X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FResidueColourSchemeTest.java;h=6978ea164feafb9b722e4f0ff42d8ca3e5b245f2;hb=2d44b9594da6c691eca72697060c166d0389affd;hp=4e8ea522de37389e4a246d050231dccffef5df0a;hpb=a09d6f5c16b0e222806e035cd38bfb4c4eb92c75;p=jalview.git diff --git a/test/jalview/schemes/ResidueColourSchemeTest.java b/test/jalview/schemes/ResidueColourSchemeTest.java index 4e8ea52..6978ea1 100644 --- a/test/jalview/schemes/ResidueColourSchemeTest.java +++ b/test/jalview/schemes/ResidueColourSchemeTest.java @@ -29,160 +29,27 @@ 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; 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") @@ -225,8 +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)); @@ -239,8 +106,9 @@ public class ResidueColourSchemeTest .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)); @@ -250,8 +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); @@ -259,14 +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); @@ -281,7 +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 @@ -301,7 +170,7 @@ public class ResidueColourSchemeTest assertTrue(cs.isApplicableTo(peptide)); } - @Test + @Test(groups = "Functional") public void testGetName() { SequenceI pep1 = new Sequence("pep1", "APQTWLS"); @@ -309,21 +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("Residue", new ResidueColourScheme().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",