Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

[jalview.git] / test / jalview / gui / SeqPanelTest.java

diff --git a/test/jalview/gui/SeqPanelTest.java b/test/jalview/gui/SeqPanelTest.java
index f163299..17e04bf 100644 (file)
--- a/test/jalview/gui/SeqPanelTest.java
+++ b/test/jalview/gui/SeqPanelTest.java
@@ -31,6 +31,7 @@ import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
@@ -40,7 +41,9 @@ import jalview.io.FileLoader;
 import jalview.util.MessageManager;
 
 import java.awt.Event;
+import java.awt.EventQueue;
 import java.awt.event.MouseEvent;
+import java.lang.reflect.InvocationTargetException;
 
 import javax.swing.JLabel;
 
@@ -249,22 +252,22 @@ public class SeqPanelTest
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
   }
 
   @Test(groups = "Functional")
   public void testFindMousePosition_wrapped_annotations()
   {
-    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "true");
-    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
+    Cache.setPropertyNoSave("SHOW_ANNOTATIONS", "true");
+    Cache.setPropertyNoSave("WRAP_ALIGNMENT", "true");
     AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     AlignViewportI av = alignFrame.getViewport();
     av.setScaleAboveWrapped(false);
     av.setScaleLeftWrapped(false);
     av.setScaleRightWrapped(false);
-    alignFrame.alignPanel.paintAlignment(false, false);
-    waitForSwing(); // for Swing thread
+
+    alignFrame.alignPanel.updateLayout();
 
     final int charHeight = av.getCharHeight();
     final int charWidth = av.getCharWidth();
@@ -371,65 +374,30 @@ public class SeqPanelTest
     assertEquals(pos.seqIndex, alignmentHeight - 1);
     assertEquals(pos.annotationIndex, -1);
 
-    /*
-     * cursor at the top of the first annotation  
-     */
-    y += 1;
-    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
-            false, 0);
-    pos = testee.findMousePosition(evt);
-    assertEquals(pos.seqIndex, alignmentHeight - 1);
-    assertEquals(pos.annotationIndex, 0); // over first annotation
-
-    /*
-     * cursor at the bottom of the first annotation  
-     */
-    y += av.getAlignment().getAlignmentAnnotation()[0].height - 1;
-    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
-            false, 0);
-    pos = testee.findMousePosition(evt);
-    assertEquals(pos.seqIndex, alignmentHeight - 1);
-    assertEquals(pos.annotationIndex, 0);
-
-    /*
-     * cursor at the top of the second annotation  
-     */
-    y += 1;
-    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
-            false, 0);
-    pos = testee.findMousePosition(evt);
-    assertEquals(pos.seqIndex, alignmentHeight - 1);
-    assertEquals(pos.annotationIndex, 1);
-
-    /*
-     * cursor at the bottom of the second annotation  
-     */
-    y += av.getAlignment().getAlignmentAnnotation()[1].height - 1;
-    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
-            false, 0);
-    pos = testee.findMousePosition(evt);
-    assertEquals(pos.seqIndex, alignmentHeight - 1);
-    assertEquals(pos.annotationIndex, 1);
-
-    /*
-     * cursor at the top of the third annotation  
-     */
-    y += 1;
-    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
-            false, 0);
-    pos = testee.findMousePosition(evt);
-    assertEquals(pos.seqIndex, alignmentHeight - 1);
-    assertEquals(pos.annotationIndex, 2);
-
-    /*
-     * cursor at the bottom of the third annotation  
-     */
-    y += av.getAlignment().getAlignmentAnnotation()[2].height - 1;
-    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
-            false, 0);
-    pos = testee.findMousePosition(evt);
-    assertEquals(pos.seqIndex, alignmentHeight - 1);
-    assertEquals(pos.annotationIndex, 2);
+    AlignmentAnnotation[] annotationRows = av.getAlignment()
+            .getAlignmentAnnotation();
+    for (int n = 0; n < annotationRows.length; n++)
+    {
+      /*
+       * cursor at the top of the n'th annotation  
+       */
+      y += 1;
+      evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+              false, 0);
+      pos = testee.findMousePosition(evt);
+      assertEquals(pos.seqIndex, alignmentHeight - 1);
+      assertEquals(pos.annotationIndex, n); // over n'th annotation
+
+      /*
+       * cursor at the bottom of the n'th annotation  
+       */
+      y += annotationRows[n].height - 1;
+      evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+              false, 0);
+      pos = testee.findMousePosition(evt);
+      assertEquals(pos.seqIndex, alignmentHeight - 1);
+      assertEquals(pos.annotationIndex, n);
+    }
 
