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.SequenceFeature;
  43 import jalview.datamodel.SequenceI;
  44 import jalview.gui.JvOptionPane;
  45 import jalview.util.DBRefUtils;
  46 import jalview.xml.binding.uniprot.DbReferenceType;
  47 import jalview.xml.binding.uniprot.Entry;
  48 import jalview.xml.binding.uniprot.FeatureType;
  49 import jalview.xml.binding.uniprot.LocationType;
  50 import jalview.xml.binding.uniprot.PositionType;
  51
  52 public class UniprotTest
  53 {
  54
  55   @BeforeClass(alwaysRun = true)
  56   public void setUpJvOptionPane()
  57   {
  58     JvOptionPane.setInteractiveMode(false);
  59     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  60   }
  61
  62   // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
  63   private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
  64           + "<uniprot xmlns=\"http://uniprot.org/uniprot\">"
  65           + "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
  66           + "<accession>A9CKP4</accession>"
  67           + "<accession>A9CKP5</accession>" + "<name>A9CKP4_AGRT5</name>"
  68           + "<name>A9CKP4_AGRT6</name>"
  69           + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName></recommendedName></protein>"
  70           + "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
  71           + "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
  72           + "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
  73           + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
  74           + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
  75           + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
  76           + "<feature type=\"sequence variant\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
  77           + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
  78           + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><location><position position=\"41\"/></location></feature>"
  79           + "<feature type=\"sequence variant\" description=\"Foo\"><variation>L</variation><variation>LMV</variation><original>M</original><location><position position=\"42\"/></location></feature>"
  80           + "<feature type=\"sequence variant\" description=\"Foo\"><variation>LL</variation><variation>LMV</variation><original>ML</original><location><begin position=\"42\"/><end position=\"43\"/></location></feature>"
  81           + "<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>"
  82           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
  83           + "</uniprot>";
  84
  85   /**
  86    * Test the method that unmarshals XML to a Uniprot model
  87    *
  88    * @throws UnsupportedEncodingException
  89    */
  90   @Test(groups = { "Functional" })
  91   public void testGetUniprotEntries() throws UnsupportedEncodingException
  92   {
  93     Uniprot u = new Uniprot();
  94     InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
  95     List<Entry> entries = u.getUniprotEntries(is);
  96     assertEquals(1, entries.size());
  97     Entry entry = entries.get(0);
  98     assertEquals(2, entry.getName().size());
  99     assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
 100     assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
 101     assertEquals(2, entry.getAccession().size());
 102     assertEquals("A9CKP4", entry.getAccession().get(0));
 103     assertEquals("A9CKP5", entry.getAccession().get(1));
 104
 105     assertEquals("MHAPL VSKDL", entry.getSequence().getValue());
 106
 107     assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
 108             .getRecommendedName().getFullName().getValue());
 109
 110     /*
 111      * Check sequence features
 112      */
 113     List<FeatureType> features = entry.getFeature();
 114     assertEquals(9, features.size());
 115     FeatureType sf = features.get(0);
 116     assertEquals("signal peptide", sf.getType());
 117     assertNull(sf.getDescription());
 118     assertNull(sf.getStatus());
 119     assertNull(sf.getLocation().getPosition());
 120     assertEquals(1, sf.getLocation().getBegin().getPosition().intValue());
 121     assertEquals(18, sf.getLocation().getEnd().getPosition().intValue());
 122     sf = features.get(1);
 123     assertEquals("propeptide", sf.getType());
 124     assertEquals("Activation peptide", sf.getDescription());
 125     assertNull(sf.getLocation().getPosition());
 126     assertEquals(19, sf.getLocation().getBegin().getPosition().intValue());
 127     assertEquals(20, sf.getLocation().getEnd().getPosition().intValue());
 128     sf = features.get(2);
 129     assertEquals("chain", sf.getType());
 130     assertEquals("Granzyme B", sf.getDescription());
 131     assertNull(sf.getLocation().getPosition());
 132     assertEquals(21, sf.getLocation().getBegin().getPosition().intValue());
 133     assertEquals(247, sf.getLocation().getEnd().getPosition().intValue());
 134
 135     sf = features.get(3);
