test/jalview/schemes/ResidueColourSchemeTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.schemes;
  22
  23 import static org.testng.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertFalse;
  25 import static org.testng.AssertJUnit.assertTrue;
  26
  27 import jalview.datamodel.Alignment;
  28 import jalview.datamodel.AlignmentAnnotation;
  29 import jalview.datamodel.AlignmentI;
  30 import jalview.datamodel.AnnotatedCollectionI;
  31 import jalview.datamodel.Annotation;
  32 import jalview.datamodel.Sequence;
  33 import jalview.datamodel.SequenceI;
  34 import jalview.gui.JvOptionPane;
  35 import jalview.io.TCoffeeScoreFile;
  36
  37 import org.testng.annotations.BeforeClass;
  38 import org.testng.annotations.Test;
  39
  40 public class ResidueColourSchemeTest
  41 {
  42   @BeforeClass(alwaysRun = true)
  43   public void setUp()
  44   {
  45
  46   }
  47
  48   @BeforeClass(alwaysRun = true)
  49   public void setUpJvOptionPane()
  50   {
  51     JvOptionPane.setInteractiveMode(false);
  52     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  53   }
  54
  55   @Test(groups = "Functional")
  56   public void testIsApplicableTo()
  57   {
  58     SequenceI pep1 = new Sequence("pep1", "APQTWLS");
  59     SequenceI pep2 = new Sequence("pep2", "AILFQYG");
  60     SequenceI dna1 = new Sequence("dna1", "ACTGAC");
  61     SequenceI dna2 = new Sequence("dna2", "TCCAAG");
  62     AlignmentI peptide = new Alignment(new SequenceI[] { pep1, pep2 });
  63     AlignmentI nucleotide = new Alignment(new SequenceI[] { dna1, dna2 });
  64
  65     /*
  66      * peptide-specific colour schemes
  67      */
  68     assertTrue(new ClustalxColourScheme(peptide, null)
  69             .isApplicableTo(peptide));
  70     assertFalse(new ClustalxColourScheme(nucleotide, null)
  71             .isApplicableTo(nucleotide));
  72     assertTrue(new Blosum62ColourScheme().isApplicableTo(peptide));
  73     assertFalse(new Blosum62ColourScheme().isApplicableTo(nucleotide));
  74     assertTrue(new BuriedColourScheme().isApplicableTo(peptide));
  75     assertFalse(new BuriedColourScheme().isApplicableTo(nucleotide));
  76     assertTrue(new HelixColourScheme().isApplicableTo(peptide));
  77     assertFalse(new HelixColourScheme().isApplicableTo(nucleotide));
  78     assertTrue(new HydrophobicColourScheme().isApplicableTo(peptide));
  79     assertFalse(new HydrophobicColourScheme().isApplicableTo(nucleotide));
  80     assertTrue(new StrandColourScheme().isApplicableTo(peptide));
  81     assertFalse(new StrandColourScheme().isApplicableTo(nucleotide));
  82     assertTrue(new TaylorColourScheme().isApplicableTo(peptide));
  83     assertFalse(new TaylorColourScheme().isApplicableTo(nucleotide));
  84     assertTrue(new TurnColourScheme().isApplicableTo(peptide));
  85     assertFalse(new TurnColourScheme().isApplicableTo(nucleotide));
  86     assertTrue(new ZappoColourScheme().isApplicableTo(peptide));
  87     assertFalse(new ZappoColourScheme().isApplicableTo(nucleotide));
  88
  89     /*
  90      * nucleotide-specific colour schemes
  91      */
  92     assertFalse(new NucleotideColourScheme().isApplicableTo(peptide));
  93     assertTrue(new NucleotideColourScheme().isApplicableTo(nucleotide));
  94     assertFalse(new PurinePyrimidineColourScheme().isApplicableTo(peptide));
  95     assertTrue(
  96             new PurinePyrimidineColourScheme().isApplicableTo(nucleotide));
  97     assertFalse(new RNAInteractionColourScheme().isApplicableTo(peptide));
  98     assertTrue(new RNAInteractionColourScheme().isApplicableTo(nucleotide));
  99
 100     /*
 101      * indifferent
 102      */
 103     assertTrue(new UserColourScheme().isApplicableTo(peptide));
 104     assertTrue(new UserColourScheme().isApplicableTo(nucleotide));
 105     assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
 106             .isApplicableTo(peptide));
 107     assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
 108             .isApplicableTo(nucleotide));
 109     ResidueColourScheme rcs = new PIDColourScheme();
 110     assertTrue(rcs.isApplicableTo(peptide));
 111     assertTrue(rcs.isApplicableTo(nucleotide));
 112     assertTrue(new PIDColourScheme().isApplicableTo(peptide));
 113     assertTrue(new PIDColourScheme().isApplicableTo(nucleotide));
 114     assertTrue(new FollowerColourScheme().isApplicableTo(peptide));
