JAL-2388 Minor fix for annotation graph, removed unit test dep on gui

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 8f91835..836a800 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -75,12 +75,12 @@ public class OverviewPanel extends Panel implements Runnable,
     sr.forOverview = true;
     fr = new FeatureRenderer(av);
 
-    boolean showAnnotation = false;
+    boolean showAnnotation = true;
     // TODO: in applet this was getSequenceConsensusHash()
     // check if it makes any functional difference: hconsensus or conservation
     if (av.getAlignmentConservationAnnotation() == null)
     {
-      showAnnotation = true;
+      showAnnotation = false;
     }
 
     od = new OverviewDimensions(av.getPosProps(), showAnnotation);

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index e399bc1..923616f 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -88,12 +88,12 @@ public class OverviewPanel extends JPanel implements Runnable
     sr.forOverview = true;
     fr = new FeatureRenderer(alPanel);
 
-    boolean showAnnotation = false;
+    boolean showAnnotation = true;
     // TODO: in applet this was getSequenceConsensusHash()
     // check if it makes any functional difference: hconsensus or conservation
     if (av.getAlignmentConservationAnnotation() == null)
     {
-      showAnnotation = true;
+      showAnnotation = false;
     }
     od = new OverviewDimensions(av.getPosProps(), showAnnotation);
 

diff --git a/test/jalview/viewmodel/OverviewDimensionsTest.java b/test/jalview/viewmodel/OverviewDimensionsTest.java
index 8184b52..e86f41b 100644 (file)
--- a/test/jalview/viewmodel/OverviewDimensionsTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsTest.java
@@ -23,23 +23,17 @@ package jalview.viewmodel;
 import static org.testng.Assert.assertEquals;
 
 import jalview.analysis.AlignmentGenerator;
-import jalview.bin.Jalview;
 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.gui.Desktop;
-import jalview.gui.JvOptionPane;
-import jalview.io.DataSourceType;
-import jalview.io.FileLoader;
 
-import java.util.List;
+import java.util.Hashtable;
 
 import org.testng.annotations.AfterClass;
-import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
@@ -67,8 +61,6 @@ public class OverviewDimensionsTest {
           "Seq5",
           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
 
-  AlignFrame af;
-  AlignViewport av;
   AlignmentI al;
   OverviewDimensions od;
 
@@ -80,12 +72,15 @@ public class OverviewDimensionsTest {
   int alheight;
   int alwidth;
 
+  ViewportPositionProps posProps;
+
+  Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+
+  ColumnSelection hiddenCols = new ColumnSelection();
+
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
-    JvOptionPane.setInteractiveMode(false);
-    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-
     // create random alignment
     AlignmentGenerator gen = new AlignmentGenerator(false);
     al = gen.generate(157, 525, 123, 5, 5);
@@ -94,107 +89,40 @@ public class OverviewDimensionsTest {
   @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
-    Jalview.main(new String[] { "-nonews", "-props",
-        "test/jalview/testProps.jvprops" });
-
-    af = new FileLoader().LoadFileWaitTillLoaded(al.toString(),
-            DataSourceType.PASTE);
-
-    /*
-     * 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);
     }
+    hiddenCols.revealAllHiddenColumns();
     
-    av = af.getViewport();
-
+    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;
 
-    while (av.isCalcInProgress())
-    {
-      try
-      {
-        Thread.sleep(50);
-      } catch (InterruptedException e)
-      {
-
-      }
-    }
-
-    av.showAllHiddenColumns();
-    av.showAllHiddenSeqs();
-    av.setSelectionGroup(null);
-    // o/w hidden seqs retain selection group, causes problems later when hiding
-    // sequences
-
-    // wait for conservation calc to complete again
-    while (av.isCalcInProgress())
-    {
-      try
-      {
-        Thread.sleep(50);
-      } catch (InterruptedException e)
-      {
-
-      }
-    }
-
-    viewHeight = av.getEndSeq() - av.getStartSeq() + 1;
-    viewWidth = av.getEndRes() - av.getStartRes() + 1;
-
-    // wait for gui to get set up
-    // this does actually appear to be necessary
-    while (viewHeight != 18 || viewWidth != 63)
-    {
-      try
-      {
-        Thread.sleep(50);
-        av.getAlignPanel().setScrollValues(0, 1);
-        av.getAlignPanel().setScrollValues(1, 0);
-        viewHeight = av.getEndSeq() - av.getStartSeq() + 1;
-        viewWidth = av.getEndRes() - av.getStartRes() + 1;
-      } catch (InterruptedException e)
-      {
-
-      }
-    }
+    ColumnSelection hiddenCols = new ColumnSelection();
 
