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.Assert;
  39 import org.testng.annotations.BeforeClass;
  40 import org.testng.annotations.Test;
  41
  42 public class UniprotTest
  43 {
  44
  45   @BeforeClass(alwaysRun = true)
  46   public void setUpJvOptionPane()
  47   {
  48     JvOptionPane.setInteractiveMode(false);
  49     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  50   }
  51
  52   // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
  53   private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
  54           + "<uniprot>"
  55           + "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
  56           + "<accession>A9CKP4</accession>"
  57           + "<accession>A9CKP5</accession>"
  58           + "<name>A9CKP4_AGRT5</name>"
  59           + "<name>A9CKP4_AGRT6</name>"
  60           + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
  61           + "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
  62           + "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
  63           + "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
  64           + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
  65           + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
  66           + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
  67           + "<feature type=\"sequence variant\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
  68           + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
  69           + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><location><position position=\"41\"/></location></feature>"
  70           + "<feature type=\"sequence variant\" description=\"Foo\"><variation>L</variation><variation>LMV</variation><original>M</original><location><position position=\"42\"/></location></feature>"
  71           + "<feature type=\"sequence variant\" description=\"Foo\"><variation>LL</variation><variation>LMV</variation><original>ML</original><location><begin position=\"42\"/><end position=\"43\"/></location></feature>"
  72           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
  73           + "</uniprot>";
  74
  75   /**
  76    * Test the method that unmarshals XML to a Uniprot model
  77    */
  78   @Test(groups = { "Functional" })
  79   public void testGetUniprotEntries()
  80   {
  81     Uniprot u = new Uniprot();
  82     Reader reader = new StringReader(UNIPROT_XML);
  83     Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
  84     assertEquals(1, entries.size());
  85     UniprotEntry entry = entries.get(0);
  86     assertEquals(2, entry.getName().size());
  87     assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
  88     assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
  89     assertEquals(2, entry.getAccession().size());
  90     assertEquals("A9CKP4", entry.getAccession().get(0));
  91     assertEquals("A9CKP5", entry.getAccession().get(1));
  92
  93     /*
  94      * UniprotSequence drops any space characters
  95      */
  96     assertEquals("MHAPLVSKDL", entry.getUniprotSequence().getContent());
  97
  98     assertEquals(2, entry.getProtein().getName().size());
  99     assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
 100             .getName().get(0));
 101     assertEquals("Henry", entry.getProtein().getName().get(1));
 102
 103     /*
 104      * Check sequence features
 105      */
 106     Vector<UniprotFeature> features = entry.getFeature();
 107     assertEquals(8, features.size());
 108     UniprotFeature sf = features.get(0);
 109     assertEquals("signal peptide", sf.getType());
 110     assertNull(sf.getDescription());
 111     assertNull(sf.getStatus());
 112     assertEquals(1, sf.getBegin());
 113     assertEquals(18, sf.getEnd());
 114     sf = features.get(1);
 115     assertEquals("propeptide", sf.getType());
 116     assertEquals("Activation peptide", sf.getDescription());
 117     assertEquals(19, sf.getPosition());
 118     assertEquals(19, sf.getBegin());
 119     assertEquals(20, sf.getEnd());
 120     sf = features.get(2);
 121     assertEquals("chain", sf.getType());
 122     assertEquals("Granzyme B", sf.getDescription());
 123     assertEquals(21, sf.getPosition());
 124     assertEquals(21, sf.getBegin());
 125     assertEquals(247, sf.getEnd());
 126
 127     sf = features.get(3);
 128     assertEquals("sequence variant", sf.getType());
 129     assertNull(sf.getDescription());
 130     assertEquals(41, sf.getPosition());
 131     assertEquals(41, sf.getBegin());
 132     assertEquals(41, sf.getEnd());
 133
