Merge branch 'Jalview-JS/develop' into merge_js_develop

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

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index 3e82547..31bd214 100644 (file)
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -27,6 +27,15 @@ import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import java.awt.Color;
+import java.util.Iterator;
+
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
@@ -48,14 +57,7 @@ import jalview.schemes.JalviewColourScheme;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.util.MessageManager;
-
-import java.awt.Color;
-import java.util.Iterator;
-
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
+import jalview.viewmodel.AlignmentViewport;
 
 public class AlignFrameTest
 {
@@ -75,7 +77,7 @@ public class AlignFrameTest
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
   }
 
   /**
@@ -86,7 +88,7 @@ public class AlignFrameTest
   public void setUp()
   {
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
-    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+    Cache.setPropertyNoSave("SHOW_IDENTITY",
             Boolean.TRUE.toString());
     af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
             DataSourceType.FILE);
@@ -94,18 +96,15 @@ public class AlignFrameTest
     /*
      * wait for Consensus thread to complete
      */
-    synchronized (this)
+    do
     {
-      while (af.getViewport().getConsensusSeq() == null)
+      try
+      {
+        Thread.sleep(50);
+      } catch (InterruptedException x)
       {
-        try
-        {
-          wait(50);
-        } catch (InterruptedException e)
-        {
-        }
       }
-    }
+    } while (af.getViewport().getCalcManager().isWorking());
   }
 
   public static void setUpJvOptionPane()
@@ -210,7 +209,7 @@ public class AlignFrameTest
   @Test(groups = "Functional")
   public void testChangeColour_background_groupsAndThresholds()
   {
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
@@ -261,8 +260,11 @@ public class AlignFrameTest
 
     /*
      * apply 30% Conservation to group
+     * (notice menu action applies to selection group even if mouse click
+     * is at a sequence not in the group)
      */
-    PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
+    PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2),
+            null);
     popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
             .toString());
     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
@@ -341,7 +343,7 @@ public class AlignFrameTest
   @Test(groups = "Functional")
   public void testColourThresholdActions()
   {
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
@@ -355,7 +357,7 @@ public class AlignFrameTest
 
     /*
      * inspect the colour of 
-     * FER_CAPAN.9(I), column 14 (14 base 0)
+     * FER_CAPAN.9(I), column 15 (14 base 0)
      * FER_CAPAN.10(SER), column 16 (15 base 0)
      */
     SequenceI ferCapan = al.findName("FER_CAPAN");
@@ -374,10 +376,14 @@ public class AlignFrameTest
     SliderPanel sp = SliderPanel.getSliderPanel();
     assertTrue(sp.isForConservation());
     assertEquals(sp.getValue(), 30); // initial slider setting
+    c = rs.findColour('I', 14, ferCapan);
+    Color i_faded = new Color(255, 255, 255);
+    assertEquals(c, i_faded);
     sp.valueChanged(10);
     assertSame(rs, av.getResidueShading());
+    assertEquals(rs.getConservationInc(), 10);
     c = rs.findColour('I', 14, ferCapan);
-    Color i_faded = new Color(196, 186, 196);
+    i_faded = new Color(196, 186, 196);
     assertEquals(c, i_faded);
     c = rs.findColour('S', 15, ferCapan);
     Color s_faded = new Color(144, 225, 144);
@@ -510,7 +516,7 @@ public class AlignFrameTest
   @Test(groups = "Functional")
   public void testNewView_colourThresholds()
   {
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
@@ -540,7 +546,8 @@ public class AlignFrameTest
     sg.setStartRes(15);
     sg.setEndRes(25);
     av.setSelectionGroup(sg);
-    PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
+    PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(0),
+            null);
     popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
             .toString());
     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
@@ -574,7 +581,7 @@ public class AlignFrameTest
      */
     af.newView_actionPerformed(null);
     assertEquals(af.alignPanel.getViewName(), "View 1");
-    AlignViewport av2 = af.getViewport();
+    AlignmentViewport av2 = af.getViewport();
     assertNotSame(av, av2);
     assertSame(av2, af.alignPanel.av);
     rs = av2.getResidueShading();