JAL-2388 Corrected overview panel behaviour, updated tests

[jalview.git] / test / jalview / viewmodel / OverviewDimensionsTest.java

diff --git a/test/jalview/viewmodel/OverviewDimensionsTest.java b/test/jalview/viewmodel/OverviewDimensionsTest.java
index cc808d6..d470c35 100644 (file)
--- a/test/jalview/viewmodel/OverviewDimensionsTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsTest.java
@@ -22,9 +22,11 @@ package jalview.viewmodel;
 
 import static org.testng.Assert.assertEquals;
 
+import jalview.analysis.AlignmentGenerator;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -37,6 +39,7 @@ 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;
@@ -45,8 +48,6 @@ import org.testng.annotations.Test;
 @Test(singleThreaded = true)
 public class OverviewDimensionsTest {
 
-  boolean showConservationSetting;
-
   SequenceI seq1 = new Sequence(
           "Seq1",
           "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
@@ -69,19 +70,15 @@ public class OverviewDimensionsTest {
 
   AlignFrame af;
   AlignViewport av;
+
+  AlignmentI al;
   OverviewDimensions od;
 
-  float scalew;
-  float scaleh;
   int boxWidth;
   int boxHeight;
-
   int viewHeight;
-
   int viewWidth;
-
   int alheight;
-
   int alwidth;
 
   @BeforeClass(alwaysRun = true)
@@ -89,6 +86,10 @@ public class OverviewDimensionsTest {
   {
     JvOptionPane.setInteractiveMode(false);
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    al = gen.generate(157, 525, 123, 5, 5);
   }
 
   @BeforeMethod(alwaysRun = true)
@@ -99,25 +100,8 @@ public class OverviewDimensionsTest {
 
     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
             Boolean.TRUE.toString());
-    af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/testdata/bigal.fa",
-            DataSourceType.FILE);
-
-    /*
-     * Wait for viewport to initialise
-     */
-    synchronized (this)
-    {
-      while (af.getViewport().getEndRes() == 0)
-      {
-        try
-        {
-          wait(50);
-        } catch (InterruptedException e)
-        {
-        }
-      }
-    }
+    af = new FileLoader().LoadFileWaitTillLoaded(al.toString(),
+            DataSourceType.PASTE);
 
     /*
      * wait for Consensus thread to complete
@@ -134,14 +118,10 @@ public class OverviewDimensionsTest {
         }
       }
     }
-
-    // get cached setting for showConservation
-    // reset it in AfterClass!
-    showConservationSetting = Cache.getDefault("SHOW_CONSERVATION", true);
     
     av = af.getViewport();
 
-    od = new OverviewDimensions(av);
+    od = new OverviewDimensions(av, true);
 
     while (av.isCalcInProgress())
     {
@@ -168,7 +148,7 @@ public class OverviewDimensionsTest {
     // o/w hidden seqs retain selection group, causes problems later when hiding
     // sequences
 
-    // wait for conservation calc to complete
+    // wait for conservation calc to complete again
     while (av.isCalcInProgress())
     {
       try
@@ -187,7 +167,7 @@ public class OverviewDimensionsTest {
     viewWidth = av.getEndRes() - av.getStartRes();
 
     // wait for gui to get set up
-    while (viewHeight != 17 || viewWidth != 59)
+    while (viewHeight != 17 || viewWidth != 62)
     {
       try
       {
@@ -215,11 +195,17 @@ public class OverviewDimensionsTest {
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
-            Boolean.toString(showConservationSetting));
+    af = null;
+    av = null;
     Desktop.instance.closeAll_actionPerformed(null);
   }
 
+  @AfterClass(alwaysRun = true)
+  public void cleanUp()
+  {
+    al = null;
+  }
+
   /**
    * Test that the OverviewDimensions constructor sets width and height
    * correctly
@@ -240,16 +226,13 @@ 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);
 
-    OverviewDimensions od = new OverviewDimensions(av1);
+    OverviewDimensions od = new OverviewDimensions(av1, true);
     int scaledHeight = 266;
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), scaledHeight);
@@ -262,7 +245,7 @@ public class OverviewDimensionsTest {
     al2.setDataset(null);
     AlignViewport av2 = new AlignViewport(al2);
 
-    od = new OverviewDimensions(av2);
+    od = new OverviewDimensions(av2, true);
     int scaledWidth = 300;
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), maxSeqHeight);
@@ -276,7 +259,7 @@ public class OverviewDimensionsTest {
     al3.setDataset(null);
     AlignViewport av3 = new AlignViewport(al3);
 
-    od = new OverviewDimensions(av3);
+    od = new OverviewDimensions(av3, true);
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), minSeqHeight);
     assertEquals(od.getWidth(), maxWidth);
@@ -289,21 +272,17 @@ public class OverviewDimensionsTest {
     al4.setDataset(null);
     AlignViewport av4 = new AlignViewport(al4);
 
-    od = new OverviewDimensions(av4);
+    od = new OverviewDimensions(av4, 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);
 
