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.Assert.assertFalse;
  24 import static org.testng.AssertJUnit.assertEquals;
  25 import static org.testng.AssertJUnit.assertNotNull;
  26 import static org.testng.AssertJUnit.assertNull;
  27 import static org.testng.AssertJUnit.assertTrue;
  28
  29 import java.io.ByteArrayInputStream;
  30 import java.io.InputStream;
  31 import java.io.UnsupportedEncodingException;
  32 import java.math.BigInteger;
  33 import java.util.List;
  34
  35 import org.testng.Assert;
  36 import org.testng.annotations.BeforeClass;
  37 import org.testng.annotations.DataProvider;
  38 import org.testng.annotations.Test;
  39
  40 import jalview.datamodel.DBRefEntry;
  41 import jalview.datamodel.DBRefSource;
  42 import jalview.datamodel.SequenceI;
  43 import jalview.gui.JvOptionPane;
  44 import jalview.util.DBRefUtils;
  45 import jalview.xml.binding.uniprot.DbReferenceType;
  46 import jalview.xml.binding.uniprot.Entry;
  47 import jalview.xml.binding.uniprot.FeatureType;
  48 import jalview.xml.binding.uniprot.LocationType;
  49 import jalview.xml.binding.uniprot.PositionType;
  50
  51 public class UniprotTest
  52 {
  53
  54   @BeforeClass(alwaysRun = true)
  55   public void setUpJvOptionPane()
  56   {
  57     JvOptionPane.setInteractiveMode(false);
  58     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  59   }
  60
  61   // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
  62   private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
  63           + "<uniprot xmlns=\"http://uniprot.org/uniprot\">"
  64           + "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
  65           + "<accession>A9CKP4</accession>"
  66           + "<accession>A9CKP5</accession>" + "<name>A9CKP4_AGRT5</name>"
  67           + "<name>A9CKP4_AGRT6</name>"
  68           + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName></recommendedName></protein>"
  69           + "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
  70           + "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
  71           + "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
  72           + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
  73           + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
  74           + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
  75           + "<feature type=\"sequence variant\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
  76           + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
  77           + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><location><position position=\"41\"/></location></feature>"
  78           + "<feature type=\"sequence variant\" description=\"Foo\"><variation>L</variation><variation>LMV</variation><original>M</original><location><position position=\"42\"/></location></feature>"
  79           + "<feature type=\"sequence variant\" description=\"Foo\"><variation>LL</variation><variation>LMV</variation><original>ML</original><location><begin position=\"42\"/><end position=\"43\"/></location></feature>"
  80           + "<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>"
  81           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
  82           + "</uniprot>";
  83
  84   /**
  85    * Test the method that unmarshals XML to a Uniprot model
  86    *
  87    * @throws UnsupportedEncodingException
  88    */
  89   @Test(groups = { "Functional" })
  90   public void testGetUniprotEntries() throws UnsupportedEncodingException
  91   {
  92     Uniprot u = new Uniprot();
  93     InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
  94     List<Entry> entries = u.getUniprotEntries(is);
  95     assertEquals(1, entries.size());
  96     Entry entry = entries.get(0);
  97     assertEquals(2, entry.getName().size());
  98     assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
  99     assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
 100     assertEquals(2, entry.getAccession().size());
 101     assertEquals("A9CKP4", entry.getAccession().get(0));
 102     assertEquals("A9CKP5", entry.getAccession().get(1));
 103
 104     assertEquals("MHAPL VSKDL", entry.getSequence().getValue());
 105
 106     assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
 107             .getRecommendedName().getFullName().getValue());
 108
 109     /*
 110      * Check sequence features
 111      */
 112     List<FeatureType> features = entry.getFeature();
 113     assertEquals(9, features.size());
 114     FeatureType sf = features.get(0);
 115     assertEquals("signal peptide", sf.getType());
 116     assertNull(sf.getDescription());
 117     assertNull(sf.getStatus());