 136     assertEquals("sequence variant", sf.getType());
 137     assertNull(sf.getDescription());
 138     assertEquals(41,
 139             sf.getLocation().getPosition().getPosition().intValue());
 140     assertNull(sf.getLocation().getBegin());
 141     assertNull(sf.getLocation().getEnd());
 142
 143     sf = features.get(4);
 144     assertEquals("sequence variant", sf.getType());
 145     assertEquals("Pathogenic", sf.getDescription());
 146     assertEquals(41,
 147             sf.getLocation().getPosition().getPosition().intValue());
 148     assertNull(sf.getLocation().getBegin());
 149     assertNull(sf.getLocation().getEnd());
 150
 151     sf = features.get(5);
 152     assertEquals("sequence variant", sf.getType());
 153     assertEquals("Pathogenic", sf.getDescription());
 154     assertEquals(41,
 155             sf.getLocation().getPosition().getPosition().intValue());
 156     assertNull(sf.getLocation().getBegin());
 157     assertNull(sf.getLocation().getEnd());
 158
 159     sf = features.get(6);
 160     assertEquals("sequence variant", sf.getType());
 161     assertEquals("Foo", sf.getDescription());
 162     assertEquals(42,
 163             sf.getLocation().getPosition().getPosition().intValue());
 164     assertNull(sf.getLocation().getBegin());
 165     assertNull(sf.getLocation().getEnd());
 166     Assert.assertEquals(Uniprot.getDescription(sf), "<html>p.Met42Leu"
 167             + "<br/>&nbsp;&nbsp;" + "p.Met42LeuMetVal Foo</html>");
 168
 169     sf = features.get(7);
 170     assertNull(sf.getLocation().getPosition());
 171     assertEquals(42, sf.getLocation().getBegin().getPosition().intValue());
 172     assertEquals(43, sf.getLocation().getEnd().getPosition().intValue());
 173     Assert.assertEquals(Uniprot.getDescription(sf), "<html>p.MetLeu42LeuLeu"
 174             + "<br/>&nbsp;&nbsp;" + "p.MetLeu42LeuMetVal Foo</html>");
 175
 176     sf = features.get(8);
 177     assertNull(sf.getLocation().getPosition());
 178     assertEquals(42, sf.getLocation().getBegin().getPosition().intValue());
 179     assertEquals(45, sf.getLocation().getEnd().getPosition().intValue());
 180     Assert.assertEquals(Uniprot.getDescription(sf), "<html>p.MLML42LeuLeu"
 181             + "<br/>&nbsp;&nbsp;" + "p.MLML42LMVK Foo Too</html>");
 182
 183     /*
 184      * Check cross-references
 185      */
 186     List<DbReferenceType> xrefs = entry.getDbReference();
 187     assertEquals(3, xrefs.size());
 188
 189     DbReferenceType xref = xrefs.get(0);
 190     assertEquals("2FSQ", xref.getId());
 191     assertEquals("PDB", xref.getType());
 192     assertEquals("X-ray",
 193             Uniprot.getProperty(xref.getProperty(), "method"));
 194     assertEquals("1.40",
 195             Uniprot.getProperty(xref.getProperty(), "resolution"));
 196
 197     xref = xrefs.get(1);
 198     assertEquals("2FSR", xref.getId());
 199     assertEquals("PDBsum", xref.getType());
 200     assertTrue(xref.getProperty().isEmpty());
 201
 202     xref = xrefs.get(2);
 203     assertEquals("AE007869", xref.getId());
 204     assertEquals("EMBL", xref.getType());
 205     assertEquals("AAK85932.1",
 206             Uniprot.getProperty(xref.getProperty(), "protein sequence ID"));
 207     assertEquals("Genomic_DNA",
 208             Uniprot.getProperty(xref.getProperty(), "molecule type"));
 209   }
 210
 211   @Test(groups = { "Functional" })
 212   public void testGetUniprotSequence() throws UnsupportedEncodingException
 213   {
 214     InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
 215     Entry entry = new Uniprot().getUniprotEntries(is).get(0);
 216     SequenceI seq = new Uniprot().uniprotEntryToSequence(entry);
 217     assertNotNull(seq);
 218     assertEquals(6, seq.getDBRefs().size()); // 2*Uniprot, PDB, PDBsum, 2*EMBL
 219     assertEquals(seq.getSequenceAsString(),
 220             seq.createDatasetSequence().getSequenceAsString());
 221     assertEquals(2, seq.getPrimaryDBRefs().size());
 222     List<DBRefEntry> res = DBRefUtils.searchRefs(seq.getPrimaryDBRefs(),
 223             "A9CKP4");
 224     assertEquals(1, res.size());
 225     assertTrue(res.get(0).isCanonical());
 226     res = DBRefUtils.searchRefsForSource(seq.getDBRefs(),
 227             DBRefSource.UNIPROT);
 228     assertEquals(2, res.size());
 229     /*
 230      * NB this test fragile - relies on ordering being preserved
 231      */
 232     assertTrue(res.get(0).isCanonical());
 233     assertFalse(res.get(1).isCanonical());
 234
 235     // check version is preserved for EMBLCDS
 236     res = DBRefUtils.searchRefs(seq.getDBRefs(), "AAK85932");
 237     assertEquals(1, res.size());
 238     // Ideally we would expect AAK85932.1 -> AAK85932
 239     // assertTrue("1".equals(res.get(0).getVersion()));
 240     // but it also passes through DBrefUtils.ensurePrimaries which adds
 241     // (promoted) to the version string
 242     // FIXME: Jim needs to specify what (promoted) means !! - or perhaps we just
 243     // ignore it !
