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.AssertJUnit.assertFalse;
  24 import static org.testng.AssertJUnit.assertTrue;
  25
  26 import jalview.io.gff.SequenceOntologyI;
  27
  28 import org.testng.annotations.BeforeClass;
  29 import org.testng.annotations.Test;
  30
  31 public class SequenceOntologyTest
  32 {
  33   private SequenceOntologyI so;
  34
  35   @BeforeClass(alwaysRun = true)
  36   public void setUp()
  37   {
  38     long now = System.currentTimeMillis();
  39     try
  40     {
  41       so = new SequenceOntology();
  42     } catch (Throwable t)
  43     {
  44       System.out.println("SOTest error ");
  45       t.printStackTrace(System.err);
  46     }
  47     long elapsed = System.currentTimeMillis() - now;
  48     System.out.println("Load and cache of Sequence Ontology took "
  49             + elapsed + "ms");
  50   }
  51
  52   @Test(groups = "Functional")
  53   public void testIsA()
  54   {
  55     assertFalse(so.isA(null, null));
  56     assertFalse(so.isA(null, "SO:0000087"));
  57     assertFalse(so.isA("SO:0000087", null));
  58     assertFalse(so.isA("complete", "garbage"));
  59
  60     assertTrue(so.isA("SO:0000087", "SO:0000704"));
  61     assertFalse(so.isA("SO:0000704", "SO:0000087"));
  62     assertTrue(so.isA("SO:0000736", "SO:0000735"));
  63
  64     // same thing:
  65     assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
  66     // direct parent:
  67     assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
  68     // grandparent:
  69     assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
  70     // great-grandparent:
  71     assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
  72
  73     // same thing by name / description:
  74     assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
  75     assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
  76     assertTrue(so.isA("SO:0000084", "SO:0000084"));
  77
  78     // SO name to description:
  79     assertTrue(so.isA("SO:0000084", "organelle_sequence"));
  80     assertTrue(so.isA("SO:0000084", "sequence_location"));
  81     assertTrue(so.isA("SO:0000084", "sequence_attribute"));
  82
  83     // description to SO name:
  84     assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
  85     assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
  86     assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
  87   }
  88
  89   @Test(groups = "Functional")
  90   public void testIsCDS()
  91   {
  92     assertTrue(so.isA("CDS", "CDS"));
  93     assertTrue(so.isA("CDS_predicted", "CDS"));
  94     assertTrue(so.isA("transposable_element_CDS", "CDS"));
  95     assertTrue(so.isA("edited_CDS", "CDS"));
  96     assertTrue(so.isA("CDS_independently_known", "CDS"));
  97     assertTrue(so.isA("CDS_fragment", "CDS"));
  98     assertFalse(so.isA("CDS_region", "CDS"));// part_of
  99     assertFalse(so.isA("polypeptide", "CDS")); // derives_from
 100   }
 101 }