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;
-
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ResidueColourSchemeTest
{
-
@BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = "Functional")
- public void testAboveThreshold()
+ public void setUp()
{
- /*
- * make up profiles for this alignment:
- * AR-Q
- * AR--
- * SR-T
- * SR-T
- */
- ProfileI[] profiles = new ProfileI[4];
- profiles[0] = new Profile(4, 0, 2, "AS");
- 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();
- rcs.setConsensus(new Profiles(profiles));
-
- /*
- * no threshold
- */
- rcs.setThreshold(0, true);
- assertTrue(rcs.aboveThreshold('a', 0));
- assertTrue(rcs.aboveThreshold('S', 0));
- assertFalse(rcs.aboveThreshold('W', 0));
- assertTrue(rcs.aboveThreshold('R', 1));
- assertFalse(rcs.aboveThreshold('W', 2));
- assertTrue(rcs.aboveThreshold('t', 3));
- assertFalse(rcs.aboveThreshold('Q', 3));
- /*
- * with threshold, include gaps
- */
- rcs.setThreshold(60, false);
- assertFalse(rcs.aboveThreshold('a', 0));
- assertFalse(rcs.aboveThreshold('S', 0));
- assertTrue(rcs.aboveThreshold('R', 1));
- assertFalse(rcs.aboveThreshold('W', 2));
- assertFalse(rcs.aboveThreshold('t', 3)); // 50% < 60%
-
- /*
- * with threshold, ignore gaps
- */
- rcs.setThreshold(60, true);
- assertFalse(rcs.aboveThreshold('a', 0));
- assertFalse(rcs.aboveThreshold('S', 0));
- assertTrue(rcs.aboveThreshold('R', 1));
- assertFalse(rcs.aboveThreshold('W', 2));
- assertTrue(rcs.aboveThreshold('t', 3)); // 67% > 60%
}
- /**
- * Test colour bleaching based on conservation score and conservation slider.
- * Scores of 10 or 11 should leave colours unchanged. Gap is always white.
- */
- @Test(groups = "Functional")
- public void testApplyConservation()
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
{
- ResidueColourScheme rcs = new ResidueColourScheme();
-
- // no conservation present - no fading
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 12));
-
- // cheat by setting conservation sequence directly
- // rather than calculating it - good enough for this test
- String consensus = "0123456789+*-";
- rcs.conservation = consensus.toCharArray();
-
- // column out of range:
- assertEquals(Color.RED,
- rcs.applyConservation(Color.RED, consensus.length()));
-
- /*
- * with 100% threshold, 'fade factor' is
- * (11-score)/10 * 100/20 = (11-score)/2
- * which is >= 1 for all scores i.e. all fade to white except +, *
- */
- rcs.setConservationInc(100);
- assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 0));
- assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 1));
- assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 2));
- assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 3));
- assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 4));
- assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 5));
- assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 6));
- assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 7));
- assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 8));
- assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 9));
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 10));
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 11));
- assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 12));
-
- /*
- * with 0% threshold, there should be no fading
- */
- rcs.setConservationInc(0);
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 0));
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 1));
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 2));
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 3));
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 4));
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 5));
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 6));
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 7));
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 8));
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 9));
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 10));
- assertEquals(Color.RED, rcs.applyConservation(Color.RED, 11));
- assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 12)); // gap
-
- /*
- * with 40% threshold, 'fade factor' is
- * (11-score)/10 * 40/20 = (11-score)/5
- * which is {>1, >1, >1, >1, >1, >1, 1, 0.8, 0.6, 0.4} for score 0-9
- * e.g. score 7 colour fades 80% of the way to white (255, 255, 255)
- */
- rcs.setConservationInc(40);
- Color colour = new Color(155, 105, 55);
- assertEquals(Color.WHITE, rcs.applyConservation(colour, 0));
- assertEquals(Color.WHITE, rcs.applyConservation(colour, 1));
- assertEquals(Color.WHITE, rcs.applyConservation(colour, 2));
- assertEquals(Color.WHITE, rcs.applyConservation(colour, 3));
- assertEquals(Color.WHITE, rcs.applyConservation(colour, 4));
- assertEquals(Color.WHITE, rcs.applyConservation(colour, 5));
- assertEquals(Color.WHITE, rcs.applyConservation(colour, 6));
- assertEquals(new Color(235, 225, 215), rcs.applyConservation(colour, 7));
- assertEquals(new Color(215, 195, 175), rcs.applyConservation(colour, 8));
- assertEquals(new Color(195, 165, 135), rcs.applyConservation(colour, 9));
- assertEquals(colour, rcs.applyConservation(colour, 10));
- assertEquals(colour, rcs.applyConservation(colour, 11));
- assertEquals(Color.WHITE, rcs.applyConservation(colour, 12));
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
@Test(groups = "Functional")
.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));
assertTrue(cs.isApplicableTo(peptide));
}
- @Test
+ @Test(groups = "Functional")
public void testGetName()
{
SequenceI pep1 = new Sequence("pep1", "APQTWLS");
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",