-    od = new OverviewDimensions(av5);
+    od = new OverviewDimensions(av5, false);
     assertEquals(od.getGraphHeight(), 0);
     assertEquals(od.getSequencesHeight(), maxSeqHeight);
     assertEquals(od.getWidth(), minWidth);
@@ -323,7 +302,7 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testSetBoxFromMouseClick()
   {
-    od.setBoxPositionByMouse(0, 0);
+    od.updateViewportFromMouse(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -417,7 +396,7 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenColsAtStart()
   {
-    od.setBoxPositionByMouse(0, 0);
+    od.updateViewportFromMouse(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -481,7 +460,7 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenColsInMiddle()
   {
-    od.setBoxPositionByMouse(0, 0);
+    od.updateViewportFromMouse(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -489,8 +468,8 @@ public class OverviewDimensionsTest {
     assertEquals(od.getScrollRow(), 0);
     
     // hide columns 60-68, no change to box position or dimensions
-    int firstHidden = 60;
-    int lastHidden = 68;
+    int firstHidden = 63;
+    int lastHidden = 73;
     hideColumns(firstHidden, lastHidden);
 
     od.setBoxPosition();
@@ -502,8 +481,8 @@ public class OverviewDimensionsTest {
 
     // move box so that it overlaps with hidden cols on one side
     // box width changes, boxX and scrollCol as for unhidden case
-    int xpos = 50 - boxWidth; // 50 is position in overview halfway between cols
-                              // 60 and 70
+    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);
@@ -518,7 +497,7 @@ public class OverviewDimensionsTest {
 
     // move box so that it completely covers hidden cols
     // box width changes, boxX and scrollCol as for hidden case
-    xpos = 30;
+    xpos = 33;
     mouseClick(od, xpos, 0);
     assertEquals(od.getBoxX(), xpos);
     assertEquals(od.getBoxY(), 0);
@@ -528,7 +507,7 @@ public class OverviewDimensionsTest {
                     * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getScrollCol(),
-            Math.round(xpos * alwidth / od.getWidth()));
+            Math.round((float) xpos * alwidth / od.getWidth()));
     assertEquals(od.getScrollRow(), 0);
 
     // move box so boxX is in hidden cols, box overhangs at right
@@ -586,7 +565,7 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenColsAtEnd()
   {
-    od.setBoxPositionByMouse(0, 0);
+    od.updateViewportFromMouse(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -737,8 +716,8 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testSetBoxFromViewportHiddenColsInMiddle()
   {
-    int firstHidden = 65;
-    int lastHidden = 75;
+    int firstHidden = 68;
+    int lastHidden = 78;
     hideColumns(firstHidden, lastHidden);
 
     // move viewport before hidden columns
@@ -765,9 +744,9 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to straddle hidden columns
-    moveViewport(60, 0);
+    moveViewport(63, 0);
     assertEquals(od.getBoxX(),
-            Math.round((float) 60 * od.getWidth() / alwidth));
+            Math.round((float) 63 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
     assertEquals(
             od.getBoxWidth(),
@@ -793,8 +772,8 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testSetBoxFromViewportHiddenColsAtEnd()
   {
-    int firstHidden = 145;
-    int lastHidden = 157;
+    int firstHidden = 152;
+    int lastHidden = 164;
     hideColumns(firstHidden, lastHidden);
 
     // move viewport before hidden columns
@@ -807,14 +786,12 @@ public class OverviewDimensionsTest {
 
     // move viewport to hidden columns
     // TODO boxwidth includes hidden in overview panel (why?)
-    moveViewport(98, 0);
+    moveViewport(102, 0);
     assertEquals(od.getBoxX(),
-            Math.round((float) 98 * od.getWidth() / alwidth));
+            Math.round((float) 102 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
-    assertEquals(
-            od.getBoxWidth(),
-            boxWidth
-                    + Math.round((float) (lastHidden - firstHidden + 1)
+    assertEquals(od.getBoxWidth(), boxWidth
+                    + Math.round((float) (lastHidden - firstHidden)
                             * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
   }
@@ -932,7 +909,7 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenRowsAtStart()
   {
-    od.setBoxPositionByMouse(0, 0);
+    od.updateViewportFromMouse(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxHeight(), boxHeight);
@@ -978,7 +955,7 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenRowsInMiddle()
   {
-    od.setBoxPositionByMouse(0, 0);
+    od.updateViewportFromMouse(0, 0);
 
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
@@ -1038,7 +1015,7 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenRowsAtEnd()
   {
-    od.setBoxPositionByMouse(0, 0);
+    od.updateViewportFromMouse(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -1132,7 +1109,7 @@ public class OverviewDimensionsTest {
    */
   private void mouseClick(OverviewDimensions od, int x, int y)
   {
-    od.setBoxPositionByMouse(x, y);
+    od.updateViewportFromMouse(x, y);
     // updates require an OverviewPanel to exist which it doesn't here
     // so call setBoxPosition() as it would be called by the AlignmentPanel
     // normally