 118     assertNull(sf.getLocation().getPosition());
 119     assertEquals(1, sf.getLocation().getBegin().getPosition().intValue());
 120     assertEquals(18, sf.getLocation().getEnd().getPosition().intValue());
 121     sf = features.get(1);
 122     assertEquals("propeptide", sf.getType());
 123     assertEquals("Activation peptide", sf.getDescription());
 124     assertNull(sf.getLocation().getPosition());
 125     assertEquals(19, sf.getLocation().getBegin().getPosition().intValue());
 126     assertEquals(20, sf.getLocation().getEnd().getPosition().intValue());
 127     sf = features.get(2);
 128     assertEquals("chain", sf.getType());
 129     assertEquals("Granzyme B", sf.getDescription());
 130     assertNull(sf.getLocation().getPosition());
 131     assertEquals(21, sf.getLocation().getBegin().getPosition().intValue());
 132     assertEquals(247, sf.getLocation().getEnd().getPosition().intValue());
 133
 134     sf = features.get(3);
 135     assertEquals("sequence variant", sf.getType());
 136     assertNull(sf.getDescription());
 137     assertEquals(41,
 138             sf.getLocation().getPosition().getPosition().intValue());
 139     assertNull(sf.getLocation().getBegin());
 140     assertNull(sf.getLocation().getEnd());
 141
 142     sf = features.get(4);
 143     assertEquals("sequence variant", sf.getType());
 144     assertEquals("Pathogenic", sf.getDescription());
 145     assertEquals(41,
 146             sf.getLocation().getPosition().getPosition().intValue());
 147     assertNull(sf.getLocation().getBegin());
 148     assertNull(sf.getLocation().getEnd());
 149
 150     sf = features.get(5);
 151     assertEquals("sequence variant", sf.getType());
 152     assertEquals("Pathogenic", sf.getDescription());
 153     assertEquals(41,
 154             sf.getLocation().getPosition().getPosition().intValue());
 155     assertNull(sf.getLocation().getBegin());
 156     assertNull(sf.getLocation().getEnd());
 157
 158     sf = features.get(6);
 159     assertEquals("sequence variant", sf.getType());
 160     assertEquals("Foo", sf.getDescription());
 161     assertEquals(42,
 162             sf.getLocation().getPosition().getPosition().intValue());
 163     assertNull(sf.getLocation().getBegin());
 164     assertNull(sf.getLocation().getEnd());
 165     Assert.assertEquals(Uniprot.getDescription(sf), "<html>p.Met42Leu"
 166             + "<br/>&nbsp;&nbsp;" + "p.Met42LeuMetVal Foo</html>");
 167
 168     sf = features.get(7);
 169     assertNull(sf.getLocation().getPosition());
 170     assertEquals(42, sf.getLocation().getBegin().getPosition().intValue());
 171     assertEquals(43, sf.getLocation().getEnd().getPosition().intValue());
 172     Assert.assertEquals(Uniprot.getDescription(sf), "<html>p.MetLeu42LeuLeu"
 173             + "<br/>&nbsp;&nbsp;" + "p.MetLeu42LeuMetVal Foo</html>");
 174
 175     sf = features.get(8);
 176     assertNull(sf.getLocation().getPosition());
 177     assertEquals(42, sf.getLocation().getBegin().getPosition().intValue());
 178     assertEquals(45, sf.getLocation().getEnd().getPosition().intValue());
 179     Assert.assertEquals(Uniprot.getDescription(sf), "<html>p.MLML42LeuLeu"
 180             + "<br/>&nbsp;&nbsp;" + "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(is).get(0);
 215     SequenceI seq = new Uniprot().uniprotEntryToSequence(entry);
 216     assertNotNull(seq);
 217     assertEquals(6, seq.getDBRefs().size()); // 2*Uniprot, PDB, PDBsum, 2*EMBL
 218     assertEquals(seq.getSequenceAsString(),
 219             seq.createDatasetSequence().getSequenceAsString());
 220     assertEquals(2, seq.getPrimaryDBRefs().size());
 221     List<DBRefEntry> res = DBRefUtils.searchRefs(seq.getPrimaryDBRefs(),
 222             "A9CKP4");
 223     assertEquals(1, res.size());
 224     assertTrue(res.get(0).isCanonical());
 225     res = DBRefUtils.searchRefsForSource(seq.getDBRefs(),
 226             DBRefSource.UNIPROT);
 227     assertEquals(2, res.size());
 228     /*
 229      * NB this test fragile - relies on ordering being preserved
 230      */
 231     assertTrue(res.get(0).isCanonical());
 232     assertFalse(res.get(1).isCanonical());
 233
 234     // check version is preserved for EMBLCDS
 235     res = DBRefUtils.searchRefs(seq.getDBRefs(), "AAK85932");
 236     assertEquals(1, res.size());
 237     // Ideally we would expect AAK85932.1 -> AAK85932
 238     // assertTrue("1".equals(res.get(0).getVersion()));
 239     // but it also passes through DBrefUtils.ensurePrimaries which adds
 240     // (promoted) to the version string
 241     // FIXME: Jim needs to specify what (promoted) means !! - or perhaps we just
 242     // ignore it !