 134     sf = features.get(4);
 135     assertEquals("sequence variant", sf.getType());
 136     assertEquals("Pathogenic", sf.getDescription());
 137     assertEquals(41, sf.getPosition());
 138     assertEquals(41, sf.getBegin());
 139     assertEquals(41, sf.getEnd());
 140
 141     sf = features.get(5);
 142     assertEquals("sequence variant", sf.getType());
 143     assertEquals("Pathogenic", sf.getDescription());
 144     assertEquals(41, sf.getPosition());
 145     assertEquals(41, sf.getBegin());
 146     assertEquals(41, sf.getEnd());
 147
 148     sf = features.get(6);
 149     assertEquals("sequence variant", sf.getType());
 150     assertEquals("Foo",
 151             sf.getDescription());
 152     assertEquals(42, sf.getPosition());
 153     assertEquals(42, sf.getBegin());
 154     assertEquals(42, sf.getEnd());
 155     Assert.assertEquals(Uniprot.getDescription(sf),
 156             "p.Met42Leu" + "\n" + "p.Met42LeuMetVal Foo");
 157
 158     sf = features.get(7);
 159     assertEquals(42, sf.getBegin());
 160     assertEquals(43, sf.getEnd());
 161     Assert.assertEquals(Uniprot.getDescription(sf),
 162             "p.MetLeu42LeuLeu" + "\n" + "p.MetLeu42LeuMetVal Foo"); /*
 163                                                                     * Check cross-references
 164                                                                     */
 165     Vector<PDBEntry> xrefs = entry.getDbReference();
 166     assertEquals(3, xrefs.size());
 167
 168     PDBEntry xref = xrefs.get(0);
 169     assertEquals("2FSQ", xref.getId());
 170     assertEquals("PDB", xref.getType());
 171     assertEquals("X-ray", xref.getProperty("method"));
 172     assertEquals("1.40", xref.getProperty("resolution"));
 173
 174     xref = xrefs.get(1);
 175     assertEquals("2FSR", xref.getId());
 176     assertEquals("PDBsum", xref.getType());
 177     assertFalse(xref.getProperties().hasMoreElements());
 178
 179     xref = xrefs.get(2);
 180     assertEquals("AE007869", xref.getId());
 181     assertEquals("EMBL", xref.getType());
 182     assertEquals("AAK85932.1", xref.getProperty("protein sequence ID"));
 183     assertEquals("Genomic_DNA", xref.getProperty("molecule type"));
 184   }
 185
 186   @Test(groups = { "Functional" })
 187   public void testGetUniprotSequence()
 188   {
 189     UniprotEntry entry = new Uniprot().getUniprotEntries(
 190             new StringReader(UNIPROT_XML)).get(0);
 191     SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
 192     assertNotNull(seq);
 193     assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
 194
 195   }
 196
 197   /**
 198    * Test the method that formats the sequence id
 199    */
 200   @Test(groups = { "Functional" })
 201   public void testGetUniprotEntryId()
 202   {
 203     UniprotEntry entry = new Uniprot().getUniprotEntries(
 204             new StringReader(UNIPROT_XML)).get(0);
 205
 206     /*
 207      * name formatted with Uniprot Entry name
 208      */
 209     String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
 210     assertEquals(expectedName,
 211             Uniprot.getUniprotEntryId(entry));
 212   }
 213
 214   /**
 215    * Test the method that formats the sequence description
 216    */
 217   @Test(groups = { "Functional" })
 218   public void testGetUniprotEntryDescription()
 219   {
 220     UniprotEntry entry = new Uniprot().getUniprotEntries(
 221             new StringReader(UNIPROT_XML)).get(0);
 222
 223     /*
 224      * recommended names concatenated with space separator
 225      */
 226     String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
 227     assertEquals(expectedDescription,
 228             Uniprot.getUniprotEntryDescription(entry));
 229   }
 230
 231   @Test(groups = { "Functional" })
 232   public void testGetDescription()
 233   {
 234     UniprotFeature uf = new UniprotFeature();
 235     assertEquals("", Uniprot.getDescription(uf));
 236
 237     uf.setDescription("Hello");
 238     assertEquals("Hello", Uniprot.getDescription(uf));
 239
 240     uf.setPosition(23);
 241     uf.setOriginal("K");
 242     Vector<String> vars = new Vector();
 243     vars.add("y");
 244     uf.setVariation(vars);
 245     assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
 246
 247     vars.clear();
 248     vars.add("z"); // unknown variant - fails gracefully
 249     uf.setVariation(vars);
 250     assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
 251
 252     uf.setVariation(null); // variant missing - is ignored
 253     assertEquals("Hello", Uniprot.getDescription(uf));
 254   }
 255 }