JAL-2388 Removing sources of non-determinism in unit tests

diff --git a/test/jalview/viewmodel/OverviewDimensionsTest.java b/test/jalview/viewmodel/OverviewDimensionsTest.java
index 7c40fe9..94fb83f 100644 (file)
--- a/test/jalview/viewmodel/OverviewDimensionsTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsTest.java
@@ -37,11 +37,12 @@ import jalview.io.FileLoader;
 
 import java.util.List;
 
-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;
 
+@Test(singleThreaded = true)
 public class OverviewDimensionsTest {
 
   boolean showConservationSetting;
@@ -84,7 +85,7 @@ public class OverviewDimensionsTest {
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  @BeforeClass(alwaysRun = true)
+  @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
     Jalview.main(new String[] { "-nonews", "-props",
@@ -112,29 +113,64 @@ public class OverviewDimensionsTest {
       }
     }
 
+    /*
+     * 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);
     
     av = af.getViewport();
+
+    if (av.isCalcInProgress())
+    {
+
+    }
+
     od = new OverviewDimensions(av);
 
+    while (av.isCalcInProgress())
+    {
+      try
+      {
+        Thread.sleep(50);
+      } catch (InterruptedException e)
+      {
+        System.out.println("Hiding cols interruption");
+      }
+    }
+
     // Initial box sizing - default path through code
     od.setBoxPosition();
+
     scalew = (float) od.getWidth()
             / (av.getAlignment().getWidth() * av.getCharWidth());
     scaleh = (float) od.getSequencesHeight()
             / (av.getAlignment().getHeight() * av.getCharHeight());
-    boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1)
+    boxWidth = Math.round((av.getEndRes() - av.getStartRes() + 1)
             * av.getCharWidth() * scalew);
-    boxHeight = (int) ((av.getEndSeq() - av.getStartSeq())
+    boxHeight = Math.round((av.getEndSeq() - av.getStartSeq())
             * av.getCharHeight() * scaleh);
 
     viewHeight = av.getEndSeq() - av.getStartSeq();
+
+    init();
   }
 
-  @BeforeMethod(alwaysRun = true)
-  public void init()
+  private void init()
   {
     av.showAllHiddenColumns();
     av.showAllHiddenSeqs();
@@ -142,11 +178,23 @@ public class OverviewDimensionsTest {
     // o/w hidden seqs retain selection group, causes problems later when hiding
     // sequences
 
+    // wait for conservation calc to complete
+    while (av.isCalcInProgress())
+    {
+      try
+      {
+        Thread.sleep(50);
+      } catch (InterruptedException e)
+      {
+
+      }
+    }
+
     mouseClick(od, 0, 0);
     moveViewport(0, 0);
   }
 
-  @AfterClass(alwaysRun = true)
+  @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
@@ -270,7 +318,7 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollRow(),
-            (int) (10 / scaleh / av.getCharHeight()));
+            Math.round(10 / scaleh / av.getCharHeight()));
     assertEquals(od.getScrollCol(), 0);
 
     // negative boxY value reset to 0
@@ -278,7 +326,8 @@ 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(6 / scalew / av.getCharWidth()));
     assertEquals(od.getScrollRow(), 0);
 
     // overly large boxX value reset to width-boxWidth
@@ -357,32 +406,34 @@ 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);
+    hideColumns(0, lastHiddenCol);
+
     od.setBoxPosition();
     assertEquals(od.getBoxX(),
-            (int) ((lastHiddenCol + 1) * scalew * av.getCharWidth()));
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+            Math.round((lastHiddenCol + 1) * scalew * av.getCharWidth()));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // try to click in hidden cols, check box does not move
     // this test currently fails as the overview box does not behave like this!
     /*    int xpos = 10;
         mouseClick(od, xpos, 0);
         assertEquals(od.getBoxX(),
-                (int) ((lastHiddenCol + 1) * scalew * av.getCharWidth()));
+                Math.round ((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()));
+                Math.round (xpos / scalew / av.getCharWidth()));
     */
     // click to right of hidden columns, box moves to click point
     testBoxIsAtClickPoint(40, 0);
     assertEquals(od.getScrollRow(), 0);
     assertEquals(od.getScrollCol(),
- (int) (40 / scalew / av.getCharWidth())
-            - lastHiddenCol, 1.5);
+            Math.round(40 / scalew / av.getCharWidth())
+ - lastHiddenCol,
+            1.5);
 
