X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fviewmodel%2FOverviewDimensionsTest.java;h=d01eaa3cb614f68370af030809ee41e4f3339d79;hb=41f78bdf2b0650fa7fde4959a7b9d58fd5c77c71;hp=39506fcdb5c7f2e08d3cbf1ae3494d3af9c8e288;hpb=29933a3d76e0a2517ac59307adb40a73204ceacf;p=jalview.git

diff --git a/test/jalview/viewmodel/OverviewDimensionsTest.java b/test/jalview/viewmodel/OverviewDimensionsTest.java
index 39506fc..d01eaa3 100644
--- a/test/jalview/viewmodel/OverviewDimensionsTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsTest.java
@@ -21,17 +21,20 @@
 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.datamodel.Alignment;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
-import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
 
 import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 public class OverviewDimensionsTest {
@@ -126,27 +129,49 @@ public class OverviewDimensionsTest {
           "Seq22",
           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
                   + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
+                  + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
+                  + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
                   + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 
   SequenceI seq23 = new Sequence(
           "Seq23",
           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 
+  AlignFrame af;
 
-  @BeforeClass(alwaysRun = true)
+  @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
-    JvOptionPane.setInteractiveMode(false);
-    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-
     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)
+    {
+      while (af.getViewport().getConsensusSeq() == null)
+      {
+        try
+        {
+          wait(50);
+        } catch (InterruptedException e)
+        {
+        }
+      }
+    }
     // get cached setting for showConservation
     // reset it in AfterClass!
     showConservationSetting = Cache.getDefault("SHOW_CONSERVATION", true);
   }
 
+
   @AfterClass(alwaysRun = true)
   public void tearDown()
   {
@@ -159,131 +184,199 @@ public class OverviewDimensionsTest {
    * correctly
    */
   @Test(groups = { "Functional" })
-      public void testConstructor()
-      {
-        SequenceI seqa = new Sequence("Seq1", "ABC");
-        SequenceI seqb = new Sequence("Seq2", "ABC");
-        SequenceI seqc = new Sequence("Seq3", "ABC");
-        SequenceI seqd = new Sequence("Seq4", "ABC");
-        SequenceI seqe = new Sequence("Seq5",
-                "ABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-        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);
-
-        OverviewDimensions od = new OverviewDimensions(av1);
-        assertEquals(od.getGraphHeight(), 20);
-        assertEquals(od.getSequencesHeight(), 266);
-        assertEquals(od.getWidth(), 400);
-        assertEquals(od.getHeight(), 286);
-
-        // 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);
-
-        od = new OverviewDimensions(av2);
-        assertEquals(od.getGraphHeight(), 20);
-        assertEquals(od.getSequencesHeight(), 300);
-        assertEquals(od.getWidth(), 300);
-        assertEquals(od.getHeight(), 320);
-
-        // test for alignment with width > height and sequence height scaled below
-        // min value
-        SequenceI[] seqs3 = new SequenceI[] { seqe };
-        Alignment al3 = new Alignment(seqs3);
-        al3.setDataset(null);
-        AlignViewport av3 = new AlignViewport(al3);
-
-        od = new OverviewDimensions(av3);
-        assertEquals(od.getGraphHeight(), 20);
-        assertEquals(od.getSequencesHeight(), 40);
-        assertEquals(od.getWidth(), 400);
-        assertEquals(od.getHeight(), 60);
-
-        // test for alignment with width < height and width scaled below min value
-        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);
-
-        od = new OverviewDimensions(av4);
-        assertEquals(od.getGraphHeight(), 20);
-        assertEquals(od.getSequencesHeight(), 300);
-        assertEquals(od.getWidth(), 120);
-        assertEquals(od.getHeight(), 320);
-
-        // 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);
-
-        od = new OverviewDimensions(av5);
-        assertEquals(od.getGraphHeight(), 0);
-        assertEquals(od.getSequencesHeight(), 300);
-        assertEquals(od.getWidth(), 120);
-        assertEquals(od.getHeight(), 300);
-      }
+  public void testConstructor()
+  {
+    SequenceI seqa = new Sequence("Seq1", "ABC");
+    SequenceI seqb = new Sequence("Seq2", "ABC");
+    SequenceI seqc = new Sequence("Seq3", "ABC");
+    SequenceI seqd = new Sequence("Seq4", "ABC");
+    SequenceI seqe = new Sequence("Seq5",
+            "ABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+    int defaultGraphHeight = 20;
+    int maxWidth = 400;
+    int minWidth = 120;
+    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);
+
+    OverviewDimensions od = new OverviewDimensions(av1);
+    int scaledHeight = 266;
+    assertEquals(od.getGraphHeight(), defaultGraphHeight);
+    assertEquals(od.getSequencesHeight(), scaledHeight);
+    assertEquals(od.getWidth(), maxWidth);
+    assertEquals(od.getHeight(), scaledHeight + defaultGraphHeight);
+
+    // 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);
+
+    od = new OverviewDimensions(av2);
+    int scaledWidth = 300;
+    assertEquals(od.getGraphHeight(), defaultGraphHeight);
+    assertEquals(od.getSequencesHeight(), maxSeqHeight);
+    assertEquals(od.getWidth(), scaledWidth);
+    assertEquals(od.getHeight(), scaledWidth + defaultGraphHeight);
+
+    // test for alignment with width > height and sequence height scaled below
+    // min value
+    SequenceI[] seqs3 = new SequenceI[] { seqe };
+    Alignment al3 = new Alignment(seqs3);
+    al3.setDataset(null);
+    AlignViewport av3 = new AlignViewport(al3);
+
+    od = new OverviewDimensions(av3);
+    assertEquals(od.getGraphHeight(), defaultGraphHeight);
+    assertEquals(od.getSequencesHeight(), minSeqHeight);
+    assertEquals(od.getWidth(), maxWidth);
+    assertEquals(od.getHeight(), minSeqHeight + defaultGraphHeight);
+
+    // test for alignment with width < height and width scaled below min value
+    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);
+
+    od = new OverviewDimensions(av4);
+    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);
+
+    od = new OverviewDimensions(av5);
+    assertEquals(od.getGraphHeight(), 0);
+    assertEquals(od.getSequencesHeight(), maxSeqHeight);
+    assertEquals(od.getWidth(), minWidth);
+    assertEquals(od.getHeight(), maxSeqHeight);
+  }
 
