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