test/jalview/ext/ensembl/EnsemblProteinTest.java

   1 package jalview.ext.ensembl;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4
   5 import org.testng.Assert;
   6 import org.testng.annotations.Test;
   7
   8 public class EnsemblProteinTest
   9 {
  10
  11   @Test(groups = "Functional")
  12   public void testIsValidReference() throws Exception
  13   {
  14     EnsemblSequenceFetcher esq = new EnsemblProtein();
  15     Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
  16     Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
  17     Assert.assertFalse(esq.isValidReference("ENST00000288602"));
  18     Assert.assertFalse(esq.isValidReference("ENSG00000288602"));
  19     // non-human species having a 3 character identifier included:
  20     Assert.assertTrue(esq.isValidReference("ENSMUSP00000099398"));
  21   }
  22
  23   @Test(groups = "Functional")
  24   public void testGetAccesionIdFromQuery() throws Exception
  25   {
  26     EnsemblSequenceFetcher esq = new EnsemblProtein();
  27     assertEquals("ENSP00000288602",
  28             esq.getAccessionIdFromQuery("ENSP00000288602"));
  29     assertEquals("ENSMUSP00000288602",
  30             esq.getAccessionIdFromQuery("ENSMUSP00000288602"));
  31
  32     // ENST converted to ENSP
  33     assertEquals("ENSP00000288602",
  34             esq.getAccessionIdFromQuery("ENST00000288602"));
  35     assertEquals("ENSMUSP00000288602",
  36             esq.getAccessionIdFromQuery("ENSMUST00000288602"));
  37
  38     // with valid separator:
  39     assertEquals("ENSP00000288604",
  40             esq.getAccessionIdFromQuery("ENSP00000288604 ENSP00000288602"));
  41
  42     // with wrong separator:
  43     assertEquals("ENSP00000288604,ENSP00000288602",
  44             esq.getAccessionIdFromQuery("ENSP00000288604,ENSP00000288602"));
  45   }
  46
  47 }