     // click to right of hidden columns such that box runs over right hand side
     // of alignment
@@ -391,14 +442,14 @@ public class OverviewDimensionsTest {
     int xpos = 100;
     mouseClick(od, xpos, 5);
     assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth(), 1.5);
-    assertEquals(od.getBoxY(), 5, 1.5);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxY(), 5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            (int) (od.getBoxX() / scalew / av.getCharWidth())
+            Math.round(od.getBoxX() / scalew / av.getCharWidth())
                     - lastHiddenCol, 1.5);
     assertEquals(od.getScrollRow(),
-            (int) (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);
+            Math.round(od.getBoxY() / scaleh / av.getCharHeight()));
 
   }
 
@@ -419,7 +470,8 @@ public class OverviewDimensionsTest {
     // hide columns 60-68, no change to box position or dimensions
     int firstHidden = 60;
     int lastHidden = 68;
-    av.hideColumns(firstHidden, lastHidden);
+    hideColumns(firstHidden, lastHidden);
+
     od.setBoxPosition();
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
@@ -432,27 +484,30 @@ public class OverviewDimensionsTest {
     int xpos = 50 - boxWidth; // 50 is position in overview halfway between cols
                               // 60 and 70
     mouseClick(od, xpos, 0);
-    assertEquals(od.getBoxX(), xpos, 1.5);
+    assertEquals(od.getBoxX(), xpos);
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth
-            + (lastHidden - firstHidden + 1) * scalew * av.getCharWidth(),
-            1.5);
+    assertEquals(
+            od.getBoxWidth(),
+            Math.round(boxWidth + (lastHidden - firstHidden + 1) * scalew
+                    * av.getCharWidth()));
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(), (int) (xpos / scalew / av.getCharWidth()), 1.5);
+    assertEquals(od.getScrollCol(),
+            Math.round(xpos / scalew / av.getCharWidth()));
     assertEquals(od.getScrollRow(), 0);
 
     // move box so that it completely covers hidden cols
     // box width changes, boxX and scrollCol as for hidden case
     xpos = 30;
     mouseClick(od, xpos, 0);
-    assertEquals(od.getBoxX(), xpos, 1.5);
+    assertEquals(od.getBoxX(), xpos);
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth
-            + (lastHidden - firstHidden + 1) * scalew * av.getCharWidth(),
-            1.5);
+    assertEquals(
+            od.getBoxWidth(),
+            Math.round(boxWidth + (lastHidden - firstHidden + 1) * scalew
+                    * av.getCharWidth()));
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            (int) (xpos / scalew / av.getCharWidth()), 1.5);
+            Math.round(xpos / scalew / av.getCharWidth()), 1.5);
     assertEquals(od.getScrollRow(), 0);
 
     // move box so boxX is in hidden cols, box overhangs at right
@@ -467,7 +522,7 @@ public class OverviewDimensionsTest {
         assertEquals(od.getBoxWidth(), boxWidth, 1.5);
         assertEquals(od.getBoxHeight(), boxHeight);
         assertEquals(od.getScrollCol(),
-                (int) (xpos / scalew / av.getCharWidth()), 1.5);
+                Math.round(xpos / scalew / av.getCharWidth()), 1.5);
         assertEquals(od.getScrollRow(), 0);*/
 
     // move box so boxX is to right of hidden cols, but does not go beyond full
@@ -483,7 +538,7 @@ public class OverviewDimensionsTest {
        testBoxIsAtClickPoint(xpos, 0);
        assertEquals(od.getScrollRow(), 0);
        assertEquals(od.getScrollCol(),
-               (int) (xpos / scalew / av.getCharWidth())
+               Math.round(xpos / scalew / av.getCharWidth())
                - lastHidden, 1.5);*/
     
     // move box so it goes beyond full width of alignment
@@ -491,15 +546,14 @@ public class OverviewDimensionsTest {
     xpos = 3000;
     mouseClick(od, xpos, 5);
     assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth(), 1.5);
-    assertEquals(od.getBoxY(), 5, 1.5);
+    assertEquals(od.getBoxY(), 5);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            (od.getBoxX() / scalew / av.getCharWidth())
-                    - (lastHidden - firstHidden + 1),
-            1.5);
+            Math.round((od.getBoxX() / scalew / av.getCharWidth())
+                    - (lastHidden - firstHidden + 1)));
     assertEquals(od.getScrollRow(),
-            (int) (od.getBoxY() / scaleh / av.getCharHeight()), 1.5);
+            Math.round(od.getBoxY() / scaleh / av.getCharHeight()));
 