 115     assertTrue(new FollowerColourScheme().isApplicableTo(nucleotide));
 116
 117     /*
 118      * TCoffee colour requires the presence of TCoffee score annotation
 119      */
 120     assertFalse(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
 121     assertFalse(
 122             new TCoffeeColourScheme(nucleotide).isApplicableTo(nucleotide));
 123     AlignmentAnnotation aa = new AlignmentAnnotation("T-COFFEE", "", null);
 124     aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
 125     peptide.addAnnotation(aa);
 126     aa = new AlignmentAnnotation("T-COFFEE", "", null);
 127     aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
 128     nucleotide.addAnnotation(aa);
 129     assertTrue(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
 130     assertTrue(
 131             new TCoffeeColourScheme(nucleotide).isApplicableTo(nucleotide));
 132
 133     /*
 134      * RNAHelices requires the presence of rna secondary structure
 135      */
 136     assertFalse(new RNAHelicesColour(peptide).isApplicableTo(peptide));
 137     assertFalse(
 138             new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
 139     // add secondary structure (small but perfectly formed)
 140     Annotation[] ss = new Annotation[2];
 141     ss[0] = new Annotation("", "", '{', 0f);
 142     ss[1] = new Annotation("", "", '}', 0f);
 143     nucleotide.addAnnotation(new AlignmentAnnotation("SS", "", ss));
 144     assertTrue(new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
 145   }
 146
 147   @Test(groups = "Functional")
 148   public void testIsApplicableTo_dynamicColourScheme()
 149   {
 150     SequenceI pep1 = new Sequence("pep1", "APQTWLS");
 151     SequenceI pep2 = new Sequence("pep2", "AILFQYG");
 152     AlignmentI peptide = new Alignment(new SequenceI[] { pep1, pep2 });
 153
 154     /*
 155      * demonstrate that we can 'plug in' a colour scheme with specified
 156      * criteria for applicability; here, that there are more than 2 sequences
 157      */
 158     ColourSchemeI cs = new UserColourScheme()
 159     {
 160       @Override
 161       public boolean isApplicableTo(AnnotatedCollectionI ac)
 162       {
 163         AlignmentI al = ac.getContext() == null ? (AlignmentI) ac
 164                 : (AlignmentI) ac.getContext();
 165         return al.getSequences().size() > 2;
 166       }
 167     };
 168     assertFalse(cs.isApplicableTo(peptide));
 169     peptide.addSequence(pep1);
 170     assertTrue(cs.isApplicableTo(peptide));
 171   }
 172
 173   @Test(groups = "Functional")
 174   public void testGetName()
 175   {
 176     SequenceI pep1 = new Sequence("pep1", "APQTWLS");
 177     AlignmentI peptide = new Alignment(new SequenceI[] { pep1 });
 178
 179     assertEquals("Blosum62", new Blosum62ColourScheme().getSchemeName());
 180     assertEquals("Buried Index", new BuriedColourScheme().getSchemeName());
 181     assertEquals("Helix Propensity",
 182             new HelixColourScheme().getSchemeName());
 183     assertEquals("Hydrophobic",
 184             new HydrophobicColourScheme().getSchemeName());
 185     assertEquals("Strand Propensity",
 186             new StrandColourScheme().getSchemeName());
 187     assertEquals("Taylor", new TaylorColourScheme().getSchemeName());
 188     assertEquals("Turn Propensity", new TurnColourScheme().getSchemeName());
 189     assertEquals("Zappo", new ZappoColourScheme().getSchemeName());
 190     assertEquals("Nucleotide",
 191             new NucleotideColourScheme().getSchemeName());
 192     assertEquals("Purine/Pyrimidine",
 193             new PurinePyrimidineColourScheme().getSchemeName());
 194     assertEquals("RNA Interaction type",
 195             new RNAInteractionColourScheme().getSchemeName());
 196     assertEquals("User Defined", new UserColourScheme().getSchemeName());
 197     assertEquals("Score",
 198             new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
 199                     .getSchemeName());
 200     assertEquals("% Identity", new PIDColourScheme().getSchemeName());
 201     assertEquals("Follower", new FollowerColourScheme().getSchemeName());
 202     assertEquals("T-Coffee Scores",
 203             new TCoffeeColourScheme(peptide).getSchemeName());
 204     assertEquals("RNA Helices",
 205             new RNAHelicesColour(peptide).getSchemeName());
 206   }
 207 }