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.SequenceI;
  30 import jalview.datamodel.xdb.uniprot.UniprotEntry;
  31 import jalview.datamodel.xdb.uniprot.UniprotFeature;
  32 import jalview.gui.JvOptionPane;
  33
  34 import java.io.Reader;
  35 import java.io.StringReader;
  36 import java.util.Vector;
  37
  38 import org.testng.annotations.BeforeClass;
  39 import org.testng.annotations.Test;
  40
  41 public class UniprotTest
  42 {
  43
  44   @BeforeClass(alwaysRun = true)
  45   public void setUpJvOptionPane()
  46   {
  47     JvOptionPane.setInteractiveMode(false);
  48     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  49   }
  50
  51   // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
  52   private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
  53           + "<uniprot>"
  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           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
  67           + "</uniprot>";
  68
  69   /**
  70    * Test the method that unmarshals XML to a Uniprot model
  71    */
  72   @Test(groups = { "Functional" })
  73   public void testGetUniprotEntries()
  74   {
  75     Uniprot u = new Uniprot();
  76     Reader reader = new StringReader(UNIPROT_XML);
  77     Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
  78     assertEquals(1, entries.size());
  79     UniprotEntry entry = entries.get(0);
  80     assertEquals(2, entry.getName().size());
  81     assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
  82     assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
  83     assertEquals(2, entry.getAccession().size());
  84     assertEquals("A9CKP4", entry.getAccession().get(0));
  85     assertEquals("A9CKP5", entry.getAccession().get(1));
  86
  87     /*
  88      * UniprotSequence drops any space characters
  89      */
  90     assertEquals("MHAPLVSKDL", entry.getUniprotSequence().getContent());
  91
  92     assertEquals(2, entry.getProtein().getName().size());
  93     assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
  94             .getName().get(0));
  95     assertEquals("Henry", entry.getProtein().getName().get(1));
  96
  97     /*
  98      * Check sequence features
  99      */
 100     Vector<UniprotFeature> features = entry.getFeature();
 101     assertEquals(3, features.size());
 102     UniprotFeature sf = features.get(0);
 103     assertEquals("signal peptide", sf.getType());
 104     assertNull(sf.getDescription());
 105     assertNull(sf.getStatus());
 106     assertEquals(1, sf.getBegin());
 107     assertEquals(18, sf.getEnd());
 108     sf = features.get(1);
 109     assertEquals("propeptide", sf.getType());
 110     assertEquals("Activation peptide", sf.getDescription());
 111     assertEquals(19, sf.getPosition());
 112     assertEquals(19, sf.getBegin());
 113     assertEquals(20, sf.getEnd());
 114     sf = features.get(2);
 115     assertEquals("chain", sf.getType());
 116     assertEquals("Granzyme B", sf.getDescription());
 117     assertEquals(21, sf.getPosition());
 118     assertEquals(21, sf.getBegin());
 119     assertEquals(247, sf.getEnd());
 120
 121     /*
 122      * Check cross-references
 123      */
 124     Vector<PDBEntry> xrefs = entry.getDbReference();
 125     assertEquals(3, xrefs.size());
 126
 127     PDBEntry xref = xrefs.get(0);
 128     assertEquals("2FSQ", xref.getId());
 129     assertEquals("PDB", xref.getType());
 130     assertEquals("X-ray", xref.getProperty("method"));
 131     assertEquals("1.40", xref.getProperty("resolution"));
 132
 133     xref = xrefs.get(1);
 134     assertEquals("2FSR", xref.getId());
 135     assertEquals("PDBsum", xref.getType());
 136     assertFalse(xref.getProperties().hasMoreElements());
 137
 138     xref = xrefs.get(2);
 139     assertEquals("AE007869", xref.getId());
 140     assertEquals("EMBL", xref.getType());
 141     assertEquals("AAK85932.1", xref.getProperty("protein sequence ID"));
 142     assertEquals("Genomic_DNA", xref.getProperty("molecule type"));
 143   }
 144
 145   @Test(groups = { "Functional" })
 146   public void testGetUniprotSequence()
 147   {
 148     UniprotEntry entry = new Uniprot().getUniprotEntries(
 149             new StringReader(UNIPROT_XML)).get(0);
 150     SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
 151     assertNotNull(seq);
 152     assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
 153
 154   }
 155
 156   /**
 157    * Test the method that formats the sequence id
 158    */
 159   @Test(groups = { "Functional" })
 160   public void testGetUniprotEntryId()
 161   {
 162     UniprotEntry entry = new Uniprot().getUniprotEntries(
 163             new StringReader(UNIPROT_XML)).get(0);
 164
 165     /*
 166      * name formatted with Uniprot Entry name
 167      */
 168     String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
 169     assertEquals(expectedName,
 170             Uniprot.getUniprotEntryId(entry));
 171   }
 172
 173   /**
 174    * Test the method that formats the sequence description
 175    */
 176   @Test(groups = { "Functional" })
 177   public void testGetUniprotEntryDescription()
 178   {
 179     UniprotEntry entry = new Uniprot().getUniprotEntries(
 180             new StringReader(UNIPROT_XML)).get(0);
 181
 182     /*
 183      * recommended names concatenated with space separator
 184      */
 185     String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
 186     assertEquals(expectedDescription,
 187             Uniprot.getUniprotEntryDescription(entry));
 188   }
 189 }