JAL-2360 refactoring for JalviewColourScheme enum,

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

diff --git a/test/jalview/schemes/ResidueColourSchemeTest.java b/test/jalview/schemes/ResidueColourSchemeTest.java
index d3a4fff..809dce3 100644 (file)
--- a/test/jalview/schemes/ResidueColourSchemeTest.java
+++ b/test/jalview/schemes/ResidueColourSchemeTest.java
@@ -24,10 +24,18 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.Profile;
 import jalview.datamodel.ProfileI;
 import jalview.datamodel.Profiles;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
+import jalview.io.TCoffeeScoreFile;
 
 import java.awt.Color;
 
@@ -176,4 +184,151 @@ public class ResidueColourSchemeTest
     assertEquals(colour, rcs.applyConservation(colour, 11));
     assertEquals(Color.WHITE, rcs.applyConservation(colour, 12));
   }
+
+  @Test
+  public void testIsApplicableTo()
+  {
+    SequenceI pep1 = new Sequence("pep1", "APQTWLS");
+    SequenceI pep2 = new Sequence("pep2", "AILFQYG");
+    SequenceI dna1 = new Sequence("dna1", "ACTGAC");
+    SequenceI dna2 = new Sequence("dna2", "TCCAAG");
+    AlignmentI peptide = new Alignment(new SequenceI[] { pep1, pep2 });
+    AlignmentI nucleotide = new Alignment(new SequenceI[] { dna1, dna2 });
+
+    /*
+     * peptide-specific colour schemes
+     */
+    assertTrue(new ClustalxColourScheme(peptide, null)
+            .isApplicableTo(peptide));
+    assertFalse(new ClustalxColourScheme(nucleotide, null)
+            .isApplicableTo(nucleotide));
+    assertTrue(new Blosum62ColourScheme().isApplicableTo(peptide));
+    assertFalse(new Blosum62ColourScheme().isApplicableTo(nucleotide));
+    assertTrue(new BuriedColourScheme().isApplicableTo(peptide));
+    assertFalse(new BuriedColourScheme().isApplicableTo(nucleotide));
+    assertTrue(new HelixColourScheme().isApplicableTo(peptide));
+    assertFalse(new HelixColourScheme().isApplicableTo(nucleotide));
+    assertTrue(new HydrophobicColourScheme().isApplicableTo(peptide));
+    assertFalse(new HydrophobicColourScheme().isApplicableTo(nucleotide));
+    assertTrue(new StrandColourScheme().isApplicableTo(peptide));
+    assertFalse(new StrandColourScheme().isApplicableTo(nucleotide));
+    assertTrue(new TaylorColourScheme().isApplicableTo(peptide));
+    assertFalse(new TaylorColourScheme().isApplicableTo(nucleotide));
+    assertTrue(new TurnColourScheme().isApplicableTo(peptide));
+    assertFalse(new TurnColourScheme().isApplicableTo(nucleotide));
+    assertTrue(new ZappoColourScheme().isApplicableTo(peptide));
+    assertFalse(new ZappoColourScheme().isApplicableTo(nucleotide));
+
+    /*
+     * nucleotide-specific colour schemes
+     */
+    assertFalse(new NucleotideColourScheme().isApplicableTo(peptide));
+    assertTrue(new NucleotideColourScheme().isApplicableTo(nucleotide));
+    assertFalse(new PurinePyrimidineColourScheme().isApplicableTo(peptide));
+    assertTrue(new PurinePyrimidineColourScheme()
+            .isApplicableTo(nucleotide));
+    assertFalse(new RNAInteractionColourScheme().isApplicableTo(peptide));
+    assertTrue(new RNAInteractionColourScheme().isApplicableTo(nucleotide));
+
+    /*
+     * indifferent
+     */
+    assertTrue(new UserColourScheme().isApplicableTo(peptide));
+    assertTrue(new UserColourScheme().isApplicableTo(nucleotide));
+    assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
+            .isApplicableTo(peptide));
+    assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
+            .isApplicableTo(nucleotide));
+    assertTrue(new ResidueColourScheme().isApplicableTo(peptide));
+    assertTrue(new ResidueColourScheme().isApplicableTo(nucleotide));
+    assertTrue(new PIDColourScheme().isApplicableTo(peptide));