   /**
    * 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
+   * 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 checkValidNoHidden()
+  public void testSetBoxFromMouseClick()
   {
-    seq23.setStart(386);
-    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
-        seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
-        seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
-    Alignment al = new Alignment(seqs);
-    al.setDataset(null);
-    AlignViewport av = new AlignViewport(al);
+    AlignViewport av = af.getViewport();
+    OverviewDimensions od = new OverviewDimensions(av);
 
     // Initial box sizing - default path through code
-    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);
+
     od.checkValid();
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), 399);
+    assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getScrollCol(), 0);
     assertEquals(od.getScrollRow(), 0);
 
     // negative boxX value reset to 0
-    od.setBoxX(-5);
-    od.checkValid();
+    mouseClick(od, -5, 10);
     assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollRow(),
+            (int) (10 / scaleh / av.getCharHeight()));
+    assertEquals(od.getScrollCol(), 0);
 
     // negative boxY value reset to 0
-    od.setBoxY(-2);
-    od.checkValid();
+    mouseClick(od, 6, -2);
     assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(), (int) (6 / scalew / av.getCharWidth()));
+    assertEquals(od.getScrollRow(), 0);
 
     // overly large boxX value reset to width-boxWidth
-    od.setBoxX(100);
-    od.checkValid();
-    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
-
-    // startRes non-zero
-    av.setStartRes(50);
-    OverviewDimensions od2 = new OverviewDimensions(av);
-    od2.setBoxPosition();
-    od2.checkValid();
-    assertEquals(od2.getBoxX(), 61);
-    assertEquals(od2.getScrollCol(), 49);
+    mouseClick(od, 100, 6);
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth(), 1.5);
+    assertEquals(od.getBoxY(), 6, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
+    assertEquals(od.getScrollRow(),
+            (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);
+
+    // 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.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getScrollCol(),
+            (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
+    assertEquals(od.getScrollRow(),
+            (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);
+
+    // click past end of alignment, as above
+    mouseClick(od, 3000, 5);
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth(), 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getScrollCol(),
+            (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
+    assertEquals(od.getScrollRow(),
+            (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);
+
+    // move viewport so startRes non-zero and then mouseclick
+    moveViewportH(av, od, 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.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getScrollCol(),
+            (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
+    assertEquals(od.getBoxY(), oldboxy + 2, 1.5);
+    assertEquals(od.getScrollRow(),
+            (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);
+
+    // click at top corner
+    mouseClick(od, 0, 0);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getScrollRow(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
   }
 
