2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
3 * Copyright (C) 2015 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.assertNotNull;
25 import static org.testng.AssertJUnit.assertNull;
27 import jalview.datamodel.PDBEntry;
28 import jalview.datamodel.SequenceFeature;
29 import jalview.datamodel.SequenceI;
30 import jalview.datamodel.UniprotEntry;
32 import java.io.Reader;
33 import java.io.StringReader;
34 import java.util.Vector;
36 import org.testng.annotations.Test;
38 public class UniprotTest
40 // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
41 private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
43 + "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
44 + "<accession>A9CKP4</accession>"
45 + "<accession>A9CKP5</accession>"
46 + "<name>A9CKP4_AGRT5</name>"
47 + "<name>A9CKP4_AGRT6</name>"
48 + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
49 + "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
50 + "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
51 + "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
52 + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
53 + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
54 + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
55 + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
59 * Test the method that unmarshals XML to a Uniprot model
61 @Test(groups = { "Functional" })
62 public void testGetUniprotEntries()
64 Uniprot u = new Uniprot();
65 Reader reader = new StringReader(UNIPROT_XML);
66 Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
67 assertEquals(1, entries.size());
68 UniprotEntry entry = entries.get(0);
69 assertEquals(2, entry.getName().size());
70 assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
71 assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
72 assertEquals(2, entry.getAccession().size());
73 assertEquals("A9CKP4", entry.getAccession().get(0));
74 assertEquals("A9CKP5", entry.getAccession().get(1));
77 * UniprotSequence drops any space characters
79 assertEquals("MHAPLVSKDL", entry.getUniprotSequence().getContent());
81 assertEquals(2, entry.getProtein().getName().size());
82 assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
84 assertEquals("Henry", entry.getProtein().getName().get(1));
87 * Check sequence features
89 Vector<SequenceFeature> features = entry.getFeature();
90 assertEquals(3, features.size());
91 SequenceFeature sf = features.get(0);
92 assertEquals("signal peptide", sf.getType());
93 assertNull(sf.getDescription());
94 assertNull(sf.getStatus());
95 assertEquals(1, sf.getPosition());
96 assertEquals(1, sf.getBegin());
97 assertEquals(18, sf.getEnd());
99 assertEquals("propeptide", sf.getType());
100 assertEquals("Activation peptide", sf.getDescription());
101 assertEquals(19, sf.getPosition());
102 assertEquals(19, sf.getBegin());
103 assertEquals(20, sf.getEnd());
104 sf = features.get(2);
105 assertEquals("chain", sf.getType());
106 assertEquals("Granzyme B", sf.getDescription());
107 assertEquals(21, sf.getPosition());
108 assertEquals(21, sf.getBegin());
109 assertEquals(247, sf.getEnd());
112 * Check cross-references
114 Vector<PDBEntry> xrefs = entry.getDbReference();
115 assertEquals(3, xrefs.size());
117 PDBEntry xref = xrefs.get(0);
118 assertEquals("2FSQ", xref.getId());
119 assertEquals("PDB", xref.getType());
120 assertEquals(2, xref.getProperty().size());
121 assertEquals("X-ray", xref.getProperty().get("method"));
122 assertEquals("1.40", xref.getProperty().get("resolution"));
125 assertEquals("2FSR", xref.getId());
126 assertEquals("PDBsum", xref.getType());
127 assertNull(xref.getProperty());
130 assertEquals("AE007869", xref.getId());
131 assertEquals("EMBL", xref.getType());
132 assertNotNull(xref.getProperty());
133 assertEquals("AAK85932.1",
134 (String) xref.getProperty().get("protein sequence ID"));
135 assertEquals("Genomic_DNA",
136 (String) xref.getProperty().get("molecule type"));
137 assertEquals(2, xref.getProperty().size());
141 @Test(groups = { "Functional" })
142 public void testGetUniprotSequence()
144 UniprotEntry entry = new Uniprot().getUniprotEntries(
145 new StringReader(UNIPROT_XML)).get(0);
146 SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
148 assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
153 * Test the method that formats the sequence id
155 @Test(groups = { "Functional" })
156 public void testGetUniprotEntryId()
158 UniprotEntry entry = new Uniprot().getUniprotEntries(
159 new StringReader(UNIPROT_XML)).get(0);
162 * name formatted as source | accession ids | names
163 * source database converted to Jalview canonical name
165 String expectedName = "UNIPROT|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
166 assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
170 * Test the method that formats the sequence description
172 @Test(groups = { "Functional" })
173 public void testGetUniprotEntryDescription()
175 UniprotEntry entry = new Uniprot().getUniprotEntries(
176 new StringReader(UNIPROT_XML)).get(0);
179 * recommended names concatenated with space separator
181 String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
182 assertEquals(expectedDescription,
183 Uniprot.getUniprotEntryDescription(entry));