-    od = new OverviewDimensions(av.getPosProps(), true);
+    od = new OverviewDimensions(posProps, true);
     // Initial box sizing - default path through code
-    od.setBoxPosition(av.getAlignment().getHiddenSequences(),
-            av.getColumnSelection(), av.getPosProps());
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
 
     mouseClick(od, 0, 0);
     moveViewport(0, 0);
 
     // calculate before hidden columns so we get absolute values
-    alheight = av.getAlignment().getHeight();
-    alwidth = av.getAlignment().getWidth();
+    alheight = posProps.getAbsoluteAlignmentHeight();
+    alwidth = posProps.getAbsoluteAlignmentWidth();
 
-    boxWidth = Math.round((float) (av.getEndRes() - av.getStartRes() + 1)
+    boxWidth = Math.round((float) (posProps.getEndRes()
+            - posProps.getStartRes() + 1)
             * od.getWidth() / alwidth);
-    boxHeight = Math.round((float) (av.getEndSeq() - av.getStartSeq() + 1)
+    boxHeight = Math.round((float) (posProps.getEndSeq()
+            - posProps.getStartSeq() + 1)
             * od.getSequencesHeight() / alheight);
-    System.out.println(boxHeight);
-
-  }
-
-  @AfterMethod(alwaysRun = true)
-  public void tearDown()
-  {
-    af = null;
-    av = null;
-    Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @AfterClass(alwaysRun = true)
@@ -226,10 +154,9 @@ public class OverviewDimensionsTest {
     // 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.getPosProps(), true);
+    OverviewDimensions od = new OverviewDimensions(props, true);
     int scaledHeight = 266;
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), scaledHeight);
@@ -239,10 +166,9 @@ 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.getPosProps(), true);
+    od = new OverviewDimensions(props, true);
     int scaledWidth = 300;
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), maxSeqHeight);
@@ -253,10 +179,9 @@ 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.getPosProps(), true);
+    od = new OverviewDimensions(props, true);
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), minSeqHeight);
     assertEquals(od.getWidth(), maxWidth);
@@ -266,20 +191,18 @@ 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.getPosProps(), true);
+    od = new OverviewDimensions(props, true);
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), maxSeqHeight);
     assertEquals(od.getWidth(), minWidth);
     assertEquals(od.getHeight(), maxSeqHeight + defaultGraphHeight);
 
     Alignment al5 = new Alignment(seqs4);
-    al5.setDataset(null);
-    AlignViewport av5 = new AlignViewport(al5);
+    props = new ViewportPositionProps(al5);
 
-    od = new OverviewDimensions(av5.getPosProps(), false);
+    od = new OverviewDimensions(props, false);
     assertEquals(od.getGraphHeight(), 0);
     assertEquals(od.getSequencesHeight(), maxSeqHeight);
     assertEquals(od.getWidth(), minWidth);
@@ -290,18 +213,12 @@ 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()
   {
-    od.updateViewportFromMouse(0, 0,
-            av.getAlignment().getHiddenSequences(),
-            av.getColumnSelection(), av.getPosProps());
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            posProps);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -395,9 +312,8 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenColsAtStart()
   {
-    od.updateViewportFromMouse(0, 0,
-            av.getAlignment().getHiddenSequences(),
-            av.getColumnSelection(), av.getPosProps());
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            posProps);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -407,10 +323,9 @@ public class OverviewDimensionsTest {
     // hide cols at start and check updated box position is correct
     // changes boxX but not boxwidth
     int lastHiddenCol = 30;
-    hideColumns(0, lastHiddenCol);
+    hiddenCols.hideColumns(0, lastHiddenCol);
 
-    od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
     assertEquals(od.getBoxX(),
             Math.round((float) (lastHiddenCol + 1) * od.getWidth()
                     / alwidth));
@@ -463,9 +378,8 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenColsInMiddle()
   {
-    od.updateViewportFromMouse(0, 0,
-            av.getAlignment().getHiddenSequences(),
-            av.getColumnSelection(), av.getPosProps());
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            posProps);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -475,10 +389,9 @@ public class OverviewDimensionsTest {
     // hide columns 63-73, no change to box position or dimensions
     int firstHidden = 63;
     int lastHidden = 73;
-    hideColumns(firstHidden, lastHidden);
+    hiddenCols.hideColumns(firstHidden, lastHidden);
 
