 
     // 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(av, od, 50);
+    moveViewportH(50);
 
     // click at viewport position
     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);
@@ -376,7 +286,7 @@ 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);
   }
 
   /**
@@ -386,21 +296,8 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenColsAtStart()
   {
-    AlignViewport av = af.getViewport();
-    OverviewDimensions od = new OverviewDimensions(av);
-
-    // Initial box sizing - default path through code
-    od.setBoxPosition();
-    float scalew = (float) od.getWidth()
-            / (av.getAlignment().getWidth() * av.getCharWidth());
-    float scaleh = (float) od.getSequencesHeight()
-            / (av.getAlignment().getHeight() * av.getCharHeight());
-    int boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1)
-            * av.getCharWidth() * scalew);
-    int boxHeight = (int) ((av.getEndSeq() - av.getStartSeq())
-            * av.getCharHeight() * scaleh);
-
-    od.checkValid();
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            posProps);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -410,36 +307,34 @@ public class OverviewDimensionsTest {
     // hide cols at start and check updated box position is correct
     // changes boxX but not boxwidth
     int lastHiddenCol = 30;
-    av.hideColumns(0, lastHiddenCol);
-    od.setBoxPosition();
+    hiddenCols.hideColumns(0, lastHiddenCol);
+
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
     assertEquals(od.getBoxX(),
-            (int) ((lastHiddenCol + 1) * scalew * av.getCharWidth()));
+            Math.round((float) (lastHiddenCol + 1) * od.getWidth()
+                    / alwidth));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // try to click in hidden cols, check box does not move
     int xpos = 10;
     mouseClick(od, xpos, 0);
-    assertEquals(od.getBoxX(),
-            (int) ((lastHiddenCol + 1) * scalew * av.getCharWidth()));
+    assertEquals(
+            od.getBoxX(),
+            Math.round((float) (lastHiddenCol + 1) * od.getWidth()
+                    / alwidth));
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollRow(), 0);
-    assertEquals(od.getScrollCol(),
-            (int) (xpos / scalew / av.getCharWidth()));
+    assertEquals(od.getScrollCol(), 0);
 
     // click to right of hidden columns, box moves to click point
-    xpos = 40;
-    mouseClick(od, xpos, 0);
-    assertEquals(od.getBoxX(),
-            (int) ((xpos - lastHiddenCol) * scalew * av.getCharWidth()));
-    assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getBoxHeight(), boxHeight);
+    testBoxIsAtClickPoint(40, 0);
     assertEquals(od.getScrollRow(), 0);
     assertEquals(od.getScrollCol(),
-            (int) (xpos / scalew / av.getCharWidth()));
+            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
@@ -447,67 +342,192 @@ public class OverviewDimensionsTest {
     // overly large boxX value reset to width-boxWidth
     xpos = 100;
     mouseClick(od, xpos, 5);
-    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth()
-            - ((int) (lastHiddenCol * scalew * av.getCharWidth())));
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
     assertEquals(od.getBoxY(), 5);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            (int) (xpos / scalew / av.getCharWidth()));
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth())
+                    - (lastHiddenCol + 1));
     assertEquals(od.getScrollRow(),
-            (int) (od.getBoxY() / scaleh / av.getCharHeight()));
-
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()));
   }
 
+  /**
+   * Test setting of the box position, when there are hidden cols in the middle
+   * of the alignment
+   */
   @Test(groups = { "Functional" })
-  public void testSetBoxPosWithHiddenColsAtEnd()
+  public void testFromMouseWithHiddenColsInMiddle()
   {
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            posProps);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
+    
+    // hide columns 63-73, no change to box position or dimensions
+    int firstHidden = 63;
+    int lastHidden = 73;
+    hiddenCols.hideColumns(firstHidden, lastHidden);
 