     /*
      * cursor in gap between wrapped widths  
@@ -465,16 +433,15 @@ public class SeqPanelTest
   @Test(groups = "Functional")
   public void testFindMousePosition_wrapped_scaleAbove()
   {
-    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "true");
-    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
+    Cache.setPropertyNoSave("SHOW_ANNOTATIONS", "true");
+    Cache.setPropertyNoSave("WRAP_ALIGNMENT", "true");
     AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     AlignViewportI av = alignFrame.getViewport();
     av.setScaleAboveWrapped(true);
     av.setScaleLeftWrapped(false);
     av.setScaleRightWrapped(false);
-    alignFrame.alignPanel.paintAlignment(false, false);
-    waitForSwing();
+    alignFrame.alignPanel.updateLayout();
 
     final int charHeight = av.getCharHeight();
     final int charWidth = av.getCharWidth();
@@ -583,65 +550,29 @@ public class SeqPanelTest
     assertEquals(pos.seqIndex, alignmentHeight - 1);
     assertEquals(pos.annotationIndex, -1);
   
-    /*
-     * cursor at the top of the first annotation  
-     */
-    y += 1;
-    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
-            false, 0);
-    pos = testee.findMousePosition(evt);
-    assertEquals(pos.seqIndex, alignmentHeight - 1);
-    assertEquals(pos.annotationIndex, 0); // over first annotation
-  
-    /*
-     * cursor at the bottom of the first annotation  
-     */
-    y += av.getAlignment().getAlignmentAnnotation()[0].height - 1;
-    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
-            false, 0);
-    pos = testee.findMousePosition(evt);
-    assertEquals(pos.seqIndex, alignmentHeight - 1);
-    assertEquals(pos.annotationIndex, 0);
-  
-    /*
-     * cursor at the top of the second annotation  
-     */
-    y += 1;
-    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
-            false, 0);
-    pos = testee.findMousePosition(evt);
-    assertEquals(pos.seqIndex, alignmentHeight - 1);
-    assertEquals(pos.annotationIndex, 1);
-  
-    /*
-     * cursor at the bottom of the second annotation  
-     */
-    y += av.getAlignment().getAlignmentAnnotation()[1].height - 1;
-    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
-            false, 0);
-    pos = testee.findMousePosition(evt);
-    assertEquals(pos.seqIndex, alignmentHeight - 1);
-    assertEquals(pos.annotationIndex, 1);
-  
-    /*
-     * cursor at the top of the third annotation  
-     */
-    y += 1;
-    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
-            false, 0);
-    pos = testee.findMousePosition(evt);
-    assertEquals(pos.seqIndex, alignmentHeight - 1);
-    assertEquals(pos.annotationIndex, 2);
-  
-    /*
-     * cursor at the bottom of the third annotation  
-     */
-    y += av.getAlignment().getAlignmentAnnotation()[2].height - 1;
-    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
-            false, 0);
-    pos = testee.findMousePosition(evt);
-    assertEquals(pos.seqIndex, alignmentHeight - 1);
-    assertEquals(pos.annotationIndex, 2);
+    AlignmentAnnotation[] annotationRows = av.getAlignment().getAlignmentAnnotation();
+    for (int n = 0; n < annotationRows.length; n++)
+    {
+      /*
+       * cursor at the top of the n'th annotation  
+       */
+      y += 1;
+      evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+              false, 0);
+      pos = testee.findMousePosition(evt);
+      assertEquals(pos.seqIndex, alignmentHeight - 1);
+      assertEquals(pos.annotationIndex, n); // over n'th annotation
+
+      /*
+       * cursor at the bottom of the n'th annotation  
+       */
+      y += annotationRows[n].height - 1;
+      evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
+              false, 0);
+      pos = testee.findMousePosition(evt);
+      assertEquals(pos.seqIndex, alignmentHeight - 1);
+      assertEquals(pos.annotationIndex, n);
+    }
   
