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.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>"
/*
* Check sequence features
*/
- Vector<SequenceFeature> features = entry.getFeature();
+ Vector<UniprotFeature> features = entry.getFeature();
assertEquals(3, features.size());
- SequenceFeature sf = features.get(0);
+ UniprotFeature sf = features.get(0);
assertEquals("signal peptide", sf.getType());
assertNull(sf.getDescription());
assertNull(sf.getStatus());
- assertEquals(1, sf.getPosition());
assertEquals(1, sf.getBegin());
assertEquals(18, sf.getEnd());
sf = features.get(1);
* 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
+
}
/**
/*
* name formatted as source | accession ids | names
+ * source database converted to Jalview canonical name
*/
- String expectedName = "UniProt/Swiss-Prot|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
+ String expectedName = "UNIPROT|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
}
{
UniprotEntry entry = new Uniprot().getUniprotEntries(
new StringReader(UNIPROT_XML)).get(0);
-
+
/*
* recommended names concatenated with space separator
*/