-  }
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    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 = 55 - boxWidth; // 55 is position in overview approx halfway
+                              // between cols 60 and 70
+    mouseClick(od, xpos, 0);
+    assertEquals(od.getBoxX(), xpos);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(
+            od.getBoxWidth(),
+            Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
+                    * od.getWidth() / alwidth));
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round(xpos * alwidth / od.getWidth()));
+    assertEquals(od.getScrollRow(), 0);
+
+    // move box so that it completely covers hidden cols
+    // box width changes, boxX and scrollCol as for hidden case
+    xpos = 33;
+    mouseClick(od, xpos, 0);
+    assertEquals(od.getBoxX(), xpos);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(
+            od.getBoxWidth(),
+            Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
+                    * od.getWidth() / alwidth));
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round((float) xpos * alwidth / od.getWidth()));
+    assertEquals(od.getScrollRow(), 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
+    // hidden region
+    xpos = 50;
+    mouseClick(od, xpos, 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(
+            od.getBoxWidth(),
+            boxWidth
+                    + Math.round((float) (lastHidden - firstHidden + 1)
+                            * od.getWidth() / alwidth));
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(), firstHidden - 1);
+    assertEquals(od.getScrollRow(), 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(),
+            Math.round(xpos * alwidth / od.getWidth())
+                    - (lastHidden - firstHidden + 1));
+    
+    // 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());
+    assertEquals(od.getBoxY(), 5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round(((float) od.getBoxX() * alwidth / od.getWidth())
+                    - (lastHidden - firstHidden + 1)));
+    assertEquals(od.getScrollRow(),
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()));
 
-  @Test(groups = { "Functional" })
-  public void testSetBoxPosWithHiddenColsMiddle()
-  {
-    AlignViewport av = af.getViewport();
-    OverviewDimensions od = new OverviewDimensions(av);
-    av.setStartRes(50);
-
-    // hiding columns before current position: changes boxX but not boxwidth
-    od.setBoxPosition();
-    int prevBoxX = od.getBoxX();
-    int prevWidth = od.getBoxWidth();
-
-    av.hideColumns(10, 20);
-    od.setBoxPosition();
-    assertEquals(od.getBoxX(), 75);
-    assertTrue(prevBoxX < od.getBoxX());
-    assertEquals(od.getBoxWidth(), prevWidth);
-
-    // hiding columns after current position: changes end position but not start
-    // so scrollCol and boxX do not change but boxWidth does
-    prevWidth = od.getBoxWidth();
-
-    av.hideColumns(108, 110);
-    od.setBoxPosition();
-    assertEquals(od.getBoxX(), prevBoxX);
-    assertEquals(od.getScrollCol(), 49);
-    // assertEquals(od2.getBoxWidth(), prevWidth + ((int) 2 * av.getCharWidth()
-    // / scalew));
   }
 
+  /**
+   * Test setting of the box position, when there are hidden cols at the end of
+   * the alignment
+   */
   @Test(groups = { "Functional" })
-  public void testSetBoxPosWithHiddenRowsAtStart()
+  public void testFromMouseWithHiddenColsAtEnd()
   {
-    AlignViewport av = af.getViewport();
-    OverviewDimensions od = new OverviewDimensions(av);
-    av.setStartRes(50);
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            posProps);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
+
+    // hide columns 140-164, no change to box position or dimensions
+    int firstHidden = 140;
+    int lastHidden = 164;
+    hiddenCols.hideColumns(firstHidden, lastHidden);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 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(),
+            Math.round((float) xpos * alwidth / od.getWidth()));
+
+    // click to left of hidden cols, with overlap
+    // boxX and scrollCol adjusted for hidden cols, width normal
+    xpos = Math.round((float) 145 * od.getWidth() / alwidth) - boxWidth;
+    mouseClick(od, xpos, 0);
+    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);
+
+    // click in hidden cols
+    // boxX and scrollCol adjusted for hidden cols, width normal
+    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((float) od.getBoxX() * alwidth / od.getWidth()));
+    assertEquals(od.getScrollRow(), 0);
 
-    // account for hidden rows
-    SequenceI[] hidden = { seq2, seq3, seq4, seq5, seq6, seq7 };
-    av.showAllHiddenColumns();
-    av.hideSequence(hidden);
-    od.checkValid();
+    // click off end of alignment
+    // boxX and scrollCol adjusted for hidden cols, width normal
+    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);
   }
 