 244     assertEquals("1 (promoted)", (res.get(0).getVersion()));
 245   }
 246
 247   /**
 248    * Test the method that formats the sequence id
 249    *
 250    * @throws UnsupportedEncodingException
 251    */
 252   @Test(groups = { "Functional" })
 253   public void testGetUniprotEntryId() throws UnsupportedEncodingException
 254   {
 255     InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
 256     Entry entry = new Uniprot().getUniprotEntries(is).get(0);
 257
 258     /*
 259      * name formatted with Uniprot Entry name
 260      */
 261     String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
 262     assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
 263   }
 264
 265   /**
 266    * Test the method that formats the sequence description
 267    *
 268    * @throws UnsupportedEncodingException
 269    */
 270   @Test(groups = { "Functional" })
 271   public void testGetUniprotEntryDescription()
 272           throws UnsupportedEncodingException
 273   {
 274     InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
 275     Entry entry = new Uniprot().getUniprotEntries(is).get(0);
 276
 277     assertEquals("Mitogen-activated protein kinase 13",
 278             Uniprot.getUniprotEntryDescription(entry));
 279   }
 280
 281   @Test(groups = { "Functional" })
 282   public void testGetDescription()
 283   {
 284     FeatureType ft = new FeatureType();
 285     assertEquals("", Uniprot.getDescription(ft));
 286
 287     ft.setDescription("Hello");
 288     assertEquals("Hello", Uniprot.getDescription(ft));
 289
 290     ft.setLocation(new LocationType());
 291     ft.getLocation().setPosition(new PositionType());
 292     ft.getLocation().getPosition().setPosition(BigInteger.valueOf(23));
 293     ft.setOriginal("K");
 294     ft.getVariation().add("y");
 295     assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(ft));
 296
 297     // multiple variants generate an html description over more than one line
 298     ft.getVariation().add("W");
 299     assertEquals("<html>p.Lys23Tyr<br/>&nbsp;&nbsp;p.Lys23Trp Hello</html>",
 300             Uniprot.getDescription(ft));
 301
 302     /*
 303      * indel cases
 304      * up to 3 bases (original or variant) are shown using 3 letter code
 305      */
 306     ft.getVariation().clear();
 307     ft.getVariation().add("KWE");
 308     ft.setOriginal("KLS");
 309     assertEquals("p.LysLeuSer23LysTrpGlu Hello",
 310             Uniprot.getDescription(ft));
 311
 312     // adding a fourth original base switches to single letter code
 313     ft.setOriginal("KLST");
 314     assertEquals("p.KLST23LysTrpGlu Hello", Uniprot.getDescription(ft));
 315
 316     // adding a fourth variant switches to single letter code
 317     ft.getVariation().clear();
 318     ft.getVariation().add("KWES");
 319     assertEquals("p.KLST23KWES Hello", Uniprot.getDescription(ft));
 320
 321     ft.getVariation().clear();
 322     ft.getVariation().add("z"); // unknown variant - fails gracefully
 323     ft.setOriginal("K");
 324     assertEquals("p.Lys23z Hello", Uniprot.getDescription(ft));
 325
 326     ft.getVariation().clear(); // variant missing - is ignored
 327     assertEquals("Hello", Uniprot.getDescription(ft));
 328   }
 329
 330   public static String Q29079 = Q29079 = new String(
 331           "<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"
 332                   + "<entry xmlns=\"http://uniprot.org/uniprot\" dataset=\"Swiss-Prot\" created=\"1997-11-01\" modified=\"2023-09-13\" version=\"103\">\n"
 333                   + "<accession>Q29079</accession>\n"
 334                   + "<accession>Q29017</accession>\n"
 335                   + "<name>PAG2_PIG</name>\n" + "<protein>\n"
 336                   + "<recommendedName>\n"
 337                   + "<fullName>Pregnancy-associated glycoprotein 2</fullName>\n"
 338                   + "<shortName>PAG 2</shortName>\n"
 339                   + "<ecNumber>3.4.23.-</ecNumber>\n"
 340                   + "</recommendedName>\n" + "</protein>\n" + "<gene>\n"
 341                   + "<name type=\"primary\">PAG2</name>\n" + "</gene>\n"
 342                   + "<organism>\n"
 343                   + "<name type=\"scientific\">Sus scrofa</name>\n"
 344                   + "<name type=\"common\">Pig</name>\n"
