+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.dbsources;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.UniprotEntry;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.xdb.uniprot.UniprotEntry;
+import jalview.datamodel.xdb.uniprot.UniprotFeature;
+import jalview.gui.JvOptionPane;
import java.io.Reader;
import java.io.StringReader;
import java.util.Vector;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class UniprotTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
// adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
+ "<uniprot>"
+ "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
+ "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
+ "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
+ + "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
+ "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
+ "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
+ "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
+ + "<feature type=\"sequence variant\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
+ + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
+ + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><location><position position=\"41\"/></location></feature>"
+ + "<feature type=\"sequence variant\" description=\"Foo\"><variation>L</variation><variation>LMV</variation><original>M</original><location><position position=\"42\"/></location></feature>"
+ + "<feature type=\"sequence variant\" description=\"Foo\"><variation>LL</variation><variation>LMV</variation><original>ML</original><location><begin position=\"42\"/><end position=\"43\"/></location></feature>"
+ + "<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>"
+ "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
+ "</uniprot>";
/**
* Test the method that unmarshals XML to a Uniprot model
*/
- @Test
+ @Test(groups = { "Functional" })
public void testGetUniprotEntries()
{
Uniprot u = new Uniprot();
/*
* UniprotSequence drops any space characters
*/
- assertEquals("MHAPLVSKDL", entry.getUniprotSequence()
- .getContent());
+ assertEquals("MHAPLVSKDL", entry.getUniprotSequence().getContent());
assertEquals(2, entry.getProtein().getName().size());
assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
/*
* Check sequence features
*/
- Vector<SequenceFeature> features = entry.getFeature();
- assertEquals(3, features.size());
- SequenceFeature sf = features.get(0);
+ Vector<UniprotFeature> features = entry.getFeature();
+ assertEquals(9, features.size());
+ UniprotFeature sf = features.get(0);
assertEquals("signal peptide", sf.getType());
assertNull(sf.getDescription());
assertNull(sf.getStatus());
- assertEquals(1, sf.getPosition()); // wrong - Castor bug??
assertEquals(1, sf.getBegin());
assertEquals(18, sf.getEnd());
sf = features.get(1);
assertEquals("propeptide", sf.getType());
assertEquals("Activation peptide", sf.getDescription());
- assertEquals(19, sf.getPosition()); // wrong - Castor bug??
+ assertEquals(19, sf.getPosition());
assertEquals(19, sf.getBegin());
assertEquals(20, sf.getEnd());
sf = features.get(2);
assertEquals("chain", sf.getType());
assertEquals("Granzyme B", sf.getDescription());
- assertEquals(21, sf.getPosition()); // wrong - Castor bug??
+ assertEquals(21, sf.getPosition());
assertEquals(21, sf.getBegin());
assertEquals(247, sf.getEnd());
+ sf = features.get(3);
+ assertEquals("sequence variant", sf.getType());
+ assertNull(sf.getDescription());
+ assertEquals(41, sf.getPosition());
+ assertEquals(41, sf.getBegin());
+ assertEquals(41, sf.getEnd());
+
+ sf = features.get(4);
+ assertEquals("sequence variant", sf.getType());
+ assertEquals("Pathogenic", sf.getDescription());
+ assertEquals(41, sf.getPosition());
+ assertEquals(41, sf.getBegin());
+ assertEquals(41, sf.getEnd());
+
+ sf = features.get(5);
+ assertEquals("sequence variant", sf.getType());
+ assertEquals("Pathogenic", sf.getDescription());
+ assertEquals(41, sf.getPosition());
+ assertEquals(41, sf.getBegin());
+ assertEquals(41, sf.getEnd());
+
+ sf = features.get(6);
+ assertEquals("sequence variant", sf.getType());
+ assertEquals("Foo",
+ sf.getDescription());
+ assertEquals(42, sf.getPosition());
+ assertEquals(42, sf.getBegin());
+ assertEquals(42, sf.getEnd());
+ Assert.assertEquals(Uniprot.getDescription(sf),
+ "<html>p.Met42Leu" + "<br/> "
+ + "p.Met42LeuMetVal Foo</html>");
+
+ sf = features.get(7);
+ assertEquals(42, sf.getBegin());
+ assertEquals(43, sf.getEnd());
+ Assert.assertEquals(Uniprot.getDescription(sf),