@@ -518,44 +538,416 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testSetBoxFromViewport()
   {
-    AlignViewport av = af.getViewport();
-    OverviewDimensions od = new OverviewDimensions(av);
-    od.setBoxPosition();
-
-    float scalew = (float) od.getWidth()
-            / (av.getAlignment().getWidth() * av.getCharWidth());
-    float scaleh = (float) od.getSequencesHeight()
-            / (av.getAlignment().getHeight() * av.getCharHeight());
-    int boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1)
-            * av.getCharWidth() * scalew);
-    int boxHeight = (int) ((av.getEndSeq() - av.getStartSeq())
-            * av.getCharHeight() * scaleh);
-
     // move viewport to start of alignment
-    moveViewport(av, od, 0, 0);
+    moveViewport(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to right
-    moveViewportH(av, od, 70);
-    assertEquals(od.getBoxX(), (int) (70 * scalew * av.getCharWidth()));
+    moveViewportH(70);
+    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(av, od, 100);
-    assertEquals(od.getBoxX(), (int) (70 * scalew * av.getCharWidth()));
-    assertEquals(od.getBoxY(), (int) (100 * scaleh * av.getCharHeight()));
+    moveViewportV(100);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 70 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(),
+            Math.round(100 * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to bottom right
-    moveViewport(av, od, 98, 508);
-    assertEquals(od.getBoxX(), (int) (98 * scalew * av.getCharWidth()));
-    assertEquals(od.getBoxY(), (int) (508 * scaleh * av.getCharHeight()));
+    moveViewport(98, 508);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 98 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(),
+            Math.round((float) 508 * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+  }
+
+  /**
+   * Test that the box position is set correctly when there are hidden columns
+   * at the start
+   */
+  @Test(groups = { "Functional" })
+  public void testSetBoxFromViewportHiddenColsAtStart()
+  {
+    int firstHidden = 0;
+    int lastHidden = 20;
+    hiddenCols.hideColumns(firstHidden, lastHidden);
+
+    // move viewport to start of alignment
+    moveViewport(0, 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) (lastHidden + 1) * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // 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((float) 98 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+  }
+
+  /**
+   * Test that the box position is set correctly when there are hidden columns
+   * in the middle
+   */
+  @Test(groups = { "Functional" })
+  public void testSetBoxFromViewportHiddenColsInMiddle()
+  {
+    int firstHidden = 68;
+    int lastHidden = 78;
+    hiddenCols.hideColumns(firstHidden, lastHidden);
+
+    // move viewport before hidden columns
+    moveViewport(3, 0);
+
+    assertEquals(od.getBoxX(),
+            Math.round((float) 3 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    System.out.println(od.getBoxWidth());
+    assertEquals(od.getBoxWidth(), boxWidth);
+    System.out.println(od.getBoxWidth());
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to left of hidden columns with overlap
+    moveViewport(10, 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 10 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(
+            od.getBoxWidth(),
+            boxWidth
+                    + Math.round((float) (lastHidden - firstHidden + 1)
+                            * od.getWidth() / alwidth));
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to straddle hidden columns
+    moveViewport(63, 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 63 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(
+            od.getBoxWidth(),
+            boxWidth
+                    + 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((float) 80 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+  }
+
+  /**
+   * Test that the box position is set correctly when there are hidden columns
+   * at the end
+   */
+  @Test(groups = { "Functional" })
+  public void testSetBoxFromViewportHiddenColsAtEnd()
+  {
+    int firstHidden = 152;
+    int lastHidden = 164;
+    hiddenCols.hideColumns(firstHidden, lastHidden);
+
+    // move viewport before hidden columns
+    moveViewport(3, 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 3 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to hidden columns
+    moveViewport(102, 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 102 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth
+                    + Math.round((float) (lastHidden - firstHidden + 1)
+                            * od.getWidth() / alwidth));
+    assertEquals(od.getBoxHeight(), boxHeight);
+  }
+
+  /**
+   * Test that the box position is set correctly when there are hidden rows at
+   * the start
+   */
+  @Test(groups = { "Functional" })
+  public void testSetBoxFromViewportHiddenRowsAtStart()
+  {
+    int firstHidden = 0;
+    int lastHidden = 20;
+    hideSequences(firstHidden, lastHidden);
+
+    // move viewport to start of alignment:
+    // box moves to below hidden rows, height remains same
+    moveViewport(0, 0);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(),
+            Math.round((float) (lastHidden + 1) * od.getSequencesHeight()
+                    / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to end of alignment
+    moveViewport(0, 525 - viewHeight - lastHidden - 1);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(
