package jalview.ws.dbsources;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
import jalview.datamodel.PDBEntry;
assertEquals("signal peptide", sf.getType());
assertNull(sf.getDescription());
assertNull(sf.getStatus());
- assertEquals(1, sf.getPosition()); // wrong - Castor bug??
+ assertEquals(1, sf.getPosition());
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());
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());
}
/**
- * Test the method that formats the sequence name in Fasta style
+ * Test the method that formats the sequence id
*/
@Test(groups = { "Functional" })
- public void testConstructSequenceFastaHeader()
+ 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 as source | accession ids | names
+ * source database converted to Jalview canonical name
+ */
+ String expectedName = "UNIPROT|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
+ assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
+ }
- // 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());
+ /**
+ * 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));
}
}