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             "p.Met42Leu" + "\n" + "p.Met42LeuMetVal Foo");
 158
 159     sf = features.get(7);
 160     assertEquals(42, sf.getBegin());
 161     assertEquals(43, sf.getEnd());
 162     Assert.assertEquals(Uniprot.getDescription(sf),
 163             "p.MetLeu42LeuLeu" + "\n" + "p.MetLeu42LeuMetVal Foo");
 164
 165     sf = features.get(8);
 166     assertEquals(42, sf.getBegin());
 167     assertEquals(45, sf.getEnd());
 168     Assert.assertEquals(Uniprot.getDescription(sf),
 169             "p.MLML42LeuLeu" + "\n" + "p.MLML42LMVK Foo Too");
 170
 171     /*
 172      * Check cross-references
 173      */
 174     Vector<PDBEntry> xrefs = entry.getDbReference();
 175     assertEquals(3, xrefs.size());
 176
 177     PDBEntry xref = xrefs.get(0);
 178     assertEquals("2FSQ", xref.getId());
 179     assertEquals("PDB", xref.getType());
 180     assertEquals("X-ray", xref.getProperty("method"));
 181     assertEquals("1.40", xref.getProperty("resolution"));
 182
 183     xref = xrefs.get(1);
 184     assertEquals("2FSR", xref.getId());
 185     assertEquals("PDBsum", xref.getType());
 186     assertFalse(xref.getProperties().hasMoreElements());
 187
 188     xref = xrefs.get(2);
 189     assertEquals("AE007869", xref.getId());
 190     assertEquals("EMBL", xref.getType());
 191     assertEquals("AAK85932.1", xref.getProperty("protein sequence ID"));
 192     assertEquals("Genomic_DNA", xref.getProperty("molecule type"));
 193   }
 194
 195   @Test(groups = { "Functional" })
 196   public void testGetUniprotSequence()
 197   {
 198     UniprotEntry entry = new Uniprot().getUniprotEntries(
 199             new StringReader(UNIPROT_XML)).get(0);
 200     SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
 201     assertNotNull(seq);
 202     assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
 203
 204   }
 205
 206   /**
 207    * Test the method that formats the sequence id
 208    */
 209   @Test(groups = { "Functional" })
 210   public void testGetUniprotEntryId()
 211   {
 212     UniprotEntry entry = new Uniprot().getUniprotEntries(
 213             new StringReader(UNIPROT_XML)).get(0);
 214
 215     /*
 216      * name formatted with Uniprot Entry name
 217      */
 218     String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
 219     assertEquals(expectedName,
 220             Uniprot.getUniprotEntryId(entry));
 221   }
 222
 223   /**
 224    * Test the method that formats the sequence description
 225    */
 226   @Test(groups = { "Functional" })
 227   public void testGetUniprotEntryDescription()
 228   {
 229     UniprotEntry entry = new Uniprot().getUniprotEntries(
 230             new StringReader(UNIPROT_XML)).get(0);
 231
 232     /*
 233      * recommended names concatenated with space separator
 234      */
 235     String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
 236     assertEquals(expectedDescription,
 237             Uniprot.getUniprotEntryDescription(entry));
 238   }
 239
 240   @Test(groups = { "Functional" })
 241   public void testGetDescription()
 242   {
 243     UniprotFeature uf = new UniprotFeature();
 244     assertEquals("", Uniprot.getDescription(uf));
 245
 246     uf.setDescription("Hello");
 247     assertEquals("Hello", Uniprot.getDescription(uf));
 248
 249     uf.setPosition(23);
 250     uf.setOriginal("K");
 251     Vector<String> vars = new Vector<>();
 252     vars.add("y");
 253     uf.setVariation(vars);
 254     assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
 255
 256     vars.add("W");
 257     assertEquals("p.Lys23Tyr\np.Lys23Trp Hello",
 258             Uniprot.getDescription(uf));
 259
 260     /*
 261      * indel cases
 262      * up to 3 bases (original or variant) are shown using 3 letter code
 263      */
 264     vars.clear();
 265     vars.add("KWE");
 266     uf.setOriginal("KLS");
 267     assertEquals(
 268             "p.LysLeuSer23LysTrpGlu Hello",
 269             Uniprot.getDescription(uf));
 270
 271     // adding a fourth original base switches to single letter code
 272     uf.setOriginal("KLST");
 273     assertEquals("p.KLST23LysTrpGlu Hello",
 274             Uniprot.getDescription(uf));
 275
 276     // adding a fourth variant switches to a condensed representation
 277     vars.clear();
 278     vars.add("KWES");
 279     assertEquals("p.KLST23KWES Hello", Uniprot.getDescription(uf));
 280
 281     vars.clear();
 282     vars.add("z"); // unknown variant - fails gracefully
 283     uf.setOriginal("K");
 284     assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
 285
 286     uf.setVariation(null); // variant missing - is ignored
 287     assertEquals("Hello", Uniprot.getDescription(uf));
 288   }
 289 }