+/*
+ * 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;
/**
* 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()
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());
}
/**
- * 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);
- // 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());
+ /*
+ * 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));
+ }
+
+ /**
+ * 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));
}
}