JAL-2360 ColourSchemes holds configured schemes, AlignFrame colour menu

[jalview.git] / test / jalview / schemes / ResidueColourSchemeTest.java

diff --git a/test/jalview/schemes/ResidueColourSchemeTest.java b/test/jalview/schemes/ResidueColourSchemeTest.java
index 4e8ea52..e6dc9e6 100644 (file)
--- a/test/jalview/schemes/ResidueColourSchemeTest.java
+++ b/test/jalview/schemes/ResidueColourSchemeTest.java
@@ -44,6 +44,11 @@ import org.testng.annotations.Test;
 
 public class ResidueColourSchemeTest
 {
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+
+  }
 
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
@@ -67,7 +72,7 @@ public class ResidueColourSchemeTest
     profiles[1] = new Profile(4, 0, 4, "R");
     profiles[2] = new Profile(4, 4, 0, "");
     profiles[3] = new Profile(4, 1, 2, "T");
-    ResidueColourScheme rcs = new ResidueColourScheme();
+    ResidueColourScheme rcs = new PIDColourScheme();
     rcs.setConsensus(new Profiles(profiles));
     
     /*
@@ -110,7 +115,7 @@ public class ResidueColourSchemeTest
   @Test(groups = "Functional")
   public void testApplyConservation()
   {
-    ResidueColourScheme rcs = new ResidueColourScheme();
+    ResidueColourScheme rcs = new PIDColourScheme();
 
     // no conservation present - no fading
     assertEquals(Color.RED, rcs.applyConservation(Color.RED, 12));
@@ -202,7 +207,8 @@ public class ResidueColourSchemeTest
             .isApplicableTo(peptide));
     assertFalse(new ClustalxColourScheme(nucleotide, null)
             .isApplicableTo(nucleotide));
-    assertTrue(new Blosum62ColourScheme().isApplicableTo(peptide));
+    // Blosum requires presence of Conservation annotation
+    assertFalse(new Blosum62ColourScheme().isApplicableTo(peptide));
     assertFalse(new Blosum62ColourScheme().isApplicableTo(nucleotide));
     assertTrue(new BuriedColourScheme().isApplicableTo(peptide));
     assertFalse(new BuriedColourScheme().isApplicableTo(nucleotide));
@@ -219,6 +225,11 @@ public class ResidueColourSchemeTest
     assertTrue(new ZappoColourScheme().isApplicableTo(peptide));
     assertFalse(new ZappoColourScheme().isApplicableTo(nucleotide));
 
+    peptide.addAnnotation(new AlignmentAnnotation("Conservation",
+            "Conservation", new Annotation[1], 0f, 11f,
+            AlignmentAnnotation.BAR_GRAPH));
+    assertTrue(new Blosum62ColourScheme().isApplicableTo(peptide));
+
     /*
      * nucleotide-specific colour schemes
      */
@@ -239,8 +250,9 @@ public class ResidueColourSchemeTest
             .isApplicableTo(peptide));
     assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
             .isApplicableTo(nucleotide));
-    assertTrue(new ResidueColourScheme().isApplicableTo(peptide));
-    assertTrue(new ResidueColourScheme().isApplicableTo(nucleotide));
+    ResidueColourScheme rcs = new PIDColourScheme();
+    assertTrue(rcs.isApplicableTo(peptide));
+    assertTrue(rcs.isApplicableTo(nucleotide));
     assertTrue(new PIDColourScheme().isApplicableTo(peptide));
     assertTrue(new PIDColourScheme().isApplicableTo(nucleotide));
     assertTrue(new FollowerColourScheme().isApplicableTo(peptide));
@@ -301,7 +313,7 @@ public class ResidueColourSchemeTest
     assertTrue(cs.isApplicableTo(peptide));
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testGetName()
   {
     SequenceI pep1 = new Sequence("pep1", "APQTWLS");
@@ -323,7 +335,6 @@ public class ResidueColourSchemeTest
     assertEquals("User Defined", new UserColourScheme().getSchemeName());
     assertEquals("Score", new ScoreColourScheme(new int[] {},
             new double[] {}, 0, 0d).getSchemeName());
-    assertEquals("Residue", new ResidueColourScheme().getSchemeName());
     assertEquals("% Identity", new PIDColourScheme().getSchemeName());
     assertEquals("Follower", new FollowerColourScheme().getSchemeName());
     assertEquals("T-Coffee Scores",