test/jalview/ws/dbsources/UniprotTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
   3  * Copyright (C) 2015 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
  27 import jalview.datamodel.PDBEntry;
  28 import jalview.datamodel.SequenceFeature;
  29 import jalview.datamodel.SequenceI;
  30 import jalview.datamodel.UniprotEntry;
  31
  32 import java.io.Reader;
  33 import java.io.StringReader;
  34 import java.util.Vector;
  35
  36 import org.testng.annotations.Test;
  37
  38 public class UniprotTest
  39 {
  40   // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
  41   private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
  42           + "<uniprot>"
  43           + "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
  44           + "<accession>A9CKP4</accession>"
  45           + "<accession>A9CKP5</accession>"
  46           + "<name>A9CKP4_AGRT5</name>"
  47           + "<name>A9CKP4_AGRT6</name>"
  48           + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
  49           + "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
  50           + "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
  51           + "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
  52           + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
  53           + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
  54           + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
  55           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
  56           + "</uniprot>";
  57
  58   /**
  59    * Test the method that unmarshals XML to a Uniprot model
  60    */
  61   @Test(groups = { "Functional" })
  62   public void testGetUniprotEntries()
  63   {
  64     Uniprot u = new Uniprot();
  65     Reader reader = new StringReader(UNIPROT_XML);
  66     Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
  67     assertEquals(1, entries.size());
  68     UniprotEntry entry = entries.get(0);
  69     assertEquals(2, entry.getName().size());
  70     assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
  71     assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
  72     assertEquals(2, entry.getAccession().size());
  73     assertEquals("A9CKP4", entry.getAccession().get(0));
  74     assertEquals("A9CKP5", entry.getAccession().get(1));
  75
  76     /*
  77      * UniprotSequence drops any space characters
  78      */
  79     assertEquals("MHAPLVSKDL", entry.getUniprotSequence().getContent());
  80
  81     assertEquals(2, entry.getProtein().getName().size());
  82     assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
  83             .getName().get(0));
  84     assertEquals("Henry", entry.getProtein().getName().get(1));
  85
  86     /*
  87      * Check sequence features
  88      */
  89     Vector<SequenceFeature> features = entry.getFeature();
  90     assertEquals(3, features.size());
  91     SequenceFeature sf = features.get(0);
  92     assertEquals("signal peptide", sf.getType());
  93     assertNull(sf.getDescription());
  94     assertNull(sf.getStatus());
  95     assertEquals(1, sf.getPosition());
  96     assertEquals(1, sf.getBegin());
  97     assertEquals(18, sf.getEnd());
  98     sf = features.get(1);
  99     assertEquals("propeptide", sf.getType());
 100     assertEquals("Activation peptide", sf.getDescription());
 101     assertEquals(19, sf.getPosition());
 102     assertEquals(19, sf.getBegin());
 103     assertEquals(20, sf.getEnd());
 104     sf = features.get(2);
 105     assertEquals("chain", sf.getType());
 106     assertEquals("Granzyme B", sf.getDescription());
 107     assertEquals(21, sf.getPosition());
 108     assertEquals(21, sf.getBegin());
 109     assertEquals(247, sf.getEnd());
 110
 111     /*
 112      * Check cross-references
 113      */
 114     Vector<PDBEntry> xrefs = entry.getDbReference();
 115     assertEquals(3, xrefs.size());
 116
 117     PDBEntry xref = xrefs.get(0);
 118     assertEquals("2FSQ", xref.getId());
 119     assertEquals("PDB", xref.getType());
 120     assertEquals(2, xref.getProperty().size());
 121     assertEquals("X-ray", xref.getProperty().get("method"));
 122     assertEquals("1.40", xref.getProperty().get("resolution"));
 123
 124     xref = xrefs.get(1);
 125     assertEquals("2FSR", xref.getId());
 126     assertEquals("PDBsum", xref.getType());
 127     assertNull(xref.getProperty());
 128
 129     xref = xrefs.get(2);
 130     assertEquals("AE007869", xref.getId());
 131     assertEquals("EMBL", xref.getType());
 132     assertNotNull(xref.getProperty());
 133     assertEquals("AAK85932.1",
 134             (String) xref.getProperty().get("protein sequence ID"));
 135     assertEquals("Genomic_DNA",
 136             (String) xref.getProperty().get("molecule type"));
 137     assertEquals(2, xref.getProperty().size());
 138
 139   }
 140
 141   @Test(groups = { "Functional" })
 142   public void testGetUniprotSequence()
 143   {
 144     UniprotEntry entry = new Uniprot().getUniprotEntries(
 145             new StringReader(UNIPROT_XML)).get(0);
 146     SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
 147     assertNotNull(seq);
 148     assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
 149
 150   }
 151
 152   /**
 153    * Test the method that formats the sequence id
 154    */
 155   @Test(groups = { "Functional" })
 156   public void testGetUniprotEntryId()
 157   {
 158     UniprotEntry entry = new Uniprot().getUniprotEntries(
 159             new StringReader(UNIPROT_XML)).get(0);
 160
 161     /*
 162      * name formatted as source | accession ids | names
 163      * source database converted to Jalview canonical name
 164      */
 165     String expectedName = "UNIPROT|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
 166     assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
 167   }
 168
 169   /**
 170    * Test the method that formats the sequence description
 171    */
 172   @Test(groups = { "Functional" })
 173   public void testGetUniprotEntryDescription()
 174   {
 175     UniprotEntry entry = new Uniprot().getUniprotEntries(
 176             new StringReader(UNIPROT_XML)).get(0);
 177
 178     /*
 179      * recommended names concatenated with space separator
 180      */
 181     String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
 182     assertEquals(expectedDescription,
 183             Uniprot.getUniprotEntryDescription(entry));
 184   }
 185 }