   }
 
@@ -520,7 +574,7 @@ public class OverviewDimensionsTest {
     // hide columns 140-157, no change to box position or dimensions
     int firstHidden = 140;
     int lastHidden = 157;
-    av.hideColumns(firstHidden, lastHidden);
+    hideColumns(firstHidden, lastHidden);
     od.setBoxPosition();
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
@@ -534,7 +588,7 @@ public class OverviewDimensionsTest {
     testBoxIsAtClickPoint(xpos, 0);
     assertEquals(od.getScrollRow(), 0);
     assertEquals(od.getScrollCol(),
-            (int) (xpos / scalew / av.getCharWidth()), 1.5);
+            Math.round(xpos / scalew / av.getCharWidth()), 1.5);
 
     // click to left of hidden cols, with overlap
     // boxX and scrollCol adjusted for hidden cols, width normal
@@ -544,13 +598,13 @@ public class OverviewDimensionsTest {
     mouseClick(od, xpos, 0);
     assertEquals(
             od.getBoxX(),
-            (int) ((firstHidden - 1) * scalew * av.getCharWidth())
+            Math.round((firstHidden - 1) * scalew * av.getCharWidth())
                     - od.getBoxWidth(), 1.5);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth, 1.5);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            (int) (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
+            Math.round(od.getBoxX() / scalew / av.getCharWidth()), 1.5);
     assertEquals(od.getScrollRow(), 0);*/
 
     // click in hidden cols
@@ -559,13 +613,13 @@ public class OverviewDimensionsTest {
     /*xpos = 115;
     assertEquals(
             od.getBoxX(),
-            (int) ((firstHidden - 1) * scalew * av.getCharWidth())
+            Math.round((firstHidden - 1) * scalew * av.getCharWidth())
                     - od.getBoxWidth(), 1.5);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth, 1.5);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            (int) (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
+            Math.round(od.getBoxX() / scalew / av.getCharWidth()), 1.5);
     assertEquals(od.getScrollRow(), 0);*/
 
     // click off end of alignment
@@ -574,13 +628,13 @@ public class OverviewDimensionsTest {
     /*    xpos = 3000;
         assertEquals(
                 od.getBoxX(),
-                (int) ((firstHidden - 1) * scalew * av.getCharWidth())
+                Math.round((firstHidden - 1) * scalew * av.getCharWidth())
                         - od.getBoxWidth(), 1.5);
         assertEquals(od.getBoxY(), 0);
         assertEquals(od.getBoxWidth(), boxWidth, 1.5);
         assertEquals(od.getBoxHeight(), boxHeight);
         assertEquals(od.getScrollCol(),
-                (int) (od.getBoxX() / scalew / av.getCharWidth()), 1.5);
+                Math.round(od.getBoxX() / scalew / av.getCharWidth()), 1.5);
         assertEquals(od.getScrollRow(), 0);*/
   }
 
@@ -595,29 +649,31 @@ public class OverviewDimensionsTest {
     moveViewport(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to right
     moveViewportH(70);
-    assertEquals(od.getBoxX(), (int) (70 * scalew * av.getCharWidth()));
+    assertEquals(od.getBoxX(), Math.round(70 * scalew * av.getCharWidth()));
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport down
     moveViewportV(100);
-    assertEquals(od.getBoxX(), (int) (70 * scalew * av.getCharWidth()));
-    assertEquals(od.getBoxY(), (int) (100 * scaleh * av.getCharHeight()));
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxX(), Math.round(70 * scalew * av.getCharWidth()));
+    assertEquals(od.getBoxY(),
+            Math.round(100 * scaleh * av.getCharHeight()));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to bottom right
     moveViewport(98, 508);
-    assertEquals(od.getBoxX(), (int) (98 * scalew * av.getCharWidth()));
-    assertEquals(od.getBoxY(), (int) (508 * scaleh * av.getCharHeight()));
+    assertEquals(od.getBoxX(), Math.round(98 * scalew * av.getCharWidth()));
+    assertEquals(od.getBoxY(),
+            Math.round(508 * scaleh * av.getCharHeight()));
     assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxHeight(), boxHeight);
   }
 
