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.SequenceI;
-import jalview.datamodel.UniprotEntry;
+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>"
+ "<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>";
/*
* 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());
assertEquals(1, sf.getBegin());
assertEquals(18, sf.getEnd());
sf = features.get(1);
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),
+ "p.Met42Leu" + "\n" + "p.Met42LeuMetVal Foo");
+
+ sf = features.get(7);
+ assertEquals(42, sf.getBegin());
+ assertEquals(43, sf.getEnd());
+ Assert.assertEquals(Uniprot.getDescription(sf),
+ "p.MetLeu42LeuLeu" + "\n" + "p.MetLeu42LeuMetVal Foo");
+
+ sf = features.get(8);
+ assertEquals(42, sf.getBegin());
+ assertEquals(45, sf.getEnd());
+ Assert.assertEquals(Uniprot.getDescription(sf),
+ "p.MLML42LeuLeu" + "\n" + "p.MLML42LMVK Foo Too");
+
/*
* Check cross-references
*/
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());
- assertNotNull(xref.getProperty());
- assertEquals("AAK85932.1",
- (String) xref.getProperty().get("protein sequence ID"));
- assertEquals("Genomic_DNA",
- (String) xref.getProperty().get("molecule type"));
- assertEquals(2, xref.getProperty().size());
-
+ assertEquals("AAK85932.1", xref.getProperty("protein sequence ID"));
+ assertEquals("Genomic_DNA", xref.getProperty("molecule type"));
}
@Test(groups = { "Functional" })
assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
}
+
/**
* Test the method that formats the sequence id
*/
new StringReader(UNIPROT_XML)).get(0);
/*
- * name formatted as source | accession ids | names
- * source database converted to Jalview canonical name
+ * name formatted with Uniprot Entry name
*/
- String expectedName = "UNIPROT|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
- assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
+ String expectedName = "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
*/
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));
+
+ vars.clear();
+ vars.add("z"); // unknown variant - fails gracefully
+ uf.setVariation(vars);
+ assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
+
+ uf.setVariation(null); // variant missing - is ignored
+ assertEquals("Hello", Uniprot.getDescription(uf));
+ }
}
git://source.jalview.org / jalview.git / blobdiff