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.assertNotNull;
  25 import static org.testng.AssertJUnit.assertNull;
  26 import static org.testng.AssertJUnit.assertTrue;
  27
  28 import jalview.datamodel.SequenceI;
  29 import jalview.gui.JvOptionPane;
  30 import jalview.xml.binding.uniprot.DbReferenceType;
  31 import jalview.xml.binding.uniprot.Entry;
  32 import jalview.xml.binding.uniprot.FeatureType;
  33 import jalview.xml.binding.uniprot.LocationType;
  34 import jalview.xml.binding.uniprot.PositionType;
  35
  36 import java.io.ByteArrayInputStream;
  37 import java.io.InputStream;
  38 import java.io.UnsupportedEncodingException;
  39 import java.math.BigInteger;
  40 import java.util.List;
  41
  42 import org.testng.Assert;
  43 import org.testng.annotations.BeforeClass;
  44 import org.testng.annotations.Test;
  45
  46 public class UniprotTest
  47 {
  48
  49   @BeforeClass(alwaysRun = true)
  50   public void setUpJvOptionPane()
  51   {
  52     JvOptionPane.setInteractiveMode(false);
  53     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  54   }
  55
  56   // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
  57   private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
  58           + "<uniprot xmlns=\"http://uniprot.org/uniprot\">"
  59           + "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
  60           + "<accession>A9CKP4</accession>"
  61           + "<accession>A9CKP5</accession>"
  62           + "<name>A9CKP4_AGRT5</name>"
  63           + "<name>A9CKP4_AGRT6</name>"
  64           + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName></recommendedName></protein>"
  65           + "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
  66           + "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
  67           + "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
  68           + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
  69           + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
  70           + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
  71           + "<feature type=\"sequence variant\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
  72           + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
  73           + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><location><position position=\"41\"/></location></feature>"
  74           + "<feature type=\"sequence variant\" description=\"Foo\"><variation>L</variation><variation>LMV</variation><original>M</original><location><position position=\"42\"/></location></feature>"
  75           + "<feature type=\"sequence variant\" description=\"Foo\"><variation>LL</variation><variation>LMV</variation><original>ML</original><location><begin position=\"42\"/><end position=\"43\"/></location></feature>"
  76           + "<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>"
  77           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
  78           + "</uniprot>";
  79
  80   /**
  81    * Test the method that unmarshals XML to a Uniprot model
  82    *
  83    * @throws UnsupportedEncodingException
  84    */
  85   @Test(groups = { "Functional" })
  86   public void testGetUniprotEntries() throws UnsupportedEncodingException
  87   {
  88     Uniprot u = new Uniprot();
  89     InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
  90     List<Entry> entries = u.getUniprotEntries(is);
  91     assertEquals(1, entries.size());
  92     Entry entry = entries.get(0);
  93     assertEquals(2, entry.getName().size());
  94     assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
  95     assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
  96     assertEquals(2, entry.getAccession().size());
  97     assertEquals("A9CKP4", entry.getAccession().get(0));
  98     assertEquals("A9CKP5", entry.getAccession().get(1));
  99
 100     assertEquals("MHAPL VSKDL", entry.getSequence().getValue());
 101
 102     assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
 103             .getRecommendedName().getFullName().getValue());
 104
 105     /*
 106      * Check sequence features
 107      */
 108     List<FeatureType> features = entry.getFeature();
