test/jalview/ext/so/SequenceOntologyTest.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.ext.so;
  22
  23 import static org.testng.Assert.assertEquals;
  24 import static org.testng.Assert.assertFalse;
  25 import static org.testng.Assert.assertNull;
  26 import static org.testng.Assert.assertTrue;
  27
  28 import jalview.datamodel.ontology.OntologyI;
  29 import jalview.gui.JvOptionPane;
  30
  31 import java.util.Arrays;
  32 import java.util.Collections;
  33 import java.util.HashSet;
  34 import java.util.List;
  35 import java.util.Set;
  36
  37 import org.testng.annotations.BeforeClass;
  38 import org.testng.annotations.Test;
  39
  40 public class SequenceOntologyTest
  41 {
  42
  43   @BeforeClass(alwaysRun = true)
  44   public void setUpJvOptionPane()
  45   {
  46     JvOptionPane.setInteractiveMode(false);
  47     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  48   }
  49
  50   private OntologyI so;
  51
  52   @BeforeClass(alwaysRun = true)
  53   public void setUp()
  54   {
  55     long now = System.currentTimeMillis();
  56     try
  57     {
  58       so = new SequenceOntology();
  59     } catch (Throwable t)
  60     {
  61       System.out.println("SOTest error ");
  62       t.printStackTrace(System.err);
  63     }
  64     long elapsed = System.currentTimeMillis() - now;
  65     System.out.println("Load and cache of Sequence Ontology took "
  66             + elapsed + "ms");
  67   }
  68
  69   @Test(groups = "Functional")
  70   public void testIsA()
  71   {
  72     assertFalse(so.isA(null, null));
  73     assertFalse(so.isA(null, "SO:0000087"));
  74     assertFalse(so.isA("SO:0000087", null));
  75     assertFalse(so.isA("complete", "garbage"));
  76
  77     assertTrue(so.isA("SO:0000087", "SO:0000704"));
  78     assertFalse(so.isA("SO:0000704", "SO:0000087"));
  79     assertTrue(so.isA("SO:0000736", "SO:0000735"));
  80
  81     // same thing:
  82     assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
  83     // direct parent:
  84     assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
  85     // grandparent:
  86     assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
  87     // great-grandparent:
  88     assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
  89
  90     // same thing by name / description:
  91     assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
  92     assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
  93     assertTrue(so.isA("SO:0000084", "SO:0000084"));
  94
  95     // SO name to description:
  96     assertTrue(so.isA("SO:0000084", "organelle_sequence"));
  97     assertTrue(so.isA("SO:0000084", "sequence_location"));
  98     assertTrue(so.isA("SO:0000084", "sequence_attribute"));
  99
 100     // description to SO name:
 101     assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
 102     assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
 103     assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
 104   }
 105
 106   @Test(groups = "Functional")
 107   public void testIsCDS()
 108   {
 109     assertTrue(so.isA("CDS", "CDS"));
 110     assertTrue(so.isA("CDS_predicted", "CDS"));
 111     assertTrue(so.isA("transposable_element_CDS", "CDS"));
 112     assertTrue(so.isA("edited_CDS", "CDS"));
 113     assertTrue(so.isA("CDS_independently_known", "CDS"));
 114     assertTrue(so.isA("CDS_fragment", "CDS"));
 115     assertFalse(so.isA("CDS_region", "CDS"));// part_of
 116     assertFalse(so.isA("polypeptide", "CDS")); // derives_from
 117   }
 118
 119   @Test(groups = "Functional")
 120   public void testIsSequenceVariant()
 121   {
 122     assertFalse(so.isA("CDS", "sequence_variant"));
 123     assertTrue(so.isA("sequence_variant", "sequence_variant"));
 124
 125     /*
 126      * these should all be sub-types of sequence_variant
 127      */
 128     assertTrue(so.isA("structural_variant", "sequence_variant"));
 129     assertTrue(so.isA("feature_variant", "sequence_variant"));
 130     assertTrue(so.isA("gene_variant", "sequence_variant"));
 131     assertTrue(so.isA("transcript_variant", "sequence_variant"));
 132     assertTrue(so.isA("NMD_transcript_variant", "sequence_variant"));
 133     assertTrue(so.isA("missense_variant", "sequence_variant"));
 134     assertTrue(so.isA("synonymous_variant", "sequence_variant"));
 135     assertTrue(so.isA("frameshift_variant", "sequence_variant"));
 136     assertTrue(so.isA("5_prime_UTR_variant", "sequence_variant"));
 137     assertTrue(so.isA("3_prime_UTR_variant", "sequence_variant"));
 138     assertTrue(so.isA("stop_gained", "sequence_variant"));
 139     assertTrue(so.isA("stop_lost", "sequence_variant"));
 140     assertTrue(so.isA("inframe_deletion", "sequence_variant"));
 141     assertTrue(so.isA("inframe_insertion", "sequence_variant"));
 142   }
 143
 144   @Test(groups = "Functional")
 145   public void testGetChildTerms()
 146   {
 147     List<String> terms = Collections.<String> emptyList();
 148     List<String> children = so.getChildTerms("exon", terms);
 149     assertTrue(children.isEmpty());
 150
 151     terms = Arrays.asList("gene", "transcript", "snRNA", "junk", "mRNA");
 152     children = so.getChildTerms("exon", terms);
 153     assertTrue(children.isEmpty());
 154     children = so.getChildTerms("transcript", terms);
 155     assertEquals(children.size(), 2);
 156     assertTrue(children.contains("snRNA"));
 157     assertTrue(children.contains("mRNA"));
 158
 159     terms = Arrays.asList("gene", "transcript", "synonymous_variant",
 160             "stop_lost", "chain");
 161     children = so.getChildTerms("sequence_variant", terms);
 162     assertEquals(children.size(), 2);
 163     assertTrue(children.contains("synonymous_variant"));
 164     assertTrue(children.contains("stop_lost"));
 165   }
 166
 167   @Test(groups = "Functional")
 168   public void testGetParentTerms()
 169   {
 170     Set<String> terms = new HashSet<>();
 171     terms.add("sequence_variant");
 172     terms.add("NMD_transcript_variant");
 173     terms.add("stop_lost");
 174     terms.add("chain"); // not an SO term
 175
 176     Set<String> parents = so.getParentTerms(terms);
 177     assertEquals(parents.size(), 2);
 178     assertTrue(parents.contains("sequence_variant"));
 179     assertTrue(parents.contains("chain"));
 180   }
 181
 182   @Test(groups = "Functional")
 183   public void testGetRootParents()
 184   {
 185     List<String> roots = so.getRootParents("xyz");
 186     assertNull(roots);
 187     roots = so.getRootParents(null);
 188     assertNull(roots);
 189
 190     roots = so.getRootParents("stop_gained");
 191     assertEquals(roots.size(), 1);
 192     assertEquals(roots.get(0), "sequence_variant");
 193
 194     roots = so.getRootParents("sequence_variant");
 195     assertEquals(roots.size(), 1);
 196     assertEquals(roots.get(0), "sequence_variant");
 197
 198     roots = so.getRootParents("alanine");
 199     assertEquals(roots.size(), 1);
 200     assertEquals(roots.get(0), "sequence_feature");
 201   }
 202 }