Merge branch 'features/JAL-1541_BioJsMSA' into develop

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

diff --git a/test/jalview/gui/AnnotationChooserTest.java b/test/jalview/gui/AnnotationChooserTest.java
index 944ab9c..33ffd32 100644 (file)
--- a/test/jalview/gui/AnnotationChooserTest.java
+++ b/test/jalview/gui/AnnotationChooserTest.java
@@ -3,13 +3,6 @@ package jalview.gui;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
 import java.awt.Checkbox;
@@ -26,6 +19,16 @@ import javax.swing.JPanel;
 import org.junit.Before;
 import org.junit.Test;
 
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.util.MessageManager;
+
 /**
  * Unit tests for AnnotationChooser
  * 
@@ -52,6 +55,16 @@ public class AnnotationChooserTest
   @Before
   public void setUp() throws IOException
   {
+    // pin down annotation sort order for test
+    Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
+            SequenceAnnotationOrder.NONE.name());
+    final String True = Boolean.TRUE.toString();
+    Cache.applicationProperties.setProperty(
+            Preferences.SHOW_AUTOCALC_ABOVE, True);
+    Cache.applicationProperties.setProperty("SHOW_QUALITY", True);
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION", True);
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY", True);
+
     AlignmentI al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
             AppletFormatAdapter.PASTE, "FASTA");
     af = new AlignFrame(al, 700, 500);
@@ -490,6 +503,7 @@ public class AnnotationChooserTest
   @Test
   public void testSelectType_showForSelected()
   {
+    // sequences 1 and 2 have annotations IUPred and Jmol
     selectSequences(1, 2);
     testee = new AnnotationChooser(parentPanel);
     final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0);
@@ -505,6 +519,7 @@ public class AnnotationChooserTest
     setSelected(selectedSequencesCheckbox, true);
     setSelected(hideCheckbox, true);
     setSelected(getTypeCheckbox("JMol"), true);
+
     assertTrue(anns[5].visible); // JMol for seq3
     assertFalse(anns[7].visible); // JMol for seq1
     // ...now show them...
@@ -738,8 +753,8 @@ public class AnnotationChooserTest
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertFalse(anns[3].visible); // IUPRED
-    assertTrue(anns[4].visible); // Beauty (not seq-related)
+    assertTrue(anns[3].visible); // Beauty (not seq-related)
+    assertFalse(anns[4].visible); // IUPRED
     assertFalse(anns[5].visible); // JMol
     assertFalse(anns[6].visible); // IUPRED
     assertFalse(anns[7].visible); // JMol