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           + "<feature type=\"sequence variant\" description=\"Foo Too\"><variation>LL</variation><variation>LMVK</variation><original>MLML</original><location><begin position=\"42\"/><end position=\"45\"/></location></feature>"
  73           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
  74           + "</uniprot>";
  75
  76   /**
  77    * Test the method that unmarshals XML to a Uniprot model
  78    */
  79   @Test(groups = { "Functional" })
  80   public void testGetUniprotEntries()
  81   {
  82     Uniprot u = new Uniprot();
  83     Reader reader = new StringReader(UNIPROT_XML);
  84     Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
  85     assertEquals(1, entries.size());
  86     UniprotEntry entry = entries.get(0);
  87     assertEquals(2, entry.getName().size());
  88     assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
  89     assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
  90     assertEquals(2, entry.getAccession().size());
  91     assertEquals("A9CKP4", entry.getAccession().get(0));
  92     assertEquals("A9CKP5", entry.getAccession().get(1));
  93
  94     /*
  95      * UniprotSequence drops any space characters
  96      */
  97     assertEquals("MHAPLVSKDL", entry.getUniprotSequence().getContent());
  98
  99     assertEquals(2, entry.getProtein().getName().size());
 100     assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
 101             .getName().get(0));
 102     assertEquals("Henry", entry.getProtein().getName().get(1));
 103
 104     /*
 105      * Check sequence features
 106      */
 107     Vector<UniprotFeature> features = entry.getFeature();
 108     assertEquals(9, features.size());
 109     UniprotFeature sf = features.get(0);
 110     assertEquals("signal peptide", sf.getType());
 111     assertNull(sf.getDescription());
 112     assertNull(sf.getStatus());
 113     assertEquals(1, sf.getBegin());
 114     assertEquals(18, sf.getEnd());
 115     sf = features.get(1);
 116     assertEquals("propeptide", sf.getType());
 117     assertEquals("Activation peptide", sf.getDescription());
 118     assertEquals(19, sf.getPosition());
 119     assertEquals(19, sf.getBegin());
 120     assertEquals(20, sf.getEnd());
 121     sf = features.get(2);
 122     assertEquals("chain", sf.getType());
 123     assertEquals("Granzyme B", sf.getDescription());
 124     assertEquals(21, sf.getPosition());
 125     assertEquals(21, sf.getBegin());
 126     assertEquals(247, sf.getEnd());
 127
 128     sf = features.get(3);
 129     assertEquals("sequence variant", sf.getType());
 130     assertNull(sf.getDescription());
 131     assertEquals(41, sf.getPosition());
 132     assertEquals(41, sf.getBegin());
 133     assertEquals(41, sf.getEnd());
 134
 135     sf = features.get(4);
 136     assertEquals("sequence variant", sf.getType());
 137     assertEquals("Pathogenic", sf.getDescription());
 138     assertEquals(41, sf.getPosition());
 139     assertEquals(41, sf.getBegin());
 140     assertEquals(41, sf.getEnd());
 141
 142     sf = features.get(5);
 143     assertEquals("sequence variant", sf.getType());
 144     assertEquals("Pathogenic", sf.getDescription());
 145     assertEquals(41, sf.getPosition());
 146     assertEquals(41, sf.getBegin());
 147     assertEquals(41, sf.getEnd());
 148
 149     sf = features.get(6);
 150     assertEquals("sequence variant", sf.getType());
 151     assertEquals("Foo",
 152             sf.getDescription());
 153     assertEquals(42, sf.getPosition());
 154     assertEquals(42, sf.getBegin());
 155     assertEquals(42, sf.getEnd());
 156     Assert.assertEquals(Uniprot.getDescription(sf),
 157             "<html>p.Met42Leu" + "<br/>&nbsp;&nbsp;"
 158                     + "p.Met42LeuMetVal Foo</html>");
 159
 160     sf = features.get(7);
 161     assertEquals(42, sf.getBegin());
 162     assertEquals(43, sf.getEnd());
 163     Assert.assertEquals(Uniprot.getDescription(sf),
 164             "<html>p.MetLeu42LeuLeu" + "<br/>&nbsp;&nbsp;"
 165                     + "p.MetLeu42LeuMetVal Foo</html>");
 166
 167     sf = features.get(8);
 168     assertEquals(42, sf.getBegin());
 169     assertEquals(45, sf.getEnd());
 170     Assert.assertEquals(Uniprot.getDescription(sf),