+    assertTrue(new PIDColourScheme().isApplicableTo(nucleotide));
+    assertTrue(new FollowerColourScheme().isApplicableTo(peptide));
+    assertTrue(new FollowerColourScheme().isApplicableTo(nucleotide));
+
+    /*
+     * TCoffee colour requires the presence of TCoffee score annotation
+     */
+    assertFalse(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
+    assertFalse(new TCoffeeColourScheme(nucleotide)
+            .isApplicableTo(nucleotide));
+    AlignmentAnnotation aa = new AlignmentAnnotation("T-COFFEE", "", null);
+    aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
+    peptide.addAnnotation(aa);
+    aa = new AlignmentAnnotation("T-COFFEE", "", null);
+    aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
+    nucleotide.addAnnotation(aa);
+    assertTrue(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
+    assertTrue(new TCoffeeColourScheme(nucleotide)
+            .isApplicableTo(nucleotide));
+
+    /*
+     * RNAHelices requires the presence of rna secondary structure
+     */
+    assertFalse(new RNAHelicesColour(peptide).isApplicableTo(peptide));
+    assertFalse(new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
+    // add secondary structure (small but perfectly formed)
+    Annotation[] ss = new Annotation[2];
+    ss[0] = new Annotation("", "", '{', 0f);
+    ss[1] = new Annotation("", "", '}', 0f);
+    nucleotide.addAnnotation(new AlignmentAnnotation("SS", "", ss));
+    assertTrue(new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
+  }
+
+  @Test
+  public void testIsApplicableTo_dynamicColourScheme()
+  {
+    SequenceI pep1 = new Sequence("pep1", "APQTWLS");
+    SequenceI pep2 = new Sequence("pep2", "AILFQYG");
+    AlignmentI peptide = new Alignment(new SequenceI[] { pep1, pep2 });
+  
+    /*
+     * demonstrate that we can 'plug in' a colour scheme with specified
+     * criteria for applicability; here, that there are more than 2 sequences
+     */
+    ColourSchemeI cs = new UserColourScheme()
+    {
+      @Override
+      public boolean isApplicableTo(AnnotatedCollectionI ac)
+      {
+        AlignmentI al = ac.getContext() == null ? (AlignmentI) ac
+                : (AlignmentI) ac.getContext();
+        return al.getSequences().size() > 2;
+      }
+    };
+    assertFalse(cs.isApplicableTo(peptide));
+    peptide.addSequence(pep1);
+    assertTrue(cs.isApplicableTo(peptide));
+  }
+
+  @Test
+  public void testGetName()
+  {
+    SequenceI pep1 = new Sequence("pep1", "APQTWLS");
+    AlignmentI peptide = new Alignment(new SequenceI[] { pep1 });
+
+    assertEquals("Blosum62", new Blosum62ColourScheme().getSchemeName());
+    assertEquals("Buried Index", new BuriedColourScheme().getSchemeName());
+    assertEquals("Helix Propensity", new HelixColourScheme().getSchemeName());
+    assertEquals("Hydrophobic", new HydrophobicColourScheme().getSchemeName());
+    assertEquals("Strand Propensity", new StrandColourScheme().getSchemeName());
+    assertEquals("Taylor", new TaylorColourScheme().getSchemeName());
+    assertEquals("Turn Propensity", new TurnColourScheme().getSchemeName());
+    assertEquals("Zappo", new ZappoColourScheme().getSchemeName());
+    assertEquals("Nucleotide", new NucleotideColourScheme().getSchemeName());
+    assertEquals("Purine/Pyrimidine",
+            new PurinePyrimidineColourScheme().getSchemeName());
+    assertEquals("RNA Interaction type",
+            new RNAInteractionColourScheme().getSchemeName());
+    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",
+            new TCoffeeColourScheme(peptide).getSchemeName());
+    assertEquals("RNA Helices",
+            new RNAHelicesColour(peptide).getSchemeName());
+  }
 }