 345                   + "<dbReference type=\"NCBI Taxonomy\" id=\"9823\"/>\n"
 346                   + "<lineage>\n" + "<taxon>Eukaryota</taxon>\n"
 347                   + "<taxon>Metazoa</taxon>\n" + "<taxon>Chordata</taxon>\n"
 348                   + "<taxon>Craniata</taxon>\n"
 349                   + "<taxon>Vertebrata</taxon>\n"
 350                   + "<taxon>Euteleostomi</taxon>\n"
 351                   + "<taxon>Mammalia</taxon>\n"
 352                   + "<taxon>Eutheria</taxon>\n"
 353                   + "<taxon>Laurasiatheria</taxon>\n"
 354                   + "<taxon>Artiodactyla</taxon>\n"
 355                   + "<taxon>Suina</taxon>\n" + "<taxon>Suidae</taxon>\n"
 356                   + "<taxon>Sus</taxon>\n" + "</lineage>\n"
 357                   + "</organism>\n" + "<reference key=\"1\">\n"
 358                   + "<citation type=\"journal article\" date=\"1995\" name=\"Biol. Reprod.\" volume=\"53\" first=\"21\" last=\"28\">\n"
 359                   + "<title>Porcine pregnancy-associated glycoproteins: new members of the aspartic proteinase gene family expressed in trophectoderm.</title>\n"
 360                   + "<authorList>\n" + "<person name=\"Szafranska B.\"/>\n"
 361                   + "<person name=\"Xie S.\"/>\n"
 362                   + "<person name=\"Green J.\"/>\n"
 363                   + "<person name=\"Roberts R.M.\"/>\n" + "</authorList>\n"
 364                   + "<dbReference type=\"PubMed\" id=\"7669851\"/>\n"
 365                   + "<dbReference type=\"DOI\" id=\"10.1095/biolreprod53.1.21\"/>\n"
 366                   + "</citation>\n"
 367                   + "<scope>NUCLEOTIDE SEQUENCE [GENOMIC DNA]</scope>\n"
 368                   + "</reference>\n" + "<reference key=\"2\">\n"
 369                   + "<citation type=\"journal article\" date=\"2001\" name=\"Mol. Reprod. Dev.\" volume=\"60\" first=\"137\" last=\"146\">\n"
 370                   + "<title>Gene for porcine pregnancy-associated glycoprotein 2 (poPAG2): its structural organization and analysis of its promoter.</title>\n"
 371                   + "<authorList>\n" + "<person name=\"Szafranska B.\"/>\n"
 372                   + "<person name=\"Miura R.\"/>\n"
 373                   + "<person name=\"Ghosh D.\"/>\n"
 374                   + "<person name=\"Ezashi T.\"/>\n"
 375                   + "<person name=\"Xie S.\"/>\n"
 376                   + "<person name=\"Roberts R.M.\"/>\n"
 377                   + "<person name=\"Green J.A.\"/>\n" + "</authorList>\n"
 378                   + "<dbReference type=\"PubMed\" id=\"11553911\"/>\n"
 379                   + "<dbReference type=\"DOI\" id=\"10.1002/mrd.1070\"/>\n"
 380                   + "</citation>\n"
 381                   + "<scope>NUCLEOTIDE SEQUENCE [GENOMIC DNA]</scope>\n"
 382                   + "<source>\n" + "<tissue>Placenta</tissue>\n"
 383                   + "</source>\n" + "</reference>\n"
 384                   + "<comment type=\"subcellular location\">\n"
 385                   + "<subcellularLocation>\n"
 386                   + "<location>Secreted</location>\n"
 387                   + "<location>Extracellular space</location>\n"
 388                   + "</subcellularLocation>\n" + "</comment>\n"
 389                   + "<comment type=\"tissue specificity\">\n"
 390                   + "<text>Expressed throughout the chorion, with the signal localized exclusively over the trophectoderm.</text>\n"
 391                   + "</comment>\n"
 392                   + "<comment type=\"developmental stage\">\n"
 393                   + "<text>Expression was detected at day 15, coinciding with the beginning of implantation, and continued throughout gestation.</text>\n"
 394                   + "</comment>\n" + "<comment type=\"similarity\">\n"
 395                   + "<text evidence=\"5\">Belongs to the peptidase A1 family.</text>\n"
 396                   + "</comment>\n"
 397                   + "<dbReference type=\"EC\" id=\"3.4.23.-\"/>\n"
 398                   + "<dbReference type=\"EMBL\" id=\"U39763\">\n"
 399                   + "<property type=\"protein sequence ID\" value=\"AAA92055.1\"/>\n"
 400                   + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 401                   + "</dbReference>\n"
