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;
}
@Test(groups = "Functional")
- public void testAboveThreshold()
- {
- /*
- * 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 PIDColourScheme();
- rcs.setConsensus(new Profiles(profiles));
-
- /*
- * no threshold
- */
- rcs.setThreshold(0, true);
- assertTrue(rcs.aboveThreshold('a', 0));
- assertTrue(rcs.aboveThreshold('S', 0));
- assertTrue(rcs.aboveThreshold('W', 0));
- assertTrue(rcs.aboveThreshold('R', 1));
- assertTrue(rcs.aboveThreshold('W', 2));
- assertTrue(rcs.aboveThreshold('t', 3));
- assertTrue(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()
- {
- ResidueColourScheme rcs = new PIDColourScheme();
-
- // 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));
- }
-
- @Test(groups = "Functional")
public void testIsApplicableTo()
{
SequenceI pep1 = new Sequence("pep1", "APQTWLS");
assertFalse(new NucleotideColourScheme().isApplicableTo(peptide));
assertTrue(new NucleotideColourScheme().isApplicableTo(nucleotide));
assertFalse(new PurinePyrimidineColourScheme().isApplicableTo(peptide));
- assertTrue(new PurinePyrimidineColourScheme()
- .isApplicableTo(nucleotide));
+ assertTrue(
+ new PurinePyrimidineColourScheme().isApplicableTo(nucleotide));
assertFalse(new RNAInteractionColourScheme().isApplicableTo(peptide));
assertTrue(new RNAInteractionColourScheme().isApplicableTo(nucleotide));
* TCoffee colour requires the presence of TCoffee score annotation
*/
assertFalse(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
- assertFalse(new TCoffeeColourScheme(nucleotide)
- .isApplicableTo(nucleotide));
+ assertFalse(
+ new TCoffeeColourScheme(nucleotide).isApplicableTo(nucleotide));
AlignmentAnnotation aa = new AlignmentAnnotation("T-COFFEE", "", null);
aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
peptide.addAnnotation(aa);
aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
nucleotide.addAnnotation(aa);
assertTrue(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
- assertTrue(new TCoffeeColourScheme(nucleotide)
- .isApplicableTo(nucleotide));
+ 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));
+ assertFalse(
+ new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
// add secondary structure (small but perfectly formed)
Annotation[] ss = new Annotation[2];
ss[0] = new Annotation("", "", '{', 0f);
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
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("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("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("Score",
+ new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
+ .getSchemeName());
assertEquals("% Identity", new PIDColourScheme().getSchemeName());
assertEquals("Follower", new FollowerColourScheme().getSchemeName());
assertEquals("T-Coffee Scores",
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