1 package jalview.ws.dbsources;
3 import static org.testng.AssertJUnit.assertEquals;
4 import static org.testng.AssertJUnit.assertNull;
6 import jalview.datamodel.PDBEntry;
7 import jalview.datamodel.SequenceFeature;
8 import jalview.datamodel.UniprotEntry;
10 import java.io.Reader;
11 import java.io.StringReader;
12 import java.util.Vector;
14 import org.testng.annotations.Test;
16 public class UniprotTest
18 // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
19 private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
21 + "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
22 + "<accession>A9CKP4</accession>"
23 + "<accession>A9CKP5</accession>"
24 + "<name>A9CKP4_AGRT5</name>"
25 + "<name>A9CKP4_AGRT6</name>"
26 + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
27 + "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
28 + "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
29 + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
30 + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
31 + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
32 + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
36 * Test the method that unmarshals XML to a Uniprot model
38 @Test(groups = { "Functional" })
39 public void testGetUniprotEntries()
41 Uniprot u = new Uniprot();
42 Reader reader = new StringReader(UNIPROT_XML);
43 Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
44 assertEquals(1, entries.size());
45 UniprotEntry entry = entries.get(0);
46 assertEquals(2, entry.getName().size());
47 assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
48 assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
49 assertEquals(2, entry.getAccession().size());
50 assertEquals("A9CKP4", entry.getAccession().get(0));
51 assertEquals("A9CKP5", entry.getAccession().get(1));
54 * UniprotSequence drops any space characters
56 assertEquals("MHAPLVSKDL", entry.getUniprotSequence().getContent());
58 assertEquals(2, entry.getProtein().getName().size());
59 assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
61 assertEquals("Henry", entry.getProtein().getName().get(1));
64 * Check sequence features
66 Vector<SequenceFeature> features = entry.getFeature();
67 assertEquals(3, features.size());
68 SequenceFeature sf = features.get(0);
69 assertEquals("signal peptide", sf.getType());
70 assertNull(sf.getDescription());
71 assertNull(sf.getStatus());
72 assertEquals(1, sf.getPosition()); // wrong - Castor bug??
73 assertEquals(1, sf.getBegin());
74 assertEquals(18, sf.getEnd());
76 assertEquals("propeptide", sf.getType());
77 assertEquals("Activation peptide", sf.getDescription());
78 assertEquals(19, sf.getPosition()); // wrong - Castor bug??
79 assertEquals(19, sf.getBegin());
80 assertEquals(20, sf.getEnd());
82 assertEquals("chain", sf.getType());
83 assertEquals("Granzyme B", sf.getDescription());
84 assertEquals(21, sf.getPosition()); // wrong - Castor bug??
85 assertEquals(21, sf.getBegin());
86 assertEquals(247, sf.getEnd());
89 * Check cross-references
91 Vector<PDBEntry> xrefs = entry.getDbReference();
92 assertEquals(2, xrefs.size());
94 PDBEntry xref = xrefs.get(0);
95 assertEquals("2FSQ", xref.getId());
96 assertEquals("PDB", xref.getType());
97 assertEquals(2, xref.getProperty().size());
98 assertEquals("X-ray", xref.getProperty().get("method"));
99 assertEquals("1.40", xref.getProperty().get("resolution"));
102 assertEquals("2FSR", xref.getId());
103 assertEquals("PDBsum", xref.getType());
104 assertNull(xref.getProperty());
108 * Test the method that formats the sequence name in Fasta style
110 @Test(groups = { "Functional" })
111 public void testConstructSequenceFastaHeader()
113 Uniprot u = new Uniprot();
114 Reader reader = new StringReader(UNIPROT_XML);
115 Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
116 UniprotEntry entry = entries.get(0);
118 // source + accession ids + names + protein names
119 String expectedName = ">UniProt/Swiss-Prot|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6 Mitogen-activated protein kinase 13 Henry";
120 assertEquals(expectedName, Uniprot.constructSequenceFastaHeader(entry)