 109     assertEquals(9, features.size());
 110     FeatureType sf = features.get(0);
 111     assertEquals("signal peptide", sf.getType());
 112     assertNull(sf.getDescription());
 113     assertNull(sf.getStatus());
 114     assertNull(sf.getLocation().getPosition());
 115     assertEquals(1, sf.getLocation().getBegin().getPosition().intValue());
 116     assertEquals(18, sf.getLocation().getEnd().getPosition().intValue());
 117     sf = features.get(1);
 118     assertEquals("propeptide", sf.getType());
 119     assertEquals("Activation peptide", sf.getDescription());
 120     assertNull(sf.getLocation().getPosition());
 121     assertEquals(19, sf.getLocation().getBegin().getPosition().intValue());
 122     assertEquals(20, sf.getLocation().getEnd().getPosition().intValue());
 123     sf = features.get(2);
 124     assertEquals("chain", sf.getType());
 125     assertEquals("Granzyme B", sf.getDescription());
 126     assertNull(sf.getLocation().getPosition());
 127     assertEquals(21, sf.getLocation().getBegin().getPosition().intValue());
 128     assertEquals(247, sf.getLocation().getEnd().getPosition().intValue());
 129
 130     sf = features.get(3);
 131     assertEquals("sequence variant", sf.getType());
 132     assertNull(sf.getDescription());
 133     assertEquals(41,
 134             sf.getLocation().getPosition().getPosition().intValue());
 135     assertNull(sf.getLocation().getBegin());
 136     assertNull(sf.getLocation().getEnd());
 137
 138     sf = features.get(4);
 139     assertEquals("sequence variant", sf.getType());
 140     assertEquals("Pathogenic", sf.getDescription());
 141     assertEquals(41,
 142             sf.getLocation().getPosition().getPosition().intValue());
 143     assertNull(sf.getLocation().getBegin());
 144     assertNull(sf.getLocation().getEnd());
 145
 146     sf = features.get(5);
 147     assertEquals("sequence variant", sf.getType());
 148     assertEquals("Pathogenic", sf.getDescription());
 149     assertEquals(41,
 150             sf.getLocation().getPosition().getPosition().intValue());
 151     assertNull(sf.getLocation().getBegin());
 152     assertNull(sf.getLocation().getEnd());
 153
 154     sf = features.get(6);
 155     assertEquals("sequence variant", sf.getType());
 156     assertEquals("Foo",
 157             sf.getDescription());
 158     assertEquals(42,
 159             sf.getLocation().getPosition().getPosition().intValue());
 160     assertNull(sf.getLocation().getBegin());
 161     assertNull(sf.getLocation().getEnd());
 162     Assert.assertEquals(Uniprot.getDescription(sf),
 163             "<html>p.Met42Leu" + "<br/>&nbsp;&nbsp;"
 164                     + "p.Met42LeuMetVal Foo</html>");
 165
 166     sf = features.get(7);
 167     assertNull(sf.getLocation().getPosition());
 168     assertEquals(42, sf.getLocation().getBegin().getPosition().intValue());
 169     assertEquals(43, sf.getLocation().getEnd().getPosition().intValue());
 170     Assert.assertEquals(Uniprot.getDescription(sf),
 171             "<html>p.MetLeu42LeuLeu" + "<br/>&nbsp;&nbsp;"
 172                     + "p.MetLeu42LeuMetVal Foo</html>");
 173
 174     sf = features.get(8);
 175     assertNull(sf.getLocation().getPosition());
 176     assertEquals(42, sf.getLocation().getBegin().getPosition().intValue());
 177     assertEquals(45, sf.getLocation().getEnd().getPosition().intValue());
 178     Assert.assertEquals(Uniprot.getDescription(sf),
 179             "<html>p.MLML42LeuLeu" + "<br/>&nbsp;&nbsp;"
 180                     + "p.MLML42LMVK Foo Too</html>");
 181
 182     /*
 183      * Check cross-references
 184      */
 185     List<DbReferenceType> xrefs = entry.getDbReference();
 186     assertEquals(3, xrefs.size());
 187
 188     DbReferenceType xref = xrefs.get(0);
 189     assertEquals("2FSQ", xref.getId());
 190     assertEquals("PDB", xref.getType());
 191     assertEquals("X-ray",
 192             Uniprot.getProperty(xref.getProperty(), "method"));
 193     assertEquals("1.40",
 194             Uniprot.getProperty(xref.getProperty(), "resolution"));
 195
 196     xref = xrefs.get(1);
 197     assertEquals("2FSR", xref.getId());
 198     assertEquals("PDBsum", xref.getType());
