test/jalview/ws/dbsources/UniprotTest.java

   1 package jalview.ws.dbsources;
   2
   3 import static org.junit.Assert.assertEquals;
   4 import static org.junit.Assert.assertNull;
   5
   6 import java.io.Reader;
   7 import java.io.StringReader;
   8 import java.util.Vector;
   9
  10 import org.junit.Test;
  11
  12 import jalview.datamodel.PDBEntry;
  13 import jalview.datamodel.SequenceFeature;
  14 import jalview.datamodel.UniprotEntry;
  15
  16 public class UniprotTest
  17 {
  18   // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
  19   private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
  20           + "<uniprot>"
  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>"
  33           + "</uniprot>";
  34
  35   /**
  36    * Test the method that unmarshals XML to a Uniprot model
  37    */
  38   @Test
  39   public void testGetUniprotEntries()
  40   {
  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));
  52
  53     /*
  54      * UniprotSequence drops any space characters
  55      */
  56     assertEquals("MHAPLVSKDL", entry.getUniprotSequence()
  57             .getContent());
  58
  59     assertEquals(2, entry.getProtein().getName().size());
  60     assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
  61             .getName().get(0));
  62     assertEquals("Henry", entry.getProtein().getName().get(1));
  63
  64     /*
  65      * Check sequence features
  66      */
  67     Vector<SequenceFeature> features = entry.getFeature();
  68     assertEquals(3, features.size());
  69     SequenceFeature sf = features.get(0);
  70     assertEquals("signal peptide", sf.getType());
  71     assertNull(sf.getDescription());
  72     assertNull(sf.getStatus());
  73     assertEquals(1, sf.getPosition()); // wrong - Castor bug??
  74     assertEquals(1, sf.getBegin());
  75     assertEquals(18, sf.getEnd());
  76     sf = features.get(1);
  77     assertEquals("propeptide", sf.getType());
  78     assertEquals("Activation peptide", sf.getDescription());
  79     assertEquals(19, sf.getPosition()); // wrong - Castor bug??
  80     assertEquals(19, sf.getBegin());
  81     assertEquals(20, sf.getEnd());
  82     sf = features.get(2);
  83     assertEquals("chain", sf.getType());
  84     assertEquals("Granzyme B", sf.getDescription());
  85     assertEquals(21, sf.getPosition()); // wrong - Castor bug??
  86     assertEquals(21, sf.getBegin());
  87     assertEquals(247, sf.getEnd());
  88
  89     /*
  90      * Check cross-references
  91      */
  92     Vector<PDBEntry> xrefs = entry.getDbReference();
  93     assertEquals(2, xrefs.size());
  94
  95     PDBEntry xref = xrefs.get(0);
  96     assertEquals("2FSQ", xref.getId());
  97     assertEquals("PDB", xref.getType());
  98     assertEquals(2, xref.getProperty().size());
  99     assertEquals("X-ray", xref.getProperty().get("method"));
 100     assertEquals("1.40", xref.getProperty().get("resolution"));
 101
 102     xref = xrefs.get(1);
 103     assertEquals("2FSR", xref.getId());
 104     assertEquals("PDBsum", xref.getType());
 105     assertNull(xref.getProperty());
 106   }
 107
 108   /**
 109    * Test the method that formats the sequence name in Fasta style
 110    */
 111   @Test
 112   public void testConstructSequenceFastaHeader()
 113   {
 114     Uniprot u = new Uniprot();
 115     Reader reader = new StringReader(UNIPROT_XML);
 116     Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
 117     UniprotEntry entry = entries.get(0);
 118
 119     // source + accession ids + names + protein names
 120     String expectedName = ">UniProt/Swiss-Prot|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6 Mitogen-activated protein kinase 13 Henry";
 121     assertEquals(expectedName, Uniprot.constructSequenceFastaHeader(entry)
 122             .toString());
 123   }
 124 }