-    od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -567,9 +480,8 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenColsAtEnd()
   {
-    od.updateViewportFromMouse(0, 0,
-            av.getAlignment().getHiddenSequences(),
-            av.getColumnSelection(), av.getPosProps());
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            posProps);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -579,9 +491,8 @@ public class OverviewDimensionsTest {
     // hide columns 140-164, no change to box position or dimensions
     int firstHidden = 140;
     int lastHidden = 164;
-    hideColumns(firstHidden, lastHidden);
-    od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+    hiddenCols.hideColumns(firstHidden, lastHidden);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -692,7 +603,7 @@ public class OverviewDimensionsTest {
   {
     int firstHidden = 0;
     int lastHidden = 20;
-    hideColumns(firstHidden, lastHidden);
+    hiddenCols.hideColumns(firstHidden, lastHidden);
 
     // move viewport to start of alignment
     moveViewport(0, 0);
@@ -721,7 +632,7 @@ public class OverviewDimensionsTest {
   {
     int firstHidden = 68;
     int lastHidden = 78;
-    hideColumns(firstHidden, lastHidden);
+    hiddenCols.hideColumns(firstHidden, lastHidden);
 
     // move viewport before hidden columns
     moveViewport(3, 0);
@@ -777,7 +688,7 @@ public class OverviewDimensionsTest {
   {
     int firstHidden = 152;
     int lastHidden = 164;
-    hideColumns(firstHidden, lastHidden);
+    hiddenCols.hideColumns(firstHidden, lastHidden);
 
     // move viewport before hidden columns
     moveViewport(3, 0);
@@ -807,7 +718,7 @@ public class OverviewDimensionsTest {
   {
     int firstHidden = 0;
     int lastHidden = 20;
-    hideSequences(firstHidden, lastHidden + 1, lastHidden + 1);
+    hideSequences(firstHidden, lastHidden);
 
     // move viewport to start of alignment:
     // box moves to below hidden rows, height remains same
@@ -839,7 +750,7 @@ public class OverviewDimensionsTest {
   {
     int firstHidden = 200;
     int lastHidden = 210;
-    hideSequences(firstHidden, lastHidden + 1, lastHidden + 1);
+    hideSequences(firstHidden, lastHidden);
 
     // move viewport to start of alignment:
     // box, height etc as in non-hidden case
@@ -870,7 +781,7 @@ public class OverviewDimensionsTest {
   {
     int firstHidden = 500;
     int lastHidden = 524;
-    hideSequences(firstHidden - 1, lastHidden, firstHidden - 1);
+    hideSequences(firstHidden, lastHidden);
 
     // move viewport to start of alignment:
     // box, height etc as in non-hidden case
@@ -900,9 +811,8 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenRowsAtStart()
   {
-    od.updateViewportFromMouse(0, 0,
-            av.getAlignment().getHiddenSequences(),
-            av.getColumnSelection(), av.getPosProps());
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            posProps);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxHeight(), boxHeight);
@@ -913,10 +823,9 @@ public class OverviewDimensionsTest {
     // hide rows at start and check updated box position is correct
     // changes boxY but not boxheight
     int lastHiddenRow = 30;
-    hideSequences(0, lastHiddenRow + 1, lastHiddenRow + 1);
+    hideSequences(0, lastHiddenRow);
 
-    od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(),
             Math.round((float) (lastHiddenRow + 1)
@@ -949,9 +858,8 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenRowsInMiddle()
   {
-    od.updateViewportFromMouse(0, 0,
-            av.getAlignment().getHiddenSequences(),
-            av.getColumnSelection(), av.getPosProps());
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            posProps);
 
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
@@ -964,10 +872,9 @@ public class OverviewDimensionsTest {
     // no changes
     int firstHiddenRow = 50;
     int lastHiddenRow = 60;
-    hideSequences(firstHiddenRow, lastHiddenRow + 1, lastHiddenRow + 1);
+    hideSequences(firstHiddenRow, lastHiddenRow);
 