   /**
@@ -629,23 +685,23 @@ public class OverviewDimensionsTest {
   {
     int firstHidden = 0;
     int lastHidden = 20;
-    av.hideColumns(firstHidden, lastHidden);
+    hideColumns(firstHidden, lastHidden);
 
     // move viewport to start of alignment
     moveViewport(0, 0);
     assertEquals(od.getBoxX(),
-            (int) ((lastHidden + 1) * scalew * av.getCharWidth()));
+            Math.round((lastHidden + 1) * scalew * av.getCharWidth()));
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to 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(), 98 * scalew * av.getCharWidth(), 1.5);
+    assertEquals(od.getBoxX(), Math.round(98 * scalew * av.getCharWidth()));
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
   }
 
   /**
@@ -657,43 +713,47 @@ public class OverviewDimensionsTest {
   {
     int firstHidden = 65;
     int lastHidden = 75;
-    av.hideColumns(firstHidden, lastHidden);
+    hideColumns(firstHidden, lastHidden);
 
     // move viewport before hidden columns
     moveViewport(3, 0);
-    assertEquals(od.getBoxX(), (int) (3 * scalew * av.getCharWidth()));
+
+    assertEquals(od.getBoxX(), Math.round(3 * scalew * av.getCharWidth()));
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    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(), (int) (10 * scalew * av.getCharWidth()));
+    assertEquals(od.getBoxX(), Math.round(10 * scalew * av.getCharWidth()));
     assertEquals(od.getBoxY(), 0);
     assertEquals(
             od.getBoxWidth(),
             boxWidth
-                    + (int) ((lastHidden - firstHidden + 1) * scalew * av
-                            .getCharWidth()), 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+                    + Math.round((lastHidden - firstHidden + 1) * scalew
+                            * av.getCharWidth()));
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to straddle hidden columns
     moveViewport(60, 0);
-    assertEquals(od.getBoxX(), (int) (60 * scalew * av.getCharWidth()));
+    assertEquals(od.getBoxX(), Math.round(60 * scalew * av.getCharWidth()));
     assertEquals(od.getBoxY(), 0);
     assertEquals(
             od.getBoxWidth(),
             boxWidth
-                    + (int) ((lastHidden - firstHidden + 1) * scalew * av
-                            .getCharWidth()), 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+                    + Math.round((lastHidden - firstHidden + 1) * scalew
+                            * av
+.getCharWidth()));
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to right of hidden columns, no overlap
     moveViewport(80 - (lastHidden - firstHidden + 1), 0);
-    assertEquals(od.getBoxX(), (int) (80 * scalew * av.getCharWidth()), 1.5);
+    assertEquals(od.getBoxX(), Math.round(80 * scalew * av.getCharWidth()));
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
   }
 
@@ -706,26 +766,28 @@ public class OverviewDimensionsTest {
   {
     int firstHidden = 145;
     int lastHidden = 157;
-    av.hideColumns(firstHidden, lastHidden);
+    hideColumns(firstHidden, lastHidden);
 
     // move viewport before hidden columns
     moveViewport(3, 0);
-    assertEquals(od.getBoxX(), (int) (3 * scalew * av.getCharWidth()), 1.5);
+    assertEquals(od.getBoxX(), Math.round(3 * scalew * av.getCharWidth()),
+            1.5);
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to hidden columns
     // TODO boxwidth includes hidden in overview panel (why?)
     moveViewport(98, 0);
-    assertEquals(od.getBoxX(), (int) (98 * scalew * av.getCharWidth()), 1.5);
+    assertEquals(od.getBoxX(), Math.round(98 * scalew * av.getCharWidth()),
+            1.5);
     assertEquals(od.getBoxY(), 0);
     assertEquals(
             od.getBoxWidth(),
             boxWidth
-                    + (int) ((lastHidden - firstHidden + 1) * scalew * av
-                            .getCharWidth()), 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+                    + Math.round((lastHidden - firstHidden + 1) * scalew
+                            * av.getCharWidth()), 1.5);
+    assertEquals(od.getBoxHeight(), boxHeight);
   }
 