 402                   + "<dbReference type=\"EMBL\" id=\"U41421\">\n"
 403                   + "<property type=\"protein sequence ID\" value=\"AAA92055.1\"/>\n"
 404                   + "<property type=\"status\" value=\"JOINED\"/>\n"
 405                   + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 406                   + "</dbReference>\n"
 407                   + "<dbReference type=\"EMBL\" id=\"U41422\">\n"
 408                   + "<property type=\"protein sequence ID\" value=\"AAA92055.1\"/>\n"
 409                   + "<property type=\"status\" value=\"JOINED\"/>\n"
 410                   + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 411                   + "</dbReference>\n"
 412                   + "<dbReference type=\"EMBL\" id=\"U39199\">\n"
 413                   + "<property type=\"protein sequence ID\" value=\"AAA92055.1\"/>\n"
 414                   + "<property type=\"status\" value=\"JOINED\"/>\n"
 415                   + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 416                   + "</dbReference>\n"
 417                   + "<dbReference type=\"EMBL\" id=\"U41423\">\n"
 418                   + "<property type=\"protein sequence ID\" value=\"AAA92055.1\"/>\n"
 419                   + "<property type=\"status\" value=\"JOINED\"/>\n"
 420                   + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 421                   + "</dbReference>\n"
 422                   + "<dbReference type=\"EMBL\" id=\"U41424\">\n"
 423                   + "<property type=\"protein sequence ID\" value=\"AAA92055.1\"/>\n"
 424                   + "<property type=\"status\" value=\"JOINED\"/>\n"
 425                   + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 426                   + "</dbReference>\n"
 427                   + "<dbReference type=\"EMBL\" id=\"U39762\">\n"
 428                   + "<property type=\"protein sequence ID\" value=\"AAA92055.1\"/>\n"
 429                   + "<property type=\"status\" value=\"JOINED\"/>\n"
 430                   + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 431                   + "</dbReference>\n"
 432                   + "<dbReference type=\"EMBL\" id=\"L34361\">\n"
 433                   + "<property type=\"protein sequence ID\" value=\"AAA81531.1\"/>\n"
 434                   + "<property type=\"molecule type\" value=\"Genomic_DNA\"/>\n"
 435                   + "</dbReference>\n"
 436                   + "<dbReference type=\"PIR\" id=\"I46617\">\n"
 437                   + "<property type=\"entry name\" value=\"I46617\"/>\n"
 438                   + "</dbReference>\n"
 439                   + "<dbReference type=\"AlphaFoldDB\" id=\"Q29079\"/>\n"
 440                   + "<dbReference type=\"SMR\" id=\"Q29079\"/>\n"
 441                   + "<dbReference type=\"MEROPS\" id=\"A01.051\"/>\n"
 442                   + "<dbReference type=\"GlyCosmos\" id=\"Q29079\">\n"
 443                   + "<property type=\"glycosylation\" value=\"2 sites, No reported glycans\"/>\n"
 444                   + "</dbReference>\n"
 445                   + "<dbReference type=\"InParanoid\" id=\"Q29079\"/>\n"
 446                   + "<dbReference type=\"Proteomes\" id=\"UP000008227\">\n"
 447                   + "<property type=\"component\" value=\"Unplaced\"/>\n"
 448                   + "</dbReference>\n"
 449                   + "<dbReference type=\"Proteomes\" id=\"UP000314985\">\n"
 450                   + "<property type=\"component\" value=\"Unplaced\"/>\n"
 451                   + "</dbReference>\n"
 452                   + "<dbReference type=\"Proteomes\" id=\"UP000694570\">\n"
 453                   + "<property type=\"component\" value=\"Unplaced\"/>\n"
 454                   + "</dbReference>\n"
 455                   + "<dbReference type=\"Proteomes\" id=\"UP000694571\">\n"
 456                   + "<property type=\"component\" value=\"Unplaced\"/>\n"
 457                   + "</dbReference>\n"
 458                   + "<dbReference type=\"Proteomes\" id=\"UP000694720\">\n"
 459                   + "<property type=\"component\" value=\"Unplaced\"/>\n"
 460                   + "</dbReference>\n"
 461                   + "<dbReference type=\"Proteomes\" id=\"UP000694722\">\n"
 462                   + "<property type=\"component\" value=\"Unplaced\"/>\n"
