+/*
+ * 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;
+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 java.io.Reader;
+ "<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>"
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());
* 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("2FSR", xref.getId());
assertEquals("PDBsum", xref.getType());
assertNull(xref.getProperty());
+
+ 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());
+
+ }
+
+ @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
+
}
/**
- * 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);
- // 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));
}
}
git://source.jalview.org / jalview.git / blobdiff