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 jalview.gui.JvOptionPane;
  26
  27 import org.testng.Assert;
  28 import org.testng.annotations.BeforeClass;
  29 import org.testng.annotations.Test;
  30
  31 public class EnsemblProteinTest
  32 {
  33
  34   @BeforeClass(alwaysRun = true)
  35   public void setUpJvOptionPane()
  36   {
  37     JvOptionPane.setInteractiveMode(false);
  38     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  39   }
  40
  41   @Test(groups = "Functional")
  42   public void testIsValidReference() throws Exception
  43   {
  44     EnsemblSequenceFetcher esq = new EnsemblProtein();
  45     Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
  46     Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
  47     Assert.assertFalse(esq.isValidReference("ENST00000288602"));
  48     Assert.assertFalse(esq.isValidReference("ENSG00000288602"));
  49     // non-human species having a 3 character identifier included:
  50     Assert.assertTrue(esq.isValidReference("ENSMUSP00000099398"));
  51   }
  52
  53   @Test(groups = "Functional")
  54   public void testGetAccesionIdFromQuery() throws Exception
  55   {
  56     EnsemblSequenceFetcher esq = new EnsemblProtein();
  57     assertEquals("ENSP00000288602",
  58             esq.getAccessionIdFromQuery("ENSP00000288602"));
  59     assertEquals("ENSMUSP00000288602",
  60             esq.getAccessionIdFromQuery("ENSMUSP00000288602"));
  61
  62     // ENST converted to ENSP
  63     assertEquals("ENSP00000288602",
  64             esq.getAccessionIdFromQuery("ENST00000288602"));
  65     assertEquals("ENSMUSP00000288602",
  66             esq.getAccessionIdFromQuery("ENSMUST00000288602"));
  67
  68     // with valid separator:
  69     assertEquals("ENSP00000288604",
  70             esq.getAccessionIdFromQuery("ENSP00000288604 ENSP00000288602"));
  71
  72     // with wrong separator:
  73     assertEquals("ENSP00000288604,ENSP00000288602",
  74             esq.getAccessionIdFromQuery("ENSP00000288604,ENSP00000288602"));
  75   }
  76
  77 }