X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FResidueColourSchemeTest.java;h=6978ea164feafb9b722e4f0ff42d8ca3e5b245f2;hb=046aff3885029c55f22027c6fdbeba8167a3a733;hp=077abd41174ac2f149624944fac23a75f27820c2;hpb=92bd4313e2f23a65df1eb965e836d178c1eacdd1;p=jalview.git diff --git a/test/jalview/schemes/ResidueColourSchemeTest.java b/test/jalview/schemes/ResidueColourSchemeTest.java index 077abd4..6978ea1 100644 --- a/test/jalview/schemes/ResidueColourSchemeTest.java +++ b/test/jalview/schemes/ResidueColourSchemeTest.java @@ -29,16 +29,11 @@ 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; - import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; @@ -58,139 +53,6 @@ public class ResidueColourSchemeTest } @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)); - 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() - { - 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"); @@ -230,8 +92,8 @@ public class ResidueColourSchemeTest 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)); @@ -256,8 +118,8 @@ public class ResidueColourSchemeTest * 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); @@ -265,14 +127,15 @@ public class ResidueColourSchemeTest 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); @@ -287,7 +150,7 @@ public class ResidueColourSchemeTest 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 @@ -315,20 +178,25 @@ public class ResidueColourSchemeTest 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",