 463                   + "</dbReference>\n"
 464                   + "<dbReference type=\"Proteomes\" id=\"UP000694723\">\n"
 465                   + "<property type=\"component\" value=\"Unplaced\"/>\n"
 466                   + "</dbReference>\n"
 467                   + "<dbReference type=\"Proteomes\" id=\"UP000694724\">\n"
 468                   + "<property type=\"component\" value=\"Unplaced\"/>\n"
 469                   + "</dbReference>\n"
 470                   + "<dbReference type=\"Proteomes\" id=\"UP000694725\">\n"
 471                   + "<property type=\"component\" value=\"Unplaced\"/>\n"
 472                   + "</dbReference>\n"
 473                   + "<dbReference type=\"Proteomes\" id=\"UP000694726\">\n"
 474                   + "<property type=\"component\" value=\"Unplaced\"/>\n"
 475                   + "</dbReference>\n"
 476                   + "<dbReference type=\"Proteomes\" id=\"UP000694727\">\n"
 477                   + "<property type=\"component\" value=\"Unplaced\"/>\n"
 478                   + "</dbReference>\n"
 479                   + "<dbReference type=\"Proteomes\" id=\"UP000694728\">\n"
 480                   + "<property type=\"component\" value=\"Unplaced\"/>\n"
 481                   + "</dbReference>\n"
 482                   + "<dbReference type=\"GO\" id=\"GO:0005615\">\n"
 483                   + "<property type=\"term\" value=\"C:extracellular space\"/>\n"
 484                   + "<property type=\"evidence\" value=\"ECO:0007669\"/>\n"
 485                   + "<property type=\"project\" value=\"UniProtKB-SubCell\"/>\n"
 486                   + "</dbReference>\n"
 487                   + "<dbReference type=\"GO\" id=\"GO:0004190\">\n"
 488                   + "<property type=\"term\" value=\"F:aspartic-type endopeptidase activity\"/>\n"
 489                   + "<property type=\"evidence\" value=\"ECO:0000318\"/>\n"
 490                   + "<property type=\"project\" value=\"GO_Central\"/>\n"
 491                   + "</dbReference>\n"
 492                   + "<dbReference type=\"GO\" id=\"GO:0006508\">\n"
 493                   + "<property type=\"term\" value=\"P:proteolysis\"/>\n"
 494                   + "<property type=\"evidence\" value=\"ECO:0000318\"/>\n"
 495                   + "<property type=\"project\" value=\"GO_Central\"/>\n"
 496                   + "</dbReference>\n"
 497                   + "<dbReference type=\"Gene3D\" id=\"6.10.140.60\">\n"
 498                   + "<property type=\"match status\" value=\"1\"/>\n"
 499                   + "</dbReference>\n"
 500                   + "<dbReference type=\"Gene3D\" id=\"2.40.70.10\">\n"
 501                   + "<property type=\"entry name\" value=\"Acid Proteases\"/>\n"
 502                   + "<property type=\"match status\" value=\"3\"/>\n"
 503                   + "</dbReference>\n"
 504                   + "<dbReference type=\"InterPro\" id=\"IPR001461\">\n"
 505                   + "<property type=\"entry name\" value=\"Aspartic_peptidase_A1\"/>\n"
 506                   + "</dbReference>\n"
 507                   + "<dbReference type=\"InterPro\" id=\"IPR001969\">\n"
 508                   + "<property type=\"entry name\" value=\"Aspartic_peptidase_AS\"/>\n"
 509                   + "</dbReference>\n"
 510                   + "<dbReference type=\"InterPro\" id=\"IPR012848\">\n"
 511                   + "<property type=\"entry name\" value=\"Aspartic_peptidase_N\"/>\n"
 512                   + "</dbReference>\n"
 513                   + "<dbReference type=\"InterPro\" id=\"IPR033121\">\n"
 514                   + "<property type=\"entry name\" value=\"PEPTIDASE_A1\"/>\n"
 515                   + "</dbReference>\n"
 516                   + "<dbReference type=\"InterPro\" id=\"IPR021109\">\n"
 517                   + "<property type=\"entry name\" value=\"Peptidase_aspartic_dom_sf\"/>\n"
 518                   + "</dbReference>\n"
 519                   + "<dbReference type=\"PANTHER\" id=\"PTHR47966\">\n"
 520                   + "<property type=\"entry name\" value=\"BETA-SITE APP-CLEAVING ENZYME, ISOFORM A-RELATED\"/>\n"
 521                   + "<property type=\"match status\" value=\"1\"/>\n"
 522                   + "</dbReference>\n"
 523                   + "<dbReference type=\"PANTHER\" id=\"PTHR47966:SF49\">\n"