-    od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
 
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
@@ -1012,9 +919,8 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenRowsAtEnd()
   {
-    od.updateViewportFromMouse(0, 0,
-            av.getAlignment().getHiddenSequences(),
-            av.getColumnSelection(), av.getPosProps());
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            posProps);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -1026,10 +932,9 @@ public class OverviewDimensionsTest {
     // no changes
     int firstHidden = 500;
     int lastHidden = 524;
-    hideSequences(firstHidden - 1, lastHidden, firstHidden - 1);
+    hideSequences(firstHidden, lastHidden);
 
-    od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -1077,10 +982,9 @@ public class OverviewDimensionsTest {
    */
   private void moveViewportH(int startRes)
   {
-    av.setStartRes(startRes);
-    av.setEndRes(startRes + viewWidth - 1);
-    od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+    posProps.setStartRes(startRes);
+    posProps.setEndRes(startRes + viewWidth - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
   }
 
   /*
@@ -1088,10 +992,9 @@ public class OverviewDimensionsTest {
    */
   private void moveViewportV(int startSeq)
   {
-    av.setStartSeq(startSeq);
-    av.setEndSeq(startSeq + viewHeight - 1);
-    od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+    posProps.setStartSeq(startSeq);
+    posProps.setEndSeq(startSeq + viewHeight - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
   }
 
   /*
@@ -1099,12 +1002,11 @@ public class OverviewDimensionsTest {
    */
   private void moveViewport(int startRes, int startSeq)
   {
-    av.setStartRes(startRes);
-    av.setEndRes(startRes + viewWidth - 1);
-    av.setStartSeq(startSeq);
-    av.setEndSeq(startSeq + viewHeight - 1);
-    od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+    posProps.setStartRes(startRes);
+    posProps.setEndRes(startRes + viewWidth - 1);
+    posProps.setStartSeq(startSeq);
+    posProps.setEndSeq(startSeq + viewHeight - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
   }
 
   /*
@@ -1112,22 +1014,24 @@ public class OverviewDimensionsTest {
    */
   private void mouseClick(OverviewDimensions od, int x, int y)
   {
-    od.updateViewportFromMouse(x, y,
-            av.getAlignment().getHiddenSequences(),
-            av.getColumnSelection(), av.getPosProps());
+    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
-    // int width = av.getEndRes() - av.getStartRes();
-    // int height = av.getEndSeq() - av.getStartSeq();
-    av.setStartRes(od.getScrollCol());
-    av.setEndRes(od.getScrollCol() + viewWidth - 1);
-    av.setStartSeq(od.getScrollRow());
-    av.setEndSeq(od.getScrollRow() + viewHeight - 1);
-    od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+
+    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);
@@ -1139,49 +1043,19 @@ public class OverviewDimensionsTest {
   }
 
   /*
-   * Hide sequences between start and end, using hideseq to do the hiding
-   * (start <= hideseq <= end. Sequence hideseq is not hidden but the others are
+   * Hide sequences between start and end
    */
-  private void hideSequences(int start, int end, int hideseq)
+  private void hideSequences(int start, int end)
   {
-    SequenceGroup sg = new SequenceGroup();
-    List<SequenceI> allseqs = av.getAlignment().getSequences();
-    for (int i = start; i <= end; ++i)
-    {
-      sg.addSequence(allseqs.get(i), false);
-    }
-    av.setSelectionGroup(sg);
-
-    /*
-     * hide group
-     */
-    av.hideSequences(allseqs.get(hideseq), true);
-
-    while (av.isCalcInProgress())
+    SequenceI[] allseqs = al.getSequencesArray();
+    SequenceGroup theseSeqs = new SequenceGroup();
+    
+    for (int i = start; i <= end; i++)
     {
-      try
-      {
-        Thread.sleep(50);
-      } catch (InterruptedException e)
-      {
-        System.out.println("Hiding seqs interruption");
-      }
+      theseSeqs.addSequence(allseqs[i], false);
+      al.getHiddenSequences().hideSequence(allseqs[i]);
     }
-  }
 
-  private void hideColumns(int firstHidden, int lastHidden)
-  {
-    av.hideColumns(firstHidden, lastHidden);
-
-    while (av.isCalcInProgress())
-    {
-      try
-      {
-        Thread.sleep(50);
-      } catch (InterruptedException e)
-      {
-        System.out.println("Hiding cols interruption");
-      }
-    }
+    hiddenRepSequences.put(allseqs[start], theseSeqs);
   }
 }