+ "<html>p.MetLeu42LeuLeu" + "<br/> "
+ + "p.MetLeu42LeuMetVal Foo</html>");
+
+ sf = features.get(8);
+ assertEquals(42, sf.getBegin());
+ assertEquals(45, sf.getEnd());
+ Assert.assertEquals(Uniprot.getDescription(sf),
+ "<html>p.MLML42LeuLeu" + "<br/> "
+ + "p.MLML42LMVK Foo Too</html>");
+
/*
* Check cross-references
*/
Vector<PDBEntry> xrefs = entry.getDbReference();
- assertEquals(2, xrefs.size());
+ assertEquals(3, xrefs.size());
PDBEntry xref = xrefs.get(0);
assertEquals("2FSQ", xref.getId());
assertEquals("PDB", xref.getType());
- assertEquals(2, xref.getProperty().size());
- assertEquals("X-ray", xref.getProperty().get("method"));
- assertEquals("1.40", xref.getProperty().get("resolution"));
+ assertEquals("X-ray", xref.getProperty("method"));
+ assertEquals("1.40", xref.getProperty("resolution"));
xref = xrefs.get(1);
assertEquals("2FSR", xref.getId());
assertEquals("PDBsum", xref.getType());
- assertNull(xref.getProperty());
+ assertFalse(xref.getProperties().hasMoreElements());
+
+ xref = xrefs.get(2);
+ assertEquals("AE007869", xref.getId());
+ assertEquals("EMBL", xref.getType());
+ assertEquals("AAK85932.1", xref.getProperty("protein sequence ID"));
+ assertEquals("Genomic_DNA", xref.getProperty("molecule type"));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetUniprotSequence()
+ {
+ UniprotEntry entry = new Uniprot().getUniprotEntries(
+ new StringReader(UNIPROT_XML)).get(0);
+ SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
+ assertNotNull(seq);
+ assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
+
}
/**
- * Test the method that formats the sequence name in Fasta style
+ * Test the method that formats the sequence id
*/
- @Test
- public void testConstructSequenceFastaHeader()
+ @Test(groups = { "Functional" })
+ public void testGetUniprotEntryId()
{
- Uniprot u = new Uniprot();
- Reader reader = new StringReader(UNIPROT_XML);
- Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
- UniprotEntry entry = entries.get(0);
+ UniprotEntry entry = new Uniprot().getUniprotEntries(
+ new StringReader(UNIPROT_XML)).get(0);
+
+ /*
+ * name formatted with Uniprot Entry name
+ */
+ String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
+ assertEquals(expectedName,
+ Uniprot.getUniprotEntryId(entry));
+ }
+
+ /**
+ * Test the method that formats the sequence description
+ */
+ @Test(groups = { "Functional" })
+ public void testGetUniprotEntryDescription()
+ {
+ UniprotEntry entry = new Uniprot().getUniprotEntries(
+ new StringReader(UNIPROT_XML)).get(0);
+
+ /*
+ * recommended names concatenated with space separator
+ */
+ String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
+ assertEquals(expectedDescription,
+ Uniprot.getUniprotEntryDescription(entry));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetDescription()
+ {
+ UniprotFeature uf = new UniprotFeature();
+ assertEquals("", Uniprot.getDescription(uf));
+
+ uf.setDescription("Hello");
+ assertEquals("Hello", Uniprot.getDescription(uf));
+
+ uf.setPosition(23);
+ uf.setOriginal("K");
+ Vector<String> vars = new Vector<>();
+ vars.add("y");
+ uf.setVariation(vars);
+ assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
+
+ // multiple variants generate an html description over more than one line
+ vars.add("W");
+ assertEquals("<html>p.Lys23Tyr<br/> p.Lys23Trp Hello</html>",
+ Uniprot.getDescription(uf));
+
+ /*
+ * indel cases
+ * up to 3 bases (original or variant) are shown using 3 letter code
+ */
+ vars.clear();
+ vars.add("KWE");
+ uf.setOriginal("KLS");
+ assertEquals("p.LysLeuSer23LysTrpGlu Hello",
+ Uniprot.getDescription(uf));
+
+ // adding a fourth original base switches to single letter code
+ uf.setOriginal("KLST");
+ assertEquals("p.KLST23LysTrpGlu Hello", Uniprot.getDescription(uf));
+
+ // adding a fourth variant switches to single letter code
+ vars.clear();
+ vars.add("KWES");
+ assertEquals("p.KLST23KWES Hello", Uniprot.getDescription(uf));
+
+ vars.clear();
+ vars.add("z"); // unknown variant - fails gracefully
+ uf.setOriginal("K");
+ assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
- // source + accession ids + names + protein names
- String expectedName = ">UniProt/Swiss-Prot|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6 Mitogen-activated protein kinase 13 Henry";
- assertEquals(expectedName, Uniprot.constructSequenceFastaHeader(entry)
- .toString());
+ uf.setVariation(null); // variant missing - is ignored
+ assertEquals("Hello", Uniprot.getDescription(uf));
}
}
git://source.jalview.org / jalview.git / blobdiff