 243     assertEquals("1 (promoted)", (res.get(0).getVersion()));
 244   }
 245
 246   /**
 247    * Test the method that formats the sequence id
 248    *
 249    * @throws UnsupportedEncodingException
 250    */
 251   @Test(groups = { "Functional" })
 252   public void testGetUniprotEntryId() throws UnsupportedEncodingException
 253   {
 254     InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
 255     Entry entry = new Uniprot().getUniprotEntries(is).get(0);
 256
 257     /*
 258      * name formatted with Uniprot Entry name
 259      */
 260     String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
 261     assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
 262   }
 263
 264   /**
 265    * Test the method that formats the sequence description
 266    *
 267    * @throws UnsupportedEncodingException
 268    */
 269   @Test(groups = { "Functional" })
 270   public void testGetUniprotEntryDescription()
 271           throws UnsupportedEncodingException
 272   {
 273     InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
 274     Entry entry = new Uniprot().getUniprotEntries(is).get(0);
 275
 276     assertEquals("Mitogen-activated protein kinase 13",
 277             Uniprot.getUniprotEntryDescription(entry));
 278   }
 279
 280   @Test(groups = { "Functional" })
 281   public void testGetDescription()
 282   {
 283     FeatureType ft = new FeatureType();
 284     assertEquals("", Uniprot.getDescription(ft));
 285
 286     ft.setDescription("Hello");
 287     assertEquals("Hello", Uniprot.getDescription(ft));
 288
 289     ft.setLocation(new LocationType());
 290     ft.getLocation().setPosition(new PositionType());
 291     ft.getLocation().getPosition().setPosition(BigInteger.valueOf(23));
 292     ft.setOriginal("K");
 293     ft.getVariation().add("y");
 294     assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(ft));
 295
 296     // multiple variants generate an html description over more than one line
 297     ft.getVariation().add("W");
 298     assertEquals("<html>p.Lys23Tyr<br/>&nbsp;&nbsp;p.Lys23Trp Hello</html>",
 299             Uniprot.getDescription(ft));
 300
 301     /*
 302      * indel cases
 303      * up to 3 bases (original or variant) are shown using 3 letter code
 304      */
 305     ft.getVariation().clear();
 306     ft.getVariation().add("KWE");
 307     ft.setOriginal("KLS");
 308     assertEquals("p.LysLeuSer23LysTrpGlu Hello",
 309             Uniprot.getDescription(ft));
 310
 311     // adding a fourth original base switches to single letter code
 312     ft.setOriginal("KLST");
 313     assertEquals("p.KLST23LysTrpGlu Hello", Uniprot.getDescription(ft));
 314
 315     // adding a fourth variant switches to single letter code
 316     ft.getVariation().clear();
 317     ft.getVariation().add("KWES");
 318     assertEquals("p.KLST23KWES Hello", Uniprot.getDescription(ft));
 319
 320     ft.getVariation().clear();
 321     ft.getVariation().add("z"); // unknown variant - fails gracefully
 322     ft.setOriginal("K");
 323     assertEquals("p.Lys23z Hello", Uniprot.getDescription(ft));
 324
 325     ft.getVariation().clear(); // variant missing - is ignored
 326     assertEquals("Hello", Uniprot.getDescription(ft));
 327   }
 328
 329   @DataProvider
 330   public Object[][] problemEntries()
 331   {
 332     return new Object[][] {
 333         new Object[]
 334         { new String(
 335                 "<uniprot xmlns=\"http://uniprot.org/uniprot\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://uniprot.org/uniprot http://www.uniprot.org/docs/uniprot.xsd\">\n"
 336                         + "<entry xmlns=\"http://uniprot.org/uniprot\" dataset=\"Swiss-Prot\" created=\"1997-11-01\" modified=\"2023-09-13\" version=\"103\">\n"
 337                         + "<accession>Q29079</accession>\n"
 338                         + "<accession>Q29017</accession>\n"
 339                         + "<name>PAG2_PIG</name>\n" + "<protein>\n"
 340                         + "<recommendedName>\n"
 341                         + "<fullName>Pregnancy-associated glycoprotein 2</fullName>\n"
 342                         + "<shortName>PAG 2</shortName>\n"
 343                         + "<ecNumber>3.4.23.-</ecNumber>\n"
 344                         + "</recommendedName>\n" + "</protein>\n"
 345                         + "<gene>\n"
 346                         + "<name type=\"primary\">PAG2</name>\n"
 347                         + "</gene>\n" + "<organism>\n"
