--- /dev/null
+package jalview.ws.dbsources;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+import java.io.Reader;
+import java.io.StringReader;
+import java.util.Vector;
+
+import org.junit.Test;
+
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.UniprotEntry;
+
+public class UniprotTest
+{
+ // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
+ private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
+ + "<uniprot>"
+ + "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
+ + "<accession>A9CKP4</accession>"
+ + "<accession>A9CKP5</accession>"
+ + "<name>A9CKP4_AGRT5</name>"
+ + "<name>A9CKP4_AGRT6</name>"
+ + "<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\"/>"
+ + "<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>"
+ + "<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
+ public void testGetUniprotEntries()
+ {
+ Uniprot u = new Uniprot();
+ Reader reader = new StringReader(UNIPROT_XML);
+ Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
+ assertEquals(1, entries.size());
+ UniprotEntry entry = entries.get(0);
+ assertEquals(2, entry.getName().size());
+ assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
+ assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
+ assertEquals(2, entry.getAccession().size());
+ assertEquals("A9CKP4", entry.getAccession().get(0));
+ assertEquals("A9CKP5", entry.getAccession().get(1));
+
+ /*
+ * UniprotSequence drops any space characters
+ */
+ assertEquals("MHAPLVSKDL", entry.getUniprotSequence()
+ .getContent());
+
+ assertEquals(2, entry.getProtein().getName().size());
+ assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
+ .getName().get(0));
+ assertEquals("Henry", entry.getProtein().getName().get(1));
+
+ /*
+ * Check sequence features
+ */
+ Vector<SequenceFeature> features = entry.getFeature();
+ assertEquals(3, features.size());
+ SequenceFeature 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.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.getBegin());
+ assertEquals(247, sf.getEnd());
+
+ /*
+ * Check cross-references
+ */
+ Vector<PDBEntry> xrefs = entry.getDbReference();
+ assertEquals(2, 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"));
+
+ xref = xrefs.get(1);
+ assertEquals("2FSR", xref.getId());
+ assertEquals("PDBsum", xref.getType());
+ assertNull(xref.getProperty());
+ }
+
+ /**
+ * Test the method that formats the sequence name in Fasta style
+ */
+ @Test
+ public void testConstructSequenceFastaHeader()
+ {
+ Uniprot u = new Uniprot();
+ Reader reader = new StringReader(UNIPROT_XML);
+ Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
+ UniprotEntry entry = entries.get(0);
+
+ // 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());
+ }
+}