   /**
@@ -291,41 +384,79 @@ public class OverviewDimensionsTest {
    * of the alignment
    */
   @Test(groups = { "Functional" })
-  public void testSetBoxPosWithHiddenColsAtStart()
+  public void testFromMouseWithHiddenColsAtStart()
   {
-    seq23.setStart(386);
-    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
-        seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
-        seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
-    Alignment al = new Alignment(seqs);
-    al.setDataset(null);
-    AlignViewport av = new AlignViewport(al);
-
-    av.setStartRes(50);
+    AlignViewport av = af.getViewport();
     OverviewDimensions od = new OverviewDimensions(av);
 
-    // hiding columns before current position: changes boxX but not scrollCol or
-    // boxwidth
-
-    // do a reset
-    av.showAllHiddenColumns();
+    // 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();
-    int prevWidth = od.getBoxWidth();
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
 
     // hide cols at start and check updated box position is correct
-    // changes boxX but not scrollCol or boxwidth
-    int lastHiddenCol = 50;
-    av.hideColumns(0, 50);
+    // changes boxX but not boxwidth
+    int lastHiddenCol = 30;
+    av.hideColumns(0, lastHiddenCol);
     od.setBoxPosition();
-    assertEquals(od.getBoxX(), 124);
-    assertEquals(od.getScrollCol(), lastHiddenCol - 1);
-    assertEquals(od.getBoxWidth(), prevWidth);
+    assertEquals(od.getBoxX(),
+            (int) ((lastHiddenCol + 1) * scalew * av.getCharWidth()));
+    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.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollRow(), 0);
+    assertEquals(od.getScrollCol(),
+            (int) (xpos / scalew / av.getCharWidth()));
+
+    // 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);
+    assertEquals(od.getScrollRow(), 0);
+    assertEquals(od.getScrollCol(),
+            (int) (xpos / scalew / av.getCharWidth()));
 
-    // set the box position by moving viewport & check it goes to the right
-    // place
+    // click to right of hidden columns such that box runs over right hand side
+    // of alignment
+    // box position is adjusted away from the edge
+    // 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.getBoxY(), 5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            (int) (xpos / scalew / av.getCharWidth()));
+    assertEquals(od.getScrollRow(),
+            (int) (od.getBoxY() / scaleh / av.getCharHeight()));
 
-    // update the box position via mouse and check it goes to the right place
   }
 
   @Test(groups = { "Functional" })
@@ -337,25 +468,28 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testSetBoxPosWithHiddenColsMiddle()
   {
-    seq23.setStart(386);
-    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
-        seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
-        seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
-    Alignment al = new Alignment(seqs);
-    al.setDataset(null);
-    AlignViewport av = new AlignViewport(al);
-
-    av.setStartRes(50);
+    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
-    float scalew = od.getWidth() / al.getWidth();
-    int prevWidth = od.getBoxWidth();
-    int prevX = od.getBoxX();
+    prevWidth = od.getBoxWidth();
+
     av.hideColumns(108, 110);
     od.setBoxPosition();
-    assertEquals(od.getBoxX(), prevX);
+    assertEquals(od.getBoxX(), prevBoxX);
     assertEquals(od.getScrollCol(), 49);
     // assertEquals(od2.getBoxWidth(), prevWidth + ((int) 2 * av.getCharWidth()
     // / scalew));
@@ -364,16 +498,9 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testSetBoxPosWithHiddenRowsAtStart()
   {
-    seq23.setStart(386);
-    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
-        seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
-        seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
-    Alignment al = new Alignment(seqs);
-    al.setDataset(null);
-    AlignViewport av = new AlignViewport(al);
-
-    av.setStartRes(50);
+    AlignViewport av = af.getViewport();
     OverviewDimensions od = new OverviewDimensions(av);
+    av.setStartRes(50);
 
