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