X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fdbsources%2FUniprotTest.java;h=c603a110559167360c087a8fb875f154bec4e37c;hb=42df19afce43090aea47fe782195f11236801be7;hp=a3c610521917c26fd8227fe3ed08169529daf78f;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git
diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index a3c6105..c603a11 100644
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
@@ -21,20 +21,33 @@
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 = ""
+ ""
@@ -46,9 +59,13 @@ public class UniprotTest
+ "Mitogen-activated protein kinase 13Henry"
+ ""
+ ""
+ + ""
+ ""
+ ""
+ ""
+ + "ML"
+ + "ML"
+ + "M"
+ "MHAPL VSKDL"
+ "";
@@ -83,61 +100,114 @@ public class UniprotTest
/*
* Check sequence features
*/
- Vector features = entry.getFeature();
- assertEquals(3, features.size());
- SequenceFeature sf = features.get(0);
+ Vector features = entry.getFeature();
+ assertEquals(6, features.size());
+ UniprotFeature sf = features.get(0);
assertEquals("signal peptide", sf.getType());
assertNull(sf.getDescription());
assertNull(sf.getStatus());
- assertEquals(1, sf.getPosition()); // wrong - Castor bug??
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());
+ sf = features.get(3);
+ assertEquals("sequence variant", sf.getType());
+ assertEquals("Variation: 'L' Original: 'M'", 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 Variation: 'L' Original: 'M'",
+ 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 Original: 'M'", sf.getDescription());
+ assertEquals(41, sf.getPosition());
+ assertEquals(41, sf.getBegin());
+ assertEquals(41, sf.getEnd());
/*
* Check cross-references
*/
Vector 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
+
}
/**
- * 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 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 with Uniprot Entry name
+ */
+ String expectedName = "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));
}
}