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.annotations.BeforeClass;
39 import org.testng.annotations.Test;
41 public class UniprotTest
44 @BeforeClass(alwaysRun = true)
45 public void setUpJvOptionPane()
47 JvOptionPane.setInteractiveMode(false);
48 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51 // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
52 private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
54 + "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
55 + "<accession>A9CKP4</accession>"
56 + "<accession>A9CKP5</accession>"
57 + "<name>A9CKP4_AGRT5</name>"
58 + "<name>A9CKP4_AGRT6</name>"
59 + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
60 + "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
61 + "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
62 + "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
63 + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
64 + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
65 + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
66 + "<feature type=\"sequence variant\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
67 + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
68 + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><location><position position=\"41\"/></location></feature>"
69 + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
73 * Test the method that unmarshals XML to a Uniprot model
75 @Test(groups = { "Functional" })
76 public void testGetUniprotEntries()
78 Uniprot u = new Uniprot();
79 Reader reader = new StringReader(UNIPROT_XML);
80 Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
81 assertEquals(1, entries.size());
82 UniprotEntry entry = entries.get(0);
83 assertEquals(2, entry.getName().size());
84 assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
85 assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
86 assertEquals(2, entry.getAccession().size());
87 assertEquals("A9CKP4", entry.getAccession().get(0));
88 assertEquals("A9CKP5", entry.getAccession().get(1));
91 * UniprotSequence drops any space characters
93 assertEquals("MHAPLVSKDL", entry.getUniprotSequence().getContent());
95 assertEquals(2, entry.getProtein().getName().size());
96 assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
98 assertEquals("Henry", entry.getProtein().getName().get(1));
101 * Check sequence features
103 Vector<UniprotFeature> features = entry.getFeature();
104 assertEquals(6, features.size());
105 UniprotFeature sf = features.get(0);
106 assertEquals("signal peptide", sf.getType());
107 assertNull(sf.getDescription());
108 assertNull(sf.getStatus());
109 assertEquals(1, sf.getBegin());
110 assertEquals(18, sf.getEnd());
111 sf = features.get(1);
112 assertEquals("propeptide", sf.getType());
113 assertEquals("Activation peptide", sf.getDescription());
114 assertEquals(19, sf.getPosition());
115 assertEquals(19, sf.getBegin());
116 assertEquals(20, sf.getEnd());
117 sf = features.get(2);
118 assertEquals("chain", sf.getType());
119 assertEquals("Granzyme B", sf.getDescription());
120 assertEquals(21, sf.getPosition());
121 assertEquals(21, sf.getBegin());
122 assertEquals(247, sf.getEnd());
124 sf = features.get(3);
125 assertEquals("sequence variant", sf.getType());
126 assertNull(sf.getDescription());
127 assertEquals(41, sf.getPosition());
128 assertEquals(41, sf.getBegin());
129 assertEquals(41, sf.getEnd());
131 sf = features.get(4);
132 assertEquals("sequence variant", sf.getType());
133 assertEquals("Pathogenic", sf.getDescription());
134 assertEquals(41, sf.getPosition());
135 assertEquals(41, sf.getBegin());
136 assertEquals(41, sf.getEnd());
138 sf = features.get(5);
139 assertEquals("sequence variant", sf.getType());
140 assertEquals("Pathogenic", sf.getDescription());
141 assertEquals(41, sf.getPosition());
142 assertEquals(41, sf.getBegin());
143 assertEquals(41, sf.getEnd());
145 * Check cross-references
147 Vector<PDBEntry> xrefs = entry.getDbReference();
148 assertEquals(3, xrefs.size());
150 PDBEntry xref = xrefs.get(0);
151 assertEquals("2FSQ", xref.getId());
152 assertEquals("PDB", xref.getType());
153 assertEquals("X-ray", xref.getProperty("method"));
154 assertEquals("1.40", xref.getProperty("resolution"));
157 assertEquals("2FSR", xref.getId());
158 assertEquals("PDBsum", xref.getType());
159 assertFalse(xref.getProperties().hasMoreElements());
162 assertEquals("AE007869", xref.getId());
163 assertEquals("EMBL", xref.getType());
164 assertEquals("AAK85932.1", xref.getProperty("protein sequence ID"));
165 assertEquals("Genomic_DNA", xref.getProperty("molecule type"));
168 @Test(groups = { "Functional" })
169 public void testGetUniprotSequence()
171 UniprotEntry entry = new Uniprot().getUniprotEntries(
172 new StringReader(UNIPROT_XML)).get(0);
173 SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
175 assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
180 * Test the method that formats the sequence id
182 @Test(groups = { "Functional" })
183 public void testGetUniprotEntryId()
185 UniprotEntry entry = new Uniprot().getUniprotEntries(
186 new StringReader(UNIPROT_XML)).get(0);
189 * name formatted with Uniprot Entry name
191 String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
192 assertEquals(expectedName,
193 Uniprot.getUniprotEntryId(entry));
197 * Test the method that formats the sequence description
199 @Test(groups = { "Functional" })
200 public void testGetUniprotEntryDescription()
202 UniprotEntry entry = new Uniprot().getUniprotEntries(
203 new StringReader(UNIPROT_XML)).get(0);
206 * recommended names concatenated with space separator
208 String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
209 assertEquals(expectedDescription,
210 Uniprot.getUniprotEntryDescription(entry));
213 @Test(groups = { "Functional" })
214 public void testGetDescription()
216 UniprotFeature uf = new UniprotFeature();
217 assertEquals("", Uniprot.getDescription(uf));
219 uf.setDescription("Hello");
220 assertEquals("Hello", Uniprot.getDescription(uf));
224 uf.setVariation("y");
225 assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
227 uf.setVariation("z"); // unknown variant - fails gracefully
228 assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
230 uf.setVariation(null); // variant missing - is ignored
231 assertEquals("Hello", Uniprot.getDescription(uf));