test/jalview/datamodel/xdb/embl/EmblFileTest.java

   1 package jalview.datamodel.xdb.embl;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4 import static org.testng.AssertJUnit.assertFalse;
   5 import static org.testng.AssertJUnit.assertNull;
   6 import static org.testng.AssertJUnit.assertTrue;
   7
   8 import jalview.datamodel.DBRefEntry;
   9
  10 import java.io.StringReader;
  11 import java.util.Vector;
  12
  13 import org.testng.annotations.Test;
  14
  15 public class EmblFileTest
  16 {
  17   // adapted from http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
  18   private static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
  19           + "<EMBL_Services>"
  20           + "<entry accession=\"X53828\" version=\"3\" lastUpdated=\"2005-04-18\" releaseCreated=\"25\" releaseLastUpdated=\"83\">"
  21           + "<description>Chicken LDH-A mRNA for lactate dehydrogenase A chain (EC 1.1.1.27)</description>"
  22           + "<keyword>L-lactate dehydrogenase</keyword><keyword>chutney</keyword>"
  23           + "<dbreference db=\"EuropePMC\" primary=\"PMC1460223\" secondary=\"9649548\" />"
  24           + "<feature name=\"CDS\"><dbreference db=\"GOA\" primary=\"P00340\" secondary=\"2.1\" /><dbreference db=\"InterPro\" primary=\"IPR001236\" />"
  25           + "<qualifier name=\"note\"><value>L-lactate dehydrogenase A-chain</value><value>pickle</value></qualifier>"
  26           + "<qualifier name=\"translation\"><value>MSLKDHLIHN</value><evidence>Keith</evidence></qualifier>"
  27           + "<location type=\"single\" complement=\"true\">"
  28           + "<locationElement type=\"range\" accession=\"X53828\" version=\"1\" complement=\"false\">"
  29           + "<basePosition type=\"simple\">60</basePosition><basePosition type=\"join\">1058</basePosition>"
  30           + "</locationElement></location></feature>"
  31           + "<sequence type=\"mRNA\" version=\"2\">GTGACG</sequence></entry></EMBL_Services>";
  32
  33   @Test(groups = { "Functional" })
  34   public void testGetEmblFile()
  35   {
  36     Vector<EmblEntry> entries = EmblFile.getEmblFile(
  37             new StringReader(TESTDATA)).getEntries();
  38     assertEquals(1, entries.size());
  39     EmblEntry entry = entries.get(0);
  40
  41     assertEquals("X53828", entry.getAccession());
  42     assertEquals(
  43             "Chicken LDH-A mRNA for lactate dehydrogenase A chain (EC 1.1.1.27)",
  44             entry.getDesc());
  45     assertEquals("2005-04-18", entry.getLastUpdated());
  46
  47     /*
  48      * FIXME these assertions fail - values are null - why?? Adding or removing
  49      * attributes in the test XML modifies behaviour. eg. inserting an attribute
  50      * _before_ lastUpdated results in a null value in this field.
  51      */
  52     // assertEquals("25", entry.getRCreated());
  53     // assertEquals("83", entry.getRLastUpdated());
  54
  55     assertEquals(2, entry.getKeywords().size());
  56     assertEquals("L-lactate dehydrogenase", entry.getKeywords().get(0));
  57     assertEquals("chutney", entry.getKeywords().get(1));
  58
  59     /*
  60      * dbrefs
  61      */
  62     assertEquals(1, entry.getDbRefs().size());
  63     DBRefEntry dbref = entry.getDbRefs().get(0);
  64     assertEquals("EuropePMC", dbref.getSource());
  65     assertEquals("PMC1460223", dbref.getAccessionId());
  66     assertEquals("9649548", dbref.getVersion());
  67
  68     /*
  69      * sequence features
  70      */
  71     assertEquals(1, entry.getFeatures().size());
  72     EmblFeature ef = entry.getFeatures().get(0);
  73     assertEquals("CDS", ef.getName());
  74     assertEquals(2, ef.getDbRefs().size());
  75     dbref = ef.getDbRefs().get(0);
  76     assertEquals("GOA", dbref.getSource());
  77     assertEquals("P00340", dbref.getAccessionId());
  78     assertEquals("2.1", dbref.getVersion());
  79     dbref = ef.getDbRefs().get(1);
  80     assertEquals("InterPro", dbref.getSource());
  81     assertEquals("IPR001236", dbref.getAccessionId());
  82     assertEquals("", dbref.getVersion());
  83     assertEquals(2, ef.getQualifiers().size());
  84
  85     // feature qualifiers
  86     Qualifier q = ef.getQualifiers().get(0);
  87     assertEquals("note", q.getName());
  88     assertEquals(2, q.getValues().length);
  89     assertEquals("L-lactate dehydrogenase A-chain", q.getValues()[0]);
  90     assertEquals("pickle", q.getValues()[1]);
  91     assertNull(q.getEvidence());
  92     q = ef.getQualifiers().get(1);
  93     assertEquals("translation", q.getName());
  94     assertEquals(1, q.getValues().length);
  95     assertEquals("MSLKDHLIHN", q.getValues()[0]);
  96     assertEquals(1, q.getEvidence().length);
  97     assertEquals("Keith", q.getEvidence()[0]);
  98
  99     // feature locations
 100     assertEquals(1, ef.getLocations().size());
 101     EmblFeatureLocations fl = ef.getLocations().get(0);
 102     assertEquals("single", fl.getLocationType());
 103     assertTrue(fl.isLocationComplement());
 104     assertEquals(1, fl.getLocElements().size());
 105     EmblFeatureLocElement le = fl.getLocElements().get(0);
 106     assertEquals("range", le.getType());
 107     assertEquals("X53828", le.getAccession());
 108     assertEquals("1", le.getVersion());
 109     assertFalse(le.isComplement());
 110     assertEquals(2, le.getBasePositions().length);
 111     BasePosition bp = le.getBasePositions()[0];
 112     assertEquals("simple", bp.getType());
 113     assertEquals("60", bp.getPos());
 114     bp = le.getBasePositions()[1];
 115     assertEquals("join", bp.getType());
 116     assertEquals("1058", bp.getPos());
 117
 118     /*
 119      * Sequence
 120      */
 121     EmblSequence seq = entry.getSequence();
 122     assertEquals("mRNA", seq.getType());
 123     assertEquals("2", seq.getVersion());
 124     assertEquals("GTGACG", seq.getSequence());
 125   }
 126 }