 348                         + "<name type=\"scientific\">Sus scrofa</name>\n"
 349                         + "<name type=\"common\">Pig</name>\n"
 350                         + "<dbReference type=\"NCBI Taxonomy\" id=\"9823\"/>\n"
 351                         + "<lineage>\n" + "<taxon>Eukaryota</taxon>\n"
 352                         + "<taxon>Metazoa</taxon>\n"
 353                         + "<taxon>Chordata</taxon>\n"
 354                         + "<taxon>Craniata</taxon>\n"
 355                         + "<taxon>Vertebrata</taxon>\n"
 356                         + "<taxon>Euteleostomi</taxon>\n"
 357                         + "<taxon>Mammalia</taxon>\n"
 358                         + "<taxon>Eutheria</taxon>\n"
 359                         + "<taxon>Laurasiatheria</taxon>\n"
 360                         + "<taxon>Artiodactyla</taxon>\n"
 361                         + "<taxon>Suina</taxon>\n"
 362                         + "<taxon>Suidae</taxon>\n" + "<taxon>Sus</taxon>\n"
 363                         + "</lineage>\n" + "</organism>\n"
 364                         + "<reference key=\"1\">\n"
 365                         + "<citation type=\"journal article\" date=\"1995\" name=\"Biol. Reprod.\" volume=\"53\" first=\"21\" last=\"28\">\n"
 366                         + "<title>Porcine pregnancy-associated glycoproteins: new members of the aspartic proteinase gene family expressed in trophectoderm.</title>\n"
 367                         + "<authorList>\n"
 368                         + "<person name=\"Szafranska B.\"/>\n"
 369                         + "<person name=\"Xie S.\"/>\n"
 370                         + "<person name=\"Green J.\"/>\n"
 371                         + "<person name=\"Roberts R.M.\"/>\n"
 372                         + "</authorList>\n"
 373                         + "<dbReference type=\"PubMed\" id=\"7669851\"/>\n"
 374                         + "<dbReference type=\"DOI\" id=\"10.1095/biolreprod53.1.21\"/>\n"
 375                         + "</citation>\n"
 376                         + "<scope>NUCLEOTIDE SEQUENCE [GENOMIC DNA]</scope>\n"
 377                         + "</reference>\n" + "<reference key=\"2\">\n"
 378                         + "<citation type=\"journal article\" date=\"2001\" name=\"Mol. Reprod. Dev.\" volume=\"60\" first=\"137\" last=\"146\">\n"
 379                         + "<title>Gene for porcine pregnancy-associated glycoprotein 2 (poPAG2): its structural organization and analysis of its promoter.</title>\n"
 380                         + "<authorList>\n"
 381                         + "<person name=\"Szafranska B.\"/>\n"
 382                         + "<person name=\"Miura R.\"/>\n"
 383                         + "<person name=\"Ghosh D.\"/>\n"
 384                         + "<person name=\"Ezashi T.\"/>\n"
 385                         + "<person name=\"Xie S.\"/>\n"
 386                         + "<person name=\"Roberts R.M.\"/>\n"
 387                         + "<person name=\"Green J.A.\"/>\n"
 388                         + "</authorList>\n"
 389                         + "<dbReference type=\"PubMed\" id=\"11553911\"/>\n"
 390                         + "<dbReference type=\"DOI\" id=\"10.1002/mrd.1070\"/>\n"
 391                         + "</citation>\n"
 392                         + "<scope>NUCLEOTIDE SEQUENCE [GENOMIC DNA]</scope>\n"
 393                         + "<source>\n" + "<tissue>Placenta</tissue>\n"
 394                         + "</source>\n" + "</reference>\n"
 395                         + "<comment type=\"subcellular location\">\n"
 396                         + "<subcellularLocation>\n"
 397                         + "<location>Secreted</location>\n"
 398                         + "<location>Extracellular space</location>\n"
 399                         + "</subcellularLocation>\n" + "</comment>\n"
 400                         + "<comment type=\"tissue specificity\">\n"
 401                         + "<text>Expressed throughout the chorion, with the signal localized exclusively over the trophectoderm.</text>\n"
 402                         + "</comment>\n"
 403                         + "<comment type=\"developmental stage\">\n"
 404                         + "<text>Expression was detected at day 15, coinciding with the beginning of implantation, and continued throughout gestation.</text>\n"
 405                         + "</comment>\n" + "<comment type=\"similarity\">\n"
 406                         + "<text evidence=\"5\">Belongs to the peptidase A1 family.</text>\n"
 407                         + "</comment>\n"