 199     assertTrue(xref.getProperty().isEmpty());
 200
 201     xref = xrefs.get(2);
 202     assertEquals("AE007869", xref.getId());
 203     assertEquals("EMBL", xref.getType());
 204     assertEquals("AAK85932.1",
 205             Uniprot.getProperty(xref.getProperty(), "protein sequence ID"));
 206     assertEquals("Genomic_DNA",
 207             Uniprot.getProperty(xref.getProperty(), "molecule type"));
 208   }
 209
 210   @Test(groups = { "Functional" })
 211   public void testGetUniprotSequence() throws UnsupportedEncodingException
 212   {
 213     InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
 214     Entry entry = new Uniprot().getUniprotEntries(
 215             is).get(0);
 216     SequenceI seq = new Uniprot().uniprotEntryToSequence(entry);
 217     assertNotNull(seq);
 218     assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
 219     assertEquals(seq.getSequenceAsString(),
 220             seq.createDatasetSequence().getSequenceAsString());
 221
 222   }
 223
 224   /**
 225    * Test the method that formats the sequence id
 226    *
 227    * @throws UnsupportedEncodingException
 228    */
 229   @Test(groups = { "Functional" })
 230   public void testGetUniprotEntryId() throws UnsupportedEncodingException
 231   {
 232     InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
 233     Entry entry = new Uniprot().getUniprotEntries(is).get(0);
 234
 235     /*
 236      * name formatted with Uniprot Entry name
 237      */
 238     String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
 239     assertEquals(expectedName,
 240             Uniprot.getUniprotEntryId(entry));
 241   }
 242
 243   /**
 244    * Test the method that formats the sequence description
 245    *
 246    * @throws UnsupportedEncodingException
 247    */
 248   @Test(groups = { "Functional" })
 249   public void testGetUniprotEntryDescription()
 250           throws UnsupportedEncodingException
 251   {
 252     InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
 253     Entry entry = new Uniprot().getUniprotEntries(is).get(0);
 254
 255     assertEquals("Mitogen-activated protein kinase 13",
 256             Uniprot.getUniprotEntryDescription(entry));
 257   }
 258
 259   @Test(groups = { "Functional" })
 260   public void testGetDescription()
 261   {
 262     FeatureType ft = new FeatureType();
 263     assertEquals("", Uniprot.getDescription(ft));
 264
 265     ft.setDescription("Hello");
 266     assertEquals("Hello", Uniprot.getDescription(ft));
 267
 268     ft.setLocation(new LocationType());
 269     ft.getLocation().setPosition(new PositionType());
 270     ft.getLocation().getPosition().setPosition(BigInteger.valueOf(23));
 271     ft.setOriginal("K");
 272     ft.getVariation().add("y");
 273     assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(ft));
 274
 275     // multiple variants generate an html description over more than one line
 276     ft.getVariation().add("W");
 277     assertEquals("<html>p.Lys23Tyr<br/>&nbsp;&nbsp;p.Lys23Trp Hello</html>",
 278             Uniprot.getDescription(ft));
 279
 280     /*
 281      * indel cases
 282      * up to 3 bases (original or variant) are shown using 3 letter code
 283      */
 284     ft.getVariation().clear();
 285     ft.getVariation().add("KWE");
 286     ft.setOriginal("KLS");
 287     assertEquals("p.LysLeuSer23LysTrpGlu Hello",
 288             Uniprot.getDescription(ft));
 289
 290     // adding a fourth original base switches to single letter code
 291     ft.setOriginal("KLST");
 292     assertEquals("p.KLST23LysTrpGlu Hello", Uniprot.getDescription(ft));
 293
 294     // adding a fourth variant switches to single letter code
 295     ft.getVariation().clear();
 296     ft.getVariation().add("KWES");
 297     assertEquals("p.KLST23KWES Hello", Uniprot.getDescription(ft));
 298
 299     ft.getVariation().clear();
 300     ft.getVariation().add("z"); // unknown variant - fails gracefully
 301     ft.setOriginal("K");
 302     assertEquals("p.Lys23z Hello", Uniprot.getDescription(ft));
 303
 304     ft.getVariation().clear(); // variant missing - is ignored
 305     assertEquals("Hello", Uniprot.getDescription(ft));
 306   }
 307 }