test/jalview/ext/ensembl/EnsemblProteinTest.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.ensembl;
  22
  23 import static org.testng.AssertJUnit.assertEquals;
  24
  25 import org.testng.Assert;
  26 import org.testng.annotations.Test;
  27
  28 public class EnsemblProteinTest
  29 {
  30
  31   @Test(groups = "Functional")
  32   public void testIsValidReference() throws Exception
  33   {
  34     EnsemblSequenceFetcher esq = new EnsemblProtein();
  35     Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
  36     Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
  37     Assert.assertFalse(esq.isValidReference("ENST00000288602"));
  38     Assert.assertFalse(esq.isValidReference("ENSG00000288602"));
  39     // non-human species having a 3 character identifier included:
  40     Assert.assertTrue(esq.isValidReference("ENSMUSP00000099398"));
  41   }
  42
  43   @Test(groups = "Functional")
  44   public void testGetAccesionIdFromQuery() throws Exception
  45   {
  46     EnsemblSequenceFetcher esq = new EnsemblProtein();
  47     assertEquals("ENSP00000288602",
  48             esq.getAccessionIdFromQuery("ENSP00000288602"));
  49     assertEquals("ENSMUSP00000288602",
  50             esq.getAccessionIdFromQuery("ENSMUSP00000288602"));
  51
  52     // ENST converted to ENSP
  53     assertEquals("ENSP00000288602",
  54             esq.getAccessionIdFromQuery("ENST00000288602"));
  55     assertEquals("ENSMUSP00000288602",
  56             esq.getAccessionIdFromQuery("ENSMUST00000288602"));
  57
  58     // with valid separator:
  59     assertEquals("ENSP00000288604",
  60             esq.getAccessionIdFromQuery("ENSP00000288604 ENSP00000288602"));
  61
  62     // with wrong separator:
  63     assertEquals("ENSP00000288604,ENSP00000288602",
  64             esq.getAccessionIdFromQuery("ENSP00000288604,ENSP00000288602"));
  65   }
  66
  67 }