 408                         + "<dbReference type=\"EC\" id=\"3.4.23.-\"/>\n"
 409                         + "<dbReference type=\"EMBL\" id=\"U39763\">\n"
 410                         + "<property type=\"protein sequence ID\" value=\"AAA92055.1\"/>\n"
 411                         + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 412                         + "</dbReference>\n"
 413                         + "<dbReference type=\"EMBL\" id=\"U41421\">\n"
 414                         + "<property type=\"protein sequence ID\" value=\"AAA92055.1\"/>\n"
 415                         + "<property type=\"status\" value=\"JOINED\"/>\n"
 416                         + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 417                         + "</dbReference>\n"
 418                         + "<dbReference type=\"EMBL\" id=\"U41422\">\n"
 419                         + "<property type=\"protein sequence ID\" value=\"AAA92055.1\"/>\n"
 420                         + "<property type=\"status\" value=\"JOINED\"/>\n"
 421                         + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 422                         + "</dbReference>\n"
 423                         + "<dbReference type=\"EMBL\" id=\"U39199\">\n"
 424                         + "<property type=\"protein sequence ID\" value=\"AAA92055.1\"/>\n"
 425                         + "<property type=\"status\" value=\"JOINED\"/>\n"
 426                         + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 427                         + "</dbReference>\n"
 428                         + "<dbReference type=\"EMBL\" id=\"U41423\">\n"
 429                         + "<property type=\"protein sequence ID\" value=\"AAA92055.1\"/>\n"
 430                         + "<property type=\"status\" value=\"JOINED\"/>\n"
 431                         + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 432                         + "</dbReference>\n"
 433                         + "<dbReference type=\"EMBL\" id=\"U41424\">\n"
 434                         + "<property type=\"protein sequence ID\" value=\"AAA92055.1\"/>\n"
 435                         + "<property type=\"status\" value=\"JOINED\"/>\n"
 436                         + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 437                         + "</dbReference>\n"
 438                         + "<dbReference type=\"EMBL\" id=\"U39762\">\n"
 439                         + "<property type=\"protein sequence ID\" value=\"AAA92055.1\"/>\n"
 440                         + "<property type=\"status\" value=\"JOINED\"/>\n"
 441                         + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 442                         + "</dbReference>\n"
 443                         + "<dbReference type=\"EMBL\" id=\"L34361\">\n"
 444                         + "<property type=\"protein sequence ID\" value=\"AAA81531.1\"/>\n"
 445                         + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 446                         + "</dbReference>\n"
 447                         + "<dbReference type=\"PIR\" id=\"I46617\">\n"
 448                         + "<property type=\"entry name\" value=\"I46617\"/>\n"
 449                         + "</dbReference>\n"
 450                         + "<dbReference type=\"AlphaFoldDB\" id=\"Q29079\"/>\n"
 451                         + "<dbReference type=\"SMR\" id=\"Q29079\"/>\n"
 452                         + "<dbReference type=\"MEROPS\" id=\"A01.051\"/>\n"
 453                         + "<dbReference type=\"GlyCosmos\" id=\"Q29079\">\n"
 454                         + "<property type=\"glycosylation\" value=\"2 sites, No reported glycans\"/>\n"
 455                         + "</dbReference>\n"
 456                         + "<dbReference type=\"InParanoid\" id=\"Q29079\"/>\n"
 457                         + "<dbReference type=\"Proteomes\" id=\"UP000008227\">\n"
 458                         + "<property type=\"component\" value=\"Unplaced\"/>\n"
 459                         + "</dbReference>\n"
 460                         + "<dbReference type=\"Proteomes\" id=\"UP000314985\">\n"
 461                         + "<property type=\"component\" value=\"Unplaced\"/>\n"
 462                         + "</dbReference>\n"
 463                         + "<dbReference type=\"Proteomes\" id=\"UP000694570\">\n"
 464                         + "<property type=\"component\" value=\"Unplaced\"/>\n"
 465                         + "</dbReference>\n"
 466                         + "<dbReference type=\"Proteomes\" id=\"UP000694571\">\n"
