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.gui.JvOptionPane;
  27 import jalview.io.gff.SequenceOntologyI;
  28
  29 import org.testng.annotations.BeforeClass;
  30 import org.testng.annotations.Test;
  31
  32 public class SequenceOntologyTest
  33 {
  34
  35   @BeforeClass(alwaysRun = true)
  36   public void setUpJvOptionPane()
  37   {
  38     JvOptionPane.setInteractiveMode(false);
  39     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  40   }
  41
  42   private SequenceOntologyI so;
  43
  44   @BeforeClass(alwaysRun = true)
  45   public void setUp()
  46   {
  47     long now = System.currentTimeMillis();
  48     try
  49     {
  50       so = new SequenceOntology();
  51     } catch (Throwable t)
  52     {
  53       System.out.println("SOTest error ");
  54       t.printStackTrace(System.err);
  55     }
  56     long elapsed = System.currentTimeMillis() - now;
  57     System.out.println(
  58             "Load and cache of Sequence Ontology took " + elapsed + "ms");
  59   }
  60
  61   @Test(groups = "Functional")
  62   public void testIsA()
  63   {
  64     assertFalse(so.isA(null, null));
  65     assertFalse(so.isA(null, "SO:0000087"));
  66     assertFalse(so.isA("SO:0000087", null));
  67     assertFalse(so.isA("complete", "garbage"));
  68
  69     assertTrue(so.isA("SO:0000087", "SO:0000704"));
  70     assertFalse(so.isA("SO:0000704", "SO:0000087"));
  71     assertTrue(so.isA("SO:0000736", "SO:0000735"));
  72
  73     // same thing:
  74     assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
  75     // direct parent:
  76     assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
  77     // grandparent:
  78     assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
  79     // great-grandparent:
  80     assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
  81
  82     // same thing by name / description:
  83     assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
  84     assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
  85     assertTrue(so.isA("SO:0000084", "SO:0000084"));
  86
  87     // SO name to description:
  88     assertTrue(so.isA("SO:0000084", "organelle_sequence"));
  89     assertTrue(so.isA("SO:0000084", "sequence_location"));
  90     assertTrue(so.isA("SO:0000084", "sequence_attribute"));
  91
  92     // description to SO name:
  93     assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
  94     assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
  95     assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
  96   }
  97
  98   @Test(groups = "Functional")
  99   public void testIsCDS()
 100   {
 101     assertTrue(so.isA("CDS", "CDS"));
 102     assertTrue(so.isA("CDS_predicted", "CDS"));
 103     assertTrue(so.isA("transposable_element_CDS", "CDS"));
 104     assertTrue(so.isA("edited_CDS", "CDS"));
 105     assertTrue(so.isA("CDS_independently_known", "CDS"));
 106     assertTrue(so.isA("CDS_fragment", "CDS"));
 107     assertFalse(so.isA("CDS_region", "CDS"));// part_of
 108     assertFalse(so.isA("polypeptide", "CDS")); // derives_from
 109   }
 110
 111   @Test(groups = "Functional")
 112   public void testIsSequenceVariant()
 113   {
 114     assertFalse(so.isA("CDS", "sequence_variant"));
 115     assertTrue(so.isA("sequence_variant", "sequence_variant"));
 116
 117     /*
 118      * these should all be sub-types of sequence_variant
 119      */
 120     assertTrue(so.isA("structural_variant", "sequence_variant"));
 121     assertTrue(so.isA("feature_variant", "sequence_variant"));
 122     assertTrue(so.isA("gene_variant", "sequence_variant"));
 123     assertTrue(so.isA("transcript_variant", "sequence_variant"));
 124     assertTrue(so.isA("NMD_transcript_variant", "sequence_variant"));
 125     assertTrue(so.isA("missense_variant", "sequence_variant"));
 126     assertTrue(so.isA("synonymous_variant", "sequence_variant"));
 127     assertTrue(so.isA("frameshift_variant", "sequence_variant"));
 128     assertTrue(so.isA("5_prime_UTR_variant", "sequence_variant"));
 129     assertTrue(so.isA("3_prime_UTR_variant", "sequence_variant"));
 130     assertTrue(so.isA("stop_gained", "sequence_variant"));
 131     assertTrue(so.isA("stop_lost", "sequence_variant"));
 132     assertTrue(so.isA("inframe_deletion", "sequence_variant"));
 133     assertTrue(so.isA("inframe_insertion", "sequence_variant"));
 134   }
 135 }