test/jalview/ws/dbsources/UniprotTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   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.
  11  *
  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.
  16  *
  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.
  20  */
  21 package jalview.ws.dbsources;
  22
  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;
  27
  28 import jalview.datamodel.PDBEntry;
  29 import jalview.datamodel.SequenceFeature;
  30 import jalview.datamodel.SequenceI;
  31 import jalview.datamodel.UniprotEntry;
  32
  33 import java.io.Reader;
  34 import java.io.StringReader;
  35 import java.util.Vector;
  36
  37 import org.testng.annotations.Test;
  38
  39 public class UniprotTest
  40 {
  41   // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
  42   private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
  43           + "<uniprot>"
  44           + "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
  45           + "<accession>A9CKP4</accession>"
  46           + "<accession>A9CKP5</accession>"
  47           + "<name>A9CKP4_AGRT5</name>"
  48           + "<name>A9CKP4_AGRT6</name>"
  49           + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
  50           + "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
  51           + "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
  52           + "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
  53           + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
  54           + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
  55           + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
  56           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
  57           + "</uniprot>";
  58
  59   /**
  60    * Test the method that unmarshals XML to a Uniprot model
  61    */
  62   @Test(groups = { "Functional" })
  63   public void testGetUniprotEntries()
  64   {
  65     Uniprot u = new Uniprot();
  66     Reader reader = new StringReader(UNIPROT_XML);
  67     Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
  68     assertEquals(1, entries.size());
  69     UniprotEntry entry = entries.get(0);
  70     assertEquals(2, entry.getName().size());
  71     assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
  72     assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
  73     assertEquals(2, entry.getAccession().size());
  74     assertEquals("A9CKP4", entry.getAccession().get(0));
  75     assertEquals("A9CKP5", entry.getAccession().get(1));
  76
  77     /*
  78      * UniprotSequence drops any space characters
  79      */
  80     assertEquals("MHAPLVSKDL", entry.getUniprotSequence().getContent());
  81
  82     assertEquals(2, entry.getProtein().getName().size());
  83     assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
  84             .getName().get(0));
  85     assertEquals("Henry", entry.getProtein().getName().get(1));
  86
  87     /*
  88      * Check sequence features
  89      */
  90     Vector<SequenceFeature> features = entry.getFeature();
  91     assertEquals(3, features.size());
  92     SequenceFeature sf = features.get(0);
  93     assertEquals("signal peptide", sf.getType());
  94     assertNull(sf.getDescription());
  95     assertNull(sf.getStatus());
  96     assertEquals(1, sf.getPosition());
  97     assertEquals(1, sf.getBegin());
  98     assertEquals(18, sf.getEnd());
  99     sf = features.get(1);
 100     assertEquals("propeptide", sf.getType());
 101     assertEquals("Activation peptide", sf.getDescription());
 102     assertEquals(19, sf.getPosition());
 103     assertEquals(19, sf.getBegin());
 104     assertEquals(20, sf.getEnd());
 105     sf = features.get(2);
 106     assertEquals("chain", sf.getType());
 107     assertEquals("Granzyme B", sf.getDescription());
 108     assertEquals(21, sf.getPosition());
 109     assertEquals(21, sf.getBegin());
 110     assertEquals(247, sf.getEnd());
 111
 112     /*
 113      * Check cross-references
 114      */
 115     Vector<PDBEntry> xrefs = entry.getDbReference();
 116     assertEquals(3, xrefs.size());
 117
 118     PDBEntry xref = xrefs.get(0);
 119     assertEquals("2FSQ", xref.getId());
 120     assertEquals("PDB", xref.getType());
 121     assertEquals("X-ray", xref.getProperty("method"));
 122     assertEquals("1.40", xref.getProperty("resolution"));
 123
 124     xref = xrefs.get(1);
 125     assertEquals("2FSR", xref.getId());
 126     assertEquals("PDBsum", xref.getType());
 127     assertFalse(xref.getProperties().hasMoreElements());
 128
 129     xref = xrefs.get(2);
 130     assertEquals("AE007869", xref.getId());
 131     assertEquals("EMBL", xref.getType());
 132     assertEquals("AAK85932.1",
 133  xref.getProperty("protein sequence ID"));
 134     assertEquals("Genomic_DNA",
 135  xref.getProperty("molecule type"));
 136   }
 137
 138   @Test(groups = { "Functional" })
 139   public void testGetUniprotSequence()
 140   {
 141     UniprotEntry entry = new Uniprot().getUniprotEntries(
 142             new StringReader(UNIPROT_XML)).get(0);
 143     SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
 144     assertNotNull(seq);
 145     assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
 146
 147   }
 148
 149   /**
 150    * Test the method that formats the sequence id
 151    */
 152   @Test(groups = { "Functional" })
 153   public void testGetUniprotEntryId()
 154   {
 155     UniprotEntry entry = new Uniprot().getUniprotEntries(
 156             new StringReader(UNIPROT_XML)).get(0);
 157
 158     /*
 159      * name formatted as source | accession ids | names
 160      * source database converted to Jalview canonical name
 161      */
 162     String expectedName = "UNIPROT|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
 163     assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
 164   }
 165
 166   /**
 167    * Test the method that formats the sequence description
 168    */
 169   @Test(groups = { "Functional" })
 170   public void testGetUniprotEntryDescription()
 171   {
 172     UniprotEntry entry = new Uniprot().getUniprotEntries(
 173             new StringReader(UNIPROT_XML)).get(0);
 174
 175     /*
 176      * recommended names concatenated with space separator
 177      */
 178     String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
 179     assertEquals(expectedDescription,
 180             Uniprot.getUniprotEntryDescription(entry));
 181   }
 182 }