 467                         + "<property type=\"component\" value=\"Unplaced\"/>\n"
 468                         + "</dbReference>\n"
 469                         + "<dbReference type=\"Proteomes\" id=\"UP000694720\">\n"
 470                         + "<property type=\"component\" value=\"Unplaced\"/>\n"
 471                         + "</dbReference>\n"
 472                         + "<dbReference type=\"Proteomes\" id=\"UP000694722\">\n"
 473                         + "<property type=\"component\" value=\"Unplaced\"/>\n"
 474                         + "</dbReference>\n"
 475                         + "<dbReference type=\"Proteomes\" id=\"UP000694723\">\n"
 476                         + "<property type=\"component\" value=\"Unplaced\"/>\n"
 477                         + "</dbReference>\n"
 478                         + "<dbReference type=\"Proteomes\" id=\"UP000694724\">\n"
 479                         + "<property type=\"component\" value=\"Unplaced\"/>\n"
 480                         + "</dbReference>\n"
 481                         + "<dbReference type=\"Proteomes\" id=\"UP000694725\">\n"
 482                         + "<property type=\"component\" value=\"Unplaced\"/>\n"
 483                         + "</dbReference>\n"
 484                         + "<dbReference type=\"Proteomes\" id=\"UP000694726\">\n"
 485                         + "<property type=\"component\" value=\"Unplaced\"/>\n"
 486                         + "</dbReference>\n"
 487                         + "<dbReference type=\"Proteomes\" id=\"UP000694727\">\n"
 488                         + "<property type=\"component\" value=\"Unplaced\"/>\n"
 489                         + "</dbReference>\n"
 490                         + "<dbReference type=\"Proteomes\" id=\"UP000694728\">\n"
 491                         + "<property type=\"component\" value=\"Unplaced\"/>\n"
 492                         + "</dbReference>\n"
 493                         + "<dbReference type=\"GO\" id=\"GO:0005615\">\n"
 494                         + "<property type=\"term\" value=\"C:extracellular space\"/>\n"
 495                         + "<property type=\"evidence\" value=\"ECO:0007669\"/>\n"
 496                         + "<property type=\"project\" value=\"UniProtKB-SubCell\"/>\n"
 497                         + "</dbReference>\n"
 498                         + "<dbReference type=\"GO\" id=\"GO:0004190\">\n"
 499                         + "<property type=\"term\" value=\"F:aspartic-type endopeptidase activity\"/>\n"
 500                         + "<property type=\"evidence\" value=\"ECO:0000318\"/>\n"
 501                         + "<property type=\"project\" value=\"GO_Central\"/>\n"
 502                         + "</dbReference>\n"
 503                         + "<dbReference type=\"GO\" id=\"GO:0006508\">\n"
 504                         + "<property type=\"term\" value=\"P:proteolysis\"/>\n"
 505                         + "<property type=\"evidence\" value=\"ECO:0000318\"/>\n"
 506                         + "<property type=\"project\" value=\"GO_Central\"/>\n"
 507                         + "</dbReference>\n"
 508                         + "<dbReference type=\"Gene3D\" id=\"6.10.140.60\">\n"
 509                         + "<property type=\"match status\" value=\"1\"/>\n"
 510                         + "</dbReference>\n"
 511                         + "<dbReference type=\"Gene3D\" id=\"2.40.70.10\">\n"
 512                         + "<property type=\"entry name\" value=\"Acid Proteases\"/>\n"
 513                         + "<property type=\"match status\" value=\"3\"/>\n"
 514                         + "</dbReference>\n"
 515                         + "<dbReference type=\"InterPro\" id=\"IPR001461\">\n"
 516                         + "<property type=\"entry name\" value=\"Aspartic_peptidase_A1\"/>\n"
 517                         + "</dbReference>\n"
 518                         + "<dbReference type=\"InterPro\" id=\"IPR001969\">\n"
 519                         + "<property type=\"entry name\" value=\"Aspartic_peptidase_AS\"/>\n"
 520                         + "</dbReference>\n"
 521                         + "<dbReference type=\"InterPro\" id=\"IPR012848\">\n"
 522                         + "<property type=\"entry name\" value=\"Aspartic_peptidase_N\"/>\n"
 523                         + "</dbReference>\n"
 524                         + "<dbReference type=\"InterPro\" id=\"IPR033121\">\n"
 525                         + "<property type=\"entry name\" value=\"PEPTIDASE_A1\"/>\n"