 524                   + "<property type=\"entry name\" value=\"PEPSIN A-5\"/>\n"
 525                   + "<property type=\"match status\" value=\"1\"/>\n"
 526                   + "</dbReference>\n"
 527                   + "<dbReference type=\"Pfam\" id=\"PF07966\">\n"
 528                   + "<property type=\"entry name\" value=\"A1_Propeptide\"/>\n"
 529                   + "<property type=\"match status\" value=\"1\"/>\n"
 530                   + "</dbReference>\n"
 531                   + "<dbReference type=\"Pfam\" id=\"PF00026\">\n"
 532                   + "<property type=\"entry name\" value=\"Asp\"/>\n"
 533                   + "<property type=\"match status\" value=\"2\"/>\n"
 534                   + "</dbReference>\n"
 535                   + "<dbReference type=\"PRINTS\" id=\"PR00792\">\n"
 536                   + "<property type=\"entry name\" value=\"PEPSIN\"/>\n"
 537                   + "</dbReference>\n"
 538                   + "<dbReference type=\"SUPFAM\" id=\"SSF50630\">\n"
 539                   + "<property type=\"entry name\" value=\"Acid proteases\"/>\n"
 540                   + "<property type=\"match status\" value=\"2\"/>\n"
 541                   + "</dbReference>\n"
 542                   + "<dbReference type=\"PROSITE\" id=\"PS00141\">\n"
 543                   + "<property type=\"entry name\" value=\"ASP_PROTEASE\"/>\n"
 544                   + "<property type=\"match status\" value=\"2\"/>\n"
 545                   + "</dbReference>\n"
 546                   + "<dbReference type=\"PROSITE\" id=\"PS51767\">\n"
 547                   + "<property type=\"entry name\" value=\"PEPTIDASE_A1\"/>\n"
 548                   + "<property type=\"match status\" value=\"1\"/>\n"
 549                   + "</dbReference>\n"
 550                   + "<proteinExistence type=\"evidence at transcript level\"/>\n"
 551                   + "<keyword id=\"KW-0064\">Aspartyl protease</keyword>\n"
 552                   + "<keyword id=\"KW-1015\">Disulfide bond</keyword>\n"
 553                   + "<keyword id=\"KW-0325\">Glycoprotein</keyword>\n"
 554                   + "<keyword id=\"KW-0378\">Hydrolase</keyword>\n"
 555                   + "<keyword id=\"KW-0645\">Protease</keyword>\n"
 556                   + "<keyword id=\"KW-1185\">Reference proteome</keyword>\n"
 557                   + "<keyword id=\"KW-0964\">Secreted</keyword>\n"
 558                   + "<keyword id=\"KW-0732\">Signal</keyword>\n"
 559                   + "<keyword id=\"KW-0865\">Zymogen</keyword>\n"
 560                   + "<feature type=\"signal peptide\" evidence=\"2\">\n"
 561                   + "<location>\n" + "<begin position=\"1\"/>\n"
 562                   + "<end position=\"15\"/>\n" + "</location>\n"
 563                   + "</feature>\n"
 564                   + "<feature type=\"propeptide\" id=\"PRO_0000026107\" description=\"Activation peptide\" evidence=\"2\">\n"
 565                   + "<location>\n" + "<begin position=\"16\"/>\n"
 566                   + "<end status=\"unknown\"/>\n" + "</location>\n"
 567                   + "</feature>\n"
 568                   + "<feature type=\"chain\" id=\"PRO_0000026108\" description=\"Pregnancy-associated glycoprotein 2\">\n"
 569                   + "<location>\n" + "<begin status=\"unknown\"/>\n"
 570                   + "<end position=\"420\"/>\n" + "</location>\n"
 571                   + "</feature>\n"
 572                   + "<feature type=\"domain\" description=\"Peptidase A1\" evidence=\"3\">\n"
 573                   + "<location>\n" + "<begin position=\"76\"/>\n"
 574                   + "<end position=\"417\"/>\n" + "</location>\n"
 575                   + "</feature>\n"
 576                   + "<feature type=\"active site\" evidence=\"4\">\n"
 577                   + "<location>\n" + "<position position=\"94\"/>\n"
 578                   + "</location>\n" + "</feature>\n"
 579                   + "<feature type=\"active site\" evidence=\"4\">\n"
 580                   + "<location>\n" + "<position position=\"277\"/>\n"
 581                   + "</location>\n" + "</feature>\n"
 582                   + "<feature type=\"glycosylation site\" description=\"N-linked (GlcNAc...) asparagine\" evidence=\"2\">\n"