+            od.getBoxY(),
+            Math.round((float) (525 - viewHeight) * od.getSequencesHeight()
+                    / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+  }
+
+  /**
+   * Test that the box position is set correctly when there are hidden rows in
+   * the middle
+   */
+  @Test(groups = { "Functional" })
+  public void testSetBoxFromViewportHiddenRowsInMiddle()
+  {
+    int firstHidden = 200;
+    int lastHidden = 210;
+    hideSequences(firstHidden, lastHidden);
+
+    // move viewport to start of alignment:
+    // box, height etc as in non-hidden case
+    moveViewport(0, 0);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to straddle hidden rows
+    moveViewport(0, 198);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), Math.round ((float)198 * od.getSequencesHeight()
+            / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(
+            od.getBoxHeight(),
+            Math.round((float) (viewHeight + lastHidden - firstHidden + 1)
+                    * od.getSequencesHeight() / alheight));
+  }
+
+  /**
+   * Test that the box position is set correctly when there are hidden rows at
+   * the bottom
+   */
+  @Test(groups = { "Functional" })
+  public void testSetBoxFromViewportHiddenRowsAtEnd()
+  {
+    int firstHidden = 500;
+    int lastHidden = 524;
+    hideSequences(firstHidden, lastHidden);
+
+    // move viewport to start of alignment:
+    // box, height etc as in non-hidden case
+    moveViewport(0, 0);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to end of alignment
+    // viewport sits above hidden rows and does not include them
+    moveViewport(0, firstHidden - viewHeight - 1);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(
+            od.getBoxY(),
+            Math.round((float) (firstHidden - viewHeight - 1)
+                    * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+  }
+
+  /**
+   * Test setting of the box position, when there are hidden rows at the start
+   * of the alignment
+   */
+  @Test(groups = { "Functional" })
+  public void testFromMouseWithHiddenRowsAtStart()
+  {
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            posProps);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
+
+    // hide rows at start and check updated box position is correct
+    // changes boxY but not boxheight
+    int lastHiddenRow = 30;
+    hideSequences(0, lastHiddenRow);
+
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(),
+            Math.round((float) (lastHiddenRow + 1)
+                    * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // click in hidden rows - same result
+    mouseClick(od, 0, 0);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(
+            od.getBoxY(),
+            Math.round((float) (lastHiddenRow + 1)
+                    * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // click below hidden rows
+    mouseClick(od, 0, 150);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 150);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+  }
+
+  /**
+   * Test setting of the box position, when there are hidden rows at the middle
+   * of the alignment
+   */
+  @Test(groups = { "Functional" })
+  public void testFromMouseWithHiddenRowsInMiddle()
+  {
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            posProps);
+
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
+
+    // hide rows in middle and check updated box position is correct
+    // no changes
+    int firstHiddenRow = 50;
+    int lastHiddenRow = 54;
+    hideSequences(firstHiddenRow, lastHiddenRow);
+
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // click above hidden rows, so that box overlaps
+    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 = 44; // 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));
+  }
+
+  /**
+   * Test setting of the box position, when there are hidden rows at the end of
+   * the alignment
+   */
+  @Test(groups = { "Functional" })
+  public void testFromMouseWithHiddenRowsAtEnd()
+  {
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            posProps);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
+
+    // hide rows at end and check updated box position is correct
+    // no changes
+    int firstHidden = 500;
+    int lastHidden = 524;
+    hideSequences(firstHidden, lastHidden);
+
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // click above hidden rows
+    int ypos = 40; // row 40
+    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);
+
+    // click above hidden rows so box overlaps
+    // boxY moved upwards, boxHeight remains same
+    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;
+    mouseClick(od, 0,
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(
+            od.getBoxY(),
+            Math.round((firstHidden - viewHeight) * od.getSequencesHeight()
+                    / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
   }
@@ -563,40 +955,33 @@ public class OverviewDimensionsTest {
   /*
    * Move viewport horizontally: startRes + previous width gives new horizontal extent. Vertical extent stays the same.
    */
-  private void moveViewportH(AlignViewport av, OverviewDimensions od,
-          int startRes)
+  private void moveViewportH(int startRes)
   {
-    int width = av.getEndRes() - av.getStartRes();
-    av.setStartRes(startRes);
-    av.setEndRes(startRes + width);
-    od.setBoxPosition();
+    posProps.setStartRes(startRes);
+    posProps.setEndRes(startRes + viewWidth - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
   }
 