 526                         + "</dbReference>\n"
 527                         + "<dbReference type=\"InterPro\" id=\"IPR021109\">\n"
 528                         + "<property type=\"entry name\" value=\"Peptidase_aspartic_dom_sf\"/>\n"
 529                         + "</dbReference>\n"
 530                         + "<dbReference type=\"PANTHER\" id=\"PTHR47966\">\n"
 531                         + "<property type=\"entry name\" value=\"BETA-SITE APP-CLEAVING ENZYME, ISOFORM A-RELATED\"/>\n"
 532                         + "<property type=\"match status\" value=\"1\"/>\n"
 533                         + "</dbReference>\n"
 534                         + "<dbReference type=\"PANTHER\" id=\"PTHR47966:SF49\">\n"
 535                         + "<property type=\"entry name\" value=\"PEPSIN A-5\"/>\n"
 536                         + "<property type=\"match status\" value=\"1\"/>\n"
 537                         + "</dbReference>\n"
 538                         + "<dbReference type=\"Pfam\" id=\"PF07966\">\n"
 539                         + "<property type=\"entry name\" value=\"A1_Propeptide\"/>\n"
 540                         + "<property type=\"match status\" value=\"1\"/>\n"
 541                         + "</dbReference>\n"
 542                         + "<dbReference type=\"Pfam\" id=\"PF00026\">\n"
 543                         + "<property type=\"entry name\" value=\"Asp\"/>\n"
 544                         + "<property type=\"match status\" value=\"2\"/>\n"
 545                         + "</dbReference>\n"
 546                         + "<dbReference type=\"PRINTS\" id=\"PR00792\">\n"
 547                         + "<property type=\"entry name\" value=\"PEPSIN\"/>\n"
 548                         + "</dbReference>\n"
 549                         + "<dbReference type=\"SUPFAM\" id=\"SSF50630\">\n"
 550                         + "<property type=\"entry name\" value=\"Acid proteases\"/>\n"
 551                         + "<property type=\"match status\" value=\"2\"/>\n"
 552                         + "</dbReference>\n"
 553                         + "<dbReference type=\"PROSITE\" id=\"PS00141\">\n"
 554                         + "<property type=\"entry name\" value=\"ASP_PROTEASE\"/>\n"
 555                         + "<property type=\"match status\" value=\"2\"/>\n"
 556                         + "</dbReference>\n"
 557                         + "<dbReference type=\"PROSITE\" id=\"PS51767\">\n"
 558                         + "<property type=\"entry name\" value=\"PEPTIDASE_A1\"/>\n"
 559                         + "<property type=\"match status\" value=\"1\"/>\n"
 560                         + "</dbReference>\n"
 561                         + "<proteinExistence type=\"evidence at transcript level\"/>\n"
 562                         + "<keyword id=\"KW-0064\">Aspartyl protease</keyword>\n"
 563                         + "<keyword id=\"KW-1015\">Disulfide bond</keyword>\n"
 564                         + "<keyword id=\"KW-0325\">Glycoprotein</keyword>\n"
 565                         + "<keyword id=\"KW-0378\">Hydrolase</keyword>\n"
 566                         + "<keyword id=\"KW-0645\">Protease</keyword>\n"
 567                         + "<keyword id=\"KW-1185\">Reference proteome</keyword>\n"
 568                         + "<keyword id=\"KW-0964\">Secreted</keyword>\n"
 569                         + "<keyword id=\"KW-0732\">Signal</keyword>\n"
 570                         + "<keyword id=\"KW-0865\">Zymogen</keyword>\n"
 571                         + "<feature type=\"signal peptide\" evidence=\"2\">\n"
 572                         + "<location>\n" + "<begin position=\"1\"/>\n"
 573                         + "<end position=\"15\"/>\n" + "</location>\n"
 574                         + "</feature>\n"
 575                         + "<feature type=\"propeptide\" id=\"PRO_0000026107\" description=\"Activation peptide\" evidence=\"2\">\n"
 576                         + "<location>\n" + "<begin position=\"16\"/>\n"
 577                         + "<end status=\"unknown\"/>\n" + "</location>\n"
 578                         + "</feature>\n"
 579                         + "<feature type=\"chain\" id=\"PRO_0000026108\" description=\"Pregnancy-associated glycoprotein 2\">\n"
 580                         + "<location>\n" + "<begin status=\"unknown\"/>\n"
 581                         + "<end position=\"420\"/>\n" + "</location>\n"
 582                         + "</feature>\n"
 583                         + "<feature type=\"domain\" description=\"Peptidase A1\" evidence=\"3\">\n"