 583                   + "<location>\n" + "<position position=\"56\"/>\n"
 584                   + "</location>\n" + "</feature>\n"
 585                   + "<feature type=\"glycosylation site\" description=\"N-linked (GlcNAc...) asparagine\" evidence=\"2\">\n"
 586                   + "<location>\n" + "<position position=\"79\"/>\n"
 587                   + "</location>\n" + "</feature>\n"
 588                   + "<feature type=\"disulfide bond\" evidence=\"1\">\n"
 589                   + "<location>\n" + "<begin position=\"107\"/>\n"
 590                   + "<end position=\"112\"/>\n" + "</location>\n"
 591                   + "</feature>\n"
 592                   + "<feature type=\"disulfide bond\" evidence=\"1\">\n"
 593                   + "<location>\n" + "<begin position=\"268\"/>\n"
 594                   + "<end position=\"272\"/>\n" + "</location>\n"
 595                   + "</feature>\n"
 596                   + "<feature type=\"disulfide bond\" evidence=\"1\">\n"
 597                   + "<location>\n" + "<begin position=\"341\"/>\n"
 598                   + "<end position=\"376\"/>\n" + "</location>\n"
 599                   + "</feature>\n"
 600                   + "<feature type=\"sequence conflict\" description=\"In Ref. 1.\" evidence=\"5\" ref=\"1\">\n"
 601                   + "<location>\n" + "<begin position=\"335\"/>\n"
 602                   + "<end position=\"367\"/>\n" + "</location>\n"
 603                   + "</feature>\n"
 604                   + "<evidence type=\"ECO:0000250\" key=\"1\"/>\n"
 605                   + "<evidence type=\"ECO:0000255\" key=\"2\"/>\n"
 606                   + "<evidence type=\"ECO:0000255\" key=\"3\">\n"
 607                   + "<source>\n"
 608                   + "<dbReference type=\"PROSITE-ProRule\" id=\"PRU01103\"/>\n"
 609                   + "</source>\n" + "</evidence>\n"
 610                   + "<evidence type=\"ECO:0000255\" key=\"4\">\n"
 611                   + "<source>\n"
 612                   + "<dbReference type=\"PROSITE-ProRule\" id=\"PRU10094\"/>\n"
 613                   + "</source>\n" + "</evidence>\n"
 614                   + "<evidence type=\"ECO:0000305\" key=\"5\"/>\n"
 615                   + "<sequence length=\"420\" mass=\"47132\" checksum=\"094153B6C1B1FCDB\" modified=\"1997-11-01\" version=\"1\" precursor=\"true\">MKWLVILGLVALSDCLVMIPLTKVKSVRESLREKGLLKNFLKEHPYNMIQNLLSKNSSHVQKFSYQPLRNYLDMVYVGNISIGTPPQQFSVVFDTGSSDLWVPSIYCKSKACVTHRSFNPSHSSTFHDRGKSIKLEYGSGKMSGFLGQDTVRIGQLTSTGQAFGLSKEETGKAFEHAIFDGILGLAYPSIAIKGTTTVIDNLKKQDQISEPVFAFYLSSDKEEGSVVMFGGVDKKYYKGDLKWVPLTQTSYWQIALDRITCRGRVIGCPRGCQAIVDTGTSMLHGPSKAVAKIHSLIKHFEKEYVVPCNARKALPDIVFTINNVDYPVPAQAYIRKYVVPCNARKALPDIVFTINNVDYPVPAQAYIRKNANNNRCYSTFEDIMDTLNQREIWILGDVFLRLYFTVYDEGQNRIGLAQAT</sequence>\n"
 616                   + "</entry>\n"
 617                   + "<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"
 618                   + "</uniprot>");
 619
 620   @DataProvider
 621   public Object[][] problemEntries()
 622   {
 623     return new Object[][] { new Object[] { Q29079 } };
 624   }
 625
 626   @Test(groups = "Functional", dataProvider = "problemEntries")
 627   public SequenceI testimportOfProblemEntries(String entry)
 628   {
 629     Uniprot u = new Uniprot();
 630     InputStream is = new ByteArrayInputStream(entry.getBytes());
 631     List<Entry> entries = u.getUniprotEntries(is);
 632     assertEquals(1, entries.size());
 633     SequenceI sq = u.uniprotEntryToSequence(entries.get(0));
 634     assertNotNull(sq);
 635     return sq;
 636   }
 637
 638   @Test(groups = "Functional")
 639   public void checkIndefiniteSequenceFeatures()
 640   {
 641     SequenceI upseq = testimportOfProblemEntries(Q29079);
 642     List<SequenceFeature> sf = upseq.getFeatures()
 643             .getPositionalFeatures("chain");
 644     assertNotNull(sf);
 645     assertTrue(sf.size() == 1);
 646     SequenceFeature chainFeaure = sf.get(0);
 647     assertTrue(chainFeaure.getBegin() == 1);
 648     assertTrue(chainFeaure.getEnd() == upseq.getEnd());
 649     assertNotNull(chainFeaure.getValueAsString("start_status"));
 650     assertNull(chainFeaure.getValueAsString("end_status"));
 651     assertTrue(
 652             "unknown".equals(chainFeaure.getValueAsString("start_status")));
 653   }
 654 }