     // account for hidden rows
     SequenceI[] hidden = { seq2, seq3, seq4, seq5, seq6, seq7 };
@@ -384,62 +511,112 @@ public class OverviewDimensionsTest {
     assertEquals(od.getScrollRow(), 0);
   }
 
-     /**
-      * Test that the box position is set correctly
-      */
+  /**
+   * Test that the box position is set correctly when set from the viewport,
+   * with no hidden rows or columns
+   */
   @Test(groups = { "Functional" })
-      public void setBoxPosition()
-      {
-
-        SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
-            seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
-            seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
-        Alignment al = new Alignment(seqs);
-        al.setDataset(null);
-        AlignViewport av = new AlignViewport(al);
-
-        // Test box is in expected location when there are no hidden rows or columns
-
-        OverviewDimensions od = new OverviewDimensions(av);
-        od.setBoxPosition();
-
-        assertEquals(od.getBoxHeight(), 81);
-        assertEquals(od.getBoxWidth(), 400);
-        assertEquals(od.getBoxX(), 0);
-        assertEquals(od.getBoxY(), 0);
-
-        // Account for hidden rows
-        SequenceI[] hidden = { seq2, seq3, seq4 };
-        av.hideSequence(hidden);
-
-        OverviewDimensions od1 = new OverviewDimensions(av);
-        od1.setBoxPosition();
+  public void testSetBoxFromViewport()
+  {
+    AlignViewport av = af.getViewport();
+    OverviewDimensions od = new OverviewDimensions(av);
+    od.setBoxPosition();
 
-        assertEquals(od1.getBoxHeight(), 80);
-        assertEquals(od1.getBoxWidth(), 400);
-        assertEquals(od1.getBoxX(), 0);
-        assertEquals(od1.getBoxY(), 0);
+    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);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
-        // Account for hidden columns
-        av.hideColumns(10, 15);
-        av.showAllHiddenSeqs();
+    // move viewport to right
+    moveViewportH(av, od, 70);
+    assertEquals(od.getBoxX(), (int) (70 * scalew * av.getCharWidth()));
+    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()));
+    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()));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+  }
 
-        OverviewDimensions od2 = new OverviewDimensions(av);
-        od2.setBoxPosition();
+  /*
+   * Move viewport horizontally: startRes + previous width gives new horizontal extent. Vertical extent stays the same.
+   */
+  private void moveViewportH(AlignViewport av, OverviewDimensions od,
+          int startRes)
+  {
+    int width = av.getEndRes() - av.getStartRes();
+    av.setStartRes(startRes);
+    av.setEndRes(startRes + width);
+    od.setBoxPosition();
+  }
 
-        assertEquals(od2.getBoxHeight(), 81);
-        assertEquals(od2.getBoxWidth(), 422);
-        assertEquals(od2.getBoxX(), 0);
-        assertEquals(od2.getBoxY(), 0);
+  /*
+   * Move viewport vertically: startSeq and endSeq give new vertical extent. Horizontal extent stays the same.
+   */
+  private void moveViewportV(AlignViewport av, OverviewDimensions od,
+          int startSeq)
+  {
+    int height = av.getEndSeq() - av.getStartSeq();
+    av.setStartSeq(startSeq);
+    av.setEndSeq(startSeq + height);
+    od.setBoxPosition();
+  }
 
-        // Account for hidden rows and cols
-        av.hideSequence(hidden);
-        OverviewDimensions od3 = new OverviewDimensions(av);
-        od3.setBoxPosition();
+  /*
+   * Move viewport horizontally and vertically.
+   */
+  private void moveViewport(AlignViewport av, OverviewDimensions od,
+          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();
+  }
 
-        assertEquals(od3.getBoxHeight(), 80);
-        assertEquals(od3.getBoxWidth(), 422);
-        assertEquals(od3.getBoxX(), 0);
-        assertEquals(od3.getBoxY(), 0);
+  /*
+   * Mouse click as position x,y in overview window
+   */
+  private void mouseClick(OverviewDimensions od, int x, int y)
+  {
+    od.setBoxX(x);
+    od.setBoxY(y);
+    od.checkValid();
+    // 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();
   }
 }