     /*
      * cursor in gap between wrapped widths  
@@ -697,16 +628,15 @@ public class SeqPanelTest
   @Test(groups = "Functional")
   public void testFindMousePosition_wrapped_noAnnotations()
   {
-    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "false");
-    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
+    Cache.setPropertyNoSave("SHOW_ANNOTATIONS", "false");
+    Cache.setPropertyNoSave("WRAP_ALIGNMENT", "true");
     AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     AlignViewportI av = alignFrame.getViewport();
     av.setScaleAboveWrapped(false);
     av.setScaleLeftWrapped(false);
     av.setScaleRightWrapped(false);
-    alignFrame.alignPanel.paintAlignment(false, false);
-    waitForSwing();
+    alignFrame.alignPanel.updateLayout();
 
     final int charHeight = av.getCharHeight();
     final int charWidth = av.getCharWidth();
@@ -786,7 +716,7 @@ public class SeqPanelTest
   @Test(groups = "Functional")
   public void testFindColumn_unwrapped()
   {
-    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "false");
+    Cache.setPropertyNoSave("WRAP_ALIGNMENT", "false");
     AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
@@ -852,16 +782,14 @@ public class SeqPanelTest
   @Test(groups = "Functional")
   public void testFindColumn_wrapped()
   {
-    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
+    Cache.setPropertyNoSave("WRAP_ALIGNMENT", "true");
     AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     AlignViewport av = alignFrame.getViewport();
     av.setScaleAboveWrapped(false);
     av.setScaleLeftWrapped(false);
     av.setScaleRightWrapped(false);
-    alignFrame.alignPanel.paintAlignment(false, false);
-    // need to wait for repaint to finish!
-    waitForSwing();
+    alignFrame.alignPanel.updateLayout();
     SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
     int x = 0;
     final int charWidth = av.getCharWidth();
@@ -895,8 +823,7 @@ public class SeqPanelTest
      * x over scale left (before drawn columns) results in -1
      */
     av.setScaleLeftWrapped(true);
-    alignFrame.alignPanel.paintAlignment(false, false);
-    waitForSwing();
+    alignFrame.alignPanel.updateLayout();
     SeqCanvas seqCanvas = testee.seqCanvas;
     int labelWidth = (int) PA.getValue(seqCanvas, "labelWidthWest");
     assertTrue(labelWidth > 0);
@@ -924,8 +851,7 @@ public class SeqPanelTest
      * x over scale right (beyond drawn columns) results in -1
      */
     av.setScaleRightWrapped(true);
-    alignFrame.alignPanel.paintAlignment(false, false);
-    waitForSwing();
+    alignFrame.alignPanel.updateLayout();
     labelWidth = (int) PA.getValue(seqCanvas, "labelWidthEast");
     assertTrue(labelWidth > 0);
     int residuesWide2 = av.getRanges().getViewportWidth();
@@ -950,14 +876,20 @@ public class SeqPanelTest
   }
 
   /**
-   * waits a few ms for Swing to do something
+   * waits for Swing event dispatch queue to empty
    */
   synchronized void waitForSwing()
   {
     try
     {
-      super.wait(10);
-    } catch (InterruptedException e)
+      EventQueue.invokeAndWait(new Runnable()
+      {
+        @Override
+        public void run()
+        {
+        }
+      });
+    } catch (InterruptedException | InvocationTargetException e)
     {
       e.printStackTrace();
     }