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.ws.dbsources;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNotNull;
26 import static org.testng.AssertJUnit.assertNull;
28 import jalview.datamodel.PDBEntry;
29 import jalview.datamodel.SequenceI;
30 import jalview.datamodel.xdb.uniprot.UniprotEntry;
31 import jalview.datamodel.xdb.uniprot.UniprotFeature;
32 import jalview.gui.JvOptionPane;
34 import java.io.Reader;
35 import java.io.StringReader;
36 import java.util.Vector;
38 import org.testng.Assert;
39 import org.testng.annotations.BeforeClass;
40 import org.testng.annotations.Test;
42 public class UniprotTest
45 @BeforeClass(alwaysRun = true)
46 public void setUpJvOptionPane()
48 JvOptionPane.setInteractiveMode(false);
49 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
52 // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
53 private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
55 + "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
56 + "<accession>A9CKP4</accession>"
57 + "<accession>A9CKP5</accession>"
58 + "<name>A9CKP4_AGRT5</name>"
59 + "<name>A9CKP4_AGRT6</name>"
60 + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
61 + "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
62 + "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
63 + "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
64 + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
65 + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
66 + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
67 + "<feature type=\"sequence variant\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
68 + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
69 + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><location><position position=\"41\"/></location></feature>"
70 + "<feature type=\"sequence variant\" description=\"Foo\"><variation>L</variation><variation>LMV</variation><original>M</original><location><position position=\"42\"/></location></feature>"
71 + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
75 * Test the method that unmarshals XML to a Uniprot model
77 @Test(groups = { "Functional" })
78 public void testGetUniprotEntries()
80 Uniprot u = new Uniprot();
81 Reader reader = new StringReader(UNIPROT_XML);
82 Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
83 assertEquals(1, entries.size());
84 UniprotEntry entry = entries.get(0);
85 assertEquals(2, entry.getName().size());
86 assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
87 assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
88 assertEquals(2, entry.getAccession().size());
89 assertEquals("A9CKP4", entry.getAccession().get(0));
90 assertEquals("A9CKP5", entry.getAccession().get(1));
93 * UniprotSequence drops any space characters
95 assertEquals("MHAPLVSKDL", entry.getUniprotSequence().getContent());
97 assertEquals(2, entry.getProtein().getName().size());
98 assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
100 assertEquals("Henry", entry.getProtein().getName().get(1));
103 * Check sequence features
105 Vector<UniprotFeature> features = entry.getFeature();
106 assertEquals(7, features.size());
107 UniprotFeature sf = features.get(0);
108 assertEquals("signal peptide", sf.getType());
109 assertNull(sf.getDescription());
110 assertNull(sf.getStatus());
111 assertEquals(1, sf.getBegin());
112 assertEquals(18, sf.getEnd());
113 sf = features.get(1);
114 assertEquals("propeptide", sf.getType());
115 assertEquals("Activation peptide", sf.getDescription());
116 assertEquals(19, sf.getPosition());
117 assertEquals(19, sf.getBegin());
118 assertEquals(20, sf.getEnd());
119 sf = features.get(2);
120 assertEquals("chain", sf.getType());
121 assertEquals("Granzyme B", sf.getDescription());
122 assertEquals(21, sf.getPosition());
123 assertEquals(21, sf.getBegin());
124 assertEquals(247, sf.getEnd());
126 sf = features.get(3);
127 assertEquals("sequence variant", sf.getType());
128 assertNull(sf.getDescription());
129 assertEquals(41, sf.getPosition());
130 assertEquals(41, sf.getBegin());
131 assertEquals(41, sf.getEnd());
133 sf = features.get(4);
134 assertEquals("sequence variant", sf.getType());
135 assertEquals("Pathogenic", sf.getDescription());
136 assertEquals(41, sf.getPosition());
137 assertEquals(41, sf.getBegin());
138 assertEquals(41, sf.getEnd());
140 sf = features.get(5);
141 assertEquals("sequence variant", sf.getType());
142 assertEquals("Pathogenic", sf.getDescription());
143 assertEquals(41, sf.getPosition());
144 assertEquals(41, sf.getBegin());
145 assertEquals(41, sf.getEnd());
147 sf = features.get(6);
148 assertEquals("sequence variant", sf.getType());
150 sf.getDescription());
151 assertEquals(42, sf.getPosition());
152 assertEquals(42, sf.getBegin());
153 assertEquals(42, sf.getEnd());
154 Assert.assertEquals(Uniprot.getDescription(sf),
155 "p.Met42Leu<br/>p.Met42LeuMetVal Foo");
157 * Check cross-references
159 Vector<PDBEntry> xrefs = entry.getDbReference();
160 assertEquals(3, xrefs.size());
162 PDBEntry xref = xrefs.get(0);
163 assertEquals("2FSQ", xref.getId());
164 assertEquals("PDB", xref.getType());
165 assertEquals("X-ray", xref.getProperty("method"));
166 assertEquals("1.40", xref.getProperty("resolution"));
169 assertEquals("2FSR", xref.getId());
170 assertEquals("PDBsum", xref.getType());
171 assertFalse(xref.getProperties().hasMoreElements());
174 assertEquals("AE007869", xref.getId());
175 assertEquals("EMBL", xref.getType());
176 assertEquals("AAK85932.1", xref.getProperty("protein sequence ID"));
177 assertEquals("Genomic_DNA", xref.getProperty("molecule type"));
180 @Test(groups = { "Functional" })
181 public void testGetUniprotSequence()
183 UniprotEntry entry = new Uniprot().getUniprotEntries(
184 new StringReader(UNIPROT_XML)).get(0);
185 SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
187 assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
192 * Test the method that formats the sequence id
194 @Test(groups = { "Functional" })
195 public void testGetUniprotEntryId()
197 UniprotEntry entry = new Uniprot().getUniprotEntries(
198 new StringReader(UNIPROT_XML)).get(0);
201 * name formatted with Uniprot Entry name
203 String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
204 assertEquals(expectedName,
205 Uniprot.getUniprotEntryId(entry));
209 * Test the method that formats the sequence description
211 @Test(groups = { "Functional" })
212 public void testGetUniprotEntryDescription()
214 UniprotEntry entry = new Uniprot().getUniprotEntries(
215 new StringReader(UNIPROT_XML)).get(0);
218 * recommended names concatenated with space separator
220 String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
221 assertEquals(expectedDescription,
222 Uniprot.getUniprotEntryDescription(entry));
225 @Test(groups = { "Functional" })
226 public void testGetDescription()
228 UniprotFeature uf = new UniprotFeature();
229 assertEquals("", Uniprot.getDescription(uf));
231 uf.setDescription("Hello");
232 assertEquals("Hello", Uniprot.getDescription(uf));
236 Vector<String> vars = new Vector();
238 uf.setVariation(vars);
239 assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
242 vars.add("z"); // unknown variant - fails gracefully
243 uf.setVariation(vars);
244 assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
246 uf.setVariation(null); // variant missing - is ignored
247 assertEquals("Hello", Uniprot.getDescription(uf));