 171             "<html>p.MLML42LeuLeu" + "<br/>&nbsp;&nbsp;"
 172                     + "p.MLML42LMVK Foo Too</html>");
 173
 174     /*
 175      * Check cross-references
 176      */
 177     Vector<PDBEntry> xrefs = entry.getDbReference();
 178     assertEquals(3, xrefs.size());
 179
 180     PDBEntry xref = xrefs.get(0);
 181     assertEquals("2FSQ", xref.getId());
 182     assertEquals("PDB", xref.getType());
 183     assertEquals("X-ray", xref.getProperty("method"));
 184     assertEquals("1.40", xref.getProperty("resolution"));
 185
 186     xref = xrefs.get(1);
 187     assertEquals("2FSR", xref.getId());
 188     assertEquals("PDBsum", xref.getType());
 189     assertFalse(xref.getProperties().hasMoreElements());
 190
 191     xref = xrefs.get(2);
 192     assertEquals("AE007869", xref.getId());
 193     assertEquals("EMBL", xref.getType());
 194     assertEquals("AAK85932.1", xref.getProperty("protein sequence ID"));
 195     assertEquals("Genomic_DNA", xref.getProperty("molecule type"));
 196   }
 197
 198   @Test(groups = { "Functional" })
 199   public void testGetUniprotSequence()
 200   {
 201     UniprotEntry entry = new Uniprot().getUniprotEntries(
 202             new StringReader(UNIPROT_XML)).get(0);
 203     SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
 204     assertNotNull(seq);
 205     assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
 206
 207   }
 208
 209   /**
 210    * Test the method that formats the sequence id
 211    */
 212   @Test(groups = { "Functional" })
 213   public void testGetUniprotEntryId()
 214   {
 215     UniprotEntry entry = new Uniprot().getUniprotEntries(
 216             new StringReader(UNIPROT_XML)).get(0);
 217
 218     /*
 219      * name formatted with Uniprot Entry name
 220      */
 221     String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
 222     assertEquals(expectedName,
 223             Uniprot.getUniprotEntryId(entry));
 224   }
 225
 226   /**
 227    * Test the method that formats the sequence description
 228    */
 229   @Test(groups = { "Functional" })
 230   public void testGetUniprotEntryDescription()
 231   {
 232     UniprotEntry entry = new Uniprot().getUniprotEntries(
 233             new StringReader(UNIPROT_XML)).get(0);
 234
 235     /*
 236      * recommended names concatenated with space separator
 237      */
 238     String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
 239     assertEquals(expectedDescription,
 240             Uniprot.getUniprotEntryDescription(entry));
 241   }
 242
 243   @Test(groups = { "Functional" })
 244   public void testGetDescription()
 245   {
 246     UniprotFeature uf = new UniprotFeature();
 247     assertEquals("", Uniprot.getDescription(uf));
 248
 249     uf.setDescription("Hello");
 250     assertEquals("Hello", Uniprot.getDescription(uf));
 251
 252     uf.setPosition(23);
 253     uf.setOriginal("K");
 254     Vector<String> vars = new Vector<>();
 255     vars.add("y");
 256     uf.setVariation(vars);
 257     assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
 258
 259     // multiple variants generate an html description over more than one line
 260     vars.add("W");
 261     assertEquals("<html>p.Lys23Tyr<br/>&nbsp;&nbsp;p.Lys23Trp Hello</html>",
 262             Uniprot.getDescription(uf));
 263
 264     /*
 265      * indel cases
 266      * up to 3 bases (original or variant) are shown using 3 letter code
 267      */
 268     vars.clear();
 269     vars.add("KWE");
 270     uf.setOriginal("KLS");
 271     assertEquals("p.LysLeuSer23LysTrpGlu Hello",
 272             Uniprot.getDescription(uf));
 273
 274     // adding a fourth original base switches to single letter code
 275     uf.setOriginal("KLST");
 276     assertEquals("p.KLST23LysTrpGlu Hello", Uniprot.getDescription(uf));
 277
 278     // adding a fourth variant switches to single letter code
 279     vars.clear();
 280     vars.add("KWES");
 281     assertEquals("p.KLST23KWES Hello", Uniprot.getDescription(uf));
 282
 283     vars.clear();
 284     vars.add("z"); // unknown variant - fails gracefully
 285     uf.setOriginal("K");
 286     assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
 287
 288     uf.setVariation(null); // variant missing - is ignored
 289     assertEquals("Hello", Uniprot.getDescription(uf));
 290   }
 291 }