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 + "<feature type=\"sequence variant\" description=\"Foo\"><variation>LL</variation><variation>LMV</variation><original>ML</original><location><begin position=\"42\"/><end position=\"43\"/></location></feature>"
72 + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
76 * Test the method that unmarshals XML to a Uniprot model
78 @Test(groups = { "Functional" })
79 public void testGetUniprotEntries()
81 Uniprot u = new Uniprot();
82 Reader reader = new StringReader(UNIPROT_XML);
83 Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
84 assertEquals(1, entries.size());
85 UniprotEntry entry = entries.get(0);
86 assertEquals(2, entry.getName().size());
87 assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
88 assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
89 assertEquals(2, entry.getAccession().size());
90 assertEquals("A9CKP4", entry.getAccession().get(0));
91 assertEquals("A9CKP5", entry.getAccession().get(1));
94 * UniprotSequence drops any space characters
96 assertEquals("MHAPLVSKDL", entry.getUniprotSequence().getContent());
98 assertEquals(2, entry.getProtein().getName().size());
99 assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
101 assertEquals("Henry", entry.getProtein().getName().get(1));
104 * Check sequence features
106 Vector<UniprotFeature> features = entry.getFeature();
107 assertEquals(8, features.size());
108 UniprotFeature sf = features.get(0);
109 assertEquals("signal peptide", sf.getType());
110 assertNull(sf.getDescription());
111 assertNull(sf.getStatus());
112 assertEquals(1, sf.getBegin());
113 assertEquals(18, sf.getEnd());
114 sf = features.get(1);
115 assertEquals("propeptide", sf.getType());
116 assertEquals("Activation peptide", sf.getDescription());
117 assertEquals(19, sf.getPosition());
118 assertEquals(19, sf.getBegin());
119 assertEquals(20, sf.getEnd());
120 sf = features.get(2);
121 assertEquals("chain", sf.getType());
122 assertEquals("Granzyme B", sf.getDescription());
123 assertEquals(21, sf.getPosition());
124 assertEquals(21, sf.getBegin());
125 assertEquals(247, sf.getEnd());
127 sf = features.get(3);
128 assertEquals("sequence variant", sf.getType());
129 assertNull(sf.getDescription());
130 assertEquals(41, sf.getPosition());
131 assertEquals(41, sf.getBegin());
132 assertEquals(41, sf.getEnd());
134 sf = features.get(4);
135 assertEquals("sequence variant", sf.getType());
136 assertEquals("Pathogenic", sf.getDescription());
137 assertEquals(41, sf.getPosition());
138 assertEquals(41, sf.getBegin());
139 assertEquals(41, sf.getEnd());
141 sf = features.get(5);
142 assertEquals("sequence variant", sf.getType());
143 assertEquals("Pathogenic", sf.getDescription());
144 assertEquals(41, sf.getPosition());
145 assertEquals(41, sf.getBegin());
146 assertEquals(41, sf.getEnd());
148 sf = features.get(6);
149 assertEquals("sequence variant", sf.getType());
151 sf.getDescription());
152 assertEquals(42, sf.getPosition());
153 assertEquals(42, sf.getBegin());
154 assertEquals(42, sf.getEnd());
155 Assert.assertEquals(Uniprot.getDescription(sf),
156 "p.Met42Leu" + "\n" + "p.Met42LeuMetVal Foo");
158 sf = features.get(7);
159 assertEquals(42, sf.getBegin());
160 assertEquals(43, sf.getEnd());
161 Assert.assertEquals(Uniprot.getDescription(sf),
162 "p.MetLeu42LeuLeu" + "\n" + "p.MetLeu42LeuMetVal Foo"); /*
163 * Check cross-references
165 Vector<PDBEntry> xrefs = entry.getDbReference();
166 assertEquals(3, xrefs.size());
168 PDBEntry xref = xrefs.get(0);
169 assertEquals("2FSQ", xref.getId());
170 assertEquals("PDB", xref.getType());
171 assertEquals("X-ray", xref.getProperty("method"));
172 assertEquals("1.40", xref.getProperty("resolution"));
175 assertEquals("2FSR", xref.getId());
176 assertEquals("PDBsum", xref.getType());
177 assertFalse(xref.getProperties().hasMoreElements());
180 assertEquals("AE007869", xref.getId());
181 assertEquals("EMBL", xref.getType());
182 assertEquals("AAK85932.1", xref.getProperty("protein sequence ID"));
183 assertEquals("Genomic_DNA", xref.getProperty("molecule type"));
186 @Test(groups = { "Functional" })
187 public void testGetUniprotSequence()
189 UniprotEntry entry = new Uniprot().getUniprotEntries(
190 new StringReader(UNIPROT_XML)).get(0);
191 SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
193 assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
198 * Test the method that formats the sequence id
200 @Test(groups = { "Functional" })
201 public void testGetUniprotEntryId()
203 UniprotEntry entry = new Uniprot().getUniprotEntries(
204 new StringReader(UNIPROT_XML)).get(0);
207 * name formatted with Uniprot Entry name
209 String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
210 assertEquals(expectedName,
211 Uniprot.getUniprotEntryId(entry));
215 * Test the method that formats the sequence description
217 @Test(groups = { "Functional" })
218 public void testGetUniprotEntryDescription()
220 UniprotEntry entry = new Uniprot().getUniprotEntries(
221 new StringReader(UNIPROT_XML)).get(0);
224 * recommended names concatenated with space separator
226 String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
227 assertEquals(expectedDescription,
228 Uniprot.getUniprotEntryDescription(entry));
231 @Test(groups = { "Functional" })
232 public void testGetDescription()
234 UniprotFeature uf = new UniprotFeature();
235 assertEquals("", Uniprot.getDescription(uf));
237 uf.setDescription("Hello");
238 assertEquals("Hello", Uniprot.getDescription(uf));
242 Vector<String> vars = new Vector();
244 uf.setVariation(vars);
245 assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
248 vars.add("z"); // unknown variant - fails gracefully
249 uf.setVariation(vars);
250 assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
252 uf.setVariation(null); // variant missing - is ignored
253 assertEquals("Hello", Uniprot.getDescription(uf));