   /**
@@ -744,9 +806,9 @@ public class OverviewDimensionsTest {
     moveViewport(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(),
-            (lastHidden + 1) * scaleh * av.getCharHeight(), 1.5);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+            Math.round((lastHidden + 1) * scaleh * av.getCharHeight()));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to end of alignment, need to account for hidden rows
     // because of how alignment panel/overview panel are implemented
@@ -790,7 +852,7 @@ public class OverviewDimensionsTest {
     // TODO also fails with boxY out by 12
     /*moveViewport(0, 198);
     assertEquals(od.getBoxX(), 0);
-    assertEquals(od.getBoxY(), (int) (198 * scaleh * av.getCharHeight()),
+    assertEquals(od.getBoxY(), Math.round (198 * scaleh * av.getCharHeight()),
             1.5);
     assertEquals(od.getBoxWidth(), boxWidth, 1.5);
     assertEquals(od.getBoxHeight(), boxHeight
@@ -814,21 +876,21 @@ public class OverviewDimensionsTest {
     moveViewport(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to end of alignment
     // TODO fails with wrong boxHeight who knows why
     /*moveViewport(0, firstHidden - viewHeight - 1);
         assertEquals(od.getBoxX(), 0);
         assertEquals(od.getBoxY(),
-     (int) ((firstHidden - viewHeight - 1)
+     Math.round ((firstHidden - viewHeight - 1)
                 * scaleh * av.getCharHeight()), 1.5);
         assertEquals(od.getBoxWidth(), boxWidth, 1.5);
         assertEquals(
                 od.getBoxHeight(),
                 boxHeight
-                        + (int) ((lastHidden - firstHidden + 1) * scaleh * av
+                        + Math.round ((lastHidden - firstHidden + 1) * scaleh * av
                                 .getCharHeight()), 1.5);*/
 
   }
@@ -843,6 +905,7 @@ public class OverviewDimensionsTest {
     od.setBoxPositionByMouse(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getScrollCol(), 0);
     assertEquals(od.getScrollRow(), 0);
@@ -855,9 +918,9 @@ public class OverviewDimensionsTest {
     od.setBoxPosition();
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(),
-            (int) ((lastHiddenRow + 1) * scaleh * av.getCharHeight()));
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+            Math.round((lastHiddenRow + 1) * scaleh * av.getCharHeight()));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // click in hidden rows
     // TODO fails because boxHeight is 27 not 25 (possible rounding issue)
@@ -866,15 +929,15 @@ public class OverviewDimensionsTest {
         assertEquals(od.getBoxY(), 0);
         assertEquals(od.getBoxWidth(), boxWidth, 1.5);
         assertEquals(od.getBoxHeight(), boxHeight
-                + (int) ((lastHiddenRow + 1) * scaleh * av.getCharHeight()),
+                + Math.round ((lastHiddenRow + 1) * scaleh * av.getCharHeight()),
                 1.5);*/
 
     // click below hidden rows
     mouseClick(od, 0, 150);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 150, 1.5);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
   }
 
   /**
@@ -884,10 +947,16 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenRowsInMiddle()
   {
+    assertEquals(od.getBoxHeight(), 10);
+
     od.setBoxPositionByMouse(0, 0);
+
+    assertEquals(od.getBoxHeight(), 10);
+
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(), 0);
     assertEquals(od.getScrollRow(), 0);
 
@@ -895,42 +964,46 @@ public class OverviewDimensionsTest {
     // no changes
     int firstHiddenRow = 50;
     int lastHiddenRow = 60;
+    assertEquals(od.getBoxHeight(), 10);
     hideSequences(firstHiddenRow, lastHiddenRow + 1, lastHiddenRow + 1);
+    assertEquals(od.getBoxHeight(), 10);
 
