X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblFileTest.java;h=fda25e3d6709b344e6b28e642ba757c217299dc3;hb=5071850e8470077a8ac2bdc6a53908c70ad5526d;hp=c6a94d7bb4c6174e6316a538728726d052e27f86;hpb=4d5c986641c7281b09e3e70c46fcf91d64f9afa7;p=jalview.git
diff --git a/test/jalview/datamodel/xdb/embl/EmblFileTest.java b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
index c6a94d7..fda25e3 100644
--- a/test/jalview/datamodel/xdb/embl/EmblFileTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
@@ -21,9 +21,7 @@
package jalview.datamodel.xdb.embl;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
-import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.DBRefEntry;
@@ -34,22 +32,21 @@ import org.testng.annotations.Test;
public class EmblFileTest
{
- // adapted from http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
+ // adapted from http://www.ebi.ac.uk/ena/data/view/x53828&display=xml
private static final String TESTDATA = ""
- + ""
- + ""
+ + ""
+ + ""
+ "Chicken LDH-A mRNA for lactate dehydrogenase A chain (EC 1.1.1.27)"
+ "L-lactate dehydrogenasechutney"
- + ""
- + ""
- + ""
+ + ""
+ + ""
+ + ""
+ + ""
+ "L-lactate dehydrogenase A-chainpickle"
+ "MSLKDHLIHNKeith"
- + ""
- + ""
- + "601058"
- + ""
- + "GTGACG";
+ + ""
+ + "GTGACG";
@Test(groups = { "Functional" })
public void testGetEmblFile()
@@ -64,6 +61,11 @@ public class EmblFileTest
"Chicken LDH-A mRNA for lactate dehydrogenase A chain (EC 1.1.1.27)",
entry.getDesc());
assertEquals("2005-04-18", entry.getLastUpdated());
+ assertEquals("mRNA", entry.getMoleculeType());
+ assertEquals("1", entry.getSequenceVersion());
+ assertEquals("3", entry.getEntryVersion());
+ assertEquals("linear", entry.getTopology());
+ assertEquals("1575", entry.getSequenceLength());
/*
* FIXME these assertions fail - values are null - why?? Adding or removing
@@ -92,11 +94,12 @@ public class EmblFileTest
assertEquals("0", dbref.getVersion());
/*
- * sequence features
+ * sequence feature for CDS
*/
assertEquals(1, entry.getFeatures().size());
EmblFeature ef = entry.getFeatures().get(0);
assertEquals("CDS", ef.getName());
+ assertEquals("60..1058", ef.getLocation());
assertEquals(2, ef.getDbRefs().size());
dbref = ef.getDbRefs().get(0);
assertEquals("GOA", dbref.getSource());
@@ -123,31 +126,10 @@ public class EmblFileTest
assertEquals(1, q.getEvidence().length);
assertEquals("Keith", q.getEvidence()[0]);
- // feature locations
- assertEquals(1, ef.getLocations().size());
- EmblFeatureLocations fl = ef.getLocations().get(0);
- assertEquals("single", fl.getLocationType());
- assertTrue(fl.isLocationComplement());
- assertEquals(1, fl.getLocElements().size());
- EmblFeatureLocElement le = fl.getLocElements().get(0);
- assertEquals("range", le.getType());
- assertEquals("X53828", le.getAccession());
- assertEquals("1", le.getVersion());
- assertFalse(le.isComplement());
- assertEquals(2, le.getBasePositions().length);
- BasePosition bp = le.getBasePositions()[0];
- assertEquals("simple", bp.getType());
- assertEquals("60", bp.getPos());
- bp = le.getBasePositions()[1];
- assertEquals("join", bp.getType());
- assertEquals("1058", bp.getPos());
-
/*
* Sequence
*/
EmblSequence seq = entry.getSequence();
- assertEquals("mRNA", seq.getType());
- assertEquals("2", seq.getVersion());
assertEquals("GTGACG", seq.getSequence());
/*