2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.datamodel.xdb.embl;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertNull;
26 import jalview.datamodel.DBRefEntry;
28 import java.util.Vector;
30 import org.testng.annotations.Test;
32 public class EmblFileTest
35 @Test(groups = { "Functional" })
36 public void testGetEmblFile()
38 Vector<EmblEntry> entries = EmblTestHelper.getEmblFile().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());
47 assertEquals("mRNA", entry.getMoleculeType());
48 assertEquals("1", entry.getSequenceVersion());
49 assertEquals("3", entry.getEntryVersion());
50 assertEquals("linear", entry.getTopology());
51 assertEquals("1575", entry.getSequenceLength());
54 * FIXME these assertions fail - values are null - why?? Adding or removing
55 * attributes in the test XML modifies behaviour. eg. inserting an attribute
56 * _before_ lastUpdated results in a null value in this field.
58 // assertEquals("25", entry.getRCreated());
59 // assertEquals("83", entry.getRLastUpdated());
61 assertEquals(2, entry.getKeywords().size());
62 assertEquals("L-lactate dehydrogenase", entry.getKeywords().get(0));
63 assertEquals("chutney", entry.getKeywords().get(1));
68 assertEquals(2, entry.getDbRefs().size());
69 DBRefEntry dbref = entry.getDbRefs().get(0);
70 assertEquals("EuropePMC", dbref.getSource());
71 assertEquals("PMC1460223", dbref.getAccessionId());
72 assertEquals("9649548", dbref.getVersion());
73 dbref = entry.getDbRefs().get(1);
74 assertEquals("MD5", dbref.getSource());
75 assertEquals("d3b68", dbref.getAccessionId());
76 // blank version has been converted to "0"
77 assertEquals("0", dbref.getVersion());
80 * sequence feature for CDS
82 assertEquals(1, entry.getFeatures().size());
83 EmblFeature ef = entry.getFeatures().get(0);
84 assertEquals("CDS", ef.getName());
85 assertEquals("60..1058", ef.getLocation());
86 assertEquals(2, ef.getDbRefs().size());
87 dbref = ef.getDbRefs().get(0);
88 assertEquals("GOA", dbref.getSource());
89 assertEquals("P00340", dbref.getAccessionId());
90 assertEquals("2.1", dbref.getVersion());
91 dbref = ef.getDbRefs().get(1);
92 assertEquals("InterPro", dbref.getSource());
93 assertEquals("IPR001236", dbref.getAccessionId());
94 // blank version converted to "0":
95 assertEquals("0", dbref.getVersion());
96 assertEquals(2, ef.getQualifiers().size());
99 Qualifier q = ef.getQualifiers().get(0);
100 assertEquals("note", q.getName());
101 assertEquals(2, q.getValues().length);
102 assertEquals("L-lactate dehydrogenase A-chain", q.getValues()[0]);
103 assertEquals("pickle", q.getValues()[1]);
104 assertNull(q.getEvidence());
105 q = ef.getQualifiers().get(1);
106 assertEquals("translation", q.getName());
107 assertEquals(1, q.getValues().length);
108 assertEquals("MSLKDHLIHN", q.getValues()[0]);
109 assertEquals(1, q.getEvidence().length);
110 assertEquals("Keith", q.getEvidence()[0]);
115 EmblSequence seq = entry.getSequence();
116 assertEquals("GTGACG", seq.getSequence());
119 * getSequence() converts empty DBRefEntry.version to "0"
121 assertEquals("0", entry.getDbRefs().get(1).getVersion());
122 assertEquals("0", entry.getFeatures().get(0).getDbRefs().get(1)