     od.setBoxPosition();
+    assertEquals(od.getBoxHeight(), 10);
+
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // click above hidden rows, so that box overlaps
     int ypos = 40;
     // TODO test fails because box does not change height - dealt with by scroll
     // values
-    /*    mouseClick(od, 0, (int) (ypos / scaleh / av.getCharHeight()));
+    /*    mouseClick(od, 0, Math.round (ypos / scaleh / av.getCharHeight()));
         assertEquals(od.getBoxX(), 0);
-        assertEquals(od.getBoxY(), (int) (ypos / scaleh / av.getCharHeight()),
+        assertEquals(od.getBoxY(), Math.round (ypos / scaleh / av.getCharHeight()),
                 1.5);
         assertEquals(od.getBoxWidth(), boxWidth, 1.5);
         assertEquals(
                 od.getBoxHeight(),
                 boxHeight
-                        + (int) ((lastHiddenRow - firstHiddenRow + 1) / scaleh / av
+                        + Math.round ((lastHiddenRow - firstHiddenRow + 1) / scaleh / av
                                 .getCharHeight()), 1.5);
     */
     // click so that box straddles hidden rows
     ypos = 48;
     // TODO test fails because box does not change height - dealt with by scroll
     // values
-    /*mouseClick(od, 0, (int) (ypos / scaleh / av.getCharHeight()));
+    /*mouseClick(od, 0, Math.round (ypos / scaleh / av.getCharHeight()));
     assertEquals(od.getBoxX(), 0);
-    assertEquals(od.getBoxY(), (int) (ypos / scaleh / av.getCharHeight()),
+    assertEquals(od.getBoxY(), Math.round (ypos / scaleh / av.getCharHeight()),
             1.5);
     assertEquals(od.getBoxWidth(), boxWidth, 1.5);
     assertEquals(
             od.getBoxHeight(),
             boxHeight
-                    + (int) ((lastHiddenRow - firstHiddenRow + 1) / scaleh / av
+                    + Math.round ((lastHiddenRow - firstHiddenRow + 1) / scaleh / av
                             .getCharHeight()), 1.5);*/
   }
 
@@ -945,6 +1018,7 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(), 0);
     assertEquals(od.getScrollRow(), 0);
 
@@ -957,28 +1031,28 @@ public class OverviewDimensionsTest {
     od.setBoxPosition();
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // click above hidden rows
     int ypos = 40; // row 40
-    mouseClick(od, 0, (int) (ypos * scaleh * av.getCharHeight()));
+    mouseClick(od, 0, Math.round(ypos * scaleh * av.getCharHeight()));
     assertEquals(od.getBoxX(), 0);
-    assertEquals(od.getBoxY(), (int) (ypos * scaleh * av.getCharHeight()),
-            1.5);
-    assertEquals(od.getBoxWidth(), boxWidth, 1.5);
-    assertEquals(od.getBoxHeight(), boxHeight, 1.5);
+    assertEquals(od.getBoxY(),
+            Math.round(ypos * scaleh * av.getCharHeight()));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // click above hidden rows so box overlaps
     // boxY moved upwards, boxHeight remains same
     // TODO fails with boxY located at row 497 - correction done by
     // setScrollValues
     /*   ypos = 497; // row 497
-       mouseClick(od, 0, (int) (ypos * scaleh * av.getCharHeight()));
+       mouseClick(od, 0, Math.round (ypos * scaleh * av.getCharHeight()));
        assertEquals(od.getBoxX(), 0);
        assertEquals(
                od.getBoxY(),
-               (int) ((firstHidden - viewHeight) * scaleh * av.getCharHeight()),
+               Math.round ((firstHidden - viewHeight) * scaleh * av.getCharHeight()),
                1.5);
        assertEquals(od.getBoxWidth(), boxWidth, 1.5);
        assertEquals(od.getBoxHeight(), boxHeight, 1.5);*/
@@ -986,11 +1060,11 @@ public class OverviewDimensionsTest {
     // click within hidden rows
     ypos = 505;
     // TODO: fails with wrong boxHeight - correction done by setScrollValues(?)
-    /*mouseClick(od, 0, (int) (ypos * scaleh * av.getCharHeight()));
+    /*mouseClick(od, 0, Math.round (ypos * scaleh * av.getCharHeight()));
     assertEquals(od.getBoxX(), 0);
     assertEquals(
             od.getBoxY(),
-            (int) ((firstHidden - viewHeight) * scaleh * av.getCharHeight()),
+            Math.round ((firstHidden - viewHeight) * scaleh * av.getCharHeight()),
             1.5);
     assertEquals(od.getBoxWidth(), boxWidth, 1.5);
     assertEquals(od.getBoxHeight(), boxHeight, 1.5);*/
@@ -1077,5 +1151,32 @@ public class OverviewDimensionsTest {
      * hide group
      */
     av.hideSequences(allseqs.get(hideseq), true);
+
+    while (av.isCalcInProgress())
+    {
+      try
+      {
+        Thread.sleep(50);
+      } catch (InterruptedException e)
+      {
+        System.out.println("Hiding seqs interruption");
+      }
+    }
+  }
+
+  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");
+      }
+    }
   }
 }