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;
public class ResidueColourSchemeTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+
+ }
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
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));
/*
rcs.setThreshold(0, true);
assertTrue(rcs.aboveThreshold('a', 0));
assertTrue(rcs.aboveThreshold('S', 0));
- assertFalse(rcs.aboveThreshold('W', 0));
+ assertTrue(rcs.aboveThreshold('W', 0));
assertTrue(rcs.aboveThreshold('R', 1));
- assertFalse(rcs.aboveThreshold('W', 2));
+ assertTrue(rcs.aboveThreshold('W', 2));
assertTrue(rcs.aboveThreshold('t', 3));
- assertFalse(rcs.aboveThreshold('Q', 3));
+ assertTrue(rcs.aboveThreshold('Q', 3));
/*
* with threshold, include gaps
@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));
assertEquals(colour, rcs.applyConservation(colour, 11));
assertEquals(Color.WHITE, rcs.applyConservation(colour, 12));
}
+
+ @Test(groups = "Functional")
+ 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));
+ 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));
+ 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(groups = "Functional")
+ 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(groups = "Functional")
+ 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("% Identity", new PIDColourScheme().getSchemeName());
+ assertEquals("Follower", new FollowerColourScheme().getSchemeName());
+ assertEquals("T-Coffee Scores",
+ new TCoffeeColourScheme(peptide).getSchemeName());
+ assertEquals("RNA Helices",
+ new RNAHelicesColour(peptide).getSchemeName());
+ }
}
git://source.jalview.org / jalview.git / blobdiff