   /*
    * Move viewport vertically: startSeq and endSeq give new vertical extent. Horizontal extent stays the same.
    */
-  private void moveViewportV(AlignViewport av, OverviewDimensions od,
-          int startSeq)
+  private void moveViewportV(int startSeq)
   {
-    int height = av.getEndSeq() - av.getStartSeq();
-    av.setStartSeq(startSeq);
-    av.setEndSeq(startSeq + height);
-    od.setBoxPosition();
+    posProps.setStartSeq(startSeq);
+    posProps.setEndSeq(startSeq + viewHeight - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
   }
 
   /*
    * Move viewport horizontally and vertically.
    */
-  private void moveViewport(AlignViewport av, OverviewDimensions od,
-          int startRes, int startSeq)
+  private void moveViewport(int startRes, int startSeq)
   {
-    int width = av.getEndRes() - av.getStartRes();
-    int height = av.getEndSeq() - av.getStartSeq();
-    av.setStartRes(startRes);
-    av.setEndRes(startRes + width);
-    av.setStartSeq(startSeq);
-    av.setEndSeq(startSeq + height);
-    od.setBoxPosition();
+    posProps.setStartRes(startRes);
+    posProps.setEndRes(startRes + viewWidth - 1);
+    posProps.setStartSeq(startSeq);
+    posProps.setEndSeq(startSeq + viewHeight - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
   }
 
   /*
@@ -604,19 +989,48 @@ public class OverviewDimensionsTest {
    */
   private void mouseClick(OverviewDimensions od, int x, int y)
   {
-    od.setBoxX(x);
-    od.setBoxY(y);
-    od.checkValid();
+    od.updateViewportFromMouse(x, y, al.getHiddenSequences(), hiddenCols,
+            posProps);
+
     // updates require an OverviewPanel to exist which it doesn't here
     // so call setBoxPosition() as it would be called by the AlignmentPanel
     // normally
-    AlignViewport av = af.getViewport();
-    int width = av.getEndRes() - av.getStartRes();
-    int height = av.getEndSeq() - av.getStartSeq();
-    av.setStartRes(od.getScrollCol());
-    av.setEndRes(od.getScrollCol() + width);
-    av.setStartSeq(od.getScrollRow());
-    av.setEndSeq(od.getScrollRow() + height);
-    od.setBoxPosition();
+
+    posProps.setStartRes(od.getScrollCol());
+    posProps.setEndRes(od.getScrollCol() + viewWidth - 1);
+    posProps.setStartSeq(od.getScrollRow());
+    posProps.setEndSeq(od.getScrollRow() + viewHeight - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+  }
+  
+  /*
+   * Test that the box is positioned with the top left corner at xpos, ypos
+   * and with the original width and height
+   */
+  private void testBoxIsAtClickPoint(int xpos, int ypos)
+  {
+    mouseClick(od, xpos, ypos);
+    assertEquals(od.getBoxX(), xpos);
+    assertEquals(od.getBoxY(), ypos);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+  }
+
+  /*
+   * Hide sequences between start and end
+   */
+  private void hideSequences(int start, int end)
+  {
+    SequenceI[] allseqs = al.getSequencesArray();
+    SequenceGroup theseSeqs = new SequenceGroup();
+    
+    for (int i = start; i <= end; i++)
+    {
+      theseSeqs.addSequence(allseqs[i], false);
+      al.getHiddenSequences().hideSequence(allseqs[i]);
+    }
+
+    hiddenRepSequences.put(allseqs[start], theseSeqs);
   }
 }