 584                         + "<location>\n" + "<begin position=\"76\"/>\n"
 585                         + "<end position=\"417\"/>\n" + "</location>\n"
 586                         + "</feature>\n"
 587                         + "<feature type=\"active site\" evidence=\"4\">\n"
 588                         + "<location>\n" + "<position position=\"94\"/>\n"
 589                         + "</location>\n" + "</feature>\n"
 590                         + "<feature type=\"active site\" evidence=\"4\">\n"
 591                         + "<location>\n" + "<position position=\"277\"/>\n"
 592                         + "</location>\n" + "</feature>\n"
 593                         + "<feature type=\"glycosylation site\" description=\"N-linked (GlcNAc...) asparagine\" evidence=\"2\">\n"
 594                         + "<location>\n" + "<position position=\"56\"/>\n"
 595                         + "</location>\n" + "</feature>\n"
 596                         + "<feature type=\"glycosylation site\" description=\"N-linked (GlcNAc...) asparagine\" evidence=\"2\">\n"
 597                         + "<location>\n" + "<position position=\"79\"/>\n"
 598                         + "</location>\n" + "</feature>\n"
 599                         + "<feature type=\"disulfide bond\" evidence=\"1\">\n"
 600                         + "<location>\n" + "<begin position=\"107\"/>\n"
 601                         + "<end position=\"112\"/>\n" + "</location>\n"
 602                         + "</feature>\n"
 603                         + "<feature type=\"disulfide bond\" evidence=\"1\">\n"
 604                         + "<location>\n" + "<begin position=\"268\"/>\n"
 605                         + "<end position=\"272\"/>\n" + "</location>\n"
 606                         + "</feature>\n"
 607                         + "<feature type=\"disulfide bond\" evidence=\"1\">\n"
 608                         + "<location>\n" + "<begin position=\"341\"/>\n"
 609                         + "<end position=\"376\"/>\n" + "</location>\n"
 610                         + "</feature>\n"
 611                         + "<feature type=\"sequence conflict\" description=\"In Ref. 1.\" evidence=\"5\" ref=\"1\">\n"
 612                         + "<location>\n" + "<begin position=\"335\"/>\n"
 613                         + "<end position=\"367\"/>\n" + "</location>\n"
 614                         + "</feature>\n"
 615                         + "<evidence type=\"ECO:0000250\" key=\"1\"/>\n"
 616                         + "<evidence type=\"ECO:0000255\" key=\"2\"/>\n"
 617                         + "<evidence type=\"ECO:0000255\" key=\"3\">\n"
 618                         + "<source>\n"
 619                         + "<dbReference type=\"PROSITE-ProRule\" id=\"PRU01103\"/>\n"
 620                         + "</source>\n" + "</evidence>\n"
 621                         + "<evidence type=\"ECO:0000255\" key=\"4\">\n"
 622                         + "<source>\n"
 623                         + "<dbReference type=\"PROSITE-ProRule\" id=\"PRU10094\"/>\n"
 624                         + "</source>\n" + "</evidence>\n"
 625                         + "<evidence type=\"ECO:0000305\" key=\"5\"/>\n"
 626                         + "<sequence length=\"420\" mass=\"47132\" checksum=\"094153B6C1B1FCDB\" modified=\"1997-11-01\" version=\"1\" precursor=\"true\">MKWLVILGLVALSDCLVMIPLTKVKSVRESLREKGLLKNFLKEHPYNMIQNLLSKNSSHVQKFSYQPLRNYLDMVYVGNISIGTPPQQFSVVFDTGSSDLWVPSIYCKSKACVTHRSFNPSHSSTFHDRGKSIKLEYGSGKMSGFLGQDTVRIGQLTSTGQAFGLSKEETGKAFEHAIFDGILGLAYPSIAIKGTTTVIDNLKKQDQISEPVFAFYLSSDKEEGSVVMFGGVDKKYYKGDLKWVPLTQTSYWQIALDRITCRGRVIGCPRGCQAIVDTGTSMLHGPSKAVAKIHSLIKHFEKEYVVPCNARKALPDIVFTINNVDYPVPAQAYIRKYVVPCNARKALPDIVFTINNVDYPVPAQAYIRKNANNNRCYSTFEDIMDTLNQREIWILGDVFLRLYFTVYDEGQNRIGLAQAT</sequence>\n"
 627                         + "</entry>\n"
 628                         + "<copyright> Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms Distributed under the Creative Commons Attribution (CC BY 4.0) License </copyright>\n"
 629                         + "</uniprot>") } };
 630   }
 631
 632   @Test(groups = "Functional", dataProvider = "problemEntries")
 633   public void testimportOfProblemEntries(String entry)
 634   {
 635     Uniprot u = new Uniprot();
 636     InputStream is = new ByteArrayInputStream(entry.getBytes());
 637     List<Entry> entries = u.getUniprotEntries(is);
 638     assertEquals(1, entries.size());
 639     SequenceI sq = u.uniprotEntryToSequence(entries.get(0));
 640     assertNotNull(sq);
 641   }
 642 }